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

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