Sam Farr U.S. Crop Improvement and Protection Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Salinas, CA 93905, USA
Xiaolun Sun
Department of Poultry Science & The Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
Qingyang Zhang
Mathematical Sciences, University of Arkansas, Fayetteville, AR 72701, USA
Yiting Xiao
Biological Engineering, University of Arkansas, Fayetteville, AR 72701, USA
Yang Tian
Program of Material Science and Engineering, Fayetteville, AR 72701, USA
Qun Luo
Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
Ibtisam Alatawi
Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
Kenani Edward Chiwina
Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
Hanan Mohammedsaeed Alkabkabi
Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
Ainong Shi
Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
This study investigates the genetic determinants of seed coat color and pattern variations in cowpea (Vigna unguiculata), employing a genome-wide association approach. Analyzing a mapping panel of 296 cowpea varieties with 110,000 single nucleotide polymorphisms (SNPs), we focused on eight unique coat patterns: (1) Red and (2) Cream seed; (3) White and (4) Brown/Tan seed coat; (5) Pink, (6) Black, (7) Browneye and (8) Red/Brown Holstein. Across six GWAS models (GLM, SRM, MLM, MLMM, FarmCPU from GAPIT3, and TASSEL5), 13 significant SNP markers were identified and led to the discovery of 23 candidate genes. Among these, four specific genes may play a direct role in determining seed coat pigment. These findings lay a foundational basis for future breeding programs aimed at creating cowpea varieties aligned with consumer preferences and market requirements.
