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Transcriptome Analysis Revealed the Dynamic and Rapid Transcriptional Reprogramming Involved in Cold Stress and Related Core Genes in the Rice Seedling Stage
Cold damage is one of the most important environmental factors influencing crop growth, development, and production. In this study, we generated a pair of near-isogenic lines (NILs), Towada and ZL31, and Towada showed more cold sensitivity than ZL31 in the rice seedling stage. To explore the transcr...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9916315/ https://www.ncbi.nlm.nih.gov/pubmed/36768236 http://dx.doi.org/10.3390/ijms24031914 |
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author | Wu, Bian Chen, Siyuan Cheng, Shiyuan Li, Changyan Li, Sanhe Chen, Junxiao Zha, Wenjun Liu, Kai Xu, Huashan Li, Peide Shi, Shaojie Yang, Guocai Chen, Zhijun Liu, Kai You, Aiqing Zhou, Lei |
author_facet | Wu, Bian Chen, Siyuan Cheng, Shiyuan Li, Changyan Li, Sanhe Chen, Junxiao Zha, Wenjun Liu, Kai Xu, Huashan Li, Peide Shi, Shaojie Yang, Guocai Chen, Zhijun Liu, Kai You, Aiqing Zhou, Lei |
author_sort | Wu, Bian |
collection | PubMed |
description | Cold damage is one of the most important environmental factors influencing crop growth, development, and production. In this study, we generated a pair of near-isogenic lines (NILs), Towada and ZL31, and Towada showed more cold sensitivity than ZL31 in the rice seedling stage. To explore the transcriptional regulation mechanism and the reason for phenotypic divergence of the two lines in response to cold stress, an in-depth comparative transcriptome study under cold stress was carried out. Our analysis uncovered that rapid and high-amplitude transcriptional reprogramming occurred in the early stage of cold treatment. GO enrichment and KEGG pathway analysis indicated that genes of the response to stress, environmental adaptation, signal transduction, metabolism, photosynthesis, and the MAPK signaling pathway might form the main part of the engine for transcriptional reprogramming in response to cold stress. Furthermore, we identified four core genes, OsWRKY24, OsCAT2, OsJAZ9, and OsRR6, that were potential candidates affecting the cold sensitivity of Towada and ZL31. Genome re-sequencing analysis between the two lines revealed that only OsWRKY24 contained sequence variations which may change its transcript abundance. Our study not only provides novel insights into the cold-related transcriptional reprogramming process, but also highlights the potential candidates involved in cold stress. |
format | Online Article Text |
id | pubmed-9916315 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-99163152023-02-11 Transcriptome Analysis Revealed the Dynamic and Rapid Transcriptional Reprogramming Involved in Cold Stress and Related Core Genes in the Rice Seedling Stage Wu, Bian Chen, Siyuan Cheng, Shiyuan Li, Changyan Li, Sanhe Chen, Junxiao Zha, Wenjun Liu, Kai Xu, Huashan Li, Peide Shi, Shaojie Yang, Guocai Chen, Zhijun Liu, Kai You, Aiqing Zhou, Lei Int J Mol Sci Article Cold damage is one of the most important environmental factors influencing crop growth, development, and production. In this study, we generated a pair of near-isogenic lines (NILs), Towada and ZL31, and Towada showed more cold sensitivity than ZL31 in the rice seedling stage. To explore the transcriptional regulation mechanism and the reason for phenotypic divergence of the two lines in response to cold stress, an in-depth comparative transcriptome study under cold stress was carried out. Our analysis uncovered that rapid and high-amplitude transcriptional reprogramming occurred in the early stage of cold treatment. GO enrichment and KEGG pathway analysis indicated that genes of the response to stress, environmental adaptation, signal transduction, metabolism, photosynthesis, and the MAPK signaling pathway might form the main part of the engine for transcriptional reprogramming in response to cold stress. Furthermore, we identified four core genes, OsWRKY24, OsCAT2, OsJAZ9, and OsRR6, that were potential candidates affecting the cold sensitivity of Towada and ZL31. Genome re-sequencing analysis between the two lines revealed that only OsWRKY24 contained sequence variations which may change its transcript abundance. Our study not only provides novel insights into the cold-related transcriptional reprogramming process, but also highlights the potential candidates involved in cold stress. MDPI 2023-01-18 /pmc/articles/PMC9916315/ /pubmed/36768236 http://dx.doi.org/10.3390/ijms24031914 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Wu, Bian Chen, Siyuan Cheng, Shiyuan Li, Changyan Li, Sanhe Chen, Junxiao Zha, Wenjun Liu, Kai Xu, Huashan Li, Peide Shi, Shaojie Yang, Guocai Chen, Zhijun Liu, Kai You, Aiqing Zhou, Lei Transcriptome Analysis Revealed the Dynamic and Rapid Transcriptional Reprogramming Involved in Cold Stress and Related Core Genes in the Rice Seedling Stage |
title | Transcriptome Analysis Revealed the Dynamic and Rapid Transcriptional Reprogramming Involved in Cold Stress and Related Core Genes in the Rice Seedling Stage |
title_full | Transcriptome Analysis Revealed the Dynamic and Rapid Transcriptional Reprogramming Involved in Cold Stress and Related Core Genes in the Rice Seedling Stage |
title_fullStr | Transcriptome Analysis Revealed the Dynamic and Rapid Transcriptional Reprogramming Involved in Cold Stress and Related Core Genes in the Rice Seedling Stage |
title_full_unstemmed | Transcriptome Analysis Revealed the Dynamic and Rapid Transcriptional Reprogramming Involved in Cold Stress and Related Core Genes in the Rice Seedling Stage |
title_short | Transcriptome Analysis Revealed the Dynamic and Rapid Transcriptional Reprogramming Involved in Cold Stress and Related Core Genes in the Rice Seedling Stage |
title_sort | transcriptome analysis revealed the dynamic and rapid transcriptional reprogramming involved in cold stress and related core genes in the rice seedling stage |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9916315/ https://www.ncbi.nlm.nih.gov/pubmed/36768236 http://dx.doi.org/10.3390/ijms24031914 |
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