Table_8_Transcriptome and Small RNA Sequencing Reveal the Mechanisms Regulating Harvest Index in Brassica napus.XLSX

Harvest index (HI), the ratio of harvested seed weight to total aboveground biomass weight, is an economically critical value reflecting the convergence of complex agronomic traits. HI values in rapeseed (Brassica napus) remain much lower than in other major crops, and the underlying regulatory network is largely unknown. In this study, we performed mRNA and small RNA sequencing to reveal the mechanisms shaping HI in B. napus during the seed-filling stage. A total of 8,410 differentially expressed genes (DEGs) between high-HI and low-HI accessions in four tissues (silique pericarp, seed, leaves, and stem) were identified. Combining with co-expression network, 72 gene modules were identified, and a key gene BnaSTY46 was found to participate in retarded establishment of photosynthetic capacity to influence HI. Further research found that the genes involved in circadian rhythms and response to stimulus may play important roles in HI and that their transcript levels were modulated by differentially expressed microRNAs (DEMs), and we identified 903 microRNAs (miRNAs), including 46 known miRNAs and 857 novel miRNAs. Furthermore, transporter activity-related genes were critical to enhancing HI in good cultivation environments. Of 903 miRNAs, we found that the bna-miR396–Bna.A06SRp34a/Bna.A01EMB3119 pair may control the seed development and the accumulation of storage compounds, thus contributing to higher HI. Our findings uncovered the underlying complex regulatory network behind HI and offer potential approaches to rapeseed improvement.

收获指数（HI），即收获种子重量与总地上生物量重量的比率，是一个经济上至关重要的数值，反映了复杂农艺性状的趋同。在油菜（Brassica napus）中，HI值远低于其他主要作物，其背后的调控网络亦鲜为人知。本研究通过对油菜种子充实阶段进行mRNA和小RNA测序，揭示了塑造B. napus HI的机制。在四个组织（角果果皮、种子、叶片和茎）中，共鉴定出8,410个差异表达基因（DEGs），这些基因在高HI和低HI品种之间存在差异。结合共表达网络，我们鉴定出72个基因模块，并发现关键基因BnaSTY46参与光合能力延迟建立，从而影响HI。进一步研究显示，参与昼夜节律和应激反应的基因可能在HI中发挥重要作用，并且其转录水平受到差异表达微小RNA（DEMs）的调控。我们鉴定出903个微小RNA（miRNAs），包括46个已知miRNAs和857个新型miRNAs。此外，与转运活性相关的基因对于在良好栽培环境中提高HI至关重要。在903个miRNAs中，我们发现bna-miR396–Bna.A06SRp34a/Bna.A01EMB3119对可能调控种子发育和储存物质的积累，从而有助于提高HI。我们的发现揭示了HI背后的复杂调控网络，并为油菜改良提供了潜在的方法。