María Muñoz-Amatriaín, University of California - RiversideFollow
Hamid Mirebrahim, University of California - Riverside
Pei Xu, Zhejiang Academy of Agricultural Sciences
Steve Wanamaker, University of California - Riverside
MingCheng Luo, University of California - DavisFollow
Hind Alhakami, University of California - Riverside
Matthew Alpert, University of California - Riverside
Ibrahim Atokple, Savanna Agricultural Research Institute
Benoit J. Batieno, Institut de l'Environnement et de Recherches Agricoles
Ousmane Boukar, International Institute of Tropical Agriculture
Serdar Bozdag, Marquette UniversityFollow
Ndiaga Cisse, Institut Sénégalais de Recherches Agricoles
Issa Drabo, Institut de l'Environnement et de Recherches Agricoles
Jeffrey D. Ehlers, University of California - Riverside
Andrew Farmer, National Center for Genome Resources
Christian Fatokun, International Institute of Tropical Agriculture
Yong Q. Gu, USDA-ARS Western Regional Research Center
Yi-Ning Guo, University of California - Riverside
Bao-Lam Huynh, University of California - Riverside
Scott A. Jackson, University of GeorgiaFollow
Francis Kusi, Savanna Agricultural Research Institute
Cynthia T. Lawley, Illumina, Inc.
Mitchell R. Lucas, University of California - Riverside
Yaqin Ma, University of California - RiversideFollow
Michael P. Timko, University of Virginia
Jiajie Wu, University of California - Davis
Frank You, University of California - Davis
Noelle A. Barkley, USDA-ARS Plant Genetic Resources Conservation Unit
Philip A. Roberts, University of California - RiversideFollow
Stefano Lonardi, University of California - RiversideFollow
Timothy J. Close, University of California - Riverside

Document Type




Format of Original

13 p.

Publication Date




Source Publication

Plant Journal

Source ISSN


Original Item ID

DOI: 10.1111/tpj.13404; PMID: 27775877


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.


Published version. Plant Journal, Vol. 89, No. 5 (October 2016): 1042-1054. DOI. © 2016 The Authors. Used with permission. Used with permission.

Creative Commons License

Creative Commons Attribution-NonCommercial 4.0 International License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License