SolCAPSolCAPSolanaceae Coordinated Agricultural Solanaceae Coordinated Agricultural ProjectProjectDedicated to the Improvement of Potato and TomatoDedicated to the Improvement of Potato and Tomato

Executive Commitee :Executive Commitee :

David Douches Walter De Jong David Douches Walter De Jong Robin Buell David Robin Buell David FrancisFrancis Alexandra Stone Lukas Mueller Alexandra Stone Lukas Mueller AllenAllenVan Van DeynzeDeynzeSupported by the National Research Initiative Plant Genome Program of USDA’s Supported by the National Research Initiative Plant Genome Program of USDA’s

Cooperative State Research , Education and Extension ServiceCooperative State Research , Education and Extension Service

Commercial Solanaceae ProductionCommercial Solanaceae ProductionUS: $5.38 billion product value (1.6 million acres)US: $5.38 billion product value (1.6 million acres)

Solanaceae Breeding Bottlenecks & ChallengesSolanaceae Breeding Bottlenecks & Challenges

• Narrow genetic baseNarrow genetic base

• Inefficient early generation selectionInefficient early generation selection

• Many pestsMany pests

• Multi-trait evaluationMulti-trait evaluation– QualityQuality– Resistance Resistance – AgronomyAgronomy

• Market differentiationMarket differentiation

• Lack of markers in elite germplasmLack of markers in elite germplasm

• Small populationsSmall populations

In Solanaceae There is a Major GapIn Solanaceae There is a Major Gap Between Genomic Information and Breeding Between Genomic Information and Breeding

• Tomato and potato breeding are based upon phenotypes, not Tomato and potato breeding are based upon phenotypes, not genotypes, despite the fact that they are being sequencedgenotypes, despite the fact that they are being sequenced

• Sol Genomics Network (SGN) database is not being utilized by Sol Genomics Network (SGN) database is not being utilized by breedersbreeders

• Similar genomes, few examples of orthologous gene discoverySimilar genomes, few examples of orthologous gene discovery

• Marker assisted breeding (MAB) is not practiced due to:Marker assisted breeding (MAB) is not practiced due to:– limited genetic diversity limited genetic diversity – lack of genetic markers linked to traits of interestlack of genetic markers linked to traits of interest

MinnesotaUniversity of Minnesota WisconsinUSDA/ARS University of WisconsinMichiganMichigan State UniversityOhio Ohio State University

Lead Institution: Michigan State University

OregonOregon State UniversityCedar Lake Research and ConsultingIdahoUSDA/ARS University of IdahoCaliforniaUC DavisCampbells R&D

New YorkCornell UniversityMarylandUSDA/ARS Beltsville

West VirginiaWest Virginia State UniversityNorth CarolinaNorth Carolina State UniversityFloridaUniversity of Florida

SolCAP Project ParticipantsSolCAP Project Participants

Principal ScientistsPrincipal Scientists

• David Douches (Michigan State, potato breeder)

• David Francis (Ohio State, tomato breeder)

• Walter De Jong (Cornell University, potato breeder)

• Allen Van Deynze (UC Davis, genotyping/sequencing)

• Robin Buell (Michigan State, sequencing/bioinformatics)

• Lukas Mueller (Boyce Thompson Inst., bioinformatics)

• Alexandra Stone (Oregon State, eXtension)

SolCAP Research ObjectivesSolCAP Research Objectives

• CSREES (CSREES (Two E’s focus of afternoon session)Two E’s focus of afternoon session)

• Primary research objective: Primary research objective: – To provide infrastructure to link allelic variation in genes to

valuable traits within the two most important vegetable crops in the Solanaceae: potato and tomato

• General objectives: General objectives: – Increase the likelihood that breeding of crops in the Solanaceae

will benefit from genotype-based selection processes

– Leverage genomic resources for the improvement of multiple crops that share taxonomic affinity and DNA homology first CAP that has a multiple species focus

• Unique challenge because, despite having close genomic structure, the breeding systems are different

– Expand beyond a single commodity to encompass multiple related species will create a broader vision for translational genomics in agricultural research.

Stakeholder-defined CoreStakeholder-defined Core Components Components

– TraitsTraits• Carbohydrate and sugar metabolism (processing traits)

– GermplasmGermplasm• Elite germplasm, Breeder driven; Appropriate outgroups

– ToolsTools• Fund existing facilities to SNP genotype germplasm panels

– Flexible fundingFlexible funding• genotyping additional populations for validation or additional traits• marker conversion

– Data mining and managementData mining and management• SGN, SolCAP websites

– ExtensionExtension• eXtension; partner with other CAPs

– Education Education • Curriculum development; breeder workshops, graduate course

How will tomato and potato breeding How will tomato and potato breeding benefit from SolCAP?benefit from SolCAP?

• Develop molecular genetic tools and infrastructure so that applied breeders can begin to use marker-assisted selection in elite germplasm.

• Develop 1536 SNP (or more as platforms expand) markers that are polymorphic in elite potato and tomato germplasm.

• SNP Genotype 480 potato clones and 480 tomato lines-- provided by North American breeders -- with these markers.

How will Tomato and potato breedingHow will Tomato and potato breeding benefit from SolCAP? benefit from SolCAP?

• Provide, as a service, genotyping of populations/ breeding clones in 2010, 2011 and 2012, submitted by the breeding community.

• Develop a breeder portal for access to SGN (sgn.cornell.edu) to improve use by applied breeders.

• Workshops for breeders, staff, and graduate students in bioinformatics, marker theory and practice.

• Develop a distance-education course in marker-assisted breeding.

• Generate and disseminate web-accessible outreach materials for the public, through an eXtension community of practice.

• Summarize all research objectives here…

ObjectivesObjectives

• Collect standardized phenotypic data across multiple Collect standardized phenotypic data across multiple environments for tomato and potato. environments for tomato and potato.

– standardized database of phenotypes for key traits across germplasm panels for each commodity, accessible through the SolCAP and Solanaceae Genome Network (SGN) websites.

Germplasm PanelsGermplasm Panels

Germplasm PanelsGermplasm Panels

• Cooperative tests- at least 2 locations for each crop under the supervision of experienced field breeders.

• Through the “cooperators guide”, we will also promote a “genomics mentality” that emphasizes increased genotypic replication and the collection of standardized and objective phenotypic data that can be linked to ontologies.

High throughput analysis of High throughput analysis of carotenoids, sugars, and carotenoids, sugars, and acids using IR Spectraacids using IR Spectra(Luis Rodruiguez-Saona, D. Francis, OSU)(Luis Rodruiguez-Saona, D. Francis, OSU)

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Lycopene QuantificationLycopene Quantification

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Germplasm Panel, e.g. PotatoGermplasm Panel, e.g. Potato

• A subset of the germplasm panel will be:

– Lines chosen based upon CHO variation

– Important varieties and advanced lines of value to the breeder

– Solanum species and accessions introgressed into 4x germplasm

– 4x mapping population from a russet x russet cross: primary CHO/ vitamin C mapping population for QTL analysis

– 2x mapping population will be used for mapping SNPs

Germplasm Panel, e.g. PotatoGermplasm Panel, e.g. Potato

• Field tested 2 years X 3 major environments for potato production (PNW northern irrigated desert/fall harvest, NC - northern humid/ fall harvest and SE southern humid/spring or summer harvest) to collect samples for CHO, vitamin C analysis and other traits.

– Evaluation of specific gravity, chip color, skin type, shape, vine maturity, tuber number, vitamin C, internal defects, bruising, anthocyanins and biotic resistances.

– K. Haynes (USDA/ARS, MD) will provide experimental design, data management (combining genotypic and phenotypic data) and statistical analysis of the phenotypic data for potato.

• Develop extensive sequence data of expressed genes, Develop extensive sequence data of expressed genes, and identify Single Nucleotide Polymorphism (SNP) and identify Single Nucleotide Polymorphism (SNP) markers associated with candidate genes for sugar, markers associated with candidate genes for sugar, carbohydrate, and vitamin biosynthetic pathways. carbohydrate, and vitamin biosynthetic pathways.

– Catalog allelic variation in structural and regulatory genes and subsequently explore correlation with corresponding traits.

Genotyping PlatformGenotyping Platform

PotatoPotato•Snowden•Atlantic•Premier Russet

LeafFlowerCallusTuber

•T5(CA fresh-market)•FL7600(Florida fresh-market)•NC84173(North Carolina fresh-market)•OH9242(Ohio processing)•PI114490(wild cherry tomato)•PI128216(wild current tomato)•H1706 (Midwest Processing; focus of Genome sequence)•TA496 (CA Processing; focus of EST sequence)

LeafFlowerCallusFruit

cDNA Libraries for SequencingcDNA Libraries for SequencingUsing illumina Genome Analyzer (Solexa)Using illumina Genome Analyzer (Solexa)

TomatoTomato

Sequencing and Marker DiscoverySequencing and Marker Discovery

• Transcript assemblies Transcript assemblies

– Represent consensus sequences of all ESTs • all alleles that are similar enough to be co-assembled under

the parameters used. – Represent the predominant allele in the underlying EST

population

• Identify SNPs via alignment to consensus transcript Identify SNPs via alignment to consensus transcript assemblies and reference genome sequence. assemblies and reference genome sequence.

– computationally identify all possible SNPs within a genotype

Add data from Robin’s eSNP discovery and cross linking to validated SNPs …

# in potato

# in tomato

Validation flags

High Throughput GenotypingHigh Throughput Genotyping

illumina Genomic Analyzer

• Establish centralized facilities for genotyping a core set Establish centralized facilities for genotyping a core set of SNPs in standard germplasm panels in tomato and of SNPs in standard germplasm panels in tomato and potatopotato. .

– a uniform database (>1.47 M data points) of integrated mapped markers and genotypes for 480 accessions of each crop.

– The genetic data will resolve population structure and facilitate association mapping in the core collections and designing further QTL mapping populations

– (For e.g. see Matt Robbins, OSU, presentation)

SNP GenotypingSNP Genotyping

Genotyping the core collections will Genotyping the core collections will impact strategies for translation.impact strategies for translation.

• Potential translational approaches: Potential translational approaches:

– 1) introgression from other populations (domesticated or wild) – 2) selection for coupling phase recombinants to establish linkage

blocks of favorable alleles (e.g. disease resistance loci)– 3) population development designed to maximize variation w/in market

classes– 4) association approaches– 5) whole genome approaches

• Other translational strategies will emerge under other Other translational strategies will emerge under other CAPs or through innovation in public research. CAPs or through innovation in public research.

• Currently traits and populations among the breeding Currently traits and populations among the breeding communities for tomato and potato exist to implement communities for tomato and potato exist to implement each of the five approaches, each of the five approaches, but there are insufficient but there are insufficient numbers of markers to do sonumbers of markers to do so..

• Address regional, individual program and emerging needs within Address regional, individual program and emerging needs within the Solanaceae community through a small grants program. the Solanaceae community through a small grants program.

• Six key areas we intend to allocate resources to are: Six key areas we intend to allocate resources to are:

– Genotyping mapping populations in the core facilities requested by the greater breeding community

– Marker conversion – developing SNP markers linked to QTL into easily assayed (e.g. CAPs or dCAPs) markers that end-users can readily apply in their own research programs

– QTL validation and MAS

– Population development to address emerging needs

– Extension or education special projects

– New directions not envisioned at the time of proposal submission.

Small Grants ProgramSmall Grants Program

• Create integrated, breeder-focused resources for Create integrated, breeder-focused resources for genotypic and phenotypic analysis by leveraging existing genotypic and phenotypic analysis by leveraging existing databases and resources at SGN and MSU. databases and resources at SGN and MSU.

– Breeders, geneticists, and bioinformaticians will work to create integrated genomic and phenotypic databases that serve the entire potato and tomato breeding and genetics community

Databases and ResourcesDatabases and Resources

Developing “Breeder Friendly” ToolsDeveloping “Breeder Friendly” Toolsconsider dropping from PAGconsider dropping from PAG

• Current SGN interfaces are aimed at the molecular biologist, with searches designed to facilitate molecular discovery– Need a portal that is trait and germplasm centered

• Ability to search by traits relevant to (and defined by) breeders

• When a marker is identified, a protocol for use in breeding will be provided.

• Search option that only yields polymorphic marker, phenotype, or QTL results from elite germplasm

• Ability to search for known parents or offspring of any given genotype

• Ability to generate a list of markers that are polymorphic between any two parents

• Detailed tutorial/definitions of terms and traits utilized within the database

Outcomes for Breeding from SolCAPOutcomes for Breeding from SolCAP

• A genome-wide set of markers A genome-wide set of markers and bioinformatic tools and bioinformatic tools accessible by breedersaccessible by breeders

– Breeders will access germplasm for crossing based upon SNP polymorphism and linked QTL of interest

– design crosses complementary for QTL and traits, and then use MAB in EGS.

• Better understanding of the allelic Better understanding of the allelic variation influencing CHOsvariation influencing CHOs

– Design crosses to create improved sugar and starch levels and starch quality.

– Crosses designed to manipulate and select variation within existing elite populations or introgress novel alleles from wild germplasm.

– More predictable and directed

breeding effort for processing and fresh market traits.

Outcomes for Breeding from SolCAPOutcomes for Breeding from SolCAP

• The discovery of orthologous genes through improved The discovery of orthologous genes through improved bioinformatic databasesbioinformatic databases

Outcomes for Breeding from SolCAPOutcomes for Breeding from SolCAP

• Changes in breeding systems. Vegetable breeding has Changes in breeding systems. Vegetable breeding has limitations not inherent in grain (cost of plot maintenance; limitations not inherent in grain (cost of plot maintenance; narrow harvest window) narrow harvest window)

Outcomes for Breeding from SolCAPOutcomes for Breeding from SolCAP

- Influence breeders to increase genotypic replication

- Make better use of breeding values through incorporation of information on population structure and kinship

- Use objective means to increase variation in breeding populations.

SolCAP Management StructureSolCAP Management Structure

http://solcap.msu.eduhttp://solcap.msu.edu