Transcriptome analysis of two contrasting rice cultivars during alkaline stress
Soil alkalinity greatly affects plant growth and crop productivity. Although RNA-Seq analyses have been conducted to investigate genome-wide gene expression in response to alkaline stress in many plants, the expressions of alkali-responsive genes in rice have not been previously investigated. In thi...
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| Veröffentlicht in: | Scientific reports 2018-06, Vol.8 (1), p.9586-16, Article 9586 |
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| creator | Li, Ning Liu, Hualong Sun, Jian Zheng, Hongliang Wang, Jingguo Yang, Luomiao Zhao, Hongwei Zou, Detang |
| description | Soil alkalinity greatly affects plant growth and crop productivity. Although RNA-Seq analyses have been conducted to investigate genome-wide gene expression in response to alkaline stress in many plants, the expressions of alkali-responsive genes in rice have not been previously investigated. In this study, the transcriptomic data between an alkaline-tolerant (WD20342) and an alkaline-sensitive (Caidao) rice cultivar were compared under alkaline stress conditions. A total of 962 important alkali-responsive (IAR) genes from highly differentially expressed genes (DEGs) were identified, including 28 alkaline-resistant cultivar-related genes, 771 alkaline-sensitive cultivar-related genes and 163 cultivar-non-specific genes. Gene ontology (GO) analysis indicated the enrichment of IAR genes involved in various stimulus or stress responses. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the IAR genes were related primarily to plant hormone signal transduction and biosynthesis of secondary metabolites. Additionally, among these 962 IAR genes, 74 were transcription factors and 15 occurred with differential alternative splicing between the different samples after alkaline treatment. Our results provide a valuable resource on alkali-responsive genes and should benefit the improvement of alkaline stress tolerance in rice. |
| doi_str_mv | 10.1038/s41598-018-27940-x |
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Although RNA-Seq analyses have been conducted to investigate genome-wide gene expression in response to alkaline stress in many plants, the expressions of alkali-responsive genes in rice have not been previously investigated. In this study, the transcriptomic data between an alkaline-tolerant (WD20342) and an alkaline-sensitive (Caidao) rice cultivar were compared under alkaline stress conditions. A total of 962 important alkali-responsive (IAR) genes from highly differentially expressed genes (DEGs) were identified, including 28 alkaline-resistant cultivar-related genes, 771 alkaline-sensitive cultivar-related genes and 163 cultivar-non-specific genes. Gene ontology (GO) analysis indicated the enrichment of IAR genes involved in various stimulus or stress responses. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the IAR genes were related primarily to plant hormone signal transduction and biosynthesis of secondary metabolites. Additionally, among these 962 IAR genes, 74 were transcription factors and 15 occurred with differential alternative splicing between the different samples after alkaline treatment. Our results provide a valuable resource on alkali-responsive genes and should benefit the improvement of alkaline stress tolerance in rice.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/s41598-018-27940-x</identifier><identifier>PMID: 29941956</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>38/39 ; 631/449/2661/2665 ; 631/449/711 ; Alkaline soils ; Alkalinity ; Alternative splicing ; Biosynthesis ; Crop production ; Cultivars ; Gene expression ; Genomes ; Humanities and Social Sciences ; Metabolites ; multidisciplinary ; Oryza ; Plant growth ; Plant hormones ; Ribonucleic acid ; Rice ; RNA ; Science ; Science (multidisciplinary) ; Secondary metabolites ; Signal transduction ; Transcription factors ; Transduction</subject><ispartof>Scientific reports, 2018-06, Vol.8 (1), p.9586-16, Article 9586</ispartof><rights>The Author(s) 2018</rights><rights>2018. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c577t-ea63c48920867d7ea63024fc1285f493594dbc0abf1e1bd50cd1de1384ae8d203</citedby><cites>FETCH-LOGICAL-c577t-ea63c48920867d7ea63024fc1285f493594dbc0abf1e1bd50cd1de1384ae8d203</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6018505/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6018505/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,41096,42165,51551,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29941956$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Ning</creatorcontrib><creatorcontrib>Liu, Hualong</creatorcontrib><creatorcontrib>Sun, Jian</creatorcontrib><creatorcontrib>Zheng, Hongliang</creatorcontrib><creatorcontrib>Wang, Jingguo</creatorcontrib><creatorcontrib>Yang, Luomiao</creatorcontrib><creatorcontrib>Zhao, Hongwei</creatorcontrib><creatorcontrib>Zou, Detang</creatorcontrib><title>Transcriptome analysis of two contrasting rice cultivars during alkaline stress</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>Soil alkalinity greatly affects plant growth and crop productivity. Although RNA-Seq analyses have been conducted to investigate genome-wide gene expression in response to alkaline stress in many plants, the expressions of alkali-responsive genes in rice have not been previously investigated. In this study, the transcriptomic data between an alkaline-tolerant (WD20342) and an alkaline-sensitive (Caidao) rice cultivar were compared under alkaline stress conditions. A total of 962 important alkali-responsive (IAR) genes from highly differentially expressed genes (DEGs) were identified, including 28 alkaline-resistant cultivar-related genes, 771 alkaline-sensitive cultivar-related genes and 163 cultivar-non-specific genes. Gene ontology (GO) analysis indicated the enrichment of IAR genes involved in various stimulus or stress responses. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the IAR genes were related primarily to plant hormone signal transduction and biosynthesis of secondary metabolites. Additionally, among these 962 IAR genes, 74 were transcription factors and 15 occurred with differential alternative splicing between the different samples after alkaline treatment. Our results provide a valuable resource on alkali-responsive genes and should benefit the improvement of alkaline stress tolerance in rice.</description><subject>38/39</subject><subject>631/449/2661/2665</subject><subject>631/449/711</subject><subject>Alkaline soils</subject><subject>Alkalinity</subject><subject>Alternative splicing</subject><subject>Biosynthesis</subject><subject>Crop production</subject><subject>Cultivars</subject><subject>Gene expression</subject><subject>Genomes</subject><subject>Humanities and Social Sciences</subject><subject>Metabolites</subject><subject>multidisciplinary</subject><subject>Oryza</subject><subject>Plant growth</subject><subject>Plant hormones</subject><subject>Ribonucleic acid</subject><subject>Rice</subject><subject>RNA</subject><subject>Science</subject><subject>Science (multidisciplinary)</subject><subject>Secondary metabolites</subject><subject>Signal transduction</subject><subject>Transcription factors</subject><subject>Transduction</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>BENPR</sourceid><recordid>eNp9kU1PxCAQhonR6Eb9Ax5MEy9eqkChhYuJ2fiVmHhZz4SldEW7ZWXadfffS62uHwe5MAPPvAzzInRE8BnBmTgHRrgUKSYipYVkOF1toRHFjKc0o3T7R7yHDgGecVycSkbkLtqjsg94PkIPk6AbMMEtWj-3iW50vQYHia-S9s0nxjdt0NC6ZpYEZ2xiurp1Sx0gKbvQn-r6RdeusQm0wQIcoJ1K12APP_d99Hh9NRnfpvcPN3fjy_vU8KJoU6vzzDAhKRZ5URZ9iimrDKGCV0xmXLJyarCeVsSSacmxKUlpSSaYtqKkONtHF4PuopvObWls32etFsHNdVgrr536fdO4JzXzS5XHiXHMo8Dpp0Dwr52FVs0dGFvXurG-A0Uxl1wQVuQRPfmDPvsuxEkNFCZEUBIpOlAmeIBgq00zBKveMjVYpmID6sMytYpFxz-_sSn5MigC2QDAoh-3Dd9v_yP7DqB6o_o</recordid><startdate>20180625</startdate><enddate>20180625</enddate><creator>Li, Ning</creator><creator>Liu, Hualong</creator><creator>Sun, Jian</creator><creator>Zheng, Hongliang</creator><creator>Wang, Jingguo</creator><creator>Yang, Luomiao</creator><creator>Zhao, Hongwei</creator><creator>Zou, Detang</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20180625</creationdate><title>Transcriptome analysis of two contrasting rice cultivars during alkaline stress</title><author>Li, Ning ; 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Although RNA-Seq analyses have been conducted to investigate genome-wide gene expression in response to alkaline stress in many plants, the expressions of alkali-responsive genes in rice have not been previously investigated. In this study, the transcriptomic data between an alkaline-tolerant (WD20342) and an alkaline-sensitive (Caidao) rice cultivar were compared under alkaline stress conditions. A total of 962 important alkali-responsive (IAR) genes from highly differentially expressed genes (DEGs) were identified, including 28 alkaline-resistant cultivar-related genes, 771 alkaline-sensitive cultivar-related genes and 163 cultivar-non-specific genes. Gene ontology (GO) analysis indicated the enrichment of IAR genes involved in various stimulus or stress responses. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the IAR genes were related primarily to plant hormone signal transduction and biosynthesis of secondary metabolites. Additionally, among these 962 IAR genes, 74 were transcription factors and 15 occurred with differential alternative splicing between the different samples after alkaline treatment. Our results provide a valuable resource on alkali-responsive genes and should benefit the improvement of alkaline stress tolerance in rice.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>29941956</pmid><doi>10.1038/s41598-018-27940-x</doi><tpages>16</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 38/39 631/449/2661/2665 631/449/711 Alkaline soils Alkalinity Alternative splicing Biosynthesis Crop production Cultivars Gene expression Genomes Humanities and Social Sciences Metabolites multidisciplinary Oryza Plant growth Plant hormones Ribonucleic acid Rice RNA Science Science (multidisciplinary) Secondary metabolites Signal transduction Transcription factors Transduction |
| title | Transcriptome analysis of two contrasting rice cultivars during alkaline stress |
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