Identification of genomic region, candidate genes and epistasis interaction using high density genetic map for drought stress tolerance in sesame (

Drought critically hampers sesame establishment and productivity; however, the genetic mechanisms underlying drought tolerance at the susceptible germination stage are poorly understood. Here, we dissected the genetic architecture of drought tolerance using 448 recombinant inbred lines (RILs) developed from contrasting parents. Using high-density quantitative trait loci (QTL) mapping, we identified nineteen (19) QTLs associated with germination-related attributes in both control and drought conditions. Among these, QTL, qGP-8 on chromosome 8, presented a small additive effect (2.31% PVE) but participated in multiple statistically significant epistatic interactions (LOD > 70), a role in a complex genetic network rather than acting as a sole determinant of drought tolerance. Notably, the epistatic architecture significantly changed from control to drought condition, indicating possible stress-specific genetic program. The qGP-8 interval (18051358–19247636 bp) discover six (06) promising candidate genes with compelling functional annotation for stress adaptation. Promoter analysis described a complex regulatory landscape, where ABA-responsive (ABRE) and drought-inducible (MYB/MYC, MBS) cis -elements were abundantly present emphasizing the sophisticated transcriptional control. Additionally, phylogenetic constructed positions of LOC105169270 and LOC105169455 in DREB2 clade suggesting a potential involvement in stress-responsive regulation that warrants further investigations. LOC105169228 and LOC105169258 clustered with stress-associated NAC transcription factors, and TAF1 and poly(A)-binding proteins, respectively, indicating a robust evolutionary conservation. The results of qRT-PCR validated a dynamic upregulation of all six genes in drought conditions, with LOC105169455 presenting a strong induction (8.955-fold) in tolerant parent. Collectively, this study identifies qGP-8 as a useful genomic resource containing potential candidate genes operating in a complex epistatic framework, providing a foundation for further functional characterization and breeding applications in sesame. This work provides useful genomic resource that, pending validation, may support marker-assisted breeding of climate-resilient sesame varieties.