title: Transcriptome and Degradome Sequencing Reveals Dormancy Mechanisms of Cunninghamia lanceolata Seeds.
abstract: Seeds with physiological dormancy usually experience primary and secondary dormancy in the nature; however, little is known about the differential regulation of primary and secondary dormancy. We combined multiple approaches to investigate cytological changes, hormonal levels, and gene expression dynamics in Cunninghamia lanceolata seeds during primary dormancy release and secondary dormancy induction. Light microscopy and transmission electron microscopy revealed that protein bodies in the embryo cells coalesced during primary dormancy release and then separated during secondary dormancy induction. Transcriptomic profiling demonstrated that expression of genes negatively regulating gibberellic acid (GA) sensitivity reduced specifically during primary dormancy release, whereas the expression of genes positively regulating abscisic acid (ABA) biosynthesis increased during secondary dormancy induction. Parallel analysis of RNA ends revealed uncapped transcripts for ∼55% of all unigenes. A negative correlation between fold changes in expression levels of uncapped versus capped mRNAs was observed during primary dormancy release. However, this correlation was loose during secondary dormancy induction. Our analyses suggest that the reversible changes in cytology and gene expression during dormancy release and induction are related to ABA/GA balance. Moreover, mRNA degradation functions as a critical posttranscriptional regulator during primary dormancy release. These findings provide a mechanistic framework for understanding physiological dormancy in seeds.
authors.affiliation: Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.).|Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.).|Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and.|Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.).
authors.forename: Dechang
authors.identifier: 0000-0002-0397-4316
authors.initials: D
authors.lastname: Cao
authors.affiliation: Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.).|Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.).|Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and.|Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.).
authors.forename: Huimin
authors.initials: H
authors.lastname: Xu
authors.affiliation: Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.).|Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.).|Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and.|Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.).
authors.forename: Yuanyuan
authors.identifier: 0000-0002-9955-2467
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.).|Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.).|Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and.|Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.).
authors.forename: Xin
authors.identifier: 0000-0002-6075-2429
authors.initials: X
authors.lastname: Deng
authors.affiliation: Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.).|Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.).|Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and.|Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.).
authors.forename: Yongxiu
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.).|Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.).|Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and.|Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.).
authors.forename: Wim J J
authors.initials: WJ
authors.lastname: Soppe
authors.affiliation: Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.); linjinxing@bjfu.edu.cn.|Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.); linjinxing@bjfu.edu.cn.|Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and linjinxing@bjfu.edu.cn.|Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.) linjinxing@bjfu.edu.cn.
authors.forename: Jinxing
authors.initials: J
authors.lastname: Lin
mesh_terms: D000040:Abscisic Acid / Q000494:pharmacology; D002473:Cell Wall / Q000187:drug effects / Q000378:metabolism; D032486:Cunninghamia / Q000166:cytology / Q000187:drug effects / Q000235:genetics* / Q000648:ultrastructure; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant; D018525:Germination / Q000187:drug effects / Q000235:genetics; D005875:Gibberellins / Q000494:pharmacology; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D058977:Molecular Sequence Annotation; D057445:Plant Dormancy / Q000187:drug effects / Q000235:genetics*; D010937:Plant Growth Regulators / Q000494:pharmacology; D020871:RNA Stability / Q000187:drug effects / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D012639:Seeds / Q000166:cytology / Q000187:drug effects / Q000235:genetics* / Q000648:ultrastructure; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000187:drug effects / Q000235:genetics*
chemical_list: D005875:Gibberellins; D035683:MicroRNAs; D010937:Plant Growth Regulators; D012333:RNA, Messenger; D000040:Abscisic Acid; C007842:gibberellic acid