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

Abstract

BackgroundGRAS 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.ResultsIn 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0590-6) contains supplementary material, which is available to authorized users.

Overexpression of a tomato miR171 target gene SlGRAS24 impacts multiple agronomical traits via regulating gibberellin and auxin homeostasis

“…SlGRAS24 is phylogenetically clustered into the HAIRY MERISTEM (HAM) subfamily of GRAS genes and shows the highest sequence identity with Arabidopsis thaliana AtSCL6 (Huang et al ., ). In 2002, a GRAS transcription factor named HAM was identified as a component of a novel non‐cell‐autonomous signalling pathway maintaining shoot indeterminacy in Petunia hybrida , ham mutants displayed arrest in lateral organ and stem production (Stuurman et al ., ).…”

“…Indeed, elevated rates of evolution in flowering plant HAM homologs indicate a refinement of HAM function in response to selective pressures (Engstrom et al ., ). In tomato, six SlGRAS genes are clustered into the HAM subfamily, including SlGRAS24 and SlGRAS40 , which are confirmed to be targeted for mRNA cleavage by miR171 , and SlGRAS8 , a suspected target gene whose translation is repressed by miR171 (Huang et al ., ). SlGRAS24 contains a conserved MIR‐binding sequence which is perfectly matched with Sly‐miR171 (Huang et al ., ).…”

“…In tomato, six SlGRAS genes are clustered into the HAM subfamily, including SlGRAS24 and SlGRAS40 , which are confirmed to be targeted for mRNA cleavage by miR171 , and SlGRAS8 , a suspected target gene whose translation is repressed by miR171 (Huang et al ., ). SlGRAS24 contains a conserved MIR‐binding sequence which is perfectly matched with Sly‐miR171 (Huang et al ., ). Despite the close evolutionary relationship between SlGRAS24 and SlGRAS40 , their transcripts in different tissues/organs and in response to hormone and abiotic stress differ greatly (Huang et al ., ), indicating that they might have different functions and participate in distinct physiological processes.…”

“…SlGRAS24 contains a conserved MIR‐binding sequence which is perfectly matched with Sly‐miR171 (Huang et al ., ). Despite the close evolutionary relationship between SlGRAS24 and SlGRAS40 , their transcripts in different tissues/organs and in response to hormone and abiotic stress differ greatly (Huang et al ., ), indicating that they might have different functions and participate in distinct physiological processes.…”

“…GRAS proteins usually act as transcription factors, but not all GRAS protein functions have been described. We previously identified a tomato ( Solanum lycopersicum ) GRAS transcription factor gene SlGRAS24 as target of tomato miR171 (Huang et al ., ) and aimed to discover more about its function in tomato development here.…”