A single nucleotide substitution in BnaC02.LBD6 promoter causes blade shape variation in Brassica napus

Leaf morphology constitutes a key component of the ideotype, and optimal leaf rolling contributes to compact plant architecture. Rapeseed (Brassica napus) is an important oilseed crop; however, the genetic mechanisms underlying leaf shape development remain poorly understood, and corresponding germplasm resources for genetic improvement are limited. In this study, we identified a dominant mutant, INSIDE-ROLLING LEAF1 (IRL1), which exhibits inward leaf rolling due to defective mesophyll cell development. The mutant also displays drooping siliques and a semi-dwarf phenotype, accompanied by a reduction of one to two effective branches. Through map-based cloning and functional complementation assays, we confirmed BnaC02G0201100ZS as the causal gene IRL1. This gene encodes LATERAL ORGAN BOUNDARIES DOMAIN6 (BnaC02.LBD6). The phenotypic alterations in the IRL1 mutant result from elevated expression of BnaC02.LBD6, driven by a single nucleotide substitution within a DNA binding site in its promoter region. Overexpression of BnaC02.LBD6 recapitulated the IRL1 mutant phenotype, confirming its functional role. Haplotype analysis revealed a rare allelic variant in the BnaC02.LBD6 promoter associated with the unique leaf morphology of IRL1. Transcriptomic profiling indicated significant differential expression of genes involved in adaxial–abaxial leaf polarity establishment, secondary metabolic pathways, and hormone signaling networks. Our findings provide novel insights into the genetic regulation of leaf morphogenesis in rapeseed and offer valuable genetic resources for optimizing plant architecture in breeding programs.