Transcriptome analysis of the winter wheat Dn1 in response to cold stress

Abstract

Background Heilongjiang Province has a long and cold winter season (the minimum temperature can reach -30 ℃), and few winter wheat varieties can safely overwinter. Dongnongdongmai1 (Dn1) is the first winter wheat variety that can safely overwinter in Heilongjiang Province. This variety fills the gap for winter wheat cultivation in the frigid region of China and greatly increases the land utilization rate. To understand the molecular mechanism of the cold response, we conducted RNA-sequencing analysis of Dn1 under cold stress. Results Approximately 120,000 genes were detected in Dn1 under cold stress. The numbers of differentially expressed genes (DEGs) in the six comparison groups (0 ℃ vs. 5 ℃, -5 ℃ vs. 5 ℃, -10 ℃ vs. 5 ℃, -15 ℃ vs. 5 ℃, -20 ℃ vs. 5 ℃ and -25 ℃ vs. 5 ℃) were 11,313, 8313, 15,636, 13,671, 14,294 and 13,979, respectively. Gene Ontology functional annotation suggested that the DEGs under cold stress mainly had “binding”, “protein kinase” and “catalytic” activities and were involved in “oxidation–reduction”, “protein phosphorylation” and “carbohydrate metabolic” processes. Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that the DEGs performed important functions in cold signal transduction and carbohydrate metabolism. In addition, major transcription factors (AP2/ERF, bZIP, NAC, WRKY, bHLH and MYB) participating in the Dn1 cold stress response were activated by low temperature. Conclusion This is the first study to explore the Dn1 transcriptome under cold stress. Our study comprehensively analysed the key genes involved in cold signal transduction and carbohydrate metabolism in Dn1 under cold stress. The results obtained by transcriptome analysis could help to further explore the cold resistance mechanism of Dn1 and provide basis for breeding of cold-resistant crops.

Proteome and phosphoproteome analysis of 2,4-epibrassinolide-mediated cold stress response in cucumber seedlings

“…So far, an extensive array of stress-responsive genes had been identified in plants, including-cold regulated ( COR ), cold-induced ( KIN ), low-temperature-induced ( LTI ), and responsive to dehydration ( RD ) ( Tao et al., 2014 ; Chilundo et al., 2017 ; Kindgren et al., 2018 ). Recently, most studies were mainly focused on transcription levels ( Ning et al., 2019 ; Tian et al., 2022 ; Zheng et al., 2022 ). It is well known that mRNA is an essential tool for protein production, and proteins ultimately carried out their functions in cells ( Kosová et al., 2018 ).…”

Cold stress triggers freezing tolerance in wheat (Triticum aestivum L.) via hormone regulation and transcription of related genes

“…Although the natural environment is complex, the adaptation of plants to the environment is the result of coordination of their own development, internal hormone regulation and response to external environmental stimuli during long-term evolution. Our team studied the metabolomics (Bao et al 2021), phenotype (Bao et al 2022) and transcriptome (Tian et al 2022) of Dn1 in response to extreme temperature stress under natural growth conditions in the field. This study will contribute to the conjoint analysis and provide a strong foundation for an in-depth analysis of the hormone regulation mechanisms of winter wheat cold resistance.…”

“…2022) and transcriptome (Tian et al . 2022) of Dn1 in response to extreme temperature stress under natural growth conditions in the field. This study will contribute to the conjoint analysis and provide a strong foundation for an in‐depth analysis of the hormone regulation mechanisms of winter wheat cold resistance.…”

Integrated transcriptomic and metabolomic analysis provides insights into cold tolerance in lettuce (Lactuca sativa L.)

“…DESeq was used for differential gene expression analysis [ 31 ]. The screening conditions for DEGs were a |log2FoldChange|> 1 and a P -value < 0.05 [ 32 ]. Bidirectional clustering was used for cluster analysis.…”