QI Ping,ZHENG Kai-jie,ZHAO Xiao-yu,et al.Transcriptome Analysis of Soybean Root System in the Early Stage of Rhizobium Infection[J].Soybean Science,2021,40(03):289-298.[doi:10.11861/j.issn.1000-9841.2021.03.0289]
根瘤菌侵染早期大豆根系的转录组分析
- Title:
- Transcriptome Analysis of Soybean Root System in the Early Stage of Rhizobium Infection
- Keywords:
- Soybean; RNA-seq; Symbiotic nitrogen fixation; WIP gene
- 文献标志码:
- A
- 摘要:
- 为了解析共生早期根瘤菌与宿主植物根组织信号交互调控作用，深入了解根瘤菌侵染早期根系的基因调控网络以及进一步解析豆科植物如何进化形成与根瘤菌共生的分子机制，本研究对根瘤菌侵染12 h后大豆的根组织材料进行转录组测序分析，对受显著调控的基因进行GO和KEGG显著性富集分析，采用qRT-PCR方法验证候选基因的表达情况，并通过构建进化树和绘制表达聚类图分析候选基因的进化及功能特征。研究共鉴定出488个在共生早期受根瘤菌侵染显著调控的基因。GO富集结果显示，上调基因中富集了参与损伤应答功能的基因，而下调基因的功能主要富集在细胞壁生物合成调控途径。KEGG通路富集分析显示，参与植物与病菌互作、植物激素转导和MAPK信号通路的基因在上调基因中富集，而编码ABC转运蛋白以及植物节律相关的蛋白基因在下调基因中富集。其中对损伤应答富集基因的分析鉴定出可能在大豆中参与根瘤菌侵染早期调控的损伤诱导短肽（Wound-Induced Peptide，WIP）家族。转录组和qRT-PCR结果显示16个WIP基因在根瘤菌侵染后受到不同程度的诱导表达。对大豆WIP家族基因序列的进化分析结果以及表达聚类分析结果均显示，受根瘤菌诱导表达的WIP基因亚家族的序列和表达均表现出与拟南芥同源的WIP基因亚家族不同的特性。
- Abstract:
- To analyze signal regulation between rhizobia and host plant in symbiosis, understand gene regulation network of the root system in the early stage of rhizobial infection, and explore the molecular mechanism of evolution of legume symbiosis, the transcriptomic profiles were performed from soybean root tissues infected by rhizobia for 12 h. The significantly regulated genes were analyzed by gene ontology (GO) and KEGG pathway enrichment analysis, the expression of candidate genes in the pathway were verified by qRT-PCR, and evolutionary and functional features of candidate genes were analyzed by phylogenetic tree and correlation cluster analysis. In this research, a total of 488 genes were identified which were significantly regulated by rhizobial infection in the early stage of symbiosis. GO enrichment analysis showed that the up-regulated genes were enriched in wounding response, while the down-regulated genes were enriched in regulation of cell wall biosynthesis. KEGG pathway enrichment analysis showed that the genes involved in plant-pathogen interaction, plant hormone transduction and MAPK signaling pathway were enriched in up-regulated genes, while the genes encoding ABC transporter and circadian rhythm were enriched in down-regulated genes. The analysis of genes enriched in wounding response identified the WIP (Wound-Induced Peptide) family that may be involved in regulation of rhizobia infection in soybeans. RNA-seq and qRT-PCR results showed that 16 WIP genes were induced after rhizobial infection. Molecular evolutionary analysis and gene expression cluster analysis showed that the sequence and expression feature of WIP subfamilies which induced by rhizobia were different from WIP subfamily homologous to Arabidopsis thaliana.
参考文献/References:
［1］Fowler D, Coyle M, Skiba U, et al. The global nitrogen cycle in the twenty-first century［J］. Philosophical Transactions of the Royal Society B: Biological Sciences, 2013, 368(1621): 20130164.［2］Schmutz J, Cannon S B, Schlueter J, et al. Genome sequence of the palaeopolyploid soybean［J］. Nature, 2010, 463(7278): 178-183.［3］Graham P H. Legumes: Importance and constraints to greater use［J］. Plant Physiology, 2003, 131(3): 872-877.［4］Iqbal A, Khalil I A, Ateeq N, et al. Nutritional quality of important food legumes［J］. Food Chemistry, 2006, 97(2): 331-335.［5］Tharanathan R N, Mahadevamma S. Grain legumes—A boon to human nutrition［J］. Trends in Food Science & Technology, 2003, 14(12): 507-518.［6］Bohra A, Mir R R, Jha R, et al. Advances in genomics and molecular breeding for legume improvement［M］∥Tuteja N, Tuteja R, Passricha N, et al. Advancement in crop improvement techniques, Elsevier: Woodhead Publishing, 2020: 129-139.［7］Fowler D, Steadman C E, Stevenson D, et al. Effects of global change during the 21st century on the nitrogen cycle［J］. Atmospheric Chemistry and Physics, 2015, 15(24): 13849-13893.［8］Franssen H J, Vijn I, Yang W C, et al. Developmental aspects of the rhizobium-legume symbiosis［J］. Plant Molecular Biology, 1992, 19(1): 89-107. ［9］Barnett M J, Fisher R F. Review article: Global gene expression in the rhizobial-legume symbiosis［J］. Symbiosis, 2006, 42(1): 1-24.［10］Oldroyd G E D, Downie J A. Coordinating nodule morphogenesis with rhizobial infection in legumes［J］. Annual Review of Plant Biology, 2008, 59: 519-546. ［11］Geurts R, Fedorova E, Bisseling T. Nod factor signaling genes and their function in the early stages of rhizobium infection［J］. Current Opinion in Plant Biology, 2005, 8(4): 346-352.［12］Zipfel C, Oldroyd G E D. Plant signalling in symbiosis and immunity［J］. Nature, 2017, 543(7645): 328-336.［13］Geurts R, Bisseling T. Rhizobium nod factor perception and signalling［J］. The Plant Cell, 2002, 14(S1): S239-S249.［14］Long S R. Genes and signals in the rhizobium-legume symbiosis［J］. Plant Physiology, 2001, 125(1): 69-72.［15］Saito K, Yoshikawa M, Yano K, et al. NUCLEOPORIN85 is required for calcium spiking, fungal and bacterial symbioses, and seed production in Lotus japonicus［J］. The Plant Cell, 2007, 19(2): 610-624. ［16］Stacey G, Libault M, Brechenmacher L, et al. Genetics and functional genomics of legume nodulation［J］. Current Opinion in Plant Biology, 2006, 9(2): 110-121. ［17］Limpens E, Bisseling T. Nod factor signal transduction in the rhizobium-legume symbiosis［M］. Springer Berlin Heidelberg, 2009: 249-276.［18］Hayashi T, Shimoda Y, Sato S, et al. Rhizobial infection does not require cortical expression of upstream common symbiosis genes responsible for the induction of Ca2+ spiking［J］. The Plant Journal, 2014, 77(1): 146-159. ［19］Wong J E M M, Nadzieja M, Madsen L H, et al. A Lotus japonicus cytoplasmic kinase connects Nod factor perception by the NFR5 LysM receptor to nodulation［J］. Proceedings of the National Academy of Sciences, 2019, 116(28): 14339-14348.［20］Antolín-Llovera M, Ried M K, Parniske M. Cleavage of the SYMBIOSIS RECEPTOR-LIKE KINASE ectodomain promotes complex formation with Nod Factor Receptor 5［J］. Current Biology, 2014, 24(4): 422-427. ［21］Kanamori N, Madsen L H, Radutoiu S, et al. A nucleoporin is required for induction of Ca2+ spiking in legume nodule development and essential for rhizobial and fungal symbiosis［J］. Proceedings of the National Academy of Sciences, 2006, 103(2): 359-364.［22］Tirichine L, Sandal N, Madsen L, et al. A gain-of-function mutation in a cytokinin receptor triggers spontaneous root nodule organogenesis［J］. Science, 2007, 315(5808): 104-107.［23］Wang Z, Gerstein M, Snyder M. RNA-Seq: A revolutionary tool for transcriptomics［J］. Nature Reviews Genetics, 2009, 10(1): 57-63.［24］Yuan S L, Li R, Chen H F, et al. RNA-Seq analysis of nodule development at five different developmental stages of soybean (Glycine max) inoculated with Bradyrhizobium japonicum strain 113-2［J］. Scientific Reports, 2017, 7(1): 1-14.［25］Niyikiza D, Piya S, Routray P, et al. Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity［J］. The Plant Journal, 2020, 103(5): 1744-1766.［26］Hayashi S, Reid D E, Lorenc M T, et al. Transient Nod factor‐dependent gene expression in the nodulation‐competent zone of soybean (Glycine max［L.］ Merr.) roots［J］. Plant Biotechnology Journal, 2012, 10(8): 995-1010.［27］Carvalho G A, Batista J S, Marcelino-Guimares F C, et al. Transcriptional analysis of genes involved in nodulation in soybean roots inoculated with Bradyrhizobium japonicum strain CPAC 15［J］. BMC Genomics, 2013, 14(1): 1-11.［28］Huerta-Cepas J, Serra F, Bork P. ETE 3: Reconstruction, analysis, and visualization of phylogenomic data［J］. Molecular Biology and Evolution, 2016, 33(6):1635-1638.［29］Libault M, Farmer A, Joshi T, et al. An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants［J］. The Plant Journal, 2010, 63(1): 86-99.［30］Karim S, Lundh D, Holmstrm K O, et al. Structural and functional characterization of AtPTR3, a stress-induced peptide transporter of Arabidopsis［J］. Journal of Molecular Modeling, 2005, 11(3): 226-236.［31］Karim S, Holmstrm K O, Mandal A, et al. AtPTR3, a wound-induced peptide transporter needed for defence against virulent bacterial pathogens in Arabidopsis［J］. Planta, 2007, 225(6): 1431-1445.［32］Yamada M, Hsiao Y C. The roles of peptide hormones and their receptors during plant root development［J］. Genes, 2021, 12(1): 22.［33］Kereszt A, Mergaert P, Montiel J, et al. Impact of plant peptides on symbiotic nodule development and functioning［J］. Frontiers in Plant Science, 2018, 9: 1026.［34］Batut J, Mergaert P, Masson-Boivin C. Peptide signalling in the rhizobium–legume symbiosis［J］. Current Opinion in Microbiology, 2011, 14(2): 181-187. ［35］Djordjevic M A, Mohd-Radzman N A, Imin N. Small-peptide signals that control root nodule number, development, and symbiosis［J］. Journal of Experimental Botany, 2015, 66(17): 5171-5181.［36］Kumagai H, Kinoshita E, Ridge R W, et al. RNAi Knock-down of ENOD40s leads to significant suppression of nodule formation in Lotus japonicus［J］. Plant and Cell Physiology, 2006, 47(8): 1102-1111.［37］Reid D E, Ferguson B J, Hayashi S, et al. Molecular mechanisms controlling legume autoregulation of nodulation［J］. Annals of Botany, 2011, 108(5): 789-795.［38］Ferguson B J, Indrasumunar A, Hayashi S, et al. Molecular analysis of legume nodule development and autoregulation［J］. Journal of Integrative Plant Biology, 2010, 52(1): 61-76.［39］Kinkema M, Gresshoff P M. Investigation of downstream signals of the soybean autoregulation of nodulation receptor kinase GmNARK［J］. Molecular Plant Microbe Interactions, 2008, 21(10): 1337-1348.［40］Tsikou D, Yan Z, Holt D B, et al. Systemic control of legume susceptibility to rhizobial infection by a mobile microRNA［J］. Science, 2018, 362(6411): 233-236.［41］Zhang C, Qi M, Zhang X, et al. Rhizobial infection triggers systemic transport of endogenous RNAs between shoots and roots in soybean［J］. Science China Life Sciences, 2020, 63(8): 1213-1226.［42］Yu L L, Wang Y W, Liu Y, et al. Wound-induced polypeptides improve resistance against Pseudomonas syringae pv. Tomato DC3000 in Arabidopsis［J］. Biochemical and Biophysical Research Communications, 2018, 504(1): 149-156.［43］Chen Y L, Lee C Y, Cheng K T, et al. Quantitative peptidomics study reveals that a wound-induced peptide from PR-1 regulates immune signaling in tomato［J］. The Plant Cell, 2014, 26(10): 4135-4148.［44］Conrath U. Priming of induced plant defense responses［J］. Advances in Botanical Research, 2009, 51: 361-395.［45］Conrath U. Molecular aspects of defence priming［J］. Trends in Plant Science, 2011, 16(10): 524-531.
相似文献/References:
[1]刘章雄,李卫东,孙石,等.1983～2010年北京大豆育成品种的亲本地理来源及其遗传贡献[J].大豆科学,2013,32(01):1.[doi:10.3969/j.issn.1000-9841.2013.01.002]
LIU Zhang-xiong,LI Wei-dong,SUN Shi,et al.Geographical Sources of Germplasm and Their Nuclear Contribution to Soybean Cultivars Released during 1983 to 2010 in Beijing[J].Soybean Science,2013,32(03):1.[doi:10.3969/j.issn.1000-9841.2013.01.002]
[2]李彩云,余永亮,杨红旗,等.大豆脂质转运蛋白基因GmLTP3的特征分析[J].大豆科学,2013,32(01):8.[doi:10.3969/j.issn.1000-9841.2013.01.003]
LI Cai-yun,YU Yong-liang,YANG Hong-qi,et al.Characteristics of a Lipid-transfer Protein Gene GmLTP3 in Glycine max[J].Soybean Science,2013,32(03):8.[doi:10.3969/j.issn.1000-9841.2013.01.003]
[3]王明霞,崔晓霞,薛晨晨,等.大豆耐盐基因GmHAL3a的克隆及RNAi载体的构建[J].大豆科学,2013,32(01):12.[doi:10.3969/j.issn.1000-9841.2013.01.004]
WANG Ming-xia,CUI Xiao-xia,XUE Chen-chen,et al.Cloning of Halotolerance 3 Gene and Construction of Its RNAi Vector in Soybean (Glycine max)[J].Soybean Science,2013,32(03):12.[doi:10.3969/j.issn.1000-9841.2013.01.004]
[4]张春宝,李玉秋,彭宝,等.线粒体ISSR与SCAR标记鉴定大豆细胞质雄性不育系与保持系[J].大豆科学,2013,32(01):19.[doi:10.3969/j.issn.1000-9841.2013.01.005]
ZHANG Chun-bao,LI Yu-qiu,PENG Bao,et al.Identification of Soybean Cytoplasmic Male Sterile Line and Maintainer Line with Mitochondrial ISSR and SCAR Markers[J].Soybean Science,2013,32(03):19.[doi:10.3969/j.issn.1000-9841.2013.01.005]
[5]卢清瑶,赵琳,李冬梅,等.RAV基因对拟南芥和大豆不定芽再生的影响[J].大豆科学,2013,32(01):23.[doi:10.3969/j.issn.1000-9841.2013.01.006]
LU Qing-yao,ZHAO Lin,LI Dong-mei,et al.Effects of RAV gene on Shoot Regeneration of Arabidopsis and Soybean[J].Soybean Science,2013,32(03):23.[doi:10.3969/j.issn.1000-9841.2013.01.006]
[6]杜景红,刘丽君.大豆fad3c基因沉默载体的构建[J].大豆科学,2013,32(01):28.[doi:10.3969/j.issn.1000-9841.2013.01.007]
DU Jing-hong,LIU Li-jun.Construction of fad3c Gene Silencing Vector in Soybean[J].Soybean Science,2013,32(03):28.[doi:10.3969/j.issn.1000-9841.2013.01.007]
[7]张力伟,樊颖伦,牛腾飞,等.大豆“冀黄13”突变体筛选及突变体库的建立[J].大豆科学,2013,32(01):33.[doi:10.3969/j.issn.1000-9841.2013.01.008]
ZHANG Li-wei,FAN Ying-lun,NIU Teng-fei?,et al.Screening of Mutants and Construction of Mutant Population for Soybean Cultivar "Jihuang13”[J].Soybean Science,2013,32(03):33.[doi:10.3969/j.issn.1000-9841.2013.01.008]
[8]盖江南,张彬彬,吴瑶,等.大豆不定胚悬浮培养基因型筛选及基因枪遗传转化的研究[J].大豆科学,2013,32(01):38.[doi:10.3969/j.issn.1000-9841.2013.01.009]
GAI Jiang-nan,ZHANG Bin-bin,WU Yao,et al.Screening of Soybean Genotypes Suitable for Suspension Culture with Adventitious Embryos and Genetic Transformation by Particle Bombardment[J].Soybean Science,2013,32(03):38.[doi:10.3969/j.issn.1000-9841.2013.01.009]
[9]王鹏飞,刘丽君,唐晓飞,等.适于体细胞胚发生的大豆基因型筛选[J].大豆科学,2013,32(01):43.[doi:10.3969/j.issn.1000-9841.2013.01.010]
WANG Peng-fei,LIU Li-jun,TANG Xiao-fei,et al.Screening of Soybean Genotypes Suitable for Somatic Embryogenesis[J].Soybean Science,2013,32(03):43.[doi:10.3969/j.issn.1000-9841.2013.01.010]
[10]刘德兴,年海,杨存义,等.耐酸铝大豆品种资源的筛选与鉴定[J].大豆科学,2013,32(01):46.[doi:10.3969/j.issn.1000-9841.2013.01.011]
LIU De-xing,NIAN Hai,YANG Cun-yi,et al.Screening and Identifying Soybean Germplasm Tolerant to Acid Aluminum[J].Soybean Science,2013,32(03):46.[doi:10.3969/j.issn.1000-9841.2013.01.011]
[11]陈锦玲,徐媛,陈玉梅,等.大豆籽粒不同发育时期的转录组分析[J].大豆科学,2019,38(04):533.[doi:10.11861/j.issn.1000-9841.2019.04.0533]
CHEN Jin-ling,XU Yuan,CHEN Yu-mei,et al.Sequencing Analysis of Transcriptome During the Different Developmental Stages in Soybean Seed[J].Soybean Science,2019,38(03):533.[doi:10.11861/j.issn.1000-9841.2019.04.0533]
[12]刘鑫磊,薛永国,唐晓飞,等.基于转录组测序的大豆体细胞胚诱导关键基因及代谢途径分析[J].大豆科学,2022,41(05):536.[doi:10.11861/j.issn.1000-9841.2022.05.0536]
LIU Xin-lei,XUE Yong-guo,TANG Xiao-fei,et al.Analysis of Metabolic Pathway and Genes Relating Somatic Embryo Induction Based on RNA Sequencing in Soybean[J].Soybean Science,2022,41(03):536.[doi:10.11861/j.issn.1000-9841.2022.05.0536]
备注/Memo
收稿日期：2021-02-04