Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)
Abstract Background GRAS transcription factors perform indispensable functions in various biological processes, such as plant growth, fruit development, and biotic and abiotic stress responses. The development of whole-genome sequencing has allowed the GRAS gene family to be identified and character...
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| Format: | Article |
| Language: | English |
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BMC
2021-11-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-021-03277-y |
| _version_ | 1818897293334544384 |
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| author | Yu Fan Xiaobao Wei Dili Lai Hao Yang Liang Feng Long Li Kexin Niu Long Chen Dabing Xiang Jingjun Ruan Jun Yan Jianping Cheng |
| author_facet | Yu Fan Xiaobao Wei Dili Lai Hao Yang Liang Feng Long Li Kexin Niu Long Chen Dabing Xiang Jingjun Ruan Jun Yan Jianping Cheng |
| author_sort | Yu Fan |
| collection | DOAJ |
| description | Abstract Background GRAS transcription factors perform indispensable functions in various biological processes, such as plant growth, fruit development, and biotic and abiotic stress responses. The development of whole-genome sequencing has allowed the GRAS gene family to be identified and characterized in many species. However, thorough in-depth identification or systematic analysis of GRAS family genes in foxtail millet has not been conducted. Results In this study, 57 GRAS genes of foxtail millet (SiGRASs) were identified and renamed according to the chromosomal distribution of the SiGRAS genes. Based on the number of conserved domains and gene structure, the SiGRAS genes were divided into 13 subfamilies via phylogenetic tree analysis. The GRAS genes were unevenly distributed on nine chromosomes, and members of the same subfamily had similar gene structures and motif compositions. Genetic structure analysis showed that most SiGRAS genes lacked introns. Some SiGRAS genes were derived from gene duplication events, and segmental duplications may have contributed more to GRAS gene family expansion than tandem duplications. Quantitative polymerase chain reaction showed significant differences in the expression of SiGRAS genes in different tissues and stages of fruits development, which indicated the complexity of the physiological functions of SiGRAS. In addition, exogenous paclobutrazol treatment significantly altered the transcription levels of DELLA subfamily members, downregulated the gibberellin content, and decreased the plant height of foxtail millet, while it increased the fruit weight. In addition, SiGRAS13 and SiGRAS25 may have the potential for genetic improvement and functional gene research in foxtail millet. Conclusions Collectively, this study will be helpful for further analysing the biological function of SiGRAS. Our results may contribute to improving the genetic breeding of foxtail millet. |
| first_indexed | 2024-12-19T19:13:52Z |
| format | Article |
| id | doaj.art-91343e5179124f0fbdcd214c92afb137 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-19T19:13:52Z |
| publishDate | 2021-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-91343e5179124f0fbdcd214c92afb1372022-12-21T20:09:11ZengBMCBMC Plant Biology1471-22292021-11-0121111910.1186/s12870-021-03277-yGenome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)Yu Fan0Xiaobao Wei1Dili Lai2Hao Yang3Liang Feng4Long Li5Kexin Niu6Long Chen7Dabing Xiang8Jingjun Ruan9Jun Yan10Jianping Cheng11College of Agriculture, Guizhou UniversityGuizhou provincial Center For Disease Control And PreventionCollege of Agriculture, Guizhou UniversityCollege of Agriculture, Guizhou UniversityChengdu Institute of Food InspectionHenan university of technologyHenan university of technologyDepartment of Nursing, Sichuan Tianyi CollegeSchool of Food and Biological engineering, Chengdu UniversityCollege of Agriculture, Guizhou UniversitySchool of Food and Biological engineering, Chengdu UniversityCollege of Agriculture, Guizhou UniversityAbstract Background GRAS transcription factors perform indispensable functions in various biological processes, such as plant growth, fruit development, and biotic and abiotic stress responses. The development of whole-genome sequencing has allowed the GRAS gene family to be identified and characterized in many species. However, thorough in-depth identification or systematic analysis of GRAS family genes in foxtail millet has not been conducted. Results In this study, 57 GRAS genes of foxtail millet (SiGRASs) were identified and renamed according to the chromosomal distribution of the SiGRAS genes. Based on the number of conserved domains and gene structure, the SiGRAS genes were divided into 13 subfamilies via phylogenetic tree analysis. The GRAS genes were unevenly distributed on nine chromosomes, and members of the same subfamily had similar gene structures and motif compositions. Genetic structure analysis showed that most SiGRAS genes lacked introns. Some SiGRAS genes were derived from gene duplication events, and segmental duplications may have contributed more to GRAS gene family expansion than tandem duplications. Quantitative polymerase chain reaction showed significant differences in the expression of SiGRAS genes in different tissues and stages of fruits development, which indicated the complexity of the physiological functions of SiGRAS. In addition, exogenous paclobutrazol treatment significantly altered the transcription levels of DELLA subfamily members, downregulated the gibberellin content, and decreased the plant height of foxtail millet, while it increased the fruit weight. In addition, SiGRAS13 and SiGRAS25 may have the potential for genetic improvement and functional gene research in foxtail millet. Conclusions Collectively, this study will be helpful for further analysing the biological function of SiGRAS. Our results may contribute to improving the genetic breeding of foxtail millet.https://doi.org/10.1186/s12870-021-03277-ySetaria italicaGRAS gene familyGenome-wide analysisDELLA proteinFruit developmentAbiotic stress |
| spellingShingle | Yu Fan Xiaobao Wei Dili Lai Hao Yang Liang Feng Long Li Kexin Niu Long Chen Dabing Xiang Jingjun Ruan Jun Yan Jianping Cheng Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.) BMC Plant Biology Setaria italica GRAS gene family Genome-wide analysis DELLA protein Fruit development Abiotic stress |
| title | Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.) |
| title_full | Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.) |
| title_fullStr | Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.) |
| title_full_unstemmed | Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.) |
| title_short | Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.) |
| title_sort | genome wide investigation of the gras transcription factor family in foxtail millet setaria italica l |
| topic | Setaria italica GRAS gene family Genome-wide analysis DELLA protein Fruit development Abiotic stress |
| url | https://doi.org/10.1186/s12870-021-03277-y |
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