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Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato.

Huang W, Xian Z, Kang X, Tang N, Li Z - BMC Plant Biol. (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China. huanghaowei1988@126.com.

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.

No MeSH data available.


Related in: MedlinePlus

Expression analysis of 39 GRAS family genes in response to hormone treatments in two different parts of seedlings. Black and gray columns stand for the expression levels of the plant shoot part and root part collected from tomato seedlings, respectively. The X-axis represents various hormone treatments. C control sample, Eth ethephon, GA3 gibberellin, IAA indole acetic acids, SA salicylic acid. The expression data of control sample were normalized to 1. Error bars show the standard error between three replicates performed
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Fig8: Expression analysis of 39 GRAS family genes in response to hormone treatments in two different parts of seedlings. Black and gray columns stand for the expression levels of the plant shoot part and root part collected from tomato seedlings, respectively. The X-axis represents various hormone treatments. C control sample, Eth ethephon, GA3 gibberellin, IAA indole acetic acids, SA salicylic acid. The expression data of control sample were normalized to 1. Error bars show the standard error between three replicates performed

Mentions: Plant hormones have been extensively studied for their roles in the regulation of various aspects of plant development. In this study, hormone treatments resulted in a wide variety of SlGRAS gene expression profiles (Figs. 8 and 10c). The expression levels of 39 GRAS genes detected vary significantly in response to different hormone treatments as well as in different tissues in response to an individual hormone treatment, suggesting that the SlGRAS genes have differences in signal-selectivity not only among different hormones but also among different tissues of tomato seedlings. In ethephon (Eth) treatment, 15 and 12 SlGRAS genes were obviously induced and inhibited, respectively. Of them, the most up-regulated gene was SlGRAS26 in roots, and the most down-regulated gene was SlGRAS36 in shoots. Similarly, GA treatment led to 10 and 9 SlGRAS genes were obviously induced and inhibited, respectively, the most up-regulated gene was SlGRAS26 in roots, while the most down-regulated gene was SlGRAS36 in roots. In IAA treatment, 6 and 17 SlGRAS were significantly induced and inhibited, respectively, and SlGRAS4 and SlGRAS14 in roots were found to be most up- and down-regulated, respectively. As for SA treatment, 20 and 9 SlGRAS genes showed dramatic increase and decrease, respectively, SlGRAS34 and SlGRAS37 in roots went through the largest increase and decrease, respectively. Notably, several genes even demonstrated opposite expression in roots and shoots when responding to the same hormone treatment. For instance, SlGRAS3 was up-regulated in shoots in response to Eth, GA3 and IAA treatments, while down-regulated in roots. Similar expression patterns were found in SlGRAS18, SlGRAS26, SlGRAS41, SlGRAS45, and SlGRAS46. The results suggest the complicated regulatory mechanism of these genes in response to hormone treatments in tomato. Taken together, these expression variations indicate that the SlGRAS gene family members were collectively regulated by a broad range of hormonal signals. Thus it is reasonable to speculate that those relevant genes might play pivotal roles in the cross-talk of hormones and should be candidates for further research in the field.Fig. 9


Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato.

Huang W, Xian Z, Kang X, Tang N, Li Z - BMC Plant Biol. (2015)

Expression analysis of 39 GRAS family genes in response to hormone treatments in two different parts of seedlings. Black and gray columns stand for the expression levels of the plant shoot part and root part collected from tomato seedlings, respectively. The X-axis represents various hormone treatments. C control sample, Eth ethephon, GA3 gibberellin, IAA indole acetic acids, SA salicylic acid. The expression data of control sample were normalized to 1. Error bars show the standard error between three replicates performed
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4549011&req=5

Fig8: Expression analysis of 39 GRAS family genes in response to hormone treatments in two different parts of seedlings. Black and gray columns stand for the expression levels of the plant shoot part and root part collected from tomato seedlings, respectively. The X-axis represents various hormone treatments. C control sample, Eth ethephon, GA3 gibberellin, IAA indole acetic acids, SA salicylic acid. The expression data of control sample were normalized to 1. Error bars show the standard error between three replicates performed
Mentions: Plant hormones have been extensively studied for their roles in the regulation of various aspects of plant development. In this study, hormone treatments resulted in a wide variety of SlGRAS gene expression profiles (Figs. 8 and 10c). The expression levels of 39 GRAS genes detected vary significantly in response to different hormone treatments as well as in different tissues in response to an individual hormone treatment, suggesting that the SlGRAS genes have differences in signal-selectivity not only among different hormones but also among different tissues of tomato seedlings. In ethephon (Eth) treatment, 15 and 12 SlGRAS genes were obviously induced and inhibited, respectively. Of them, the most up-regulated gene was SlGRAS26 in roots, and the most down-regulated gene was SlGRAS36 in shoots. Similarly, GA treatment led to 10 and 9 SlGRAS genes were obviously induced and inhibited, respectively, the most up-regulated gene was SlGRAS26 in roots, while the most down-regulated gene was SlGRAS36 in roots. In IAA treatment, 6 and 17 SlGRAS were significantly induced and inhibited, respectively, and SlGRAS4 and SlGRAS14 in roots were found to be most up- and down-regulated, respectively. As for SA treatment, 20 and 9 SlGRAS genes showed dramatic increase and decrease, respectively, SlGRAS34 and SlGRAS37 in roots went through the largest increase and decrease, respectively. Notably, several genes even demonstrated opposite expression in roots and shoots when responding to the same hormone treatment. For instance, SlGRAS3 was up-regulated in shoots in response to Eth, GA3 and IAA treatments, while down-regulated in roots. Similar expression patterns were found in SlGRAS18, SlGRAS26, SlGRAS41, SlGRAS45, and SlGRAS46. The results suggest the complicated regulatory mechanism of these genes in response to hormone treatments in tomato. Taken together, these expression variations indicate that the SlGRAS gene family members were collectively regulated by a broad range of hormonal signals. Thus it is reasonable to speculate that those relevant genes might play pivotal roles in the cross-talk of hormones and should be candidates for further research in the field.Fig. 9

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China. huanghaowei1988@126.com.

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.

No MeSH data available.


Related in: MedlinePlus