Summary: Silique number is the most important component of yield in rapeseed (Brassica napus L.). To dissect the mechanism underlying the natural variation of silique number in rapeseed germplasm, a series of studies were performed. A panel of 331 core lines was employed to genome‐wide association study (GWAS), and 27 loci (including 20 novel loci) were identified. The silique number difference between the more‐ and fewer‐silique lines can be attributed to the accumulative differences in flower number and silique setting rate. Each of them accounted for 75.2% and 24.8%, respectively. The silique number was highly associated with the total photosynthesis and biomass. Microscopic analysis showed that the difference between extremely more‐ and fewer‐silique lines normally occurred at the amount of flower bud but not morphology. Transcriptome analysis of shoot apical meristem (SAM) suggested that most of enriched groups were associated with the auxin biosynthesis/metabolism, vegetative growth and nutrition/energy accumulation. By integrating GWAS and RNA‐seq results, six promising candidate genes were identified, and some of them were related to biomass accumulation. In conclusion, the natural variation of silique number is largely affected by the biomass and nutrition accumulation, which essentially reflects the positive regulatory relationship between the source and sink. Our study provides a comprehensive and systematic explanation for natural variation of silique number in rapeseed, which provides a foundation for its improvement.

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.

Currently, the research on earliness traits of rapeseed mainly focused on flowering time. Although there was a significant positive correlation between the flowering period and the growth period, it was not completely consistent. There are few reports on the genetic studies and QTL mapping of traits related to rapeseed growth and development after flowering. We carried out phenotypic survey (flowering time, flowering period duration, silique period duration etc.) and QTL mapping with the DH population constructed by ‘Huaqianzao’ and ‘Global’ as material. A total of 30 QTL loci for earliness traits were detected. Among them, 12, 5, 4 and 9 QTL loci were detected in the flowering time, flowering period duration, silique period duration and full growth period, respectively, explaining 5.8%–22.4% phenotypic variance. The 2, 4, and 1 QTL confidence intervals of full growth period were found overlap in part or in whole with flowering time, flowering period duration and silique period duration respectively. The 29 candidate genes were screened, which affected the earliness traits by regulating flowering or silique development in rapeseed growth and development processes. Therefore, in the study of earliness traits, we could consider flowering time and silique development process at the same time, which not only helps to advance the maturity period, but also reduces the adverse effects of early flowering.