基于转录组测序对紫花苜蓿细胞质雄性不育系相关代谢通路的鉴定
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摘要
【目的】研究紫花苜蓿(Medicago sative L.)细胞质雄性不育(CMS)的机理,为紫花苜蓿利用不育系的育种工作提供理论基础。【方法】本研究以紫花苜蓿细胞质雄性不育系MSGN1A及其保持系MSGN1B为材料,进行转录组测序(RNA-Seq)以及基因功能注释,筛选与不育系机理相关的差异表达基因及代谢通路。【结果】Illumina测序共得到紫花苜蓿95 679条功能基因,经过差异表达分析筛选出187个显著差异表达的基因(DEGs),其中包括18个上调基因,169个下调基因。采用GO、KEGG、COG注释库分别对187个DEGs进行功能注释,其主要涉及催化活性、代谢活动、信号传导机制、合成、膜功能、碳水化合物运输和代谢、能量代谢等相关通路。【结论】筛选出与紫花苜蓿细胞质雄性不育性相关的代谢通路,初步探讨了紫花苜蓿细胞质雄性不育系的分子机理。
【Objective】 The cytoplasmic male sterility(CMS) mechanism was studied to enhance the use of sterile lines of alfalfa in breeding.【Method】 RNA-sequencing was performed to identify genes involving in CMS line MSGN1A and maintainer line MSGN1B.The genes function annotation analysis was conducted and the differences in gene expression and correlated metabolism pathways were investigated.【Result】 A total of 95 679 unigenes were obtained by Illumina sequencing and 187 differentially expressed genes(DEGs) were identified with 18 up-regulated genes and 169 down-regulated genes. Based on GO,KEGG,and COG database,these DEGs were related to catalytic activity,metabolic process,signal transduction mechanisms,binding,membrance function,carbohydrate transport and metabolism,as well as energy metabolism.【Conclusion】 The CMS related metabolism pathways were identified and the molecular mechanism of sterile lines of alfalfa was preliminarily revealed.
【Objective】 The cytoplasmic male sterility(CMS) mechanism was studied to enhance the use of sterile lines of alfalfa in breeding.【Method】 RNA-sequencing was performed to identify genes involving in CMS line MSGN1A and maintainer line MSGN1B.The genes function annotation analysis was conducted and the differences in gene expression and correlated metabolism pathways were investigated.【Result】 A total of 95 679 unigenes were obtained by Illumina sequencing and 187 differentially expressed genes(DEGs) were identified with 18 up-regulated genes and 169 down-regulated genes. Based on GO,KEGG,and COG database,these DEGs were related to catalytic activity,metabolic process,signal transduction mechanisms,binding,membrance function,carbohydrate transport and metabolism,as well as energy metabolism.【Conclusion】 The CMS related metabolism pathways were identified and the molecular mechanism of sterile lines of alfalfa was preliminarily revealed.
引文
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[19] Dong X,Kim W,Lim Y,et al.Ogura-CMS in Chinese cabbage (Brassica rapa ssp.pekinensis) causes delayed expression of many nuclear genes [J].Plant Sci,2013(199/200):7-17.
[20] Cao Y.Anomalous changes in Ca2+-ATPase distribution during the process of pollen abortion in Populus tomentosa Carr [J].Journal of Beijing Forestry University,2012(34):10-17.
[21] 杨福愉.氧化磷酸化机制的研究近况 [J].生物学通报,1988(9):16-18,32.Yang F Y.Recent research on oxidative phosphorylation mechanism [J].Bulletin of Biology,1988(9):16-18,32.
[22] Rato C,Monteiro D,Hepler P K,et al.Calmodulin activity and camp signaling modulate growth and apical secretion in pollen tubes [J].Plant Journal,2004(38),887-897.
[23] Yang S.Comparative transcriptome analysis between cytoplasmic male sterile line NJCMS1A and its maintainer NJCMS1B in soybean (Glycine max (L.) Merr) [J].PLoS ONE,2015(10):e0126771.
[2] Wang S,Wang C,Zhang X X,et al.Transcriptome de novo,assembly and analysis of differentially expressed genes related to cytoplasmic male sterility in cabbage [J].Plant Physiology & Biochemistry,2016(105):224-232.
[3] Han Z,Qin Y,Deng Y,et al.Expression profiles of a cytoplasmic male sterile line of Gossypium harknessii and its fertility restorer and maintainer lines revealed by RNA-seq [J].Plant Physiology & Biochemistry,2017(116):106-115.
[4] Qiu Y,Liao L,Jin X,et al.Analysis of the meiotic transcriptome reveals the genes related to the regulation of pollen abortion in cytoplasmic male-sterile pepper (Capsicum annuum L.) [J].Gene,2018(641):8-17.
[5] Yuan Q,Song C,Gao L,et al.Transcriptome de novo assembly and analysis of differentially expressed genes related to cytoplasmic male sterility in onion [J].Plant Physiology & Biochemistry,2018(125):35-44.
[6] 杨青川,孙彦.紫花苜蓿在北京市种植业结构调整中的作用 [J].北京农业科学,2000,18(3):38-40.Yang Q C,Sun Y.The role of alfalfa in the structural adjustment of Beijing planting industry [J].Beijing Agricultural Sciences,2000,18(3):38-40.
[7] 贾瑞,于洪柱,徐博,等.苜蓿不同品种与雄性不育系MS-GN杂交F1代草产量和品质分析 [J].西北农林科技大学学报(自然科学版),2015,43(5):12-20.Jia R,Yu H Z,Xu B,et al.Yield and quality of hybrid F1 grass of different alfalfa varieties with male sterile line MS-GN [J].Journal of Northwest A & F University (Nat Sci Ed),2015,43(5):12-20.
[8] 吴永敷.苜蓿雄性不育系的选育 [J].中国草原,1980,2(2):36-38.Wu Y F.The breeding of alfalfa male sterile lines [J].China’s Grassland,1980,2(2):36-38.
[9] 于洪柱,徐安凯,栾博宇,等.紫花苜蓿雄性不育系的研究 [J].黑龙江畜牧兽医,2013(17):81-82.Yu H Z,Xu A K,Luan B Y,et al.Study on male sterile line of Medicago sativa [J].Heilongjiang Animal Science and Veterinary Medicine,2013(17):81-82.
[10] Denoeud F,Aury J M,Da S C,et al.Annotating genomes with massive-scale RNA sequencing [J].Genome Biology,2008,9(12):1-12.
[11] Schuster S C.Next-generation sequencing transforms today’s biology [J].Nat Methods,2008(5):16-18.
[12] Ansorge W J.Next-generation DNA sequencing techniques [J].N Biotechnol,2009(25):195-203.
[13] Zenoni S,Ferrarini A,Giacomelli E,et al.Characterization of transcriptional complexity during berry development in vitis vinifera using RNA-seq [J].Plant Physiol,2010(152):1787-1795.
[14] Suzuki H,Rodriguez-Uribe L,Xu J,et al.Transcriptome analysis of cytoplasmic male sterility and restoration in CMS-D8 cotton [J].Plant Cell Reports,2013(32):1531-1542.
[15] Li J,Han S,Ding X,et al.Comparative transcriptome analysis between the cytoplasmic male sterile line NJCMS1A and its maintainer NJCMS1B in soybean (Glycine max (L.) Merr.) [J].PLoS ONE,2015(10):e0126771.
[16] Garg R,Patel R K,Tyagi A K,et al.De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification [J].DNA Research,2011,18(1):53-63.
[17] Miernyk J,Pretová A,Olmedilla A,et al.Using proteomics to study sexual reproduction in angiosperms [J].Sex Plant Reprod,2011(24):9-22.
[18] 尚丽.拟南芥糖反应相关基因TANG1的克隆及功能分析 [D].北京:中国科学院大学,2016.Shang L.Cloning and functional analysis of TANG1 gene related to Arabidopsis thaliana carbohydrate response [D].Beijing:University of Chinese Academy of Sciences,2016.
[19] Dong X,Kim W,Lim Y,et al.Ogura-CMS in Chinese cabbage (Brassica rapa ssp.pekinensis) causes delayed expression of many nuclear genes [J].Plant Sci,2013(199/200):7-17.
[20] Cao Y.Anomalous changes in Ca2+-ATPase distribution during the process of pollen abortion in Populus tomentosa Carr [J].Journal of Beijing Forestry University,2012(34):10-17.
[21] 杨福愉.氧化磷酸化机制的研究近况 [J].生物学通报,1988(9):16-18,32.Yang F Y.Recent research on oxidative phosphorylation mechanism [J].Bulletin of Biology,1988(9):16-18,32.
[22] Rato C,Monteiro D,Hepler P K,et al.Calmodulin activity and camp signaling modulate growth and apical secretion in pollen tubes [J].Plant Journal,2004(38),887-897.
[23] Yang S.Comparative transcriptome analysis between cytoplasmic male sterile line NJCMS1A and its maintainer NJCMS1B in soybean (Glycine max (L.) Merr) [J].PLoS ONE,2015(10):e0126771.