Global Sesame Germplasm Harbors Untapped Genetic Potential for Crop Improvement

Background Sesame (Sesamum indicum L.) is one of the oldest oilseed crops. Its seeds accumulate lignans and antioxidants that determine their nutritional value. Global demand for sesame is rising rapidly, but climate change increasingly threatens sesame yields and seed quality. Here, we analyzed a worldwide panel of 300 sesame accessions to explore the genetic basis of key adaptive and quality traits, specifically flowering time, seed lignan content, and seed antioxidant capacity. Results Whole-genome resequencing revealed previously unreported genetic diversity, expanding the resources available for sesame breeding. By integrating k-mer-based genome-wide association analysis with a graph-based sesame genome, we identified structural variants associated with differences in flowering time and lignan accumulation. A 9.4-kb deletion on chromosome 6 that disrupted SIN_1018434 (an ortholog of Arabidopsis PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1) and a 6.2-kb Copia-type retrotransposon insertion upstream of SIN_1004470 on chromosome 11 were associated with early flowering. The intact alleles at both loci were associated with delayed flowering and were predominant in low-latitude accessions. High seed lignan content was associated with non-synonymous mutations and copy number variants in glycosyl hydrolase genes on chromosome 6 and an 8.2-kb deletion spanning SIN_1019378 on chromosome 13. Association signals for seed antioxidant traits coincided with loci involved in abiotic stress responses and seed-coat pigmentation. Conclusions These findings highlight the importance of exploring diverse germplasm to uncover previously unrecognized adaptive and quality-associated genomic variation. The loci identified here provide molecular targets for developing climate-adapted cultivars with improved seed quality.