Division of Plant and Crop Sciences, School of Biosciences and Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, United Kingdom.
Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9709-14. doi: 10.1073/pnas.1100958108. Epub 2011 May 18.
Seed germination is a complex trait of key ecological and agronomic significance. Few genetic factors regulating germination have been identified, and the means by which their concerted action controls this developmental process remains largely unknown. Using publicly available gene expression data from Arabidopsis thaliana, we generated a condition-dependent network model of global transcriptional interactions (SeedNet) that shows evidence of evolutionary conservation in flowering plants. The topology of the SeedNet graph reflects the biological process, including two state-dependent sets of interactions associated with dormancy or germination. SeedNet highlights interactions between known regulators of this process and predicts the germination-associated function of uncharacterized hub nodes connected to them with 50% accuracy. An intermediate transition region between the dormancy and germination subdomains is enriched with genes involved in cellular phase transitions. The phase transition regulators SERRATE and EARLY FLOWERING IN SHORT DAYS from this region affect seed germination, indicating that conserved mechanisms control transitions in cell identity in plants. The SeedNet dormancy region is strongly associated with vegetative abiotic stress response genes. These data suggest that seed dormancy, an adaptive trait that arose evolutionarily late, evolved by coopting existing genetic pathways regulating cellular phase transition and abiotic stress. SeedNet is available as a community resource (http://vseed.nottingham.ac.uk) to aid dissection of this complex trait and gene function in diverse processes.
种子萌发是一个具有关键生态和农艺意义的复杂特征。尽管已经鉴定出少数调节萌发的遗传因素，但它们协同作用控制这一发育过程的方式在很大程度上仍是未知的。我们利用拟南芥的公开基因表达数据，生成了一个全局转录相互作用的条件相关网络模型（SeedNet），该模型显示了开花植物中进化保守的证据。SeedNet 图形的拓扑结构反映了生物学过程，包括与休眠或萌发相关的两个状态相关的相互作用集。SeedNet 突出了该过程中已知调节剂之间的相互作用，并预测了与它们连接的未表征的枢纽节点与萌发相关的功能，准确率为 50%。休眠和萌发子域之间的中间过渡区域富含参与细胞阶段转变的基因。来自该区域的细胞过渡调节剂 SERRATE 和 EARLY FLOWERING IN SHORT DAYS 影响种子萌发，表明保守机制控制植物细胞身份的转变。SeedNet 的休眠区域与营养生物胁迫反应基因强烈相关。这些数据表明，种子休眠是一种适应性特征，它是在进化后期出现的，是通过利用调节细胞阶段转变和非生物胁迫的现有遗传途径进化而来的。SeedNet 作为一个社区资源（http://vseed.nottingham.ac.uk）提供，以帮助解析这个复杂特征和不同过程中的基因功能。
