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Abstract：
Soybean (Glycine max) is an important crop providing oil and protein for both human and animal consumption. Knowing which biological processes take place in specific tissues in a temporal manner will enable directed breeding or synthetic approaches to improve seed quantity and quality. We analyzed a genome-wide transcriptome dataset from embryo, endosperm, endothelium, epidermis, hilum, outer and inner integument and suspensor at the global, heart and cotyledon stages of soybean seed development. The tissue specificity of gene expression was greater than stage specificity, and only three genes were differentially expressed in all seed tissues. Tissues had both unique and shared enriched functional categories of tissue-specifically expressed genes associated with them. Strong spatio-temporal correlation in gene expression was identified using weighted gene co-expression network analysis, with the most co-expression occurring in one seed tissue. Transcription factors with distinct spatiotemporal gene expression programs in each seed tissue were identified as candidate regulators of expression within those tissues. Gene ontology (GO) enrichment of orthogroup clusters revealed the conserved functions and unique roles of orthogroups with similar and contrasting expression patterns in transcript abundance between soybean and Arabidopsis during embryo proper and endosperm development. Key regulators in each seed tissue and hub genes connecting those networks were characterized by constructing gene regulatory networks. Our findings provide an important resource for describing the structure and function of individual soybean seed compartments during early seed development.
摘要：
大豆(Glycinemax)是为人类和动物消费提供油和蛋白质的重要作物。知道哪些生物过程以时间方式在特定组织中发生将能够实现定向育种或合成方法以改善种子数量和质量。我们分析了来自胚胎的全基因组转录组数据集，胚乳,内皮,表皮,宫门,全球的外貌和内貌，大豆种子发育的心脏和子叶阶段。基因表达的组织特异性大于阶段特异性，只有三个基因在所有种子组织中差异表达。组织具有与其相关的组织特异性表达基因的独特和共有的丰富功能类别。使用加权基因共表达网络分析鉴定了基因表达的强时空相关性，最多的共表达发生在一个种子组织中。在每个种子组织中具有不同时空基因表达程序的转录因子被鉴定为这些组织中表达的候选调节因子。正统簇的基因本体论（GO）富集揭示了正统簇的保守功能和独特作用，在胚胎和胚乳发育过程中，大豆和拟南芥之间的转录物丰度具有相似和对比的表达模式。通过构建基因调控网络来表征每个种子组织和连接这些网络的枢纽基因中的关键调控因子。我们的发现为描述早期种子发育过程中单个大豆种子区室的结构和功能提供了重要资源。
