Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors under Multiple Stresses in Brassica napus
WRKY transcription factors play important roles in responses to environmental stress stimuli. Using a genome-wide domain analysis, we identified 287 WRKY genes with 343 WRKY domains in the sequenced genome of Brassica napus, 139 in the A sub-genome and 148 in the C sub-genome. These genes were class...
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| Published in: | PloS one Vol. 11; no. 6; p. e0157558 |
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| Main Authors: | , , , , , , , |
| Format: | Journal Article |
| Language: | English |
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20.06.2016
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| ISSN: | 1932-6203, 1932-6203 |
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| Abstract | WRKY transcription factors play important roles in responses to environmental stress stimuli. Using a genome-wide domain analysis, we identified 287 WRKY genes with 343 WRKY domains in the sequenced genome of Brassica napus, 139 in the A sub-genome and 148 in the C sub-genome. These genes were classified into eight groups based on phylogenetic analysis. In the 343 WRKY domains, a total of 26 members showed divergence in the WRKY domain, and 21 belonged to group I. This finding suggested that WRKY genes in group I are more active and variable compared with genes in other groups. Using genome-wide identification and analysis of the WRKY gene family in Brassica napus, we observed genome duplication, chromosomal/segmental duplications and tandem duplication. All of these duplications contributed to the expansion of the WRKY gene family. The duplicate segments that were detected indicated that genome duplication events occurred in the two diploid progenitors B. rapa and B. olearecea before they combined to form B. napus. Analysis of the public microarray database and EST database for B. napus indicated that 74 WRKY genes were induced or preferentially expressed under stress conditions. According to the public QTL data, we identified 77 WRKY genes in 31 QTL regions related to various stress tolerance. We further evaluated the expression of 26 BnaWRKY genes under multiple stresses by qRT-PCR. Most of the genes were induced by low temperature, salinity and drought stress, indicating that the WRKYs play important roles in B. napus stress responses. Further, three BnaWRKY genes were strongly responsive to the three multiple stresses simultaneously, which suggests that these 3 WRKY may have multi-functional roles in stress tolerance and can potentially be used in breeding new rapeseed cultivars. We also found six tandem repeat pairs exhibiting similar expression profiles under the various stress conditions, and three pairs were mapped in the stress related QTL regions, indicating tandem duplicate WRKYs in the adaptive responses to environmental stimuli during the evolution process. Our results provide a framework for future studies regarding the function of WRKY genes in response to stress in B. napus. |
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| AbstractList | WRKY transcription factors play important roles in responses to environmental stress stimuli. Using a genome-wide domain analysis, we identified 287 WRKY genes with 343 WRKY domains in the sequenced genome of Brassica napus, 139 in the A sub-genome and 148 in the C sub-genome. These genes were classified into eight groups based on phylogenetic analysis. In the 343 WRKY domains, a total of 26 members showed divergence in the WRKY domain, and 21 belonged to group I. This finding suggested that WRKY genes in group I are more active and variable compared with genes in other groups. Using genome-wide identification and analysis of the WRKY gene family in Brassica napus, we observed genome duplication, chromosomal/segmental duplications and tandem duplication. All of these duplications contributed to the expansion of the WRKY gene family. The duplicate segments that were detected indicated that genome duplication events occurred in the two diploid progenitors B. rapa and B. olearecea before they combined to form B. napus. Analysis of the public microarray database and EST database for B. napus indicated that 74 WRKY genes were induced or preferentially expressed under stress conditions. According to the public QTL data, we identified 77 WRKY genes in 31 QTL regions related to various stress tolerance. We further evaluated the expression of 26 BnaWRKY genes under multiple stresses by qRT-PCR. Most of the genes were induced by low temperature, salinity and drought stress, indicating that the WRKYs play important roles in B. napus stress responses. Further, three BnaWRKY genes were strongly responsive to the three multiple stresses simultaneously, which suggests that these 3 WRKY may have multi-functional roles in stress tolerance and can potentially be used in breeding new rapeseed cultivars. We also found six tandem repeat pairs exhibiting similar expression profiles under the various stress conditions, and three pairs were mapped in the stress related QTL regions, indicating tandem duplicate WRKYs in the adaptive responses to environmental stimuli during the evolution process. Our results provide a framework for future studies regarding the function of WRKY genes in response to stress in B. napus. |
| Audience | Academic |
| Author | Mao, Shaoshuai Li, Jiana Gao, Yulong Wu, Daoming He, Yajun Cui, Yixin Qian, Wei Zhu, Liying |
| AuthorAffiliation | Huazhong university of Science and Technology, CHINA 1 College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China 2 Yunnan Academy of Tobacco Agricultural Sciences, Yuxi 653100, China |
| AuthorAffiliation_xml | – name: 1 College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China – name: 2 Yunnan Academy of Tobacco Agricultural Sciences, Yuxi 653100, China – name: Huazhong university of Science and Technology, CHINA |
| Author_xml | – sequence: 1 givenname: Yajun surname: He fullname: He, Yajun – sequence: 2 givenname: Shaoshuai surname: Mao fullname: Mao, Shaoshuai – sequence: 3 givenname: Yulong surname: Gao fullname: Gao, Yulong – sequence: 4 givenname: Liying surname: Zhu fullname: Zhu, Liying – sequence: 5 givenname: Daoming surname: Wu fullname: Wu, Daoming – sequence: 6 givenname: Yixin surname: Cui fullname: Cui, Yixin – sequence: 7 givenname: Jiana surname: Li fullname: Li, Jiana – sequence: 8 givenname: Wei surname: Qian fullname: Qian, Wei |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/27322342$$D View this record in MEDLINE/PubMed |
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| Copyright | COPYRIGHT 2016 Public Library of Science 2016 He et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2016 He et al 2016 He et al |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Competing Interests: The authors have declared that no competing interests exist. Conceived and designed the experiments: YH WQ. Performed the experiments: YH DW YC. Analyzed the data: YH SM YG LZ. Wrote the paper: YH JL WQ. |
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| SubjectTerms | Adaptation, Physiological - genetics Agronomy Amino Acid Motifs Amino Acid Sequence Analysis Arabidopsis Arabidopsis - genetics Biology and Life Sciences Biotechnology Brassica Brassica napus Brassica napus - genetics Brassica napus - physiology Brassica oleracea Brassica rapa Breeding Chromosomes, Plant - genetics Computer Simulation Conserved Sequence Cultivars Databases, Genetic Divergence DNA microarrays Drought Ecology and Environmental Sciences Environmental effects Environmental stress Evolution Gene Duplication Gene expression Gene Expression Regulation, Plant Genes Genes, Plant Genome, Plant Genome-wide association studies Genomes Genomics Glycine max Identification Information sources Low temperature Molecular biology Multigene Family Oryza Phylogenetics Phylogeny Physical Sciences Plant Proteins - chemistry Plant Proteins - genetics Plant Proteins - metabolism Polyethylene glycol Protein Domains Proteins Quantitative trait loci Quantitative Trait Loci - genetics Rape (Plant) Rape plants Rapeseed Reproduction (copying) Research and Analysis Methods Sclerotinia sclerotiorum Sorghum Stimuli Stress response Stress, Physiological - genetics Stresses Transcription factors Transcription Factors - chemistry Transcription Factors - genetics Transcription Factors - metabolism Trends |
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| Title | Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors under Multiple Stresses in Brassica napus |
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