Pleiotropic SNPs and genes linked to enhanced seed longevity and vigor for climate resilient pearl millet production

Seed longevity and vigor are critical factors for sustainable crop production, particularly in environments prone to stress, where consistent germination and seedling establishment are crucial. This study investigates the genetic architecture underlying seed longevity and vigor traits in pearl millet (Pennisetum glaucum [L.] R. Br.) through genome-wide association studies (GWAS). The GWAS panel comprising 201 inbred lines representing B and R lines was phenotyped under both control and accelerated aging (AA) conditions for 27 seed longevity and seedling vigor traits and their relative measures. Phenotypic analysis revealed significant changes in seed traits following AA in germination percentages, seedling vigor indices and mean germination times. A 4K mid-density SNP panel was used for genotyping, producing 2,015 high-confidence SNPs after stringent filtering for GWAS. The Bayesian information and linkage disequilibrium iteratively nested keyway (BLINK) and Multi-locus mixed model (MLMM) models identified 413 significant marker-trait associations (MTAs), with 185 MTAs common to both models. A pleiotropic SNP, PMSnpB394 on chromosome 2, was linked to 14 seed longevity traits. Key genes associated with these traits include hormone signaling (Auxin response factor, DOG1), stress response (LEA_2, 10 kDa heat shock protein), metabolism (Glyceraldehyde-3-phosphate dehydrogenase, Beta-galactosidase) and seed coat structure (Peroxidase, 3-Ketoacyl-CoA synthase). These MTAs and candidate genes provide valuable insights into the molecular mechanisms underlying seed longevity and vigor and serve as promising targets for marker-assisted selection and breeding strategies aimed at developing climate-resilient cultivars in the rainfed ecologies.