Integrated Meta-QTL and Genome-wide Association Study of Ethiopian Sesame (Sesamum indicum L.) Identifies Novel Loci for Plant Height and Seed Coat Color

Sesame (Sesamum indicum L.) is a nutrient-rich oilseed valued for its high-quality oil and protein-rich seeds. Sesame breeding can be accelerated by unlocking the untapped genetic variation present in African landraces. This study integrated a global meta-quantitative trait loci (QTL) analysis with genome‑wide association study (GWAS) of Ethiopian germplasm to identify molecular markers for two key agronomic traits: plant height and seed coat color. To address inconsistencies among published studies, we explicitly documented the genetic maps, marker systems, mapping populations, linkage mapping and GWAS analysis methods used in each source study before conducting the meta-analysis. Only QTL whose markers could be reliably anchored to the sesame reference genome v3.0 were retained. Meta-analysis of eight published studies identified six conserved QTL hotspots on chromosomes 3, 4, 6, 8, 9, and 11. Field evaluation of 200 Ethiopian accessions over two seasons revealed wide phenotypic variation and high heritability (H² > 0.85). Using 3,633 genome-wide SNPs, GWAS detected 36 significant marker-trait associations, including multiple novel loci on chromosomes 12 and 13 not reported in Asian germplasm-focused studies. Key SNPs explained up to 14.2% (plant height) and 9.2% (seed coat color) of phenotypic variance. Candidate genes linked to significant SNPs included brassinosteroid-related CYP90B1 and ethylene-responsive AP2/ERF for plant height, and transcription factors WRKY23, DOF3.1, and SBP-like for seed coat color. Population structure showed two distinct groups (K = 2), and linkage disequilibrium decayed rapidly (~204 kb), enabling fine‑mapping. The study provides validated meta‑QTL intervals, trait-associated SNPs, and candidate genes that form a molecular foundation for marker-assisted selection in sesame improvement programs.