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Genome-wide analysis of Dof family transcription factors and their responses to abiotic stresses in Chinese cabbage

BACKGROUND: Chinese cabbage is an important leaf vegetable that experienced long-term cultivation and artificial selection. Dof (DNA-binding One Zinc Finger) transcription factors, with a highly conserved Dof domain, are members of a major plant-specific transcription factor family that play importa...

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Autores principales: Ma, Jing, Li, Meng-Yao, Wang, Feng, Tang, Jun, Xiong, Ai-Sheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4320540/
https://www.ncbi.nlm.nih.gov/pubmed/25636232
http://dx.doi.org/10.1186/s12864-015-1242-9
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author Ma, Jing
Li, Meng-Yao
Wang, Feng
Tang, Jun
Xiong, Ai-Sheng
author_facet Ma, Jing
Li, Meng-Yao
Wang, Feng
Tang, Jun
Xiong, Ai-Sheng
author_sort Ma, Jing
collection PubMed
description BACKGROUND: Chinese cabbage is an important leaf vegetable that experienced long-term cultivation and artificial selection. Dof (DNA-binding One Zinc Finger) transcription factors, with a highly conserved Dof domain, are members of a major plant-specific transcription factor family that play important roles in many plant biological processes. The Dof family transcription factors, one of the most important families of transcriptional regulators in higher plants, are involved in massive aspects of plant growth, development, and response to abiotic stresses. Our study will supply resources for understanding how Dof transcription factors respond to abiotic stress and the interaction network of these genes in tolerance mechanism. RESULTS: In this study, we performed a comprehensive analysis of Dof family factors in Chinese cabbage. In total, 76 genes encoding BraDof family transcription factor were identified from Chinese cabbage, and those BraDof factors were divided into nine classes. Fifteen motifs were found based on Dof amino acid sequence alignments. Chromosome locations and gene duplications of BraDof family genes were also analyzed. Ten duplicate events of BraDof genes were discovered in Chinese cabbage chromosomes. The uneven distribution of BraDof genes in Brassica chromosomes may cause the expansion of BraDof genes. In the Dof family, 37 and 7 orthologous genes were identified between Chinese cabbage and Arabidopsis and between Chinese cabbage and Oryza sativa, respectively. The interaction networks of Dof factors in Chinese cabbage were also constructed. Expression profiles of nine selected genes from different nine classes subjected to four abiotic stresses (cold, heat, salt and drought) were further investigated by quantitative real-time PCR to obtain a better understanding of the functions and regulation mechanisms of BraDof family transcription factors in two Chinese cabbage varieties, ‘Lubaisanhao’ and ‘Qingdao 87-114’. CONCLUSIONS: Dof-family transcription factors were analyzed in genome of Chinese cabbage. Chromosomal locations showed that duplication might result in expansion. Response to abiotic stresses was elucidated in Chinese cabbage varieties. The results provide novel insights into the stress responses of BraDof genes and promote a better understanding of the construction and function of Dofs in Chinese cabbage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1242-9) contains supplementary material, which is available to authorized users.
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spelling pubmed-43205402015-02-08 Genome-wide analysis of Dof family transcription factors and their responses to abiotic stresses in Chinese cabbage Ma, Jing Li, Meng-Yao Wang, Feng Tang, Jun Xiong, Ai-Sheng BMC Genomics Research Article BACKGROUND: Chinese cabbage is an important leaf vegetable that experienced long-term cultivation and artificial selection. Dof (DNA-binding One Zinc Finger) transcription factors, with a highly conserved Dof domain, are members of a major plant-specific transcription factor family that play important roles in many plant biological processes. The Dof family transcription factors, one of the most important families of transcriptional regulators in higher plants, are involved in massive aspects of plant growth, development, and response to abiotic stresses. Our study will supply resources for understanding how Dof transcription factors respond to abiotic stress and the interaction network of these genes in tolerance mechanism. RESULTS: In this study, we performed a comprehensive analysis of Dof family factors in Chinese cabbage. In total, 76 genes encoding BraDof family transcription factor were identified from Chinese cabbage, and those BraDof factors were divided into nine classes. Fifteen motifs were found based on Dof amino acid sequence alignments. Chromosome locations and gene duplications of BraDof family genes were also analyzed. Ten duplicate events of BraDof genes were discovered in Chinese cabbage chromosomes. The uneven distribution of BraDof genes in Brassica chromosomes may cause the expansion of BraDof genes. In the Dof family, 37 and 7 orthologous genes were identified between Chinese cabbage and Arabidopsis and between Chinese cabbage and Oryza sativa, respectively. The interaction networks of Dof factors in Chinese cabbage were also constructed. Expression profiles of nine selected genes from different nine classes subjected to four abiotic stresses (cold, heat, salt and drought) were further investigated by quantitative real-time PCR to obtain a better understanding of the functions and regulation mechanisms of BraDof family transcription factors in two Chinese cabbage varieties, ‘Lubaisanhao’ and ‘Qingdao 87-114’. CONCLUSIONS: Dof-family transcription factors were analyzed in genome of Chinese cabbage. Chromosomal locations showed that duplication might result in expansion. Response to abiotic stresses was elucidated in Chinese cabbage varieties. The results provide novel insights into the stress responses of BraDof genes and promote a better understanding of the construction and function of Dofs in Chinese cabbage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1242-9) contains supplementary material, which is available to authorized users. BioMed Central 2015-01-31 /pmc/articles/PMC4320540/ /pubmed/25636232 http://dx.doi.org/10.1186/s12864-015-1242-9 Text en © Ma et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Ma, Jing
Li, Meng-Yao
Wang, Feng
Tang, Jun
Xiong, Ai-Sheng
Genome-wide analysis of Dof family transcription factors and their responses to abiotic stresses in Chinese cabbage
title Genome-wide analysis of Dof family transcription factors and their responses to abiotic stresses in Chinese cabbage
title_full Genome-wide analysis of Dof family transcription factors and their responses to abiotic stresses in Chinese cabbage
title_fullStr Genome-wide analysis of Dof family transcription factors and their responses to abiotic stresses in Chinese cabbage
title_full_unstemmed Genome-wide analysis of Dof family transcription factors and their responses to abiotic stresses in Chinese cabbage
title_short Genome-wide analysis of Dof family transcription factors and their responses to abiotic stresses in Chinese cabbage
title_sort genome-wide analysis of dof family transcription factors and their responses to abiotic stresses in chinese cabbage
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4320540/
https://www.ncbi.nlm.nih.gov/pubmed/25636232
http://dx.doi.org/10.1186/s12864-015-1242-9
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