Association analysis of cowpea mosaic virus (CPMV) resistance in the USDA cowpea germplasm collection

Cowpea Vigna unguiculata (L.) Walp.] is an important legume crop, widely grown in Africa, South America, South Asia, Southeast Asia, and the southern United States. Cowpea is consumed as both fresh vegetable and dry grain, and as an animal feed and fodder, and it is a major dietary protein source that complements cereal-based diet. Cowpea mosaic virus (CPMV) causes a severe yield loss of cowpea in many areas worldwide notably in the Africa. Utilization of host genetic resistance is the most effective control method for the viral disease. The objective of this research is to conduct genome-wide association analysis and identify single nucleotide polymorphism (SNP) markers associated with CPMV resistance in cowpea. Three hundred and thirty-three cowpea germplasm accessions, originally collected from 39 different countries and 1033 SNPs identified from genotyping by sequencing approach were used in this study. Single marker regression, general linear model, and mixed linear model in Tassel 5 were used for association analysis of CPMV resistance. Six SNP markers (C35069548_1883, scaffold65342_6794, scaffold66293_6549, scaffold95805_2175, C35081948_540, and scaffold17319_4417) were strongly associated with the CPMV resistance, of which the first three were associated for immune and the remaining three were associated with hypersensitive response. SNP markers identified in this research will be a potential tool to use in cowpea molecular breeding to develop CPMV resistant cultivars through marker-assisted selection.