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

Abstract

These authors contributed equally. SUMMARYCowpea (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.

Quantitative trait loci analysis of brown blotch resistance in cowpea variety KN1

“…The genetic map size of 763.4 cM was consistent with previous maps of cowpea, although slightly smaller than those reported recently (Muñoz-Amatriaín et al 2016). Overall genome coverage was generally consistent despite the relatively few markers used for mapping.…”

“…2). Additional SNPs previously identified in this genomic interval (Muñoz-Amatriaín et al 2016) could also be converted to PCR markers if further markers were needed for fine mapping or introgression into other susceptible genetic backgrounds. Although the genetic distance between flanking markers was approximately 7 cM, a 1-LOD confidence interval delineated qBBDR1 to a 3-cM interval from 29 to 32 cM on Vu02.…”

“…An increasing pool of genomic data (Timko et al 2008; Muñoz-Amatriaín et al 2016; Vigna unguiculata v1.0, NSF, UCR, USAID, DOE-JGI, http://phytozome.jgi.doe.gov/) has facilitated the identification of genetic markers and quantitative trait loci (QTL) associated with resistance to several important cowpea pests and diseases. These pests and diseases include Striga gesnerioides (Ouédraogo et al 2001, 2002b; Li and Timko 2009; Ouedraogo et al 2012), aphids (Huynh et al 2015; Kusi et al 2018), thrips (Omo-Ikerodah et al 2008; Muchero et al 2010), root-knot nematodes (Ouédraogo et al 2002a; Huynh et al 2016), Fusarium wilt (Ouédraogo et al 2002a; Pottorff et al 2012), Macrophomina phaseolina (Muchero et al 2011), Cercospora leaf spot (Duangsong et al 2016), bacterial blight (Shi et al 2016), and various mosaic viruses (Ouédraogo et al 2002a).…”

Genomic regions, cellular components and gene regulatory basis underlying pod length variations in cowpea (V. unguiculata L. Walp)

“…The recently developed Cowpea iSelect Consortium Array (Illumina, Inc.) provides an opportunity to further dissect pod length and other domestication traits. This array contains 51 128 SNPs that derive from WGS sequencing of 37 diverse cowpea accessions (33 grain cowpeas and four asparagus bean) (Muñoz-Amatria ın et al, 2016). Using this assay, a cowpea consensus genetic map was constructed with SNP data from five mapping populations (Muñoz-Amatria ın et al, 2016).…”

Genomic and transcriptomic approaches towards the genetic improvement of an underutilised crops: The case of Bambara groundnut

“…Historically, genomic and molecular genetic analysis has been focused towards major species, but now with the advancement in high-throughput sequencing technologies, such as NGS, and the reduction in their costs and also the availability of bioinformatic tools (Table 3), it is becoming possible to transfer information to crops and related-species. With the availability of genomic resources and the completion of reference genome sequences of legume crops, such as Medicago truncatula (Young and Udvardi, 2009), Common bean (Schmutz et al, 2014), Soybean (Glycine max) (Schmutz et al, 2010) and Cowpea (Muñoz-Amatriaín et al, 2016), it is now possible to dissect information and transfer genomic and transcriptomic data to other legume crops such as bambara groundnut. For example, the USEARCH sequence analysis tool can be used for comparing sequences between closely related species (Ward and Moreno-Hagelsieb, 2014), enabling advances in genetic marker development, location of orthologues and decoding of the genetic mechanism and pathways involved in drought tolerance in less studied crops, such as bambara groundnut through genomic and transcriptomic comparative analysis.…”