Physiological and genetic characterization of seed dormancy and pre-harvest sprouting in sorghum

Pre-harvest sprouting (PHS) is a major agronomic constraint in sorghum, triggered by rainfall, high humidity, and temperature fluctuations during physiological maturity. The resulting premature germination reduces both grain yield and quality. To elucidate the physiological and genetic basis of PHS tolerance, this research integrated phenotypic evaluation and genome-wide analysis using the Sorghum Association Panel, which represents extensive genetic and geographic diversity. In the first experiment, 172 accessions were evaluated for dormancy-related traits under controlled conditions across two years. Germination Index (GI) and arcsine-transformed germination percentage (ArcG%) were used as proxy traits for dormancy. A genome-wide association study (GWAS) using ~4.8 million high-quality SNPs identified 99 QTLs, with major clusters on chromosomes Sb04 and Sb05. Haplotype analysis refined these regions to 15 haplotype blocks with significant phenotypic contrasts. Candidate-gene mining highlighted seven strong candidates, functionally linked to dormancy and sprouting regulation. Several loci co-localized with known sorghum dormancy genes and orthologs in other cereals, revealing conserved ABA–GA regulatory mechanisms. In the second experiment, a novel intact-panicle phenotyping protocol was developed to simulate rainfall and diurnal temperature cycles under controlled conditions. Evaluation of 19 diverse genotypes identified 30/20°C (day/night) as the optimal regime for inducing sprouting within 48 hours and captured distinct genotypic variation in PHS response. Contrasting tolerant (SC399, SC425) and susceptible (44M, SC1494) lines were identified. Hormonal profiling validated the phenotyping assay, showing that tolerant lines accumulated higher levels of abscisic acid (ABA), indole-3-acetic acid (IAA), and salicylic acid (SA), consistent with stronger dormancy maintenance and stress resilience. Collectively, these results provide both genetic resources and an improved phenotyping framework to accurately distinguish tolerant and susceptible genotypes. The integration of trait mapping, haplotype analysis, and hormone-based validation offers practical tools for breeding climate-adaptive, PHS-resilient sorghum cultivars.