3
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Gene co-expression network analysis to identify critical modules and candidate genes of drought-resistance in wheat

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Aim

          To establish a gene co-expression network for identifying principal modules and hub genes that are associated with drought resistance mechanisms, analyzing their mechanisms, and exploring candidate genes.

          Methods and findings

          42 data sets including PRJNA380841 and PRJNA369686 were used to construct the co-expression network through weighted gene co-expression network analysis (WGCNA). A total of 1,896,897,901 (284.30 Gb) clean reads and 35,021 differentially expressed genes (DEGs) were obtained from 42 samples. Functional enrichment analysis indicated that photosynthesis, DNA replication, glycolysis/gluconeogenesis, starch and sucrose metabolism, arginine and proline metabolism, and cell cycle were significantly influenced by drought stress. Furthermore, the DEGs with similar expression patterns, detected by K-means clustering, were grouped into 29 clusters. Genes involved in the modules, such as dark turquoise, yellow, and brown, were found to be appreciably linked with drought resistance. Twelve central, greatly correlated genes in stage-specific modules were subsequently confirmed and validated at the transcription levels, including TraesCS7D01G417600. 1 (PP2C), TraesCS5B01G565300. 1 (ERF), TraesCS4A01G068200. 1 (HSP), TraesCS2D01G033200. 1 (HSP90), TraesCS6B01G425300. 1 (RBD), TraesCS7A01G499200. 1 (P450), TraesCS4A01G118400. 1 (MYB), TraesCS2B01G415500. 1 (STK), TraesCS1A01G129300. 1 (MYB), TraesCS2D01G326900. 1 (ALDH), TraesCS3D01G227400. 1 (WRKY), and TraesCS3B01G144800. 1 (GT).

          Conclusions

          Analyzing the response of wheat to drought stress during different growth stages, we have detected three modules and 12 hub genes that are associated with drought resistance mechanisms, and five of those genes are newly identified for drought resistance. The references provided by these modules will promote the understanding of the drought-resistance mechanism. In addition, the candidate genes can be used as a basis of transgenic or molecular marker-assisted selection for improving the drought resistance and increasing the yields of wheat.

          Related collections

          Most cited references55

          • Record: found
          • Abstract: not found
          • Article: not found

          Rising temperatures reduce global wheat production

            Bookmark
            • Record: found
            • Abstract: not found
            • Article: not found

            Crops that feed the world 10. Past successes and future challenges to the role played by wheat in global food security

              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Overexpression of an R1R2R3 MYB gene, OsMYB3R-2, increases tolerance to freezing, drought, and salt stress in transgenic Arabidopsis.

              We used a cDNA microarray approach to monitor the expression profile of rice (Oryza sativa) under cold stress and identified 328 cold-regulated genes. Thirteen such genes encoding MYB, homeodomain, and zinc finger proteins with unknown functions showed a significant change in expression under 72-h cold stress. Among them, OsMYB3R-2 was selected for further study. Unlike most plant R2R3 MYB transcription factors, OsMYB3R-2 has three imperfect repeats in the DNA-binding domain, the same as in animal c-MYB proteins. Expression of OsMYB3R-2 was induced by cold, drought, and salt stress. The Arabidopsis (Arabidopsis thaliana) transgenic plants overexpressing OsMYB3R-2 showed increased tolerance to cold, drought, and salt stress, and the seed germination of transgenic plants was more tolerant to abscisic acid or NaCl than that of wild type. The expression of some clod-related genes, such as dehydration-responsive element-binding protein 2A, COR15a, and RCI2A, was increased to a higher level in OsMYB3R-2-overexpressing plants than in wild type. These results suggest that OsMYB3R-2 acts as a master switch in stress tolerance.
                Bookmark

                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ValidationRole: Writing – original draft
                Role: Investigation
                Role: Validation
                Role: Data curation
                Role: Validation
                Role: Data curation
                Role: Investigation
                Role: Investigation
                Role: Supervision
                Role: Supervision
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                31 August 2020
                2020
                : 15
                : 8
                : e0236186
                Affiliations
                [1 ] Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Crop Genetics and Breeding Laboratory of Hebei, Shijiazhuang, China
                [2 ] Institute of Dryland Farming Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
                Murdoch University, AUSTRALIA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Article
                PONE-D-20-08497
                10.1371/journal.pone.0236186
                7458298
                32866164
                16296120-c00b-4056-8f1a-7ced6572163c
                © 2020 Lv et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 30 April 2020
                : 30 June 2020
                Page count
                Figures: 6, Tables: 1, Pages: 18
                Funding
                Funded by: HAAFS Agriculture Science and Technology Innovation Project
                Award ID: 2019-4-6-02
                Award Recipient :
                Funded by: Special Foundation of Hebei Academy of Agriculture and Forestry Sciences
                Award ID: 2018060303
                Award Recipient :
                Funded by: HAAFS Agriculture Science and Technology Innovation Project
                Award ID: 4-09-04-01
                Award Recipient :
                Funded by: Earmarked Fund for Hebei Wheat Innovation Team of Modern Agro-industry Technology Research System
                Award ID: HBCT2018010201
                Award Recipient :
                Funded by: Key Research and Development Program of china(CN)
                Award ID: 2017YF00100603
                Award Recipient :
                This study was financially supported by the HAAFS Agriculture Science and Technology Innovation Project (2019-4-6-02;4-09-04-01) to LL; Special Foundation of Hebei Academy of Agriculture and Forestry Sciences (2018060303) to LL; Earmarked Fund for Hebei Wheat Innovation Team of Modern Agro-industry Technology Research System (HBCT2018010201) to HL; Key Research and Development Program of china (CN) (2017YF00100603) to LL; Natural Science Foundation of Hebei Province (C2020301004) to LL. We have received funds for covering the costs to publish in open access. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Organisms
                Eukaryota
                Plants
                Grasses
                Wheat
                Biology and Life Sciences
                Genetics
                Gene Expression
                Biology and Life Sciences
                Physiology
                Plant Physiology
                Plant Defenses
                Plant Resistance to Abiotic Stress
                Biology and Life Sciences
                Plant Science
                Plant Physiology
                Plant Defenses
                Plant Resistance to Abiotic Stress
                Biology and Life Sciences
                Plant Science
                Plant Pathology
                Plant Resistance to Abiotic Stress
                Biology and Life Sciences
                Ecology
                Plant Ecology
                Plant-Environment Interactions
                Plant Resistance to Abiotic Stress
                Ecology and Environmental Sciences
                Ecology
                Plant Ecology
                Plant-Environment Interactions
                Plant Resistance to Abiotic Stress
                Biology and Life Sciences
                Plant Science
                Plant Ecology
                Plant-Environment Interactions
                Plant Resistance to Abiotic Stress
                Biology and Life Sciences
                Cell Biology
                Cell Processes
                Cellular Stress Responses
                Biology and Life Sciences
                Cell Biology
                Cell Processes
                Cellular Stress Responses
                Heat Shock Response
                Biology and Life Sciences
                Genetics
                Gene Expression
                Gene Regulation
                Biology and life sciences
                Biochemistry
                Proteins
                DNA-binding proteins
                Transcription Factors
                Biology and Life Sciences
                Genetics
                Gene Expression
                Gene Regulation
                Transcription Factors
                Biology and Life Sciences
                Biochemistry
                Proteins
                Regulatory Proteins
                Transcription Factors
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Transcriptome Analysis
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Transcriptome Analysis
                Custom metadata
                The RNA sequencing data are available from the NCBI Sequence Read Archive under the Bioprojects PRJNA380841 and PRJNA369686. Samples are descried by Biosamples SAMN06649910-SAMN06649915, SAMN06649934-SAMN06649952 and SAMN06291347-SAMN06291364.

                Uncategorized
                Uncategorized

                Comments

                Comment on this article