Molecular marker development for salt tolerance in cowpea: insights from genome-wide association analysis at the early vegetative stage.

key messageThis study identified efficient marker combinations consisting of two significant SNPs associated with salt tolerance in cowpea, providing genomic insights and candidate frameworks for future validation and breeding applications. Salt stress is a major abiotic factor that severely reduces crop productivity, particularly in arid and semi-arid regions. Its effects are further exacerbated by climate change and the continuous buildup of salts in the soil. Although cowpea (Vigna unguiculata L.) is regarded as a promising crop in drought- and heat-prone areas, it remains especially susceptible to salt stress during its early developmental stages. To investigate the genetic foundation of salt tolerance, a genome-wide association study (GWAS) was carried out using 401 genetically diverse cowpea germplasms. This analysis integrated phenotypic assessments under 200 mM NaCl treatment at the early vegetative stage with 34,704 high-quality single-nucleotide polymorphisms (SNPs). Four morpho-physiological traits were chosen to assess responses to salt stress, including leaf scorch score (LSS), leaf chlorophyll content (LCC), and the contents of leaf sodium ions (LSI) and leaf chloride ions (LCI). GWAS identified several significant marker-trait associations, among which six SNPs with the highest statistical significance across the four traits were selected. Candidate genes associated with these SNPs were involved in ion transport, regulation of reactive oxygen species (ROS), and secondary metabolite biosynthesis, which are fundamental mechanisms in salt tolerance. Moreover, the combination of two SNPs, 2_52855 and 2_38343, proved to be the most effective marker for distinguishing salt-tolerant germplasms. Germplasms containing the GC genotype at this combination, meaning the G allele at the SNP 2_52855 and the C allele at the SNP 2_38343, consistently demonstrated enhanced salt tolerance. These findings enhance our understanding of the genetic architecture of salt stress response in cowpea and provide a foundation for identifying molecular markers that can be validated and applied in future breeding efforts.