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

Sesame (<i>Sesamum indicum</i> 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 3683 SNPs, detected 36 significant associations, including novel loci on chromosomes 12 and 13 not reported in Asian-focused research. Candidate genes assigned to these loci implicated key hormonal and transcriptional mechanisms: brassinosteroid biosynthesis (<i>CYP90B1</i>) and ethylene signaling (<i>AP2/ERF</i>) probably regulate plant architecture, while transcription factors (<i>WRKY23</i>, <i>DOF3.1</i>, and <i>SBP-like</i>) 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), which allows fine-mapping. The present study presents validated molecular markers and candidate genes for marker-assisted selection in sesame breeding.