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

Wei Huang,Xia Kang,Ning Tang,Zhiqiang Xian,Zhengguo Li

doi:10.1186/s12870-015-0590-6

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.

Highlights

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
BLASTP analysis using the amino acid (AA) sequences of characterized AtGRAS proteins as queries obtained 51 previously annotated GRAS members in tomato WGS Chromosomes (SL2.50), which were all included in the 53 GRAS genes identified above
All of the 53 tomato GRAS genes were mapped onto the 12 tomato chromosomes and renamed based on their distributions and relative linear orders among the respective chromosome (Fig. 2), among which, SlDELLA and SlLs were kept as their already existed name, and so did the SlGRAS1 to SlGRAS17, which were previously described by Mayrose et al [37]

Summary

Introduction

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. GRAS proteins are named after GAI, RGA and SCR [2,3,4], the first three functionally identified members in this family. Only small number of GRAS proteins were functionally characterized, including some members identified in Zea mays, Petunia hybrida, Medicago truncatula, Lilium longiflorum [13,14,15,16]. These genes play crucial roles in diverse fundamental processes of plant growth and development. Two independent studies demonstrated that endodermisexpressed SCL3 acted as an integrator downstream of the GA/DELLA and SCR/SHR pathways, mediating the

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Conclusion