Genome-wide association study for drought tolerance in cowpea (Vigna unguiculata (L.) Walp.) at seedling stage using a whole genome resequencing approach

Authors: RAVELOMBOLA, WALTRAM - Texas A&M University; XIONG, HAIZHENG - University Of Arkansas; BHATTARAI, GEHENDRA - University Of Arkansas; MANLEY, AURORA - Texas A&M University; CASON, JOHN - Texas A&M Agrilife; PHAM, HANH - Texas A&M Agrilife; ZIA, BAZGHA - Clemson University; Mou, Beiquan; SHI, AINONG - University Of Arkansas

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/4/2025
Publication Date: 6/7/2025
Citation: Ravelombola, W., Xiong, H., Bhattarai, G., Manley, A., Cason, J., Pham, H., Zia, B., Mou, B., Shi, A. 2025. Genome-wide association study for drought tolerance in cowpea (Vigna unguiculata (L.) Walp.) at seedling stage using a whole genome resequencing approach. International Journal of Molecular Sciences. 26(12). Article 5478. https://doi.org/10.3390/ijms26125478.
DOI: https://doi.org/10.3390/ijms26125478

Interpretive Summary: Even though cowpea is one of the more drought-tolerant legumes, some varieties with a high yield under well-watered conditions have been shown to be susceptible to drought stress, thus requiring further improvement. The objectives of this study were to conduct a genetic study for drought tolerance in cowpea. A total of 331 cowpea varieties were evaluated for drought tolerance. A total of 5,884,299 DNA markers were found in the study . 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. Results showed: 1) a cluster of 196 markers located on chromosome 5 was identified to be a good gene candidate for tolerance to trifoliate leaf chlorosis under drought stress in cowpea. This chromosome region harbored genes encoding for hormone-induced proteins, 2) markers were found towards the end of chromosome 1 and this area was a good candidate gene for tolerance to unifoliate leaf chlorosis under drought stress in cowpea. An additional set of more than 500 markers located on chromosomes 8 and 10 were also found to be linked to tolerance to unifoliate leaf chlorosis under drought stress in cowpea, 3) a total of 25 markers located on chromosomes 1, 3, 5, and 11 were significantly associated with plant greenness under drought stress, and 4) a total of 12 common markers were found between genes for tolerance to trifoliate leaf chlorosis and plant greenness. To the best of our knowledge, this is the first such genetic study using DNA sequencing data in cowpea.

Technical Abstract: Even though cowpea is one of the more drought-tolerant legumes, some genotypes with a high yield under well-watered conditions have been shown to be susceptible to drought stress, thus requiring further improvement. The objectives of this study were to conduct a genome-wide association study (GWAS) for drought tolerance in cowpea. A total of 331 cowpea genotypes were evaluated for drought tolerance. After SNP filtering, 5,884,299 SNPs were used to conduct GWAS using BLINK. Results showed: 1) a significant GWAS peak defined by a cluster of 196 significant SNPs and mapped on a 210-kb region of chromosome 5 was identified to be a good locus candidate for tolerance to trifoliate leaf chlorosis under drought stress in cowpea. This genomic region harbored genes encoding for hormone-induced proteins, 2) a strong GWAS peak was found towards the end of chromosome 1 and this peak was a good candidate locus for tolerance to unifoliate leaf chlorosis under drought stress in cowpea. An additional set of more than 500 SNPs located on chromosomes 8 and 10 were also found to be significantly with tolerance to unifoliate leaf chlorosis under drought stress in cowpea, 3) a total of 25 SNPs located on chromosomes 1, 3, 5, and 11 were significantly associated with plant greenness under drought stress, and 4) a total of 12 common SNPs were found between loci of tolerance to trifoliate leaf chlorosis and plant greenness. To the best of our knowledge, this is the first GWAS study using a whole genome resequencing data in cowpea.