title: Genome resources for climate-resilient cowpea, an essential crop for food security.
abstract: Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to 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 most other major crops. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include a whole-genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4355 BACs. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51 128 SNPs, which was then applied to five bi-parental RIL populations to produce a consensus genetic map containing 37 372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. 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.
authors: Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.
authors: María
authors: M
authors: Muñoz-Amatriaín
authors: Department of Computer Science and Engineering, University of California, Riverside, CA, USA.
authors: Hamid
authors: H
authors: Mirebrahim
authors: Institute of Vegetables, Zhejiang Academy of Agricultural Sciences (ZAAS), Hangzhou, 310021, China.
authors: Pei
authors: P
authors: Xu
authors: Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.
authors: Steve I
authors: SI
authors: Wanamaker
authors: Department of Plant Sciences, University of California, Davis, CA, USA.
authors: MingCheng
authors: M
authors: Luo
authors: Department of Computer Science and Engineering, University of California, Riverside, CA, USA.
authors: Hind
authors: H
authors: Alhakami
authors: Department of Computer Science and Engineering, University of California, Riverside, CA, USA.
authors: Matthew
authors: M
authors: Alpert
authors: Council for Scientific and Industrial Research, Savanna Agricultural Research Institute, Tamale, Ghana.
authors: Ibrahim
authors: I
authors: Atokple
authors: Institut de l'Environnement et de Recherches Agricoles, Saria, Burkina Faso.
authors: Benoit J
authors: BJ
authors: Batieno
authors: International Institute of Tropical Agriculture, Kano, Nigeria.
authors: Ousmane
authors: O
authors: Boukar
authors: Department of Computer Science and Engineering, University of California, Riverside, CA, USA.|Department of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, USA.
authors: Serdar
authors: S
authors: Bozdag
authors: Institut Sénégalais de Recherches Agricoles, Thiès, Senegal.
authors: Ndiaga
authors: N
authors: Cisse
authors: Institut de l'Environnement et de Recherches Agricoles, Saria, Burkina Faso.
authors: Issa
authors: I
authors: Drabo
authors: Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.|The Bill & Melinda Gates Foundation, Seattle, WA, USA.
authors: Jeffrey D
authors: JD
authors: Ehlers
authors: National Center for Genome Resources, Santa Fe, NM, USA.
authors: Andrew
authors: A
authors: Farmer
authors: International Institute of Tropical Agriculture, Ibadan, Nigeria.
authors: Christian
authors: C
authors: Fatokun
authors: USDA-ARS Western Regional Research Center, Albany, CA, USA.
authors: Yong Q
authors: YQ
authors: Gu
authors: Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.
authors: Yi-Ning
authors: YN
authors: Guo
authors: Department of Nematology, University of California, Riverside, CA, USA.
authors: Bao-Lam
authors: BL
authors: Huynh
authors: Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.
authors: Scott A
authors: SA
authors: Jackson
authors: Council for Scientific and Industrial Research, Savanna Agricultural Research Institute, Tamale, Ghana.
authors: Francis
authors: F
authors: Kusi
authors: Illumina, Inc., San Francisco, CA, USA.
authors: Cynthia T
authors: CT
authors: Lawley
authors: Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.
authors: Mitchell R
authors: MR
authors: Lucas
authors: Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.|Department of Plant Sciences, University of California, Davis, CA, USA.
authors: Yaqin
authors: Y
authors: Ma
authors: Department of Biology, University of Virginia, Charlottesville, VA, USA.
authors: Michael P
authors: MP
authors: Timko
authors: Department of Plant Sciences, University of California, Davis, CA, USA.
authors: Jiajie
authors: J
authors: Wu
authors: Department of Plant Sciences, University of California, Davis, CA, USA.|Agriculture and Agri-Food Canada, Morden, MB, Canada.
authors: Frank
authors: F
authors: You
authors: USDA-ARS Plant Genetic Resources Conservation Unit, Griffin, GA, USA.
authors: Noelle A
authors: NA
authors: Barkley
authors: Department of Nematology, University of California, Riverside, CA, USA.
authors: Philip A
authors: PA
authors: Roberts
authors: Department of Computer Science and Engineering, University of California, Riverside, CA, USA.
authors: Stefano
authors: S
authors: Lonardi
authors: Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.
authors: Timothy J
authors: TJ
authors: Close
mesh_terms: D022202:Chromosomes, Artificial, Bacterial; D032461:Chromosomes, Plant / Q000235:genetics; D002980:Climate; D018556:Crops, Agricultural / Q000235:genetics* / Q000502:physiology*; D005523:Food Supply; D018745:Genome, Plant / Q000235:genetics; D005838:Genotype; D000070658:Vigna / Q000235:genetics* / Q000502:physiology*
keywords: BAC sequencing; Phaseolus vulgaris L.; Vigna unguiculata L. Walp.; WGS sequencing; West Africa; consensus genetic map; cowpea; genetic anchoring; iSelect genotyping array; synteny