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

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.

Fig. 1

The information of 53 GRAS transcription factors identified in tomato genome. SlGRAS19, SlGRAS20, SlGRAS29, SlGRAS35, SlGRAS50, whose full amino acid length less than 300 were distributed to “No group” and were excluded from some of the following analyses

Fig. 2

Positions of GRAS gene family members on the Solanum lycopersicum chromosomes. Tandemly duplicated genes were indicated in red colour

Fig. 3

Multiple sequence alignment of the 48 GRAS domain from tomato GRAS genes obtained by ClustalX and manual correction. The most conserved motif of GRAS domain, VHIID, was underlined

Fig. 4

Phylogenetic analysis of GRAS proteins. The phylogenetic tree was generated by Neighbor-Joining method derived from ClustalX alignment of 48, 32, 14, 14, and 16GRAS amino acid sequences from tomato, Arabidopsis, Populus, P.mume, and rice, respectively. Members in the same sub-branch were marked by circle filled with same color

Fig. 5

Cleavage sites of miR171 at complementary sequences of SlGRAS24 and SlGRAS40 determined by 5’-RACE. The electrophoretogram shows the PCR products representing the 3’-cleavage fragments that were cloned and sequenced for each gene. Both SlGRAS24 and SlGRAS40 were cleaved between 10^th and 11^th, 13^th and 14^th nt of mature miR171 sequence (arrows)

Fig. 6

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

Fig. 7

Expression patterns exhibited by 40 SlGRAS family genes during fruit-set stage of tomato. The X-axis represents 3 different stages, -2 dpa 2 days before anthesis, 0 dpa the first day of anthesis, 2 dpa 2 days post anthesis. Solid lines depict the expression patterns of ovaries while dotted lines stand for stamens. The expression data of -2 dpa stamens were normalized to 1. Error bars show the standard error between three replicates performed

Fig. 8

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

Fig. 9

Expression analysis of 40 GRAS family genes in response to abiotic treatments. The X-axis represents different abiotic stresses. C control sample, SS salt stress, DS drought stress, CS cold stress, HS heat stress, OsmS osmotic stress, OxiS oxidative stress. The expression data of control sample were normalized to 1. Error bars show the standard error between three replicates performed

Fig. 10

The expression profiles of SlGRAS genes visualized as heatmaps with respect to different tissues (a), floral organs (b), hormone treatments (c), and stress treatments (d). Members in the same subfamily based on the phylogenetic tree (Fig. 4) were grouped together. The color scale represents log10 expression values. The relative expression levels of root, -2 dpa stamen, and untreated control samples were normalized to 0