Genetic Dissection of Diverse Seed Coat Patterns in Cowpea through a Comprehensive GWAS Approach

Haizheng Xiong; Yilin Chen; Waltram Ravelombola; Beiquan Mou; Xiaolun Sun; Qingyang Zhang; Yiting Xiao; Yang Tian; Qun Luo; Ibtisam Alatawi; Kenani Edward Chiwina; Hanan Mohammedsaeed Alkabkabi; Ainong Shi

doi:10.3390/plants13091275

Plants (May 2024)

Genetic Dissection of Diverse Seed Coat Patterns in Cowpea through a Comprehensive GWAS Approach

Haizheng Xiong,
Yilin Chen,
Waltram Ravelombola,
Beiquan Mou,
Xiaolun Sun,
Qingyang Zhang,
Yiting Xiao,
Yang Tian,
Qun Luo,
Ibtisam Alatawi,
Kenani Edward Chiwina,
Hanan Mohammedsaeed Alkabkabi,
Ainong Shi

Affiliations

Haizheng Xiong: Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
Yilin Chen: Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
Waltram Ravelombola: Texas A&M AgriLife Research, 11708 Highway 70 South, Vernon, TX 76384, USA
Beiquan Mou: 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

DOI: https://doi.org/10.3390/plants13091275
Journal volume & issue: Vol. 13, no. 9
p. 1275

Abstract

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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.

Published in Plants

ISSN: 2223-7747 (Online)
Publisher: MDPI AG
Country of publisher: Switzerland
LCC subjects: Science: Botany
Website: http://www.mdpi.com/journal/plants

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