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| Status |
Public on Oct 24, 2022 |
| Title |
Dynamics of leaf transcriptome during cold acclimation in wheat |
| Organism |
Triticum aestivum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
This dataset is associated with two publications
1. Elucidating the biochemical basis of trans-16:1 fatty acid change in leaves during cold acclimation in wheat. http://doi.org/10.1002/pei3.10044
In this study, comparative RNA-seq analyses with leaf tissues undergoing cold acclimation reveal concerted transcriptome shifts indicating a reduced chloroplast lipid pathway activity and increased cytosolic ER membrane lipid synthesis. To explore the underlying metabolic and transcriptional mechanisms responsible for the reduction of the t16:1 under cold, a detailed lipid analysis and comparative transcriptome study were conducted with four wheat cultivars during cold treatment. The RNA-seq dataset includes four wheat cultivars (Manitou, Winter Manitou, Norstar and Spring Norstar) treated with cold paired with control. The data as a whole show that leaf tissues experience a gradual decrease in chloroplast lipid pathway activity and the variation in the decline of chloroplast lipid synthesis in different cultivars manifest in the rate of decrease in t16:1decrease in leaf tissues. Future efforts are required to determine if and how the down regulation of the chloroplast lipid pathway is related to the development of winter hardiness.
2. Computational genomics insights into cold acclimation in wheat. https://doi.org/10.3389/fgene.2022.1015673
In this study, integrated computational approaches was employed to investigate the transcriptomics and lipidomics data associated with cold acclimation and vernalization in the 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 transcriptome 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.
Citations:
http://doi.org/10.1002/pei3.10044
https://doi.org/10.3389/fgene.2022.1015673
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| Overall design |
RNA-seq data were collected from leaf tissues of the four wheat varieties (Manitou, Winter Manitou, Norstar and Winter Norstar) respectively at normal condition and cold treatment condition. There are three biological replicates for each sample, total 24 RNA-seq samples.
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| Web link |
https://www.frontiersin.org/articles/10.3389/fgene.2022.1015673/full
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| Contributor(s) |
Li Q, Li Y, Liu Z, Pan Y, Zou J |
| Citation(s) |
36338961 |
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| Submission date |
Aug 14, 2020 |
| Last update date |
Nov 17, 2022 |
| Contact name |
Ziying Liu |
| E-mail(s) |
ziying.liu@nrc-cnrc.gc.ca
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| Phone |
6139930829
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| Organization name |
National Research Council, Canada
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| Street address |
1200 Montreal Road
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| City |
Ottawa |
| State/province |
ON |
| ZIP/Postal code |
K1A0R6 |
| Country |
Canada |
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| Platforms (1) |
| GPL18862 |
Illumina HiSeq 2500 (Triticum aestivum) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA657302 |
| SRA |
SRP277577 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE156300_MappedToIWGSC-RefSeq2.1.xlsx |
26.0 Mb |
(ftp)(http) |
XLSX |
| GSE156300_MappedToIWGSC_surveyGenome_V2.2.xlsx |
23.0 Mb |
(ftp)(http) |
XLSX |
| GSE156300_Readme.txt |
3.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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