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Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato.
BMC Plant Biol. 2015 Aug 25; 15:209.BP

Abstract

BACKGROUND

GRAS transcription factors usually act as integrators of multiple growth regulatory and environmental signals, including axillary shoot meristem formation, root radial pattering, phytohormones, light signaling, and abiotic/biotic stress. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model plant for crop species with fleshy fruits.

RESULTS

In this study, 53 GRAS genes were identified and renamed based on tomato whole-genome sequence and their respective chromosome distribution except 19 members were kept as their already existed name. Multiple sequence alignment showed typical GRAS domain in these proteins. Phylogenetic analysis of GRAS proteins from tomato, Arabidopsis, Populus, P.mume, and Rice revealed that SlGRAS proteins could be divided into at least 13 subfamilies. SlGRAS24 and SlGRAS40 were identified as target genes of miR171 using5'-RACE (Rapid amplification of cDNA ends). qRT-PCR analysis revealed tissue-/organ- and development stage-specific expression patterns of SlGRAS genes. Moreover, their expression patterns in response to different hormone and abiotic stress treatments were also investigated.

CONCLUSIONS

This study provides the first comprehensive analysis of GRAS gene family in the tomato genome. The data will undoubtedly be useful for better understanding the potential functions of GRAS genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species.

Authors+Show Affiliations

Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China. huanghaowei1988@126.com.Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China. shane19851@gmail.com.Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China. 1060530628@qq.com.Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China. sabrina-0810@hotmail.com.Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China. zhengguoli@cqu.edu.cn.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

26302743

Citation

Huang, Wei, et al. "Genome-wide Identification, Phylogeny and Expression Analysis of GRAS Gene Family in Tomato." BMC Plant Biology, vol. 15, 2015, p. 209.
Huang W, Xian Z, Kang X, et al. Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato. BMC Plant Biol. 2015;15:209.
Huang, W., Xian, Z., Kang, X., Tang, N., & Li, Z. (2015). Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato. BMC Plant Biology, 15, 209. https://doi.org/10.1186/s12870-015-0590-6
Huang W, et al. Genome-wide Identification, Phylogeny and Expression Analysis of GRAS Gene Family in Tomato. BMC Plant Biol. 2015 Aug 25;15:209. PubMed PMID: 26302743.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato. AU - Huang,Wei, AU - Xian,Zhiqiang, AU - Kang,Xia, AU - Tang,Ning, AU - Li,Zhengguo, Y1 - 2015/08/25/ PY - 2015/03/09/received PY - 2015/08/11/accepted PY - 2015/8/26/entrez PY - 2015/8/26/pubmed PY - 2016/1/27/medline SP - 209 EP - 209 JF - BMC plant biology JO - BMC Plant Biol VL - 15 N2 - BACKGROUND: GRAS transcription factors usually act as integrators of multiple growth regulatory and environmental signals, including axillary shoot meristem formation, root radial pattering, phytohormones, light signaling, and abiotic/biotic stress. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model plant for crop species with fleshy fruits. RESULTS: In this study, 53 GRAS genes were identified and renamed based on tomato whole-genome sequence and their respective chromosome distribution except 19 members were kept as their already existed name. Multiple sequence alignment showed typical GRAS domain in these proteins. Phylogenetic analysis of GRAS proteins from tomato, Arabidopsis, Populus, P.mume, and Rice revealed that SlGRAS proteins could be divided into at least 13 subfamilies. SlGRAS24 and SlGRAS40 were identified as target genes of miR171 using5'-RACE (Rapid amplification of cDNA ends). qRT-PCR analysis revealed tissue-/organ- and development stage-specific expression patterns of SlGRAS genes. Moreover, their expression patterns in response to different hormone and abiotic stress treatments were also investigated. CONCLUSIONS: This study provides the first comprehensive analysis of GRAS gene family in the tomato genome. The data will undoubtedly be useful for better understanding the potential functions of GRAS genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species. SN - 1471-2229 UR - https://www.unboundmedicine.com/medline/citation/26302743/Genome_wide_identification_phylogeny_and_expression_analysis_of_GRAS_gene_family_in_tomato_ L2 - https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-015-0590-6 DB - PRIME DP - Unbound Medicine ER -