Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Oct 20:13:1015673.
doi: 10.3389/fgene.2022.1015673. eCollection 2022.

Computational genomics insights into cold acclimation in wheat

Youlian Pan  1 , Yifeng Li  1   2 , Ziying Liu  1 , Jitao Zou  3 , Qiang Li  3   4
Affiliations

Computational genomics insights into cold acclimation in wheat

Youlian Pan et al. Front Genet. .

Abstract

Development of cold acclimation in crops involves transcriptomic reprograming, metabolic shift, and physiological changes. Cold responses in transcriptome and lipid metabolism has been examined in separate studies for various crops. In this study, integrated computational approaches was employed to investigate the transcriptomics and lipidomics data associated with cold acclimation and vernalization in four wheat genotypes of distinct cold tolerance. Differential expression was investigated between cold treated and control samples and between the winter-habit and spring-habit wheat genotypes. Collectively, 12,676 differentially expressed genes (DEGs) were identified. Principal component analysis of these DEGs indicated that the first, second, and third principal components (PC1, PC2, and PC3) explained the variance in cold treatment, vernalization and cold hardiness, respectively. Differential expression feature extraction (DEFE) analysis revealed that the winter-habit wheat genotype Norstar had high number of unique DEGs (1884 up and 672 down) and 63 winter-habit genes, which were clearly distinctive from the 64 spring-habit genes based on PC1, PC2 and PC3. Correlation analysis revealed 64 cold hardy genes and 39 anti-hardy genes. Cold acclimation encompasses a wide spectrum of biological processes and the involved genes work cohesively as revealed through network propagation and collective association strength of local subnetworks. Integration of transcriptomics and lipidomics data revealed that the winter-habit genes, such as COR413-TM1, CIPKs and MYB20, together with the phosphatidylglycerol lipids, PG(34:3) and PG(36:6), played a pivotal role in cold acclimation and coordinated cohesively associated subnetworks to confer cold tolerance.

Keywords: RNA-seq; cold acclimation; differential expression feature extraction; lipidomics; phosphatidylglycerol lipid; transcriptomics; wheat.

PubMed Disclaimer

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Transcriptome overview based on the 12,676 DEGs. (A) Frequency distribution (insert) and top 40 patterns of P series of DEFE analysis; (B) Heatmap; (C) Principal component analysis, where PC1 and PC2 are principal components 1 and 2, respectively.
FIGURE 2
FIGURE 2
Distinction of genes associated with cold acclimation from the others. (A) Distinction of the 63 WHGs from the other three groups of DEGs identified in DEFE analysis as revealed by their scores of the first three principal components. (B) Distinction of the 64 cold hardy genes from the 39 anti-hardy genes revealed by their scores of the first two principal components. Where, PC1, PC2, and PC3 are the principal components 1, 2, and 3.
FIGURE 3
FIGURE 3
Expression of peroxiredoxins across all samples. (A) peroxiredoxin-2F, mitochondrial isoform X1, (B) peroxiredoxin-2E-2, chloroplastic-like. Error bars are one standard error of the mean of three replicates.
FIGURE 4
FIGURE 4
The cold acclimation genes directly associated with the Cold acclimation protein COR413-TM1 highlighted. Details are available in Supplementary File S3.
FIGURE 5
FIGURE 5
Expression of two homoeologs of COR413-TM1 gene in different experimental conditions.
FIGURE 6
FIGURE 6
Expression of vernalization genes in different experimental conditions. (A) VRN1, (B) VRN2, (C) VRN3. Error bars are one standard error of the mean of three replicates. More details are available in Supplementary File S7.
See this image and copyright information in PMC

References

    1. Abdul Kayum M., Nath U. K., Park J. I., Biswas M. K., Choi E. K., Song J. Y., et al. (2018). Genome-wide identification, characterization, and expression profiling of glutathione S-transferase (GST) family in pumpkin reveals likely role in cold-stress tolerance. Genes (Basel) 9, 84. 10.3390/genes9020084 - DOI - PMC - PubMed
    1. Al-Attar R., Wijenayake S., Storey K. B. (2019). Metabolic reorganization in winter: Regulation of pyruvate dehydrogenase (PDH) during long-term freezing and anoxia. Cryobiology 86, 10–18. 10.1016/j.cryobiol.2019.01.006 - DOI - PubMed
    1. Amasino R. M. (2005). Vernalization and flowering time. Curr. Opin. Biotechnol. 16, 154–158. 10.1016/j.copbio.2005.02.004 - DOI - PubMed
    1. Aslam M., Greaves J. G., Jakada B. H., Fakher B., Wang X., Qin Y. (2022). AcCIPK5, a pineapple CBL-interacting protein kinase, confers salt, osmotic and cold stress tolerance in transgenic Arabidopsis. Plant Sci. 320, 111284. 10.1016/j.plantsci.2022.111284 - DOI - PubMed
    1. Blighe K., Lun A. (2022). PCAtools: Everything principal components analysis. Available at: https://bioconductor.org/packages/devel/bioc/vignettes/PCAtools/inst/doc... .

LinkOut - more resources