Genetic architecture of salt tolerance in cowpea (Vigna unguiculata (L.) Walp.) at seedling stage using a whole genome resequencing approach

Authors: RAVELOMBOLA, WALTRAM - Texas A&M University; DONG, LINDGI - Hebei Academy Of Agriculture & Forestry; BARICKMAN, CASEY - Mississippi State University; XIONG, HAIZHENG - 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: 10/16/2023
Publication Date: 10/18/2023
Citation: Ravelombola, W., Dong, L., Barickman, C.T., Xiong, H., Manley, A., Cason, J., Pham, H., Zia, B., Mou, B., Shi, A. 2023. Genetic architecture of salt tolerance in cowpea (Vigna unguiculata (L.) Walp.) at seedling stage using a whole genome resequencing approach. International Journal of Molecular Sciences. 24(20). Article 15281. https://doi.org/10.3390/ijms242015281.
DOI: https://doi.org/10.3390/ijms242015281

Interpretive Summary: Cowpea [Vigna unguiculata (L.) Walp.] is a legume crop used for human consumption, feed for livestock, and green manure. Earlier reports have shown that salinity has been a growing threat to cowpea cultivation. The objectives of this study were to conduct a genetic study to identify DNA markers , and to investigate genes for salt tolerance in cowpea. 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. A total of 331 cowpea varieties were evaluated for salt tolerance. The cowpea varieties were analyzed using a DNA resequencing approach. A total of 14,465,516 DNA markers were obtained, and 5,884,299 of them were selected for this study. Results showed: 1) a region on chromosome 2 harboring a significant cluster of plant enzyme (epimerase/dehydratase) genes was linked to leaf chlorophyll content under salt stress in cowpea, 2) relative tolerance index for chlorophyll was associated with chromosomes 1 and 2, including a cluster of 10 DNA markers on chromosome 1 and a cluster of 53 markers on chromosome 2, and 3) a region on chromosome 3 within the structure of a potassium channel gene was associated with leaf injury. To the best of our knowledge, this is one the earliest reports examining salt tolerance of cowpea using DNA sequencing data.

Technical Abstract: Cowpea [Vigna unguiculata (L.) Walp.] is a diploid legume crop used for human consumption, feed for livestock, and cover crop. Earlier reports have shown that salinity has been a growing threat to cowpea cultivation. The objectives of this study were to conduct a genome-wide association study (GWAS) to identify SNP markers, and to investigate candidate genes for salt tolerance in cowpea. A total of 331 cowpea genotypes were evaluated for salt tolerance. The cowpea panel was genotyped using a whole genome resequencing approach. A total of 14,465,516 SNPs were obtained, and 5,884,299 SNPs were used after SNP filtering. GWAS was conducted on a total of 296 cowpea genotypes that were quality-checked. BLINK was used for conducting GWAS. Results showed: 1) a strong GWAS peak on an 890-bk region of chromosome 2 for leaf SPAD chlorophyll under salt stress in cowpea and harboring a significant cluster of NAD dependent epimerase/dehydratase genes such as Vigun02g128900.1, Vigun02g129000.1, Vigun02g129100.1, Vigun02g129200.1, and Vigun02g129500.1, 2) two GWAS peaks associated with relative tolerance index for chlorophyll were identified on chromosomes 1 and 2. The peak on chromosome 1 was defined by a cluster of 10 significant SNPs mapped on a 5-kb region and was located in the vicinity of Vigun01g086000.1, encoding for a GATA transcription factor. The GWAS peak on chromosome 2 was defined by a cluster of 53 significant SNPs and mapped on a 68-bk region of chromosome 2, and 3) the highest GWAS peak was identified on chromosome 3 and this locus was associated with leaf injury. This peak was within the structure of a potassium channel gene (Vigun03g144700.1). To the best of our knowledge, this is one the earliest reports on salt tolerance study of cowpea using a whole genome resequencing data.