Article(id=1309575125658338149, tenantId=1146029695717560320, journalId=1308397196074385509, issueId=1309575113855562513, articleNumber=null, orderNo=null, doi=10.11733/j.issn.1007-0435.2026.09.006, pmid=null, cstr=null, oa=null, hot=0, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1773158400000, receivedDateStr=2026-03-11, revisedDate=1776182400000, revisedDateStr=2026-04-15, acceptedDate=null, acceptedDateStr=null, onlineDate=1790156640686, onlineDateStr=2026-09-23, pubDate=null, pubDateStr=null, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1790156640686, onlineIssueDateStr=2026-09-23, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1790156640686, creator=13701087609, updateTime=1790156640686, updator=13701087609, issue=Issue{id=1309575113855562513, tenantId=1146029695717560320, journalId=1308397196074385509, year='2026', volume='34', issue='9', pageStart='3141', pageEnd='3524', issueExtLink='null', onlineDate='null', pubDate='1789401600000', pubDateStr='2026-09-15', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=1, specialIssue=null, createTime=1790156637871, creator='13701087609', updateTime=1790156973247, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1309576520587374966, tenantId=1146029695717560320, journalId=1308397196074385509, issueId=1309575113855562513, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1309576520587374967, tenantId=1146029695717560320, journalId=1308397196074385509, issueId=1309575113855562513, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=3197, endPage=3210, ext={EN=ArticleExt(id=1309575126014853991, articleId=1309575125658338149, tenantId=1146029695717560320, journalId=1308397196074385509, language=EN, title=Genome-Wide Identification and Cold Stress Expression Analysis of the WRKY Gene Family in Pennisetum alopecuroides, columnId=null, journalTitle=Acta Agrestia Sinica, columnName=null, runingTitle=null, highlight=null, articleAbstract=To clarify the molecular characteristics of the WRKY gene family in highly cold-resistant Pennisetum alopecuroides and their functions in cold stress response, in this study we conducted systematic identification, phylogenetic analysis and cold stress-related expression pattern analysis of the WRKY gene family via combined genome-wide and transcriptome analyses. The results showed that a total of 104 PaWRKY genes with complete WRKY domains were identified, which were unevenly distributed on nine chromosomes. All the encoded proteins were hydrophilic, and most of them had poor in vitro stability and were susceptible to degradation. Based on phylogenetic analysis, the taxa were divided into seven subtribes, and Subtribe IIc comprises the most members, and ten core conserved motifs were predicted in total. Extensive homologous collinearity was found between this gene family and Oryza sativa subsp. japonica. The promoter regions of PaWRKY genes were enriched with numerous cis-acting elements responsive to abiotic stresses and phytohormones. Transcriptome data revealed that eight PaWRKY genes were differentially expressed under cold stress, including four upregulated and four downregulated genes, all of which harbored MeJA-responsive elements. This study clarified the molecular and evolutionary characteristics of the WRKY gene family in Pennisetum alopecuroides and screened out key cold stress-responsive genes, which laid a theoretical foundation for cold-tolerant molecular breeding of Pennisetum alopecuroides and evolutionary research of the WRKY gene family in Panicoideae., authors=SHI Zhi-fu1,2, WANG Xin2, YUE Yue-sen2, TENG Ke2, ZHOU Le2, LIU Ling-yun2, YUAN Su-fan2, FAN Xi-feng2, MU Na2, authorsList=SHI Zhi-fu, WANG Xin, YUE Yue-sen, TENG Ke, ZHOU Le, LIU Ling-yun, YUAN Su-fan, FAN Xi-feng, MU Na, authorCompany=1 Beijing University of Agriculture, Beijing 102206, China; 2. Institute of Grassland, Flowers and Landscape Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China, correspAuthors=null, authorNote=null, correspAuthorsNote=null, copyrightStatement=null, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, fund=null), CN=ArticleExt(id=1309575125930967910, articleId=1309575125658338149, tenantId=1146029695717560320, journalId=1308397196074385509, language=CN, title=狼尾草WRKY基因家族全基因组鉴定与冷胁迫表达分析, columnId=1309565024058835950, journalTitle=草地学报, columnName=研究论文, runingTitle=null, highlight=null, articleAbstract=为解析高抗寒性狼尾草(Pennisetum alopecuroides) WRKY基因家族的分子特征及其在冷胁迫响应中的作用,本研究采用全基因组与转录组联合分析,对 WRKY 基因家族进行系统鉴定、进化分析及冷胁迫表达模式研究。结果表明:共鉴定出104个含完整 WRKY 结构域的 PaWRKY 基因,这些基因不均匀分布于9条染色体;编码蛋白均为亲水蛋白,多数体外稳定性较弱,易降解。经系统进化分析,将其分为7个亚族,Ⅱc 亚族成员最多,共预测10个核心保守基序;该家族与粳稻存在广泛同源共线性关系。PaWRKY 基因启动子区富集大量逆境与激素响应顺式作用元件。转录组数据表明,8个 PaWRKY 基因在冷胁迫下出现差异表达,其中4个上调,4个下调,且均含有茉莉酸甲酯响应元件。本研究明确了狼尾草 WRKY 家族的分子与进化特征,筛选获得冷胁迫响应关键基因,为狼尾草抗寒分子育种及黍亚科 WRKY 家族进化研究提供理论依据。, authors=史志福1,2, 王鑫2, 岳跃森2, 滕珂2, 周仂2, 刘凌云2, 袁苏凡2, 范希峰2, 穆娜2, authorsList=史志福, 王鑫, 岳跃森, 滕珂, 周仂, 刘凌云, 袁苏凡, 范希峰, 穆娜, authorCompany=1 北京农学院, 北京 102206; 2 北京市农林科学院草业花卉与景观生态研究所, 北京 100097, correspAuthors=null, authorNote=史志福(2001-),男,汉族,河北邯郸人,硕士研究生,主要从事狼尾草育种研究,E-mail:3405966520@qq.com, correspAuthorsNote=null, copyrightStatement=null, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=BKvB29xdsEubeTulwkBDxQ==, pdfFileSize=11373324, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, 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Frontiers in Plant Science,2022,12:816156 WEI W,LIANG D W,BIAN X H,et al. GmWRKY54 improves drought tolerance through activating genes in abscisic acid and Ca2+ signaling pathways in transgenic soybean[J]. The Plant Journal,2019,100(2):384-398 TAO Z,KOU Y J,LIU H B,et al. OsWRKY45 alleles play different roles in abscisic acid signalling and salt stress tolerance but similar roles in drought and cold tolerance in rice[J]. Journal of Experimental Botany,2011,62(14):4863-4874 VAN ECK L,DAVIDSON R M,WU S C,et al. The transcriptional network of WRKY53 in cereals links oxidative responses to biotic and abiotic stress inputs[J]. Functional & Integrative Genomics,2014,14(2):351-362 ISHIGURO S,NAKAMURA K. Characterization of a cDNA encoding a novel DNA-binding protein,SPF1 that recognizes SP8 sequences in the 5' upstream regions of genes coding for sporamin and β-amylase from sweet potato[J]. Molecular and General Genetics,1994,244(6):563-571 EULGEM T,RUSHTON P J,ROBATZEK S,et al. The WRKY superfamily of plant transcription factors[J]. Trends in Plant Science,2000,5(5):199-206 WANG S Y,WU G Q,WEI M. Functional mechanisms of WRKY transcription factors in regulating plant response to abiotic stresses[J]. Chinese Journal of Biotechnology,2024,40(1):35-52 王淑叶,伍国强,魏明. WRKY转录因子调控植物逆境胁迫响应的作用机制[J]. 生物工程学报,2024,40(1):35-52 JIANG J J,MA S H,YE N H,et al. WRKY transcription factors in plant responses to stresses[J]. Journal of Integrative Plant Biology,2017,59(2):86-101 CHEN X J,LI C,WANG H,et al. WRKY transcription factors: evolution,binding,and action[J]. Phytopathology Research,2019,1(1):13 WEI K F,CHEN J,CHEN Y F,et al. Molecular phylogenetic and expression analysis of the complete WRKY transcription factor family in maize[J]. DNA Research,2012,19(2):153-164 GULZAR F,FU J Y,ZHU C Y,et al. Maize WRKY transcription factor ZmWRKY79 positively regulates drought tolerance through elevating ABA biosynthesis[J]. International Journal of Molecular Sciences,2021,22(18):10080 BAILLO E H,HANIF M S,GUO Y H,et al. Genome-wide Identification of WRKY transcription factor family members in sorghum (Sorghum bicolor (L.) moench)[J]. PLoS One,2020,15(8):e0236651 CHEN W,WANG Z K,TAO C Z,et al. SbWRKY50 promotes drought tolerance of sorghum by regulating lateral root formation[J]. Plant,Cell & Environment,2026,49(2):954-967 TENG K,GUO Q,LIU L Y,et al. Chromosome-level reference genome assembly provides insights into the evolution of Pennisetum alopecuroides[J]. Frontiers in Plant Science,2023,14:1195479 PAYSAN-LAFOSSE T,ANDREEVA A,BLUM M,et al. The Pfam protein families database: embracing AI/ML[J]. Nucleic Acids Research,2025,53(D1):D523-D534 ALTSCHUL S F,GISH W,MILLER W,et al. Basic local alignment search tool[J]. Journal of Molecular Biology,1990,215(3):403-410 JIN J P,TIAN F,YANG D C,et al. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants[J]. Nucleic Acids Research,2017,45(D1):D1040-D1045 GURUPRASAD K,BHASKER REDDY B V,PANDIT M W. Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence[J]. Protein Engineering,1990,4(2):155-161 KYTE J,DOOLITTLE R F. A simple method for displaying the hydropathic character of a protein[J]. Journal of Molecular Biology,1982,157(1):105-132 DENG Y R,LIU Y,WU L X,et al. Functions of plant WRKY transcription factors in nutrient uptake and utilization as well as detoxification of heavy metals[J]. Journal of Plant Nutrition and Fertilizers,2023,29(10):1932-1943 邓雅茹,柳燕,吴丽霞,等. WRKY转录因子调控植物养分吸收利用及重金属解毒的研究进展[J]. 植物营养与肥料学报,2023,29(10):1932-1943 LETUNIC I,BORK P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation[J]. Bioinformatics,2007,23(1):127-128 BAILEY T L,BODEN M,BUSKE F A,et al. MEME Suite: tools for motif discovery and searching[J]. Nucleic Acids Research,2009,37(suppl_2):W202-W208 LESCOT M,DÉHAIS P,THIJS G,et al. PlantCARE,a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences[J]. Nucleic Acids Research,2002,30(1):325-327 ZHANG L,TAN P H,TENG K,et al. Screening of reference genes for real-time fluorescence quantitative PCR in Kentucky bluegrass[J]. Acta Prataculturae Sinica,2017,26(3):75-81 张兰,檀鹏辉,滕珂,等. 草地早熟禾荧光定量PCR分析中内参基因的筛选[J]. 草业学报,2017,26(3):75-81 HU W J,REN Q Y,CHEN Y L,et al. Genome-wide identification and analysis of WRKY gene family in maize provide insights into regulatory network in response to abiotic stresses[J]. BMC Plant Biology,2021,21(1):427 YAN L,JIN H T,RAZA A,et al. WRKY genes provide novel insights into their role against Ralstonia solanacearum infection in cultivated peanut (Arachis hypogaea L.)[J]. Frontiers in Plant Science,2022,13:986673 MAO C L,ZHANG J,ZHANG Y N,et al. Genome-wide analysis of the WRKY gene family and their response to low-temperature stress in elephant grass[J]. BMC Genomics,2024,25(1):947 KHOSO M A,HUSSAIN A,RITONGA F N,et al. WRKY transcription factors (TFs): molecular switches to regulate drought,temperature,and salinity stresses in plants[J]. Frontiers in Plant Science,2022,13:1039329 YU Y P,JIANG Y J,SUN X Y,et al. Identification of the WRKY family genes and thier expression analysis in response to drought stress in centipedegrass[J]. Acta Agrestia Sinica,2024,32(5):1378-1391 于元平,蒋宇佳,孙向一,等. 假俭草WRKY家族基因鉴定及其响应干旱胁迫表达分析[J]. 草地学报,2024,32(5):1378-1391 WANG C T,RU J N,LIU Y W,et al. The maize WRKY transcription factor ZmWRKY40 confers drought resistance in transgenic Arabidopsis[J]. International Journal of Molecular Sciences,2018,19(9):2580 GUO M Y,YANG F J,ZHU L J,et al. Loss of cold tolerance is conferred by absence of the WRKY34 promoter fragment during tomato evolution[J]. Nature Communications,2024,15:6667 ZHANG J Y,LIANG Y H,ZHANG S M,et al. Global landscape of alternative splicing in maize response to low temperature[J]. Journal of Agricultural and Food Chemistry,2022,70(50):15715-15725)
Genome-Wide Identification and Cold Stress Expression Analysis of the WRKY Gene Family in Pennisetum alopecuroides
SHI Zhi-fu1,2, WANG Xin2, YUE Yue-sen2, TENG Ke2, ZHOU Le2, LIU Ling-yun2, YUAN Su-fan2, FAN Xi-feng2, MU Na2
Affiliations
1 Beijing University of Agriculture, Beijing 102206, China; 2. Institute of Grassland, Flowers and Landscape Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
To clarify the molecular characteristics of the WRKY gene family in highly cold-resistant Pennisetum alopecuroides and their functions in cold stress response, in this study we conducted systematic identification, phylogenetic analysis and cold stress-related expression pattern analysis of the WRKY gene family via combined genome-wide and transcriptome analyses. The results showed that a total of 104 PaWRKY genes with complete WRKY domains were identified, which were unevenly distributed on nine chromosomes. All the encoded proteins were hydrophilic, and most of them had poor in vitro stability and were susceptible to degradation. Based on phylogenetic analysis, the taxa were divided into seven subtribes, and Subtribe IIc comprises the most members, and ten core conserved motifs were predicted in total. Extensive homologous collinearity was found between this gene family and Oryza sativa subsp. japonica. The promoter regions of PaWRKY genes were enriched with numerous cis-acting elements responsive to abiotic stresses and phytohormones. Transcriptome data revealed that eight PaWRKY genes were differentially expressed under cold stress, including four upregulated and four downregulated genes, all of which harbored MeJA-responsive elements. This study clarified the molecular and evolutionary characteristics of the WRKY gene family in Pennisetum alopecuroides and screened out key cold stress-responsive genes, which laid a theoretical foundation for cold-tolerant molecular breeding of Pennisetum alopecuroides and evolutionary research of the WRKY gene family in Panicoideae.
SHI Zhi-fu, WANG Xin, YUE Yue-sen, TENG Ke, ZHOU Le, LIU Ling-yun, YUAN Su-fan, FAN Xi-feng, MU Na.
Genome-Wide Identification and Cold Stress Expression Analysis of the WRKY Gene Family in Pennisetum alopecuroides[J].
Acta Agrestia Sinica,
2026
, 34
(9)
: 3197
-3210
.
DOI: 10.11733/j.issn.1007-0435.2026.09.006
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Genome-wide analysis of the WRKY gene family and their response to low-temperature stress in elephant grass[J]. BMC Genomics,2024,25(1):947 KHOSO M A,HUSSAIN A,RITONGA F N,et al. WRKY transcription factors (TFs): molecular switches to regulate drought,temperature,and salinity stresses in plants[J]. Frontiers in Plant Science,2022,13:1039329 YU Y P,JIANG Y J,SUN X Y,et al. Identification of the WRKY family genes and thier expression analysis in response to drought stress in centipedegrass[J]. Acta Agrestia Sinica,2024,32(5):1378-1391 于元平,蒋宇佳,孙向一,等. 假俭草WRKY家族基因鉴定及其响应干旱胁迫表达分析[J]. 草地学报,2024,32(5):1378-1391 WANG C T,RU J N,LIU Y W,et al. The maize WRKY transcription factor ZmWRKY40 confers drought resistance in transgenic Arabidopsis[J]. International Journal of Molecular Sciences,2018,19(9):2580 GUO M Y,YANG F J,ZHU L J,et al. Loss of cold tolerance is conferred by absence of the WRKY34 promoter fragment during tomato evolution[J]. 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