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Gene Coexpression Analysis Identifies Genes Associated with Chlorophyll Content and Relative Water Content in Pearl Millet
Pearl millet is a significant crop that is tolerant to abiotic stresses and is a staple food of arid regions. However, its underlying mechanisms of stress tolerance are not fully understood. Plant survival is regulated by the ability to perceive a stress signal and induce appropriate physiological c...
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/PMC10057621/ https://www.ncbi.nlm.nih.gov/pubmed/36987099 http://dx.doi.org/10.3390/plants12061412 |
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author | Shinde, Harshraj Dudhate, Ambika Sathe, Atul Paserkar, Neha Wagh, Sopan Ganpatrao Kadam, Ulhas Sopanrao |
author_facet | Shinde, Harshraj Dudhate, Ambika Sathe, Atul Paserkar, Neha Wagh, Sopan Ganpatrao Kadam, Ulhas Sopanrao |
author_sort | Shinde, Harshraj |
collection | PubMed |
description | Pearl millet is a significant crop that is tolerant to abiotic stresses and is a staple food of arid regions. However, its underlying mechanisms of stress tolerance are not fully understood. Plant survival is regulated by the ability to perceive a stress signal and induce appropriate physiological changes. Here, we screened for genes regulating physiological changes such as chlorophyll content (CC) and relative water content (RWC) in response to abiotic stress by using “weighted gene coexpression network analysis” (WGCNA) and clustering changes in physiological traits, i.e., CC and RWC associated with gene expression. Genes’ correlations with traits were defined in the form of modules, and different color names were used to denote a particular module. Modules are groups of genes with similar patterns of expression, which also tend to be functionally related and co-regulated. In WGCNA, the dark green module (7082 genes) showed a significant positive correlation with CC, and the black (1393 genes) module was negatively correlated with CC and RWC. Analysis of the module positively correlated with CC highlighted ribosome synthesis and plant hormone signaling as the most significant pathways. Potassium transporter 8 and monothiol glutaredoxin were reported as the topmost hub genes in the dark green module. In Clust analysis, 2987 genes were found to display a correlation with increasing CC and RWC. Furthermore, the pathway analysis of these clusters identified the ribosome and thermogenesis as positive regulators of RWC and CC, respectively. Our study provides novel insights into the molecular mechanisms regulating CC and RWC in pearl millet. |
format | Online Article Text |
id | pubmed-10057621 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-100576212023-03-30 Gene Coexpression Analysis Identifies Genes Associated with Chlorophyll Content and Relative Water Content in Pearl Millet Shinde, Harshraj Dudhate, Ambika Sathe, Atul Paserkar, Neha Wagh, Sopan Ganpatrao Kadam, Ulhas Sopanrao Plants (Basel) Communication Pearl millet is a significant crop that is tolerant to abiotic stresses and is a staple food of arid regions. However, its underlying mechanisms of stress tolerance are not fully understood. Plant survival is regulated by the ability to perceive a stress signal and induce appropriate physiological changes. Here, we screened for genes regulating physiological changes such as chlorophyll content (CC) and relative water content (RWC) in response to abiotic stress by using “weighted gene coexpression network analysis” (WGCNA) and clustering changes in physiological traits, i.e., CC and RWC associated with gene expression. Genes’ correlations with traits were defined in the form of modules, and different color names were used to denote a particular module. Modules are groups of genes with similar patterns of expression, which also tend to be functionally related and co-regulated. In WGCNA, the dark green module (7082 genes) showed a significant positive correlation with CC, and the black (1393 genes) module was negatively correlated with CC and RWC. Analysis of the module positively correlated with CC highlighted ribosome synthesis and plant hormone signaling as the most significant pathways. Potassium transporter 8 and monothiol glutaredoxin were reported as the topmost hub genes in the dark green module. In Clust analysis, 2987 genes were found to display a correlation with increasing CC and RWC. Furthermore, the pathway analysis of these clusters identified the ribosome and thermogenesis as positive regulators of RWC and CC, respectively. Our study provides novel insights into the molecular mechanisms regulating CC and RWC in pearl millet. MDPI 2023-03-22 /pmc/articles/PMC10057621/ /pubmed/36987099 http://dx.doi.org/10.3390/plants12061412 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 | Communication Shinde, Harshraj Dudhate, Ambika Sathe, Atul Paserkar, Neha Wagh, Sopan Ganpatrao Kadam, Ulhas Sopanrao Gene Coexpression Analysis Identifies Genes Associated with Chlorophyll Content and Relative Water Content in Pearl Millet |
title | Gene Coexpression Analysis Identifies Genes Associated with Chlorophyll Content and Relative Water Content in Pearl Millet |
title_full | Gene Coexpression Analysis Identifies Genes Associated with Chlorophyll Content and Relative Water Content in Pearl Millet |
title_fullStr | Gene Coexpression Analysis Identifies Genes Associated with Chlorophyll Content and Relative Water Content in Pearl Millet |
title_full_unstemmed | Gene Coexpression Analysis Identifies Genes Associated with Chlorophyll Content and Relative Water Content in Pearl Millet |
title_short | Gene Coexpression Analysis Identifies Genes Associated with Chlorophyll Content and Relative Water Content in Pearl Millet |
title_sort | gene coexpression analysis identifies genes associated with chlorophyll content and relative water content in pearl millet |
topic | Communication |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10057621/ https://www.ncbi.nlm.nih.gov/pubmed/36987099 http://dx.doi.org/10.3390/plants12061412 |
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