Association mapping of aphid resistance in USDA cowpea (Vigna unguiculata L. Walp.) core collection using SNPs

Abstract

Cowpea aphid (Aphis craccivora) is a destructive insect pest of cowpea, as well as other legume crops including alfalfa, beans, chickpea, lentils, lupins and peanuts. The utilization of aphid resistance in cowpea breeding is one of the most efficient and environmental friendly methods to control aphids. Using marker-assisted selection will expedite cowpea breeding procedures, but it is limited by the lack of information on marker associations of the aphid resistance. The objective of this study was to identify single nucleotide polymorphism (SNP) markers associated with aphid resistance in cowpea and to conduct genetic diversity analysis for aphid resistant resources. In this study, 338 cowpea accessions from the cowpea core collection in United States Department of Agriculture (USDA) Germplasm Resources Information Network (GRIN), originally collected from 40 countries, were evaluated for their aphid resistance and 1047 SNPs identified from genotyping by sequencing (GBS) were used as the genotypic data. Single marker regression, general linear model, and mixed linear model in TASSEL were used for association analysis between the SNPs and the phenotypic data. Three clusters for the association panel of the 338 cowpea accessions were inferred by STRUCTURE analysis, in good agreement with the phylogenetic tree drawn by MEGA 6 based on the maximum likelihood model with the neighbor joining method. A genome-wide association study revealed that two SNP markers, C35011941_894 and Scaffold30061_3363, were strongly associated with aphid resistance across three models with the log of odds (LOD) value greater than 2.5. The results will provide useful information for selecting aphid resistance in cowpea molecular breeding.