1. Genome resources for climate-resilient cowpea, an essential crop for food security
- Author
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Francis Kusi, Christian Fatokun, Ibrahim Atokple, Steve Wanamaker, Hind Alhakami, Ming-Cheng Luo, Hamid Mirebrahim, Cindy Lawley, Mitchell R. Lucas, Frank M. You, Matthew Alpert, Ousmane Boukar, Jeffrey D. Ehlers, Jiajie Wu, María Muñoz-Amatriaín, Scott A. Jackson, Timothy J. Close, Yi-Ning Guo, Bao-Lam Huynh, Pei Xu, Noelle A. Barkley, Andrew Farmer, Stefano Lonardi, Ndiaga Cisse, Yong Q. Gu, Serdar Bozdag, Benoit Joseph Batieno, Philip A. Roberts, Yaqin Ma, Michael P. Timko, and Issa Drabo
- Subjects
0106 biological sciences ,0301 basic medicine ,Germplasm ,Chromosomes, Artificial, Bacterial ,Climate ,Plant Biology ,BAC sequencing ,Plant Science ,01 natural sciences ,Genome ,Food Supply ,iSelect genotyping array ,Food security ,genetic anchoring ,consensus genetic map ,synteny ,Bacterial ,food and beverages ,WGS sequencing ,Artificial ,Zero Hunger ,Genome, Plant ,Biotechnology ,Crops, Agricultural ,Genotype ,Plant Biology & Botany ,Genomics ,Crops ,Biology ,Chromosomes, Plant ,Chromosomes ,03 medical and health sciences ,Vigna unguiculata L. Walp ,West Africa ,Genetics ,Plant breeding ,Synteny ,Genetic diversity ,Agricultural ,business.industry ,Vigna ,Phaseolus vulgaris L ,Cell Biology ,Plant ,cowpea ,030104 developmental biology ,Agriculture ,Biochemistry and Cell Biology ,business ,010606 plant biology & botany - Abstract
Summary 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 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 4,355 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 biparental 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. This article is protected by copyright. All rights reserved.
- Published
- 2017