Fine mapping and transcriptomic analysis reveal BnaMMS, a novel locus regulating multi-main-stem phenotype via auxin pathway in rapeseed

The multi-main-stem (MMS) trait presents considerable potential for improving plant architecture and increasing yield in rapeseed ( Brassica napus L.). However, the molecular mechanism underlying MMS formation remains poorly understood. In this study, we characterized a dominant MMS material, 1030R. Genetic analysis indicated that the MMS phenotype is controlled by a single dominant gene, designated BnaMMS . Utilizing BSA-seq combined with fine mapping, BnaMMS was localized to a 70 kb physical interval on chromosome A6, representing a novel genetic locus for MMS regulation. This region contains 17 annotated genes. Sequence analysis revealed multiple SNP and Indel variations between the parental lines. Transcriptome profiling further demonstrated that, among these candidates, two genes ( BnaA06G0092000ZS and BnaA06G0092200ZS ) were differentially expressed between near-isogenic lines (NILs) displaying MMS and single-main-stem (SMS) phenotypes. Mechanistic investigations suggested that, with no significant changes observed in the expression of core WUS-CLV pathway genes in our transcriptome data, BnaMMS likely regulates MMS formation by disrupting auxin biosynthesis and distribution. Our work identifies a novel genetic locus controlling MMS and provides valuable genetic resources and a theoretical framework for elucidating the molecular mechanisms of stem development and for breeding high-yielding rapeseed varieties with optimized plant architecture.