Genome-wide association studies reveals new candidate genes associated with resistance to Striga gesneroides in Cowpea [Vigna unguiculata (L.) Walp.] accessions from sub-Saharan Africa

Abstract

Parasitic plant Striga gesneroides reduces cowpea productivity in sub-Saharan Africa, leading to substantial yield losses. This weed is the major reason for land abandonment by many farmers. While various methods have been proposed for managing Striga invasion and parasitism, host-plant resistance remains the most effective and affordable option for small-scale farmers in the sub-region. This study aims to expedite the improvement of Striga resistance breeding through marker-assisted selection by identifying genomic regions and candidate genes associated with Striga resistance indicator traits using association mapping. A panel of 188 cowpea accessions assembled from five gene banks in West Africa were phenotyped for two years under Striga-infested and non-infested research conditions. These accessions were equally genotyped using the medium-density genotyping of the Diversity Arrays Technology sequencing (DArTseq) platform to obtain marker information. High broad-sense heritability estimates were observed for Striga resistance status (SRS), number of Striga per plot (NSPlot), and Pod weight (PW) while low heritability estimates were observed for fodder weight (FW) and Plant Aspect (PASP). Twenty-four SNP markers were identified across SRS, NSPlot, FW, PASP, and PW under Striga-infested conditions. Under non-infested conditions, 17 SNPs were identified across FW, PASP, and PW. Gene annotation of the significant SNPs revealed candidate genes such as ubiquitin ligase activity, cell wall reinforcement protein, and pathogenesis-related protein. These genes function in plant growth regulation, development, and defense mechanisms. This study offers valuable insights for marker selection, validation, and deployment in cowpea improvement for Striga resistance in SSA.