US Department of Agriculture, Agriculture Research Service, Midwest Area, Plant Genetics Research at Donald Danforth Plant Sciences Center, 975 N Warson Road, St, Louis, MO 63132, USA.
BMC Plant Biol. 2011 Jun 13;11:105. doi: 10.1186/1471-2229-11-105.
Seed germination is a complex multi-stage developmental process, and mainly accomplished through concerted activities of many gene products and biological pathways that are often subjected to strict developmental regulation. Gibberellins (GA) and abscisic acid (ABA) are two key phytohormones regulating seed germination and seedling growth. However, transcriptional regulatory networks underlying seed germination and its associated biological pathways are largely unknown.
The studies examined transcriptomes of barley representing six distinct and well characterized germination stages and revealed that the transcriptional regulatory program underlying barley germination was composed of early, late, and post-germination phases. Each phase was accompanied with transcriptional up-regulation of distinct biological pathways. Cell wall synthesis and regulatory components including transcription factors, signaling and post-translational modification components were specifically and transiently up-regulated in early germination phase while histone families and many metabolic pathways were up-regulated in late germination phase. Photosynthesis and seed reserve mobilization pathways were up-regulated in post-germination phase. However, stress related pathways and seed storage proteins were suppressed through the entire course of germination. A set of genes were transiently up-regulated within three hours of imbibition, and might play roles in initiating biological pathways involved in seed germination. However, highly abundant transcripts in dry barley and Arabidopsis seeds were significantly conserved. Comparison with transcriptomes of barley aleurone in response to GA and ABA identified three sets of germination responsive genes that were regulated coordinately by GA, antagonistically by ABA, and coordinately by GA but antagonistically by ABA. Major CHO metabolism, cell wall degradation and protein degradation pathways were up-regulated by both GA and seed germination. Those genes and metabolic pathways are likely to be important parts of transcriptional regulatory networks underlying GA and ABA regulation of seed germination and seedling growth.
The studies developed a model depicting transcriptional regulatory programs underlying barley germination and GA and ABA regulation of germination at gene, pathway and systems levels, and established a standard transcriptome reference for further integration with various -omics and biological data to illustrate biological networks underlying seed germination. The studies also generated a great amount of systems biological evidence for previously proposed hypotheses, and developed a number of new hypotheses on transcriptional regulation of seed germination for further experimental validation.
种子萌发是一个复杂的多阶段发育过程，主要通过许多基因产物和生物途径的协同活动来完成，这些生物途径通常受到严格的发育调控。赤霉素（GA）和脱落酸（ABA）是调节种子萌发和幼苗生长的两种关键植物激素。然而，种子萌发及其相关生物途径的转录调控网络在很大程度上尚不清楚。
该研究检测了代表六个不同且特征明确的萌发阶段的大麦转录组，结果表明，大麦萌发的转录调控程序由早期、晚期和萌发后三个阶段组成。每个阶段都伴随着不同生物途径的转录上调。细胞壁合成和调控成分，包括转录因子、信号和翻译后修饰成分，在早期萌发阶段特异性和短暂上调，而组蛋白家族和许多代谢途径在晚期萌发阶段上调。萌发后阶段，光合作用和种子贮藏物质动员途径上调。然而，整个萌发过程中与应激相关的途径和种子贮藏蛋白受到抑制。一组基因在吸水后三个小时内短暂上调，可能在启动种子萌发涉及的生物途径中发挥作用。然而，在干燥的大麦和拟南芥种子中高度丰富的转录本显著保守。与大麦糊粉层对 GA 和 ABA 响应的转录组比较，鉴定出三组萌发响应基因，这些基因受 GA 协同调控，受 ABA 拮抗调控，受 GA 协同调控但受 ABA 拮抗调控。主要的 CHO 代谢、细胞壁降解和蛋白质降解途径受 GA 和种子萌发的上调。这些基因和代谢途径可能是 GA 和 ABA 调节种子萌发和幼苗生长的转录调控网络的重要组成部分。
该研究在基因、途径和系统水平上构建了大麦萌发和 GA、ABA 调节萌发的转录调控程序模型，并建立了一个标准的转录组参考，以进一步与各种组学和生物数据整合，以说明种子萌发的生物网络。该研究还为先前提出的假说提供了大量系统生物学证据，并为进一步的实验验证提出了一些关于种子萌发转录调控的新假说。
