Association Analysis of Seed Antioxidant Content and Aphid Resistance in Cowpea

The goals of this research were to conduct association analysis of two important traits in cowpea (Vigna unguiculata L. Walp.): seed antioxidant content, a health-promoting compound for humans, and cowpea aphid (Aphis craccivora) resistance and identification of SNP markers associated with the two traits. USDA-GRIN cowpea core collection was used for both phenotyping and genotyping. Genotyping by Sequencing (GBS) was used for SNP discovery, which was used as genotypic data in association analysis. The STRUCTURE 2, and MEGA 6 software programs were used to analyze the population structure and genetic diversity. Single marker regression (SMR), general linear model (GLM), and mixed linear model (MLM) in Tassel were used for association analysis between the SNPs and the phenotypic data of the seed antioxidant content and aphid resistance. Results indicated that: (1) three structured populations for the cowpea accessions in both association panels 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; (2) although different SNP markers were found to be associated with seed antioxidant content with different models, the two SNP markers, Scaffold7139_14363 and scaffold29110_4657 were strongly associated with antioxidant content; and (3) 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. These SNP markers could potentially be used in marker-assisted breeding to accelerate genetic improvement of cowpea for higher seed antioxidant content and aphid resistance.