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 to Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six subpopulations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. In the most complete assembly (IT97K-499-35), 26,026 core and 4963 noncore genes were identified, with 35,436 pan genes when considering all seven accessions. GO terms associated with response to stress and defense response were

The pattern of genetic variability in a core collection of 2,021 cowpea accessions

“…Although genetic resources for cowpea are underdeveloped compared to cereal crops such as maize, rice, and wheat, cowpea benefits from several available sequenced genomes (Lonardi et al 2019;Liang et al 2023) as well as a high quality genotyping array (Muñoz-Amatriaín et al 2017) . Several quantitative trait locus (QTL) mapping populations have been developed to link genotype to phenotype in this species and have been useful in identifying QTL for diverse traits such as flowering time (Andargie et al 2013;Huynh et al 2018;Lo et al 2018;Olatoye et al 2019) , disease resistance (Huynh et al 2016;Santos et al 2018) , seed coat color and patterning (Herniter et al 2018(Herniter et al , 2019 , perenniality (Lo et al 2020) , and several domestication-related traits such as seed shattering and yield (Lo et al 2018) .…”

Exploring the genomics of abiotic stress tolerance and crop resilience to climate change

“…Furthermore, many genes absent in reference accessions possess functions of potential adaptive significance, making the creation of a pan-genome a crucial task for globally important crops. To identify the genomic diversity existing within cowpea domesticates, Liang et al (2023) generated de novo genome assemblies and constructed a pangenome containing 26,026 core, 4963 noncore, and 35,436 pan genes. Among the noncore genes, gene ontology terms related to stress and defense response were highly enriched among noncore genes, whereas core genes exhibited enrichment in terms linked to transcription factor activity and metabolic processes.…”

Identification of candidate genes controlling red seed coat color in cowpea (Vigna unguiculata[L.] Walp)

“…The -log10(p) values were plotted against the physical coordinates of the SNPs [26]. A Bonferroni correction was applied to correct for multiple testing error in GWAS, with the significance cut-off set at α/n, where α is 0.05 and n is the number of tested markers, resulting in a cut-off of -log10(p) = 5.93.…”

“…In particular, new populations have been developed for higher-resolution mapping including a minicore collection representing a worldwide cross-section of cultivated cowpea ("UCR Minicore") [24] and an eight-parent Multi-parent Advanced Generation Inter-Cross (MAGIC) population [25]. In addition, a reference genome sequence of cowpea (phytozome-next.jgi.doe.gov) [22] and genome assemblies of six additional diverse accessions [26];…”