Genome-Wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm
Grain appearance quality and milling quality are the main determinants of market value of rice. Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through m...
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| creator | Qiu, Xianjin Pang, Yunlong Yuan, Zhihua Xing, Danying Xu, Jianlong Dingkuhn, Michael Li, Zhikang Ye, Guoyou |
| description | Grain appearance quality and milling quality are the main determinants of market value of rice. Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through marker-assisted selection. Here, we reported a genome-wide association study in indica rice to identify QTL associated with 10 appearance and milling quality related traits, including grain length, grain width, grain length to width ratio, grain thickness, thousand grain weight, degree of endosperm chalkiness, percentage of grains with chalkiness, brown rice rate, milled rice rate and head milled rice rate. A diversity panel consisting of 272 indica accessions collected worldwide was evaluated in four locations including Hangzhou, Jingzhou, Sanya and Shenzhen representing indica rice production environments in China and genotyped using genotyping-by-sequencing and Diversity Arrays Technology based on next-generation sequencing technique called DArTseq™. A wide range of variation was observed for all traits in all environments. A total of 16 different association analysis models were compared to determine the best model for each trait-environment combination. Association mapping based on 18,824 high quality markers yielded 38 QTL for the 10 traits. Five of the detected QTL corresponded to known genes or fine mapped QTL. Among the 33 novel QTL identified, qDEC1.1 (qGLWR1.1), qBRR2.2 (qGL2.1), qTGW2.1 (qGL2.2), qGW11.1 (qMRR11.1) and qGL7.1 affected multiple traits with relatively large effects and/or were detected in multiple environments. The research provided an insight of the genetic architecture of rice grain quality and important information for mining genes/QTL with large effects within indica accessions for rice breeding. |
| doi_str_mv | 10.1371/journal.pone.0145577 |
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Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through marker-assisted selection. Here, we reported a genome-wide association study in indica rice to identify QTL associated with 10 appearance and milling quality related traits, including grain length, grain width, grain length to width ratio, grain thickness, thousand grain weight, degree of endosperm chalkiness, percentage of grains with chalkiness, brown rice rate, milled rice rate and head milled rice rate. A diversity panel consisting of 272 indica accessions collected worldwide was evaluated in four locations including Hangzhou, Jingzhou, Sanya and Shenzhen representing indica rice production environments in China and genotyped using genotyping-by-sequencing and Diversity Arrays Technology based on next-generation sequencing technique called DArTseq™. A wide range of variation was observed for all traits in all environments. A total of 16 different association analysis models were compared to determine the best model for each trait-environment combination. Association mapping based on 18,824 high quality markers yielded 38 QTL for the 10 traits. Five of the detected QTL corresponded to known genes or fine mapped QTL. Among the 33 novel QTL identified, qDEC1.1 (qGLWR1.1), qBRR2.2 (qGL2.1), qTGW2.1 (qGL2.2), qGW11.1 (qMRR11.1) and qGL7.1 affected multiple traits with relatively large effects and/or were detected in multiple environments. The research provided an insight of the genetic architecture of rice grain quality and important information for mining genes/QTL with large effects within indica accessions for rice breeding.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0145577</identifier><identifier>PMID: 26714258</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Agricultural production ; Agriculture ; Analysis ; Association analysis ; Breeding ; Crop science ; Data mining ; Ecology ; Edible Grain - anatomy & histology ; Education ; Endosperm ; Engineering research ; Environment ; Food Quality ; Gene mapping ; Genes ; Genetic Markers - genetics ; Genetics ; Genome-wide association studies ; Genome-Wide Association Study ; Genomes ; Genomics ; Genotyping ; Germplasm ; Grain ; Linkage Disequilibrium ; Marker-assisted selection ; Market value ; Mine wastes ; Oryza - anatomy & histology ; Oryza - cytology ; Oryza - genetics ; Oryza - growth & development ; Oryza sativa indica ; Phenotype ; Plant biology ; Plant breeding ; Population ; Quality ; Quantitative genetics ; Quantitative trait loci ; Quantitative Trait Loci - genetics ; Rice ; Studies ; Wetlands</subject><ispartof>PloS one, 2015-12, Vol.10 (12), p.e0145577-e0145577</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 Qiu 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>2015 Qiu et al 2015 Qiu et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-9a0631b7990b1caaf768b1bd5a594f30ede2a88e36cead8fc6237a726a52ae7f3</citedby><cites>FETCH-LOGICAL-c692t-9a0631b7990b1caaf768b1bd5a594f30ede2a88e36cead8fc6237a726a52ae7f3</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/PMC4694703/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4694703/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,729,782,786,866,887,2106,2932,23875,27933,27934,53800,53802</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26714258$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Yadav, Rattan Singh</contributor><creatorcontrib>Qiu, Xianjin</creatorcontrib><creatorcontrib>Pang, Yunlong</creatorcontrib><creatorcontrib>Yuan, Zhihua</creatorcontrib><creatorcontrib>Xing, Danying</creatorcontrib><creatorcontrib>Xu, Jianlong</creatorcontrib><creatorcontrib>Dingkuhn, Michael</creatorcontrib><creatorcontrib>Li, Zhikang</creatorcontrib><creatorcontrib>Ye, Guoyou</creatorcontrib><title>Genome-Wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Grain appearance quality and milling quality are the main determinants of market value of rice. Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through marker-assisted selection. Here, we reported a genome-wide association study in indica rice to identify QTL associated with 10 appearance and milling quality related traits, including grain length, grain width, grain length to width ratio, grain thickness, thousand grain weight, degree of endosperm chalkiness, percentage of grains with chalkiness, brown rice rate, milled rice rate and head milled rice rate. A diversity panel consisting of 272 indica accessions collected worldwide was evaluated in four locations including Hangzhou, Jingzhou, Sanya and Shenzhen representing indica rice production environments in China and genotyped using genotyping-by-sequencing and Diversity Arrays Technology based on next-generation sequencing technique called DArTseq™. A wide range of variation was observed for all traits in all environments. A total of 16 different association analysis models were compared to determine the best model for each trait-environment combination. Association mapping based on 18,824 high quality markers yielded 38 QTL for the 10 traits. Five of the detected QTL corresponded to known genes or fine mapped QTL. Among the 33 novel QTL identified, qDEC1.1 (qGLWR1.1), qBRR2.2 (qGL2.1), qTGW2.1 (qGL2.2), qGW11.1 (qMRR11.1) and qGL7.1 affected multiple traits with relatively large effects and/or were detected in multiple environments. The research provided an insight of the genetic architecture of rice grain quality and important information for mining genes/QTL with large effects within indica accessions for rice breeding.</description><subject>Agricultural production</subject><subject>Agriculture</subject><subject>Analysis</subject><subject>Association analysis</subject><subject>Breeding</subject><subject>Crop science</subject><subject>Data mining</subject><subject>Ecology</subject><subject>Edible Grain - anatomy & histology</subject><subject>Education</subject><subject>Endosperm</subject><subject>Engineering research</subject><subject>Environment</subject><subject>Food Quality</subject><subject>Gene mapping</subject><subject>Genes</subject><subject>Genetic Markers - genetics</subject><subject>Genetics</subject><subject>Genome-wide association studies</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotyping</subject><subject>Germplasm</subject><subject>Grain</subject><subject>Linkage Disequilibrium</subject><subject>Marker-assisted selection</subject><subject>Market value</subject><subject>Mine wastes</subject><subject>Oryza - anatomy & histology</subject><subject>Oryza - cytology</subject><subject>Oryza - genetics</subject><subject>Oryza - growth & development</subject><subject>Oryza sativa indica</subject><subject>Phenotype</subject><subject>Plant biology</subject><subject>Plant breeding</subject><subject>Population</subject><subject>Quality</subject><subject>Quantitative genetics</subject><subject>Quantitative trait loci</subject><subject>Quantitative Trait Loci - genetics</subject><subject>Rice</subject><subject>Studies</subject><subject>Wetlands</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk1Fv0zAQxyMEYmPwDRBEQkLw0GLHsZ28IFUVlEpDExuwR-viXDpPjl3sBLZvj7t204r2gCzF1uX3_198ucuyl5RMKZP0w6UfgwM7XXuHU0JLzqV8lB3SmhUTURD2-N75IHsW4yUhnFVCPM0OCiFpWfDqMLtaoPM9Ts5Ni_ksRq8NDMa7_GwY2-vcd_kigHH5bL1GCOA05uDa_Kux1rhV_m0Ea4brPBGQn_tg2z8bo7m3FvWNT3JYutZoyE9NEi8w9GsLsX-ePenARnyx24-yH58_fZ9_mRyfLJbz2fFEi7oYJjUQwWgj65o0VAN0UlQNbVoOvC47RrDFAqoKmdAIbdVpUTAJshDAC0DZsaPs9dZ3bX1Uu6JFRSUvGGcsPY-y5ZZoPVyqdTA9hGvlwaibgA8rBWEw2qIqkYBknJYNK8qUthG84bwjgrZAeMOS18ddtrHpsdXohgB2z3T_jTMXauV_q1LUpSQbg3c7g-B_jRgH1Zuo0Vpw6Mftd8tKCk4T-uYf9OHb7agVpAsY1_mUV29M1ayUNLVIqmiipg9QabXYG506rDMpvid4vydIzIBXwwrGGNXy7PT_2ZOf--zbe-wFgh0uorfjppfiPlhuQR18jAG7uyJTojYDclsNtRkQtRuQJHt1_wfdiW4ngv0FFvkLIg</recordid><startdate>20151229</startdate><enddate>20151229</enddate><creator>Qiu, Xianjin</creator><creator>Pang, Yunlong</creator><creator>Yuan, Zhihua</creator><creator>Xing, Danying</creator><creator>Xu, Jianlong</creator><creator>Dingkuhn, Michael</creator><creator>Li, Zhikang</creator><creator>Ye, Guoyou</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>7X5</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>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BEZIV</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>K6~</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>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20151229</creationdate><title>Genome-Wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm</title><author>Qiu, Xianjin ; Pang, Yunlong ; Yuan, Zhihua ; Xing, Danying ; Xu, Jianlong ; Dingkuhn, Michael ; Li, Zhikang ; Ye, Guoyou</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-9a0631b7990b1caaf768b1bd5a594f30ede2a88e36cead8fc6237a726a52ae7f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Agricultural production</topic><topic>Agriculture</topic><topic>Analysis</topic><topic>Association analysis</topic><topic>Breeding</topic><topic>Crop science</topic><topic>Data mining</topic><topic>Ecology</topic><topic>Edible Grain - 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Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through marker-assisted selection. Here, we reported a genome-wide association study in indica rice to identify QTL associated with 10 appearance and milling quality related traits, including grain length, grain width, grain length to width ratio, grain thickness, thousand grain weight, degree of endosperm chalkiness, percentage of grains with chalkiness, brown rice rate, milled rice rate and head milled rice rate. A diversity panel consisting of 272 indica accessions collected worldwide was evaluated in four locations including Hangzhou, Jingzhou, Sanya and Shenzhen representing indica rice production environments in China and genotyped using genotyping-by-sequencing and Diversity Arrays Technology based on next-generation sequencing technique called DArTseq™. A wide range of variation was observed for all traits in all environments. A total of 16 different association analysis models were compared to determine the best model for each trait-environment combination. Association mapping based on 18,824 high quality markers yielded 38 QTL for the 10 traits. Five of the detected QTL corresponded to known genes or fine mapped QTL. Among the 33 novel QTL identified, qDEC1.1 (qGLWR1.1), qBRR2.2 (qGL2.1), qTGW2.1 (qGL2.2), qGW11.1 (qMRR11.1) and qGL7.1 affected multiple traits with relatively large effects and/or were detected in multiple environments. The research provided an insight of the genetic architecture of rice grain quality and important information for mining genes/QTL with large effects within indica accessions for rice breeding.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26714258</pmid><doi>10.1371/journal.pone.0145577</doi><tpages>e0145577</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | PloS one, 2015-12, Vol.10 (12), p.e0145577-e0145577 |
| issn | 1932-6203 1932-6203 |
| language | eng |
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| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Agricultural production Agriculture Analysis Association analysis Breeding Crop science Data mining Ecology Edible Grain - anatomy & histology Education Endosperm Engineering research Environment Food Quality Gene mapping Genes Genetic Markers - genetics Genetics Genome-wide association studies Genome-Wide Association Study Genomes Genomics Genotyping Germplasm Grain Linkage Disequilibrium Marker-assisted selection Market value Mine wastes Oryza - anatomy & histology Oryza - cytology Oryza - genetics Oryza - growth & development Oryza sativa indica Phenotype Plant biology Plant breeding Population Quality Quantitative genetics Quantitative trait loci Quantitative Trait Loci - genetics Rice Studies Wetlands |
| title | Genome-Wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-11-30T22%3A44%3A37IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genome-Wide%20Association%20Study%20of%20Grain%20Appearance%20and%20Milling%20Quality%20in%20a%20Worldwide%20Collection%20of%20Indica%20Rice%20Germplasm&rft.jtitle=PloS%20one&rft.au=Qiu,%20Xianjin&rft.date=2015-12-29&rft.volume=10&rft.issue=12&rft.spage=e0145577&rft.epage=e0145577&rft.pages=e0145577-e0145577&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0145577&rft_dat=%3Cgale_plos_%3EA471193768%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1752353352&rft_id=info:pmid/26714258&rft_galeid=A471193768&rft_doaj_id=oai_doaj_org_article_4e0a73514b324a88b65b55f061da05b3&rfr_iscdi=true |