Leaf angle (LA) is an important trait of plant architecture, and individuals with narrow LA can better capture canopy light under high-density planting, which is beneficial for increasing the overall yield per unit area. To study the genetic basis and molecular regulation mechanism of leaf angle in rapeseed, we carried out a series of experiments. Quantitative trait loci (QTL) mapping was performed using the RIL population, and seven QTLs were identified. Transcriptome analysis showed that the cell wall formation/biogenesis processes and biosynthesis/metabolism of cell wall components were the most enrichment classes. Most differentially expressed genes (DEGs) involved in the synthesis of lignin, xylan, and cellulose showed down-regulated expression in narrow leaf material. Microscopic analysis suggested that the cell size affected by the cell wall in the junction area of the stem and petiole was the main factor in leaf petiole angle (LPA) differences. Combining QTL mapping and RNA sequencing, five promising candidate genes BnaA01G0125600ZS, BnaA01G0135700ZS, BnaA01G0154600ZS, BnaA10G0154200ZS, and BnaC03G0294200ZS were identified in rapeseed, and most of them were involved in cell wall biogenesis and the synthesis/metabolism of cell wall components. The results of QTL, transcriptome analysis, and cytological analysis were highly consistent, collectively revealing that genes related to cell wall function played a crucial role in regulating the LA trait in rapeseed. The study provides further insights into LA traits, and the discovery of new QTLs and candidate genes is highly beneficial for genetic improvement.

Silique number is an important yield trait in rapeseed. Identifying the genetic loci and analyzing the molecular mechanism of this trait are of great significance for increasing rapeseed yield. In this study, we conducted a quantitative trait loci (QTL) analysis for silique number using a recombinant inbred line (RIL) population, and detected seven QTLs for silique number across two environments, explaining 5.97%–9.05% of the phenotypic variation. The transcriptome sequencing analysis of extreme lines with more silique and less silique showed sulfur and glycosyl compounds metabolism is crucial for flower bud differentiation in shoot apical meristem (SAM) of rapeseed. By integrating the QTL mapping results with transcriptome data, we identified four candidate genes involved in regulating silique number, including BnaA06g27290D, BnaA06g27360D, BnaC06g10070D and BnaC06g10100D . The findings not only enhance the understanding of the genetic and molecular basis of silique formation but also provide valuable genetic loci and gene resources for molecular breeding aimed at yield improvement in rapeseed.