Population structure analysis and association mapping of seed antioxidant content in USDA cowpea (Vigna unguiculata L. Walp.) core collection using SNPs

Authors: QIN, JUN - University Of Arkansas; XIONG, HAIZHENG - University Of Arkansas; SHI, AINONG - University Of Arkansas; Mou, Beiquan; MOTES, DENNIS - University Of Arkansas; LU, WEIGUO - University Of Arkansas; CREIGHTON MILLER JR., J. - Texas A&M University; SCHEURING, DOUGLAS - Texas A&M University; NZARAMBA, M. - Texas A&M University; WENG, YUEJIN - University Of Arkansas; YANG, WEI - University Of Arkansas

Submitted to: Canadian Journal of Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/16/2016
Publication Date: 6/9/2016
Citation: Qin, J., Xiong, H., Shi, A., Mou, B., Motes, D., Lu, W., Creighton Miller Jr., J., Scheuring, D., Nzaramba, M.N., Weng, Y., Yang, W. 2016. Population structure analysis and association mapping of seed antioxidant content in USDA cowpea (Vigna unguiculata L. Walp.) core collection using SNPs. Canadian Journal of Plant Science. 96: 1026-1036. doi: 10.1139/cjps-2016-0090.

Interpretive Summary: Cowpea (Vigna unguiculata (L) Walp.) is an important legume and the antioxidants in cowpea seeds have been recognized as health-promoting compounds for human. The objectives of this study were to analyze the populations of cowpea varieties using single nucleotide polymorphism (SNP) molecular markers associated with the seed antioxidant content in cowpea. A total of 1047 SNPs were used to analyze 369 accessions of a USDA cowpea core collection, originally collected from 47 countries worldwide. The STRUCTURE, TASSEL, and MEGA software programs were used to analyze the population structure and genetic diversity for associations between the SNPs and the data of the seed antioxidant context and seedcoat color. Results indicated that: (1) there was a wide range of genetic variations of seed antioxidant content and coat color in the cowpea population; there were three clusters existed in the 369 accessions based on SNP data; and the germplasm collected from India, South Africa, and USA showed broader genetic backgrounds. (2) Although different SNP markers were identified to be associated with seed antioxidant content and seedcoat colors with different software models, two SNP markers were strongly associated with antioxidant content; and three SNP markers, were strongly associated with seedcoat color across three models. (3) Significant correlations were detected between the seed antioxidant content and seed black or red coat color. (4) Two SNP markers were associated with both seed antioxidant content and seedcoat color, simultaneously. The SNP markers identified in this study could potentially be used in breeding to accelerate genetic improvement of cowpea for higher seed antioxidant content.

Technical Abstract: Cowpea (Vigna unguiculata (L) Walp.) is an important legume and the antioxidants in cowpea seeds have been recognized as health-promoting compounds for human. The objectives of this study were to analyze the population structure of cowpea collections using single nucleotide polymorphism (SNP) and to identify SNP markers associated with the seed antioxidant content in cowpea. A total of 1047 SNPs were used to analyze 369 accessions of a cowpea core collection, originally collected from 47 countries worldwide. The STRUCTURE, TASSEL, and MEGA software programs were used to analyze the population structure and genetic diversity. Single marker regression (SMR), general linear model (GLM), and mix linear model (MLM) in Tassel were used for association analysis between the SNPs and the phenotypic data of the seed antioxidant context and seedcoat color. Results indicated that: (1) there was a wide range of genetic variations of seed antioxidant content and coat color in the cowpea population; there were three clusters existed in the 369 accessions based on SNP data; and the germplasm collected from India, South Africa, and USA showed broader genetic backgrounds. (2) Although different SNP markers were identified to be associated with seed antioxidant content and seedcoat colors with different models, the two SNP markers, Scaffold7139_14363 and scaffold29110_4657 were strongly associated with antioxidant content; and three SNP markers, C35063613_1497, scaffold81493_886, and scaffold84620_6785 were strongly associated with seedcoat color across three models. (3) Significant correlations were detected between the seed antioxidant content and seed black color (correlation coefficient= 0.45), between seed antioxidant content and seed red coat color (r = 0.50). (4) Two SNP markers, Scaffold42008_191 and C35082838_2258 were associated with both seed antioxidant content and seedcoat color, simultaneously. The SNP markers identified in this study could potentially be used in marker-assisted breeding to accelerate genetic improvement of cowpea for higher seed antioxidant content.