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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Publications at this Location » Publication #329432

Research Project: Small Grains Database and Bioinformatics Resources

Location: Crop Improvement and Genetics Research

Title: Genome resources for climate-resilient cowpea, an essential crop for food security

Author
item MUNOZ-AMATRIAIN, M - University Of California
item MIREBRAHIM, H - University Of California
item XU, P - Zhejiang Academy Of Agricultural Sciences
item WANNAMAKER, S - University Of California
item LUO, M - University Of California
item ALHAKAMI, H - University Of California
item ALPERT, M - University Of California
item ATOKPLE, IBRAHIM - Savanna Agricultural Research
item BATIENO, J - Institute Of Environmental And Agricultural Research - Burkina Faso (FORMERLY: UPPER VOLTA)
item BOUKAR, O - International Institute Of Tropical Agriculture (IITA)
item BOZDAG, S - University Of California
item CISSE, N - Institut Senegalais De Recherches Agricoles
item DRABO, I - Institute Of Environmental And Agricultural Research - Burkina Faso (FORMERLY: UPPER VOLTA)
item EHLERS, J - University Of California
item FARMER, A - National Center For Genome Resources
item FATOKUN, C - International Institute Of Tropical Agriculture (IITA)
item Gu, Yong
item GUO, Y - University Of California
item HUYNH, B-L - University Of California
item JACKSON, S - University Of Georgia
item KUSI, F - Savanna Agricultural Research
item LAWLEY, CYNTHIA - Illumina, Inc
item LUCAS, MITCHELL - University Of California
item MA, YAQIN - University Of California
item TIMKO, MICHAEL - University Of Virginia
item WU, JIAJIE - University Of California
item YOU, FRANK - Agriculture And Agri-Food Canada
item Angline, Noelle
item ROBERTS, PHILIP - University Of California
item LONARDI, STEFANO - University Of California
item CLOSE, TIMOTHY - University Of California

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/28/2016
Publication Date: 3/1/2017
Citation: Munoz-Amatriain, M., Mirebrahim, H., Xu, P., Wannamaker, S., Luo, M., Alhakami, H., Alpert, M., Atokple, I.K., Batieno, J., Boukar, O., Bozdag, S., Cisse, N., Drabo, I., Ehlers, J., Farmer, A., Fatokun, C., Gu, Y.Q., Guo, Y., Huynh, B., Jackson, S., Kusi, F., Lawley, C.T., Lucas, M.R., Ma, Y., Timko, M.P., Wu, J., You, F., Barkley, N.L., Roberts, P.A., Lonardi, S., Close, T.J. 2017. Genome resources for climate-resilient cowpea, an essential crop for food security. Plant Journal. 89:1042-1054 doi: 10.1111/tpj.13404.

Interpretive Summary: Cowpea is a native African legume crop that is a primary source of protein in sub-Saharan Africa, where it is grown for fresh and dry grains, foliage, and forage. Cowpea is also an important crop in parts of Asia, South America, and the USA. Because of its adaptability to harsh conditions, cowpea is a successful crop in arid and semiarid regions where few other crops perform well. Cowpea is important to the nutrition and income of smallholder farmers in Africa, while also contributing to sustainability of the cropping system through fixation of atmospheric nitrogen and prevention of soil erosion. Despite its relevance to agriculture in the developing world and its stress resilience, actual yields of cowpea are much lower than the known yield potential, and cowpea genome resources have lagged behind those developed for other major crop plants. Here we generate useful cowpea genomics resources including bacterial artificial chromosome (BAC) libraries and a BAC-based physical map of the chromosomes, sequences of 4,355 BACs, as well as a whole-genome shotgun (WGS) version of the cowpea genome sequence. These resources and WGS sequences from an additional 36 diverse cowpea accessions supported the development of a genetic map containing 37,372 molecular markers and assessment of the genetic diversity within cowpea breeding programs. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited-input small-holder farming and climate stress.

Technical Abstract: Cowpea is a legume crop that is resilient in hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind those of most other major crop plants. Here we describe foundational genome resources and their application to analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include bacterial artificial chromosome (BAC) libraries and a BAC-based physical map, assembled sequences from 4,355 BACs, as well as a whole-genome shotgun (WGS) assembly. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for over 50,000 SNPs, which was then applied to five biparental RIL populations to produce a consensus genetic map containing 37,372 SNPs. This genetic map enabled the anchoring of 100 Mbp of WGS and 420 Mbp of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny relationships between cowpea and common bean. The genomes of West African breeding lines and landraces have regions of marked depletion of diversity, some of which coincide with QTLs that may be the result of artificial selection or environmental adaptation. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited-input small-holder farming and climate stress.