Source: UNIVERSITY OF CALIFORNIA, DAVIS submitted to NRP
DEVELOPMENT OF MOLECULAR TOOLS FOR BREEDING IN LEGUME SPECIES
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
1008063
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Oct 1, 2015
Project End Date
Sep 30, 2020
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS,CA 95616-8671
Performing Department
Plant Pathology
Non Technical Summary
Breeding for climate resilience as well as other high value traits in pulse legumes will be greatly accelerated if we can expand the range of adaptations accessible to breeders. We will address this need in chickpea, the world's second most important pulse legume, by harnessing the capacity of chickpea's wild relatives to survive in harsh environments. Chickpea is a global commodity of critical importance to food security in low income, food deficit countries of sub-Saharan Africa (Ethiopia, Malawi, Sudan, Kenya and Tanzania) and South Asia (India, Myanmar, and Pakistan), and also of importance in advanced developing economies (Turkey), and developed countries (USA, Australia and Canada). Effective use of wild germplasm in chickpea improvement will require new and systematic surveys of genotypes from natural environments, identification of adaptive alleles to environmental extremes, and incorporation of the diversity of wild alleles into phenology-normalized backgrounds for trait analysis and breeding. The activities we propose combine relevant cutting-edge science, with a high-caliber interdisciplinary research partnership, and effective leveraging of resources from multiple donor organizations. In doing so we bring a new paradigm to trait selection methods, with a focus on generating breeding stocks with superior abiotic stress tolerance and nutrient density.
Animal Health Component
30%
Research Effort Categories
Basic
70%
Applied
30%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
1021419110020%
2061419104010%
2011419108130%
2021419107010%
2031419108130%
Knowledge Area
206 - Basic Plant Biology; 102 - Soil, Plant, Water, Nutrient Relationships; 203 - Plant Biological Efficiency and Abiotic Stresses Affecting Plants; 202 - Plant Genetic Resources; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1419 - Leguminous vegetables, general/other;

Field Of Science
1040 - Molecular biology; 1070 - Ecology; 1081 - Breeding; 1100 - Bacteriology;
Goals / Objectives
Chickpea is the world's second most important pulse legume, with particular importance in the semi-arid tropics of sub-Saharan Africa and South Asia, but also in the north-western US. Like the majority of cultivated legumes, chickpea has exceedingly narrow genetic and phenotypic diversity. This has consequences for breeding of climate-resilient crop varieties, because much of the historical phenotypic plasticity necessary to tolerate environmental extremes has been lost through domestication. Thus breeding only within cultivated material will have steeply diminishing returns, and there is an urgent need for new sources of diversity.Breeding for climate resilience as well as other high value traits will be greatly accelerated if we can expand the range of adaptations accessible to breeders. Towards this end, we propose to characterize wild Cicer species from a representative range of environments; introduce wild diversity into phenology-normalized backgrounds so that it is amenable for trait assessment and breeding; characterize the material by systematic phenotyping; develop a digital information network that explicitly identifies and quantifies the contributions of agronomically useful alleles.Objective 1. Characterize a comprehensive collection of wild species focused on C. reticulatum, the wild progenitor of cultivated chickpea.Objective 2. Create reverse-introgression and advanced backcross introgression lines to (a) remove phenological barriers that otherwise impede the use of wild germplasm in breeding, (b) establish a resource for association mapping of climate-resilience traits, and (c) initiate breeding with superior wild alleles.Objective 3. Phenotype reverse-introgressed and advanced backcross introgression lines for a range of high-priority traits related to developing high-yielding, climate-resilient chickpea.Objective 4. Develop a predictive network of genotype-phenotype associations that identifies genes and genome regions from wild species that improve chickpea's yield resilience to climatic extremes.
Project Methods
Objective 1. Develop and characterize a comprehensive collection of wild species focused on C. reticulatum, the wild progenitor of cultivated chickpea. Here we will combine ecology, genomics and quantitative biology to digitize genotype-environment interactions in wild progenitor populations. We have collected seed and will sequence the genomes of 250 individuals from 20 wild C. reticulatum populations. For an additional 1,000 lines we will collect DNA and sequence their genomes. In parallel, we will quantify key environmental parameters related to climate, edaphic constraints and co-occurring species, work that is undertaken by a concurrent NSF-supported project. The resulting information will identify genomic adaptations for performance in specific environments. Understanding gained in Obj. 1 will substantially augment observations made in Obj. 3 and analyses performed in Obj. 4, creating a powerful digital platform for gene-to-trait identification and molecular breeding. In Obj. 1 we will also deposit the full set of wild germplasm to public germplasm repositories, which will address the acute inadequacy of the current collection of chickpea wild crop relatives.Objective 2. Create two purpose-driven populations that are synergistic for trait discovery and breeding. (2.1) Create reverse-introgressed lines (reVILs) to (a) remove phenological barriers that otherwise impede the use of wild germplasm in breeding, (b) establish a resource for association mapping of climate-resilience traits, and (c) initiate breeding with superior wild alleles. (2.2) Create advanced backcross introgression lines (ABIs) that forward introgress wild genome segments into farmer-preferred varieties, leading to accelerated use of reVIL phenotypes in breeding and variety development. We will combine a massively-parallel crossing scheme with low-cost/high-density genotyping to "reverse-introgress" cultivated alleles for flowering time and plant architecture into a full suite of wild species' genome diversity. Reverse introgression will be from elite varieties adapted to the major chickpea growing regions of the world, thereby maximizing impact on global chickpea production. The activity will be carried out by a network of international partners who are breeders and germplasm specialists, ensuring both (i) the immediate use of this resource, and (ii) greater awareness of its availability. Among the outcomes of Obj. 2 will be an immortalized RIL collection of quasi-domesticated wild alleles, an extensive and fully sequenced nested association mapping panel, and a full suite of bi-parental mapping populations. Moreover, when combined with the results of Obj. 3 and Obj. 4, reverse introgressed lines and data derived therefrom will provide a solid starting point for formal breeding activities. ABI lines will be developed to complement reVIL populations, providing a library of genome segment introgression events that are at an advanced backcross stage and ready to use for breeding and variety development when trait-marker associations emerge from the reVIL analysis.Objective 3. Phenotype reverse-introgressed and ABI lines for a range of high-priority traits related to developing high-yielding, climate-resilient chickpea. For reVIL lines, we will conduct phenotyping at multiple sites, representing the primary chickpea production areas: Ethiopia, Turkey, India, Canada and Australia. The primary theme will be climate-resilience, especially tolerance to drought and heat and reproductive phase chilling, as these factors constrain chickpea's yield potential, and contribute to both reduced livelihoods of smallholder farmers and childhood malnutrition in Ethiopia and throughout the semi-arid tropics of India and Africa. In parallel, we will analyze the contribution of wild alleles to chickpea's nutrient content, providing an opportunity to "re-domesticate" these important properties. These high priority traits will be analyzed at all partner locations using common phenotyping protocols, which will serve the dual purposes of increasing replication and testing the environmental stability and penetrance of these important traits. The outcome of Obj. 3 will be new and detailed knowledge about the influence of wild alleles on climate resilience and nutrition, providing the basis to precisely identify candidate causal loci in Obj. 4. In parallel to phenotyping of reVIL lines, ABI lines will be directly phenotyped for climate resiliency, especially tolerance to heat and drought and early flowering, providing an opportunity for rapid deployment of major effect genes into breeding and variety development.Objective 4. Develop a predictive network of genotype-phenotype associations that identifies genes and genome regions from wild species that improve chickpea's yield resilience to climatic extremes. The association between genomic and environmental variation in natural populations (Obj. 1) combined with trait-genotype associations established through phenotyping of reverse-introgressed lines (Obj. 3) will enable the identification of agronomically valuable alleles with great precision. A key premise is that favorable alleles for climate resilience will have been under selection in one or more of the sampled natural environments; thus we can correlate specific genomic-by-environment associations established in natural populations of C. reticulatum (Obj. 1) with genotype-trait associations established in the reverse-introgressed populations (Obj 2). The combination of these two independent association experiments will greatly increase statistical power, while the nature of C. reticulatum populations, including their large size, structured sampling, and extensive recombination history, will enable great precision for the identification of candidate adaptive alleles. The resulting information will feed directly into breeding programs by providing candidate genes with corresponding trait values, enhancing the rate and approach by which starter backcross populations established in Obj. 2 can be incorporated into breeding schemes, and guiding new crosses that pyramid valuable alleles into superior varieties. Detailed knowledge of candidate genes may also impact breeding through gene cloning and genetic transformation.

Progress 10/01/15 to 09/30/20

Outputs
Target Audience:• US chickpea farmers and commodity groups. • US seed companies and inoculant industries. • US processed food companies. • US public with interests in sustainable agricultural practices. • International commodity groups and companies. • Target countries of the US Agency for International Development. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?As part of my lab's efforts, I founded and direct the Chickpea Innovation Lab (http://chickpealab.ucdavis.edu), which ultimately generated 19 million in funding. Key among these awards were projects funded by the US National Science Foundation and a related award from the US Agency for International Development's Feed the Future initiative. From 2014-2019 the Lab expanded to involve 21 sponsors, including competitive science funding, industry partners and philanthropic organizations. The research network involved 4 domestic and 28 partner, with institutions in 12 countries. In addition to a broad research portfolio and activities that span both developing and developed world scenarios, the Chickpea Innovation Lab trained a total of 51 students, postdocs and scholars. How have the results been disseminated to communities of interest?Research results have been disseminated through a combination of means. • Numerous peer-reviewed publications, including landmark manuscripts in Nature Communications and PNAS. The specific publications are reported here and in prior progress reports for this 5-year period. • Communicated outcomes in the form of 81 oral or poster presentations at scientific and policy meetings. • Three project web sites. The main website (http://chickpealab.ucdavis.edu), a germplasm and plant metadata web site (https://ics.hutton.ac.uk/cwr/chickpea/), and an NCBI umbrella BioProject (https://www.ncbi.nlm.nih.gov/bioproject/? term=PRJNA353637) with 12 sub-bioprojects. • The Chickpea Lab was featured in Episode 6 of the British Broadcasting Corporation Worldwide documentary on Follow the Food. The ~5 minute segment describes our strategy and outcomes from using wild relative as a source of variation for crop improvement. https://www.bbc.co.uk/future/bespoke/follow-the-food/how-to-fix-our-broken-food-system.html https://www.bbc.com/reel/video/p07fpr6l/the-hidden-hunger-affecting-billions • The Financial Times of London wrote an article for their weekend magazine, focused on activities of the Chickpea Lab. This is the most widely read financial newspaper in the world. https://www.ft.com/content/60d9e4e0-faab-11e9-98fd-4d6c20050229 • The Chickpea Innovation Lab was featured in a U.S. Feed The Future online news article posted September 24, 2019 by Brandon Jetter titled, "The Challenge of Taking Chickpea Innovations from the Lab to the Field" • Chickpea research and the need for diversity is the focus of a crops and commodities opinion article called, Beyond Hummus, by Foodtank. The article features the Chickpea Innovation Lab and Douglas Cook. Article --> •The article by Amanda Mull, "In the Future, Everything Will Be Made of Chickpeas: America is finally embracing an ingredient that much of the world has relied on for millennia", in The Atlantic (March 2019) discusses the health benefits of chickpea as referenced by Douglas Cook, UC Davis Professor and Chickpea Lab Director. Article --> • Keynote presentations at the World Bank (http://chickpealab.ucdavis.edu/index.php/videos/2016-world-bank-presentation/), at the United Nations Food and Agricultural Organization (http://www.fao.org/webcast/home/en/item/4032/icode/), at the US Government's Global Food Security Research Strategy meeting at the National Press Club 2017 (http://chickpealab.ucdavis.edu/index.php/videos/2017-bifad-meeting/), and at the Nestles Annual Meeting (http://chickpealab.ucdavis.edu/index.php/videos/plant-breeding-presentation/). • Full videos of our 2017 Annual Meeting are on-line (http://chickpealab.ucdavis.edu/index.php/videos/2017-chickpea-lab- meeting/) What do you plan to do during the next reporting period to accomplish the goals?My lab will continue to work on chickpea genetics and microbial symbionts and pathogens of chickpea. We are very interested in translating the outcomes of our efforts to farmers and plan to establish a network of field trials in the Pacific Northwest of the US, in Australia, and potentially in California.

Impacts
What was accomplished under these goals? Previous yearly progress reports summarize outcomes from this project. Here, the 5-year summary of progress is briefly reported relative to the initial objectives: Objective 1. Characterize a comprehensive collection of wild species focused on C. reticulatum, the wild progenitor of cultivated chickpea. We assembled one of the largest single-effort collections of crop wild relatives for any crop species. Collection was guided by principles of ecology and population genetics, and the nature of the collection was described through a combination of genome sequencing, computational methods and phenotyping. In parallel, we collected microbes from the crop's center of origin. Phenotyping was conducted for a range of traits, but most detailed in the case of nitrogen fixation efficiency, drought tolerance and seed coat characteristics. Two high profile manuscripts were published in Nature Communications (2018) and PNAS (2019), in addition to numerous lower profile manuscripts. A detailed description of gene transcription differences between wild and cultivated species was published in a leading disciplinary journal, the Plant Journal. Several additional manuscripts describing these collections are in preparation, including a manuscript describing the diversity and function of the crop relatives' microbiome. These plant genetic materials were deposited to the multi-lateral system of crop germplasm, under the Standard Material Transfer Agreement (SMTA) of the International Treaty on Plant Genetic Resources. Objective 2. Create reverse-introgression and advanced backcross introgression lines to (a) remove phenological barriers that otherwise impede the use of wild germplasm in breeding, (b) establish a resource for association mapping of climate-resilience traits, and (c) initiate breeding with superior wild alleles. Genetic crosses were made between four cultivated female recipient parents and >20 wild relative accessions. Crop accessions represent breeding adaptation to different agro-climatic zones. Wild parents represent the genetic and environmental breadth of the wild collections. 9,970 lineages were advanced to F4 and deposited into the multi-lateral system through the Australian Grains Genebank under the SMTA. Metadata related to lineage relationships and simple agronomic phenotypes accompanied the germplasm submission, while the same data is available in a public database developed by colleagues at the University of Edinburgh and for which we provided and curated the associated data. Objective 3. Phenotype reverse-introgressed and advanced backcross introgression lines for a range of high-priority traits related to developing high-yielding, climate-resilient chickpea. At F2, 2,400 individual plants were phenotyped for a range of traits. Data related to agronomic-style traits was collected from single plants, including flower time, days to maturity, seed size, harvest index, pod shattering and plant architecture. In subsequent cycles of recombinant inbred line development, a subset of these same traits were scored. Subsets of these materials have been phenotypes for nitrogen fixation efficiency, tolerance to acid soils, and resistance to fungal pathogens. Objective 4. Develop a predictive network of genotype-phenotype associations that identifies genes and genome regions from wild species that improve chickpea's yield resilience to climatic extremes. An initial round of genotyping using RAD-GBS was conducted at F2. Traits related to domestication and with potential agronomic value have been genetically mapped using a combination of QTL and association mapping methodologies. Loci controlling harvest index, pod shattering, plant biomass, seed coat characteristics, among others, have been genetically determined. Genetic analysis of tolerance to acidic soils and to agronomically important pathogens are ongoing and yielding data suitable for genomic introgression approaches in breeding. To facilitate molecular breeding, we have developed high quality chromosomal-level genome assemblies for the cultivated species (Cicer arietinum) and its two wild relatives (C. recitulatum and C. echniospermum). An iSelect genotyping array is under development and will provide a power bridge between phenotyping and genetic data. Specific successes: • Identified improved nitrogen fixation in plants and microbes. • Identified wild accessions with improved water use efficiency. • Mapped genetic loci control seed coat traits likely causal to flavor. • Mapped genetic loci controlling agronomic traits (shattering, seed size, yield, plant architecture, flowering time). • Mapped a single recessive locus for Fusarium wilt resistance. • Identified Phytophthora as the cause of mis-diagnosed Fusarium wilt in numerous farmers' fields. • Confirmed segregation for Ascochyta blight and Fusarium wilt tolerance in pre-breeding populations. • Advanced 9,700 lines to F4 and deposited to the multi-lateral system of germplasm. • Advanced 2,400 lines to F5. • Deposited data on ~22 thousand accessions to a public chickpea database, developed by partners in Scotland. • Identified significant species-level differences in transcriptional patterns that provide a correlate of genetic diversity. • Identified many hundreds of host genes that respond to nitrogen status, bacterial symbiont genotype and water stress.

Publications

  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Moenga S, Gai Y, Carrasquilla-Garcia N, Perilla-Henao LM and Cook DR (2020) Gene co-expression analysis reveals transcriptome divergence between wild and cultivated chickpea under drought stress. Plant Journal doi:10.1111/TPJ.14988.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Raubach S, Kilian B, Dreher K, Amri A, Bassi FM, Boukar O, Cook D, Cruickshank A, Fatokun C, El Haddad N, Humphries A, Jordan D, Kehel Z, Kumar S, Labarosa SJ, Nguyen LH, Mace E, McCouch S, McNally K, Marshall DF, Mikwa EO, Milne I, Odeny DA, Plazas M, Prohens J, Rieseberg LH, Schafleitner R, Sharma S, Stephen G, Tin HW, Togola A, Warschefsky E, Werner P, Shaw PD. (2020) From bits to bites: Advancement of the Germinate platform to support informatics for crop wild relatives. Crop Science DOI:10.1002/csc2.20248.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Alena Sokolkova, Sergey V. Bulyntsev, Peter L. Chang, Noelia Carrasquila-Garcia, Anna Igolkina, Nina V. Noujdina, Eric von Wettberg, Margarita A. Vishnyakova, Douglas R. Cook, Sergey V. Nuzhdin and Maria G. Samsonova1 (2020) Genomic analysis of Vavilovs historic chickpea landraces reveal footprints of environmental and human selection. Int. J. Mol. Sci. 21:3952 doi:10.3390/ijms21113952
  • Type: Journal Articles Status: Under Review Year Published: 2021 Citation: Bekele D, Tesfaye K, Fikre A and Cook DR. The Extent and Association of Chickpea Fusarium Wilt and Root Rot Disease Pressure with Major Biophysical Factors in Ethiopia. Journal of Plant Pathology Journal of Plant Pathology, in review.


Progress 10/01/18 to 09/30/19

Outputs
Target Audience:US chickpea farmers and commodity groups. US seed companies and inoculant industries. US processed food companies. US public with interests in sustainable agricultural practices. International commodity groups and companies. Target countries of the US Agency for International Development. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project contributed to the training of six UC Davis graduate students, 10 international scholars, 4 UC Davis undergraduate students, several technicians and professional scientists. Training was provided in the form or research mentoring, regular lab meetings, attendance and presentation at major scientific meetings, and authorship on peer-reviewed publications. How have the results been disseminated to communities of interest?Peer-reviewed publications, listed above. Invited presentations: Cook, D.R. Domesticating the Legume-Rhizobium Symbiosis: From Wild Systems to Agricultural Applications. Plant and Animal Genome Conference XXVI, San Diego, CA, January 12-16, 2019. Cook, D.R. Biotechnologies for Chickpea Improvement. International Symposium on Biotechnology for Food-Nutritional Security and Organic Agriculture. Assam Agricultural University, India, March 25-26, 2019. Cook, D.R. Harvesting plants, genes and microbes from the ancestors of modern agriculture. Keynote Speaker. University of California Riverside Microbiome Initiative Symposium, September 23, 2019. Cook, D.R. Plenary Address. Genomic footprints and functional impact of domestication on symbiotic nitrogen fixation. The 21st International Congress on Nitrogen Fixation, Wuhan, China, October 10-15, 2019. Print and video media: • The Chickpea Lab was featured in Episode 6 of the British Broadcasting Corporation Worldwide documentary on Follow the Food. The ~5 minute segment describes our strategy and outcomes from using wild relative as a source of variation for crop improvement. (https://www.bbc.co.uk/future/bespoke/follow-the-food/how-to-fix-our-broken-food-system.html) (https://www.bbc.com/reel/video/p07fpr6l/the-hidden-hunger-affecting-billions) • The Financial Times of London wrote an article for their weekend magazine, focused solely on activities of the Chickpea Lab. This is the most widely read financial newspaper in the world. (https://www.ft.com/content/60d9e4e0-faab-11e9-98fd-4d6c20050229). • The Chickpea Lab was featured in a U.S. Feed The Future online news article posted September 24, 2019 by Brandon Jetter titled, "The Challenge of Taking Chickpea Innovations from the Lab to the Field". (https://foodtank.com/news/2019/06/opinion-beyond-hummus/). • The Chickpea Lab was featured in an article published by Foodtank. "Beyond Hummus", focusing on crops and commodities. (https://foodtank.com/news/2019/06/opinion-beyond-hummus/). • An article by Amanda Mull, "In the Future, Everything Will Be Made of Chickpeas: America is finally embracing an ingredient that much of the world has relied on for millennia", was published in The Atlantic (March 2019) discussing the health benefits of chickpea and refernced Douglas Cook (https://www.theatlantic.com/health/archive/2019/03/chickpea-products-have-exploded-popularity-us/584956/). • In May 2018, Agrilinks published an interview with Douglas Cook, Director of the Feed the Future Innovation Lab for Climate Resilient Chickpea, as the first article in a series for climate, weather and resilient agriculture. The article titled, "Toward a More Resilient Chickpea: Q&A with Innovation Lab Director Doug Cook" (https://www.agrilinks.org/post/toward-more-resilient-chickpea-qa-innovation-lab-director-doug-cook). What do you plan to do during the next reporting period to accomplish the goals?During 2019-2020, my major focus will be completing peer-reviewed manuscripts for which data has been generated in prior years. In parallel, we have started to screen new phenotypes related to root system architecture, the response of root systems to acidic and high aluminum conditions.

Impacts
What was accomplished under these goals? Summary The Chickpea Lab harnesses the genetic diversity of wild chickpea varieties to improve the productivity of chickpea farmers. By combining advanced genomic technologies with analysis of plant traits, researchers identify new and desirable genes harbored by chickpea's closest wild relatives, then introduce these novel genes into the breeding programs at UC Davis and at global partners. The project aims to improve the yield, climate resilience, pest and disease resistance, nutritional value, and nitrogen-fixing properties of chickpea varieties. The Chickpea Lab also conducts research on chickpea's symbiotic microbes, with the goal of understanding fundamental principles and eventually applying new knowledge to enhance agricultural productivity. FY19 Performance 2018-2019 was a year of trait and gene discovery, and of release of massive quantities of genomic, phenotypic and germplasm resources into the public domain. Analysis of traits identifies superior performance in the program's germplasm for disease resistance, drought tolerance, acid soils tolerance, nitrogen fixation. Analysis of cultivated systems clarified the role of an important new plant pathogen, tested the effectiveness of improved microbial inoculants, and increased the capacity of partners through research and training opportunities. The project published several peer-reviewed manuscripts, including a ground breaking study in the Proceedings of the National Academy of Sciences. The program was the subject of the British Broadcasting Corporation's Episode 6 of "Follow the Food", and featured in an article in the Financial Times, in addition to several other popular news items. Successes • Identified improved nitrogen fixation in plants and microbes. • Identified wild accessions with improved water use efficiency. • Mapped genetic loci control seed coat traits likely causal to flavor. • Mapped genetic loci controlling agronomic traits (shattering, seed size, yield, plant architecture, flowering time). • Mapped a single recessive locus for Fusarium wilt resistance. • Identified Phytophthora as the cause of mis-diagnosed Fusarium wilt in numerous farmers' fields. • Confirmed segregation for Ascochyta blight and Fusarium wilt tolerance in pre-breeding populations. • Advanced 9,500 lines to F4 and deposited to the multi-lateral system of germplasm. • Advanced 2,400 lines to F5. • Deposited data on ~22 thousand accessions to a public chickpea database, developed by partners in Scotland. • Identified significant species-level differences in transcriptional patterns that provide a correlate of genetic diversity. • Identified many hundreds of host genes that respond to nitrogen status, bacterial symbiont genotype and water stress.

Publications

  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Ortega R, et al (2019) Altered expression of an FT cluster underlies a major locus onctrolling domestication-related changes to chickpea phenology and growth habit. Frontiers in Plant Science DOI 10.3389/fpls.2019.00824.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Konstantin K, Singh A, Berger J, Cook D, Aydogan A, Kahraman A, Nuzhdin S and Samsonova M (2019) Non-linear regression models for time to flowering in wild chickpea combined genetic and climatic factors. BMC Plant Biology. DOI 10.1186/s12870-019-1685-2.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Greenlon A, Chang PL, Damtew ZM, Muleta A, Carrasquilla-Garcia N and Cook DR (2019) Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria. Proc. Natl. Acad. Sci. 116:15200-15209. doi/10.1073/pnas.1900056116.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Shin MG, Bulyntsev SV, Chang PL, Korbu LB, Carrasquila-Garcia N, Vishnyakova MA, Samsonova MG, Cook DR and Nuzhdin SV (2019) Multi-trait analysis of domestication genes in Cicer arietinum  Cicer reticulatum hybrids with a multidimensional approach: modeling wide crosses for crop improvement. Plant Science 285: 122-131 DOI 10.1016/j.plantsci.2019.04.018.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Sivasakthi, K, et al (2019) Functional dissection of the chickpea (Cicer arietinum L.) stay-green phenotype associated with molecular variation at an ortholog of Mendels I gene for cotyledon color: implications for crop production and carotenoid biofortification. International Journal of Molecular Sciences 20:5562 doi:10.3390/ijms20225562.


Progress 10/01/17 to 09/30/18

Outputs
Target Audience:1. Chickpea breeders. 2. Chickpea farmers. 3. Chickpea consumers. 4. Breeders and scientists working other legume systems. 5. Food Industry. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project, supported financially by NSF and USAID as well as nineteen additional sponsors, has trained fifty-one twenty undergraduate and graduate students, postdoctoral scholars and visiting scientists. A majority of these individuals receive training at UC Davis, either as enrolled graduate students on campus or as visiting scholars. We also contribute to the professional development of faculty and researchers both in the US and internationally, with partners in 32 institutions world wide. How have the results been disseminated to communities of interest?The primary mechanism for of dissemination has been by means of published manuscripts, seminars and invited talks. These include talks to grower groups, academic and research venues, and presentations to policy makers at international institutions. A list of presentations given during the current 12 month review period follows: Cook, D.R. "Feeding the World in a Changing Environment". UC Davis Regional Event on Food Security. The National Press Club, Washington DC, October 4, 2017. Cook, D.R. Using Chickpea's Wild Relative Plants and Microbes to Expand Agricultural Diversity and Address Agricultural Challenges in the Developing World. Plant and Animal Genome Conference XXVI, San Diego, CA, January 13-17, 2018. Cook, D.R. Cicer international consortium: Aims, scope, highlights for chickpea improvement. Wild Cicer project meeting, March 22-23, 2018, Perth, Australia. Cook, D.R. Mining diversity from the wild crop and microbial progenitors of chickpea. Commonwealth Scientific and Industrial Research Organization, March 23, 2018, Perth, Australia. Cook, D.R. Geographic influences on chickpea diversity: harnessing local adaptations among wild accessions for crop improvement. Legume Federation Workshop, National Center for Genome Resources, Santa Fe, NM, March 28, 2018. Cook, D.R. Harvesting plants, genes and microbes from the ancestors of modern agriculture. Thermo Fisher Scientific, Santa Clara, CA, April 16, 2018. Cook, D.R. Tapping wild species of plants and microbes to improve nitrogen fixation in the chickpea crop. International Food Legume Research Conference. Marrakesh, Morocco, May 6-8, 2018. Cook, D.R. Harvesting Crop Wild Relatives to Improve Chickpea Cultivation in Food-Insecure Countries. Cargill Seminar, University of Saskatchewan, September 18, 2018. What do you plan to do during the next reporting period to accomplish the goals?Focus in the coming year is on germplasm curation, database of germplasm data, further characterization of traits for nitrogen fixation, the microbiome, seed characters, drought tolerance and disease resistance.

Impacts
What was accomplished under these goals? Executive Summary Chickpea is a pulse legume of critical importance in low-income food insecure countries, in advanced developing economies, and in developed countries. Paradoxically, countries with the highest nutritional demand for chickpea are also those with the lowest yields, often ½ to ¼ of yields found in the developed world. Whole genome sequencing reveals that ~95% of genomic variation was lost from modern elite cultivars during domestication. This has profound implications, because corresponding reductions to trait variation limit the ability to adapt the crop to changing environments and to meet emerging needs, raising an urgent need for new sources of diversity. We address these needs by harnessing the expanded genetic potential of chickpea's wild relatives, focusing on traits related to tolerance to biotic and abiotic stress, improved seed nutrient density, agronomic characters and symbiotic nitrogen fixation. In previous reports we described the collection, analysis and systematic introgression of novel genetic diversity from wild species into the cultivated gene pool. Here we report continuation of those activities, with increasing emphasis on analysis and testing of identified traits with agronomic utility, including field trials with hybrid crop germplasm and bioinoculants in our target countries of Ethiopia and India. Phenotyping in 2018 confirms prior observations of crop traits that can enhance (i) the sustainability of chickpea production, including resistance to the three most important biological stressors (Ascochyta blight, Fusarium wilt and pod borer), tolerance to abiotic stress (drought and heat), and more effective nitrogen fixation; (ii) agricultural efficiency (flowering time and plant architecture); (iii) nutritional value of chickpea seed to humans (increased protein content of seed); and (iv) microbial traits that enhance plant performance (efficient strains of Mesorhizobium for nitrogen fixation and potential beneficial organisms from the plant rhizosphere). Our germplasm and inoculum resources are in the hands of international partners who are well positioned to deliver novel traits to improved cultivars; realistically, achieving the full potential of the project's vision of expanding crop resilience through wild diversity will not be possible in the absence of sustained US-led efforts. Among the most significant current challenges to the project is the need to curate, archive and make available germplasm resources and related metadata. During the past year, UC Davis has advanced ~12,000 lineages to the F4 generation, with >1,000 accessions remaining to be advanced to F4. An additional ~10K unique lineages are with partners in Turkey, Canada and Australia. The UC Davis material is being phenotyped for simple agronomic traits (seed size, seed per pod, plant architecture, time to harvest, etc) that will allow users to prioritize materials for further use. Working with the Global Crop Diversity Trust, we are implementing a public relational database to provide open access to the multi-generation data, which will be linked to germplasm collections and to field and laboratory data related to the full range of traits under study by the Chickpea Innovation Lab. Though the USAID-funding is insufficient to achieve these full objectives, we recently co-funding (~$400,000 USD) from the Australian Grains Research and Development Corporation that meets ~50% of this need. We completed high quality genomes for the cultivated species and one wild relative, with the second wild relative genome in the final stages. These genome reference sequences are substantially more complete than previous versions, and will greatly facilitate the use of molecular breeding approaches. In parallel we have identified genome regions linked to numerous yield-related traits, which is the first step towards a predictive breeding platform that could greatly accelerate the pace of crop improvement. With the goal of increasing the quality of data collection for crop improvement, we purchased and initiated training of our Ethiopian students on a tablet-based field phenotyping system. The system facilitates and standardizes phenotyping, and ensures stable electronic data storage and retrieval. The system utilizes a web-connected database that we maintain on servers at UC Davis, while project-specific experimental designs are implemented locally. We currently have three such protocols running in Ethiopia and one at UC Davis. We continue to expand our network of collaborators, trainees and funding sources. The National Institute of Agricultural Botany in Cambridge UK and the University of Sydney in Australia have joined the project, providing biochemical analysis of seed nutrient profiles and metabolite biomarker analyses of crop drought response, respectively. Two additional trainees joined the project as trainees at UC Davis in 2018, both of whom are female: Dr. Swarnalakshmi Karivaradharajan from the Indian Institute of Agricultural Research and Ms. Amna Fayyaz from the University of Agriculture Faisalabad in Pakistan. We also received an additional $527K in funding from sponsors in Australia, Germany, India and the US who share the vision of the Chickpea Innovation Lab. In total, the project involves thirty-two partner institutions, fifty-two trainees (26 female, 26 male), and twenty-one financial sponsors. We continue to maintain a clear focus on research-for-development, with all upstream activities predicated on the need to facilitate downstream phenotyping and breeding activities. The Chickpea Innovation Lab's long-term impact will derive from the value of the biological tools and resources that we develop, the genomic and phenotyping data that we archive and make available, and the increased capacity for research and agricultural applications that our students acquire and express.

Publications

  • Type: Journal Articles Status: Under Review Year Published: 2019 Citation: Greenlon A, Chang PL, Damtew ZM, Muleta A, Carrasquilla-Garcia N and Cook DR (201X) Domesticating symbiosis: Genome exchange and biogeography of chickpeas bacterial symbionts. In review.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: von Wettberg EJB, Chang PL, Ba?demir F, Carrasquila-Garcia N, Korbu LB, Moenga SM, Bedada G, Greenlon A, Moriuchi KS, Singh V, Cordeiro MA, Noujdina NV, Dinegde KN, Sani SGAS, Getahun F, Vance LC, Bergmann E, Lindsay D, Mamo BE, Warschefsky EJ, Dacosta-Calheiros E, Marques E, Yilmaz MA, Cakmak A, Rose J, Migneault A, Krieg CP, Saylak S, Temel H, Friesen ML, Siler E, Akhmetov Z, Ozcelik H, Kholova J, Can J, Gaur P, Yildirim M, Sharma H, Vadez V, Tesfaye K, Fikre A Woldemedhin, Tar⿿an B, Aydogan A, Bukun B, Penmetsa RV, Berger J, Kahraman A, Nuzhdin SV, Cook DR (2018). Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation. Nature Communications DOI 10.1038/s41467-018-02867-z.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Yimer, S.M., Ahmed, S., Fininsa, C., Tadesse, N., Hamwieh, A., Cook, D.R. (2018) Distribution and factors influending chickpea wild and root rot epidemics in Ethiopia. Crop Protection 106:150-155.
  • Type: Journal Articles Status: Under Review Year Published: 2019 Citation: Min-Gyoung Shin MG, Bulyntsev SV, Chang PL, Korbu LB, Carrasquila-Garcia N, Vishnyakova MA, Samsonova MG, Cook DR and Nuzhdin SV (201X) Multi-trait analysis of domestication genes in Cicer arietinum ⿿ Cicer reticulatum hybrids with a multidimensional approach: modeling wide crosses for crop improvement. In review.
  • Type: Journal Articles Status: Under Review Year Published: 2019 Citation: Konstantin K, Singh A, Berger J, Cook D, Aydogan A, Kahraman A, Nuzhdin S and Samsonova M (201X) Non-linear regression models for time to flowering in wild chickpea combined genetic and climatic factors. In review.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Green H, Broun P, Cook D, Cooper K, Drewnowski A, Fanzo J, Moloney M, Pollard D, Sweeney G and Roulin A (2018). Healthy and Sustainable Diets. Journal for the Science of Food and Agriculture. DOI 10.1002/jsfa.8953.


Progress 10/01/16 to 09/30/17

Outputs
Target Audience:1. Chickpea breeders. 2. Chickpea farmers. 3. Chickpea consumers. 4. Breeders and scientists working other legume systems. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project, supported financially by NSF and USAID as well as international sponsors, trains more than twenty graduate students and postdocs. A majority of these individuals receive training at UC Davis, either as enrolled graduate students on campus or as visiting scholars. We also contribute to the professional development of faculty and researchers both in the US and internationally, with partners in more than 25 institutions world wide. How have the results been disseminated to communities of interest?The primary mechanism for of dissemination has been by means of seminars and invited talks. These include talks to grower groups, academic and research venues, and presentations to policy makers at international institutions. In addition to typical academic research presentations, during this reporting period, Dr. Cook gave presentations at the World Bank and at the Board for International Food and Agricultural Development (BIFAD) Public Meeting to announce the U.S. Government's Global Food Security Research Strategy A list of presentations is as follows: Cook, D.R. "Taking a walk on the wild side: combining ecology and genomics to deduce the function of legume-microbe interactions in natural and agricultural systems "Texas A&M University, September 21, 2016. Cook, D.R. "Pulses: The Heroes of Nutrition and Agricultural Sustainability". World Bank, Washington DC, October 5, 2016. Cook, D.R. "Molecular breeding in chickpea for resource-poor farmers". International Conference on Sustainable Agriculture in Pakistan, November 17-19, 2016, Faisalabad Agricultural University, Pakistan. Cook, D.R. "Conducting agricultural science in and for the developing world". University of Wisconsin-Madison, December 15, 2016. Cook, D.R. "Ecology and community genomics of an important crop wild relative as a prelude to agricultural innovation". DivSeek Workshop, Plant and Animal Genome Conference XXV, San Diego, CA, January 13-18, 2017. Cook, D.R. "Toward Agricultural Innovation from Wild Systems: Harnessing Biogeographical Patterns in Chickpea's Ancestral Microbial Communities". Plant Pathogen Symposium and Workshop, University of California-Berkeley, January 24-26, 2017. Cook, D.R. "The Chickpea Innovation Lab". Indo-US Bilateral Workshop on Genomic Approaches for Yield Enhancement and Biological Nitrogen Fixation in Chickpea, IARI campus, New Delhi, India, January 30-31, 2017. Cook, D.R. "Taking a walk on the wild side: combining ecology and genomics to deduce the function of legume-microbe interactions in natural and agricultural systems". Amherst College, February 15, 2017. Cook, D.R. "Legumes in agriculture". UC Davis Organic Production Meeting, Woodland, CA, February 22, 2017. Cook, D.R. "Ecology and community genomics of an important crop wild relative and its microbes as a prelude to agricultural innovation". IPK Gatersleben, Leibniz-Institut fur Pflanzengenetik und Kulturpflanzenforschung, Germany, March 8, 2017. Cook, D.R. "Ecology and community genomics of an important crop wild relative and its microbes as a prelude to agricultural innovation". Institute of Plant Sciences Paris Saclay, Orsay, France, March 13, 2017. Cook, D.R. "Biogeography and population genomics of wild microbiomes at the origin of agriculture and their domestication-related shifts" University of Arizona, Tucson, April 18, 2017. Cook, D.R. Keynote Presentation: "Understanding the biogeography of crops and their microbes as a prelude to agricultural innovation". Sainsbury Laboratory Annual Science Retreat, Suffolk, UK, May 2-3, 2017. Cook, D.R. "Ecology and community genomics of an important crop wild relative and its microbes as a prelude to agricultural innovation". Donald Danforth Plant Science Center June 14, 2017. Cook, D.R. "Ecology and community genomics of an important crop wild relative and its microbes as a prelude to agricultural innovation". Planting Seeds for the Future II. Nestle Headquarters, Vevey, Switzerland, July 6-7, 2017. Cook, D.R. "Harnessing an international network to deliver focused upstream research to real world outcomes in farmer fields" U.S. Government's Global Food Security Research Strategy: From Upstream Research to Development Impact. BIFAD Public Meeting, National Press Club, Washington D.C., September 12, 2017. Cook, D.R. Opening Plenary Talk: "Mining agricultural traits from wild systems". International Congress on Legume Genetics and Genomics, Lake Balaton, Hungary, September 18-22, 2017. What do you plan to do during the next reporting period to accomplish the goals?Crop improvement (1) to generate high quality plant phenotype data for key traits (drought, heat, disease and pest tolerance among them), (2) to accelerate the discovery of trait marker associations and deploy the resulting information for marker-assisted introgression of high value wild alleles. Inoculum development (1) identify high performing strains of either (a) complete collections in India, (b) main effects across environments, or (c) environment-specific high performers for tailored inoculum applications, and (2) facilitate discussions in India and Ethiopia about inoculum industry requirements. Nutrition Pilot scale projects have been initiated to examine variation for protein nutrition within our pre-breeding populations, in particular to determine if there is potential to increase nutritional value through breeding with wild relatives. Germplasm Finish curation and storage of F2 populations that form the basis of our pre-breeding efforts. Continue to advance selected materials as recombinant inbred lines. Increase seed availability for replicated testing of high value genotypes.

Impacts
What was accomplished under these goals? Objective 1. Characterize a comprehensive collection of wild species focused on C. reticulatum, the wild progenitor of cultivated chickpea. This objective is essentially complete, with a recently accepted manuscript in Nature Communications describing the outcomes. Objective 2. Create reverse-introgression and advanced backcross introgression lines. Introgression population development. Among ~10,000 project-generated independent lineages, roughly 5,700 lineages were produced at UC Davis and 4,500 were produced at Harran University in Turkey. International partners in Canada and Australia produced several thousand additional lineages. Populations range in development from F3 to F5. To simplify analysis, we have focused genotyping and phenotyping on progeny of a single cultivated parent (an early flowering Indian variety "ICCV96029") crossed with the panel of wild donor genotypes. ~2,500 independent F3 lineages from this population were imported to India and Ethiopia and advanced to F4 in the fall of 2016, with a subset is under advancement to F5 in the fall of 2017. Objective 3. Phenotype reverse-introgressed and advanced backcross introgression lines for a range of high-priority traits related to developing high-yielding, climate-resilient chickpea. Drought phenotyping. We have quantified significant variation in wild donor genotypes for physiological responses to limiting soil moisture (classical drought) and to vapor pressure deficit (atmospheric drought). Wild genotypes are often more tolerant of soil and atmospheric drought than the best tolerant cultivated checks. Interestingly, as we hypothesized in our original proposal, the tolerance of wild accessions to moisture deficit is correlated with moisture availability at field locations where they originated. We are currently exploring drought responses and related whole plant phenotypes in segregating pre-breeding populations using field-based lysimetry and imaging of the plant canopy. Transcriptional profiling reveals differences in drought responses between wild and cultivated accessions, and between tolerant and susceptible genotypes, providing a complement to the ongoing physiological and breeding work. Pod borer phenotyping. A lack of resources prevented further progress on pod borer breeding. However our earlier observations of high levels of pod borer resistance in wild genotypes, combined with the magnitude of pod borer losses globally, make developing genetic resistance against this pest a high priority. Heat tolerance. Field testing at has identified high levels of heat tolerance (seed set at >40°C) in our pre-breeding populations. Trait values in segregating populations, calculated as percentage seed set under typically non-permissive temperatures, often significantly exceeded those of the most tolerant cultivated checks. Selected accessions are being prepared for additional field testing in Ethiopia and India. Ascochyta blight. Two field trials were planted in Ethiopia at field sites in Alementa and Dera. These field locations are characterized by high Ascochyta blight pressure, which was unusually extreme in the late summer of 2017. Representative families from our pre-breeding populations were planted in replicate between the two field sites. We observed a range of disease tolerance phenotypes (tolerant to immune) in a subset of F4 families, with the same families performing well at both locations. These results are consistent with simple genetic control of Ascochyta resistance, which if so should be amenable to breeding. Whole genome sequencing of the pathogen and disease resistance assays under controlled conditions are being initiated. Nitrogen fixation. ~85 additional symbiont strains were isolated in pure culture and their genomes sequenced. New strains from Ethiopia are primarily from low pH soils with the objective of pH resistant inocula, while strains from India represent the beginning of a living strain collection that will enable inoculum trials with endemic diversity. Our corporate partner, Rhizobacter Inc, is developing commercial grade liquid inoculum, providing capacity to uniformly inoculate 100's of thousands of seed. Sachets of inoculum were delivered to UC Davis and to our partners in Ethiopia, where a field trial is currently ongoing. We have developed greenhouse methods to quantify nitrogen fixation effectiveness and we are exploring host factors that determine effective symbiosis, providing a rational basis to evaluate and compare additional strains as a prelude to field-testing. Fusarium genomics and phenotyping. We completed the DNA sequencing of 280 Fusarium oxysporum genomes that we collected in a systematic survey of chickpea growing regions in Ethiopia. We tested and optimized a bioinformatics pipeline for genome assembly and analysis. Genomic and phylogenetic diversity analyses, combined with GIS coordinate of strain origins, allowed us to reject the hypothesis that genomic diversity is related to geographic distribution. Multi-locus phylogenies with ~2,000 conserved genes provide an unprecedented view of species diversity, which we anticipate can guide breeding strategies in the crop. Objective 4. Develop a predictive network of genotype-phenotype associations that identifies genes and genome regions from wild species that improve chickpea's yield resilience to climatic extremes. Whole genome sequencing. We have developed error corrected Pacific Biosciences assemblies for each of our target species (C. arietinum, C. reticulatum and C. echinospermum). These genomes are significantly improved over previously published genomes and should greatly facilitate the use of genomics in crop improvement. They contain 34%-60% more DNA sequence within the non-gapped contig fraction, and an order of magnitude increase in sequence contiguity. Efforts are currently underway to scaffold these assemblies using optical mapping for which the data is complete; high-density linkage mapping is ongoing to anchor, order and orient these molecules. Genome annotation is being conducted by the National Center for Biotechnology Information. All sequencing data can be found in the NCBI Umbrella BioProject PRJNA353637, which includes Illumina data from genotyping-by-sequencing (GBS) data for of over 1,000 wild Cicer accessions (PRJNA416006), landraces (PRJNA396092), whole genome sequencing (WGS) for 280 plant accessions (PRJNA416007), the trace reads for Fusarium genomes (PRJNA412392), and reference genome assemblies for C. arietinum (PRJNA418058), C. reticulatum (PRJNA418059) and C. echinospermum (PRJNA418060). Trait-marker associations. We have made significant progress in the discovery of yield-related traits through genome wide association studies (GWAS) and QTL analysis. DNA was extracted from 5,700 F2 individuals, and ~2,500 progeny were genotyped using genotyping-by-sequencing approaches. An initial round of SNP discovery was conducted using an older genome draft of the Cicer arietinum genome (Nature Biotechnology 2013). With that data we have filtered for fixed differences between wild and cultivated accessions and performed GWAS, discovering major loci for seed shattering, 100 seed weight, biomass conversion efficiency, plant architecture, total biomass and total seed yield. These data should increase in precision and accuracy as we begin to incorporate the improved genome drafts that we have developed.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: R. Varma Penmetsa, Noelia Carrasquilla-Garcia, Emily M Bergmann, Lisa Vance, Brenna Castro, Mulualem T. Kassa, Birinchi K. Sarma, Subhojit Datta, Anuja Dubey, Neha Gujaria, Jong-Min Baek1, Jimmy E Woodward, Andrew D Farmer, Clarice J Coyne, Eric J.B. von Wettberg, Rajeev K Varshney, Douglas R Cook (2016) Multiple post-domestication origins of kabuli chickpea through allelic variation in a diversification-associated transcription factor. New Phytologist 211:1440-1451.
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Bisseling T and Cook D (2017) Live on Air: Rizobium and legumes, the nitrogen fixing nodule symbiosism. In Mighty Microbes: the amazing world of microorganisms, pp 98-100. Microanaon Founation/Stitching Microcanon, The Netherlands.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Plekhanova E, Vishnyakova MA, Bulyntsev S, Chang PL, Carrasquilla-Garcia N, Negash K, von Wettberg E, Noujdina N, Cook DR, Samsonova MG, and Nuzhdin SV (2017) Genomic and phenotypic analysis of Vavilovs historic landraces reveals the impact of environment and genomic islands of agronomic traits. Scientific Reports 7: 4816 | DOI:10.1038/s41598-017-05087-5.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Kahraman, A., Pandey, A., Khan, M.K., Lindsay, D., Moenga, S., Vance, L., Bergmann, E., Carrasquilla-Garcia, N., Shin, M-G., Chang, P.L., von Wettberg, E.J.V., Taran, B., Cook, D.R. and Penmetsa, R.V. (2017) Distinct subgroups of Cicer echiospermum are associated with hybrid sterility and hybrid breakdown in interspecific crosses with cultivated chickpea. Crop Sci doi:10.2135/cropsci2017.06.0335.
  • Type: Journal Articles Status: Accepted Year Published: 2018 Citation: von Wettberg EJB, Chang PL, Ba?demir F, Carrasquila-Garcia N, Korbu LB, Moenga SM, Bedada G, Greenlon A, Moriuchi KS, Singh V, Cordeiro MA, Noujdina NV, Dinegde KN, Sani SGAS, Getahun F, Vance LC, Bergmann E, Lindsay D, Mamo BE, Warschefsky EJ, Dacosta-Calheiros E, Marques E, Yilmaz MA, Cakmak A, Rose J, Migneault A, Krieg CP, Saylak S, Temel H, Friesen ML, Siler E, Akhmetov Z, Ozcelik H, Kholova J, Can J, Gaur P, Yildirim M, Sharma H, Vadez V, Tesfaye K, Fikre A Woldemedhin, Taran B, Aydogan A, Bukun B, Penmetsa RV, Berger J, Kahraman A, Nuzhdin SV, Cook DR (2018). Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation. Nature Communications in press.
  • Type: Journal Articles Status: Accepted Year Published: 2018 Citation: Green H, Broun P, Cook D, Cooper K, Drewnowski A, Fanzo J, Moloney M, Pollard D, Sweeney G and Roulin A (2018). Healthy and Sustainable Diets. Journal for the Science of Food and Agriculture, in press.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Sani, S.G.A.S., Chang, P.L., Zubair, A., Carrasquilla-Garcia, N., Cordeiro, M., Penmetsa, R.V., M. Farooq H. Munis, M.F.H., Nuzhdin, S.V., Cook, D.R., von Wettberg, E.J.B. (2017) Genetic diversity and population structure in chickpea (Cicer arietinum) landraces from Pakistan correlates with climatic variation. Plant Genome doi: 10.3835/plantgenome2017.08.0067.


Progress 10/01/15 to 09/30/16

Outputs
Target Audience:1. Chickpea breeders. 2. Chickpea farmers. 3. Chickpea consumers. 4. Breeders and scientists working other legume systems. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project, supported financially by NSF and USAID as well as international sponsors, trains more than twenty graduate students and postdocs. A majority of these individuals receive training at UC Davis, either as enrolled graduate students on campus or as visiting scholars. We also contribute to the professional development of faculty and researchers both in the US and internationally, with partners in more than 25 institutions world wide. How have the results been disseminated to communities of interest?The primary for of dissemination has been by means of seminars and invited talks. These include talks to grower groups, academic and research venues, and presentations to policy makers at international institutions. In addition to typical academic research presentations, during this reporting period, Dr. Cook gave presentations at the World Bank, at the United National Food and Agricultural Organization, and at the American Society for Nutrition. A list of presentations is as follows: Cook, D.R. "Examining the impact of domestication on symbiotic nitrogen fixation in legume and microbial genomes". International Congress on Nitrogen Fixation. Asilomar, California, October 4 - 9, 2015. Cook, D.R. "In situ analysis and collection of chickpea's wild relatives and their co-occurring microbes". Joint meeting of the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. Minneapolis, MN, November 15-18, 2015. Cook, D.R. "Biogeography and Community Genomics of Legumes and their Microbial Associates". North American Conference on Symbiotic Nitrogen Fixation, Ixtapa, Mexico, December 6-10, 2015. Cook, D.R. "Harvesting climate adaptations from wild crop relatives". International Climate Resilient Crop Genomics Consortium Workshop, Plant and Animal Genome meeting XXIV, January 9-13, 2016. Cook, D.R. "Biogeography and population genomics of plants and their microbes at the origin of agriculture and their domestication-related shifts", Washington State University, Vancouver, WA, February 1, 2016. Cook, D.R. "Biogeography and population genomics of plants and their microbes at the origin of agriculture and their domestication-related shifts", University of Nebraska Lincoln, Feb 10, 2016. Cook, D.R. "Molecular breeding in legumes for resource-poor farmers: Chickpea for Ethiopia and India", International Symposium on Agricultural Biotechnologies, United Nations Food and Agricultural Organization, Rome, Italy, February 15-17, 2016. Cook, D.R. "Legumes under stress", Joint PanAfrican Grain Legume and World Cowpea Conference, Livingstone, Zambia, session on Enhancing yield potential and resilience to abiotic stress through genetic improvement of grain legumes, February 28-March 4, 2016. Cook, D.R. "Harvesting climatic adaptations from the wild progenitors of chickpea and its symbiotic bacteria", Joint Pan African Grain Legume and World Cowpea Conference, Livingstone, Zambia, session on Enhancing yield potential and resilience to abiotic stress through genetic improvement of grain legumes, February 28-March 4, 2016. Cook, D.R. "Genomics of Natural Systems". Argentinian Society of Plant Physiology, meeting on Hot Topics on Stress Tolerance, Phenomics, Genomics and Metagenomics in Plants, Mara del Plata, Argentina, March 7-9, 2016. Cook, D.R. "Genomics of the Plant Microbiome". Argentinian Society of Plant Physiology, meeting on Hot Topics on Stress Tolerance, Phenomics, Genomics and Metagenomics in Plants, Mara del Plata, Argentina, March 7-9, 2016. Cook, D.R. "Prospecting for agricultural traits in crop wild progenitors". Eldorado County Master Gardeners, March 24, 2016. Cook, D.R. "Harvesting natural variation for climate resilience, biotic stress and nutrient density from chickpea's wild progenitors". Satellite Symposium of the American Society of Nutrition and Federation of American Societies of Experimental Biology, Annual Meeting, April 2-6, 2016, San Diego, CA. Cook, D.R. "Harvesting the potential of wild crop relatives for chickpea improvement", University of Sydney, Legume Symposium, July 12, 2016. Cook, D.R. "Feed the Future Chickpea Innovation Lab". Mars Plant Science Symposium, August 8-11, 2016, University of California-Davis. What do you plan to do during the next reporting period to accomplish the goals?We will continue activities on all objectives of the project, with a special emphasis on plant and microbe phenotyping, and moving trait-marker tools towards breeding and crop improvement.

Impacts
What was accomplished under these goals? Objective 1. Characterize a comprehensive collection of wild species focused on C. reticulatum, the wild progenitor of cultivated chickpea. During this reporting period, we continued the collection of Mesorhizobium strains and chickpea nodules from major chickpea growing areas around the world. In particular, we completed sampling from seven regions in India and Pakistan, representing the historical center of chickpea cultivation of the past six millennia, as well as recent expansion of chickpea cultivation into southern India. Including the new 378 genomes from India, our global set of Mesorhizobium genomes is composed of 1,281 strains, sampling the primary locations of chickpea's wild and agricultural history, and using a hierarchical sampling strategy that permits quantitative evaluation of species evolution and biogeography. Mesorhizobium strains from Indian and Ethiopia have been used for seed treatment and assessment in multi-location field trials in Indian and Ethiopia. Outcomes of these field trials will be reported in the subsequent progress report. Overall the objective of these field trials is to develop improved inoculum for nitrogen fixation. We have analyzed wild microbial communities by means of 16S sequencing and collection of a living collection of the predominant plant-associated microbial species. We have sequences ~800 microbial communities from chickpea's wild progenitor species, revealing a main effect of the plant on reshaping soil microbial communities that is much greater than the impact of diverse soil chemistries and environmental variation. We have assembled a living collection of ~700 microbial isolates, analyzed using 16S sequencing to further reduce the set to 192 diverse taxa that we have sequenced to completion using Illumina short read data. We also completed sampling of microbial communities from diverse field sites in India, to determine the differences among microbial communities in diverse, longstanding cultivated situations. Objective 2. Create reverse-introgression and advanced backcross introgression lines to (a) remove phenological barriers that otherwise impede the use of wild germplasm in breeding, (b) establish a resource for association mapping of climate-resilience traits, and (c) initiate breeding with superior wild alleles. Working in conjunction with personnel from a parallel-funded NSA and USAID projects, we initiated development of a nested association mapping panel that incorporates a diverse set of wild donor genotypes crossed into a recurrent set of cultivated recipient lines. The final set of parents includes 24 wild accessions and 4 cultivated recipient genotypes. ~Eight thousand F2 seed were sown in fields at UC Davis from which 5,700 independent F2 plants reached maturity and were collected for seed. These same plants were phenotyped for a range of easily-scored traits (e.g., pod shattering, seed size and plant biomass) and DNA was extracted for RAD genotyping. Collaborators in Canada, Turkey and Australia are developing additional populations, bringing the anticipated scale of the segregating populations to greater than 10 thousand individuals. The power of recombination represented by this collection is enormous. The logistical challenges of managing the seed stocks and associated metadata are also large and unsustainable, causing to think about writing a proposal specific to collection maintenance. Association genetic analysis has been initiated for wild traits related to seed size and seed coat color. ~2,500 lineages from the wild x cultivated populations have been transferred to breeders in India and Ethiopia. Objective 3. Phenotype reverse-introgressed and advanced backcross introgression lines for a range of high-priority traits related to developing high-yielding, climate-resilient chickpea. Phenotyping of wild x cultivated lines and of the parents of these populations has been initiated for insect pest resistance (pod borer), Fusarium wilt resistance, drought tolerance, heat tolerance, nitrogen fixation, seed characteristics, and yield-related traits (total biomass, seed yield, plant volume). DNA has been extracted from ~7,000 lineages. RAD genotyping has been initiated on a subset of 2,500 lines, with the goal of advancing trait-marker association analysis that will facilitate molecular breeding. Objective 4. Develop a predictive network of genotype-phenotype associations that identifies genes and genome regions from wild species that improve chickpea's yield resilience to climatic extremes. Ongoing.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: R. Varma Penmetsa, Noelia Carrasquilla-Garcia, Emily M Bergmann, Lisa Vance, Brenna Castro, Mulualem T. Kassa, Birinchi K. Sarma, Subhojit Datta, Anuja Dubey, Neha Gujaria, Jong-Min Baek1, Jimmy E Woodward, Andrew D Farmer, Clarice J Coyne, Eric J.B. von Wettberg, Rajeev K Varshney, Douglas R Cook (2016) Multiple post-domestication origins of kabuli chickpea through allelic variation in a diversification-associated transcription factor. New Phytologist 211:1440-1451.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2017 Citation: Bisseling T and Cook D (2017) Live on Air: Rhizobium and legumes, the nitrogen fixing nodule symbiosis. Microanaon, in press.