RNA-seq profiling the transcriptome of secondary seed dormancy in canola (Brassica napus L.)

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• 作者：Fuxia Liu ; Xiangqiang Zhao ; Lihua Zhang ; Tang Tang…
• 关键词：Brassica napus ; Secondary dormancy ; Seed transcriptome ; RNA ; seq
• 刊名：Chinese Science Bulletin
• 出版年：2014
• 出版时间：November 2014
• 年：2014
• 卷：59
• 期：32
• 页码：4341-4351
• 全文大小：453 KB
• 参考文献：1. Adler LS, Wickler K, Wyndham PS et al (1993) Potential for persistence of genes escaped from canola: germination cues in crop, wild, and crop–wild hybrid / Brassica rapa. Funct Ecol 7:736-45 CrossRef
  2. Pessel FD, Lecomte J, Emeriau V et al (2001) Persistence of oilseed rape ( / Brassica napus L.) outside of cultivated fields. Theor Appl Genet 102:841-46 CrossRef
  3. Chadoeuf R, Darmency H, Maillet J et al (1998) Survival of buried seeds of interspecific hybrids between oilseed rape, hoary mustard and wild radish. Field Crops Res 58:197-04 CrossRef
  4. Beckie HJ, Harker KN, Hall LM et al (2006) A decade of herbicide-resistant crops in Canada. Can J Plant Sci 86:1243-264 CrossRef
  5. Finch-Savage WE, Leubner-Metzger G (2006) Seed dormancy and the control of germination. New Phytol 171:501-23 CrossRef
  6. Amen RD (1968) A model of seed dormancy. Bot Rev 34:1-1 CrossRef
  7. Momoh EJ?J, Zhou WJ, Kristiansson B (2002) Variation in the development of secondary dormancy in oilseed rape genotypes under conditions of stress. Weed Res 42:446-55 CrossRef
  8. Gulden RH, Shirtliffe SJ, Thomas AG (2003) Secondary seed dormancy prolongs persistence of volunteer canola ( / Brassica napus) in western Canada. Weed Sci 51:904-13 CrossRef
  9. Finkelstein R, Reeves W, Ariizumi T et al (2008) Molecular aspects of seed dormancy. Annu Rev Plant Biol 59:387-15 CrossRef
  10. Gruber S, Emrich K, Claupein W (2009) Classification of canola ( / Brassica napus) winter cultivars by secondary dormancy. Can J Plant Sci 89:613-19 CrossRef
  11. Webera EA, Gruber S, Stockmann F et al (2013) Can low-dormancy oilseed rape ( / Brassica napus) genotypes be used to minimize volunteer problems? Field Crops Res 147:32-9 CrossRef
  12. Holdsworth MJ, Finch-Savage WE, Grappin P et al (2008) Post-genomics dissection of seed dormancy and germination. Trends Plant Sci 13:7-3 CrossRef
  13. Fei H, Tsang E, Cutler AJ (2007) Gene expression during seed maturation in / Brassica napus in relation to the induction of secondary dormancy. Genomics 89:419-28 CrossRef
  14. Fei H, Ferhatoglu Y, Tsang E et al (2009) Metabolic and hormonal processes associated with the induction of secondary dormancy in / Brassica napus seeds. Botany 87:585-96 CrossRef
  15. Parkin IA, Gulden SM, Sharpe AG et al (2005) Segmental structure of the / Brassica napus genome based on comparative analysis with / Arabidopsis thaliana. Genetics 171:765-81 CrossRef
  16. Harper AL, Trick M, Higgins J et al (2012) Associative transcriptomics of traits in the polyploid crop species / Brassica napus. Nat Biotech 30:798-02 CrossRef
  17. Pekrun C, Lutman PJW, Baeumer K (1997) Induction of secondary dormancy in rape seeds ( / Brassica napus L.) by prolonged imbibition under conditions of water stress or oxygen deficiency in darkness. Euro J Agron 6:245-55 CrossRef
  18. Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotech 29:644-52 CrossRef
  19. Thimm O, Blasing O, Gibon Y et al (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37:914-39 CrossRef
  20. Maere S, Heymans K, Kuiper M (2005) BiNGO: a cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21:3448-449 CrossRef
  21. Mortazavi A, Williams BA, McCue K et al (2008) Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods 5:621-28 CrossRef
  22. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357-59 CrossRef
  23. Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7:986-95
  24. Wang X, Wang H, Wang J et al (2011) The genome of the mesopolyploid crop species / Brassica rapa. Nat Genet 43:1035-039 CrossRef
  25. Dave A, Hernandez ML, He Z et al (2011) 12-oxo-phytodienoic acid accumulation during seed development represses seed germination in / Arabidopsis. Plant Cell 23:583-99 CrossRef
  26. Nambara E, Marion-Poll A (2005) Abscisic acid biosynthesis and catabolism. Annu Rev Plant Biol 56:165-85 CrossRef
  27. Yamaguchi S (2008) Gibberellin metabolism and its regulation. Annu Rev Plant Biol 59:225-51 CrossRef
  28. Weiner JJ, Peterson FC, Volkman BF et al (2010) Structural and functional insights into core ABA signaling. Curr Opin Plant Biol 13:495-02 CrossRef
  29. Daviere JM, Achard P (2013) Gibberellin signaling in plants. Development 140:1147-151 CrossRef
  30. Chiu RS, Nahal H, Provart NJ et al (2012) The role of the / Arabidopsis FUSCA3 transcription factor during inhibition of seed germination at high temperature. BMC Plant Biol 12:15 CrossRef
  31. Penfield S, Josse EM, Halliday KJ (2010) A role for an alternative splice variant of / PIF6 in the control of / Arabidopsis primary seed dormancy. Plant Mol Biol 73:89-5 CrossRef
  32. Pinfield-Wells H, Rylott EL, Gilday AD et al (2005) Sucrose rescues seedling establishment but not germination of / Arabidopsis mutants disrupted in peroxisomal fatty acid catabolism. Plant J 43:861-72 CrossRef
  33. Pracharoenwattana I, Cornah JE, Smith SM (2005) / Arabidopsis peroxisomal citrate synthase is required for fatty acid respiration and seed germination. Plant Cell 17:2037-048 CrossRef
  34. Cadman CS, Toorop PE, Hilhorst HW et al (2006) Gene expression profiles of / Arabidopsis Cvi seeds during dormancy cycling indicate a common underlying dormancy control mechanism. Plant J 46:805-22 CrossRef
  35. Carrera E, Holman T, Medhurst A et al (2007) Gene expression profiling reveals defined functions of the ATP-binding cassette transporter COMATOSE late in phase II of germination. Plant Physiol 143:1669-679 CrossRef
  36. Barrero JM, Millar AA, Griffiths J et al (2010) Gene expression profiling identifies two regulatory genes controlling dormancy and ABA sensitivity in / Arabidopsis seeds. Plant J 61:611-22 CrossRef
  37. Monke G, Seifert M, Keilwagen J et al (2012) Toward the identification and regulation of the / Arabidopsis thaliana ABI3 regulon. Nucleic Acids Res 40:8240-254 CrossRef
  38. Nishimura N, Kitahata N, Seki M et al (2005) Analysis of ABA hypersensitive germination2 revealed the pivotal functions of PARN in stress response in / Arabidopsis. Plant J 44:972-84 CrossRef
  39. Liu Y, Geyer R, van Zanten M et al (2011) Identification of the / Arabidopsis / REDUCED DORMANCY 2 gene uncovers a role for the polymerase associated factor I complex in seed dormancy. PLoS One 6:e22241 CrossRef
  40. Carrera E, Holman T, Medhurst A et al (2008) Seed after-ripening is a discrete developmental pathway associated with specific gene networks in / Arabidopsis. Plant J 53:214-24 CrossRef
  41. Okamoto M, Tatematsu K, Matsui A et al (2010) Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of / Arabidopsis using tiling arrays. Plant J 62:39-1 CrossRef
  42. Footitt S, Marquez J, Schmuths H et al (2006) Analysis of the role of COMATOSE and peroxisomal beta-oxidation in the determination of germination potential in / Arabidopsis. J Exp Bot 57:2805-814 CrossRef
  
• 作者单位：Fuxia Liu (1)
  Xiangqiang Zhao (2)
  Lihua Zhang (4)
  Tang Tang (1)
  Changming Lu (3)
  Guiming Chen (1)
  Xinlong Wang (1) (2)
  Cuiping Bu (1)
  Xiangxiang Zhao (1)
  
  1. Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, Huaian, 223300, China
  2. School of Life Sciences, Nantong University, Nantong, 226019, China
  4. Plant science department, South Dakota State University, Brookings, SD 57006, USA
  3. Genetic Engineering and GMO Biosafety Lab of Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
  
• ISSN：1861-9541

文摘

Secondary seed dormancy (SSD) is responsible for volunteer plants in canola fields, which causes a series of problems in canola production and serves as an important trait for the environmental safety assessment of transgenic canola. A canola cultivar with strong SSD was used to establish insight into seed transcriptomes in its secondarily dormant seeds and control seeds without dormancy by RNA-seq analysis, aiming to determine the molecular ecological characterizations of SSD. A dataset (more than 4?Gb) of valid sequences was obtained from each sample, which was combined to carry out the de novo assembling. The assembled sequences consisted of 314,261 fragments with length?>?100?bp, including 29,740 long transcripts of length?≥?00?bp. Functional annotation indicated that 1,641 long transcripts could be categorized into 24 cluster of orthologous groups of proteins (COGs) and 16,515 transcripts were linked to 2,648 gene ontology (GO) terms. There were 452 long transcripts with significantly different expression identified by a threshold of?>?2-fold expression change (P?Arabidopsis genes. The plant hormones abscisic acid and gibberellins were known as the pivotal regulators of seed dormancy and germination. Although genes responsible for either biosynthesis or signaling of each hormone could be widely verified from the SSD transcriptome, theirs expression evidences failed to correlate with the induction of SSD. Based on the enriched terms of gene ontology and KEGG orthology, as well as the expression models of candidate genes of SSD, we proposed that fatty acid metabolism might implicate in SSD in canola. The information reported here may play a significant role in further understanding of environmental safety assessment of SSD in transgenic canola.