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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Autores principales:	Yu Fan, Xiaobao Wei, Dili Lai, Hao Yang, Liang Feng, Long Li, Kexin Niu, Long Chen, Dabing Xiang, Jingjun Ruan, Jun Yan, Jianping Cheng
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Setaria italica GRAS gene family Genome-wide analysis DELLA protein Fruit development Abiotic stress Botany QK1-989
Acceso en línea:	https://doaj.org/article/91343e5179124f0fbdcd214c92afb137
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spelling	oai:doaj.org-article:91343e5179124f0fbdcd214c92afb1372021-11-07T12:09:31ZGenome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)10.1186/s12870-021-03277-y1471-2229https://doaj.org/article/91343e5179124f0fbdcd214c92afb1372021-11-01T00:00:00Zhttps://doi.org/10.1186/s12870-021-03277-yhttps://doaj.org/toc/1471-2229Abstract 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.Yu FanXiaobao WeiDili LaiHao YangLiang FengLong LiKexin NiuLong ChenDabing XiangJingjun RuanJun YanJianping ChengBMCarticleSetaria italicaGRAS gene familyGenome-wide analysisDELLA proteinFruit developmentAbiotic stressBotanyQK1-989ENBMC Plant Biology, Vol 21, Iss 1, Pp 1-19 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Setaria italica GRAS gene family Genome-wide analysis DELLA protein Fruit development Abiotic stress Botany QK1-989
spellingShingle	Setaria italica GRAS gene family Genome-wide analysis DELLA protein Fruit development Abiotic stress Botany QK1-989 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.)
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.
format	article
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
title	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_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_sort	genome-wide investigation of the gras transcription factor family in foxtail millet (setaria italica l.)
publisher	BMC
publishDate	2021
url	https://doaj.org/article/91343e5179124f0fbdcd214c92afb137
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Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)

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