Abstract
Capsule shattering in sesame is a major agronomic constraint that reduces yield stability and limits mechanized harvesting efficiency. To address this challenge, 200 genetically diverse sesame genotypes from Sudan were genotyped using genotyping-by-sequencing (GBS) and evaluated for three consecutive seasons under field conditions for shattering type (ST), type of capsule beak (TCB), and bicarpellate capsule shape (BS). The resulting phenotypic and genotypic data were integrated into a multi-model genome-wide association study (GWAS) framework (BLINK, FarmCPU, and MLMM) to elucidate the genetic architecture of capsule-shattering traits. Two marker-trait associations (MTAs) were consistently identified across the GWAS models, comprising Chr1_19419575 associated with the TCB and Chr2_15649330 linked to ST. Additional MTAs, including Chr8_31466064 for ST and Chr8_19392181 and Chr8_30292484 for TCB, were also detected in this study, further highlighting the complex genetic regulation of capsule traits. Allelic effect analysis further validated the functional role of key allelic variants at Chr2_15649330 and Chr8_31466064, demonstrating significant differences in shattering responses among genotypic subgroups. In silico functional enrichment analysis using a candidate gene approach identified 68 homologous genes associated with pod shattering in Brassica napus, of which FLZ3, RZF1, MKK5, and COR27 showed distinct expression patterns that correlated with shattering susceptibility during pod development. These results provide new insights into the genetic regulation of capsule shattering, providing valuable targets for marker-assisted selection and development of sesame cultivars with enhanced resistance to shattering.