SUN Chong-yuan,CUI Rui-fan,WANG Rui-yang,et al.Bioinformatics Analysis on Soybean ERF Family Genes and Their Response to Low Phosphorus Stress[J].Soybean Science,2021,40(06):748-758.[doi:10.11861/j.issn.1000-9841.2021.06.0748]
大豆ERF家族基因生物信息学分析及其对低磷胁迫的响应
- Title:
- Bioinformatics Analysis on Soybean ERF Family Genes and Their Response to Low Phosphorus Stress
- Keywords:
- Glycine max; ERF gene family; Bioinformatics; Low-phosphorus stress
- 文献标志码:
- A
- 摘要:
- 为分析大豆乙烯响应因子(Ethylene Response Factor,ERF)基因家族的特征及其在低磷胁迫下的响应作用,本研究首先利用生物信息学方法从大豆基因组数据库中鉴定获得ERF家族基因,进行进化分析、染色体分布和基因结构分析,并研究其在大豆发育过程中不同组织的表达模式及在低磷胁迫下的表达情况。结果显示:59个大豆ERF家族基因分布在除4号染色体外的整个大豆染色体组上,其中3号、10号、13号、18号和19号染色体分布较多。基因结构分析显示整个家族具有典型的AP2结构域。同源序列比对和进化分析将该家族的基因分为4组,分别包括15,5,19和20个基因。基于Soybase数据库的组织表达分析表明该家族基因在大豆的不同组织中均有表达;qRT-PCR结果表明该家族基因低磷胁迫条件下的大豆根、茎和叶中均被诱导表达。结果说明大豆ERF基因结构较保守,能够参与低磷胁迫响应。
- Abstract:
- In order to analyze the characteristics of soybean Ethylene Response Factor (ERF) genes and their response to low phosphorus stress, this study identified ERF family genes from soybean genome database by bioinformatics methods. And then we analyzed the evolution, chromosome distribution and gene structure of the family genes and their gene expression patterns in different tissues during soybean development, and the expression of the family genes under low phosphorus stress. The results showed that the gene family was distributed in the whole soybean genome except chromosome 4, among which chromosome 3, 10, 13, 18 and 19 were more distributed. The gene structure analysis showed that the whole family had a typical AP2 domain. Homologous sequence alignment and evolutionary analysis divided the genes of this family into 4 groups, including 15, 5, 19 and 20 genes, respectively. Tissue expression analysis based on Soybase database showed that the family genes were expressed in different tissues of soybean. qRT-PCR results showed that the family genes were induced in soybean roots, stems and leaves under low phosphorus stress. The results showed that the structure of soybean ERF genes were conservative, and were involved in the response to low phosphorus stress.
参考文献/References:
[1]沈鸣, 陈受宜, 张劲松. 乙烯对豆科植物生长发育和根瘤形成的影响[J]. 大豆科学, 2016, 35(2): 330-336. (Shen M, Chen S Y, Zhang J S, et al. Effects of ethylene on growth and development and nodule formation of legume plants[J]. Soybean Science, 2016, 35(2): 330-336.)[2]Zhang J, Xu M, Dwiyanti M S, et al. A soybean deletion mutant that moderates the repression of flowering by cool temperatures[J]. Front Plant Science, 2020(11): 429.[3]Zhang Z J, Huang R F. Enhanced tolerance to freezing in tobacco and tomato overexpressing transcription factor TERF2/LeERF2 is modulated by ethylene biosynthesis[J]. Plant Molecular Biology, 2010, 73(3): 241-249.[4]Lee S B, Lee S J, Kim S Y. AtERF15 is a positive regulator of ABA response[J]. Plant Cell Reports, 2015, 34(1): 71-81.[5]Muller M, Munne-Bosch S. Ethylene response factors: A key re-gulatory hub in hormone and stress signaling[J]. Plant Physiology, 2015, 169(1): 32-41.[6]Licausi F, Masaru O T, Pierdomenico P. Apetala 2/Ethylene re-sponsive factor (Ap 2/Erf) transcription factors: Mediators of stress responses and developmental programs[J]. New Phytologist 2013, 199(3): 639-649.[7]Riechmann J L, Meyerowitz E M. The AP2/EREBP family of plant transcription factors[J]. Biological Chemistry, 1998, 379(6): 633-646.[8]Zhu Q, Zhang J, Gao X, et al.The Arabidopsis AP2/ERF transcription factor RAP2.6 participates in ABA, salt and osmotic stress responses[J]. Gene, 2010, 457(1-2): 1-12.[9]Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type-A response regulator of cytokinin signaling[J]. Plant Journal, 2011, 67(3): 472-484.[10]Hirota A, Kato T, Fukaki H, et al. The auxin-regulated AP2/EREBP gene PUCHI is required for morphogenesis in the early lateral root primordium of Arabidopsis[J]. Plant Cell, 2007, 19(7): 2156-2168.[11]Andriankaja A, Boisson-Demier A, Frances L, et al. AP2-ERF transcription factors mediate nod factor-dependent mt ENOD11 activation in root hairs via a novel cis-regulatory motif[J]. Plant Cell,2007, 19(9): 2866-2885.[12]Marsch-Martinez N, Greco R, Becker J D, et al. BOLITA, an Arabidopsis AP2/ERF-like transcription factor that affects cell expansion and proliferation/differentiation pathways[J]. Plant Molecular Biology, 2006, 62(6): 825-843.[13]Salvi S, Sponza G, Morgante M, et al. Conserved noncoding gen-omic sequences associated with a flowering-time quantitative trait locus in maize[J]. Proceedings of the National Academy of Sciences of the United States of America, 2007, 104(27): 11376-11381.[14]Chuck G, Meeley R, Hake S. Floral meristem initiation and meri-stem cell fate are regulated by the maize AP2 genes ids1 and sid1[J]. Development, 2008, 135(18): 3013-3019.[15]Komatsu M, Chujo A, Nagato Y, et al. FRIZZY PANICLE is required to prevent the formation of axillary meristems and to establish floral meristem identity in rice spikelets[J]. Development, 2003, 130(16): 3841-3850.[16]Liu J, Li J, Wang H, et al. Identification and expression analysis of ERF transcription factor genes in petunia during flower senescence and in response to hormone treatments[J]. Journal of Experimental Botany, 2011, 62(2): 825-840.[17]Jofuku K D, Omidyar P K, Gee Z, et al. Control of seed mass and seed yield by the floral homeotic gene APETALA2[J]. Proceedings of the National Academy of Sciences of the United States of America, 2005, 102(8): 3117-3122.[18]Thiel J, Weier D, Sreenivasulu N, et al. Different hormonal regulation of cellular differentiation and function in nucellar projection and endosperm transfer cells: A microdissection-based transcriptome study of young barley grains[J]. Plant Physiology, 2008, 148(3): 1436-1452.[19]El-Sharkawy I, Sherif S, Mila I, et al. Molecular characterization of seven genes encoding ethylene-responsive transcriptional factors during plum fruit development and ripening[J]. Journal of Experimental Botany, 2009, 60(3): 907-922.[20]Pietsch C, Sreenivasulu N, Wobus U, et al. Linkage mapping of putative regulator genes of barley grain development characterized by expression profiling[J]. BMC Plant Biology, 2009, 9(1): 4.[21]Soares V L, Rodrigues S M, de Oliveira T M, et al. Unraveling new genes associated with seed development and metabolism in Bixa orellana L. by expressed sequence tag (EST) analysis[J]. Molecular Biology Report, 2011, 38(2): 1329-1340.[22]Ramaiah M, Jain A, Raghothama K G. ETHYLENE RESPONSE FACTOR070 regulates root development and phosphate starvation-mediated responses[J]. Plant Physiology, 2014, 164(3): 1484-1498.[23]Karanja B K, Xu L, Wang Y, et al. Genome-wide characte-rization of the AP2/ERF gene family in radish (Raphanus sativus L.): Unveiling evolution and patterns in response to abiotic stresses[J]. Gene, 2019, 718: 144048.[24]Song L, Liu D. Ethylene and plant responses to phosphate defic-iency[J]. Front Plant Science, 2015, 6: 796.[25]Wang G, Wang H, Zhu J, et al. An expression analysis of 57 transcription factors derived from ESTs of developing seeds in maize(Zea mays)[J]. Plant Cell Report, 2010, 29(6): 545-559.[26]Wang X P, Liu S D, Tian H N, et al. The small ethylene resp-onse factor ERF96 is involved in the regulation of the abscisic acid response in Arabidopsis[J]. Frontiers in Plant Science, 2015(6): 1064.[27]Zhai Y,Shao S L,Sha W,et al.Overexpression of soybean GmERF9 enhances the tolerance to drought and cold in the transgenic tobacoo[J].Plant Cell Tissue and Organ Culture,2017,128(3):607-618.[28]Zhao Y, Chang X, Qi D, et al. A novel soybean ERF transcription factor, GmERF113, increases resistance to Phytophthora sojae infection in soybean[J]. Frontiers in Plant Science, 2017, 8(47): 299.[29]Lestari R, Rio M, Martin F, et al. Overexpression of Hevea bra-siliensis ethylene response factor HbERF-IXc5 enhances growth and tolerance to abiotic stress and affects laticifer differentiation[J]. Plant Biotechnology Journal, 2018, 16(1): 322-336.[30]Bustos R, Castrillo G, Linhares F, et al. A central regulatory system largely controls transcriptional activation and repression responses to phosphate starvation in Arabidopsis[J]. PLoS Genetics, 2010, 6(9): e1001102.[31]Upadhyay R K, Soni D K, Singh R, et al. SlERF36, an EAR-motif-containing ERF gene from tomato, alters stomatal density and modulates photosynthesis and growth[J]. Journal of Experimental Botany, 2013, 64(11): 3237-3247.[32]张淑珍, 华彩峰, 董利东, 等. ERF 转录因子及在大豆中的研究进展[J]. 大豆科学, 2015,34(3): 512-517. (Zhang S Z, Hua C F, Dong L D, et al. ERF transcription factors and research progress in soybean[J]. Soybean Science, 2015, 34(3): 512-517.)[33]Zhang D, Zhang H, Chu S, et al. Integrating QTL mapping and transcriptomics identifies candidate genes underlying QTLs associated with soybean tolerance to low-phosphorus stress[J]. Plant Molecular Biology, 2016, 93(1-2): 137-150.[34]魏海超, 刘媛, 豆明珠, 等. 大豆AP2/ERF基因家族的分子进化分析[J]. 植物生理学报 2015, 51(10): 1706-1718. (Wei H C, Liu Y, Dou M Z, et al. Molecular evolution analysis of soybean AP2 / ERF gene family[J]. Plant Physiology Report, 2015, 51(10): 1706-1718.)[35]袁伟, 万红建, 杨悦俭. 植物实时荧光定量 PCR 内参基因的特点及选择[J]. 植物学报, 2012, 47(4): 427-436. (Yuan W, Wan H J, Yang Y J, et al. The characteristics and selection of reference genes in plant real-time fluorescence quantitative PCR[J]. Phytology, 2012, 47(4): 427-436.)[36]Zhou Y, Tan W J, Xie L J, et al. Polyunsaturated linolenoyl-CoA modulates ERF-VII-mediated hypoxia signaling in Arabidopsis[J]. Journal of Integrative Plant Biology, 2020, 62(3): 330-348.[37]Livak K J, Schmittgen T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2 -ΔΔCT method[J] Elsevier, 2001, 25(4): 402-408.[38]Liu M, Chen Y, Chen Y, et al. The tomato Ethylene Response Factor Sl-ERF.B3 integrates ethylene and auxin signaling via direct regulation of Sl-Aux/IAA27[J]. New Phytology, 2018, 219(2): 631-640.[39]Xu J J, Zhang X F, Xue H W. Rice aleurone layer specific OsNF-YB1 regulates grain filling and endosperm development by interacting with an ERF transcription factor[J].Journal of Experimental Botany, 2016, 67(22): 6399-6411.[40]Zhang G, Chen M, Chen X, et al. Phylogeny, gene structures, and expression patterns of the ERF gene family in soybean (Glycine max L.) [J]. Journal of Experimental Botany, 2008, 59(15): 4095-4107.[41]Zhang G, Chen M, Li L, et al. Overexpression of the soybean GmERF3 gene, an AP2/ERF type transcription factor for increased tolerances to salt, drought, and diseases in transgenic tobacco[J]. Journal of Experimental Botany, 2009, 60(13): 3781-3796.[42]Zhao M J, Yin L J, Liu Y, et al. The ABA-induced soybean ERF transcription factor gene GmERF75 plays a role in enhancing osmotic stress tolerance in Arabidopsis and soybean[J]. BMC Plant Biology, 2019, 19(1): 506.[43]Chen C, Chen H, Zhang Y, et al. TBtools: An integrative toolkit developed for interactive analyses of big biological data[J]. Molecular Plant, 2020, 13(8): 1194-1202.
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备注/Memo
收稿日期:2021-03-17