De Novo Transcriptome Analysis for Kentucky Bluegrass Dwarf Mutants Induced by Space Mutation
Kentucky bluegrass (Poa pratensis L.) is a major cool-season turfgrass requiring frequent mowing. Utilization of cultivars with slow growth is a promising method to decrease mowing frequency. In this study, two dwarf mutant selections of Kentucky bluegrass (A12 and A16) induced by space mutation wer...
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| creator | Gan, Lu Di, Rong Chao, Yuehui Han, Liebao Chen, Xingwu Wu, Chao Yin, Shuxia |
| description | Kentucky bluegrass (Poa pratensis L.) is a major cool-season turfgrass requiring frequent mowing. Utilization of cultivars with slow growth is a promising method to decrease mowing frequency. In this study, two dwarf mutant selections of Kentucky bluegrass (A12 and A16) induced by space mutation were analyzed for the differentially expressed genes compared with the wild type (WT) by the high-throughput RNA-Seq technology. 253,909 unigenes were obtained by de novo assembly. 24.20% of the unigenes had a significant level of amino acid sequence identity to Brachypodium distachyon proteins, followed by Hordeum vulgare with 18.72% among the non-redundant (NR) Blastx top hits. Assembled unigenes were associated with 32 pathways using KEGG orthology terms and their respective KEGG maps. Between WT and A16 libraries, 4,203 differentially expressed genes (DEGs) were identified, whereas there were 883 DEGs between WT and A12 libraries. Further investigation revealed that the DEG pathways were mainly involved in terpenoid biosynthesis and plant hormone metabolism, which might account for the differences of plant height and leaf blade color between dwarf mutant and WT plants. Our study presents the first comprehensive transcriptomic data and gene function analysis of Poa pratensis L., providing a valuable resource for future studies in plant dwarfing breeding and comparative genome analysis for Pooideae plants. |
| doi_str_mv | 10.1371/journal.pone.0151768 |
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Utilization of cultivars with slow growth is a promising method to decrease mowing frequency. In this study, two dwarf mutant selections of Kentucky bluegrass (A12 and A16) induced by space mutation were analyzed for the differentially expressed genes compared with the wild type (WT) by the high-throughput RNA-Seq technology. 253,909 unigenes were obtained by de novo assembly. 24.20% of the unigenes had a significant level of amino acid sequence identity to Brachypodium distachyon proteins, followed by Hordeum vulgare with 18.72% among the non-redundant (NR) Blastx top hits. Assembled unigenes were associated with 32 pathways using KEGG orthology terms and their respective KEGG maps. Between WT and A16 libraries, 4,203 differentially expressed genes (DEGs) were identified, whereas there were 883 DEGs between WT and A12 libraries. Further investigation revealed that the DEG pathways were mainly involved in terpenoid biosynthesis and plant hormone metabolism, which might account for the differences of plant height and leaf blade color between dwarf mutant and WT plants. Our study presents the first comprehensive transcriptomic data and gene function analysis of Poa pratensis L., providing a valuable resource for future studies in plant dwarfing breeding and comparative genome analysis for Pooideae plants.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0151768</identifier><identifier>PMID: 27010560</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Amino acid sequence ; Amino acids ; Analysis ; Biology and Life Sciences ; Biosynthesis ; Bluegrasses ; Brachypodium distachyon ; Breeding ; Cultivars ; Data processing ; Extraterrestrial Environment ; Function analysis ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene mapping ; Gene Ontology ; Genes ; Genes, Plant ; Genetic aspects ; Genomes ; Genomics ; Grasses ; Hordeum vulgare ; Kentucky ; Metabolism ; Mowing ; Mutagenesis ; Mutants ; Mutation ; Orthology ; Pathways ; Physiological aspects ; Plant breeding ; Plant growth ; Plant hormones ; Plants (botany) ; Poa - genetics ; Poa - growth & development ; Poa pratensis ; Proteins ; Ribonucleic acid ; RNA ; RNA sequencing ; Seeds ; Seeds - genetics ; Seeds - growth & development ; Turfgrasses</subject><ispartof>PloS one, 2016-03, Vol.11 (3), p.e0151768</ispartof><rights>COPYRIGHT 2016 Public Library of Science</rights><rights>2016 Gan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2016 Gan et al 2016 Gan et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-92af47cea9035ae863d231fbc30048d861b2efbdd5b3e9c96d3c53f61113b5053</citedby><cites>FETCH-LOGICAL-c692t-92af47cea9035ae863d231fbc30048d861b2efbdd5b3e9c96d3c53f61113b5053</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/PMC4807101/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4807101/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27010560$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Gan, Lu</creatorcontrib><creatorcontrib>Di, Rong</creatorcontrib><creatorcontrib>Chao, Yuehui</creatorcontrib><creatorcontrib>Han, Liebao</creatorcontrib><creatorcontrib>Chen, Xingwu</creatorcontrib><creatorcontrib>Wu, Chao</creatorcontrib><creatorcontrib>Yin, Shuxia</creatorcontrib><title>De Novo Transcriptome Analysis for Kentucky Bluegrass Dwarf Mutants Induced by Space Mutation</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Kentucky bluegrass (Poa pratensis L.) is a major cool-season turfgrass requiring frequent mowing. Utilization of cultivars with slow growth is a promising method to decrease mowing frequency. In this study, two dwarf mutant selections of Kentucky bluegrass (A12 and A16) induced by space mutation were analyzed for the differentially expressed genes compared with the wild type (WT) by the high-throughput RNA-Seq technology. 253,909 unigenes were obtained by de novo assembly. 24.20% of the unigenes had a significant level of amino acid sequence identity to Brachypodium distachyon proteins, followed by Hordeum vulgare with 18.72% among the non-redundant (NR) Blastx top hits. Assembled unigenes were associated with 32 pathways using KEGG orthology terms and their respective KEGG maps. Between WT and A16 libraries, 4,203 differentially expressed genes (DEGs) were identified, whereas there were 883 DEGs between WT and A12 libraries. Further investigation revealed that the DEG pathways were mainly involved in terpenoid biosynthesis and plant hormone metabolism, which might account for the differences of plant height and leaf blade color between dwarf mutant and WT plants. Our study presents the first comprehensive transcriptomic data and gene function analysis of Poa pratensis L., providing a valuable resource for future studies in plant dwarfing breeding and comparative genome analysis for Pooideae plants.</description><subject>Amino acid sequence</subject><subject>Amino acids</subject><subject>Analysis</subject><subject>Biology and Life Sciences</subject><subject>Biosynthesis</subject><subject>Bluegrasses</subject><subject>Brachypodium distachyon</subject><subject>Breeding</subject><subject>Cultivars</subject><subject>Data processing</subject><subject>Extraterrestrial Environment</subject><subject>Function analysis</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Plant</subject><subject>Gene mapping</subject><subject>Gene Ontology</subject><subject>Genes</subject><subject>Genes, Plant</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Grasses</subject><subject>Hordeum vulgare</subject><subject>Kentucky</subject><subject>Metabolism</subject><subject>Mowing</subject><subject>Mutagenesis</subject><subject>Mutants</subject><subject>Mutation</subject><subject>Orthology</subject><subject>Pathways</subject><subject>Physiological aspects</subject><subject>Plant breeding</subject><subject>Plant growth</subject><subject>Plant hormones</subject><subject>Plants (botany)</subject><subject>Poa - genetics</subject><subject>Poa - growth & development</subject><subject>Poa pratensis</subject><subject>Proteins</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA sequencing</subject><subject>Seeds</subject><subject>Seeds - genetics</subject><subject>Seeds - growth & development</subject><subject>Turfgrasses</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNkltrFDEYhgdR7EH_gWhAKHixazI5zMyNsLYeFqsFW72TkMlhNtvZyZpkqvvvzXanZQcUJBcJX57vzZeXN8ueIThFuECvl673nWina9fpKUQUFax8kB2iCucTlkP8cO98kB2FsISQ4pKxx9lBXkAEKYOH2Y8zDb64GweuvOiC9HYd3UqDWVLeBBuAcR580l3s5fUGvG173XgRAjj7JbwBn_souhjAvFO91ArUG3C5FlLfXkTruifZIyPaoJ8O-3H27f27q9OPk_OLD_PT2flEsiqPkyoXhhRSiwpiKnTJsMoxMrXEEJJSlQzVuTa1UrTGupIVU1hSbBhCCNc0_eo4e7HTXbcu8MGZwFFRUJYXhFSJmO8I5cSSr71dCb_hTlh-W3C-4cJHK1vNpYYllUZghSHBCtWaQqLyUiCskoEqab0ZXuvrlVYy2eNFOxId33R2wRt3w0kJCwRREng5CHj3s9ch_mPkgWpEmsp2xiUxubJB8hmhmBSQUJio6V-otJReWZmyYWyqjxpejRoSE_Xv2Ig-BD6__Pr_7MX3MXuyxy60aOMiuLbf5iCMQbIDpXcheG3unUOQb6N95wbfRpsP0U5tz_ddv2-6yzL-A1Zo88E</recordid><startdate>20160324</startdate><enddate>20160324</enddate><creator>Gan, Lu</creator><creator>Di, Rong</creator><creator>Chao, Yuehui</creator><creator>Han, Liebao</creator><creator>Chen, Xingwu</creator><creator>Wu, Chao</creator><creator>Yin, Shuxia</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20160324</creationdate><title>De Novo Transcriptome Analysis for Kentucky Bluegrass Dwarf Mutants Induced by Space Mutation</title><author>Gan, Lu ; Di, Rong ; Chao, Yuehui ; Han, Liebao ; Chen, Xingwu ; Wu, Chao ; Yin, Shuxia</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-92af47cea9035ae863d231fbc30048d861b2efbdd5b3e9c96d3c53f61113b5053</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Amino acid sequence</topic><topic>Amino acids</topic><topic>Analysis</topic><topic>Biology and Life Sciences</topic><topic>Biosynthesis</topic><topic>Bluegrasses</topic><topic>Brachypodium distachyon</topic><topic>Breeding</topic><topic>Cultivars</topic><topic>Data processing</topic><topic>Extraterrestrial Environment</topic><topic>Function analysis</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation, Plant</topic><topic>Gene mapping</topic><topic>Gene Ontology</topic><topic>Genes</topic><topic>Genes, Plant</topic><topic>Genetic aspects</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Grasses</topic><topic>Hordeum vulgare</topic><topic>Kentucky</topic><topic>Metabolism</topic><topic>Mowing</topic><topic>Mutagenesis</topic><topic>Mutants</topic><topic>Mutation</topic><topic>Orthology</topic><topic>Pathways</topic><topic>Physiological aspects</topic><topic>Plant breeding</topic><topic>Plant growth</topic><topic>Plant hormones</topic><topic>Plants (botany)</topic><topic>Poa - 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Utilization of cultivars with slow growth is a promising method to decrease mowing frequency. In this study, two dwarf mutant selections of Kentucky bluegrass (A12 and A16) induced by space mutation were analyzed for the differentially expressed genes compared with the wild type (WT) by the high-throughput RNA-Seq technology. 253,909 unigenes were obtained by de novo assembly. 24.20% of the unigenes had a significant level of amino acid sequence identity to Brachypodium distachyon proteins, followed by Hordeum vulgare with 18.72% among the non-redundant (NR) Blastx top hits. Assembled unigenes were associated with 32 pathways using KEGG orthology terms and their respective KEGG maps. Between WT and A16 libraries, 4,203 differentially expressed genes (DEGs) were identified, whereas there were 883 DEGs between WT and A12 libraries. Further investigation revealed that the DEG pathways were mainly involved in terpenoid biosynthesis and plant hormone metabolism, which might account for the differences of plant height and leaf blade color between dwarf mutant and WT plants. Our study presents the first comprehensive transcriptomic data and gene function analysis of Poa pratensis L., providing a valuable resource for future studies in plant dwarfing breeding and comparative genome analysis for Pooideae plants.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>27010560</pmid><doi>10.1371/journal.pone.0151768</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Amino acid sequence Amino acids Analysis Biology and Life Sciences Biosynthesis Bluegrasses Brachypodium distachyon Breeding Cultivars Data processing Extraterrestrial Environment Function analysis Gene expression Gene Expression Profiling Gene Expression Regulation, Plant Gene mapping Gene Ontology Genes Genes, Plant Genetic aspects Genomes Genomics Grasses Hordeum vulgare Kentucky Metabolism Mowing Mutagenesis Mutants Mutation Orthology Pathways Physiological aspects Plant breeding Plant growth Plant hormones Plants (botany) Poa - genetics Poa - growth & development Poa pratensis Proteins Ribonucleic acid RNA RNA sequencing Seeds Seeds - genetics Seeds - growth & development Turfgrasses |
| title | De Novo Transcriptome Analysis for Kentucky Bluegrass Dwarf Mutants Induced by Space Mutation |
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