Genetic Diversity and Genome-Wide Association in Cowpeas (Vigna unguiculata L. Walp)

Abstract

Cowpea is one of the most popular dry-land legumes cultivated for food and forage in arid and semi-arid areas. Genetic diversity for global germplasm can be organized into core collections providing optimum resources to serve breeding requirements. Here, we present diversity analysis and genome-wide association study (GWAS) results for part of the cowpea core collection of the United States Department of Agriculture (USDA) along with breeding line controls. Included in the analysis were a total of 373 accessions analyzed with 6880 Single Nucleotide Polymorphism (SNP) markers from Genotyping by Sequencing (GBS). Population structure differentiated accessions into two groups irrespective of geographical origin and formed three clusters based on taxa upon phylogenetic analysis. A total of 56 SNPs were significantly associated to nine traits including pod length (25 Quantitative Trait Nucleotides, QTNs), seed anti-oxidant content (7 QTNs), dry pod color (7 QTNs), plant maturity (5 QTNs), flower color (5 QTNs), seed weight (4 QTNs), tolerance to low phosphate (1 QTN), growth habit (1 QTN), and response to rock phosphate (1 QTN) using Bayesian-information, Linkage-disequilibrium Iteratively Nested Keyway (BLINK), and Fixed and random model Circulating Probability Unification (FarmCPU) association models. Key genes related to all significant SNPs were identified based on annotations of the cowpea reference genome, including a flavonoid gene controlling flower color (Vigun08g040200.1), a root nodulation regulator for tolerance to low phosphate (Vigun11g168000.1), and numerous genes involved in signaling, biosynthesis, metabolite transport, and abiotic stress. Our results highlight the importance of maintaining public phenotyping databases at USDA and strengthening collaborations for data collection in cowpea to maximize research impacts.