Brassica rapa is an important oilseed and vegetable crop species and is the A subgenome donor of two important oilseed Brassica crops, Brassica napus and Brassica juncea. Although seed size (SZ), seed color (SC), and oil content (OC) substantially affect seed yield and quality, the mechanisms regulating these traits in Brassica crops remain unclear. We collected seeds from a pair of B. rapa accessions with significantly different SZ, SC, and OC at seven seed developmental stages (every 7 days from 7 to 49 days after pollination), and identified 28,954 differentially expressed genes (DEGs) from seven pairwise comparisons between accessions at each developmental stage. K-means clustering identified a group of cell cycle-related genes closely connected to variation in SZ of B. rapa. A weighted correlation analysis using the WGCNA package in R revealed two important co-expression modules comprising genes whose expression was positively correlated with SZ increase and negatively correlated with seed yellowness, respectively. Upregulated expression of cell cycle-related genes in one module was important for the G2/M cell cycle transition, and the transcription factor Bra.A05TSO1 seemed to positively stimulate the expression of two CYCB1;2 genes to promote seed development. In the second module, a conserved complex regulated by the transcription factor TT8 appear to determine SC through downregulation of TT8 and its target genes TT3, TT18, and ANR. In the third module, WRI1 and FUS3 were conserved to increase the seed OC, and Bra.A03GRF5 was revealed as a key transcription factor on lipid biosynthesis. Further, upregulation of genes involved in triacylglycerol biosynthesis and storage in the seed oil body may increase OC. We further validated the accuracy of the transcriptome data by quantitative real-time PCR of 15 DEGs. Finally, we used our results to construct detailed models to clarify the regulatory mechanisms underlying variations in SZ, SC, and OC in B. rapa. This study provides insight into the regulatory mechanisms underlying the variations of SZ, SC, and OC in plants based on transcriptome comparison. The findings hold great promise for improving seed yield, quality and OC through genetic engineering of critical genes in future molecular breeding.

中文翻译：

---

破译控制芸苔种子大小、颜色和含油量的转录调控网络。

油菜是一种重要的油料和蔬菜作物物种，是两种重要的油料芸苔属作物——欧洲油菜和芥菜的 A 亚基因组供体。尽管种子大小 (SZ)、种子颜色 (SC) 和含油量 (OC) 显着影响种子产量和质量，但在芸苔属作物中调节这些性状的机制仍不清楚。我们在七个种子发育阶段（授粉后 7 至 49 天每 7 天）从一对具有显着不同 SZ、SC 和 OC 的 rapa 种质中收集种子，并从 7 个成对中鉴定出 28,954 个差异表达基因 (DEG)每个发育阶段的种质之间的比较。K-means 聚类确定了一组与青菜 SZ 变异密切相关的细胞周期相关基因。使用 R 中的 WGCNA 包进行的加权相关分析揭示了两个重要的共表达模块，包括分别与 SZ 增加呈正相关和与种子黄度呈负相关的基因。一个模块中细胞周期相关基因的上调表达对G2/M细胞周期转变很重要，转录因子Bra.A05TSO1似乎正刺激两个CYCB1;2基因的表达以促进种子发育。在第二个模块中，由转录因子 TT8 调节的保守复合物似乎通过下调 TT8 及其靶基因 TT3、TT18 和 ANR 来决定 SC。在第三个模块中，WRI1 和 FUS3 被保留以增加种子 OC，并且 Bra.A03GRF5 被揭示为脂质生物合成的关键转录因子。更远，参与三酰基甘油生物合成和储存在种子油体中的基因的上调可能会增加 OC。我们通过 15 度的实时定量 PCR 进一步验证了转录组数据的准确性。最后，我们使用我们的结果构建了详细的模型，以阐明 B. rapa 中 SZ、SC 和 OC 变化的调控机制。本研究基于转录组比较深入了解植物中 SZ、SC 和 OC 变异的调控机制。这些发现为通过对未来分子育种中的关键基因进行基因工程来提高种子产量、质量和 OC 带来了巨大的希望。最后，我们使用我们的结果构建了详细的模型，以阐明 B. rapa 中 SZ、SC 和 OC 变化的调控机制。本研究基于转录组比较深入了解植物中 SZ、SC 和 OC 变异的调控机制。这些发现为通过对未来分子育种中的关键基因进行基因工程来提高种子产量、质量和 OC 带来了巨大的希望。最后，我们使用我们的结果构建了详细的模型，以阐明 B. rapa 中 SZ、SC 和 OC 变化的调控机制。本研究基于转录组比较深入了解植物中 SZ、SC 和 OC 变异的调控机制。这些发现为通过对未来分子育种中的关键基因进行基因工程来提高种子产量、质量和 OC 带来了巨大的希望。