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. 2024 Jan 13;24(1):46.
doi: 10.1186/s12870-023-04674-1.

GRAS gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses

Yu Fan  1 , Xianqi Wan  2 , Xin Zhang  1 , Jieyu Zhang  1 , Chunyu Zheng  3 , Qiaohui Yang  1 , Li Yang  1 , Xiaolong Li  1 , Liang Feng  4 , Liang Zou  5 , Dabing Xiang  6
Affiliations

GRAS gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses

Yu Fan et al. BMC Plant Biol. .

Abstract

Background: The GRAS transcription factor family plays a crucial role in various biological processes in different plants, such as tissue development, fruit maturation, and environmental stress. However, the GRAS family in rye has not been systematically analyzed yet.

Results: In this study, 67 GRAS genes in S. cereale were identified and named based on the chromosomal location. The gene structures, conserved motifs, cis-acting elements, gene replications, and expression patterns were further analyzed. These 67 ScGRAS members are divided into 13 subfamilies. All members include the LHR I, VHIID, LHR II, PFYRE, and SAW domains, and some nonpolar hydrophobic amino acid residues may undergo cross-substitution in the VHIID region. Interested, tandem duplications may have a more important contribution, which distinguishes them from other monocotyledonous plants. To further investigate the evolutionary relationship of the GRAS family, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. The response characteristics of 19 ScGRAS members from different subfamilies to different tissues, grains at filling stages, and different abiotic stresses of rye were systematically analyzed. Paclobutrazol, a triazole-based plant growth regulator, controls plant tissue and grain development by inhibiting gibberellic acid (GA) biosynthesis through the regulation of DELLA proteins. Exogenous spraying of paclobutrazol significantly reduced the plant height but was beneficial for increasing the weight of 1000 grains of rye. Treatment with paclobutrazol, significantly reduced gibberellin levels in grain in the filling period, caused significant alteration in the expression of the DELLA subfamily gene members. Furthermore, our findings with respect to genes, ScGRAS46 and ScGRAS60, suggest that these two family members could be further used for functional characterization studies in basic research and in breeding programmes for crop improvement.

Conclusions: We identified 67 ScGRAS genes in rye and further analysed the evolution and expression patterns of the encoded proteins. This study will be helpful for further analysing the functional characteristics of ScGRAS genes.

Keywords: DELLA; Expression pattern; GRAS gene family; Secale cereale.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Unrooted phylogenetic tree showing relationships among GRAS domains of Secale cereale (Sc), Arabidopsis thaliana (At) and Oryza sativa (Os). The phylogenetic tree was derived using the neighbor-joining method in MEGA7.0. The tree shows the 13 phylogenetic subfamilies. GRAS proteins from S. cereale are highlighted in red
Fig. 2
Fig. 2
Phylogenetic relationships, gene structure analysis, and motif distributions of S. cereale GRAS genes. A Phylogenetic tree was constructed using the neighbor-joining method with 1000 replicates for each node. B Exons and introns are indicated by yellow rectangles and grey lines, respectively. The green, yellow, and red rectangles represent the UTR, CDS, and GRAS conserved domains, respectively. C Amino acid motifs in the ScGRAS proteins (1–10) are represented by colored boxes. The black lines indicate relative protein lengths
Fig. 3
Fig. 3
Schematic representation of the chromosomal distribution of the S. cereale GRAS genes. Vertical bars represent the chromosomes of S. cereale. The chromosome number is indicated to the left of each chromosome. The scale on the left represents chromosome length. Gene pairs with tandem repeat relationships are marked in red. The tandem gene pairs between pairs are connected by U-shaped lines
Fig. 4
Fig. 4
Schematic representation of the chromosomal distribution and interchromosomal relationships of S. cereale GRAS genes. Colored lines indicate all synteny blocks in the S. cereale genome, and the red lines indicate duplicated GRAS gene pairs. The chromosome number is indicated at the bottom of each chromosome
Fig. 5
Fig. 5
Synteny analyses of the GRAS genes between Secale cereale and six representative plant species (Triticum aestivum, Aegilops tauschii, Hordeum vulgare, Oryza sativa subsp. Indica, Zea mays, and Arabidopsi thaliana). Gray lines on the background indicate the collinear blocks in S. cereale and other plant genomes; red lines highlight the syntenic S. cereale GRAS gene pairs
Fig. 6
Fig. 6
Phylogenetic relationship and motif composition of the GRAS proteins from S. cereale with six different plant species (T. aestivum, A. tauschii, H. vulgare, O. sativa subsp. Indica, Z. mays, and A. thaliana). Outer panel: an unrooted phylogenetic tree constructed using Geneious R11 with the neighbor-joining method. Inner panel: distribution of conserved motifs in GRAS proteins. The differently colored boxes represent different motifs and their positions in each GRAS protein sequence. The sequence information for each motif is provided in Table S2
Fig. 7
Fig. 7
Expression patterns of selected 19 S. cereale GRAS genes. A Expression patterns of 19 S. cereale GRAS genes in the root, stem, leave, flower, and grain were examined via qRT-PCR. Relative expression level was shown as mean (± SE) from three independent experiments. B Expression patterns of 19 S. cereale GRAS genes were examined during different grain development stages: 7 DPA (early-filling stage), 14 DPA (mid-filling stage), 21 DPA (early-ripening stage), 28 DPA (mid-ripening stage), and 35 DPA (full-ripening stage). Lowercase letters above the bars indicate significant differences (α = 0.05, LSD) among the treatments
Fig. 8
Fig. 8
Grain development of S. cereale under exogenous paclobutrazol and gibberellin treatment. A The plant height, 1000 grain weight, and gibberellin content during grain development. B Differences in the expression of DELLA subfamily genes under exogenous paclobutrazol and gibberellin treatment during grain development. Mock: the same amount of water treatment, Paclobutrazol: 250 mg/L paclobutrazol treatment. Gibberellin: 100 μm gibberellin treatment. Error bars were obtained from three measurements. We need information that asterisk described significant differences (α = 0.05/0.01/0.001, LSD) among the treatments. *, **, and *** indicate significant correlations at the 0.05, 0.01 and 0.001 levels, respectively
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