A view of the pan-genome of domesticated cowpea (Vigna unguiculata[L.] Walp.)

Abstract

Cowpea, Vigna unguiculata L. Walp., is a diploid warm-season legume of critical importance as both food and fodder in sub-Saharan Africa. This species is also grown in Northern Africa, Europe, Latin America, North America and East/Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six sub-populations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. A total of 44,861 genes were identified in the resulting pan-genome, including 21,330 core and 23,531 non-core genes. Therefore, the total number of genes in the domesticated cowpea pan-genome is more than double the number of genes in any of the individual genomes. GO-Terms associated with response to stress, defense response in particular, were highly enriched among the non-core genes, while core genes were significantly enriched in terms associated with catabolic processes, transport and cellular homeostasis, among others. Over 5 million SNPs relative to each individual assembly and over 40 structural variants >1 Mb in size were identified by comparing genomes. Vu10 was the chromosome with the highest frequency of SNPs and Vu04 had the most structural variants of all sizes. While similar numbers of synonymous SNPs and in-frame indels were found in core and non-core genes, non-core genes had much higher numbers of missense, stop gain, and frameshift mutations. These results suggest that non-core genes make a large contribution to diversity within domesticated cowpeas, and may be particularly important in terms of the contribution of large-effect variants.

Cowpea Constraints and Breeding in Europe

“…In recent years, genome sequencing resulted in significant progress through genetic quantitative trait loci (QTLs) identification, using either linkage mapping or association mapping and revealing the linkage of these genomic regions to phenotype [ 107 ]. As a reference the genome of IT97K-499-35 breeding line from Nigeria was sequenced [ 108 ], with an assembled genome size of 519.44 Mb [ 109 ].…”

Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration

“…Advances in next-generation sequencing-based approaches and bioinformatic analyses have facilitated the identification of target genomic regions conferring disease resistance in various crops, including grain legumes ( Thudi et al., 2020 ; Gangurde et al., 2022 ). Further, these technologies have enabled WGRS of large-scale global germplasm and pangenome construction for various legumes, including soybean ( Li et al., 2014 ), chickpea ( Varshney et al., 2021 ), pigeon pea ( Zhao et al., 2020 ), cowpea ( Liang et al., 2022 ), and mungbean ( Liu et al., 2022b ). Thus, these genomic resources could help underpin novel presence/absence variations contributing to various viral-disease-resistance genes and pathogenesis genes for developing next-generation viral-disease-resistant grain legumes.…”

Development of a mobile, high-throughput, and low-cost image-based plant growth phenotyping system

“…The seeds of 5 cowpea accessions (CB5-2, IT97K-499, Sanzi, Suvita-2, UCR799), representative of the wider diversity within cowpea were germinated in 4-inch pots filled with soil (Cornell Mix + Osmocote) (Liang et al, 2023). We used seven biological replicates per accession per treatment for this experiment.…”

“…S10). Within the cowpea pangenome (Liang et al, 2022), the majority of the sequence variation resides within the gene coding region (5 SNPS, Fig. 10A) and 5'UTR (2 SNPs, 1 indel mutations).…”