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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

The expression profiles of 45 SlGRAS genes analyzed using qPCR during eight stages of development. Y-axis represents relative expression values and X-axis represents stages of development as follows: R root, S stem, L leaf, Bud bud flower, Ant anthesis flower, IM immature green stages, Br breaker stage, and RF red ripe stage of fruit development. The expression data of root were normalized to 1. Error bars show the standard error between three replicates performed
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Fig6: The expression profiles of 45 SlGRAS genes analyzed using qPCR during eight stages of development. Y-axis represents relative expression values and X-axis represents stages of development as follows: R root, S stem, L leaf, Bud bud flower, Ant anthesis flower, IM immature green stages, Br breaker stage, and RF red ripe stage of fruit development. The expression data of root were normalized to 1. Error bars show the standard error between three replicates performed

Mentions: To investigate the potential functions of SlGRAS genes during tomato development, their expression patterns were carried out in different tissues including root, stem, leaf, bud, anthesis flower and three stages of fruit development using qRT-PCR. In the qPCR analysis, genes exhibiting Ct value > 36 were treated as non-expressors. As shown in Figs. 6 and 10a, a total of 45 SlGRAS gene transcripts were obtained, while 8 other SlGRAS genes could not be detected because of their low expression levels or might be pseudogenes. It is apparent that the expression levels in different tissues vary widely among the tomato GRAS genes, as well as among different tissues for individual GRAS genes. Of them, 23, 10, and 8 genes were found exhibit the highest expression in stems, anthesis flowers, and roots, respectively. During fruit development, generally higher transcript abundance can be observed in immature fruits than mature fruits, which suggests that those genes might relate to early fruit development. Nevertheless, several genes show dramatic increase at the breaker stage compared to the immature stage. For example, SlGRAS38, SlGRAS35, and SlGRAS47 display relatively strong and specific expression during fruit ripening, indicating that they might have functional significance during the onset of ripening.Fig. 6


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)

The expression profiles of 45 SlGRAS genes analyzed using qPCR during eight stages of development. Y-axis represents relative expression values and X-axis represents stages of development as follows: R root, S stem, L leaf, Bud bud flower, Ant anthesis flower, IM immature green stages, Br breaker stage, and RF red ripe stage of fruit development. The expression data of root 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

Fig6: The expression profiles of 45 SlGRAS genes analyzed using qPCR during eight stages of development. Y-axis represents relative expression values and X-axis represents stages of development as follows: R root, S stem, L leaf, Bud bud flower, Ant anthesis flower, IM immature green stages, Br breaker stage, and RF red ripe stage of fruit development. The expression data of root were normalized to 1. Error bars show the standard error between three replicates performed
Mentions: To investigate the potential functions of SlGRAS genes during tomato development, their expression patterns were carried out in different tissues including root, stem, leaf, bud, anthesis flower and three stages of fruit development using qRT-PCR. In the qPCR analysis, genes exhibiting Ct value > 36 were treated as non-expressors. As shown in Figs. 6 and 10a, a total of 45 SlGRAS gene transcripts were obtained, while 8 other SlGRAS genes could not be detected because of their low expression levels or might be pseudogenes. It is apparent that the expression levels in different tissues vary widely among the tomato GRAS genes, as well as among different tissues for individual GRAS genes. Of them, 23, 10, and 8 genes were found exhibit the highest expression in stems, anthesis flowers, and roots, respectively. During fruit development, generally higher transcript abundance can be observed in immature fruits than mature fruits, which suggests that those genes might relate to early fruit development. Nevertheless, several genes show dramatic increase at the breaker stage compared to the immature stage. For example, SlGRAS38, SlGRAS35, and SlGRAS47 display relatively strong and specific expression during fruit ripening, indicating that they might have functional significance during the onset of ripening.Fig. 6

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