Transcriptome profiling reveals gene regulatory network governing seed size in Brassica napus

Seed size is a critical trait influencing yield and quality in oilseed crops such as Brassica napus. Despite their economic importance, the genetic and molecular mechanisms regulating seed size remain unclear, particularly in polyploid species, such as B. napus. To deepen our understanding of seed size regulation, we performed a comprehensive transcriptomic analysis across four developmental stages (heart, torpedo, green, and mature) and three distinct seed organs: the seed coat, embryo, and endosperm. Differential expression analysis between B. napus var. Zhongshuang (ZS11) and B. napus cv. Ragged Jack (RJ) was performed to uncover regulatory networks involved in seed size control. Our results uncovered dynamic gene regulatory networks (GRNs) and pinpointed key regulators, including well-established factors like ABI5 and BRI1, as well as novel candidate genes such as KNAT5, ARF11, SUS2, UGT72B1, UGT89A2, and SBT1.7. The present research provides an understanding of the regulatory networks governing seed size in B. napus. These findings not only enhance our knowledge of seed biology but also offer valuable resources for future breeding strategies aimed at optimizing seed size and yield in polyploid oilseed crops.