Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of <i>qDTYs</i> to Reproductive-Stage Drought Stress in Rice (<i>Oryza sativa</i> L.)
Rice (<i>Oryza sativa</i> L.) is more sensitive to drought stress than other cereals. To dissect molecular mechanisms underlying drought-tolerant yield in rice, we applied differential expression and co-expression network approaches to transcriptomes from flag-leaf and emerging panicle t...
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2020-09-01
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| Online Access: | https://www.mdpi.com/2073-4425/11/10/1124 |
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| author | Jeshurun Asher Tarun Ramil Mauleon Juan David Arbelaez Sheryl Catausan Shalabh Dixit Arvind Kumar Patrick Brown Ajay Kohli Tobias Kretzschmar |
| author_facet | Jeshurun Asher Tarun Ramil Mauleon Juan David Arbelaez Sheryl Catausan Shalabh Dixit Arvind Kumar Patrick Brown Ajay Kohli Tobias Kretzschmar |
| author_sort | Jeshurun Asher Tarun |
| collection | DOAJ |
| description | Rice (<i>Oryza sativa</i> L.) is more sensitive to drought stress than other cereals. To dissect molecular mechanisms underlying drought-tolerant yield in rice, we applied differential expression and co-expression network approaches to transcriptomes from flag-leaf and emerging panicle tissues of a drought-tolerant yield introgression line, DTY-IL, and the recurrent parent Swarna, under moderate reproductive-stage drought stress. Protein turnover and efficient reactive oxygen species scavenging were found to be the driving factors in both tissues. In the flag-leaf, the responses further included maintenance of photosynthesis and cell wall reorganization, while in the panicle biosynthesis of secondary metabolites was found to play additional roles. Hub genes of importance in differential drought responses included an expansin in the flag-leaf and two peroxidases in the panicle. Overlaying differential expression data with allelic variation in DTY-IL quantitative trait loci allowed for the prioritization of candidate genes. They included a differentially regulated auxin-responsive protein, with DTY-IL-specific amino acid changes in conserved domains, as well as a protein kinase with a DTY-IL-specific frameshift in the C-terminal region. The approach highlights how the integration of differential expression and allelic variation can aid in the discovery of mechanism and putative causal contribution underlying quantitative trait loci for drought-tolerant yield. |
| first_indexed | 2024-03-10T16:04:52Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T16:04:52Z |
| publishDate | 2020-09-01 |
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| record_format | Article |
| series | Genes |
| spelling | doaj.art-9ab990f64e9e4decaf875862528b0bcc2023-11-20T15:00:50ZengMDPI AGGenes2073-44252020-09-011110112410.3390/genes11101124Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of <i>qDTYs</i> to Reproductive-Stage Drought Stress in Rice (<i>Oryza sativa</i> L.)Jeshurun Asher Tarun0Ramil Mauleon1Juan David Arbelaez2Sheryl Catausan3Shalabh Dixit4Arvind Kumar5Patrick Brown6Ajay Kohli7Tobias Kretzschmar8Department of Crop Sciences, College of Agricultural, Consumer & Environmental Sciences, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USASouthern Cross Plant Science, Southern Cross University, Military Rd, East Lismore NSW 2480, AustraliaDepartment of Crop Sciences, College of Agricultural, Consumer & Environmental Sciences, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USAInternational Rice Research Institute, Los Baños, Laguna 4031, PhilippinesInternational Rice Research Institute, Los Baños, Laguna 4031, PhilippinesInternational Rice Research Institute, Los Baños, Laguna 4031, PhilippinesDepartment of Plant Sciences, University of California Davis, One Shields Avenue, Davis, CA 95616, USAInternational Rice Research Institute, Los Baños, Laguna 4031, PhilippinesSouthern Cross Plant Science, Southern Cross University, Military Rd, East Lismore NSW 2480, AustraliaRice (<i>Oryza sativa</i> L.) is more sensitive to drought stress than other cereals. To dissect molecular mechanisms underlying drought-tolerant yield in rice, we applied differential expression and co-expression network approaches to transcriptomes from flag-leaf and emerging panicle tissues of a drought-tolerant yield introgression line, DTY-IL, and the recurrent parent Swarna, under moderate reproductive-stage drought stress. Protein turnover and efficient reactive oxygen species scavenging were found to be the driving factors in both tissues. In the flag-leaf, the responses further included maintenance of photosynthesis and cell wall reorganization, while in the panicle biosynthesis of secondary metabolites was found to play additional roles. Hub genes of importance in differential drought responses included an expansin in the flag-leaf and two peroxidases in the panicle. Overlaying differential expression data with allelic variation in DTY-IL quantitative trait loci allowed for the prioritization of candidate genes. They included a differentially regulated auxin-responsive protein, with DTY-IL-specific amino acid changes in conserved domains, as well as a protein kinase with a DTY-IL-specific frameshift in the C-terminal region. The approach highlights how the integration of differential expression and allelic variation can aid in the discovery of mechanism and putative causal contribution underlying quantitative trait loci for drought-tolerant yield.https://www.mdpi.com/2073-4425/11/10/1124co-expression networkdrought-tolerant-yieldreproductive-stage drought<i>qDTY</i>sricetranscriptomics |
| spellingShingle | Jeshurun Asher Tarun Ramil Mauleon Juan David Arbelaez Sheryl Catausan Shalabh Dixit Arvind Kumar Patrick Brown Ajay Kohli Tobias Kretzschmar Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of <i>qDTYs</i> to Reproductive-Stage Drought Stress in Rice (<i>Oryza sativa</i> L.) Genes co-expression network drought-tolerant-yield reproductive-stage drought <i>qDTY</i>s rice transcriptomics |
| title | Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of <i>qDTYs</i> to Reproductive-Stage Drought Stress in Rice (<i>Oryza sativa</i> L.) |
| title_full | Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of <i>qDTYs</i> to Reproductive-Stage Drought Stress in Rice (<i>Oryza sativa</i> L.) |
| title_fullStr | Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of <i>qDTYs</i> to Reproductive-Stage Drought Stress in Rice (<i>Oryza sativa</i> L.) |
| title_full_unstemmed | Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of <i>qDTYs</i> to Reproductive-Stage Drought Stress in Rice (<i>Oryza sativa</i> L.) |
| title_short | Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of <i>qDTYs</i> to Reproductive-Stage Drought Stress in Rice (<i>Oryza sativa</i> L.) |
| title_sort | comparative transcriptomics and co expression networks reveal tissue and genotype specific responses of i qdtys i to reproductive stage drought stress in rice i oryza sativa i l |
| topic | co-expression network drought-tolerant-yield reproductive-stage drought <i>qDTY</i>s rice transcriptomics |
| url | https://www.mdpi.com/2073-4425/11/10/1124 |
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