Genome-wide identification and analysis of the WRKY gene family in Sainfoin (Onobrychis viciifolia) and their response to drought, salt, and alkali stress
Abstract Background The WRKY gene family plays important roles in plant growth, development, and response to various stresses. Despite the significance of Sainfoin (Onobrychis viciifolia) as an important forage legume species, WRKY genes in this species have not been studied thoroughly. The aim of t...
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2025-05-01
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| Online Access: | https://doi.org/10.1186/s12864-025-11646-2 |
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| author | Wenxiang Li Yinuo Yan Yanxia Liang Shiyao Yue Yaling Liu Feng Yuan Mengrong Xu Dengxia Yi Jun Li Yan Zhao Lili Nan Wenbo Jiang |
| author_facet | Wenxiang Li Yinuo Yan Yanxia Liang Shiyao Yue Yaling Liu Feng Yuan Mengrong Xu Dengxia Yi Jun Li Yan Zhao Lili Nan Wenbo Jiang |
| author_sort | Wenxiang Li |
| collection | DOAJ |
| description | Abstract Background The WRKY gene family plays important roles in plant growth, development, and response to various stresses. Despite the significance of Sainfoin (Onobrychis viciifolia) as an important forage legume species, WRKY genes in this species have not been studied thoroughly. The aim of this study was to identify WRKY genes family in Sainfoin genome, particularly those linked to response to drought, salt, and alkali stresses. Results A total of 253 WRKY genes (OvWRKY) were identified in Sainfoin. Phylogenetic analysis and conserved domain analysis divided these genes into seven subfamilies with similar conserved motifs but different gene structures. Collinearity analysis identified 232 duplicated gene pairs, including four tandem repeat pairs, indicating role of segmental duplication in the expansion of the OvWRKY gene family. Transcriptome analysis revealed that highly expressed genes under drought, salt, and alkali stress mostly belonged to groups I, III, IId, IIa, and IIb. OvWRKY89 was down-regulated, and OvWRKY147 was up-regulated by drought, salt, and alkali treatments. OvWRKY240 and OvWRKY164 were down-regulated by both drought and salt stress, and OvWRKY36, OvWRKY107, OvWRKY65, and OvWRKY200 were down-regulated by both salt and alkali stress. Protein association network analysis using STRING suggested that OvWRKY89 is functionally associated with five other WRKY proteins and four stress-related proteins. Conclusions In this study, we identified and analyzed the WRKY gene family members in Sainfoin for their physicochemical properties, gene structures, conserved motifs, phylogenetic relationships, and expression under drought, salt, and alkali stresses. Some key genes were identified based on enrichment analysis, potential protein network, and the expression under drought, salt, and alkali stress. This study provides insights into the diversity of the WRKY gene family and their roles in drought, salt, and alkali stress responses in Sainfoin. |
| format | Article |
| id | doaj-art-7a1734cc2d944774a33fed39fc7260bf |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-7a1734cc2d944774a33fed39fc7260bf2025-08-20T03:52:19ZengBMCBMC Genomics1471-21642025-05-0126111710.1186/s12864-025-11646-2Genome-wide identification and analysis of the WRKY gene family in Sainfoin (Onobrychis viciifolia) and their response to drought, salt, and alkali stressWenxiang Li0Yinuo Yan1Yanxia Liang2Shiyao Yue3Yaling Liu4Feng Yuan5Mengrong Xu6Dengxia Yi7Jun Li8Yan Zhao9Lili Nan10Wenbo Jiang11Institute of Animal Science, Chinese Academy of Agricultural SciencesInstitute of Animal Science, Chinese Academy of Agricultural SciencesInstitute of Animal Science, Chinese Academy of Agricultural SciencesInstitute of Animal Science, Chinese Academy of Agricultural SciencesInner Mongolia Pratacultural Technology Innovation Center Co. LtdInner Mongolia Pratacultural Technology Innovation Center Co. LtdInstitute of Animal Science, Chinese Academy of Agricultural SciencesInstitute of Animal Science, Chinese Academy of Agricultural SciencesKey Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia UniversityCollege of Grassland, Resources and Environment, Key Laboratory of Grassland Resources, Ministry of Education, Inner Mongolia Agricultural UniversityKey Laboratory of Grassland Ecosystem of Ministry of Education, College of Pratacultural Science, Gansu Agricultural UniversityInstitute of Animal Science, Chinese Academy of Agricultural SciencesAbstract Background The WRKY gene family plays important roles in plant growth, development, and response to various stresses. Despite the significance of Sainfoin (Onobrychis viciifolia) as an important forage legume species, WRKY genes in this species have not been studied thoroughly. The aim of this study was to identify WRKY genes family in Sainfoin genome, particularly those linked to response to drought, salt, and alkali stresses. Results A total of 253 WRKY genes (OvWRKY) were identified in Sainfoin. Phylogenetic analysis and conserved domain analysis divided these genes into seven subfamilies with similar conserved motifs but different gene structures. Collinearity analysis identified 232 duplicated gene pairs, including four tandem repeat pairs, indicating role of segmental duplication in the expansion of the OvWRKY gene family. Transcriptome analysis revealed that highly expressed genes under drought, salt, and alkali stress mostly belonged to groups I, III, IId, IIa, and IIb. OvWRKY89 was down-regulated, and OvWRKY147 was up-regulated by drought, salt, and alkali treatments. OvWRKY240 and OvWRKY164 were down-regulated by both drought and salt stress, and OvWRKY36, OvWRKY107, OvWRKY65, and OvWRKY200 were down-regulated by both salt and alkali stress. Protein association network analysis using STRING suggested that OvWRKY89 is functionally associated with five other WRKY proteins and four stress-related proteins. Conclusions In this study, we identified and analyzed the WRKY gene family members in Sainfoin for their physicochemical properties, gene structures, conserved motifs, phylogenetic relationships, and expression under drought, salt, and alkali stresses. Some key genes were identified based on enrichment analysis, potential protein network, and the expression under drought, salt, and alkali stress. This study provides insights into the diversity of the WRKY gene family and their roles in drought, salt, and alkali stress responses in Sainfoin.https://doi.org/10.1186/s12864-025-11646-2SainfoinWRKY familyDroughtSaltAlkaliGenome-wide analysis |
| spellingShingle | Wenxiang Li Yinuo Yan Yanxia Liang Shiyao Yue Yaling Liu Feng Yuan Mengrong Xu Dengxia Yi Jun Li Yan Zhao Lili Nan Wenbo Jiang Genome-wide identification and analysis of the WRKY gene family in Sainfoin (Onobrychis viciifolia) and their response to drought, salt, and alkali stress BMC Genomics Sainfoin WRKY family Drought Salt Alkali Genome-wide analysis |
| title | Genome-wide identification and analysis of the WRKY gene family in Sainfoin (Onobrychis viciifolia) and their response to drought, salt, and alkali stress |
| title_full | Genome-wide identification and analysis of the WRKY gene family in Sainfoin (Onobrychis viciifolia) and their response to drought, salt, and alkali stress |
| title_fullStr | Genome-wide identification and analysis of the WRKY gene family in Sainfoin (Onobrychis viciifolia) and their response to drought, salt, and alkali stress |
| title_full_unstemmed | Genome-wide identification and analysis of the WRKY gene family in Sainfoin (Onobrychis viciifolia) and their response to drought, salt, and alkali stress |
| title_short | Genome-wide identification and analysis of the WRKY gene family in Sainfoin (Onobrychis viciifolia) and their response to drought, salt, and alkali stress |
| title_sort | genome wide identification and analysis of the wrky gene family in sainfoin onobrychis viciifolia and their response to drought salt and alkali stress |
| topic | Sainfoin WRKY family Drought Salt Alkali Genome-wide analysis |
| url | https://doi.org/10.1186/s12864-025-11646-2 |
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