Pan-genome analysis uncovers extensive structural variations in Africa’s indigenous legume crop cowpea

Cowpea (Vigna unguiculata L. Walp.) is an Africa-originated legume providing a vital source of protein for millions across resource constrained areas of Africa, Asia and Latin America. Understanding genetic diversity in cowpea is pivotal to its genetic improvement. Here, we assemble 20 high-quality genomes representing cowpea global diversity and construct a graph-based pan-genome to characterize genetic variation. The pan-genome comprises 29,557 orthogroups, with approximately 73% conserved across all accessions. Extensive structural variations (SVs) are uncovered, affecting thousands of coding sequences and gene expression. Thousands of SVs are found under selection between two cowpea subspecies, highlighting their roles in subspecies divergence. We pinpoint key SVs underlying variation in pod length and seed number per pod. Two SV clusters appear to modulate pod length through altering expression and function of VuWAK and VuGA2ox2 genes. These findings provide insights into cowpea genetic diversity and establish a fundamental resource for cowpea genetic improvement. Cowpea is a nutritious legume that provides an important source of plant-based protein worldwide. Here, the authors assemble 20 genomes representing global diversity and construct a pan-genome to characterize genetic variations and their associations with pod length and seed number per pod.