甘蓝型油菜矮化突变体的茎秆发育转录组分析
|
摘要
甘蓝型油菜矮化突变体"NDF-1"是从高秆油菜"3529"理化诱变群体中分离的矮化突变体,它的株高只有高秆亲本的1/3,是一个优良的甘蓝型油菜矮化资源.本文应用RNA-Seq测序技术分析了"NDF-1"茎开始伸长的抽薹期和花期转录组,为深入了解油菜茎秆发育机理提供基因组层面的参考.抽薹期和花期的测序数据通过筛选得到了4.55亿条质量合格的clean reads.经过对高质量序列的组装注释,筛选得到"NDF-1"和"3529"间的2147条差异表达基因(DEGs).选择其中的20个差异表达基因进行了荧光定量PCR验证.通过GO和KEGG分析,发现"NDF-1"的矮化与赤霉素、生长素和油菜素内酯相关,细胞伸长异常和细胞壁的不正常形成也影响"NDF-1"的茎秆发育.从差异基因中筛选出与植物矮化性状相关的基因,为利用矮化基因改善性状和矮化机理的研究和提供了更多信息.
"NDF-1"is a Brassica napus L.dwarf mutant,which was derived from physical and chemical mutagenesis of a high stemmed line "3529",possesses a stable dwarf phenotype of approximately one third the height of high stalk parent"3529".It is an excellent resource dwarf Brassica napus L.RNASeq based transcriptome analysis on stem elongation of the dwarf mutant from Bolting Stage(BS)and Florescence Stage(FS),which was conducted to provide a reference for the genome level in order to understand the mechanism of rapeseed stem development.A total of 455 million clean reads were obtained from two different stages include Bolting Stage(BS)and Florescence Stage(FS).Then 2,147 differentially expressed genes(DEGs)were found which detected between"NDF-1"and"3529"after assembled them.Furthermore,twenty differentially expressed genes were selected for RT-PCR validation.With the GO and KEGG pathway analysis,"NDF-1"stems elongation most regulated by the gibberellin、auxin and brassinosteroids,cell wall formation or cells Elongation is not normal but also play an important role in"NDF-1"dwarf.Screening genes associated with plant dwarfing traits from DEGs,which provide a reference for further use of these genes on traits improvement and dwarfing mechanism research.
"NDF-1"is a Brassica napus L.dwarf mutant,which was derived from physical and chemical mutagenesis of a high stemmed line "3529",possesses a stable dwarf phenotype of approximately one third the height of high stalk parent"3529".It is an excellent resource dwarf Brassica napus L.RNASeq based transcriptome analysis on stem elongation of the dwarf mutant from Bolting Stage(BS)and Florescence Stage(FS),which was conducted to provide a reference for the genome level in order to understand the mechanism of rapeseed stem development.A total of 455 million clean reads were obtained from two different stages include Bolting Stage(BS)and Florescence Stage(FS).Then 2,147 differentially expressed genes(DEGs)were found which detected between"NDF-1"and"3529"after assembled them.Furthermore,twenty differentially expressed genes were selected for RT-PCR validation.With the GO and KEGG pathway analysis,"NDF-1"stems elongation most regulated by the gibberellin、auxin and brassinosteroids,cell wall formation or cells Elongation is not normal but also play an important role in"NDF-1"dwarf.Screening genes associated with plant dwarfing traits from DEGs,which provide a reference for further use of these genes on traits improvement and dwarfing mechanism research.
引文
[1]Kim S G,Lee S,Kim Y S,et al.Activation tagging of an Arabidopsis SHI-RELATED SE-QUENCE gene produces abnormal anther dehiscence and floral development[J].Plant Mol Biol,2010,74:337.
[2]Liu S S,Chen J,Li S C,et al.Comparative transcriptome analysis of genes involved in GA-GID1-DELLA regulatory module in symbiotic and asymbiotic seed germination of anoectochilus roxburghii(Wall.)Lindl.(Orchidaceae)[J].Int J Mol Sci,2015,16:30190.
[3]Wang R,Liu M,Yuan M,et al.The brassinosteroidactivated BRI1receptor kinase is switched off by dephosphorylation mediated by cytoplasm-localized PP2AB'subunits[J].Mol Plant,2015,9:148.
[4]Chalhoub B,Denoeud F,Liu S,et al.Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome[J].Science,2014,345:950.
[5]Zhang J,Ren A,Chen H,et al.Transcriptome analysis and its application in identifying genes associated with fruiting body development in Basidiomycete Hypsizygus marmoreus[J].PloS One,2015,10:e0123025.
[6]吴燕,颜朗,李雪丹,等.甘薯耐旱和耐盐基因的挖掘和表达分析[J].四川大学学报:自然科学版,2016,53:5.
[7]Freiman Z E,Doron-Faigenboim A,Dasmohapatra R,et al.High-throughput sequencing analysis of common fig(Ficus carica L.)transcriptome during fruit ripening[J].Tree Genet Genomes,2014,10:923.
[8]Li X,Nair A,Wang S,et al.Quality control of RNA-seq experiments[J].Bioinformatics,2015,28:2184.
[9]Benjamini Y,Hochberg Y.Controlling the false discovery rate-apractical and powerful approach to multiple testing[J].J R Stat Soc,1995,57:289.
[10]Chen S,Yuan H M,Liu G F,et al.Genome-wide analysis of a TaLEA-introduced transgenic Populus simonii×Populus nigra dwarf mutant[J].Mol Biol Rep,2012,13:2744.
[11]Bo Z,Lin J,Peng W,et al.Dwarfism in Brassica napus L.induced by the over-expression of a gibberellin 2-oxidase gene from Arabidopsis thaliana[J].Mol Breed,2012,29:115.
[12]Song D,Shen J,Li L.Characterization of cellulose synthase complexes in Populus xylem differentiation[J].New Phytol,2010,187:777.
[13]Roudier F,Fernandez AG,Fujita M,et al.CO-BRA,an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein,specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation[J].Plant Cell,2005,17:1749.
[14]Ueguchitanaka M,Nakajima M,Motoyuki A,et al.Gibberellin receptor and its role in gibberellin signaling in plants[J].Annu Rev Plant Biol,2007,58:183.
[15]Collins C,Maruthi N M,Jahn C E.CYCD3D-type cyclins regulate cambial cell proliferation and secondary growth in Arabidopsis[J].J Exp Bot,2015,66:351.
[16]Clouse SD,Mcmorris TC.A brassinosteroid-insensitive mutant in Arabidopsis thaliana exhibits multiple defects in growth and development[J].Plant Physiol,1996,111:671.
[17]Petrásek J,Friml J.Auxin transport routes in plant development[J].Development,2009,136:2675.
[18]Song C,Zhang D,Zhang J,et al.Expression analysis of key auxin synthesis,transport,and metabolism genes in different young dwarfing apple trees[J].Acta Physiol Plant,2016,38:1.
[19]Wang R,Liu M,Yuan M,et al.The brassinosteroidactivated BRI1receptor kinase is switched off by dephosphorylation mediated by cytoplasm-localized PP2AB'subunits[J].Mol Plant,2015,9:148.
[20]Kataya A R,Heidari B,Lillo C.Protein phosphatase 2A regulatory subunits affecting plant innate immunity,energy metabolism,and flowering time--joint functions among B'ηsubfamily members[J].Plant Signal Behav,2015,10:e1026024.
[21]Hagen G,Martin G,Li Y,et al.Auxin-induced expression of the soybean GH3promoter in transgenic tobacco plants[J].Plant Mol Biol,1991,17:567.
[2]Liu S S,Chen J,Li S C,et al.Comparative transcriptome analysis of genes involved in GA-GID1-DELLA regulatory module in symbiotic and asymbiotic seed germination of anoectochilus roxburghii(Wall.)Lindl.(Orchidaceae)[J].Int J Mol Sci,2015,16:30190.
[3]Wang R,Liu M,Yuan M,et al.The brassinosteroidactivated BRI1receptor kinase is switched off by dephosphorylation mediated by cytoplasm-localized PP2AB'subunits[J].Mol Plant,2015,9:148.
[4]Chalhoub B,Denoeud F,Liu S,et al.Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome[J].Science,2014,345:950.
[5]Zhang J,Ren A,Chen H,et al.Transcriptome analysis and its application in identifying genes associated with fruiting body development in Basidiomycete Hypsizygus marmoreus[J].PloS One,2015,10:e0123025.
[6]吴燕,颜朗,李雪丹,等.甘薯耐旱和耐盐基因的挖掘和表达分析[J].四川大学学报:自然科学版,2016,53:5.
[7]Freiman Z E,Doron-Faigenboim A,Dasmohapatra R,et al.High-throughput sequencing analysis of common fig(Ficus carica L.)transcriptome during fruit ripening[J].Tree Genet Genomes,2014,10:923.
[8]Li X,Nair A,Wang S,et al.Quality control of RNA-seq experiments[J].Bioinformatics,2015,28:2184.
[9]Benjamini Y,Hochberg Y.Controlling the false discovery rate-apractical and powerful approach to multiple testing[J].J R Stat Soc,1995,57:289.
[10]Chen S,Yuan H M,Liu G F,et al.Genome-wide analysis of a TaLEA-introduced transgenic Populus simonii×Populus nigra dwarf mutant[J].Mol Biol Rep,2012,13:2744.
[11]Bo Z,Lin J,Peng W,et al.Dwarfism in Brassica napus L.induced by the over-expression of a gibberellin 2-oxidase gene from Arabidopsis thaliana[J].Mol Breed,2012,29:115.
[12]Song D,Shen J,Li L.Characterization of cellulose synthase complexes in Populus xylem differentiation[J].New Phytol,2010,187:777.
[13]Roudier F,Fernandez AG,Fujita M,et al.CO-BRA,an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein,specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation[J].Plant Cell,2005,17:1749.
[14]Ueguchitanaka M,Nakajima M,Motoyuki A,et al.Gibberellin receptor and its role in gibberellin signaling in plants[J].Annu Rev Plant Biol,2007,58:183.
[15]Collins C,Maruthi N M,Jahn C E.CYCD3D-type cyclins regulate cambial cell proliferation and secondary growth in Arabidopsis[J].J Exp Bot,2015,66:351.
[16]Clouse SD,Mcmorris TC.A brassinosteroid-insensitive mutant in Arabidopsis thaliana exhibits multiple defects in growth and development[J].Plant Physiol,1996,111:671.
[17]Petrásek J,Friml J.Auxin transport routes in plant development[J].Development,2009,136:2675.
[18]Song C,Zhang D,Zhang J,et al.Expression analysis of key auxin synthesis,transport,and metabolism genes in different young dwarfing apple trees[J].Acta Physiol Plant,2016,38:1.
[19]Wang R,Liu M,Yuan M,et al.The brassinosteroidactivated BRI1receptor kinase is switched off by dephosphorylation mediated by cytoplasm-localized PP2AB'subunits[J].Mol Plant,2015,9:148.
[20]Kataya A R,Heidari B,Lillo C.Protein phosphatase 2A regulatory subunits affecting plant innate immunity,energy metabolism,and flowering time--joint functions among B'ηsubfamily members[J].Plant Signal Behav,2015,10:e1026024.
[21]Hagen G,Martin G,Li Y,et al.Auxin-induced expression of the soybean GH3promoter in transgenic tobacco plants[J].Plant Mol Biol,1991,17:567.