Identification of the major QTL related to stipe length based on QTL mapping and BSA ‐Seq in oyster mushroom

Abstract BACKGROUND The length of the stipe is a key commercial trait in oyster mushrooms, but the genes and molecular mechanisms regulating its development remain unclear. This study aimed to identify genes linked to stipe length in oyster mushrooms. RESULTS An F 2 segregating population associated with stipe length was developed and used for phenotypic analysis. The results showed that stipe length followed a typical normal distribution, indicating that this trait is polygenic in nature. Quantitative trait locus (QTL) mapping and bulked segregant analysis (BSA‐Seq) were used to identify genomic regions linked to stipe length. A high‐density genetic map with 17 604 SNP (single‐nucleotide polymorphism) markers was constructed for QTL mapping. A significant QTL associated with stipe length was identified on linkage group 7, located on contig00004 (1 771 973 to 2 139 983 bp). This region contains 122 putative candidate genes. In the BSA‐Seq analysis, three significant candidate regions were identified on contig00004, contig00016, and contig00018, collectively containing 26 potential candidate genes. Genes identified through BSA‐Seq and QTL mapping are enriched in the cell wall biosynthesis pathway, which plays a key role in stipe elongation. Integrating QTL mapping with BSA‐Seq results, a refined candidate region was pinpointed on contig00004 (2 049 583 to 2 063 927 bp). This region contains four candidate genes, which potentially regulating stipe length in oyster mushrooms. CONCLUSION The combined QTL mapping and BSA‐Seq approach proved effective for identifying genetic regions associated with stipe length. The candidate genes identified in this study provide valuable insights for future research and applications in stipe‐length‐related breeding programs for oyster mushrooms. © 2026 Society of Chemical Industry.