CWR global and US presentation Wag 2011

The ecogeographic distribution of crop wild relatives: implications for

conservation and useInitial Steps

Colin Khoury [email protected] [email protected]

mailto:[email protected]




Feeding the Future

Source: Dery P. and Anderson B. 2007. Peak Phosphorus. Available online at http://www.theoildrum.com/node/2882

http://www.theoildrum.com/node/2882

http://www.theoildrum.com/node/2882

Source: Battisti, D.S., 2009. personal communication

Distributions of average (summer) temperature for 20th century (blue), and climate model projections for 2080-2100 (red) (y=number of

summers, x=departure from long-term 20th century mean)

Predicted changes in total production (per cent) in SSA from climate change in 2046–2065 relative to 1961–2000. The median predicted impact is shown as solid line, while the box shows the 25–75 percentile range. Whiskers extend to the 5 and 95 percentile

Source: Schlenker W and Lobell D. B. 2010. Robust negative impacts of climate change on African agriculture. Environmental Research Letters 5, no. 1: 014010.

Feeding the Future

How can the world produce more food, under more challenging conditions, with less energy, on at most the same amount of land, in a more ecologically sustainable manner?

The Challenge

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Sources of Cereal Production Growth (2000-2050)

EAP: East Asia and the Pacific; MENA: Middle East and North Africa; LAC: Latin America and the Caribbean; SSA: Sub-Saharan Africa

Source: Hubert et al. 2010. The Future of Food: Scenarios for 2050. Crop Sci 50.

CWR of Rice

Source: Brar D.S. (2010). What are the main bottlenecks to the use of CWR in breeding? How can they be overcome? Presentation for ‘Adapting Agriculture to Climate Change: The Need for Crop Wild Relatives’, Bellagio, 7-9 September 2010.

The Evolution of Wheat

Source: Payne T and Braun H (2010) Presentation for ‘Adapting Agriculture to Climate Change: The Need for Crop Wild Relatives’, Bellagio, 7-9 September 2010. Data from Evolution of Wheat, Wheat Genetics Resource Center, KSU.

Source: McCouch S (2010) Is there convincing evidence that we are more likely to find traits for dealing with climate change in crop wild relatives (CWR) than in the cultivated gene pool? Presentation for ‘Adapting Agriculture to Climate Change: The Need for Crop Wild Relatives’, Bellagio, 7-9 September 2010. Data from Tanksley and McCouch (1997) Science 277.

CWR and Genetic Diversity

Musa acuminata- black sigatoka resistance

Manihot glaziovii- cassava mosaic disease

(CMD) resistanceAegilops tauschii- hessian fly resistance

Source: Okogbenin E (2010) The Use and Challenges of CWR in Breeding. Presentation for ‘Adapting Agriculture to Climate Change: The Need for Crop Wild Relatives’, Bellagio, 7-9 September 2010.

Pest and Disease Resistance from CWR

Source: Brar D.S. (2010). What are the main bottlenecks to the use of CWR in breeding? How can they be overcome? Presentation for ‘Adapting Agriculture to Climate Change: The Need for Crop Wild Relatives’, Bellagio, 7-9 September 2010.

Disease Resistance from CWR of Rice

tungro virus tolerant

Source: Okogbenin E (2010) The Use and Challenges of CWR in Breeding. Presentation for ‘Adapting Agriculture to Climate Change: The Need for Crop Wild Relatives’, Bellagio, 7-9 September 2010. Data from Tanksley and McCouch (1997) Science 277.

Don’t Judge a Book by its Cover!

(a) Lycopersicon hirsutum, a wild species that does not turn red upon ripening.

(b) Left- fruit of a modern processing tomato cultivar. Right- fruit from a breeding line in

which a QTL for increased pigment has been transferred from L. hirsutum

(c) Top left- wild tomato L. pimpinellifolium. Top right- fruit of a modern processing

tomato cultivar. Bottom- fruit of a backcrossed breeding line of the modern

processing tomato, with QTL for increased fruit size from L. pimpinellifolium

Source: Valls J F M (2010) What specific changes in the current way genebanks and breeders to business and interact will be necessary to increase use of Crop Wild Relatives? Presentation for ‘Adapting Agriculture to Climate Change: The Need for Crop Wild Relatives’, Bellagio, 7-9 September 2010. Photo adapted from Tollefson J (2010) Nature 466: 554-556.

2055

Source: Jarvis, A., Ferguson, M., Williams, D., Guarino, L., Jones, P., Stalker, H., Valls, J., Pittman, R., Simpson, C. & Bramel, P. 2003. Biogeography of Wild Arachis: Assessing Conservation Status and Setting Future Priorities. Crop Science 43, 1100-1108.

Threats to CWR In Situ

Impacts of Climate Change on Crop Wild Relatives

Arachis species Change in area of distribution (%)

Predicted state in 2055

batizocoi -100 Extinctcardenasii -100 Extinctcorrentina -100 Extinctdecora -100 Extinctdiogoi -100 Extinctduranensis -91 Threatenedglandulifera -17 Stablehelodes -100 Extincthoehnii -100 Extinctkempff-mercadoi -69 Near-Threatenedkuhlmannii -100 Extinctmagna -100 Extinctmicrosperma -100 Extinctpalustris -100 Extinctpraecox -100 Extinctstenosperma -86 Threatenedvillosa -51 Near-Threatened

Arachis (peanut, groundnut)- wild species distributions

Source: Jarvis, A., Ferguson, M., Williams, D., Guarino, L., Jones, P., Stalker, H., Valls, J., Pittman, R., Simpson, C. & Bramel, P. 2003. Biogeography of Wild Arachis: Assessing Conservation Status and Setting Future Priorities. Crop Science 43, 1100-1108.

Impacts of Climate Change on Crop Wild Relatives

Jarvis et al. (2008) By 2055, 16-‐22% of Arachis, Solanum and Vigna CWR will be exCnct

Thuiller (2005)-‐ By 2080, 50% of 1350 studied plant species would be vulnerable or threatened by climate change

Liva et al (2009). By 2060, 40 of 69 protected areas would no longer have the right climate to support currently exisCng populaCons of all 8 Mexican

cucurbit CWR

represented (>10 accessions)28%

under or unrepresented72%

Gaps in the Ex Situ Conservation of CWR

Of est. 260,000 total accessions,4,453 wild accessions

Accessions Species

Of 85 taxa in Phaseolus, 35 not represented in genebanks and26 have <10 accessions

Source: Ramírez-Villegas J, Khoury C, Jarvis A, Debouck DG, and Guarino L (2010). A Gap Analysis Methodology for Collecting Crop Genepools: a Case Study with Phaseolus Bean. PLoS ONE 5(10): e13497. doi:10.1371/journal.pone.0013497; FAO WIEWS 2009

cultivated98%

wild2%

Biodiversity Conservation

Agricultural Development

Climate Change Adaptation

Food Security

Adapting Agriculture to Climate ChangeCollecting, Protecting and Preparing Crop Wild Relatives

Project Timeline

Crop TaxaAlfalfa (Medicago) 13Apple 12Bambara Groundnut 27Banana 31Barley 2Bean (Phaseolus) 37Carrot 27Chickpea 4Cowpea 12Eggplant 32Faba Bean 1Finger Millet 4Grasspea 12Lentil 4Oat 12Pea 9Pearl Millet 4Pigeon Pea 8Potato 83Rice 19Rye 4Sorghum 5Sunflower 11Sweet Potato 14Vetch 9Wheat 55 Total 451

AlfalfaApple

Bambara Groundnut

Banana

Barley

Bean

Chickpea

Cowpea

Eggplant

Faba Bean

Finger Millet

Grasspea

Lentil

Oat

Pea

Pearl Millet

Pigeon Pea

Potato

Rice

Rye Sorghum

Sunflower

Sweet Potato

Vetch

Wheat

Priority Genepools and Taxa

Analyze State of Ex Situ

Conservation

Produce taxon database

Perform gap analysis

Produce collecting guides

Prioritize collecting sites

Collect

Coordinate with national partners and experts

CWR Research Methodology

Pilot Pre-breeding and Evaluation

Source: Ramírez-Villegas J, Khoury C, Jarvis A, Debouck DG, and Guarino L (2010). A Gap Analysis Methodology for Collecting Crop Genepools: a Case Study with Phaseolus Bean. PLoS ONE 5(10): e13497. doi:10.1371/journal.pone.0013497

Research: Gap Analysis

Collecting Guides

Source: Smith P. (2010). Prioritizing crop wild relatives for collection, long term storage and use. Presentation for ‘Adapting Agriculture to Climate Change: The Need for Crop Wild Relatives’, Bellagio, 7-9 September 2010.

Research: State of Ex Situ Conservation of CWR in Genebanks


Collecting


Trust and Kew MSB Partnerships

Photos: ICRISAT 2009; IRRI 2009; Mari Tefre; Global Crop Diversity Trust

Conservation

Groundnut Breeding with CWR

Source: Valls J F M (2010) What specific changes in the current way genebanks and breeders to business and interact will be necessary to increase use of Crop Wild Relatives? Presentation for ‘Adapting Agriculture to Climate Change: The Need for Crop Wild Relatives’, Bellagio, 7-9 September 2010. Photo adapted from Tollefson J (2010) Nature 466: 554-556.

Determine appropriate genomics toolsDetermine genetic diversity (Genotyping)

Use other data as well

Figure out what diversity is presentChoose maximum diversity set for

breedingIn select cases, pick accessions with

known genes of interest

Pick the most diversity

Cross, cross, crossBreed CWR set with appropriate

modern varietiesBackcross to head toward modern

varieties

Evaluate crosses for traits of interest (Phenotyping), specifically for climate change (i.e. heat tolerance, drought

tolerance, salt tolerance, etc.)

Figure out if its good

Make it availableRelease to breeding programs

integrate in information systems

CWR Pre-Breeding and Evaluation

"It's a bit like crossing a house cat with a wildcat...You don't automatically get a big docile pussycat. What you get is a lot of

wildness that you probably don't want Iying on your sofa."

Source: Rhoades, Robert E. “The World’s Food Supply at Risk,” National Geographic (April 1991), 74-105.

Source: http://www.genesys-pgr.org/.

Information Systems

http://www.genesys-pgr.org

http://www.genesys-pgr.org

Priority Crops and GenepoolsAgropyron Colocasia Ipomoea Pistacia

Allium Corylus Isatis Pisum (incl. Vavilovia)

Ananas Crambe Juglans Prunus

Arachis Cucumis Lablab Pyrus

Armoracia Cucurbita Lactuca Raphanus (incl. Raphanobrassica)

Artocarpus Cynara Lathyrus Ribes

Asparagus Daucus Lens Rorippa

Avena Digitaria Lepidium Saccarhum

Barbarea Dioscorea Lupinus Secale

Bertholletia Diplotaxis Malus Sesamum

Beta Echinochloa Mangifera Setaria

Brassica Elaeis Manihot Sinapis

Cajanus Elettaria Medicago Solanum (incl. Lycopersicon)

Camellia Eleusine Musa (incl. Ensete) Sorghum

Capsicum Elymus Olea Spinacia

Carica Eruca Oryza Theobroma

Carthamnus Ficus Panicum Triticum (incl. Triticosecale, Aegilops, others)

Chenopodium Fragaria (incl. as Potentilla) Pennisetum Vicia

Cicer Glycine Persea Vigna

Citrullus Gossypium Phaseolus Vitellaria

Citrus (incl. Fortunella and Poncirus) Helianthus Phoenix Vitis

Cocos Hordeum Pimenta Xanthosoma

Coffea Ilex Piper Zea (incl. Tripsacum)

https://nacms.co.uk/croptrust/



Research: Gap Analysis

Determine gaps in collections

Model distributions

Gather taxonomic data

Gather occurrence data

Make collecting recommendations

Georeferencing

Source: concept and images from Jarvis et al. 2009. Value of a Coordinate: geographic analysis of agricultural biodiversity. Presentation for Biodiversity Information Standards (TDWG), November 2009.

Occurrence data sources

GBIF- 44.7 million plant occurrences

Data quality- 840,449 (88.5%) out of 950,000 records good quality


But there are gaps

Source: Castaneda N (2011)


• Online data- eg GBIF, Genesys

• Directly from researchers- eg Phaseolus, Solanum, Oryza

• Herbarium and genebank databases

• Published literature

• Herbarium visits- more than 15,000 photos taken at NY, PH, US, MO, CAS, UC, WAG. Still gathering data from Kew, BM, E, P, Leiden, Portugal, Spain, others

Taxon occurrence database will eventually contain ca. 3 million geo-referenced records

Data gaps- China, India, South-east Asia, Central Asia

Geo-referencing

Gap analysis

Source: Ramírez-Villegas J, Khoury C, Jarvis A, Debouck DG, and Guarino L (2010). A Gap Analysis Methodology for Collecting Crop Genepools: a Case Study with Phaseolus Bean. PLoS ONE 5(10): e13497. doi:10.1371/journal.pone.0013497;

Gap analysis- different gaps


Gap analysis- gross representation


Gap analysis- modeling distributions


Gap analysis- geographic gaps


Gap analysis- climatic gaps

Species Sampling (%) Coverage (%) Distribution (%) Outlier (%) Rarity Score

albiviolaceus 0.0 N/A N/A N/A N/A 0.00 amabilis 0.0 N/A N/A N/A N/A 0.00 chacoensis 0.0 N/A N/A N/A N/A 0.00 diversifolius 0.0 N/A N/A N/A N/A 0.00 elongatus 0.0 N/A N/A N/A N/A 0.00 fraternus 0.0 N/A N/A N/A N/A 0.00 laxiflorus 0.0 N/A N/A N/A N/A 0.00 micranthus 10.0 N/A N/A N/A N/A 0.00 mollis 0.0 N/A N/A N/A N/A 0.00 nitensis 0.0 N/A N/A N/A N/A 0.00 opacus 0.0 N/A N/A N/A N/A 0.00 pachycarpus 0.0 N/A N/A N/A N/A 0.00 texensis 10.0 N/A N/A N/A N/A 0.00 trifidus 0.0 N/A N/A N/A N/A 0.00 xolocotzii 0.0 N/A N/A N/A N/A 0.00 anisophyllus 0.0 N/A N/A N/A N/A 0.00 oaxa canus 0.0 N/A N/A N/A N/A 0.00 pauper 0.0 N/A N/A N/A N/A 0.00 plagiocylix 0.0 N/A N/A N/A N/A 0.00 rosei 0.0 N/A N/A N/A N/A 0.00 sonorensis 0.0 N/A N/A N/A N/A 0.00 falciformis 0.0 N/A N/A N/A N/A 0.00 marechalii 6.7 N/A N/A N/A N/A 0.00 rotundatu s 6.7 N/A N/A N/A N/A 0.00 salicifolius 3.3 N/A N/A N/A N/A 0.00 altimontanus 7.5 N/A N/A N/A N/A 0.00 esquincensis 0.0 N/A N/A N/A N/A 0.00 novoleonensis 5.0 N/A N/A N/A N/A 0.00 tenellus 0.0 N/A N/A N/A N/A 0.00 albiflorus 10.0 N/A N/A N/A N/A 0.00 macrolepis 8.0 N/A N/A N/A N/A 0.00 reticulatus 2.0 N/A N/A N/A N/A 0.00 jaliscanus 1.7 N/A N/A N/A N/A 0.00 macvaughii 3.3 N/A N/A N/A N/A 0.00 magnilobatus 3.3 N/A N/A N/A N/A 0.00 venosus 0.0 N/A N/A N/A N/A 0.00 carteri 7.1 N/A N/A N/A N/A 0.00 formosus 0.0 N/A N/A N/A N/A 0.00 polymorphus 2.9 N/A N/A N/A N/A 0.00 esperanzae 8.8 N/A N/A N/A N/A 0.00 perplexus 1.3 N/A N/A N/A N/A 0.00 polystachios 0.1 0.1 0.0 0.0 8.3 0.45 amblyosepalus 0.0 0.0 0.0 N/A 10.0 1.00 nelsonii 0.0 0.0 0.0 N/A 10. 0 1.00 pluriflorus 1.4 1.3 2.5 N/A 10.0 2.56 pedicellatus 0.9 2.7 3.3 0.0 9.5 2.56 angustissimus 0.5 1.2 6.7 0.6 6.1 2.83 grayanus 5.2 2.0 4.0 0.0 7.5 3.72 parvulus 1.3 5.0 5.0 0.0 8.6 3.82 tuerckheimii 1.5 10.0 0.0 0.0 8.2 3.86 pauciflorus 0.2 4.0 6.7 N/A 10.0 4.27 lunatus 3.9 3.3 5.6 3.9 8.9 4.47

parvifolius 4.5 2.2 5.0 N/A 10.0 4.50 filiformis 1.6 5.6 6.7 0.0 9.9 4.66 maculatus 2.2 4.4 8.0 1.0 9.1 4.89 talamancensis 1.1 10.0 4.0 2.0 7.1 4.97 leptostachyus 2.9 6.5 6.7 0.0 9.9 5.32 glabellus 5.3 6.0 4.0 N/A 10.0 5.60 pachyrrhizoides 8.8 6.5 2.9 0.0 6.7 5.77 costaricensis 2.3 10.0 6.0 1.1 8.0 5.96 coccineus 4.8 8.1 5.7 0.0 9.7 6.06 oligospermus 3.4 10.0 5.0 10.0 9.5 6.51 hintonii 7.7 4.3 7.5 N/A 10.0 6.86 microcarpus 5.9 8.6 6.7 0.0 9.8 6.86 acutifolius 6.4 8.3 8.0 0.0 9.9 7.30 augusti 7.4 10.0 4.3 10.0 9.5 7.49 neglectus 5.3 10.0 6.7 N/A 10.0 7.60 vulgaris 8.7 9.9 5.4 3.8 7.4 7.76 dumosus 5.3 10.0 8.6 6.0 8.8 7.89 xanthotrichus 8.4 10.0 5.7 10.0 9.0 8.19 chiapasanus 9.0 9.5 7.5 N/A 10.0 8.80 zimapanensis 8.8 10.0 10.0 N/A 10.0 9.63


Gap analysis- results


Gap analysis- results


Gap analysis- validating results

man versus the machine

Source: Jarvis A. 2009.

Gap analysis- results for African Vigna

complementarity analysis

Gap analysis- results for wild tomatoes

Source: Castaneda N (2011)

Source: Jarvis A., Ramirez J. 2009. personal communication

Gap analysis- results for 12 genepools

Source: Jarvis et al. 2009. Value of a Coordinate: geographic analysis of agricultural biodiversity. Presentation for Biodiversity Information Standards (TDWG), November 2009.

http://gisweb.ciat.cgiar.org/GapAnalysis/

Gap Analysis Website

the future- automated, iterative results

Predicted change in taxon richness in 2050

Low evidence of potential traits for adapting wheat crops to climate change

CWR of millet have unique climatic adaptations potentially relevant for crop improvement

Will we find what we are looking for?

Low but statistically significant correlation between pairwise difference in climate and morphological, agronomical and molecular traits

Climate at collection point could also be a rapid means of screening for diversity in a collection

Will we find what we are looking for?

Toward a US National Strategy for the Conservation of Crop Wild Relatives

Strategy Flowchart

National Inventory

• Inventory includes a wide range of utilized and potentially useful taxa, including both native and naturalized taxa occurring in the US

o Taxa directly used for food, fiber, forage, medicine, ornamental, and restoration purposes

o CWR taxa

• Inventory currently lists over 3,000 taxa

Taxonomic Priorities- what taxa are likely to be most useful?

• A rational, effective strategy requires prioritization of taxa based upon their potential use value in contributing to breeding and therefore to crop production.

• This focuses the priorities on those genepools of major crops with active breeding programs

• Primary focus on food crops, but also forage, medicinal, ornamental, etc.

• Gather data on major crops globally (FAOSTAT, published literature, ITPGRFA)

• Prioritize the list (Priority 1, Priority 2)

• Identify genera in genepools of priority crops

• Results: 242 World’s Top Crops (268 genera)

o 101 crops (119 genera) in Priority 1

o 141 crops (149 genera) in Priority 2

• This list includes all the most important agricultural crops around the world by a number of measures, and covers all crops listed in FAOSTAT for US production and food supply, with virtually all

• Apply World’s Top Crops list to the national inventory and to GRIN taxonomy to derive a priority list of CWR occurring in the US

• Review inventory and add a few additional genepools to priorities- brome (Bromus), Cuphea, groundcherry (Physalis), St. John’s Wort (Hypericum), liquorice (Glycyrrhiza), pitanga (Eugenia), and Echinacea to Priority 2 CWR

• sugar maple (Acer saccharum), wild rice (Zizania spp.), medicinal species of Echinacea, pine nut species of Pinus, pecan (Carya illinoinensis, jojoba (Simmondsia chinensis) and the alcohol/sugar taxa of Agave- utilized taxa were added to Priority 1, as iconic wild species crops occurring in the US

Priorities for the US

• 2,014 taxa of 159 priority genera occur in the US

o 905 taxa of 74 Priority 1 genera

o 1,108 taxa of 85 Priority 2 genera.

• Important crops with rich native genepools include Allium (onion), Cucurbita (squash), Fragaria (strawberry), Helianthus (sunflower), Ipomoea (sweet potato), Lactuca (lettuce), Phaseolus (bean), Prunus (cherry, almond, peach), Ribes (currant), Rubus (raspberry), Saccharum (sugar cane), Vaccinium (blueberry, cranberry), and Vitis (grape), among others.


• National Strategy will focus on Priority 1 genepools. This focus includes the richest genepools of native diversity occurring in the US that have the potential to contribute to crop improvement, and also attempts to cover the major wild species directly utilized for food or medicine.

• Closely related taxa (generally GP1/2), plus any additional taxa known to be of use to crop breeding, will be subjected to a full gap analysis for identification of collecting priorities, and for in situ conservation considerations.

• Given these parameters, the major effort will focus on ca. 250-300 taxa.

• Distantly related taxa (GP3)- a superficial gap analysis will identify taxa not conserved ex situ by at least a few populations, and prioritize these for additional collecting. Generally no in situ analysis for Genepool 3 taxa.

• Non-native populations of taxa will generally not be considered within the analysis, aside from particular populations of interest to the breeding community. Any taxa identified as rare or threatened will be given particular attention in conservation recommendations.


• Expert revision of priority genepools- inputs requested for forming a final list of the priority crop genepools to be researched, deadline end November.

• http://cwroftheus.wordpress.com/

Next Steps

http://cwroftheus.wordpress.com/

http://cwroftheus.wordpress.com/

Research DirectionsPrioritizing CWR populations for conservation and use, based on potential use valueAre CWR potentially useful for adaptation to climate change? Who, Where, how and why?

Ecogeographic characterization of taxa through GIS- how can GIS complement morphological and molecular data in discerning closely related CWR?

How robust are genetic reserves in protected areas (in situ conservation) under projected climate change?

What are the global patterns of distribution of richness of CWR? Why are they distributed as they are? How well is that richness conserved ex situ? What are the constraints to filling the gaps?

How well conserved are crop genepools with an emphasis on use value?

What can the global patterns of CWR diversity tell us about why certain related plants were domesticated, and not others? What does these patterns tell us about the domestication process and history of domestication?

What are the differences between different crop genepools in population biology that should be taken into consideration with the question of adequate conservation of the genetic diversity within the genepool?

How does the distribution of the CWR of the world’s major crops create interdependence in agriculture and breeding?

Centers of Origin of Selected Crops

Source: adapted from Flores Palacios F. 1998. Contribution to the Estimation of Countries’ Interdependence in the Area of Plant Genetic Resources. Rep. 7, Rev. 1, UN Food. Agric. Org. Comm. Genet. Resour. Food Agric., Rome, Italy. taken from Fowler C. and Hodgkin T. 2004. Plant Genetic Resources for

Food and Agriculture: Assessing Global Availability. Annu Rev Environ Resour 29: 10.1-10.37.

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Interdependence of Genetic Resources in Crops= % food energy supply from crops not

indigenous to country = % food energy supply from crops

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CWR global and US presentation Wag 2011

Technology

Transcript of CWR global and US presentation Wag 2011