Genome-wide identification and expression analysis of the GRAS gene family under abiotic stresses in wheat (Triticum aestivum L.)

Abstract

The GRAS transcription factors are multifunctional proteins involved in various biological processes, encompassing plant growth, metabolism, and responses to both abiotic and biotic stresses. Wheat is an important cereal crop cultivated worldwide. However, no systematic study of the GRAS gene family and their functions under heat, drought, and salt stress tolerance and molecular dynamics modeling in wheat has been reported. In the present study, we identified the GRAS gene in Triticum aestivum through systematically performing gene structure analysis, chromosomal location, conserved motif, phylogenetic relationship, and expression patterns. A total of 177 GRAS genes were identified within the wheat genome. Based on phylogenetic analysis, these genes were categorically placed into 14 distinct subfamilies. Detailed analysis of the genetic architecture revealed that the majority of TaGRAS genes had no intronic regions. The expansion of the wheat GRAS gene family was proven to be influenced by both segmental and tandem duplication events. The study of collinearity events between TaGRAS and analogous orthologs from other plant species provided valuable insights into the evolution of the GRAS gene family in wheat. It is noteworthy that the promoter regions of TaGRAS genes consistently displayed an array of cis-acting elements that are associated with stress responses and hormone regulation. Additionally, we discovered 14 miRNAs that target key genes involved in three stress-responsive pathways in our study. Moreover, an assessment of RNA-seq data and qRT-PCR results revealed a significant increase in the expression of TaGRAS genes during abiotic stress. These findings highlight the crucial role of TaGRAS genes in mediating responses to different environmental stresses. Our research delved into the molecular dynamics and structural aspects of GRAS domain-DNA interactions, marking the first instance of such information being generated. Overall, the current findings contribute to our understanding of the organization of the GRAS genes in the wheat genome. Furthermore, we identified TaGRAS27 as a candidate gene for functional research, and to improve abiotic stress tolerance in the wheat by molecular breeding.

Figure 1

Characterised sequences of five species (wheat, Arabidopsis, rice, barley and oilseed rape) were used to draw this phylogenetic tree (Maximum Likelihood) with the wheat GRAS proteins using MEGA X. Combined phylogenetic analysis of GRAS proteins from T. aestivum (Ta), A. thaliana (At), O. sativa (Os), H. vulgare (Hv) and B. napus (Bn). The GRAS proteins are clustered into 14 subgroups, marked by different colours.

Figure 2

Distribution of TaGRAS genes on 21 wheat (T. aestivum) chromosomes constructed using Mapchart.

Figure 3

(a) Interspecies synteny of T. aestivum and A. thaliana (b) T. aestivum and O. sativa on the basis of orthologous genes. Gray lines in the background indicate the collinear blocks within T. estivum (Ta) and A. thaliana (At), T. aestivum (Ta) and O. sativa (Os) while the red lines highlight the syntenic GRAS gene pairs by using TBtools.

Figure 4

The synteny analysis of TaGRAS family in T. aestivum. Different colours represent GRAS subfamilies on A, B and D sub-genome red lines indicate duplicated TaGRAS subfamily gene pairs on A sub-genome, green lines indicated on B sub-genome and blue represented D sub-genome. The chromosome number is indicated at the bottom of each chromosome by using TBtools.

Figure 5

Interaction network among TaGRAS families in wheat. Specific protein interactions between GRAS transcription factors in wheat were determined using String.

Figure 6

qRT-PCR based differential expression analysis of 20 TaGRAS genes under abiotic stress. (A) drought stress at 20% (v/v) PEG treatment in C306 and WL711 for 24 h leaf tissues, (B) Salt stress treatment at 150 mM NaCl in Kharchia65 and HD2687 at 0 h, 24 h and 48 h leaf tissues, (C) Heat stress treatment in Raj3765 and HD2009 at 37 °C and  42 ⁰C.

Figure 6

qRT-PCR based differential expression analysis of 20 TaGRAS genes under abiotic stress. (A) drought stress at 20% (v/v) PEG treatment in C306 and WL711 for 24 h leaf tissues, (B) Salt stress treatment at 150 mM NaCl in Kharchia65 and HD2687 at 0 h, 24 h and 48 h leaf tissues, (C) Heat stress treatment in Raj3765 and HD2009 at 37 °C and  42 ⁰C.

Figure 7

MDS analysis (a) Root Mean Square Deviation, (b) Root Mean Square Fluctuations, (c) Ribbon shape superimposed structure of GARS_126, (d) GARS_161, (e) GARS_151 are shown, the orange colour structure is the initial phase of the system at 0 ns and the blue colour structure is the final phase of the system after 20 ns of Molecular Dynamics Simulation. GARS domain is shown in red and dark blue for the pre- and post MDS structures generated using the Rosettafold.