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Computational genomics insights into cold acclimation in wheat

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...

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Autores principales: Pan, Youlian, Li, Yifeng, Liu, Ziying, Zou, Jitao, Li, Qiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9632429/
https://www.ncbi.nlm.nih.gov/pubmed/36338961
http://dx.doi.org/10.3389/fgene.2022.1015673
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author Pan, Youlian
Li, Yifeng
Liu, Ziying
Zou, Jitao
Li, Qiang
author_facet Pan, Youlian
Li, Yifeng
Liu, Ziying
Zou, Jitao
Li, Qiang
author_sort Pan, Youlian
collection PubMed
description 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.
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spelling pubmed-96324292022-11-04 Computational genomics insights into cold acclimation in wheat Pan, Youlian Li, Yifeng Liu, Ziying Zou, Jitao Li, Qiang Front Genet Genetics 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. Frontiers Media S.A. 2022-10-20 /pmc/articles/PMC9632429/ /pubmed/36338961 http://dx.doi.org/10.3389/fgene.2022.1015673 Text en Copyright © 2022 His Majesty the King in Right of Canada. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Pan, Youlian
Li, Yifeng
Liu, Ziying
Zou, Jitao
Li, Qiang
Computational genomics insights into cold acclimation in wheat
title Computational genomics insights into cold acclimation in wheat
title_full Computational genomics insights into cold acclimation in wheat
title_fullStr Computational genomics insights into cold acclimation in wheat
title_full_unstemmed Computational genomics insights into cold acclimation in wheat
title_short Computational genomics insights into cold acclimation in wheat
title_sort computational genomics insights into cold acclimation in wheat
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9632429/
https://www.ncbi.nlm.nih.gov/pubmed/36338961
http://dx.doi.org/10.3389/fgene.2022.1015673
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