Genetic dissection of diverse seed coat patterns in cowpea through a comprehensive GWAS approach

Authors: XIONG, HAIZHENG - University Of Arkansas; CHEN, YILIN - University Of Arkansas; RAVELOMBOLA, WALTRAM - Texas A&M Agrilife; Mou, Beiquan; SUN, XIAOLUN - University Of Arkansas; ZHANG, QINGYANG - University Of Arkansas; XIAO, YITING - University Of Arkansas; TIAN, YANG - University Of Arkansas; LUO, QUN - University Of Arkansas; ALATAWI, IBTISAM - University Of Arkansas; CHIWINA, KENANI - University Of Arkansas; ALKABKABI, HANAN - University Of Arkansas; SHI, AINONG - University Of Arkansas

Submitted to: Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/2/2024
Publication Date: 5/5/2024
Citation: Xiong, H., Chen, Y., Ravelombola, W., Mou, B., Sun, X., Zhang, Q., Xiao, Y., Tian, Y., Luo, Q., Alatawi, I., Chiwina, K.E., Alkabkabi, H.M., Shi, A. 2024. Genetic dissection of diverse seed coat patterns in cowpea through a comprehensive GWAS approach. Plants. 13(9). Article 1275. https://doi.org/10.3390/plants13091275.
DOI: https://doi.org/10.3390/plants13091275

Interpretive Summary: This research explores the genetic basis of seed coat color and pattern diversity in cowpea (Vigna unguiculata), in a study of 296 cowpea varieties using DNA markers. A DNA marker is a particular sequence of DNA associated with a specific location on a chromosome. DNA marker technology enables plant breeders to select individual plants based on their marker pattern (genotype) rather than their observable traits (phenotype). This process is called marker assisted breeding (MAB) or marker assisted selection (MAS), which can increase the speed and efficiency of the crop breeding. Focused on eight distinct coat patterns— (1) red and (2) cream seed; (3) white and (4) brown/tan seed coat; (5) pink, (6) black, (7) brown eye and (8) red/brown Holstein—the study identified 13 significant DNA markers. Further analysis of these markers unveiled 19 candidate genes, among which the gene Vigun05g039300, which regulates anthocyanin synthesis, was highlighted for its potential direct role in seed coat pigmentation. This study's findings provide a critical foundation for future breeding strategies, emphasizing the potential for using genetic markers to develop cowpea varieties that meet consumer preferences and market demands.

Technical Abstract: This research explores the genetic basis of seed coat color and pattern diversity in cowpea (Vigna unguiculata), utilizing a Genome-Wide Association Study (GWAS) with a 296-cowpea mapping panel and 11K SNPs. Focused on eight distinct coat patterns— (1) red and (2) cream seed; (3) white and (4) brown/tan seed coat; (5) pink, (6) black, (7) brown eye and (8) red/brown Holstein—the study identified 13 significant SNP markers across six GWAS models (GLM, SRM, MLM, MLMM, FarmCPU from GAPIT3, and TASSEL5). Proximity analysis of these loci unveiled 19 candidate genes, among which the gene Vigun05g039300 (myb domain protein 114) was highlighted for its potential direct role in seed coat pigmentation. This study's findings provide a critical foundation for future breeding strategies, emphasizing the potential for using genetic markers to develop cowpea varieties that meet consumer preferences and market demands.