Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos

Soybean (Glycine max) seeds are an important source of seed storage compounds, including protein, oil, and sugar used for food, feed, chemical, and biofuel production. We assessed detailed temporal transcriptional and metabolic changes in developing soybean embryos to gain a systems biology view of developmental and metabolic changes and to identify potential targets for metabolic engineering. Two major developmental and metabolic transitions were captured enabling identification of potential metabolic engineering targets specific to seed filling and to desiccation. The first transition involved a switch between different types of metabolism in dividing and elongating cells. The second transition involved the onset of maturation and desiccation tolerance during seed filling and a switch from photoheterotrophic to heterotrophic metabolism. Clustering analyses of metabolite and transcript data revealed clusters of functionally related metabolites and transcripts active in these different developmental and metabolic programs. The gene clusters provide a resource to generate predictions about the associations and interactions of unknown regulators with their targets based on guilt-by-association relationships. The inferred regulators also represent potential targets for future metabolic engineering of relevant pathways and steps in central carbon and nitrogen metabolism in soybean embryos and drought and desiccation tolerance in plants. Overall design: Total mRNA profiles of 10 time course samples of Soybean developing embryos with three replicates per sample were generated by deep sequencing, using Illumina HiSeq 2000

大豆（Glycine max）种子是种子贮藏化合物的重要来源，这类化合物涵盖可应用于食品、饲料、化工及生物燃料生产的蛋白质、油脂与糖类。本研究针对发育进程中的大豆胚开展了精细的时序转录与代谢动态变化分析，以期从系统生物学视角解析其发育与代谢调控规律，并挖掘代谢工程改造的潜在靶点。本实验捕捉到两次关键的发育与代谢转换事件，借此可分别鉴定出与种子填充及脱水耐受相关的特异性代谢工程靶点。第一次转换对应分裂细胞与伸长细胞间的代谢类型切换；第二次转换则启动了种子填充阶段的成熟进程与脱水耐受机制，并伴随从光合异养代谢向异养代谢的转变。对代谢物与转录本数据的聚类分析，揭示了在上述不同发育与代谢程序中发挥功能的代谢物与转录本功能簇。这些基因簇可作为研究资源，基于牵连有罪（guilt-by-association）原则，预测未知调控因子与其靶标间的关联与互作关系。所鉴定出的调控因子，同时可作为未来改造大豆胚中央碳、氮代谢相关通路与步骤，以及提升植物抗旱与脱水耐受能力的潜在靶点。整体实验设计：采用Illumina HiSeq 2000平台开展深度测序，获取了10个时间点的大豆发育胚样本的总mRNA表达谱，每个样本设置3次生物学重复。