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. 2023 Jul 21;12(14):2719.
doi: 10.3390/plants12142719.

Integrating Full-Length Transcriptome and RNA Sequencing of Siberian Wildrye (Elymus sibiricus) to Reveal Molecular Mechanisms in Response to Drought Stress

Qingqing Yu  1   2 , Yi Xiong  1 , Xiaoli Su  1 , Yanli Xiong  1 , Zhixiao Dong  1 , Junming Zhao  1 , Xin Shu  1 , Shiqie Bai  2 , Xiong Lei  2 , Lijun Yan  2 , Xiao Ma  1
Affiliations

Integrating Full-Length Transcriptome and RNA Sequencing of Siberian Wildrye (Elymus sibiricus) to Reveal Molecular Mechanisms in Response to Drought Stress

Qingqing Yu et al. Plants (Basel). .

Abstract

Drought is one of the most significant limiting factors affecting plant growth and development on the Qinghai-Tibet Plateau (QTP). Mining the drought-tolerant genes of the endemic perennial grass of the QTP, Siberian wildrye (Elymus sibiricus), is of great significance to creating new drought-resistant varieties which can be used in the development of grassland livestock and restoring natural grassland projects in the QTP. To investigate the transcriptomic responsiveness of E. sibiricus to drought stress, PEG-induced short- and long-term drought stress was applied to two Siberian wildrye genotypes (drought-tolerant and drought-sensitive accessions), followed by third- and second-generation transcriptome sequencing analysis. A total of 40,708 isoforms were detected, of which 10,659 differentially expressed genes (DEGs) were common to both genotypes. There were 2107 and 2498 unique DEGs in the drought-tolerant and drought-sensitive genotypes, respectively. Additionally, 2798 and 1850 DEGs were identified in the drought-tolerant genotype only under short- and long-term conditions, respectively. DEGs numbering 1641 and 1330 were identified in the drought-sensitive genotype only under short- and long-term conditions, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that all the DEGs responding to drought stress in E. sibiricus were mainly associated with the mitogen-activated protein kinase (MAKP) signaling pathway, plant hormone signal transduction, the linoleic acid metabolism pathway, the ribosome pathway, and plant circadian rhythms. In addition, Nitrate transporter 1/Peptide transporter family protein 3.1 (NPF3.1) and Auxin/Indole-3-Acetic Acid (Aux/IAA) family protein 31(IAA31) also played an important role in helping E. sibiricus resist drought. This study used transcriptomics to investigate how E. sibiricus responds to drought stress, and may provide genetic resources and references for research into the molecular mechanisms of drought resistance in native perennial grasses and for breeding drought-tolerant varieties.

Keywords: Elymus sibiricus; WGCNA; comparative transcriptomics; drought stress; endemic forage.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The Venn diagram of the isoform numbers annotated to four databases (A). GO annotation results of all isoforms (B). Distribution of isoforms annotated in Nr database in different species (C). Distribution of transcription factor families predicted by all isoforms (D). The data constructed by the figure (A–D) is based on the three-generation full-length transcriptome data.
Figure 2
Figure 2
Quality control analysis of second-generation transcriptome data. The hierarchy of 30 samples (A). The 2D map of PCA (B). The heatmap of Pearson’s correlation of 30 samples (C).
Figure 3
Figure 3
Histogram of DEGs in 25 comparison groups (A); Venn diagram of DEGs (B), X represents drought-tolerant genotype and W represents drought-sensitive genotype.
Figure 4
Figure 4
Venn diagram that shows the differentially expressed genes (DEGs) identified in four comparison groups of the X genotype (A) and W genotype (B). Additionally, KEGG enrichment pathway maps were generated to display the DEGs shared by the four comparison groups of the X genotype (C) and W genotype (E), while GO enrichment pathway maps were used to illustrate the DEGs shared by the four comparison groups of the X genotype (D) and W genotype (F). X represents drought-tolerant genotype and W represents drought-sensitive genotype.
Figure 5
Figure 5
KEGG enrichment pathway map of DEGs by X genotype only under short-term (A) and long-term (B) drought stress; KEGG enrichment pathway map of DEGs by W genotype only under short-term (C) and long-term (D) drought stress. X represents drought-tolerant genotype and W represents drought-sensitive genotype.
Figure 6
Figure 6
Trend analysis of all genes in X genotype (A) and W genotype (B). Histogram of the number of genes per profile in X genotype (C) and W genotype (D). The Venn diagram of DEGs and genes of profile in X genotypes and W genotypes, (E) represent profile 19 and (F) represent profile 0; KEGG enrichment pathway map of DEGs in profile 19 (G) and profile 0 (H). X represents drought-tolerant genotype and W represents drought-sensitive genotype.
Figure 7
Figure 7
Plant hormone signaling pathway in response to drought stress in E. sibiricus based on the KEGG database. The values of the heatmap represent the fold difference between the comparison groups. X represents drought-tolerant genotype and W represents drought-sensitive genotype.
Figure 8
Figure 8
MAPK signaling pathway in response to drought stress in E. sibiricus based on the literature and KEGG database. The values of the heatmap represent the fold difference between the comparison groups. X represents drought-tolerant genotype and W represents drought-sensitive genotype.
Figure 9
Figure 9
Linoleic acid metabolic pathway in response to drought stress in E. sibiricus based on the literature and KEGG database. The values of the heatmap represent the fold difference between the comparison groups. X represents drought-tolerant genotype and W represents drought-sensitive genotype.
Figure 10
Figure 10
Diagram of the results of WGCNA using 40,708 genes with REC and RWC and 10 samples (A); heatmap of Pearson’s correlation of 19 modules with REC and RWC and 10 samples (B), the value represents R2, and the value in parentheses represents the p value. Expression heatmap of differentially expressed transcription factor of darkolivegreen (C) and darkseagreen4 (D) module in the two genotypes. X represents drought-tolerant genotype and W represents drought-sensitive genotype.
Figure 11
Figure 11
The top 15 hub genes in the proposed modules and relationships within the module. (A) represents darkolivegreen and (B) represents darkseagreen4.
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