Single Nucleotide polymorphic (SNP) markers of f 98 cowpea accessions

Exploring genes linked with drought tolerance and photosynthesis in cowpea could accelerate breeding of climate-resilient cowpea varieties. A Genome-wide association study (GWAS) was conducted to identify genomic regions linked with agronomic and photosynthetic traits under well-watered and water-stressed conditions. One hundred and twelve cowpea accessions from IITA were phenotyped for agronomic and photosynthetic traits across three locations in two years: Ibadan, Ikenne (2020 and 2021) and Kano (2021 and 2022). The accessions were genotyped using 19,000 DArT-Seq SNP markers from which 9,210 markers were utilized for GWAS analysis. Using the BLINK and mixed linear model (MLM) with correction for population structure, 38 associated SNP markers were identified, and 21 candidate genes uncovered closely positioned within the GWAS hits. Two stable SNP associated with grain yield under well-watered and water-stressed conditions and SNP markers linked with leaf temperature differential, relative chlorophyll content and ΦPSII were all located on chromosome 4 and 8. Gene annotations revealed Vigun04g169000, Vigun08g168900, Vigun09g020600 and Vigun03g370600 genes have functional roles in plant development and response to environmental stress. Vigun08g126600, Vigun04g146250 and Vigun05g129600 genes were found to be involved in driving photosynthetic process of ΦPSII, abiotic stress response and non-photochemical quenching. The identified SNP markers and candidate genes upon validation would be valuable in marker-assisted selection and useful for cowpea breeders to harness the role of photosynthesis in genetic enhancement of cowpea tolerance to drought.