Genome-wide characterization of the GRF family and their roles in response to salt stress in Gossypium
Abstract Background Cotton (Gossypium spp.) is the most important world-wide fiber crop but salt stress limits cotton production in coastal and other areas. Growth regulation factors (GRFs) play regulatory roles in response to salt stress, but their roles have not been studied in cotton under salt s...
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2020-08-01
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Series: | BMC Genomics |
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Online Access: | http://link.springer.com/article/10.1186/s12864-020-06986-0 |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Jun-Feng Cao Jin-Quan Huang Xia Liu Chao-Chen Huang Zi-Shou Zheng Xiu-Fang Zhang Xiao-Xia Shangguan Ling-Jian Wang Yu-Gao Zhang Jonathan F. Wendel Corrinne E. Grover Zhi-Wen Chen |
spellingShingle |
Jun-Feng Cao Jin-Quan Huang Xia Liu Chao-Chen Huang Zi-Shou Zheng Xiu-Fang Zhang Xiao-Xia Shangguan Ling-Jian Wang Yu-Gao Zhang Jonathan F. Wendel Corrinne E. Grover Zhi-Wen Chen Genome-wide characterization of the GRF family and their roles in response to salt stress in Gossypium BMC Genomics Growth regulating factor Cotton Phylogenetics Organ-specific expression Salt stress |
author_facet |
Jun-Feng Cao Jin-Quan Huang Xia Liu Chao-Chen Huang Zi-Shou Zheng Xiu-Fang Zhang Xiao-Xia Shangguan Ling-Jian Wang Yu-Gao Zhang Jonathan F. Wendel Corrinne E. Grover Zhi-Wen Chen |
author_sort |
Jun-Feng Cao |
title |
Genome-wide characterization of the GRF family and their roles in response to salt stress in Gossypium |
title_short |
Genome-wide characterization of the GRF family and their roles in response to salt stress in Gossypium |
title_full |
Genome-wide characterization of the GRF family and their roles in response to salt stress in Gossypium |
title_fullStr |
Genome-wide characterization of the GRF family and their roles in response to salt stress in Gossypium |
title_full_unstemmed |
Genome-wide characterization of the GRF family and their roles in response to salt stress in Gossypium |
title_sort |
genome-wide characterization of the grf family and their roles in response to salt stress in gossypium |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2020-08-01 |
description |
Abstract Background Cotton (Gossypium spp.) is the most important world-wide fiber crop but salt stress limits cotton production in coastal and other areas. Growth regulation factors (GRFs) play regulatory roles in response to salt stress, but their roles have not been studied in cotton under salt stress. Results We identified 19 GRF genes in G. raimondii, 18 in G. arboreum, 34 in G. hirsutum and 45 in G. barbadense, respectively. These GRF genes were phylogenetically analyzed leading to the recognition of seven GRF clades. GRF genes from diploid cottons (G. raimondii and G. arboreum) were largely retained in allopolyploid cotton, with subsequent gene expansion in G. barbadense relative to G. hirsutum. Most G. hirsutum GRF (GhGRF) genes are preferentially expressed in young and growing tissues. To explore their possible role in salt stress, we used qRT-PCR to study expression responses to NaCl treatment, showing that five GhGRF genes were down-regulated in leaves. RNA-seq experiments showed that seven GhGRF genes exhibited decreased expression in leaves under NaCl treatment, three of which (GhGRF3, GhGRF4, and GhGRF16) were identified by both RNA-seq and qRT-PCR. We also identified six and three GRF genes that exhibit decreased expression under salt stress in G. arboreum and G. barbadense, respectively. Consistent with its lack of leaf withering or yellowing under the salt treatment conditions, G. arboreum had better salt tolerance than G. hirsutum and G. barbadense. Our results suggest that GRF genes are involved in salt stress responses in Gossypium. Conclusion In summary, we identified candidate GRF genes that were involved in salt stress responses in cotton. |
topic |
Growth regulating factor Cotton Phylogenetics Organ-specific expression Salt stress |
url |
http://link.springer.com/article/10.1186/s12864-020-06986-0 |
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doaj-b99c379bc33f4fd59dc3d8d2b9c1eb742020-11-25T03:43:50ZengBMCBMC Genomics1471-21642020-08-0121111610.1186/s12864-020-06986-0Genome-wide characterization of the GRF family and their roles in response to salt stress in GossypiumJun-Feng Cao0Jin-Quan Huang1Xia Liu2Chao-Chen Huang3Zi-Shou Zheng4Xiu-Fang Zhang5Xiao-Xia Shangguan6Ling-Jian Wang7Yu-Gao Zhang8Jonathan F. Wendel9Corrinne E. Grover10Zhi-Wen Chen11National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesNational Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesEsquel GroupNational Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesNational Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesNational Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesNational Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesNational Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesEsquel GroupDepartment of Ecology, Evolution and Organismal Biology, Iowa State UniversityDepartment of Ecology, Evolution and Organismal Biology, Iowa State UniversityNational Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesAbstract Background Cotton (Gossypium spp.) is the most important world-wide fiber crop but salt stress limits cotton production in coastal and other areas. Growth regulation factors (GRFs) play regulatory roles in response to salt stress, but their roles have not been studied in cotton under salt stress. Results We identified 19 GRF genes in G. raimondii, 18 in G. arboreum, 34 in G. hirsutum and 45 in G. barbadense, respectively. These GRF genes were phylogenetically analyzed leading to the recognition of seven GRF clades. GRF genes from diploid cottons (G. raimondii and G. arboreum) were largely retained in allopolyploid cotton, with subsequent gene expansion in G. barbadense relative to G. hirsutum. Most G. hirsutum GRF (GhGRF) genes are preferentially expressed in young and growing tissues. To explore their possible role in salt stress, we used qRT-PCR to study expression responses to NaCl treatment, showing that five GhGRF genes were down-regulated in leaves. RNA-seq experiments showed that seven GhGRF genes exhibited decreased expression in leaves under NaCl treatment, three of which (GhGRF3, GhGRF4, and GhGRF16) were identified by both RNA-seq and qRT-PCR. We also identified six and three GRF genes that exhibit decreased expression under salt stress in G. arboreum and G. barbadense, respectively. Consistent with its lack of leaf withering or yellowing under the salt treatment conditions, G. arboreum had better salt tolerance than G. hirsutum and G. barbadense. Our results suggest that GRF genes are involved in salt stress responses in Gossypium. Conclusion In summary, we identified candidate GRF genes that were involved in salt stress responses in cotton.http://link.springer.com/article/10.1186/s12864-020-06986-0Growth regulating factorCottonPhylogeneticsOrgan-specific expressionSalt stress |