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Transcriptome Analysis of Bread Wheat Genotype KRL3-4 Provides a New Insight Into Regulatory Mechanisms Associated With Sodicity (High pH) Tolerance
Globally, sodicity is one of the major abiotic stresses limiting the wheat productivity in arid and semi-arid regions. With due consideration, an investigation of the complex gene network associated with sodicity stress tolerance is required to identify transcriptional changes in plants during abiot...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8864244/ https://www.ncbi.nlm.nih.gov/pubmed/35222517 http://dx.doi.org/10.3389/fgene.2021.782366 |
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author | Prasad, Geeta Mittal, Shikha Kumar, Arvind Chauhan, Divya Sahu, Tanmaya Kumar Kumar, Sundeep Singh, Rakesh Yadav, Mahesh C. Singh, Amit Kumar |
author_facet | Prasad, Geeta Mittal, Shikha Kumar, Arvind Chauhan, Divya Sahu, Tanmaya Kumar Kumar, Sundeep Singh, Rakesh Yadav, Mahesh C. Singh, Amit Kumar |
author_sort | Prasad, Geeta |
collection | PubMed |
description | Globally, sodicity is one of the major abiotic stresses limiting the wheat productivity in arid and semi-arid regions. With due consideration, an investigation of the complex gene network associated with sodicity stress tolerance is required to identify transcriptional changes in plants during abiotic stress conditions. For this purpose, we sequenced the flag leaf transcriptome of a highly tolerant bread wheat germplasm (KRL 3–4) in order to extend our knowledge and better understanding of the molecular basis of sodicity tolerance. A total of 1,980 genes were differentially expressed in the flag leaf due to sodicity stress. Among these genes, 872 DEGs were upregulated and 1,108 were downregulated. Furthermore, annotation of DEGs revealed that a total of 1,384 genes were assigned to 2,267 GO terms corresponding to 502 (biological process), 638 (cellular component), and 1,127 (molecular function). GO annotation also revealed the involvement of genes related to several transcription factors; the important ones are expansins, peroxidase, glutathione-S-transferase, and metal ion transporters in response to sodicity. Additionally, from 127 KEGG pathways, only 40 were confidently enriched at a p-value <0.05 covering the five main KEGG categories of metabolism, i.e., environmental information processing, genetic information processing, organismal systems, and cellular processes. Most enriched pathways were prioritized using MapMan software and revealed that lipid metabolism, nutrient uptake, and protein homeostasis were paramount. We have also found 39 SNPs that mapped to the important sodicity stress-responsive genes associated with various pathways such as ROS scavenging, serine/threonine protein kinase, calcium signaling, and metal ion transporters. In a nutshell, only 19 important candidate genes contributing to sodicity tolerance in bread wheat were identified, and these genes might be helpful for better understanding and further improvement of sodicity tolerance in bread wheat. |
format | Online Article Text |
id | pubmed-8864244 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-88642442022-02-24 Transcriptome Analysis of Bread Wheat Genotype KRL3-4 Provides a New Insight Into Regulatory Mechanisms Associated With Sodicity (High pH) Tolerance Prasad, Geeta Mittal, Shikha Kumar, Arvind Chauhan, Divya Sahu, Tanmaya Kumar Kumar, Sundeep Singh, Rakesh Yadav, Mahesh C. Singh, Amit Kumar Front Genet Genetics Globally, sodicity is one of the major abiotic stresses limiting the wheat productivity in arid and semi-arid regions. With due consideration, an investigation of the complex gene network associated with sodicity stress tolerance is required to identify transcriptional changes in plants during abiotic stress conditions. For this purpose, we sequenced the flag leaf transcriptome of a highly tolerant bread wheat germplasm (KRL 3–4) in order to extend our knowledge and better understanding of the molecular basis of sodicity tolerance. A total of 1,980 genes were differentially expressed in the flag leaf due to sodicity stress. Among these genes, 872 DEGs were upregulated and 1,108 were downregulated. Furthermore, annotation of DEGs revealed that a total of 1,384 genes were assigned to 2,267 GO terms corresponding to 502 (biological process), 638 (cellular component), and 1,127 (molecular function). GO annotation also revealed the involvement of genes related to several transcription factors; the important ones are expansins, peroxidase, glutathione-S-transferase, and metal ion transporters in response to sodicity. Additionally, from 127 KEGG pathways, only 40 were confidently enriched at a p-value <0.05 covering the five main KEGG categories of metabolism, i.e., environmental information processing, genetic information processing, organismal systems, and cellular processes. Most enriched pathways were prioritized using MapMan software and revealed that lipid metabolism, nutrient uptake, and protein homeostasis were paramount. We have also found 39 SNPs that mapped to the important sodicity stress-responsive genes associated with various pathways such as ROS scavenging, serine/threonine protein kinase, calcium signaling, and metal ion transporters. In a nutshell, only 19 important candidate genes contributing to sodicity tolerance in bread wheat were identified, and these genes might be helpful for better understanding and further improvement of sodicity tolerance in bread wheat. Frontiers Media S.A. 2022-02-09 /pmc/articles/PMC8864244/ /pubmed/35222517 http://dx.doi.org/10.3389/fgene.2021.782366 Text en Copyright © 2022 Prasad, Mittal, Kumar, Chauhan, Sahu, Kumar, Singh, Yadav and Singh. 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 Prasad, Geeta Mittal, Shikha Kumar, Arvind Chauhan, Divya Sahu, Tanmaya Kumar Kumar, Sundeep Singh, Rakesh Yadav, Mahesh C. Singh, Amit Kumar Transcriptome Analysis of Bread Wheat Genotype KRL3-4 Provides a New Insight Into Regulatory Mechanisms Associated With Sodicity (High pH) Tolerance |
title | Transcriptome Analysis of Bread Wheat Genotype KRL3-4 Provides a New Insight Into Regulatory Mechanisms Associated With Sodicity (High pH) Tolerance |
title_full | Transcriptome Analysis of Bread Wheat Genotype KRL3-4 Provides a New Insight Into Regulatory Mechanisms Associated With Sodicity (High pH) Tolerance |
title_fullStr | Transcriptome Analysis of Bread Wheat Genotype KRL3-4 Provides a New Insight Into Regulatory Mechanisms Associated With Sodicity (High pH) Tolerance |
title_full_unstemmed | Transcriptome Analysis of Bread Wheat Genotype KRL3-4 Provides a New Insight Into Regulatory Mechanisms Associated With Sodicity (High pH) Tolerance |
title_short | Transcriptome Analysis of Bread Wheat Genotype KRL3-4 Provides a New Insight Into Regulatory Mechanisms Associated With Sodicity (High pH) Tolerance |
title_sort | transcriptome analysis of bread wheat genotype krl3-4 provides a new insight into regulatory mechanisms associated with sodicity (high ph) tolerance |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8864244/ https://www.ncbi.nlm.nih.gov/pubmed/35222517 http://dx.doi.org/10.3389/fgene.2021.782366 |
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