@article {Mu{\~n}oz-Amatria{\'\i}n059261, author = {Mar{\'\i}a Mu{\~n}oz-Amatria{\'\i}n and Hamid Mirebrahim and Pei Xu and Steve I. Wanamaker and MingCheng Luo and Hind Alhakami and Matthew Alpert and Ibrahim Atokple and Benoit Joseph Batieno and Ousmane Boukar and Serdar Bozdag and Ndiaga Cisse and Issa Drabo and Jeffrey D. Ehlers and Andrew Farmer and Christian Fatokun and Yong Q. Gu and Yi-Ning Guo and Bao-Lam Huynh and Scott A. Jackson and Francis Kusi and Cynthia T. Lawley and Mitchell R. Lucas and Yaqin Ma and Michael P. Timko and Jiajie Wu and Frank You and Philip A. Roberts and Stefano Lonardi and Timothy J. Close}, title = {Genome resources for climate-resilient cowpea, an essential crop for food security}, elocation-id = {059261}, year = {2016}, doi = {10.1101/059261}, publisher = {Cold Spring Harbor Laboratory}, 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 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 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 genomes of West African breeding lines and landraces have regions of marked depletion of diversity, some of which coincide with QTL that may be the result of artificial selection or environmental adaptation. The new publicly available 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.}, URL = {https://www.biorxiv.org/content/early/2016/06/15/059261}, eprint = {https://www.biorxiv.org/content/early/2016/06/15/059261.full.pdf}, journal = {bioRxiv} }