Genome‐wide association and haplotype analyses reveal genetic architecture of seed dormancy in grain sorghum with implications for preharvest sprouting tolerance

Preharvest sprouting (PHS), triggered primarily by wet or humid conditions at maturity and further influenced by temperature, causes premature grain germination in sorghum (Sorghum bicolor (L.) Moench), reducing yield and grain quality. To elucidate the genetic architecture of seed dormancy and germination responses related to PHS tolerance, 172 genetically diverse Sorghum Association Panel accessions were evaluated under controlled conditions across two years. Germination index (GI) and arcsine-transformed germination percentage (ArcG%) were used to characterize dormancy-related variation. Genome-wide association studies based on ∼4.8 million high-quality single-nucleotide polymorphisms identified 99 quantitative trait loci (QTLs) for GI and ArcG%, several of which were stable across datasets. Notably, clusters of ArcG%-associated QTL on chromosomes Sb4 and Sb5 represented major genetic hotspots enriched for dormancy-related variation. Haplotype analysis refined these QTLs into 36 blocks, with 15 showing significant phenotypic differentiation. Favorable haplotypes consistently associated with lower GI or ArcG% indicated stronger dormancy and reduced germination under sprouting-inducing conditions. Candidate-gene mining within these regions identified 29 genes, of which 11 were prioritized for their functional similarity to known dormancy and sprouting regulators. Gene-based haplotype analysis highlighted seven strong candidates, each showing a robust association with dormancy-related traits. Several QTLs also colocalized with known sorghum dormancy genes (e.g., SbVP1, SbABI1, SbGA2ox1, SbPKABA1) and orthologs of cereal dormancy regulators (e.g., TaAFP, TaMYB10, TaPYL5, Sdr4, ABI5), suggesting conserved mechanisms across cereals. Collectively, these findings identify key genomic regions, favorable haplotypes, and high-priority candidate genes associated with seed dormancy and germination response, providing valuable genomic resources for breeding sorghum cultivars with improved PHS tolerance.