Integrative QTL mapping and transcriptomic profiling uncover molecular mechanisms underlying lodging resistance in Brassica napus

Abstract Lodging remains a significant agronomic challenge that limiting the yield potential of Brassica napus globally, making the elucidation of its molecular basis critical for breeding new germplasm. Lignocellulose components (including lignin, cellulose, and hemicellulose) play an essential role in the mechanical strength of the stem, and they are regarded as the key determinants of lodging. In a doubled haploid (DH) population, 61 consensus quantitative trait loci (QTLs) associated with the lignocellulose content in the stem were identified through QTL analysis. Integrating QTL mapping with transcriptomic data revealed 1035 candidate genes potentially involved in stem lignocellulose biosynthesis, of which 52 high-confidence candidates were selected. Among them, BnaC01.MYB85, BnaA04.WRKY12, and BnaC03.ASMT exhibited stem-specific expression. A stem-specific lignocellulose biosynthetic pathway characterized by the coordinated expression of these high-confidence genes was delineated. Haplotype analysis in a natural population showed that BnaC03.ASMT segregated into two major haplotypes, with hap01 exhibiting a significantly higher hemicellulose content (HC) than hap02. These findings provide novel insights into the genetic regulation of lodging resistance and offer a valuable foundation for breeding B. napus cultivars with higher stem strength and lodging tolerance.