Genome-wide identification, structural characterization and gene expression analysis of the WRKY transcription factor family in pea (Pisum sativum L.)
Abstract Background The WRKY gene family is one of the largest families of transcription factors in higher plants, and WRKY transcription factors play important roles in plant growth and development as well as in response to abiotic stresses; however, the WRKY gene family in pea has not been systema...
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| Format: | Article |
| Language: | English |
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BMC
2024-02-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-024-04774-6 |
| _version_ | 1827328041202745344 |
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| author | Ruiqi Xiong Zhonghua Peng Hui Zhou Guoxing Xue Ailing He Xin Yao Wenfeng Weng Weijiao Wu Chao Ma Qing Bai Jingjun Ruan |
| author_facet | Ruiqi Xiong Zhonghua Peng Hui Zhou Guoxing Xue Ailing He Xin Yao Wenfeng Weng Weijiao Wu Chao Ma Qing Bai Jingjun Ruan |
| author_sort | Ruiqi Xiong |
| collection | DOAJ |
| description | Abstract Background The WRKY gene family is one of the largest families of transcription factors in higher plants, and WRKY transcription factors play important roles in plant growth and development as well as in response to abiotic stresses; however, the WRKY gene family in pea has not been systematically reported. Results In this study, 89 pea WRKY genes were identified and named according to the random distribution of PsWRKY genes on seven chromosomes. The gene family was found to have nine pairs of tandem duplicates and 19 pairs of segment duplicates. Phylogenetic analyses of the PsWRKY and 60 Arabidopsis WRKY proteins were performed to determine their homology, and the PsWRKYs were classified into seven subfamilies. Analysis of the physicochemical properties, motif composition, and gene structure of pea WRKYs revealed significant differences in the physicochemical properties within the PsWRKY family; however, their gene structure and protein-conserved motifs were highly conserved among the subfamilies. To further investigate the evolutionary relationships of the PsWRKY family, we constructed comparative syntenic maps of pea with representative monocotyledonous and dicotyledonous plants and found that it was most recently homologous to the dicotyledonous WRKY gene families. Cis-acting element analysis of PsWRKY genes revealed that this gene family can respond to hormones, such as abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellin (GA), methyl jasmonate (MeJA), and salicylic acid (SA). Further analysis of the expression of 14 PsWRKY genes from different subfamilies in different tissues and fruit developmental stages, as well as under five different hormone treatments, revealed differences in their expression patterns in the different tissues and fruit developmental stages, as well as under hormone treatments, suggesting that PsWRKY genes may have different physiological functions and respond to hormones. Conclusions In this study, we systematically identified WRKY genes in pea for the first time and further investigated their physicochemical properties, evolution, and expression patterns, providing a theoretical basis for future studies on the functional characterization of pea WRKY genes during plant growth and development. |
| first_indexed | 2024-03-07T15:11:16Z |
| format | Article |
| id | doaj.art-a02f2fb2ca0b441185749bacea794828 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-03-07T15:11:16Z |
| publishDate | 2024-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-a02f2fb2ca0b441185749bacea7948282024-03-05T18:38:23ZengBMCBMC Plant Biology1471-22292024-02-0124111810.1186/s12870-024-04774-6Genome-wide identification, structural characterization and gene expression analysis of the WRKY transcription factor family in pea (Pisum sativum L.)Ruiqi Xiong0Zhonghua Peng1Hui Zhou2Guoxing Xue3Ailing He4Xin Yao5Wenfeng Weng6Weijiao Wu7Chao Ma8Qing Bai9Jingjun Ruan10College of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversitySichuan Province Seed StationCollege of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversityAbstract Background The WRKY gene family is one of the largest families of transcription factors in higher plants, and WRKY transcription factors play important roles in plant growth and development as well as in response to abiotic stresses; however, the WRKY gene family in pea has not been systematically reported. Results In this study, 89 pea WRKY genes were identified and named according to the random distribution of PsWRKY genes on seven chromosomes. The gene family was found to have nine pairs of tandem duplicates and 19 pairs of segment duplicates. Phylogenetic analyses of the PsWRKY and 60 Arabidopsis WRKY proteins were performed to determine their homology, and the PsWRKYs were classified into seven subfamilies. Analysis of the physicochemical properties, motif composition, and gene structure of pea WRKYs revealed significant differences in the physicochemical properties within the PsWRKY family; however, their gene structure and protein-conserved motifs were highly conserved among the subfamilies. To further investigate the evolutionary relationships of the PsWRKY family, we constructed comparative syntenic maps of pea with representative monocotyledonous and dicotyledonous plants and found that it was most recently homologous to the dicotyledonous WRKY gene families. Cis-acting element analysis of PsWRKY genes revealed that this gene family can respond to hormones, such as abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellin (GA), methyl jasmonate (MeJA), and salicylic acid (SA). Further analysis of the expression of 14 PsWRKY genes from different subfamilies in different tissues and fruit developmental stages, as well as under five different hormone treatments, revealed differences in their expression patterns in the different tissues and fruit developmental stages, as well as under hormone treatments, suggesting that PsWRKY genes may have different physiological functions and respond to hormones. Conclusions In this study, we systematically identified WRKY genes in pea for the first time and further investigated their physicochemical properties, evolution, and expression patterns, providing a theoretical basis for future studies on the functional characterization of pea WRKY genes during plant growth and development.https://doi.org/10.1186/s12870-024-04774-6Pisum sativum L.WRKY gene familyGenome-wide identificationTranscription factorHormone treatment |
| spellingShingle | Ruiqi Xiong Zhonghua Peng Hui Zhou Guoxing Xue Ailing He Xin Yao Wenfeng Weng Weijiao Wu Chao Ma Qing Bai Jingjun Ruan Genome-wide identification, structural characterization and gene expression analysis of the WRKY transcription factor family in pea (Pisum sativum L.) BMC Plant Biology Pisum sativum L. WRKY gene family Genome-wide identification Transcription factor Hormone treatment |
| title | Genome-wide identification, structural characterization and gene expression analysis of the WRKY transcription factor family in pea (Pisum sativum L.) |
| title_full | Genome-wide identification, structural characterization and gene expression analysis of the WRKY transcription factor family in pea (Pisum sativum L.) |
| title_fullStr | Genome-wide identification, structural characterization and gene expression analysis of the WRKY transcription factor family in pea (Pisum sativum L.) |
| title_full_unstemmed | Genome-wide identification, structural characterization and gene expression analysis of the WRKY transcription factor family in pea (Pisum sativum L.) |
| title_short | Genome-wide identification, structural characterization and gene expression analysis of the WRKY transcription factor family in pea (Pisum sativum L.) |
| title_sort | genome wide identification structural characterization and gene expression analysis of the wrky transcription factor family in pea pisum sativum l |
| topic | Pisum sativum L. WRKY gene family Genome-wide identification Transcription factor Hormone treatment |
| url | https://doi.org/10.1186/s12870-024-04774-6 |
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