Integrating Meta-QTL Analysis and Genome-Wide Association Mapping in Ethiopian Sesame (<em>Sesamum indicum</em> L.) Reveals Novel Loci for Plant Height and Seed Coat Color

Sesame (Sesamum indicum L.) is a nutrient-rich oilseed crop whose improvement can be accelerated by unlocking untapped genetic variation in African landraces. We integrated a global meta-quantitative trait loci (QTL) analysis with a genome-wide association study (GWAS) of Ethiopian germplasm to identify molecular markers for plant height and seed coat color. Meta-analysis of eight available data sources revealed six conserved QTL hotspots on chromosomes 3, 4, 6, 8, 9 and 11. Subsequently, GWAS on 200 Ethiopian accessions, represented by 3,683 SNPs, detected 36 significant associations, including novel loci on chromosomes 12 and 13 that were not reported in Asian-focused research. Candidate gene analysis implicated key hormonal and transcriptional mechanisms, including brassinosteroid biosynthesis (CYP90B1) and ethylene signaling (AP2/ERF), which probably regulate plant architecture. In contrast, transcription factors (WRKY23, DOF3.1, and SBP-like) modulate flavonoid pathways, controlling seed coat pigmentation. Analyses of population structure revealed two distinct groups (K = 2), and linkage disequilibrium (LD) decayed rapidly (~190 kb). This rapid decay facilitates fine‑mapping of trait-associated regions and highlights the high genetic diversity within the Ethiopian panel. The present study presents validated molecular markers and candidate genes for marker-assisted selection in sesame breeding, providing a foundation for improving sesame in Africa and beyond.