Genome-wide association mapping for charcoal rot (Macrophomina phaseolina (Tassi) Goid.) in sesame (Sesamum indicum L.) germplasm

Sesame (Sesamum indicum L.) is a valuable, ancient oilseed crop with high oil content (45-63%), rich antioxidants such as sesamin and sesamol, and significant nutritional value, making it economically important. However, its production is severely threatened by biotic stress factors such as charcoal rot caused by the soil-borne fungus Macrophomina phaseolina. This disease leads to blockage in the vascular tissues, tissue necrosis, protein loss, and yield losses of up to 100%. In this study, M. phaseolina isolates collected from Diyarbakır and Şanlıurfa, Turkey, were characterized using morphological, molecular, and pathogenicity tests. DNA obtained from 100 sesame genotypes was analyzed using genotyping-by-sequencing (GBS) and the phenotypic responses of these genotypes were evaluated using a standard disease rating scale. Out of 100 genotypes, 47 were classified as fully tolerant, 23 as moderately tolerant, 14 as slightly tolerant, 6 as moderately susceptible, 6 as susceptible, and 4 as highly susceptible to charcoal rot. A total of 49, 297 SilicoDArT markers and 19, 568 SNP markers were generated during DArT sequencing and 13,500 SNP markers which are shown high reproducibility were analyzed in the TASSEL program, a significant SNP marker associated with resistance to charcoal root rot was identified on chromosome 4 (position 3292, 100008622; P = 4.87 × 10⁻⁴) and this marker was found to have potential for marker-assisted selection. STRUCTURE and neighbor-joining analyses revealed distinct genetic clustering among genotypes. These findings provide valuable insights for the development of sesame varieties resistant to coal root rot through marker-assisted selection.