2

Table of Contents Overview of Structure and Activities ............................................................................................................ 3

History ...................................................................................................................................................... 3

SIPS Section Overviews ........................................................................................................................... 4

Strategic Direction and Progress ............................................................................................................... 6

Facilities ..................................................................................................................................................... 10

Research Program Strength ......................................................................................................................... 11

Funding ............................................................................................................................................... 11

Rankings ............................................................................................................................................. 14

Research connected to our Grand Challenges ............................................................................................. 15

Grand Challenge: Foundational Knowledge ........................................................................................... 15

Foundation Knowledge: Plants as Model Organisms ......................................................................... 15

Foundation Knowledge: Soil Properties and Impact .......................................................................... 17

Foundation Knowledge: Plant-Associated Microbes .......................................................................... 18

Grand Challenge: Food Security ............................................................................................................. 19

Food Security: Crop Systems .............................................................................................................. 19

Food Security: Biotic Interactions ...................................................................................................... 20

Food Security: Enhanced Food Value ................................................................................................ 21

Grand Challenge: Environmental Conservation ..................................................................................... 23

Grand Challenge: Human Health & Well-being ..................................................................................... 24

Faculty Strength .......................................................................................................................................... 26

Teaching Program: Undergraduate ............................................................................................................. 28

Teaching Program: MS/PhD Graduate Education ...................................................................................... 31

Teaching Program: MPS Programs............................................................................................................. 34

Extension and Public Engagement .............................................................................................................. 35

Future Directions ........................................................................................................................................ 38

Appendix A: SIPS Strategic Plan - 2015 .................................................................................................... 39

Appendix B: Section Profiles ...................................................................................................................... 47

Section profile: Horticulture ................................................................................................................... 47

Section profile: Plant Biology ................................................................................................................. 50

Section profile: Plant Breeding and Genetics ......................................................................................... 56

Section profile: Plant Pathology & Plant Microbe Biology .................................................................... 62

Section profile: Soil & Crop Sciences .................................................................................................... 65

3

Overview of Structure and Activities The Cornell University School of Integrative Plant Science (SIPS) was launched by the College

of Agriculture and Life Sciences (CALS) in June 2014 to provide a unifying framework for five

Sections (formerly Departments) with interrelated activities in the plant sciences at Cornell:

Horticulture, Plant Biology, Plant Breeding & Genetics, Plant Pathology & Plant-Microbe

Biology, and Soil & Crop Sciences. The Sections are associated with distinct disciplines,

graduate fields, and knowledge bases, but are connected by urgent challenges and revolutionary

tools relevant to all plant scientists. While the School is led by a Director, each Section is led by

a Section Chair and two Sections have program leaders who manage the faculty and staff at

Cornell AgriTech (in Geneva NY). The Director is counseled by the Executive Committee which

includes the SIPS Director, the five Section Chairs, the Director of Undergraduate Studies (Plant

Sciences Major), the Chair of the Council of Extension Leaders, the Chair of the Directors of

Graduate Studies Council, the SIPS Assistant Director, and the SIPS Senior Administrative

Director.

Note: Given the page limitation, hyperlinks are used extensively throughout the self-study to

provide additional details and background information. A list of documents generated for the

self-study can be found here.

History Cornell University was founded in 1865, and the doors of Morrill Hall (the first building

constructed on the Ithaca campus) first opened in 1868. The history of plant science and the

land-grant mission trace back to the opening of the university, with George Caldwell directing

groundbreaking research in soil fertility in 1868, and the founding of the Cornell herbarium in

1869. Shortly thereafter, in 1874, Isaac Roberts initiated some of the first work on enhancing

crop production and began ‘resident instruction in agricultural practices’ (an early form of

extension). In 1885, J.C. Arthur became Cornell’s first recipient of a Doctor of Science degree,

using Koch’s Postulates to demonstrate Erwinia amylovora’s role in fire blight. Liberty Hyde

Bailey became the first Chair of Horticulture in 1888, and after becoming Dean in 1903, he

established the Department of Plant Breeding in 1907, and the Department of Botany in 1913.

The New York State Agricultural Experiment Station (renamed Cornell AgriTech in 2018) was

established in 1880 and became part of Cornell University in 1923. The rich and diverse history

of plant science at Cornell has a unique attribute – plant science departments involved in a

spectrum of activities from the most fundamental to applied have resided within CALS since its

founding, combining research, teaching, and the land-grant mission. An historical overview of

how the five Department/Sections have evolved since Cornell’s founding is shown in Figure 1.

4

Figure 1. Historical Overview of the SIPS Sections

SIPS Section Overviews SIPS was created to provide a unifying framework for five Sections (formerly Departments) with

interrelated activities in the plant sciences at Cornell: Horticulture, Plant Biology, Plant Breeding

& Genetics, Plant Pathology & Plant-Microbe Biology, and Soil & Crop Sciences. The Sections

are associated with distinct disciplines, graduate fields, and knowledge bases, as well as having

unique historical trajectories at Cornell. Numbers of personnel associated with each Section are

shown in Table 1.

Section profiles - including historical milestones and areas of strength in research, outreach and

extension, and teaching - have been provided by the Section Chairs and are included as links and

as a text Appendix B. The missions of the individual Sections are summarized.

Horticulture. To serve professionals, students and citizens of New York State, the nation, and

the world by collaborating with our diverse partners to identify challenging issues of primary

concern and generating and extending knowledge about fruits, vegetables, and landscape plants

for the purpose of sustaining the environment, enhancing economic vitality, and improving the

quality of life of individuals and their communities. (Section profile)

5

Plant Biology. To discover fundamental processes, mechanisms and molecular components

within plants, and the evolutionary processes that have driven these processes and their

incredible diversity for millions of years across the plant kingdom. These fundamental insights

will help drive innovations in translational and applied plant research. (Section profile)

Plant Breeding and Genetics. Genetic improvement of vegetable crops, agronomic crops and

forages for the benefit of society through the development of novel breeding methodologies, the

discovery, genetic study, and transfer of economically important traits or genes into genetic

stocks, the development and release of novel germplasm and varieties, and the training of new

generations of plant breeders. (Section profile)

Plant Pathology and Plant-Microbe Biology. To conduct research that will advance our

understanding of the interactions between plants and microbes as well as the causes of and

management options for plant diseases, and to transfer research-based information and

technology to stakeholders in New York State, the nation, and the world. (Section profile)

Soil and Crop Sciences. To advance and communicate knowledge relevant to agroecosystems

and their sustainable management within the context of accelerating global change. (Section

profile)

Table 1. Personnel numbers associated with the SIPS Sections

6

SIPS Vision/Mission

SIPS was launched to provide a framework for interrelated activities in the plant sciences at

Cornell. To quote from the 2014 proposal for SIPS creation:

In the coming decades, the world must arrive at solutions to the major challenges of feeding a

burgeoning population, mitigating and adapting to climate change, and preserving biodiversity

and essential ecosystem services. Plants underpin all agricultural and natural ecosystems and

environmental impacts on plant systems will cascade at local, regional, national, and

international scales. But plants will also be the basis for solutions. Through research, education,

extension and outreach, SIPS will help secure a sustainable future for coming generations.

The SIPS community envisions fundamental insights as the foundation for achieving better

plants, sustainably grown, serving the world.

Grand Challenges

In developing the 2015 SIPS Strategic Plan (Appendix A), five local and global needs/grand

challenges were identified.

Foundational knowledge of the structure, function, and evolution of plants, the soils in

which they grow, and the microbes and other organisms with which they interact

Empowered students and engaged and informed societal leaders and citizens

Informed and engaged growers and consumers: from New York State, to the US, to

developing countries

Food security and human health, nutrition, and economic vitality in the face of climate,

population, and resource limitation pressures

Environmental conservation and sustainable landscapes in the face of climate change and

urbanization

Strategic Direction and Progress We envision these grand challenges as organizing tools with several properties: (1) each meets a

local or global need; (2) they build on strengths within Cornell regarding research, education,

and land-grant missions; (3) they serve as a guide for development of new faculty positions and

help attract top candidates; (4) they represent an organizational framework for coordinating

activity among faculty across Sections; (5) they attract philanthropic and large-project

competitive funding; (6) they are clearly understood and supported by the public and

stakeholders; (7) they inspire and foster global collaborations on global problems.

The principal goal of SIPS, as stated in our founding document, is to:

…coordinate strategic planning and faculty hiring in the plant sciences and thereby allow

strength and innovation in areas of key importance in research, teaching and extension and to

grow the undergraduate major. The School of Integrative Plant Science will provide a visible

entity to match the College’s investment in the plant sciences. One aim of the school will be to

track societal and scientific needs going forward and to innovate and lead in these contexts. The

7

School will promote synergies due to structured interactions and juxtapositions that follow from

the School organization.

As shown in Figure 3, the SIPS organizational plan reflects these priorities. Furthermore, the

SIPS vision and organization, as described in the Strategic Plan Overview, align closely with

CALS and Cornell University priorities, particularly those that emphasize cross-unit

coordination and collaboration, interdisciplinary training, and enhanced visibility.

Figure 3. SIPS Organizational Plan

Integrated committees and administrative teams. As an important step toward

achieving our strategic vision, integrated administrative teams and cross-Sectional academic

committees have been established to guide the School’s educational and outreach missions and

to improve the quality and effectiveness of the School through improved coordination and

adoption of administrative best practices. A complete listing can be found in Specific Areas of

Structural Integration.

Staff coordination. SIPS administrative staff involved in management, financial reporting,

event planning, teaching support, student services, communications, and Section support

coordinate their activities across the School, greatly enhancing their overall effectiveness and

consistent coverage of essential functions. Staff teams hold regular meetings as well as meeting

with the SIPS Director twice yearly to provide input on the direction and operation of the School.

8

SIPS staff consistently reflect that the School-wide coordination and administrative structure has

improved the quality of their work experience. See the SIPS Admin Org Chart.

Communications. Lack of awareness of activities outside research specializations or specific

administrative units has been an historical barrier to collaboration and strategic coordination. To

enhance information flow, communications are coordinated SIPS-wide with a central web site,

curated cross-Sectional listservs, and regular meetings of a Communications and Logistics

Committee. A SIPS-wide newsletter (example) is sent out weekly by the Assistant Director to all

School personnel and other interested parties to inform the community about SIPS-related news,

relevant seminars and events, and recent publications from the SIPS faculty. News items are

identified from Cornell and outside sources, social media, or generated internally by the SIPS

communications staff to enhance visibility of School activities.

Coordinated faculty renewal is critical to the strategic direction of SIPS. It has been

difficult to identify the most effective method to build unity around faculty renewal in the first

few years of SIPS. This difficulty has been, in part, due to the ever-increasing need for new

faculty in all Sections. SIPS had 104 faculty when founded in 2014. As a result of retirements,

SIPS now has 84 faculty with many additional pending retirements. In 2018, the faculty renewal

process from the SIPS founding document was modified to increase faculty input and

coordination between Sections. SIPS faculty renewal is now an iterative process that begins with

long term visioning, includes several opportunities for coordinated input, and will culminate with

the SIPS Faculty Renewal Committee and Director identifying position descriptions to be sent to

the CALS Dean in April 2019.

SIPS is also involved in University-wide academic initiatives including the Provost’s Radical

Collaboration faculty recruitment effort. Of the seven strategic discipline areas, SIPS faculty are

represented on the taskforces for Data Science, Genome Biology, Sustainability, and Infection

Biology.

Diversity and inclusion. These efforts have been at the forefront of the SIPS strategic

direction. SIPS takes pride in the ways in which the land grant mission calls us to address the

needs of diverse stakeholders as well as our long tradition of international engagement. Building

on these core values, we are continuing to actively work at identifying barriers faced by

underrepresented groups among faculty, staff, and students and to insure that SIPS provides a

welcoming environment.

A Diversity Audit was conducted during the 2017/18 academic year to provide baseline

information for efforts to strengthen diversity and inclusion, and engaged students, staff,

and faculty. See report and also SIPS diversity data - Fall 2017

ABC Working Group (Achieving Belonging in our Community). As a follow up to the

audit, students, post-docs, faculty, and staff have come together to better educate the

SIPS community about inclusive and supportive behavior.

Diversity Preview Weekend. SIPS graduate students co-led and organized this event in

2018 and will do so again in Spring 2019. The event is aimed at familiarizing

underrepresented minorities with the grad school application process.

9

Changes in graduate recruitment practices. Upon recommendation of students, the

Graduate Field of Plant Pathology and Plant-Microbe Biology is evaluating 2019

applications GRE-blind to encourage a more holistic assessment of applicant potential.

Enhanced coordination with other Cornell units and campus-wide initiatives. The SIPS Sections and individual researchers have a long history of collaboration with other

units in CALS and Cornell and many of our faculty and senior researchers have appointments in

other academic units and centers. As a centralized hub for plant and agriculture-related science at

Cornell, SIPS has facilitated expansion of this network through coordinated participation in

cross-cutting initiatives such as the Cornell Institute for Digital Agriculture (CIDA), the

Industrial Hemp Initiative, and Organics@Cornell. SIPS is also partnering with service units

such as Cornell High Energy Synchrotron Source (CHESS) and Cornell NanoScale Science and

Technology Facility (CNF), to promote joint research related to plants and agriculture.

SIPS additionally represents a central hub for development of strategic partnerships with industry

and philanthropic groups interested in investing in plant and agriculture research. Marius

Weigert, the recently hired SIPS Strategic Partnerships Liaison, coordinates with Cornell

Technology Licensing (CTL), Alumni Affairs and Development, and others to increase industry

investment in SIPS research and expand opportunities for student internships. The network of

connections between SIPS and other units within CALS and Cornell is illustrated in Figure 4.

Figure 4. SIPS integration with other units at Cornell

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Facilities

Adequate facilities are critical to our ability to effectively address our grand challenges. Faculty

affiliated with SIPS are located primarily on the Ithaca campus and at Cornell AgriTech in

Geneva, NY. These together with satellite campuses, farms, and infrastructure resources are

significant in size, but upgrades and continued maintenance are desperately needed. Here there is

good news! Two buildings that faculty in SIPS occupy are scheduled for $65 million major

renovations. Bradfield Hall will undergo an upgrade of the HVAC system beginning in 2019.

While there are many other issues in Bradfield Hall (such as a lack of windows), the air handling

upgrade is critical. The Plant Science Building will undergo a near-complete renovation

beginning in 2021. The planning and design phase has been conducted and the architect is being

selected. Plant Science was built in 1929, and despite many partial renovations since then, much

of the current space is inappropriate for use as 21st century research and teaching space. These

renovations are critical, as SIPS will not be able to recruit or retain faculty, students and staff in

the current facilities. $5 millions have been approved for Phase I of a greenhouse upgrade in

Ithaca, but additional funds and upgrades will be needed on both the Ithaca campus and for aging

facilities at AgriTech. See maps of Ithaca based and Agritech facilities.

Field facilities are necessary for many SIPS faculty and we have access to farms and outstanding

field staff through our two Experiment Stations – the Cornell University Agricultural Experiment

Station (CUAES) and the New York State Agricultural Experiment Station (AgriTech) (Figure

4). However, the cutting-edge equipment necessary to complete our work is not always available.

We are working with the newly formed (2018) Cornell Initiative for Digital Agriculture, New

York State, and other funding agencies to identify a path to improvement. Additionally,

laboratory facilities such as a mass spectroscopy training facility are necessary to ensure our

students have the training and skills needed to succeed. Highlights of our facilities are the SIPS

Biodiversity Collections which include the living collection in our L.H. Bailey Conservatory

along with plant and fungal herbaria, and paleobotanical and plant anatomy collections. We are

fortunate to have the Plant Transformation Facility (PTF), Plant Disease Diagnostic Clinic,

Nutrient Analysis Lab (CNAL), Soil Health Lab, and Institute for Resource Information Sciences

(IRIS) reside within SIPS. The SIPS community also utilizes the Biotechnology Resource Center

(BRC), which hosts a comprehensive set of core sequencing and imaging facility services.

SIPS-occupied buildings on the Ithaca central campus SIPS-occupied buildings on the AgriTech central campus

11

Research Program Strength

Funding

A summary of funds from sponsored research can be found in Figure 5. Faculty receive funding

from foundations, federal, regional, state, and commodity sources. Many of the sponsored

projects are multidisciplinary with connections to other Departments and units at Cornell, along

with collaborators across the country and around the world. (See listing of research partners)

Figure 5. SIPS revenue, expenses and funding sources. See expanded explanation

Our strategic vision is guided by a combination of faculty-driven initiatives, emerging areas of

research, teaching and engagement, and stakeholder priorities. Several current major research

projects aligned with our vision and the amounts and sources of their funding are listed.

12

Digital Agriculture:

Deep Learning Unmanned Aircraft Systems for high-Throughput Agricultural Disease

Phenotyping

NSF award to Michael Gore (PI) and Rebecca Nelson (co-PI) $1,149,273, 2015 – 2019

Fostering Agricultural ReMote Sensing (FARMS) - use of unmanned aerial systems to

enable precision agriculture

NSF award to Sarah Pethybridge (co-PI) $746,844, 2018 – 2021

Accelerated breeding:

Next Generation Cassava Breeding Project

Gates Foundation award to Ronnie Coffman (PI), Tim Setter (Team Leader)

$29,999,458, 2017 – 2022

Quantitative Trait Locus Editing for Crop Improvement

NSF award to Adam Bogdanove (PI) and Susan McCouch (co-PI)

$5,577,710, 2015 – 2019

A Genome-level Approach to Balancing the Vitamin Content of Maize Grain

NSF Award to Michael Gore (co-PI) $3,722,030, 2016 – 2021

Controlled Environment Agriculture:

Strategic FEW and Workforce investments to Enhance Viability of Controlled

Environment Agriculture in Metropolitan Areas

NSF award to Neil Mattson (PI) $2,423,476, 2017 – 2020

Crop Development:

Developing an eastern broccoli industry through cultivar development, economically and

environmentally sustainable production and delivery

USDA NIFA award to Thomas Bjorkman (PI) $4,977,142, 2016 – 2021

Vitisgen2: Application of next generation technologies to accelerate grapevine cultivar

development

USDA NIFA award to Bruce Reisch (PI) $6,550,976, 2017 – 2021

Accelerating the development, evaluation, and adoption of new apple rootstock

technologies to improve apple growers profitability and sustainability

USDA NIFA award to Lailiang Cheng (PI) $4,281,618, 2016 – 2021

Industrial Hemp Research Initiative in New York State

The Cornell Hemp research program encompasses many areas of research in SIPS,

including basic metabolomics, seed science, microbiome research, disease, insect and

weed identification and management, cultivar trials, growth in controlled environments,

tissue culture and transformation, and a robust public breeding program. The program is

supported by $3,765,000 from New York State, providing funding to 10 faculty and 10

extension educators across the state. Research is complemented by state-wide extension

programming, a new undergraduate course on hemp, and an on-line certificate program

and one-year MPS program in Cannabis Science beginning in begin Fall 2020.

13

Fundamental processes:

Chloroplast soluble proteases and their physiological substrates

NSF award to Klaas van Wijk (PI) $997,393, 2016 – 2019

Transcriptional regulation of Cu homeostasis in cereals and its relationship with fertility

and grain yield

USDA NIFA award to Olena Vatamaniuk (PI) and Mark Sorrells (co-PI)

$499,838, 2018 – 2021

Transcriptomics and metabolomics to identify drivers of seed composition in oat

USDA NIFA award to Mark Sorrells (PI) $980,000, 2017 – 2020

Long distance signaling of iron deficiency via phloem

NSF award to Olena Vatamaniuk (co-PI) $870,864, 2018 – 2021

Initiation of Cell Size Patterning in Arabidopsis

NSF award to Adrienne Roeder (PI) $740,000, 2016 – 2021

Synthesis of Microcompartments in Plants for Enhanced Carbon Fixation

NSF award to Maureen Hanson (PI) $984,401, 2016 – 2020

Decadal nitrogen partitioning and retention: insights from whole-ecosystem, laboratory,

and molecular studies

USDA AFRI award to Enid Martinez (PI) $488,900, 2016 – 2019

Microbiome Research:

Microbial metabolic dependency and its impacts on the soil carbon cycle

DOE award to Dan Buckley (PI) and Johannes Lehmann (co-PI)

$2,031,644, 2016 – 2019

Multi-Scale Coupled Natural-Human System Dynamics of Nitrogen in Residential

Landscapes

NSF award to Jenny Kao-Kniffin (co-PI) $1,600,000, 2016 – 2019

Organic Agriculture:

Creating cover crops that organic farmers need: delivering regionally-adapted varieties

across America

USDA NIFA award to Matt Ryan (PI) and Laurie Drinkwater (co-PI)

$499,607, 2016 – 2019

14

Rankings

Cornell is frequently ranked among the top programs in Plant and Animal Science and in

Agriculture (US News). In NRC and other rankings, Cornell Plant Science ranks favorably, with

Plant Breeding frequently ranking first in the country. However, we are not aware of direct

comparisons between SIPS and Schools or Departments at other universities owing to our

unusual composition. While many universities have combined various plant science departments

into a single unit, Cornell’s organization of all plant science departments (now Sections) in the

same college (CALS) and same school (SIPS) is unique. The closest in similarity to SIPS may be

the Department of Plant Sciences at UC-Davis; however, at Davis the Department of Plant

Biology and the Department of Plant Pathology remain separate. Scientists in SIPS involved in

fundamental studies identify with peer institutions such as UC-Berkeley, Stanford, and Michigan

State, while other faculty see universities such as UC-Davis and University of Wisconsin as their

closest peers. (See summary of peer institution data). As a single School, SIPS unique strength in

research, scholarship, and creativity is rooted in our ability to rapidly identify and assemble

diverse teams of experts to address specific questions and stakeholder priorities as they arise. For

example, the progress our industrial hemp team has made in enabling NY farmers grow, harvest,

and process this crop is only possible because of the breadth of expertise across all five Sections.

Figure 6. Significance of foundational research to the grand challenges

15

Research connected to our Grand Challenges

Areas of research strength associated with the grand challenges in our strategic vision are

described below, highlighting selected examples of SIPS faculty research programs. While some

of these overlap with the previous listing of funded projects, this section more fully illustrates the

scope of our research activities. Following completion of the program review we look forward to

developing a revised strategic plan (currently scheduled for 2020), informed by perspectives

from the review team. Note that SIPS has many adjunct faculty (ADJ) with primary

appointments at the Boyce Thompson Institute (BTI), USDA and other Cornell units. These

faculty are included in the summary lists at the end of each section to underscore areas of

collective strength and are designated (BTI, USDA, or ADJ). Senior Research Associates (SRA)

and Senior Extension Associates (SEA) are also indicated.

Grand Challenge: Foundational Knowledge The SIPS community envisions achievement of fundamental insights on plants, soil, and plant-

associated microbes as the foundation for progress toward our grand challenges of food security,

environmental conservation, and human health and well-being.

Foundation Knowledge: Plants as Model Organisms

SIPS researchers are making breakthroughs in understanding the important and fundamental

processes at work in plants and their environments, as well as understanding the principles

underlying plant evolution and diversification.

Molecular mechanisms of plant development

Margaret Frank uses grafting as a tool to look at the

coordination of growth and development between root

and shoot systems, and the molecular mechanisms

underlying grafting-induced traits.

Jian Hua’s research explores the molecular

mechanisms underlying how plants respond to

temperature variation and associated regulation of

development and immunity.

Robert Turgeon investigates the physiology of phloem

transport and its relation to leaf development and the

structure and function of plasmodesmata.

Kenong Xu is focused on characterization of

regulatory networks in apple with an emphasis on

those involved in stress resistance and fruit quality and longevity.

Margaret Frank works on mechanisms

underlying grafting

16

Increased plant productivity through manipulation of chloroplasts and

photosynthesis

Klaas van Wijk investigates the role of proteolysis and plastoglobules in biogenesis and

other developmental transitions of chloroplasts in C3 and C4 plants

Maureen Hanson has re-engineeered chloroplasts of higher plants with high efficiency

Rubisco from an alga and is working to optimize efficiency under normal atmospheric

conditions.

Mike Scanlon investigates the developmental biology of leaves, revealing new strategies for

optimizing leaf angles so light is more efficiently captured by the whole plant.

Identification of new targets for enhancing agronomic

qualities

Olena Vatamaniuk is identifying proteins involved in metal

transport and signaling with potential use in creation of iron

fortified foods

Lailiang Cheng is finding new ways to manipulate the sugar and

acid content in apples in ways that enhance fruit quality.

Susheng Gan is focused on regulation of senescence as a strategy

for increasing crop yield and minimizing post-harvest loss

Advanced imaging technologies provide novel insights

into plant development

Adrienne Roeder analyzes plant developmental patterning over time by generating

computational models from confocal microscope images (news)

Wojtek Pawlowski studies meiotic recombination using genetics, biochemistry and several

advanced microscopy methods, such as restorative deconvolution, multiphoton excitation,

and structured illumination microscopy.

Taryn Bauerle images very fine-scale spatial relationships between competing tree roots in a

3D space using X-ray computed tomography.

New technologies for computational analysis

Gaurav Moghe’s research involves in silico process odeling and creation of predictive

computational models to reveal enzyme function, pathway organization, and secondary

metabolite pools (news)

Joss Rose is developing new protocols and computational tools to characterize cell wall

proteins with particular emphasis on cell wall changes during fruit development and

molecular interactions with pathogens

Faculty and senior researchers with involvement in these areas: Taryn Bauerle - Lailiang

Cheng - Giulia Friso - Susheng Gan - Maureen Hanson - Jian Hua - Margaret Frank - Tom

Olena Vatamaniuk conducts

research on Fe distribution

in Arabidopsis

17

Owens - Wojciech Pawlowski - Adrienne Roeder - Joss Rose - Mike Scanlon - Bob Turgeon -

Klaas van Wijk - Olena Vatamaniuk - Randy Wayne - Carmen Catala (BTI) - Zhangjun Fei

(BTI, USDA) - James Giovannoni (BTI) - Dan Klessig (BTI) - Joanne Labate (USDA) - Li Li

(USDA) - Lukas Mueller (BTI)

Systematics and Biodiversity

Biodiversity resources such as the L.H. Bailey Hortorium and Cornell Plant Pathology

Herbarium are becoming ever more important resources for genomic study of biodiversity and

evolution

Chelsea Specht investigates the processes and patterns involved in the evolution and

diversification of monocots, with a focus on the Zingiberales.

M. Alejandra Gandolfo’s research centers on paleobotany, answering questions about the

origin of angiosperms, the evolution of seed plant characters, and evolution of floras in the

Southern Hemisphere.

Kevin Nixon focuses on evolution and systematics of angiosperms with emphasis on the

Fagaceae. He has also written software packages used for phylogenetic analysis.

Jeff Doyle’s research concerns the origin and evolution of polyploidy in plants, also

focusing on legume systematics and the evolution of nodulation

Kathie Hodge works on the biodiversity and ecology of fungi with a focus on insect-

associated and food-spoilage fungi and is a national expert on fungal identification and

poisoning

Faculty and senior researchers with involvement in Systematics and Biodiversity: Bill

Crepet - M. Alejandra Gandolfo - Jerrold Davis - Kevin Nixon - Jeff Doyle - Chelsea Specht -

Kathie Hodge - Gaurav Moghe

Foundation Knowledge: Soil Properties and Impact

Understanding the properties of soils, soil impact on plant productivity, and the soil microbial

communities is foundational to both environmental conservation and food security.

Characterization and manipulation of soil microbes

Dan Buckley investigates the soil microbiome and its impacts on ecosystem health, the

plants we grow, the water we drink, and the air we breathe.

Jenny Kao-Kniffin investigates how soil microbes can be used to confer selective growth

benefits to plants, providing a potential strategy for promoting growth of desirable plants

and suppressing weeds without the use of chemicals

Janice Thies looks at the fate of insecticidal Bt-toxin in the soil, the role of the rhizosphere

microbial community, and how different agricultural practices alter soil properties.

18

Understanding and manipulating nutrient cycling in the soil

Johannes Lehmann’s research is focused on

understanding of biogeochemical cycles of carbon

and nutrient elements in soil, developing methods for

soil carbon sequestration with biochar, resource

recycling from waste to fertilizers, and providing

important insight into regional and global element

cycles. (news)

Harold Van Es’s program concerns precision soil

management, with emphases on a holistic soil health

management framework, and a computational tool for

precision nitrogen management (Adapt-N) that was

recently commercialized (news)

Enid Martínez focuses on molecular scale investigations of the interaction of organic carbon

and nitrogen at mineral surfaces and the movement of major, trace, and toxic elements

through plants and soil.

Faculty and senior researchers with involvement in these areas: Dan Buckley - Jenny Kao-

Kniffin - Johannes Lehmann - Enid Martínez - Janice Thies - David Wolfe - Dawit Solomon

(SRA) - Jeffrey Melkonian (SRA)

Foundation Knowledge: Plant-Associated Microbes

In the School of Integrative Plant Science (SIPS) we are making breakthroughs in understanding

how microbes and other organisms interact with plants leading either to beneficial interactions or

disease.

Identification of virulence factors and their targets to uncover sources of

susceptibility and resistance

Adam Bogdanove works on TAL effector proteins

in bacterial pathogens. TAL effectors are additionally

used as biotechnological tools for DNA

modification.

Marc Fuchs explores the molecular determinants of

virus disease of grapevine and interaction with

insect vectors as part of his program on detection

and control of viral diseases

Alan Collmer works on the bacterial pathogen

Pseudomonas syringae and the means by which

Model of nitrogen run-off developed by

Harold van Es's Adapt-N team

Graduate student Morgan Carter in the

Bogdanove lab examines her samples

19

individual toxins and type III effectors interfere with plant defense pathways.

Greg Martin identifies defense pathways and proteins in tomato. By screening for variation in

responses among different cultivars and relatives, Martin's group is identifying novel sources

of host resistance.

Exploring beneficial interactions with other organisms to more effectively

promote plant health

Teresa Pawlowska studies arbuscular mycorrizhal fungi and how bacterial endosymbionts

of the fungi contribute to the symbiotic relationship.

Faculty and senior researchers with involvement in these areas: Adam Bogdanove - Alan

Collmer - Marc Fuchs - Kathie Hodge - Gregory Martin - Michael Milgroom - Teresa

Pawlowska - Gillian Turgeon - Keith Perry - Clare Casteel (July 2019) - Magdalen Lindeberg

(SRA) - Xiaohong Wang (USDA) - Michelle Heck (USDA) - Melanie Filiatrault (USDA) -

Stewart Gray (USDA) - Bryan Swingle (USDA) - Maria Harrison (BTI) - Georg Jander (BTI)

Grand Challenge: Food Security Global and national food security is one the greatest challenges we face. SIPS researchers are

working on many fronts to develop strategies for increased food production including improved

cropping systems, research on biotic interactions, and efforts directed at enhancing food value.

Food Security: Crop Systems

Development and deployment of crop systems that use plant genomic diversity and field-data

systems to maximize productivity, minimize resource inputs, and increase stress tolerance is

integral to food security. Several focus areas are highlighted, though there are clear links to

research areas described under other grand challenges.

Optimizing growing conditions to maximize productivity

Greg Peck researches strategies for increasing the production of value-added fruit-based

products such as hard cider using sustainable management practices (news)

Steve Reiners focuses on cultural practices and variety selection for the processing vegetable

industry, with particular interest in using cover crops to maximize nutrient cycling and

reducing disease incidence

Terence Robinson is dedicated to improving fruit production through identification of

rootstocks most suitable for New York growers and development of orchard management

practices that improve fruit size and quality

Justine Vanden Heuvel researches how light and temperature influence flavor and aroma

in wine grapes and how these environmental variables can be optimized to improve fruit

quality (news)

Marvin Pritts focuses on berry production and how cultivation practices such as environment

management with high and low tunnels can enhance growth in colder climates

20

Chris Watkins, in addition to his responsibilities as Director of Cornell Cooperative

Extension, researches management strategies for extending post-harvest storage of apples.

Tim Martinson, Northern Grapes Project leader, focuses on how best to integrate varieties

and cultural practices to maximize productivity and fruit quality in the New York

environment (SEA) (news)

Controlled Environment Agriculture

Neil Mattson investigates how different environmental

variables affect the growth of greenhouse crops and how

variables such as lighting and greenhouse infrastructure can

optimize indoor crop production (news)

Digital Agriculture

Learn more about the Cornell Initiative for Digital Agriculture

(CIDA), an initiative involving multiple SIPS faculty

Michael Gore’s research includes a major project focuses

on development and application of field-based, high-

throughput phenotyping tools for plant breeding and genetics research, and, in

collaboration with Rebecca Nelson, image analysis for diagnosis of Northern corn leaf blight

(news)

Sarah Pethybridge has generated image analysis tools such as Leaf Doctor and Estimate for

diagnosis of fungal diseases, as part of their work on the epidemiology and control of

diseases of processing vegetables (news)

Terry Bates collects and integrates data from soil, canopy, and crop sensors to understand

spatial relationships and improve management of Concord vineyards (SRA)

Faculty and senior researchers with involvement in these areas: Neil Mattson - Jason Londo

- Marvin Pritts - Steve Reiners - Terence Robinson - David G. Rossiter - Tim Setter - Justine

Vanden Heuvel - Michael Gore - Sarah Pethybridge - Greg Peck - Rebecca Nelson - Terry Bates

(SRA) - Tim Martinson (SEA)

Food Security: Biotic Interactions

Plants fight to grow and thrive in the face of threats from weeds and pathogens including viruses,

bacteria, fungi, and oomycetes. SIPS researchers are investigating ways of combating these

threats using a range of strategies including early detection, reduction in inoculum, and chemical

control. Several focus areas are highlighted, though there are clear links to research listed under

our other grand challenges.

Neil Mattson evaluates hydroponic

trials of leafy greens

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Strategies for effective and sustainable weed control

Toni DiTommaso’s and Matt Ryan’s research focuses on understanding how different

environments influence weed species and how soil properties and biological agents, and

cultivation practices can be used in weed control

Strategies for pathogen detection and control

Gary Bergstrom conducts research on disease of small grains, maize, and soybean focusing

on factors that increase the risk and spread of disease, and the efficacy of different control

methods for fungal diseases (news)

Kerik Cox investigates fungal pathogens of fruit crops such as apples, stone fruit, and bush

berries, and how different management practices alter the pathogen life cycle

David Gadoury explores innovative ways of controlling

powdery mildew disease with UV-B light (news)

Keith Perry, Director of the New York State Foundation Seed

Potato Program, has developed macroarrays for virus

detection in potato and grapevine, facilitating the screening

of plant material for large numbers of pathogens and having

applications in quarantine and clean seed programs

Margaret McGrath is focused on management of vegetable

crop diseases grown on Long Island using both

conventional and organic production

Chris Smart’s research involves detection and management of

fungal, oomycete and bacterial diseases of vegetables.

Smart collaborates with the Mazourek program on selection

of disease resistant lines.

Alan Taylor is focused on seed biology and development of

seed treatments that protect against insect pests and pathogens

Faculty and senior researchers with involvement in these areas: Gary Bergstrom - Kerik

Cox - Antonio DiTommaso - Marc Fuchs - Margaret McGrath - Keith Perry - Sarah Pethybridge

- Matt Ryan - Chris Smart - Alan Taylor - Courtney Weber - Michael Gore - Rebecca Nelson -

Margery Daughtrey (SEA), David Gadoury (SRA) – Juliet Carroll (SEA) - Lance Cadle-

Davidson (USDA)

Food Security: Enhanced Food Value

Development of new cultivated plants and analytical strategies that make use of the latest

genomic tools is integral to regional, national, and global food security. The highlighted focus

areas are clearly connected to research listed under our other grand challenges including

foundational research on plant genomics. See also: Plant varieties licensed by SIPS faculty

Summer scholar in the Smart lab

conducts a pathogenicity assay

22

Development of new cultivated plants with enhanced food value

Thomas Björkman is involved in development of commercial broccoli varieties from existing

germplasm that are capable of thriving in growing conditions of northeastern states, thereby

minimizing the flavor-killing lag between harvest and consumption that occurs when

broccoli is imported from more temperate regions (news)

Susan Brown studies apple genetics and uses marker assisted breeding and transgene

technology to develop new apple varieties including the recently released SnapDragon and

RubyFrost.

Walter De Jong works on genetic improvement of potato by conventional and molecular

genetic means as well as identification of genes that control tuber color and shape. (news)

Phillip Griffiths is focused on genetic

improvement of snap bean and brassica

crops, with particular focus on traits

conferring resistance to plant diseases.

Susan McCouch conducts genetic analysis of

rice and identification of genes and

quantitative trait loci in wild and exotic

species that enhance productivity of modern

rice cultivars (news)

Martha Mutschler-Chu works on the genetic

improvement of tomatoes and onion with a

particular focus on pathogen and insect pest resistance.

Bruce Reisch specializes in development of new grape varieties with the aid of marker-

assisted breeding technology. Wine quality, disease resistance, and cold tolerance are

among the traits of greatest interest. (news)

Margaret Smith focuses on genetic improvement of maize with an emphasis on traits that

enhance performance in marginal environments

Mark Sorrells is engaged in genomic analysis of small grains and the mapping and

characterization of candidate genes associated with stem rust resistance, nutritional

quality and other kernel properties (news)

Development of new strategies for genome-assisted breeding

While many SIPS researchers make use of genome assisted breeding technologies, the Robbins

program, in addition to others associated primarily with USDA, are focused on development of

these strategies

Kelly Robbins conducts advanced modeling and computational analyses for improving the

efficiency of breeding programs and increasing understanding of complex traits

Faculty and senior researchers with involvement in these areas: Thomas Björkman - Susan

Brown - Walter De Jong - Jeff Doyle - Michael Gore - Phillip Griffiths - Neil Mattson - Susan

Walter De Jong breeds potatoes widely adopted

for the chipping market

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McCouch - Martha Mutschler-Chu - Rebecca Nelson - Marvin Pritts - Stephen Reiners - Bruce

Reisch - Kelly Robbins - Terence Robinson - Margaret Smith - Mark Sorrells - Alan Taylor -

Chris Watkins - Gennaro Fazio (USDA) - Edward Buckler (USDA) - Jean-Luc Jannink (USDA)

- Tim Martinson (SEA) - Maricelis Acevedo (ADJ)

Application of breeding methods and agriculture strategies targeted to the

developing world

SIPS researchers with interests in plant breeding and environmental conservation have a long

history of involvement in international research, with collaborations in Asia, Africa, the Middle

East and Latin America and with a wide range of organizations. Selected international activities,

not included under other focus areas, are described here. Read more about CALS International

Programs

Ronnie Coffman, Cornell’s Director of International Programs, is engaged in developing

world agriculture on several fronts including the Durable Rust Resistance in Wheat project

and the NextGen Cassava Project

Rebecca Nelson is Scientific Director for The McKnight Foundation's Collaborative Crop

Research Program that funds agricultural research in developing countries. Her research

program investigates natural genetic diversity for quantitative disease resistance in maize.

Andrew Mcdonald (new hire) comes to SIPS from CIMMYT in Nepal and brings extensive

experience in the global area to his position in international cropping systems

Faculty and senior researchers with involvement in International Agriculture: Ronnie

Coffman - Susan McCouch – Tim Setter - Johannes Lehmann - Rebecca Nelson - Julie Lauren –

Marvin Pritts – Kelly Robbins - Janice Thies - Harold van Es - Jian Hua - Phillip Griffiths -

Michael Gore – Mark Sorrells - Andrew Mcdonald (new hire) - Dawit Solomon (SRA) - Frank

Shotkoski (ADJ) - Sarah Davidson Evanega (ADJ) - Peter Hobbs (ADJ) - Vernon Gracen (ADJ)

- Peter Gregory (ADJ) - Kandukuri Raman (ADJ) - Hale Ann Tufan (ADJ) - Maricelis Acevedo

(ADJ) - Jean-Luc Jannink (USDA)

Grand Challenge: Environmental Conservation This grand challenge concerns the development of sustainable agroecosystems that improve soil

health and provide forage, fuel, and fiber. Three focus areas are described in detail, though all are

closely linked to foundational research, food security, and human health and well-being.

Agroecosystem management for soil health and conservation

See the Soil Health web site for additional information

Matt Ryan is focuses on enhancing sustainability of agroecosystems through improved

cover crop management, ecological weed management, and conservation agriculture

(news) (see also Organic@Cornell)

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David Wolfe's research includes improved accounting of soil carbon and greenhouses

gasses and prediction of climate change impact on agriculture

Laurie Drinkwater focuses on the role of variables such as cover crops and agricultural

practices (organic/conventional) on retention of soil nitrogen

Imaging technology for environmental analysis, resource management, and

digital agriculture

See the Institute for Resource Information Sciences (IRIS) for additional information

Ying Sun, uses remote sensing of solar-induced

chlorophyll fluorescence and land surface modeling

to quantify photosynthesis and its response to

changing climate/stress (news)

Susan Hoskins, Remote Sensing Program Leader at

IRIS, collects and summarizes information on the

type and location of land use and land cover, as

well as on other renewable and non-renewable

resources (SRA)

Stephen Smith, GIS Program Leader at IRIS, is

focused on methods of spatial analysis, statistics

and cartography, and their many applications to environmental analysis (SRA)

Development of sustainable agro-industry

See the Industrial Hemp and Willowpedia web sites for additional information

Larry Smart investigates breeding and cultivation of willow and industrial hemp, and the

genetics of biomass and yield to maximize potential as sources of bioenergy

Jerome Cherney researches the profitable and sustainable production of forage crops for

use as biofuels and livestock feed

Don Viands and Julie Hanson focus on genetics of perennial, herbaceous plant species for

forage, biofuels, and other uses.

Faculty and senior researchers involved in Environmental Conservation:

Johannes Lehmann - Harold Van Es - Jerome Cherney - Laurie Drinkwater - Murray McBride -

Matthew Ryan - Larry Smart - Donald Viands - David Wolfe - Ying Sun - Toni DiTommaso -

Susan Hoskins (SRA) - Stephen Smith (SRA) - Jean Bonhotal (SRA) - Deborah Grantham

(SRA) - Julie Hansen (SRA) - Julie Lauren (SRA) - Jeffrey Melkonian (SRA) – Anu Rangarajan

(SRA) - Juliet Carroll (SEA)

Grand Challenge: Human Health & Well-being Plants produce a vast array of natural products which can enhance our lives through flavor and

health benefits. Plant also contribute to health and well-being by their presence in public spaces.

Christine Yao-Yun Chang in the Sun program

measures photosynthesis

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Culinary and Health Benefits

Michael Mazourek is focused in part on development of specialty vegetables such as small,

extra sweet squash and peppers with altered taste profiles for enhancement of the aesthetic

and culinary appeal of New York produce.

Mike Gore engages in genetic dissection of metabolic seed traits to increase content of

nutrients such as vitamin A and provitamin A carotenoids

Courtney Weber develops improved berry varieties with

emphasis on disease and insect resistance, fruit quality,

and beneficial phytochemicals (news)

Promote growth of plants in urban and other

developed settings

Nina Bassuk improves the quality of urban life by

enhancing the functions of plants within the urban

ecosystem. Read more at Urban Horticulture Institute.

Neil Mattson directs the Controlled Environment

Agriculture group, researching advances in lighting and

greenhouse technologies that can reduce the carbon footprint of local greenhouse-grown

produce (news)

Murray McBride investigates the presence and uptake of heavy metals in urban garden

settings and former orchard sites

Provide horticultural resources for growers and producers of turf and

ornamentals

Mark Bridgen, Director of the Long Island

Horticultural Research and Extension Center,

focuses on new plant development, breeding,

and propagation of herbaceous ornamentals and

flowers

Bill Miller researches floricultural crop

production and postharvest physiology, with a

focus on growth control, ethylene effects on

plants, carbohydrate metabolism in bulbous

plants, and physiological disorders.

Frank Rossi addresses practical problems in

turfgrass management with emphasis on environmental compatibility and economic

feasibility (news)

'Dickens' strawberry released in

2018 by the Weber program

Frank Rossi talks with students about the turf

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Promote the significance of public gardens and natural areas to health and

education

Don Rakow specializes in the design, history, and management of public gardens, and has

worked to bond students with nature through Nature Rx@Cornell.

Lori Brewer works with CCE educators and Master Gardener Volunteers to promote

successful gardening experiences for NYS households

Marcia Eames-Sheavly is focused on enhancing aesthetic appreciation of plants and

promoting connection with plants through garden-based learning

Christopher Dunn, Director of Cornell Botanic Gardens, oversees Cornell’s 3500 acres of

botanical gardens, arboretum, and network of natural preserves, and promotes a mission of

conservation and community engagement.

Faculty and senior researchers working in Human Health and Well-being:

Nina Bassuk - Lori Brewer - Mark Bridgen - Marcia Eames-Sheavly - Michael Mazourek - Bill

Miller - Donald Rakow - Frank Rossi - Anu Rangarajan (SRA), Christopher Dunn (ADJ)

See also: SIPS faculty research and extension activities organized by crop

Faculty Strength

Recruitment and Retention. Since the formation of SIPS, we have recruited eleven

outstanding new faculty (Clare Casteel (July 2019), Margaret Frank, Alejandra Gandolfo, Awais

Khan, Chelsea Specht, Andy McDonald, Gaurav Moghe, Greg Peck, Sarah Pethybridge, Kelly

Robbins, and Ying Sun) and there are four searches currently underway. Our new faculty have

invigorated the School and brought new ideas and enthusiasm to our research, teaching and

extension programs. Looking to the future, ten new faculty positions and nine retirements are

expected between now and the end of 2021. An additional 16 SIPS faculty are 65 or older.

Our faculty are sought after by other universities and we have successfully worked with CALS

administration to retain six faculty members since SIPS founding. Retention packages were

developed as a collaboration between the faculty member, Section Chair, SIPS Director, and

CALS Sr. Associate Dean. Salary and program financial incentives along with dual career

partner accommodations were critical to keeping faculty at Cornell. In several instances

additional or improved laboratory space, and the development of a future interdisciplinary lab

were also part of the retention package.

Sections within SIPS are critical for disciplinary and faculty strength. Section Chairs are

responsible for (1) leading strategic planning and faculty hiring for the Section in the context of

the School strategic plan, (2) mentoring and review of faculty, (3) managing tenure and

promotion, including selecting representatives for the SIPS committee on Promotion and Tenure,

(4) working with the Plant Sciences Curriculum Committee to manage teaching assignments, (5)

identification of Section Extension leaders, and (6) fiscal management of their Section. They also

represent the Section at administrative meetings. A full description of duties and responsibilities

27

of the Director and Section Chair is enumerated in the SIPS founding document. Importantly,

Section Chairs are responsible for establishing a mentoring committee for each new faculty

member as well as having responsibility for post-tenure review.

While the SIPS administration has no funds to incentivize collaboration, cross-Sectional

interactions among faculty have been encouraged by initiatives such as digital agriculture,

organic agriculture, and industrial hemp, in addition to the long-standing program work teams

focused on various specialty crops and commodities. Growing areas of interest such as

microbiome research, adaptation to climate change, and controlled environment agriculture are

inspiring coordinated faculty searches. The renovation of the Plant Science Building will greatly

aid in breaking down historic physical boundaries.

Our graduate students are at the forefront of enhanced cross-Sectional interaction, with

coordinated recruitment, career development, and social events. The Schmittau-Novak Small

Grants Program was specifically designed in 2016 to incentivize graduate student collaboration

across SIPS.

Examples of recent cross-sectional activities within SIPS:

Publication: Seasonal changes in amino acids and phenolic compounds in fruits from

hybrid cross populations of American grapes differing in disease resistance.

Bruce Reisch (Horticulture) and Peter Davies (Plant Biology)

Publication: The heavy metal budget of an urban rooftop farm.

Tom Whitlow and Nina Bassuk (Horticulture) and Jonathan Russell-Anelli and Mike

Rutzke (Soil and Crop Sciences)

U.S. Patent App: Gene expression monitoring for risk assessment of apple and pear fruit

storage stress and physiological disorders.

Chris Watkins (Horticulture) and Jim Giovannoni (Plant Biology)

NSF Award: Quantitative Trait Locus Editing for Crop Improvement

Adam Bogdanove (Plant Pathology) and Susan McCouch (Plant Breeding)

Awards. The excellence of our research, extension and teaching is reflected in the range of

high profile honors awarded to many among our faculty. A few examples since SIPS’ founding

include the election of Susan McCouch to the U.S. National Academy of Science, Johannes

Lehmann to the German National Academy of Science, Kenong Xu’s receiving of a Presidential

Early Career Award, and the awarding of the $1 million Tulane Prize to Harold van Es on behalf

of Adapt-N. SIPS faculty have also received numerous awards from CALS, Cornell, and the

SUNY Chancellor in addition to recognition from professional societies, other universities, and

industry groups. Sections are responsible for the majority of award nominations, with some

Sections having award nomination committees, and others using a more ad hoc process. (See list

of faculty awards since the formation of SIPS)

Publications represent an important measure of productivity. Faculty publications are tracked

with Web of Science reports and shared on the SIPS News Site and in the weekly all-SIPS

newsletter to familiarize the community with the breadth of SIPS research activities. Funding is

28

tracked by financial reporting staff with awards, editorships, with invited talks being largely self-

reported.

Faculty in SIPS publish research articles and extension and outreach materials in a wide array of

journals in addition to fact sheets, book chapters, and books. Owing to our sheer size we

collectively produce more published output than peer departments. Five of our faculty have been

listed for one or more years among the most cited researchers in the world. (See a list of faculty

publications since the formation of SIPS) Note that awards and publications lists do not include

USDA, BTI, and other adjunct faculty.

International Collaborations. Faculty from all the SIPS Sections are engaged in

international research, teaching and outreach. Our connection to IP-CALS is strong and vibrant,

underscored by our recent hire of Andy McDonald, a research and extension expert in

international cropping systems. As IP-CALS goes through potential changes with the formation

of a new Global Development group in CALS, SIPS will work hard to ensure that plant scientists

remain engaged with the Cornell international agriculture team, and with the Plant Sciences

Major.

Teaching Program: Undergraduate Students from many undergraduate majors take courses taught by SIPS faculty, but Plant

Sciences is the only undergraduate major wholly administered by SIPS. Other closely allied

majors include Agricultural Sciences, Biological Sciences, Viticulture and Enology,

Environmental and Sustainability Sciences, and International Agriculture and Rural

Development. The Biological Sciences Major is unique in that it is administered by the Office of

Undergraduate Biology and is cross-college. SIPS is a significant contributor to the Biological

Sciences Major, with many faculty teaching and advising Biology students, in addition to direct

participation in several concentrations including: Microbiology, Plant Science, and Systematics

& Biotic Diversity. Of the 159 classes offered in SIPS, 42 are intro level undergraduate, 75 are

upper-division undergraduate, and 42 are graduate level courses. Across all categories, less than

1 % of classes are taught by assistant professors and 20% are taught by non-tenure track

academic appointees. Teaching responsibilities fall under the purview of the SIPS Plant Sciences

Curriculum Committee, and this committee works together with section chairs to assign

responsibilities.

The Plant Sciences teaching program has undergone a significant transformation over the past

five years into what we believe is now a flagship major in the college and university. In the past,

Plant Sciences Majors selected their course of study in no particular order from lists of

requirements. Enrollment was low, students had relatively little opportunity for connection and

camaraderie, and acceptance rates were high relative to the rest of the college. CALS, which

admits directly to majors, was reluctant to accept more Plant Sciences majors because the quality

of the applicant pool was lower, on average, than for many other majors.

Early in the formation of SIPS, steps were taken to address deficiencies in the major and

curriculum. Many of these changes were based on the 2014 Purdue-Gallup survey on student

engagement which found that students greatly benefit when they feel that faculty actively care

29

about them, engage with them, and encourage their interests. In addition, students who were able

to apply classroom learning to longer-term projects doubled these measures of success.

Four significant changes were implemented to incorporate these findings:

1. Curriculum. Seven learning outcomes were developed to guide the curriculum, with a core

curriculum of 10 courses developed as a requirement for all students in the major.

Concentrations were developed based on possible career paths rather than on former Department

designations. Currently there are 10 concentrations that students choose from, with the option to

design one’s own concentration. All majors now graduate with breadth in plant sciences and

depth in their focus area.

2. Curriculum Enhancements. Starting in 2015, a 1-credit supplement to general

chemistry was created to help Plant Science Majors better understand the subject material. This

has resulted in significant improvements in student performance.

Many of our upper level classes have labs and field trips so students can learn by seeing and

doing. All students are now required to complete an out-of-classroom experience for at least one

semester or summer and complete a guided reflection on the experience (PLSCI 4900) be it an

internship or research experience. Each student must attend and summarize 14 plant-related

seminars as a graduation requirement and is required to take a course on presentation skills

(PLSCI 4950). A senior symposium is held each May where soon-to-be graduates deliver a

presentation on their out-of-classroom experience in front of faculty and peers.

Special courses offer students the opportunity for international experience with recent trips

organized to Chile, Costa Rica, India, Myanmar, Belize, Argentina, Nicaragua and Cuba. About

30% of our students have an abroad experience before they graduate. SIPS faculty are involved

in teaching Cornell courses in China and Chile for credit, with programs being developed in

Argentina.

3. Student Support. A new course (PLSCI 1110) was developed for first-year students that

familiarizes them with support services at Cornell, introduces them to faculty, exposes them to

opportunities for study abroad and graduate school, and takes them to local natural areas.

Leadership experiences are built into the course and students engage in a service project in the

community. They also begin to create an ePortfolio which they build over the course of their

Cornell career, with achievements organized by the seven learning outcomes for the major. Upon

graduation, students have an electronic record of their accomplishments and examples of their

work that they can share with employers or those whom they ask for letters of recommendation.

Peer mentoring has been implemented to ease the transition of first year students. Upperclass

volunteers are selected and trained in mentorship and each is assigned 5 or 6 students. Milestones

are established for mentors and mentees. There are also many opportunities for social gathering

among the Plant Sciences Majors. They have their own lounge for studying and there are several

active clubs, including Hortus Forum, Fungi Fanatics, and the Dilmun Hill student organic farm.

30

Each Plant Sciences undergraduate student has a faculty advisor. First-year students are all

advised by the Director of Undergraduate Studies for the first semester. During the Fall semester,

SIPS has dinners where faculty and students get to know one another, and students can than

choose their faculty advisor by the end of the first semester. Transfer students are assigned an

advisor that matches their stated career goals. The Plant Sciences major has advisor training each

August, and advisors generally meet with advisees twice per semester. The college provides an

annual report that evaluates the effectiveness of our advising based on student surveys.

Additionally, we have an end of year lunch with our graduating seniors and ask for feedback on

all aspects of their undergraduate education including advising.

4. Peer dialog. Each course undergoes peer dialog/review every third time it is taught. Faculty

are encouraged to invite reviewers from a Section other than their own and instructors are

provided with the CWSEI Teaching Practices Inventory. The Undergraduate Teaching

Coordinator receives confidential feedback and anonymously summarizes the good practices that

were observed to share among the SIPS

community. Faculty are free to use the

letter in promotion packages, but are

not required to do so. The intent of

peer dialog is to encourage

constructive, non-threatening

conversation about instructional best

practices. SIPS faculty also gather a

few times each semester to discuss

items of interest to teachers.

New reality. The changes

described have had a positive impact

on the number and quality of our

students. There are currently 117

students in the Plant Sciences Major.

Acceptance rates have fallen to the

low 20% range, with applications

increasing from 39 in 2011 to 94 in

2018. Yield rate (enrolled/admitted)

was an astounding 91% for 2018.

Enrollment in our courses has

increased 50% in the past 5 years

(2304 students in 2013; 3456 in

2018). To further enhance our

curricular strength we have recently

applied for and received a $1 million

grant from Cornell - Enhancing the

core curriculum of the Plant Sciences

Major through active learning.

Figure 7. Post-graduation career paths for 2018 graduates

in the Plant Sciences and related majors

31

Plant Science Minor. We additionally offer 8 minors that are managed by SIPS, including

the Plant Science Minor.

Leadership Minor. The University’s leadership minor is directed out of SIPS. This minor is

a little over a year old with 50+ declared participants representing most colleges in the

university. It aims to integrate co-curricular leadership training with formal coursework and

experiential learning. The minor partners with the Big Red Leadership Institute, the Public

Service Center, Cornell Outdoor Education, ROTC and Engaged Cornell to complete Tier I of a

four tier process. The last tier requires a semester-long experience involving learning outcomes

and a coach, and the completion of a reflective ePortfolio. It is coordinated with the fellows

program in the College of Business and with the Cornell Institute for Public Affairs.

Non-majors. SIPS faculty teach several courses that attract non-majors to plant science.

Examples include: Art of Horticulture; Green World, Blue Planet; Hands-On Horticulture;

Hollywood Biology; Magical Mushrooms, Mischievous Molds; Plants, Genes and Global Food

Production; and Vines to Wine. These students often go on to take additional plant science

classes.

Post-graduation. While roughly half of Plant Sciences Majors attend graduate school

following graduation from Cornell, many others find opportunities in industry, government, and

public service. Representative examples for 2018 are shown in Figure 7 for graduates of the

Plant Sciences Major as well as Agricultural Sciences and Viticulture and Enology, both of

which depend significantly on our course offerings.

Teaching Program: MS/PhD Graduate Education

Graduate Fields and concentrations

Graduate study at Cornell is organized using a Field structure. Graduate Fields are composed of

faculty members from a number of Departments and/or Sections (in the case of SIPS) who come

together around a shared intellectual interest, and may draw from different campuses or colleges.

Graduate students are admitted to Fields of Study. Within each Field, students select major and

minor subjects. One of the advantages of the Field structure is that they broadly span disciplines

and incorporate faculty from other units at Cornell. For example, students in Soil & Crop

Sciences can have Field members on their special committee from Natural Resources or Earth

and Atmospheric Sciences. Students in Plant Biology can have committee members from

Entomology or Ecology and Evolutionary Biology. The student’s special committee serves as the

primary source of mentorship.

There are five Graduate Fields in SIPS corresponding to the five Sections with multiple

concentrations in each. Collectively these Fields provide a wealth of opportunities for graduate

students to connect disciplines, creatively solve problems, and integrate complex systems, with

the goal of preparing them for diverse careers and futures as professional and societal leaders.

32

Courses. The Graduate Fields within SIPS do not have strict course requirements because the

number and nature of courses taken varies greatly depending on the recommendations of a

student’s special committee. Insight into this curricular diversity can be seen from examples of

courses taken by several of our recent graduates.

Graduate Field of Horticulture:

Enrollment and Degree data

Comprehensive course listings

Links to recent theses

Graduate Field of Plant Biology:

Enrollment and Degree data

Comprehensive course listings

Links to recent theses

Graduate Field of Plant Breeding:

Enrollment and Degree data

Comprehensive course listings

Links to recent theses

Graduate Field of Plant Pathology and

Plant-Microbe Biology:

Enrollment and Degree data

Comprehensive course listings

Links to recent theses

Graduate Field of Soil and Crop Sciences:

Enrollment and Degree data

Comprehensive course listings

Links to recent theses

Improved climate for graduate students since the formation of SIPS

Since creation of SIPS, graduate students in

the five Sections are much more connected

as a community. This starts with a SIPS-

wide graduate recruitment event and SIPS-

wide orientation to graduate school where

students in the five Sections can meet one

another. There is also a SIPS-wide Graduate

Student Association that selects and

sponsors high profile seminar speakers,

hosts career talks, and organizes social

events for the SIPS graduate student body.

The spring chili cook-off is a perennial

favorite!

Students within each of the five Graduate Fields are mentored and advised by a major professor

in addition to other members of their special committee. PhD students have a minimum of three

committee members while MS students have a minimum of two members. While the major

advisor takes the lead, this committee works as a team to advise and mentor each of our graduate

students.

2018 Cornell AgriTech Student Symposium speakers

33

Career preparation. Students are interested in a range of careers outside academia and SIPS

is finding ways to facilitate appropriate experience and training.

Teaching and instructional skills. Cornell has many resources for TA support and

training. SIPS has recently applied for and been awarded an internal grant to support

conversion of core Plant Sciences courses to active learning. This will enable increased

training of graduate student TAs in strategies for incorporating active learning into

classes

Career perspectives. The SIPS Graduate Student Association in collaboration with the

SIPS post-doc organization regularly sponsors visits and video talks from SIPS alumni

and others working in ag biotech, small start-ups, publishing, and government agencies to

learn more about a range of career paths after graduate school.

Leadership training. Marvin Pritts teaches “Leadership Skills for Graduate Students”

(LEAD 5100), a 2-credit leadership training course designed specifically for the needs of

graduate students.

Organizational training. SIPS graduate students are provided with opportunities to

serve on faculty searches and other SIPS committees, as well as to plan and host

scientific symposia:

o Pioneer Symposium (2018, 2017) hosted by Synapsis, the academic and social

organization of the SIPS Section of Plant Breeding and Genetics

o Cornell AgriTech Symposium (2018, 2017) hosted by SAGES, the student

organization at Cornell AgriTech

o SIPS Graduate Student Symposium speakership, hosted by the SIPS Graduate

Student Association

Broad foundational skill development

Grantsmanship. SIPS graduate students have a strong track record of attracting competitive

external funding to support both PhD research and subsequent post-doctoral research.

Mentorship. Many SIPS graduate students devote significant time and energy to mentorship

of undergraduate researchers. To highlight and reward these activities, the Sellew Family

Excellence-in-Mentoring Fellowship, instituted in 2016 and endowed by Cornell alumni Mark

and Lisa Sellew, is awarded to SIPS graduate students who have demonstrated an exceptional

record of undergraduate mentorship. The fellowship recipient and mentees report on their joint

research as part of an annual spring symposium. (2018 Sellew recipient, 2017 Sellew recipient).

Collaboration. Another alumni bequest has been used to fund the Schmittau-Novack Small

Grants Program. This program is designed to allow student to explore new ideas, realize

emerging opportunities, and form new collaborations. Projects are designed, written, and

reviewed by graduate students with priority given to projects that involve cross-Section and

inter-Departmental collaborations. Approximately 10 awards in the amount of $5-10,000 are

made each year. (Schmittau-Novak recipients for 2018, Schmittau-Novak recipients for 2017)

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Science communication and outreach. SIPS graduate students engage in a variety of

activities directed at communicating science and the benefits of science education to various

audiences.

Plant science outreach in the public schools: graduate students teach science to the

elementary grades in Ithaca, Geneva, New York City

Expanding your Horizons: graduate students, faculty and staff present lead workshops

for girls in grades 7-9 (2017, 2016)

Summer Research Scholars Program: This program provides undergraduate interns

with the opportunity to work with faculty, graduate students, postdocs, and staff on

laboratory or field-based research projects. Many SIPS faculty also host summer REU

students as part of BTI’s Plant Genome Research Program.

Science Advocacy: congressional visits, March for Science

Skills for Public Engagement: This course provides students with skills for

communicating science using text, video, and social media, as well as tools for effective

engagement in diverse cultural settings

Graduate student recognition. The time and energy spent by graduate students to both excel in

their research and improve life in SIPS, its component Sections, and the greater Cornell

community is evident from the many awards they have received. (See list of selected awards)

Teaching Program: MPS Programs (starting Fall 2019)

The Master of Professional Studies (MPS) degree offered through SIPS is a one-year, course-

based master's degree, ideal for individuals who are interested in in-depth study of the issues and

advancements in plant and soil sciences. The MPS degree program prepares students for the

21st century workplace through knowledge development and career skill set refinement. A

unique aspect of our programs is that half of the coursework is dedicated to professional

development and students in all specializations take those courses. The mix of coursework and a

capstone project equips students with the skill set and knowledge necessary for careers in

industry, government, or non-profit agencies.

Program Description. The program has two main components: specialized, course-based

instruction led by world-class faculty and a capstone project aimed at solving a real-world

problem. As part of their coursework, students work with a faculty advisor to map out their

individualized course of study based on their area(s) of interest. While the majority of courses

(20 credits) will be in CALS, students have the flexibility to take courses across Cornell. For

their capstone project, students work under the guidance of a faculty advisor, on solving a real-

world problem.

MPS Specializations. While students have the opportunity to customize their own course of

study with their faculty advisor, the School of Integrative Plant Science offers several areas of

specialization for MPS degree candidates. With specializations focused on the latest

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advancements in plant and soil sciences, the MPS emphasizes useful plant improvements that

progress human health and advance environmental sustainability. Specializations include:

Controlled Environment Agriculture (CEA), one of the fastest growing areas of

agriculture. This specialization emphasizes specific skills to understand lighting,

hydroponic production, pest control, and horticultural aspects of production.

Viticulture is the science, production and study of grapes. With Cornell’s ideal location

in the Finger Lakes region, students will be exposed to every aspect of grape growing and

wine making.

Public Garden Leadership. This specialization emphasizes leadership, strategic

decision making, and business management, preparing students for managerial and

leadership roles in the public garden field. Learn more about Cornell's Botanic Gardens

Geospatial Applications. This specialization provides education in the geospatial

application, including GIS, to develop data management and decision-making skills for a

wide range of data. Students will also become licensed and experienced in the use of

UAVs.

Plant Biotechnology is a set of methods used to adapt plants for specific needs or

opportunities. This specialization provides skills in plant gene editing, plant propagation,

and molecular tools needed for jobs in this area.

Extension and Public Engagement

The research and teaching that make SIPS a top-ranked unit nationally and globally are the basis

for an equally robust, vibrant, high quality, and far-reaching set of extension and outreach

efforts. Our extension and outreach programs are central to getting the results of plant science

research translated into use by farmers and stakeholders in NY and beyond; to improving public

understanding of the role of plant science in food, feed, fiber and energy production as well as

managed landscapes; and to building and interacting with the global community of researchers

and practitioners of plant science. A program like Cornell Small Farms exemplifies our land-

grant mission, providing resources to new entrants into the farm economy with the goal of

building human capacity, supplying regional food systems, and fostering ecological resilience.

At the same time, collections ranging from the L.H. Bailey Conservatory to the Cornell Orchards

bring in hundreds of K-12 students each year. Our herbaria and other biodiversity collections are

used for education and loaned out around the globe in the form of specimens and high quality

images.

Integration with CCE. Our extension work is embedded within Cornell Cooperative

Extension (CCE), which was formally established in 1914 but has its roots with Liberty Hyde

Bailey (1858-1954), among others. In 1888, Bailey began a program in “practical and

experimental horticulture” (in which agriculture was an academic discipline) with the purpose of

education to “serve the people”. This early extension movement gained strength through farm

visits and demonstrations, lectures, and accessible bulletins and became a national model. Today,

the CCE system flourishes as a partnership between federal, state, and county governments and

Cornell University. Each county (along with New York City) maintains its own independent not-

for-profit extension association, altogether employing more than 1,000 staff members. County-

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campus linkages and support of county associations are facilitated by an administrative office at

the Cornell Ithaca campus. Many counties have also banded together to form teams of regional

specialists who work closely with Cornell faculty to support field crop, vegetable, tree fruit, and

grape producers across New York State.

Extension Faculty. Many SIPS faculty have formal extension appointments (38 out of 85

faculty) with appointments varying between 5 and 70%, comprising cumulatively about 11

FTEs. In addition there are just over 12 FTEs associated with non-tenure track Extension

Associates and Sr. Extension Associates. Faculty/Associates are based in Ithaca and at other

Cornell research campuses including: Cornell AgriTech in Geneva, NY; the Long Island

Horticultural Research and Extension Center in Riverhead, NY; the Hudson Valley Research

Laboratory in Highland, NY; and the Cornell Lake Erie Research and Extension Laboratory in

Portland, NY.

Faculty/Associates with formal

extension appointments

typically lead or contribute to a

concerted extension

“program”. While each formal

extension program is different,

they have similar components

including: a target audience

(this spans a wide range from

farmers/producers, to policy

makers, K-12 students and

educators, and the general

public), goals or learning

outcomes (what the target audience will learn, and what we will learn from them), and strategies

for evaluation/assessment. Many faculty without extension appointments also contribute to

formal extension programs as described above (e.g. presenting at workshops for producers,

writing extension articles based on applied research, etc.). Furthermore, many SIPS faculty

engage in outreach activities independent of CCE and formal extension appointments but in

some cases tied to federal funding and greatly contributing to the broader impacts of these

projects. These efforts are carried out using traditional approaches (field days, meetings, trade

articles) as well as many innovative approaches that capitalize on digital technologies (apps,

podcasts, webinars). One measure of extension/outreach activity is contact hours with

stakeholders. In 2017, SIPS led CALS units with 49,531 NYS extension/outreach contact hours.

This, however, is the tip of the iceberg, with many faculty contributing substantially both to

traditional extension and to diverse outreach activities.

SIPS Extension Council. Within SIPS, there is a culture of valuing faculty outreach and

extension efforts. The SIPS Extension Council (composed of the five Section Extension Leaders)

fosters information exchange between extension and SIPS administration and faculty; for

example, making faculty aware of training, funding, and reporting deadlines within the

Gary Bergstrom leads tour of malting barley trials

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extension/outreach sphere. The Extension Council Chair also sits on the SIPS Executive

Committee (attending their meetings every two weeks). Ongoing major efforts of the Extension

Council are: an assessment of critical extension/ outreach needs for SIPS over the next five

years, providing faculty with easy to follow instructions for extension/outreach reporting in

Activity Insight, and communicating the importance of fully reporting extension and outreach

activities.

Assessment of critical extension/outreach needs for SIPS over the next five years has been a top

priority, ensuring that extension resources are deployed strategically. The Extension Council

surveyed each Section and obtained a list of areas that are currently under-served and also new

areas of opportunity/need. The extension council compiled the needs list and provided it to the

SIPS Executive Committee. The list was approved by the Executive Committee and also

provided to the CALS Executive Dean Max Pfeffer. Because of changing needs, the list will be

reviewed on an annual basis. (See 2018 strategic extension hiring).

Funding for extension. Many research questions studied by SIPS faculty are driven by

stakeholder needs and problems facing agriculture in New York and beyond. Both research and

extension and outreach activities are funded through a variety of sources on a competitive basis

including Federal Capacity Funds (ex: Smith-Lever), state funds (ex: Ag and Markets, New York

Farm Viability Institute, New York State Energy Research & Development Authority, state

budget line items), stakeholder associations and commodity groups (ex: NYS Wine & Grape

Foundation, NYS Flower Industries, NYS Vegetable Growers Association), and federal grants

that include a translational component (e.g., NSF, NIFA Specialty Crops Research Initiative,

NIFA Organic Research & Extension Initiative, NIFA Sustainable Agriculture Research &

Education). In some cases SIPS activities are funded through ‘fee for service’. Examples include:

sample submission fees (Plant Disease Diagnostic Clinic, the Cornell Nutrient Analysis

Laboratory, Cornell Soil Health), registration fees for workshops, and travel reimbursement to

present at some stakeholder conferences. The primary source of funds for our extension/outreach

activities is through individual faculty-funded competitive grants.

Students and Extension. SIPS equips students with the necessary skill sets for effective

communication and engagement with industry stakeholders and the general public. SIPS research

and teaching activities dovetail with our extension and outreach activities. Several courses

explicitly include training in

extension/outreach, such as “Skills for Public

Engagement” (PLSCI 3940) and “Seed to

Supper: Community Facilitation Practicum”

(PLHRT 4271) All Plant Science and

Agricultural Science majors must participate

in an experiential learning project (internship,

research project, etc.). SIPS partners with

CCE to offer several internships each summer

where students work directly out of a CCE

office. Graduate students are trained in SIPS students and staff host workshops for middle school girls as

part of 'Expanding your Horizons’

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extension/outreach through farm visits and trials, presentations at extension programs, orchard

tours with elementary schools, etc. Annually, several graduate students are supported with

Extension Assistantships to support their work with extension programs. Students also

participate extensively in community science outreach including Judy’s Day (2018 theme: Plants

have Families too!), sponsored by Cornell Botanic Gardens, and the SIPS-sponsored BioBlitz,

which engaged the community in assessing local biodiversity.

Program Work Teams. In many cases, extension programs centering on a specific

subject/audience have developed formal Program Work Teams (PWTs) to facilitate interaction

among involved faculty, county-based extension educators, and stakeholders. Faculty with

formal extension appointments generally have a close working relationship with CCE and

regional extension educators, which facilitates information exchange to and from stakeholders in

many ways including informing research priorities and providing political support for research

funding.

Mechanisms for assessing outputs/impacts. Outputs (e.g., extension articles,

presentations, number of producers trained) are reported through annual Federal Capacity Fund

progress reports and annual Cornell Activity Insight reporting. Success is linked to impact,

which is assessed through a range of (somewhat imperfect) mechanisms, such as contact hours,

surveying stakeholders to determine changes in practice and profitability, and case study and

impact statements. The performance standards SIPS follows for evaluating individuals as part of

annual/biennial performance reviews and tenure and promotion are as noted in the CALS Faculty

Effort Distribution Guidelines.

Future Directions

As SIPS moves forward, we will continue to unify Sections and enhance synergies among our

research, teaching, and extension activities. While we have made great strides since the

formation of the School in 2014, we still need to increase advocacy for one another and speak

with a unified voice. Faculty renewal will be critical to maintaining our cutting edge research, to

providing outstanding educational opportunities for our students, and to serving our stakeholders.

While the Plant Sciences Major has grown in the past four years, we will continue to incorporate

active learning into our classes and provide targeted internship opportunities. Our graduate

students are a source of inspiration, providing ideas and enthusiasm to improve our research

programs, enhance diversity, and build cohesion within SIPS. We will continue to identify

opportunities to coordinate activities of our Graduate Fields and ensure that students have a voice

as we plan for the future. A critical need in the near future is the renovation of the Plant Science

Building. Additional renovations are needed in Bradfield Hall and in our greenhouse complexes.

We will diligently work with CALS and University administration to ensure that these

renovations are fully funded. The SIPS strategic plan was completed in 2015 and includes a

timeline specifying development of the next strategic plan in 2020. The SIPS executive

committee looks forward to revisiting our strategic direction, incorporating feedback from this

program review.

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Appendix A: SIPS Strategic Plan - 2015

School of Integrative Plant Science

College of Agriculture and Life Sciences, Cornell University

March 23, 2015

Timeline for Development and Implementation of the SIPS Strategic Plan

9 September 2014 to 2 February 2015 the SIPS Executive Committee met 16 times to

work on general planning for SIPS and to develop a draft Strategic Plan. The planning

process was informed by discussions with SIPS Section faculty, leaders of units and

groups working with plants beyond SIPS, and other members of the wider SIPS

community.

5 February 2015 discussion of the draft SIPS Strategic Plan began in the five Sections, as

led by the Section chairs.

23 February 2015 the suggestions from the five Sections were integrated by the

Executive Committee into a near-final draft.

27 February 2015 the near-final draft was distributed to the SIPS community with an

invitation for further comment on the plan and its implementation.

6 March 2015 the comment period closed, and the (few) suggestions were integrated.

11 March 2015 from 2:00-3:00 PM a SIPS Town Hall Meeting was held in B25 Warren

Hall (with connections to the Geneva campus and the Long Island Horticultural Research

and Extension Center) to discuss (with general approval) the SIPS Strategic Plan and its

implementation.

23 March 2015 the SIPS Strategic Plan is presented to Dean Boor and the CALS

Leadership team.

April 2015 formal implementation of the plan begins (as coordinated and documented

through a newly developed SIPS intranet system), and the Vision and Grand Challenges

sections of the plan are used as components of a completely revised SIPS website.

2017 the 2015 SIPS Strategic Plan is evaluated by the SIPS Executive Committee and the

community to determine if any updates are needed based on the first two years of School

activities.

2020 a new SIPS Strategic Plan is developed.

Preface

In the coming decades, the world must arrive at solutions to the major challenges of feeding a

burgeoning population, mitigating and adapting to climate change, and preserving biodiversity

and essential ecosystem functions. Plants underpin all agricultural and natural ecosystems and

environmental impacts on plant systems will cascade at local, regional, national, and

international scales. But plants will also be the basis for solutions. Innovative approaches and

revolutionary breakthroughs in plant sciences will be used to meet these challenges and help

secure a sustainable future for coming generations.

These words introduced the Proposal for Creating the School of Integrative Plant Science in the

College of Agriculture and Life Sciences, a framework document for SIPS as it was formally

40

launched 6 June 2014. That framework has now been strengthened with an Administrative

Support Structure Plan, completed November 2014, and a variety of new operational links

between the five Sections that compose the School: Horticulture, Plant Biology, Plant Breeding

& Genetics, Plant Pathology & Plant-Microbe Biology, and Soil & Crop Sciences. Importantly,

the framework has a new foundation in Knowledge with a Public Purpose in a Changing World:

CALS Strategic Plan 2014, which describes an overarching mission, values, and goals in six

thematic areas for the College, and the rationale for the creation of the School.

The SIPS Strategic Plan introduces a vision for the School and three sets of goals addressing the

following interrelated questions:

What are the most important local and global needs that Cornell plant scientists can

address, and what grand challenges can focus SIPS efforts to meet those needs?

What SIPS capabilities must be strengthened to enhance work on the grand challenges?

What synergies between the operation of the School and its constituent Sections will

improve our ability to serve CALS and SIPS goals?

Vision

Discovery that connects: From fundamental insights to better plants, sustainably grown, serving

the world

The process of fundamental discovery underpins all work in the plant sciences: from the soils in

which plants grow to the microbes and other organisms that interact with plants. At its core, plant

biology explores the mechanisms that convert genetic information into functioning cells and full

organisms and, ultimately, through evolution, into the diversity of plants that define the Earth’s

terrestrial environments and support the human population. Revolutions in areas such as

systematic theory, structural biology, cellular imaging, and “omics” (from genome to phenome)

have unified all biology, yielding gratifying insights into molecular mechanisms and

evolutionary processes but also revealing staggering levels of diversity and system complexity.

Fundamental discoveries enlarge our understanding of the natural world, engender awe in

students, reveal unexpected beneficial applications, and provide foundational knowledge for

modern agriculture. Without continuing excellence and innovation in fundamental plant sciences,

we will be limited to recycling previous advances in addressing societal needs involving food

security and global sustainability. An operating principle of the School will be to affirm and

nurture the creative potential of fundamental research on plant, soil, and interorganismal

interactions that has made Cornell a worldwide leader in the plant sciences.

“Connectedness” is emerging as a property of the discoveries and activities that have the most

explanatory power and beneficial impact, and it is a defining property of systems. Advances in

fundamental biology, agriculture, communications technology, and food production highlight the

importance of natural and human-made systems and the connections within them. An operating

principle of the School will be to identify and maximize empowering connections – from

molecules to ecosystems, plants to people, and scientists to citizens.

41

We envision fundamental insights as actuating three broad aims that can act sequentially: better

plants, sustainably grown, serving the world. Regarding better plants, we anticipate that a

growing queue for improvements will be generated by new insights into plant cellular systems,

plant interactions with emerging pests and pathogens, stresses of a changing climate, better-

understood human nutritional needs, culinary preferences, and other uses for plants. Similarly,

novel and precision agriculture methods will have the potential to dramatically alter

agroecosystems in favor of environmental sustainability and prolonged productivity. All of these

advances will have the potential to improve human health, economic activity, and well-being in

New York State, the US, and internationally. However, it is important to note that these three

broad activities are interdependent. For example, the full success of advancing agricultural

practices may depend on plant breeders appropriately optimizing plants, and crops with

improved nutritional properties may not benefit many people without appropriate marketing and

engaged communication with the public. Thus, an operating principle of the School will be to

maximize information flow in all directions across the broad activities aimed at “better plants,

sustainably grown, serving the world.”

I. Grand Challenges Aimed at Plant-Related Local and Global Needs

We see five local and global needs for the SIPS community to address:

Foundational knowledge of the structure, function, and evolution of plants, the soils in

which they grow, and the microbes and other organisms with which they interact

Empowered students and engaged and informed societal leaders and citizens

Informed and engaged growers and consumers: from New York State, to the US, to

developing countries

Food security and human nutrition, health, and economic vitality in the face of climate,

population, and resource limitation pressures

Environmental conservation and sustainable landscapes in the face of climate change and

urbanization

We envision the grand challenges as organizing tools with several properties: (1) meet a local or

global need; (2) build on strengths within Cornell regarding research, education, and land-grant

missions; (3) guide the development of new faculty positions and help attract top candidates; (4)

coordinate activity at multiple levels of project engagement among faculty across Sections; (5)

attract philanthropic and large-project competitive funding; (6) be understood and supported by

the public and stakeholders; (7) inspire and foster global collaborations on global problems. The

grand challenges are presented below in association with the needs they serve.

Foundational knowledge of the structure, function, and evolution of plants, the soils in which

they grow, and the microbes and other organisms with which they interact

1. Investigate plants as model organisms for understanding basic biology, as evolving

systems displaying both the unity and diversity of life and as living systems that scale

from genome to organism to biosphere.

42

2. Understand the physical-chemical properties of soils and the basis for soil impact on

plant productivity and microbial communities, as well as carbon, nutrient, and related

fluxes.

3. Understand the diversity of plant-associated microbes and the rapidly evolving

molecular/cellular contacts between microbes and plants that explain interactions ranging

from beneficial to pathogenic.

Empowered students and engaged and informed societal leaders and citizens

1. Attract and educate undergraduate and graduate students who can connect disciplines,

creatively solve problems, integrate complex systems, pursue diverse careers, engage the

public, and become professional and societal leaders.

2. Engage policy makers, alumni, philanthropists, and other leaders in society with

empowering awareness of advances in plant and soil sciences and the benefits of healthy

agricultural and natural ecosystems, using media and direct interactions.

3. Reach out to K-12 students, citizens, and consumers to enhance their appreciation and

enjoyment of plants and promote their informed decision making.

Informed and engaged growers and consumers: from New York State, to the US, to developing

countries

1. Work with all members of the farm-to-consumer continuum and extension partners to

maximize two-way knowledge flow to improve economic vitality, ecological

sustainability, and human health in New York State.

2. Engage growers and landscape managers as research partners to utilize their expertise and

ensure relevance to local needs.

3. Extend research advances and outreach internationally through partnerships, internships,

international courses, and training of students interested in international research/service.

Food security and human nutrition, health, and economic vitality in the face of climate,

population, and resource limitation pressures

1. Develop and deploy crop systems that use resources efficiently and have greater tolerance

of abiotic stresses, particularly flooding, acid and nutrient-limited soils, drought, and

heat.

2. Manage biotic interactions with plants for improved productivity, sustainability, and food

safety and security.

3. Discover plant taxa with beneficial attributes, and improve cultivated plants with value-

added traits to benefit human health, well-being, and income generation: from aesthetics

to plant products.

4. Develop resources, such as improved varieties and management practices, that contribute

to economic development in New York State and beyond and enhance well-being and

ecosystem services.

Environmental conservation and sustainable landscapes in the face of climate change and

urbanization

43

1. Characterize and preserve diversity in natural ecosystems to promote system stability and

protect genetic resources for agriculture and human health applications.

2. Develop and deploy sustainable agroecosytems and urban landscapes that are productive,

climate-friendly, and feature soil management approaches that increase resource use

efficiency, contribute toward mitigation of climate change, and improve soil health.

3. Contribute to enhanced well-being and enjoyment of life by enriching the connections

between plants and human experience.

II. Goals Aimed at Enhancing Work on the Grand Challenges

1. Promote School-wide expertise, basic competency, and supporting resources in three

critical skills:

o bioinformatic tools for genomics and other “omics” views of living systems –

from organismal systems to the genomics/phylogenetics interface

o “big data” computer/mathematical modeling of systems – from systems biology to

natural ecosystems to geospatial systems to agro/eco/food systems

o engaged communication that more effectively connects people –for education,

problem solving, and public benefit

2. Develop infrastructure for technologies that enable critical new directions for SIPS

research:

a. “omics”: genome > transcriptome > proteome > metabolome, including needed

instrumentation and supporting expertise to study chemical diversity in plants and plant-

associated microbes

b. infrastructure for high throughput phenotyping

c. infrastructure for genome editing and associated tools

d. Plant Transformation Facility and other Biotechnology Resource Center tools

e. access to natural areas and cutting-edge field research resources and facilities that

efficiently support problem-solving research and interrelated studies on pathogen

evolution, diversity, ecology, soil dynamics, and other fundamental issues uniquely

addressable in agroecosystems and which support the concepts of “nature and agriculture

as a laboratory”

1. Maximize utilization of our unique herbaria and other biological collections and our

extensive document and image archives for synergistic research and outreach

2. While embracing established plant model systems, promote the value of domesticated

plants as model systems for fundamental biology and improve translational pipelines for

a few targeted crops through the collaborative effort of multiple groups

a. focus crops: tomato, apple, grape, berries, maize, wheat, rice, potato, cassava (list to be

under ongoing review)

b. genotype to phenotype challenge

1. Enhance the sustainability of funding for SIPS research, extension, and outreach projects

through entrepreneurial activities and better alignment with big-problem oriented

government and philanthropic funding sources

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a. include sustained fundability as a component in the design of projects

b. broaden sources of income for projects through educating SIPS members about

intellectual property and commercialization opportunities and resources supporting the

translation of discovery into application

c. educate regulators and the public about the benefits of plants with genomes that are

edited with Generally Recognized As Safe (GRAS) principles as a source of improved

varieties that will enable land-grant institutions to support many special needs of

stakeholders

d. measure and better publicize the economic impact and scientific advances of SIPS and

the general importance of plants in the world

1. Optimize SIPS operations:

o to promote success and connectedness of constituent Sections, administrative

staff, academic and technical staff, postdoctoral scientists and visiting fellows,

and graduate students

o improve logistical connections within SIPS between the Ithaca and Geneva

campuses and other locations in New York State, such as the Long Island

Horticultural Research & Extension Center, the Hudson Valley Research

Laboratory, and the Cornell Lake Erie Research & Extension Laboratory

o strengthen collaborations with affiliated institutions: BTI and USDA/ARS

o strengthen collaborations with relevant Cornell units and groups: IP CALS,

Plantations, Landscape Architecture, Atkinson Center, Chemical Ecology, Cornell

Center for Comparative and Population Genomics

o strengthen collaborations with relevant faculty programs in the basic biological

sciences, the Departments of Entomology, Food Science, Microbiology, Natural

Resources, and Nutrition, the Hotel School and Dyson School, and elsewhere in

Cornell

o coordinate utilization of resources such as farms, greenhouses, growth chambers,

and Cornell natural areas

o strategically prioritize, advocate, and plan for consolidations and/or major

upgrades to facilities that are expensively energy inefficient, obsolete, or out of

compliance with current standards for work spaces with natural light

2. Attract and hire the next generation of faculty leaders in the plant sciences for SIPS and

its affiliates at Cornell

(III and IV) Synergisms between the School and Its Constituent Sections

As noted in Knowledge with a Public Purpose in a Changing World: CALS Strategic Plan 2014:

“The five current plant-science related departments in CALS have been consolidated into the

School of Integrative Plant Science (SIPS). This consolidation will result in a School that:

Provides a unifying framework to integrate and coordinate key administrative functions

across the current plant science units, while preserving their unique character and

purpose;

45

Enables these units to work together in a more strategic and cohesive way on matters

related to faculty hiring, curricular development and resource allocation;

Creates a new face for plant science at Cornell, increasing its prominence to a level equal

with its scientific and educational importance, and raising its profile to encourage greater

student interest in pursuing study in the plant sciences.”

III. Benefits of maintaining identity, prominence, and "unique character and purpose" of the five

discipline-based Sections

1. Represent disciplines with irreplaceable historical traditions (maintained despite name

changes over the years)

2. Align with established, recognizable graduate fields

3. Have links to alumni, donors, and stakeholders who relate to specific disciplines

4. Have links to scientific societies with special opportunities for student presentations,

networking, leadership, and awards systems

5. Are recognized units for various national rankings (especially the graduate fields)

6. Represent groups with closely interrelated knowledge and activity

7. Enable SIPS to launch "interdisciplinary" initiatives based on internal collaborations

8. Represent "family sized" functional social and supervisory groups

IV. Benefits of the School to the Sections

1. Strategic planning for sustainable activities of maximum impact, including infrastructure

development and farsighted, coordinated hiring of faculty with strong internal and

external leadership potential

2. Streamlined interactions with the CALS Communications Office, which can raise both

public and institutional awareness of our accomplishments and is an important resource

for internal communication with students and other groups

3. Improved web-based extension/outreach (and recruitment) by attracting a broader

audience and then providing more coordinated and useful information

4. Better ability to attract support from alumni, philanthropists, foundations, training grants,

and various government sources because we are a bigger group capable of addressing

grand challenges

5. More efficient negotiation for various resources, such as fellowships, infrastructure, and

biological collections, through representation by a large and coordinated group of users

6. Enhanced performance in college metrics through bonuses resulting from the collective

activity of SIPS

7. Enhanced best practices for Sections, for example, in faculty and staff mentoring and

interactions with scientific societies, alumni, and potential donors, etc.

8. Better coordination of activities that are common across Sections, such as administrative

services, seminar announcements, social events, award nominations, etc.

9. Streamlined management of information flow to students, staff, and/or faculty across

Sections

10. Development of more connections and collaborations through awareness of research and

other activities in different Sections and through socializing and working with colleagues

in SIPS-wide activities

46

11. Coordinated approaches to curriculum development and student services, such as a web-

based concept- diagrammed and searchable system for connecting undergraduates to the

diverse research programs in SIPS

12. Strengthened education of graduate students in the five graduate fields through an

integrated seminar system, development of shared courses addressing laboratory and

professional skills, an undergraduate mentoring program with associated fellowships, and

SIPS-wide educational/social events

13. Enhanced recruitment of undergraduates to the Plant Sciences major and graduate

students to the five graduate fields in SIPS

14. Better coordinated development, use, and support of common resources, from photo

archives to instrumentation to farms

Acknowledgements

SIPS Executive Committee members were the primary authors of the Strategic Plan. The

committee members (and responsibilities) were: Alan Collmer (Director of SIPS), Gary

Bergstrom (Chair Plant Pathology & Plant-Microbe Biology Section), Bill Crepet (Chair Plant

Biology Section), Jeff Doyle (Chair Plant Breeding & Genetics Section), Marvin Pritts (Chair

Horticulture Section), Tim Setter (Chair Soil & Crop Sciences Section), Chris Smart (Chair of

the Council of Extension Leaders), Mike Scanlon (Director of Undergraduate Studies), and

Magdalen Lindeberg (SIPS Communications and Development, beginning December 2014). We

also acknowledge thoughtful guidance on the development of the School from Jan Nyrop, critical

suggestions regarding administrative issues from Andy Vail, proofreading by Leah Cook, helpful

suggestions from Pamela Strausser regarding the comment and town hall meeting process, input

from Bill Fry that critically improved an early draft, a stimulating SIPS Plenary Seminar by Ed

Buckler that launched community engagement in the strategic planning process, development

of the online comment system by Jase Base, and the thoughtful input from many faculty, staff,

and other members of the SIPS community.

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Appendix B: Section Profiles

Section profile: Horticulture

Section Description: Horticulture at Cornell has a rich history, beginning with the appointment

of Liberty Hyde Bailey as its first chair in 1888. We pride ourselves on research programs that

range from the very applied to the basic, in both breadth and depth. Our program maintains a

strong link to extension educators around the state as well as the world and a commitment to

teaching that includes a strong comprehensive curriculum with research opportunities,

experiential learning, presentation skills, and an ePortfolio. We focus on Horticulture as both an

art and a science and offer a horticulture minor with a focus in the fine arts. We have

tremendous field resources not only in Ithaca and Geneva, but in Portland and Riverhead, New

York as well. Our undergraduate Plant Science major, which encompasses classes throughout

the School of Integrative Plant Science, is growing. More than 100 students are enrolled this

academic year. Our faculty also contribute to the Agricultural Sciences, Viticulture and

Enology, and Environmental and Sustainable Sciences majors. Our graduate program continues

to excel. Our students find employment as professors, researchers, plant breeders, crop

specialists, and extension educators.

Our accomplishments are impressive and varied. This includes: the development of the biolistic

particle delivery system (Gene Gun), allowing for the introduction of DNA into plant genomes,

“Cornell Mix,” the synthetic greenhouse growing media used worldwide, and “CU Structural

Soil” which allows urban trees to thrive. We have developed 66 apple cultivars including:

Empire, Jonagold, and our newest Snapdragon; more than 50 wine, juice, and table grapes;

dozens of berries including the Heritage raspberry, the number one cultivar in the world;

hundreds of high yielding, pest resistant lines of vegetables; highly resistant apple rootstocks;

and ornamental plants like Alstroemeria “Tangerine Tango.” We established the tall spindle

planting system for apples that revolutionized the way apples are grown as well as the apple tree

carbon balance model for fruit thinning. We developed and refined controlled atmosphere

technology for long-term apple storage. We invented the Geneva Double Curtain, which

improved Concord grape productivity as well as mechanical harvesting of grapes.

Although our history is rich, we are focused on the future. Recent plant breeding efforts will

have global impacts. We created a digital microtensiometer that allows continuous

measurements of tree water status that has the potential to revolutionize irrigation. We

discovered the first resistance gene against the necrotrophic fungus Alternaria in apple that is

regulated by sorbitol. Other efforts include taking horticultural therapy to a new level with

Nature Rx @Cornell, which bonds students with nature to improve mood and overall sense of

well-being. Our faculty have received prestigious awards, the most recent being the USDA’s

2016 Presidential Early Career Award for Scientists and Engineers (PECASE), which “recognize

some of the finest scientists and engineers who, while early in their research careers, show

exceptional potential for leadership at the frontiers of scientific knowledge during the twenty-

first century.”

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Although two separate departments since their founding, the Ithaca Horticulture Department and

Geneva’s Horticultural Sciences Department merged in 2010 under the leadership of Marvin

Pritts. The merger was smooth, as faculty programs already worked closely together. In July

2014, the Department of Horticulture, along with Soil and Crop Sciences, Plant Breeding and

Genetics, Plant Pathology and Plant-Microbe Biology, and Plant Biology, joined in the new

School of Integrative Plant Science. The mission of the Horticulture Section is to serve

professionals, students and citizens of New York State, the nation, and the world by

collaborating with our diverse partners to identify challenging issues of primary concern and

generating and extending knowledge about fruits, vegetables, and landscape plants for the

purpose of sustaining the environment, enhancing economic vitality, and improving the quality

of life of individuals and their communities.

The section of Horticulture has 31 faculty members, including four senior extension associates,

one senior research associate, and one lecturer. Of these, 18 are based in Ithaca, 11 in Geneva,

with one each at Stations in Portland and Riverhead, New York. We currently have 25 tenure

track positions. The distribution of effort among tenure track faculty is 4.7 FTE teaching, 14.25

FTE research and 6.05 FTE extension. Since 2010, the section has seen a loss of 11 positions

with only three additions, a net loss of eight. In addition, several faculty have significant

administrative duties within the College of Agriculture and Life Sciences (CALS), SIPS, and

Cornell AgriTech. This has led to gaps in teaching and research and especially in extension with

losses across the board in fruits, vegetables, turf, and ornamentals. Over the next ten years, half

of our current faculty members will likely retire. This comes at a time when new challenges and

opportunities are emerging in Controlled Environment Agriculture; climate change as it relates to

fruit crops, vegetables and urban landscapes; new invasive pests requiring an ICM approach; and

new specialty crops like cider apples, hemp, and hops.

Section research covers all aspects of horticulture and is focused on four major programmatic

areas which are aligned with the priorities of the College of Agriculture and Life Sciences: 1)

production and management systems (CALS land-grant mission); 2) biology of horticulture

crops (new life sciences); 3) environmental stewardship (environmental sciences); and 4) plants

and human well-being (applied social sciences). The emphasis is on the whole plant, or on

horticultural systems, but there is a growing concentration on cellular and molecular processes.

Support for the research program comes from a range of sources, including federal, state, and

horticultural industry research funds.

1. Production and Management Systems: This program involves developing and introducing

new cultivars, technologies, and management practices that promote the competitiveness and

sustainability of horticultural businesses. We develop, test, and introduce improved cultivars of

fruits, vegetables, ornamentals, and other plants which are adapted to New York and provide

producers, distributors, processors, and consumers with high-quality products. We develop,

modify, and evaluate new technologies and management practices and translate findings from

fundamental research on the biology and genomics of horticultural crops to improve product

quality, profitability, and sustainability. We develop strategies for urban landscape remediation

and planting to provide green infrastructure and ecosystem benefits. We develop crop curricula

for extension staff that synthesize new production practices, submit impact statements, and

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communicate the results of our research in extension meetings, newsletters, and appropriate

media.

2. Biology of Horticultural Crops: This program involves improving the understanding and

application of fundamental biological research to production agriculture, landscape stewardship,

and the food system. We study the environmental and biotic effects on the growth, productivity,

and quality of horticultural crops, attempt to better understand the genomic basis of important

horticultural traits and plant-pest interactions to improve breeding and management, and study

weather and climate effects on crop biology to address short- and long-term effects of

environment on horticultural crops. We provide education on the practical application of

molecular biology to agriculture through applied courses and informally by explaining to the

public the impact of fundamental biology principles on horticultural crops through extension

programming and web-based educational resources.

3. Environmental Stewardship: This program involves improving the health of food systems,

urban landscapes, and communities. We develop new environmentally sustainable practices and

systems that improve soil health, grower profitability, enhance product quality and create

landscapes that provide ecosystem benefits. We analyze environmental impacts that affect the

viability of New York fruit and vegetable producers and the commercial and urban landscapes.

We provide scientific expertise to policy makers and community leaders on regulatory issues

facing horticulture producers and commercial and urban landscape managers. We study

bioenergy and climate issues in cooperation with other programs.

4. Plants and Human Well-Being: This program involves the use of quantitative and qualitative

research methods to explore, describe, and quantify the impact that plants have on people and

communities. It involves understandings of why plants have these positive benefits and the

creation of opportunities to enhance human-plant interactions. We teach courses that explore the

interrelationship between plants and human well-being, encourage graduate students to integrate

social science into their research projects, and work with external stakeholders and decision

makers to demonstrate the positive impacts that plants have on human well-being. We

collaborate with industry, community leaders, educators, and policy-makers to explore,

demonstrate, and share with others the positive impacts of plants on human well-being. We

communicate with the public through extension learning networks, and through social media,

distance learning, and other appropriate venues. We strive to involve students in preparing

educators and volunteers to foster garden-based educational programs that build relationships

with community audiences to integrate local experience and research based knowledge; expand

learning networks and ecological gardening skills towards greater resilience and connections;

and provide adult, youth and family participants with enhanced health and wellness, food

security, ecological literacy, environmental stewardship, and sustainable community practices.

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Section profile: Plant Biology

I. Mission and Role of the Section of Plant Biology (PB) The Section of PB aims to teach and

research plant evolution, diversity, form, function and the molecular underpinnings. At its center

is the evolution and diversity of plant life (from non-angiosperms to angiosperms) which

provides a rich ground for investigating and understanding the molecular mechanisms in plant

development, growth, reproduction and responses to the environment. PB aims to train future

generations in the essentials of plant biology, including evolution and plant diversity, and to

provide fundamental knowledge and cutting-edge techniques to improve plants and crops for

agriculture, health and global sustainability. PB is unique within SIPS in that it is not directly

focused on breeding better crops, or developing and optimizing agricultural practices. Instead PB

aims to discover fundamental processes, mechanisms and molecular components within plants,

and the evolutionary processes that have driven these fundamental processes and their incredible

diversity for millions of years across the plant kingdom. It is these fundamental insights that will

drive innovations in translational and applied plant research.

II. History of Plant biology, its faculty and teaching staff The department of PB was formed

in 1999 by joining the former Section of Plant Biology (within the Division of Biological

Sciences) with the L.H. Bailey Hortorium, with W.L. Crepet as Chair until Dec 2017. After 6

months as associate chair to help transition the leadership, K. van Wijk took over the chair

position in Jan 2018. Since the formation of PB, there have been six Faculty retirements

(Spanswick, Parthasarathy, M. Nasrallah, Davies, Luckow, Rodriquez) and a cluster hire in 2001

as part of the Cornell Genome Initiative (van Wijk, Rose and Hua), followed by hiring of

Scanlon in 2006 and Roeder (2011) housed in the Weill Institute for Cell and Molecular Biology.

In recent years, Gan moved from the Section Crop & Soil to PB, whereas Doyle formally moved

out of the PB section to become chair of Plant Breeding & Genetics. After a hiatus of more than

10 years, there been a further four hires (Specht and Moghe in 2017; Gandolfo and Frank in

2018). The faculty currently consists of two assistant, five associate and 13 full professors, and

two joint members with other Cornell units (Vatamaniuk and Hanson). However, three more

faculty will retire in the next 18 months (Niklas, Owens, Davis). Finally, PB has one full time

senior lecturer (Silva) teaching several large core classes and one part time (20%) lecturer (Friso)

teaching two new courses related to medicinal plants.

III. Teaching, training and advising by plant biology

Teaching Contributions by Plant Biology Faculty The PB section has a strong tradition in

teaching fundamental courses in e.g. Plant Physiology, Plant Evolution, Plant Systematics, Plant

Anatomy and Morphology, as well as Plant Biochemistry. Several of these courses are now part

of the core curriculum for CALS Plant Science Majors. The PB section also plays a campus-wide

role in teaching core Biological Science Major courses, as well as courses about the societal

impact of plants to large cohorts of Cornell undergraduates across different colleges and majors

(e.g. Foundations of Biology, Comparative Physiology, Green World/Blue Planet). PB also

teaches/taught more specialized and often higher level classes in a wide array of topics, such as

molecular systematics, medicinal plants and drug discovery, molecular biology and genetic

engineering, plant proteomics & mass spectrometry and plant hormones. The recent hires will

take over some of the teaching responsibilities of retired/retiring faculty, and also teach newly

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developed courses such as Concepts and Techniques in Computational Biology (Moghe) or

participating in large undergraduate classes (Introduction to Evolutionary Biology and Diversity

– Specht). In the context of internationalization, the PB section (spearheaded by Nixon)

developed a unique and successful undergraduate course ‘Global Plant Biodiversity and

Vegetation’, and its associated three-week field trip to Patagonia; this is a long standing

collaboration with colleagues and the ‘Museo Paleontologico Egidio Feruglio’ in Argentina

(several have PB visiting professor status). This field course is scheduled to be broadened to

include e.g. zoology and culture through contributions from other Cornell units in CALS and

Arts & Sciences.

Undergraduate student advising and independent research The PB faculty serve as advisors to

undergraduates majoring in Plant Sciences within SIPS, and as advisors for >150 students in

other Majors, such as ‘Biological Sciences’ and ‘Biology and Society’ – these majors are

offered through CALS and the College of Arts & Sciences, and include many pre-med students.

Many of the PB faculty provide independent research opportunities throughout the semesters to

Cornell students, and in the summer also to undergraduates for other colleges and universities,

frequently through sponsored outreach programs.

The Graduate Field of Plant Biology The PB Graduate Field currently has 34 graduate students

and nearly 40 faculty field members, encompassing all of the PB Faculty, several other SIPS

faculty, the departments of Neurobiology & Behavior (Raguso, Kessler), as well as faculty in the

BTI (Martin, Harrison, Jander, Stern) and USDA (Giovannoni, Li). The graduate students

receive broad and in-depth training in fundamentals of plant biology, with specializations in e.g.

organelle function, plant development and cell signaling, molecular genetics and epigenetics,

physiology and metabolism, (a) biotic interactions, system biology (‘omics’) and modeling, as

well as systematics, evolution, and plant diversity. All students do three-four lab rotations in

their first year, after which they join a selected lab; obtaining fellowships for their 1st year is a

huge bottleneck in our graduate student recruitment. Students graduate on average within 5.5

years and graduates pursue careers in academics, industry, government and non-profit

organizations (see Appendix 111- SIPS graduate fields ). The position of DGS rotates (~4-5 year

period) across the Plant Biology Faculty section (currently Scanlon). Yearly recruitment is done

through a rotating admission committee and a visiting weekend. In the last few years, the

recruitment visit is coordinated with the other four SIPS graduate fields with several shared

activities, making a positive impact on the recruitment and enhancing integration across the

sections.

Postdoctoral training Postdoctoral fellows funded by federal grants or (inter)national

fellowships and awards (e.g. USDA, NSF, Humboldt, Human Frontiers, Fulbright, as well as

national fellowships such as DAD, SNF, BARD) play an important role in driving research

programs in the PB section. Many former fellows have continued in career in academics in the

US or in countries across the globe. With the formation of SIPS, postdocs in PB and the other

sections have formed a highly beneficial postdoc association

https://sips.cals.cornell.edu/people/postdoctoral-association/.

IV. Research interests, accomplishments, connections and funding

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Research by PB faculty Consistent with the diverse historical foundations of the section and its

leading role in teaching the fundamentals of plant biology, the section encompasses several

research areas, with particular strength in (i) Plant Evolution and Systematics, (ii) Plant Cell and

Developmental Biology, and (iii) Plant Metabolism and Biochemistry. Since the formation of

PB, and with the advent of ‘omics’ techniques, the molecular research mostly involved model

and crop plant species within the Brassicaceae (in particular Arabidopsis thaliana), Fabaceae

(Leguminosae), maize, rice and tomato, as well as the moss Physcomitrella patens. However,

cheap genome sequencing and genome editing techniques are now providing vast opportunities

to expand plant molecular research to more diverse sets of plant species, as reflected in recent

research and grant applications by PB faculty (e.g. charophycean green algae, the ‘living fossil’

Equisetum, and Morning Glory species). The group of faculty focused on systematics and

evolution include specialists in particular taxa and topics, such as oaks, grasses, legumes,

angiosperm fossils, the flora of Patagonia, and with the arrival of Specht also non-grass

monocots in particular the Zingiberales. PB faculty have a long history of contributions to

systematic theory.

Unique Collections serving in Research, Education and Outreach The section of PB has a long

tradition in the recording, collecting and researching of extant and fossil plants. PB actively

maintains major collections of international importance, namely the L.H. Bailey Herbarium

(860,000 specimens), the CU Plant Anatomy Collection (CU-PAC), the Ethel Z. Bailey

Horticultural Catalogue Collection, the L.H. Bailey Library, and the L.H. Bailey Conservatory

(Greenhouse in front of the Plant Science building serving many daily visitors, including alumni)

with living plants (See Appendix - SIPS Biodiversity Collections). The herbarium includes the

largest collection of cultivated plant specimens (ca. 270,000) in the US, documenting the entire

history of horticulture in North America (starting in late 1700s), and can be used for various

studies, e.g. tracking the origin and early spread of invasive plants, earliest records of some

introduced plant diseases and of early heirloom vegetable plants. The collections support an

array of SIPS internal and external NY state, national and international activities, including

requests for plant identification.

Other Outreach Most of the faculty in PB do not have formal ‘extension’ appointments, with the

exception of Nixon and Crepet related to the PB collections (see above). However, the faculty is

actively engaged in outreach activities often associated with funded projects by the NSF.

Furthermore, each summer many faculty have high school and undergraduate students in their

labs, e.g. through NSF sponsored REU programs. Several PB faculty (and others in SIPS) have

also provided leadership and actual teaching hours to the Cornell Prison Education Program, see

http://cpep.cornell.edu/. To coordinate outreach activities, build new synergies and collaborative

outreach activities, PB is currently collecting information of all our outreach activities and their

impact, to be displayed through the PB-SIPS webpages.

National and International connections, contributions and leadership The Faculty in PB has

strong connections and collaborations at the national level through multi-PI grants, in particular

NSF genome, and at the international level, e.g. through international collaborative grants such

as ERACAPS, BARD, Human Frontiers. Faculty are active in a number of professional societies

through leadership positions, and by organizing and participating in societal conferences

organized by e.g. ASPB, ICAR, ASMS, SEB, BSA, ASPT, as well as many smaller and

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specialized meetings such as Gordon Research Conferences. PB also partners with the New York

Botanical Garden in a Graduate Studies Program.

Funding Research by PB faculty is mostly funded by the National Science Foundation, with a

smaller portion of funding from NIH, USDA and DOE, as well international collaborative grants

such as BARD, BSF, Human Frontiers, ERACAPS, etc. Some of the faculty also have funding

through the extension programs, such as Hatch. The external funding profile of research in PB

underlines the fundamental nature of the research in the section. However, PB is actively seeking

to diversify its funding sources. The formation of SIPS and the resulting increased interactions

across sections will help in this funding diversification objective.

We started analysis and discussions about the PB funding profile and funding diversification at

the Faculty retreat on 14 Oct 2017. This was followed by subsequent discussions at several

faculty meetings. As an immediate practical response, the PB section now maintain an active

document (via Google Docs) with funding opportunities. We review this information at our

monthly faculty meetings and discuss specific new opportunities. The address the need for

graduate student support, the PB section and associate PB graduate field has submitted proposals

for NSF graduate training grant in 2017 (rejected but otherwise with highly favorable reviews)

and 2018 (pending). We are also preparing a ‘white paper’ for the PB collections (e.g. the

herbarium) aimed at funding raising for private donors. Several faculty are involved in

developing cross-college innovation grants for the CU digital Agronomy Initiative (due in April

2019). PB faculty also try to expand into emerging research areas such as medicinal plants and

drug discovery, exemplified by submission of a seed grant to Weil-CU with colleagues at the Vet

School and Weil in NY city and potential for NIH funding. Another area of potential new

funding opportunities is Synthetic Biology focused on metabolic engineering in plants and non-

plants systems. This will provide new multi-disciplinary opportunities with chemical

engineering, computational biology and biological chemistry and funding through NIH. At the

next Faculty Retreat (May/June 2019), we will again specifically address funding and brainstorm

about possible center grants, and large new thematic initiatives.

Recognition of PB faculty Many of the PB faculty have been recognized to national and

international awards for their outstanding research, but also within Cornell for their teaching,

service and innovation. To mention just a recent few: 2018 ASPB early career award (Moghe),

2018 Stadler Mid-Career Maize Genetics Award (Scanlon), 2016/2017 SUNY Chancellor's

Award for Excellence (Crepet/Doyle), 2015 U.S. Secretary of Agriculture's Honor Award for

increasing global food security (Rose), 2014 Botanical Society of America Distinguished

Fellow/Merit Award (Doyle), 2013 Charles Reid Barnes Lifetime Achievement Award ASPB

(Turgeon), 2012 Humboldt Research Award (van Wijk), 2012 Stephen H. Weiss Presidential

Fellow Cornell (Niklas). We also note the 2003 Martin Gibbs Medal ASPB and Elected Member

of US National Academy of Sciences for J Nasrallah.

V. Plant Biology and the Cornell Community, BTI and USDA PB has strong ties to the

Boyce Thomson Institute (BTI) and the local USDA, both located in close physical proximity on

Cornell Campus. Multiple BTI and USDA faculty are integrated with PB through shared

research interests and projects (e.g. tomato fruit ripening, evolution, chloroplast biology) formal

appointments as adjunct faculty and/or graduate membership in the field of Plant Biology, as

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well as the summer REU student programs. However, they typically make only minor

contributions to teaching. PB is also well connected to other SIPS sections through shared

research projects and interests, as well as teaching. Since formation of SIPS, the ties between PB

and other sections have greatly strengthened through vastly increased communication and

exchange at the level of faculty, (under)graduate students and postdocs, around SIPS seminars,

social activities, organizational meetings, and importantly the course curriculum. This has

resulted in an increase in research collaborations and shared grant applications. A great example

is the study of molecular signaling during grafting of various horticultural crops by Margaret

Frank, the most recent hire in PB, with faculty in the section of Horticulture. Finally, as part of

its mission, PB has a strong tradition in organizing a high quality seminar series with invited

‘outside’ speakers (at significant expense to the PB budget) with a focus on basic research topics

aligned with the interests of PB faculty. These PB seminars draw a large audience from across

SIPS and other units and are an important component of career development of our graduate

students and postdocs. Over the last 2 years, we have used this seminar series to create more

awareness of the excellent science across campus, including research involving non-plant

systems. PB aims to strengthen multi-disciplinary collaborations taking advantage of Cornell’s

strength in engineering, computer science and campus-wide initiatives.

VI. Vision and Future of the Section of Plant Biology To shape the future and contributions of

PB, over the last year the section has collectively engaged in a series of internal events, including

a full day faculty retreat, two half days with faculty ‘vision’ talks, two teaching discussion and

evaluation meetings, and several recent meetings specifically focused on setting priorities for

short and long term faculty hiring. These meetings are helping to build collective strength,

internal communication and a unified vision for the future of the Section, as part of SIPS and the

wider community. PB will continue strategic discussion meetings in the coming year to

strengthen our science, identify new collaboration opportunities and just enjoy talking science.

Strategic faculty hiring A number of key elements for faculty hires emerged from our

discussions: (i) The candidates need to contribute to core Plant Science courses, as well as larger

undergraduate classes, in addition to more specialized courses in their research area, (ii) The

candidates will incorporate/take advantage of recent technological / methodological advances,

such as synthetic biology, nanoscale sensors that can measure (sub)cellular parameters (e.g.

[ATP], pH, [Ca2+], various metabolites), single cell techniques (i.e. to determine cell-type

specific biology) and computational biology (with application in e.g. growth and metabolic

modeling, analysis of large metabolomics data sets), (iii) Consideration of scales in biology –

from molecule to subcellular compartment, cell, organ, organism, population – is important as it

will allows for better and more collaborative research, (iv) Non-angiosperm photosynthetic

organisms, in particular cyanobacteria and algae, as they greatly contribute to biological

diversity, are very informative in studying plant evolution, are a rich resource for new materials,

metabolites, important species for synthetic biology, and play a key role in the global carbon

balance, (v) Articulated relevance for global climate changes, the global carbon balance, and/or

food security should be part of research, training and education. Faculty positions around topics

such as Plant Signaling, Synthetic Plant Biology, Cyanobacteria and Algae, Post-genome

regulation, Computational Plant Modeling, Evolutionary Plant Biology in field and/or

collections-based research all received broad support with the PB section. Following extensive

Faculty discussions in the Fall of 2018 and unanimous vote, the PB section submitted two faculty

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position descriptions (for hires in 2019/2020) for consideration to the FRC of SIPS (Faculty

Renewal Committee) – these are i) Plant Synthetic Biology and ii) Plant Signaling. These

comprehensive descriptions provide also strategic arguments for these positions. Long term

faculty leadership of the collections must be considered given anticipated (in addition to

planned) retirements in the next 5 years.

Outreach & Extension PB would like to hire an extension/outreach specialist to expand and

coordinate the diverse array of PB outreach activities and support stakeholder’s requests for plant

identification, including horticultural plants, invasive species, weeds, and toxic plants and plant

products, Additionally, the extension specialist would help to create a web-based, updated

version of the Hortus Third (1976), the authoritative reference work of the plants of North

American horticulture; this will include web-based identification tools. This extension activity

will utilize and update the exceptional resources within the Herbarium and PB, and aligns well

with needs of the stakeholders of SIPS. (See Appendix - SIPS Biodiversity Collections)

Infrastructural needs There are two urgent infrastructural needs, namely a Plant Metabolomics

Training & Research Facility (PMTRF) and an Automated Indoor Plant Phenotyping Facility

(AIPPF). A NSF-MRI preproposal for the PMTRF is now pending for internal Cornell review

and, if successful, this will be submitted in Jan 2019. Possible avenues for funding for an AIPPF

could be through the new NSF program ‘Infrastructure Capacity for Biology (ICB) or perhaps

the Cornell Digital Agriculture Initiative; Several PB faculty are involved with this initiative. A

new mass spectrometer dedicated to proteomics (van Wijk) will be acquired through combined

funding from NSF, the Dean and SIPS.

Untapped collaborative opportunities The PB section also sees many untapped opportunities for

collaborations within SIPS, as well as other units on CU campus and Weil Cornell in NY city.

These include collaborations with Chemical Engineering in particular within the realm of

synthetic biology, Computational Biology for large scale data analysis in the context of

metabolomics, the department of MBG for developmental biology and the Weil Institute for Cell

and Molecular Biology for e.g. collaborations in protein biochemistry and structural biology. It is

great to see that the newest faculty recruits to PB are very active in developing collaborations

across and beyond SIPS

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Section profile: Plant Breeding and Genetics

Plant Breeding as a Discipline: Plant Breeding is not a static art, but a vibrant, rapidly-

evolving scientific discipline that incorporates crop genetics and genomics advances, innovations

in phenotyping and statistical prediction, as well as advances in other allied disciplines

(horticulture/agronomy, plant biochemistry, plant pathology/entomology, ecology, food science,

etc) for the development of superior crop varieties that resolve critical issues in crop production,

quality, and sustainability. Plant breeding is mission-based, focused on solving important

problems in agriculture, nested in stakeholder needs, and employs the most effective and

efficient combinations of methods to meet targeted goals. The Plant Breeding & Genetics

Section is unique within SIPS in that the plants themselves are the dynamic part of the system,

resulting in new and valuable germplasm, lines and varieties. Plant Breeding & Genetics thus

complements the other sections, providing tremendous opportunities for cooperative efforts.

Mission of Plant Breeding & Genetics Section: The genetic improvement of vegetable crops,

agronomic crops and forages for the benefit of society through the development of novel

breeding methodologies, the discovery, genetic study, and transfer of economically important

traits or genes into genetic stocks, the development and release of novel germplasm and

varieties, and the training of new generations of plant breeders.

Plant Breeding History at Cornell. Our department, now section, has a rich history dating from

1907 when Dean Liberty Hyde Bailey hired Herbert J. Webber to head the Department of Plant

Breeding. Much of our history was captured in the book, The Evolution of Cornell Plant

Breeding (Murphy and Kass, 2007) and will not be repeated here. In 1914, Rollins A. Emerson

succeeded Webber, who had expanded the department activities to include research and teaching

of plant breeding, genetics, and biometry. The period from 1920-1940, sometimes referred to as

the “Golden Era of Genetics”, was remarkable for the large number of students who went on to

become great scientists and leaders in plant breeding. Two students from that era, George W.

Beadle and Barbara McClintock, were named Nobel Laureates. The period from 1953 to 1980

was a period where Cornell became preeminent in vegetable breeding, with Henry Munger

releasing a range of materials that still underlie many currently grown varieties in multiple

genera, and training graduate students who went on to become leaders of vegetable seed

companies, plant breeding faculty at other land grant universities, or held critical positions in

agriculture in their home countries. The current Section faculty includes three members of the

US National Academy of Sciences: Susan McCouch, Ed Buckler (adjunct member), and Steve

Tanksley (emeritus).

From the beginning, Plant Breeding & Genetics has welcomed international students and has had

significant interests in agricultural development in other countries. A major involvement, led by

H.H. Love, was in China from 1925 until World War II. During this time, we had many

graduate students from China. With financial support from Foundations (Rockefeller and Ford)

and United States Assistance programs (now USAID) Cornell was instrumental in establishing

the first International Agriculture Center. The Section has continued to contribute heavily to

international development, more recently with the Africa Center for Crop Improvement (ACCI)

in South Africa and the West Africa Center for Crop Improvement (WACCI) in Ghana. Our

alumni hold prominent positions in academia and government agencies throughout the world.

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Numerous prominent international scholars are among the many Adjunct and Joint Professors

who play active and important roles in the Section. Also included are several joint members

(from the Horticulture and Plant Biology Sections; including three in Geneva and one on Long

Island); three scientists from USDA; and several researchers from the Boyce Thompson Institute.

Cornell has vigorously maintained its historical strength in the discipline of plant breeding while

developing a world-class strength in plant genomics and its applications in plant breeding. The

creation of the School of Integrative Plant Science (SIPS) cross-linked Plant Breeding and

Genetics with other sections of SIPS in a larger, interactive network. The Plant Breeding and

Genetics Section remains highly regarded worldwide for our innovative, productive research

programs that contribute to the enhancement of our discipline. We now look to the future

anticipating that new selection methods will be developed, informed by high throughput

phenotyping, application of genomic information, and other techniques.

Highlights of breeding successes in diverse crops

Cucurbits: Historically this program is the source of disease resistances still used

globally in cucumber, winter and summer squash, and melon. Recent successes include

Robin’s Koginut culinary pumpkin (ca. 1/2 million pounds grown in its first season in

2018); Honeynut butternut squash with enhanced flavor and nutrition, distributed

nationally and the darling of farm to table chefs; and cucumbers that are the first with

resistance to the reemerged downy mildew pathogen.

Pepper: Habanada captures the flavor of habanero without the heat; distributed in US

and Europe.

Tomato: the first lines combining resistances to oomycete/fungal diseases Late Blight,

Septoria Leaf spot, and Early Blight, sharply reducing the number of fungicide

applications needed for combined control, underlying the fungal resistant hybrids Iron

Lady, Stellar, BrandyWise, and Summer Sweetheart. First transfer of late blight

resistance, combined with resistance to other fungal, virus and nematode pathogens plum

tomato, resulting in the multi-resistant hybrid Plum Perfect. Creation of acylsugar-

producing tomato lines with broad-spectrum resistance to insects and insect-transmitted

virus that could eliminate insecticides, and are used in entomology/virology labs at 6 land

grant universities.

Onion: Production of doubled haploid lines with substantially reduced inbreeding

depression, two of which were adopted by international cooperators as the basis for the

onion genome map and sequence. Transfer of resistance to Botrytis Leaf Blight across

strong barriers from a weedy Allium.

Potatoes: Lamoka and Waneta have outstanding fry color out of long-term cold storage

that allows growers to store potatoes for several months longer than was possible just a

few years ago; about 1/5 of potato chips in the USA are now made from these two clones.

Lehigh is a high yielding yellow potato that is widely grown in the East. All three are

resistant to golden nematode and common scab.

Wheat/small grains: Medina soft white winter wheat is an excellent pastry wheat but an

added bonus is that it is excellent for malting and use in wheat beer brewing. Erie soft red

winter wheat is an excellent pastry wheat with resistance to five different diseases.

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Alfalfa/forages: Regen alfalfa selected for root regeneration to survive when roots are

damaged mechanically or by disease, rodents, and insects. N-R-Gee alfalfa: the only

variety bred for higher levels of pectin to increase quality of alfalfa for dairy animals.

Seedway 9558 SBR alfalfa: the only variety with some resistance to alfalfa snout beetle.

SW315 LH alfalfa with a very high level of resistance to potato leafhopper. Pardee

birdsfoot trefoil: the only trefoil variety with resistance to Fusarium wilt.

Highlights of extension, international efforts, and non-breeding research

Extension: Our extension and outreach program (0.75 FTEs) connects with

stakeholders, county extension educators, seed industry representatives, consumers, high

school and elementary school educators, and policy makers, both domestically and

internationally, to deliver information about our discipline and the products we develop

and to support grower access to regionally appropriate seed.

Environmental Sciences. Plant Breeding and Genetics research is inextricably

associated with environmental science and supports the development of sustainable agro-

ecosystems. Development of plant varieties with resistance to insects and diseases

reduces exposure of the environment to pesticides. Biodiversity is the life-blood of plant

breeding research and is the focus of many of our activities from methods of assessment

to novel applications. All of our courses incorporate topics that teach environmental

stewardship and the paramount role of the genotype by environment interaction.

Applied Social Sciences: We have played a major role in educating the public about the

risks and benefits of genetically modified crops. Our faculty also teach topics on

international agriculture policy and intellectual property rights, both of which have

emerged as major global issues. The International Treaty on Biological Diversity has

transformed biodiversity from a common heritage of humankind to a commodity subject

to laws that restrict distribution and allow ownership of germplasm.

International: PB&G is especially active in international research with collaborations in

Asia, Africa, the Middle East and Latin America with a wide range of

organizations. Many of the International Agricultural Research Centers involved with

plant breeding collaborate closely with our department as do a number of national

agricultural research systems and private sector programs.

Education

Training graduate students/postdocs

Our field/section has the highest graduate student/faculty ratio, and also a very high Post

doc/faculty ratio. Our students tend to be funded on faculty grants rather than TA lines.

Synapsis is a vibrant plant breeding graduate student organization founded 110 years ago.

In addition to bonding our students through social functions, the group is also the vehicle

for student engagement with section decisions on courses and faculty hiring, curriculum,

and is active in professional events like NAPB and hosting the Pioneer symposium.

Training undergraduate students

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Faculty in our section advise students in the increasingly popular ‘plant breeding and

genetics concentration’ of the Plant Science major

Courses

Plants, Genes and Global Food Production (PLBRG2010) is a gateway course that gives

undergraduate students the opportunity to discover the appeal of our discipline. Plant Genetics

(PLBRG2250) is the largest required course in the Plant Science major and serves ~60 students

annually. Serving both undergraduate and graduate is Genetic Improvement of Crop Plants

(PLBRG4030) and its accompanying lab PLBRG4060; this is our principal plant breeding

course. Quantitative Genetics (PLBRG 7170) has been recently modernized with a new faculty

hire. Perspectives in Plant Breeding Strategies (PLBRG 7160) is a capstone literature course.

Additional coursework is typically in statistics, computational biology and within students’

selected minors (commonly international agriculture and pathology).

Challenges:

Plant breeding section staffing

GOAL 1: To rebuild Plant Breeding and Genetics Section Faculty

PB&G is the smallest section of SIPS. Other current sections of SIPS were formed

following mergers of other departments (Hort. and PPPMB merged departments from

Geneva and Ithaca campuses, Plant Biology was combined with the Hortorium, etc) and

so were large or very large in faculty size, while Plant Breeding was very small and

remained small when SIPS was formed in 2014. With the reduction in SIPS faculty from

104 to 84 since then, most SIPS sections have been reduced in size, but Plant Breeding &

Genetics remains uniquely and critically small in size.

Plant Breeding has had great accomplishments with a small group of faculty, but is at risk

of being reduced below sustainable levels as recent and anticipated faculty retirements

outpace the current model for hiring. We have eleven faculty with PBG as their primary

appointment; of these, seven are 62 years old or older, and only five have full time

appointments within the section largely due the administrative service our faculty are

called upon to provide to the college.

While other land grant institutions are investing in plant breeding faculty hires, and/or

have created centers or institutes where there was no prior named unit, Plant Breeding at

Cornell was allowed to shrink prior to the formation of SIPS.We were ranked top in the

nation in plant breeding in the most recent (2010) NRC study of doctoral programs, and

need to hire faculty at a pace that will allow us to recover a critical mass. Without

specific steps to resolve the situation, and with a number of the existing plant breeding

faculty retiring or reaching an age when additional retirements are likely, we face the

challenge of maintaining the sustainability of this section, as well as its balance of

breeding and critical allied disciplines/programs.

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GOAL 2: to maintain a balance between outstanding plant breeding and basic scientific research

in key research areas that contribute to breeding advances, as well as maintain a balance in

breeding and genetics programs among crops

Plant Breeding at Cornell has long had a tradition of including among its faculty excellent

scientists focused on breeding/genetics of specific crops, and excellent scientists with

strengths in allied fields and an interest in applying those capabilities to breeding, often in

cooperation with the breeding faculty.In the current situation, with many breeding faculty

retiring or likely to retire soon, it will be necessary to focus new hires on faculty whose

primary focus is on the breeding/genetics of a crop, rather than a primary focus on an

allied field.

Grains have emerged as powerful systems for research and training so our recent hiring

efforts have been grain-focused in their research. With germplasm and cultivar

development being central to our identity, we need to maintain a cohort of faculty

working directly in this breeding area.

While we cover many vegetable needs, this is through the efforts of a few faculty each

covering multiple crops. Vegetable breeding is in critical need of more attention, through

additional faculty, to prevent loss of programs and maintain excellence in this area.

Breeding efforts could also be expanded into new plant species such as non-forage

legumes, ornamentals, or sources of specialized metabolites for nutrition and flavor (such

as hops) if additional positions could be created.

Teaching undergrads/grad

GOAL: As staffing issues are addressed, we can simultaneously strengthen our curriculum by

contributing specific courses in Plant Breeding and Genetics as well as interdisciplinary teaching

to support education in food, sustainability, policy, big data and engineering.

PLBRG2010 Plants, Genes and Global Food production has long served as a first

exposure to plant breeding, helping students discover a passion and career in the

discipline, but was cancelled when McCouch recently became director of the new Cornell

Institute of Digital Agriculture

PLBRG4030 is our core course in plant breeding.Gore now teaches this.By relieving

Gore of triage coverage of PLBRG4030, he can develop new coursework to engage

engineering students in collaborations with plant breeders to innovate production and

phenotyping

Infrastructure

GOAL: Invest in infrastructure necessary for plant breeding to both enable research and

secure existing investments

Adequate, local storage for field equipment: fundraising for field machinery is

challenging and storage spaces promote longevity by preventing rust and

corrosion.Storage near point of use reduces risk to operator and equipment from

accidents while in transport on roadways.

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Appropriate field and greenhouse space that meet plant breeder’s needs. At times plant

breeders inoculate and need appropriate facilities that both promote disease yet contain

the pathogen; at other times breeders need disease-free field and greenhouse space to

generate healthy seed that can be shared globally. Cost saving measures that reduce

available space are challenging these needs and putting valuable program materials at

risk.

Many of our facilities for processing plant samples and acquiring data are several decades

old. Some of these structures would be in violation of code if not “grandfathered”,

including conditions that risk personnel health and safety.These facilities need to be

expanded (and upgraded).

Seed storage is reaching capacity and will become insufficient to preserve the archive of

precious germplasm that will otherwise slowly die.

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Section profile: Plant Pathology & Plant Microbe Biology

History: The study of plant pathology at Cornell dates back to the university’s founding in

1868, with classes in parasitic fungi taught by Albert Prentiss, the first chair of Botany. In 1885,

JC Arthur, Cornell’s first recipient of a Doctor of Science degree, used Koch’s Postulates to

demonstrate Erwinia amylovora’s role in fire blight. Cornell’s Department of Plant Pathology,

founded in 1907, was one of the first of its kind in the nation. Plant pathology research and

extension at the NYS Agriculture Experiment Station in Geneva dates back to the station’s

founding in the early 1880s, with a Geneva based Plant Pathology Department created in 1933.

In 2007 the Geneva and Ithaca departments were renamed “Plant Pathology and Plant-Microbe

Biology” (PPPMB) and administratively merged in 2010 to create a single academic center for

the study of the causes and management of plant disease and the fundamental interactions

between plants and microbes.

Areas of excellence

Mycology: Cornell has a long history of world renowned mycological research, with George

Atkinson (hired 1892) and Harry Fitzpatrick (hired 1913) conducting high profile work in fungal

taxonomy and playing founding roles in both the American Botanical Society and Mycological

Society of America. Richard Korf, hired in 1951, served as the Director of the Cornell

University Plant Pathology Herbarium (CUP), one of the largest fungal herbariums in the United

States, co-founded the journal Mycotaxon, and was considered a world expert on Discomycete

branch of fungi. At least 19 fungal species are names for him. Kathie Hodge, current professor of

mycology, continues to maintain CUP and is a national expert in fungal taxonomy, highly

regarded for her teaching and outreach. Several other of our faculty are engaged in detection and

control of fungal and oomycete diseases, as well as the fundamental mechanisms of fungal-plant

interactions.

Fundamental mechanisms of pathogenesis and host-microbe interaction: Cornell has a

strong program in fundamental nature of pathogenesis, promoted by the hiring of DF Bateman in

1970 and carried on by many subsequent faculty. Molecular genetic studies of phytoalexins and

fungal toxins, and development of molecular methods by the Yoder and Van Etten programs

were instrumental in advancing fungal molecular biology. Gillian Turgeon, Michael Milgroom,

Rebecca Nelson, and Teresa Pawlowska continue to make groundbreaking discoveries in the

areas of fungal genetics and genomics and fungal symbioses.

On the bacterial front, Alan Collmer and Greg Martin have developed the Pseudomonas

syringae/tomato pathosystem into a model for understanding the interactions of hemi-biotrophic

bacterial pathogens with plant defense responses. Adam Bogdanove, recruited in 2012, leads a

research program that has made groundbreaking insights into interactions of Xanthomonas TAL

effectors and development of TAL-based gene editing.

As new methods and tools for understanding mechanisms of virulence and resistance have

become more accessible, they are being applied increasingly to non-model, economically

important pathosystems such as apple, grape, and others.

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Meeting state and regional needs: Cornell maintains a long history of nimble and effective

response to state and regional plant disease challenges, particularly impressive in light of the

reduction in faculty lines. These include diagnostic testing and maintenance of quarantine

programs, addressing new and emerging diseases such as Dickeya on potatoes (Perry, McGrath),

highly virulent Phytophthera isolates (Smart, McGrath), new virus disease of potato and grape

(Perry, Fuchs), and emergent fungal diseases of fruits (Cox), vegetables (Pethybridge, Smart),

and small grains and forage crops (Bergstrom). Cornell plant pathologists are also working to

meet the challenges of newly important crops for New York State such as industrial hemp as

well as hops and grains used for the state’s growing brewing industry. Gary Bergstrom’s

program is focused on pathology and control of hemp and small grain diseases, and David

Gadoury’s on hops. Cornell plant pathologists are also playing a significant role in Cornell’s

Digital Agriculture Initiative with Sarah Pethybridge and Rebecca Nelson both engaged in UAV-

based disease diagnostics and phenotyping.

Virology: Cornell plant pathologists have made many contributions to virus pathology,

detection, and control. The potential for viruses in disease control has a particularly storied

history with Systemic Acquired Resistance being first described by Frank Ross in the early

1960s. Milt Zaitlin made significant discoveries in the area of pathogen-derived resistance, a

concept ultimately use by Denis Gonsalves for development of virus resistant squash and papaya.

The virus resistant papaya lines have been credited with saving the $47 million Hawaiian papaya

industry and remain the best known example of disease control using genetic

biotechnology. Marc Fuchs and Keith Perry currently conduct research in identification and

characterization of emerging virus diseases such as Red Blotch of grape.

International Agriculture: Cornell plant pathology has a long tradition of partnering with

institutions and initiatives directed at enhancing global food security. John Niederhauser, an

alumnus and extension pathologist in the department was awarded the 1990 World Food Prize

for his work in Mexico. David Thurston, the first faculty member with specific responsibilities

for international agriculture, was succeeded by Rebecca Nelson, 1998 winner of a MacArthur

Fellowship for her work at the International Potato Center and current program director for the

McKnight Foundation Collaborative Crop Research Program. Many other PPPMB faculty also

maintain international collaborations.

Goals and Objectives of training in the graduate field:

Plant Pathology and Plant-Microbe Biology is a multi-faceted discipline that comprises many

diverse subjects. To reflect this diversity, the section is organized into the following three

programs of graduate study. (i) Plant Pathology encompasses Biology and Ecology,

Epidemiology and Population Biology, and Etiology, Diagnosis, and Management of Plant

Diseases. (ii) Plant-Microbe Biology encompasses Molecular and Cellular Basis of Inter-

organismal Interactions, Functional Genomics and Proteomics, and Plant Responses to

Symbionts and Pathogens. (iii) Fungal and Oomycete Biology encompasses Genetics and

Genomics, Cell and Developmental Biology, and Systematics, Ecology, and Evolution.

Upon completing their graduate degree, students are expected to have demonstrated Mastery of

knowledge in their chosen program of study, advanced research skills that synthesize existing

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knowledge and critical analysis, developed effective communication skills and the ability to

effectively receive feedback, and acquired a commitment to ongoing personal and professional

development.

Important affiliations outside of SIPS

Many faculty affiliated with the PPPMB Section have primary appointments at the Boyce

Thompson Institute (BTI) and with the Agricultural Research Units in Ithaca and

Geneva. Affiliated faculty at BTI include Maria Harrison, Michelle Heck, Zhangjun Fei, and

Dan Klessig. Affiliated faculty at ARS include Xiaohong Wang, Bryan Swingle, Melanie

Filiatrault, Stewart Gray, Jason Londo, and Lance Cadle-Davidson. BTI and ARS affiliates

provide vitally important contributions as collaborators, as major and minor advisors for

graduate students, service to the section, and as a complementary scientific knowledge base.

Members of the section also have significant collaborations with engineers and computer

scientists at Cornell and other institutions including Columbia University, RIT, and RPI, much of

these being driven by recent initiatives in digital agriculture.

Affiliations with other sections since creation of SIPS

Commodity based affinity groups: Pathologists focused on crops such as grape, potato, apple,

vegetables, or field crops participate in commodity working groups and shared field days with

faculty in other sections such as plant breeding and horticulture. New initiatives: New cross-

section collaborations have emerged around Initiatives such as industrial hemp and digital

agriculture, with faculty in different sections involved in different, complementary aspects of

these challenges. New synergies: Examples of unexpected synergies between research programs

include recent collaboration between Gillian Turgeon and Lailiang Cheng in the Horticulture

Section. Margaret Frank, a recent hire in the Plant Biology Section, is also collaborating with

pathologists on the biology of grafting and its contribution to host resistance.

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Section profile: Soil & Crop Sciences

History of the Soil and Crop Sciences Section at Cornell. The history of the Soil and Crop

Sciences Section reflects its deep connections with disciplines spanning cropping systems,

weather, and soil geochemistry. Section history can be traced back to George Caldwell and Isaac

Roberts in 1868 and 1874 – pioneering researchers in soil fertility and crop production, for

whom Roberts and Caldwell Halls are now named. Cornell’s program excelled throughout the

early 20th century in the analysis of the fate of chemicals in soils and their delivery to water. The

department was also among the first to establish overseas research programs, gaining a

preeminent international reputation in agronomy. The changing priorities of society during the

1960's led to the growth of research on environmental and health-related problems along with

emphasis on soil resources, forage crops and weeds that continued through the 1970's and 1980's.

The configuration and name of the department changed several times during the 20th century,

with Earth and Atmospheric Sciences splitting from Crop and Soil Sciences in 2000. The name

was officially changed to Soil and Crop Sciences upon the incorporation of the department into

SIPS. Since 2006, the department has become an integral part of new curricula in Agricultural

Sciences and Environmental and Sustainability Sciences, which provide undergraduate students

with integrated and diverse opportunities for studies.

Mission of the Soil and Crop Sciences Section. The mission of the Soil and Crop Sciences

Section is to advance and communicate knowledge relevant to agroecosystems and their

sustainable management within the context of accelerating global change. Our vision is to build

on our status as a world leader in research targeting the intersection between food, feed, and fuel

production systems and the environment, to educate tomorrow’s leaders in agricultural

management and environmental stewardship locally and globally, and to serve stakeholders of

New York State by providing information resources and services that promote the sustainable

management of agricultural and environmental resources.

We fulfill our mission by (i) focusing our scholarship at the productive interface between

agriculture, the environment, and the new life sciences, (ii) exploiting the interdisciplinary nature

of our faculty and experiential learning environments that attract and educate tomorrow’s leaders

in crop biology, agricultural sustainability, and environmental stewardship, (iii) extending our

programs to enhance lifelong learning opportunities for stakeholders locally and globally, and

(iv) fostering a climate in which members of our section community can achieve personal and

professional goals.

We will continue to sustain growth in the quality of our programs and foster a unit climate that

continues to value excellence in research and education. Strategies for achieving our research

goals include fostering multidisciplinary research teams that achieve national prominence in

understanding and managing sustainable landscapes, strengthening productive areas of research

that lie at the intersection of agriculture and the environment, and continuing our tradition of

excellence in investigating and advancing sustainable agroecosystem management. Strategies for

improving our curriculum focus on our continued leadership and contributions to several

undergraduate majors include: leveraging the interdisciplinary nature of our faculty, taking

advantage of our small class sizes to enhance faculty-student interaction, and fostering an

environment of instructional excellence that will enhance the learning outcomes of our students.

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Programmatic Themes and Areas of Excellence

Scientific disciplines represented in the section include crop, environmental, and soil sciences.

Crop science disciplines focus on crop biology, grain and forage crop agronomy, and weed

science. Environmental science disciplines focus on global change in managed ecosystems,

agriculture-environment interface, and environmental information science and modeling. Soil

science disciplines focus on soil biological, chemical, and physical properties and processes. Our

programmatic themes are structured to complement university grand challenges, college

priorities, School and Section missions, and faculty expertise. The three strategic themes are

especially timely areas of inquiry, span the intellectual goals and disciplinary strengths

Theme 1: Crop Biology – Sub-theme: Environmental Stress Biology. Global climate change,

which involves both warming and more frequent incidence of weather extremes, is predicted to

increase crop losses due to stress from heat, drought, and flooding. Crop production is being

shifted to more marginal lands that are susceptible to problems with mineral nutrient fertility,

toxic soil components, drought, flooding and poor water holding capacity. Tim Setter’s program

is investigating the basis of maize and cassava sensitivity to drought during reproduction. Genes

involved in the response are being identified using microarray and bioinformatics/comparative

genome mapping, and transient expression tests. Olena Vatamaniuk’s program focuses on

mechanisms of heavy-metal toxicity in plants and in the nematode Caenorhabditis elegans, a

model for heavy metal sensitivity and disease in humans. The emphasis of these studies is on

generating novel tools for cost-efficient phytoremediation approaches for clean-up of soils and

water polluted with heavy metals; generating “heavy metal-free” crops; and developing new

approaches for preventing and treating heavy metal poisoning in humans.

Theme 2: Agricultural Sustainability – Sub-theme: Integrated Crop Production Systems.

Discussions about sustainable agriculture must go far beyond what happens within the

boundaries of any individual farm. Farming is now viewed as a much larger system with many

interacting parts, including environmental, economic, and social components. It is the complex

interactions and balance among all of these parts that have brought us together to discuss

sustainability, determine how we move towards this broader goal, and how an agroecological

perspective focused on sustainable agroecosystems is a way to achieve such long term

objectives. Matt Ryan, Jerry Cherney, Antonio DiTommaso, and Andrew McDonald work

on field and forage cropping systems and weed management. With the increasing interest in

diversified cropping systems both within conventional and organic farming, they are using their

expertise to broadly address needs of New York growers as well as growers nationally and

internationally. The programs of Harold Van Es and Johannes Lehmann also broadly fall

within the Sub-theme: Soil and Nutrient Conservation for Soil Health and Climate

Resilience. Van Es’s program is focused on precision soil management, with emphases on a

holistic soil health management framework, and a computational tool for precision nitrogen

management (Adapt-N) that was recently commercialized. Johannes Lehmann’s research is

focused on understanding of biogeochemical cycles of carbon and nutrient elements in soil,

developing methods for soil carbon sequestration and resource recycling from waste to

fertilizers, and providing important insight into regional and global element cycles. This field of

research has global and local relevance with implications for climate change, resource use

efficiency, and environmental pollution.

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Theme 3: Environmental Stewardship – Sub-theme: Global Change in Managed

Ecosystems. Agricultural landscapes are inherently linked with the environment. Land

management decisions have powerful impacts on local ecosystems and agriculture is a

tremendous driver of global environmental change. The Soil and Crop Sciences Section seeks to

maintain and expand its role as a global leader in efforts to examine and reduce the

environmental impact of agriculture while maintaining the productivity and profitability of

agricultural systems. Biogeochemical cycles in soils drive soil organic matter dynamics, the

availability and fate of soil nutrients (such as N, P, S, and trace minerals) and soil toxicants (such

as heavy metals and other soil contaminants), and the consumption and production of greenhouse

gasses such as N2O and CH4. These processes are driven by a wide range of microbiological and

chemical processes which remain poorly characterized. We seek to understand the interactions

between microbial communities, soil organic matter dynamics, and the biochemical and

chemical reactions that govern soil function. This field of research has global and local relevance

with implications for soil fertility, climate change, and environmental pollution. In addition to

the Van Es and Lehmann research programs that focus on this sub-theme, Murray McBride

studies bioavailability of toxic and trace metals in soils to crops, animals, and humans,

considering all of the properties of soils that modify this bioavailability. Ultimately, this research

has several goals, protecting food crops from toxic metal contaminants, minimizing trace

element deficiencies, and developing methods for testing and remediating contaminated soils.

Enid Martinez’s program focuses on molecular scale investigations of the interaction of organic

carbon and nitrogen at mineral surfaces and biomolecular signature in soils with depth in

addition to the biogeochemistry of trace minerals. The research programs of microbial ecologists,

Daniel Buckley and Janice Thies make use of innovative population genomics tools to map

microbial food webs in the soil and for investigating soil and plant microbiomes and their

impacts on ecosystem health, the plants we grow, the water we drink, and the air we breathe.

Sub-theme: Environmental Information Science and Modeling.

Advanced aerospace imagery can be used to improve resource inventory and to inform

management decisions. However, effective utilization of these tools requires the development of

spatial models that incorporate multi-spectral and multi-temporal data from Earth-orbiting

satellites with edaphic variables for mapping ecological communities. These models can then be

used to generate resource inventory data for use in spatially-explicit simulation models of

nutrient and pesticide fate and transport in mixed use landscapes. Such environmental

information will provide fundamental insights on regional interactions between agriculture and

the environment and will provide valuable tools for use in developing effective farm

management practices and policy. SCS faculty member Ying Sun is at the forefront of using

remote sensing of Solar-Induced chlorophyll Fluorescence (SIF) and land surface modeling (i.e.,

the NCAR Community Land Model) to quantify the spatial-temporal dynamics photosynthesis

and its response to changing climate/stress.

Goals and Objectives of Graduate Training in the field. Students in the Field of Soil and Crop

Sciences work on projects spanning a range of topics such as advances in management practices

for sustainable field crop production, soil biogeochemistry in relation to climate change and

environmental concerns, geospatial land processes, and molecular genomic aspects of crop plants

and soil microbes. Many faculty members have research programs focused on international

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agricultural and environmental issues in tropical and subtropical regions. A limited number of

students can complete most or all of their research overseas. Reflecting this diversity, programs

of graduate study are organized under the following concentrations. (i) Agronomy concerns

development of improved management practices with an integrated consideration of field crops

and soils. (ii) Field Crop Science encompasses weed science, seed science, crop physiology, and

nutrient management. (iii) Soil Science concerns processes and properties of the soil

environment. (iv) Environmental Information Systems is focused on the use of geospatial

environmental information systems to advance our understanding of biophysical processes and

the sustainable development and management of Earth’s resources.

Undergraduate Education. Our faculty are actively involved in undergraduate teaching,

academic and research advising. They are key contributors to several undergraduate majors

including, Agricultural Sciences, Environmental and Sustainability Sciences, International

Agriculture and Rural Development, Plant Sciences, and Biology and Society. Section faculty

serve as academic advisers for 150 undergraduate students in these five majors. Antonio

DiTommaso holds a leadership role in the multi-departmental and multidisciplinary Agricultural

Sciences major. Several SCS undergraduate courses are required in multiple majors including

PLSCS 1900: Sustainable Agriculture: Food, Farming, and the Future PLSCS 2110: Field Crop

Systems, and PLSCS 2600: Soil Science.

Important Collaborations within and outside of SIPS. Commodity based affinity groups: Soil

and Crop Sciences faculty actively participate in commodity (field crops, forages) working

groups and shared field days with faculty in other SIPS sections such as plant breeding, plant

pathology and horticulture. New initiatives: New cross-section collaborations have emerged

around initiatives such as industrial hemp, digital agriculture, food security, and

Organics@Cornell, with faculty in different sections involved in different, complementary

aspects of these challenges. Shared priorities: Cornell’s soil health team is composed of faculty

drawn from both Soil and Crop Sciences and Horticulture.

Faculty in Soil and Crop Sciences have extensive connections outside of SIPS with faculty in

engineering, Earth & Atmospheric Sciences, Entomology, and the USDA-ARS Unit in Ithaca.

Examples include Olena Vatamaniuk who collaborates with staff at Cornell’s synchrotron in

investigation of mineral distribution in plant material. Tim Setter participates in the Next Gen

Cassava project led by ARS and BTI faculty. Johannes Lehmann works with faculty in chemical

engineering on resource recycling and fertilizer production from agricultural wastes, and with

colleagues in entomology, CEE, and the Lab of Ornithology on sound detection in soil. Antonio

DiTommaso collaborates with faculty in the Department of Entomology to better understand the

ecological value of weeds in the landscape for insect pollinators and natural enemies of crop

insect pests. Most recently, this work has shifted to assessing the value of mixed plantings for

pollinators and natural enemies of crop insect pests on solar power generating farms.