Three-year QTL mapping discovers a novel locus and candidate gene BnC09.LMI1 regulating the leaf complexity of Brassica napus

Leaf shape diversity in Brassica napus provides critical insights into the molecular basis of leaf complexity and its evolutionary implications in rapeseed. Two predominant leaf morphotypes were characterized in B. napus: serrated-margin and deeply lobed leaves. Serrated leaves were further subdivided based on the presence or absence of petiolar lobes, establishing a novel phenotypic classification system. Through QTL mapping of the APL01/Holly recombinant inbred line population (n = 2,755 markers) across three environments, we identified 10 consensus loci associated with non-lobed petioles. A major-effect QTL (qNLP.C9-3) spanning a 951-kb interval on chromosome C9 accounted for 9.43–21.66% of phenotypic variation in the APL01 genetic background. Within this interval, 148 annotated genes were identified, among which BnC09.LMI1 was prioritized as a candidate gene regulating petiole lobe formation and leaf complexity based on phylogenetic analysis and differential expression. These results advance our understanding of leaf morphological diversity in B. napus and provide a molecular framework for dissecting the genetic architecture of leaf complexity.