Identification of Key Genes in ‘Luang Pratahn’, Thai Salt-Tolerant Rice, Based on Time-Course Data and Weighted Co-expression Networks
Salinity is an important environmental factor causing a negative effect on rice production. To prevent salinity effects on rice yields, genetic diversity concerning salt tolerance must be evaluated. In this study, we investigated the salinity responses of rice (Oryza sativa) to determine the critica...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-12-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2021.744654/full |
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| author | Pajaree Sonsungsan Pheerawat Chantanakool Apichat Suratanee Teerapong Buaboocha Teerapong Buaboocha Luca Comai Supachitra Chadchawan Supachitra Chadchawan Kitiporn Plaimas Kitiporn Plaimas |
| author_facet | Pajaree Sonsungsan Pheerawat Chantanakool Apichat Suratanee Teerapong Buaboocha Teerapong Buaboocha Luca Comai Supachitra Chadchawan Supachitra Chadchawan Kitiporn Plaimas Kitiporn Plaimas |
| author_sort | Pajaree Sonsungsan |
| collection | DOAJ |
| description | Salinity is an important environmental factor causing a negative effect on rice production. To prevent salinity effects on rice yields, genetic diversity concerning salt tolerance must be evaluated. In this study, we investigated the salinity responses of rice (Oryza sativa) to determine the critical genes. The transcriptomes of ‘Luang Pratahn’ rice, a local Thai rice variety with high salt tolerance, were used as a model for analyzing and identifying the key genes responsible for salt-stress tolerance. Based on 3' Tag-Seq data from the time course of salt-stress treatment, weighted gene co-expression network analysis was used to identify key genes in gene modules. We obtained 1,386 significantly differentially expressed genes in eight modules. Among them, six modules indicated a significant correlation within 6, 12, or 48h after salt stress. Functional and pathway enrichment analysis was performed on the co-expressed genes of interesting modules to reveal which genes were mainly enriched within important functions for salt-stress responses. To identify the key genes in salt-stress responses, we considered the two-state co-expression networks, normal growth conditions, and salt stress to investigate which genes were less important in a normal situation but gained more impact under stress. We identified key genes for the response to biotic and abiotic stimuli and tolerance to salt stress. Thus, these novel genes may play important roles in salinity tolerance and serve as potential biomarkers to improve salt tolerance cultivars. |
| first_indexed | 2024-12-14T14:11:28Z |
| format | Article |
| id | doaj.art-d0904ce211f642aa9b6709f84d31ee4b |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-14T14:11:28Z |
| publishDate | 2021-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-d0904ce211f642aa9b6709f84d31ee4b2022-12-21T22:58:18ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2021-12-011210.3389/fpls.2021.744654744654Identification of Key Genes in ‘Luang Pratahn’, Thai Salt-Tolerant Rice, Based on Time-Course Data and Weighted Co-expression NetworksPajaree Sonsungsan0Pheerawat Chantanakool1Apichat Suratanee2Teerapong Buaboocha3Teerapong Buaboocha4Luca Comai5Supachitra Chadchawan6Supachitra Chadchawan7Kitiporn Plaimas8Kitiporn Plaimas9Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, ThailandCenter of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, ThailandDepartment of Mathematics, Faculty of Applied Science, King Mongkut’s University of Technology North Bangkok, Bangkok, ThailandMolecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, ThailandOmics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, ThailandDepartment of Plant Biology, College of Biological Sciences, College of Biological Sciences, University of California, Davis, Davis, CA, United StatesCenter of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, ThailandOmics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, ThailandOmics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, ThailandAdvanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, ThailandSalinity is an important environmental factor causing a negative effect on rice production. To prevent salinity effects on rice yields, genetic diversity concerning salt tolerance must be evaluated. In this study, we investigated the salinity responses of rice (Oryza sativa) to determine the critical genes. The transcriptomes of ‘Luang Pratahn’ rice, a local Thai rice variety with high salt tolerance, were used as a model for analyzing and identifying the key genes responsible for salt-stress tolerance. Based on 3' Tag-Seq data from the time course of salt-stress treatment, weighted gene co-expression network analysis was used to identify key genes in gene modules. We obtained 1,386 significantly differentially expressed genes in eight modules. Among them, six modules indicated a significant correlation within 6, 12, or 48h after salt stress. Functional and pathway enrichment analysis was performed on the co-expressed genes of interesting modules to reveal which genes were mainly enriched within important functions for salt-stress responses. To identify the key genes in salt-stress responses, we considered the two-state co-expression networks, normal growth conditions, and salt stress to investigate which genes were less important in a normal situation but gained more impact under stress. We identified key genes for the response to biotic and abiotic stimuli and tolerance to salt stress. Thus, these novel genes may play important roles in salinity tolerance and serve as potential biomarkers to improve salt tolerance cultivars.https://www.frontiersin.org/articles/10.3389/fpls.2021.744654/fullsalt tolerant rice3' Tag Seqtime-series dataweighted co-expression networktwo-state co-expression networknetwork-based analysis |
| spellingShingle | Pajaree Sonsungsan Pheerawat Chantanakool Apichat Suratanee Teerapong Buaboocha Teerapong Buaboocha Luca Comai Supachitra Chadchawan Supachitra Chadchawan Kitiporn Plaimas Kitiporn Plaimas Identification of Key Genes in ‘Luang Pratahn’, Thai Salt-Tolerant Rice, Based on Time-Course Data and Weighted Co-expression Networks Frontiers in Plant Science salt tolerant rice 3' Tag Seq time-series data weighted co-expression network two-state co-expression network network-based analysis |
| title | Identification of Key Genes in ‘Luang Pratahn’, Thai Salt-Tolerant Rice, Based on Time-Course Data and Weighted Co-expression Networks |
| title_full | Identification of Key Genes in ‘Luang Pratahn’, Thai Salt-Tolerant Rice, Based on Time-Course Data and Weighted Co-expression Networks |
| title_fullStr | Identification of Key Genes in ‘Luang Pratahn’, Thai Salt-Tolerant Rice, Based on Time-Course Data and Weighted Co-expression Networks |
| title_full_unstemmed | Identification of Key Genes in ‘Luang Pratahn’, Thai Salt-Tolerant Rice, Based on Time-Course Data and Weighted Co-expression Networks |
| title_short | Identification of Key Genes in ‘Luang Pratahn’, Thai Salt-Tolerant Rice, Based on Time-Course Data and Weighted Co-expression Networks |
| title_sort | identification of key genes in luang pratahn thai salt tolerant rice based on time course data and weighted co expression networks |
| topic | salt tolerant rice 3' Tag Seq time-series data weighted co-expression network two-state co-expression network network-based analysis |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2021.744654/full |
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