title: An integrated RNA-Seq and network study reveals a complex regulation process of rice embryo during seed germination.
abstract: Seed germination is a crucial stage for plant development and agricultural production. To investigate its complex regulation process, the RNA-Seq study of rice embryo was conducted at three time points of 0, 12 and 48 h post imbibition (HPI). Dynamic transcriptional alterations were observed, especially in the early stage (0-12 HPI). Seed related genes, especially those encoding desiccation inducible proteins and storage reserves in embryo, decreased drastically after imbibition. The expression profiles of phytohormone related genes indicated distinct roles of abscisic acid (ABA), gibberellin (GA) and brassinosteroid (BR) in germination. Moreover, network analysis revealed the importance of protein phosphorylation in phytohormone interactions. Network and gene ontology (GO) analyses suggested that transcription factors (TFs) played a regulatory role in functional transitions during germination, and the enriched TF families at 0 HPI implied a regulation of epigenetic modification in dry seeds. In addition, 35 germination-specific TF genes in embryo were identified and seven genes were verified by qRT-PCR. Besides, enriched TF binding sites (TFBSs) supported physiological changes in germination. Overall, this study expands our comprehensive knowledge of multiple regulation factors underlying rice seed germination.
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Ting
authors.initials: T
authors.lastname: Wei
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Zilong
authors.initials: Z
authors.lastname: He
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: XinYu
authors.initials: X
authors.lastname: Tan
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Xue
authors.initials: X
authors.lastname: Liu
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Yuan
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: luoyf@big.ac.cn.
authors.forename: Yingfeng
authors.initials: Y
authors.lastname: Luo
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: husn@big.ac.cn.
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
mesh_terms: D000040:Abscisic Acid / Q000378:metabolism; D060406:Brassinosteroids / Q000378:metabolism; D004058:Diffusion; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D018525:Germination / Q000235:genetics*; D005875:Gibberellins / Q000378:metabolism; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000196:embryology / Q000235:genetics* / Q000378:metabolism; D010766:Phosphorylation; D010937:Plant Growth Regulators / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*; D012639:Seeds / Q000196:embryology / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics; D014158:Transcription, Genetic; D014867:Water / Q000378:metabolism; D017155:Wettability
chemical_list: D060406:Brassinosteroids; D005875:Gibberellins; D010937:Plant Growth Regulators; D010940:Plant Proteins; D018749:RNA, Plant; D014157:Transcription Factors; D014867:Water; D000040:Abscisic Acid
keywords: Network; Phytohormone; RNA-Seq; Rice; Seed germination; Transcription factor (TF)