Association Analysis of the Amino Acid Contents in Rice
The main objective of the present study was to identify simple sequence repeat （SSR） markers associated with the amino acid content of rice （Oryza sativa L.）. SSR markers were selected by prescreening for the relationship to amino acid content. Eighty-four rice landrace accessions from Korea were ev...
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| Veröffentlicht in: | Journal of integrative plant biology 2009-12, Vol.51 (12), p.1126-1137 |
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| container_title | Journal of integrative plant biology |
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| creator | Zhao, Weiguo Park, Eun-Jin Chung, Jong-Wook Park, Yong-Jin Chung, Ill-Min Ahn, Joung-Kuk Kim, Gwang-Ho |
| description | The main objective of the present study was to identify simple sequence repeat （SSR） markers associated with the amino acid content of rice （Oryza sativa L.）. SSR markers were selected by prescreening for the relationship to amino acid content. Eighty-four rice landrace accessions from Korea were evaluated for 16 kinds of amino acids in brown rice and ganotyped with 25 SSR markers. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium （LD） patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r^2 value for all intrachromosomal loci pairs was 0.033. LD between linked markers decreased with distance. Marker-trait associations were investigated using the unified mixed-model approach, considering both population structure （Q） and kinship （K）. A total of 42 marker-trait associations with amino acids （P 〈 0.05） were identified using 15 different SSR markers covering three chromosomes and explaining more than 40% of the total variation. These results suggest that association analysis in rice is a viable alternative to quantitative trait loci mapping and should help rice breeders develop strategies for improving rice quality. |
| doi_str_mv | 10.1111/j.1744-7909.2009.00883.x |
| format | Article |
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SSR markers were selected by prescreening for the relationship to amino acid content. Eighty-four rice landrace accessions from Korea were evaluated for 16 kinds of amino acids in brown rice and ganotyped with 25 SSR markers. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium （LD） patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r^2 value for all intrachromosomal loci pairs was 0.033. LD between linked markers decreased with distance. Marker-trait associations were investigated using the unified mixed-model approach, considering both population structure （Q） and kinship （K）. A total of 42 marker-trait associations with amino acids （P 〈 0.05） were identified using 15 different SSR markers covering three chromosomes and explaining more than 40% of the total variation. These results suggest that association analysis in rice is a viable alternative to quantitative trait loci mapping and should help rice breeders develop strategies for improving rice quality.</description><identifier>ISSN: 1672-9072</identifier><identifier>EISSN: 1744-7909</identifier><identifier>DOI: 10.1111/j.1744-7909.2009.00883.x</identifier><identifier>PMID: 20021560</identifier><language>eng</language><publisher>Melbourne, Australia: Melbourne, Australia : Blackwell Publishing Asia</publisher><subject>Amino acid content ; Amino Acids - analysis ; association mapping ; Chromosome Mapping ; Genetic Variation ; Linkage Disequilibrium ; Microsatellite Repeats ; Oryza - chemistry ; Oryza - genetics ; Phenotype ; population structure ; simple sequence repeats ; SSR标记 ; 人口结构 ; 数量性状位点 ; 标记性状 ; 氨基酸含量 ; 水稻育种 ; 简单序列重复</subject><ispartof>Journal of integrative plant biology, 2009-12, Vol.51 (12), p.1126-1137</ispartof><rights>2009 Institute of Botany, the Chinese Academy of Sciences</rights><rights>Copyright © Wanfang Data Co. Ltd. All Rights Reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4873-d5edfdbd4b6801bb9a463f357d17beacc758a1f5aeb6f188cb9766f5a946545c3</citedby><cites>FETCH-LOGICAL-c4873-d5edfdbd4b6801bb9a463f357d17beacc758a1f5aeb6f188cb9766f5a946545c3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://image.cqvip.com/vip1000/qk/94176A/94176A.jpg</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1744-7909.2009.00883.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1744-7909.2009.00883.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20021560$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhao, Weiguo</creatorcontrib><creatorcontrib>Park, Eun-Jin</creatorcontrib><creatorcontrib>Chung, Jong-Wook</creatorcontrib><creatorcontrib>Park, Yong-Jin</creatorcontrib><creatorcontrib>Chung, Ill-Min</creatorcontrib><creatorcontrib>Ahn, Joung-Kuk</creatorcontrib><creatorcontrib>Kim, Gwang-Ho</creatorcontrib><title>Association Analysis of the Amino Acid Contents in Rice</title><title>Journal of integrative plant biology</title><addtitle>Journal of Integrative Plant Biology</addtitle><description>The main objective of the present study was to identify simple sequence repeat （SSR） markers associated with the amino acid content of rice （Oryza sativa L.）. SSR markers were selected by prescreening for the relationship to amino acid content. Eighty-four rice landrace accessions from Korea were evaluated for 16 kinds of amino acids in brown rice and ganotyped with 25 SSR markers. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium （LD） patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r^2 value for all intrachromosomal loci pairs was 0.033. LD between linked markers decreased with distance. Marker-trait associations were investigated using the unified mixed-model approach, considering both population structure （Q） and kinship （K）. A total of 42 marker-trait associations with amino acids （P 〈 0.05） were identified using 15 different SSR markers covering three chromosomes and explaining more than 40% of the total variation. These results suggest that association analysis in rice is a viable alternative to quantitative trait loci mapping and should help rice breeders develop strategies for improving rice quality.</description><subject>Amino acid content</subject><subject>Amino Acids - analysis</subject><subject>association mapping</subject><subject>Chromosome Mapping</subject><subject>Genetic Variation</subject><subject>Linkage Disequilibrium</subject><subject>Microsatellite Repeats</subject><subject>Oryza - chemistry</subject><subject>Oryza - genetics</subject><subject>Phenotype</subject><subject>population structure</subject><subject>simple sequence repeats</subject><subject>SSR标记</subject><subject>人口结构</subject><subject>数量性状位点</subject><subject>标记性状</subject><subject>氨基酸含量</subject><subject>水稻育种</subject><subject>简单序列重复</subject><issn>1672-9072</issn><issn>1744-7909</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNUE1v1DAUjBCIlpa_ABES4pTFH4ntHDikKyhFFW2B0uOT7dhbb7N2G2fVXX49Dln2XB-en-WZefMmy3KMZjidj8sZ5mVZ8BrVM4JSQUgIOts8yw73H89TzzgpasTJQfYqxiVCVCBGXmYHiUNwxdBhxpsYg3ZycMHnjZfdNrqYB5sPtyZvVs6HvNGuzefBD8YPMXc-_-G0Oc5eWNlF83p3H2XXXz7_mn8tzi9Oz-bNeaFLwWnRVqa1rWpLxQTCStWyZNTSireYKyO15pWQ2FbSKGaxEFrVnLH0rktWlZWmR9n7SfdReiv9ApZh3SebEf48btS4O05FJNyHCXffh4e1iQOsXNSm66Q3YR2BU8o4R4wmpJiQug8x9sbCfe9Wst8CRjCmC0sYQ4QxRBgnwL90YZOob3ZD1mpl2j3xf5wJ8Gnn1nVm-2Rh-HZ2eZK6xC8mvouD2ez5sr8Dximv4Ob7KWB2-fuKJM2bhH874a0MIBe9i3D9kyBMEeaIMzIqvtttexv84sGlBJXUdzb5A0oYEyXl9C-_kKpK</recordid><startdate>200912</startdate><enddate>200912</enddate><creator>Zhao, Weiguo</creator><creator>Park, Eun-Jin</creator><creator>Chung, Jong-Wook</creator><creator>Park, Yong-Jin</creator><creator>Chung, Ill-Min</creator><creator>Ahn, Joung-Kuk</creator><creator>Kim, Gwang-Ho</creator><general>Melbourne, Australia : Blackwell Publishing Asia</general><general>Blackwell Publishing Asia</general><general>Department of Plant Resources, College of Industnal Science, Kongju National University, Yesan 340-802, Korea%Department of Applied Bioscience, Konkuk University, Seou1143-701, Korea%Department of Plant Resources, College of Industnal Science, Kongju National University, Yesan 340-802, Korea</general><general>Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Jiangsu University of Science and Technology, Zhenjiang 212018, China</general><general>Department of Applied Bioscience, Konkuk University, Seou1143-701, Korea</general><scope>2RA</scope><scope>92L</scope><scope>CQIGP</scope><scope>W95</scope><scope>~WA</scope><scope>FBQ</scope><scope>BSCLL</scope><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>7X8</scope><scope>2B.</scope><scope>4A8</scope><scope>92I</scope><scope>93N</scope><scope>PSX</scope><scope>TCJ</scope></search><sort><creationdate>200912</creationdate><title>Association Analysis of the Amino Acid Contents in Rice</title><author>Zhao, Weiguo ; Park, Eun-Jin ; Chung, Jong-Wook ; Park, Yong-Jin ; Chung, Ill-Min ; Ahn, Joung-Kuk ; Kim, Gwang-Ho</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4873-d5edfdbd4b6801bb9a463f357d17beacc758a1f5aeb6f188cb9766f5a946545c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Amino acid content</topic><topic>Amino Acids - analysis</topic><topic>association mapping</topic><topic>Chromosome Mapping</topic><topic>Genetic Variation</topic><topic>Linkage Disequilibrium</topic><topic>Microsatellite Repeats</topic><topic>Oryza - chemistry</topic><topic>Oryza - genetics</topic><topic>Phenotype</topic><topic>population structure</topic><topic>simple sequence repeats</topic><topic>SSR标记</topic><topic>人口结构</topic><topic>数量性状位点</topic><topic>标记性状</topic><topic>氨基酸含量</topic><topic>水稻育种</topic><topic>简单序列重复</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhao, Weiguo</creatorcontrib><creatorcontrib>Park, Eun-Jin</creatorcontrib><creatorcontrib>Chung, Jong-Wook</creatorcontrib><creatorcontrib>Park, Yong-Jin</creatorcontrib><creatorcontrib>Chung, Ill-Min</creatorcontrib><creatorcontrib>Ahn, Joung-Kuk</creatorcontrib><creatorcontrib>Kim, Gwang-Ho</creatorcontrib><collection>中文科技期刊数据库</collection><collection>中文科技期刊数据库-CALIS站点</collection><collection>中文科技期刊数据库-7.0平台</collection><collection>中文科技期刊数据库-农业科学</collection><collection>中文科技期刊数据库- 镜像站点</collection><collection>AGRIS</collection><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Wanfang Data Journals - Hong Kong</collection><collection>WANFANG Data Centre</collection><collection>Wanfang Data Journals</collection><collection>万方数据期刊 - 香港版</collection><collection>China Online Journals (COJ)</collection><collection>China Online Journals (COJ)</collection><jtitle>Journal of integrative plant biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhao, Weiguo</au><au>Park, Eun-Jin</au><au>Chung, Jong-Wook</au><au>Park, Yong-Jin</au><au>Chung, Ill-Min</au><au>Ahn, Joung-Kuk</au><au>Kim, Gwang-Ho</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Association Analysis of the Amino Acid Contents in Rice</atitle><jtitle>Journal of integrative plant biology</jtitle><addtitle>Journal of Integrative Plant Biology</addtitle><date>2009-12</date><risdate>2009</risdate><volume>51</volume><issue>12</issue><spage>1126</spage><epage>1137</epage><pages>1126-1137</pages><issn>1672-9072</issn><eissn>1744-7909</eissn><abstract>The main objective of the present study was to identify simple sequence repeat （SSR） markers associated with the amino acid content of rice （Oryza sativa L.）. SSR markers were selected by prescreening for the relationship to amino acid content. Eighty-four rice landrace accessions from Korea were evaluated for 16 kinds of amino acids in brown rice and ganotyped with 25 SSR markers. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium （LD） patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r^2 value for all intrachromosomal loci pairs was 0.033. LD between linked markers decreased with distance. Marker-trait associations were investigated using the unified mixed-model approach, considering both population structure （Q） and kinship （K）. A total of 42 marker-trait associations with amino acids （P 〈 0.05） were identified using 15 different SSR markers covering three chromosomes and explaining more than 40% of the total variation. These results suggest that association analysis in rice is a viable alternative to quantitative trait loci mapping and should help rice breeders develop strategies for improving rice quality.</abstract><cop>Melbourne, Australia</cop><pub>Melbourne, Australia : Blackwell Publishing Asia</pub><pmid>20021560</pmid><doi>10.1111/j.1744-7909.2009.00883.x</doi><tpages>12</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1672-9072 |
| ispartof | Journal of integrative plant biology, 2009-12, Vol.51 (12), p.1126-1137 |
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| source | MEDLINE; Wiley Online Library Journals Frontfile Complete; Alma/SFX Local Collection |
| subjects | Amino acid content Amino Acids - analysis association mapping Chromosome Mapping Genetic Variation Linkage Disequilibrium Microsatellite Repeats Oryza - chemistry Oryza - genetics Phenotype population structure simple sequence repeats SSR标记 人口结构 数量性状位点 标记性状 氨基酸含量 水稻育种 简单序列重复 |
| title | Association Analysis of the Amino Acid Contents in Rice |
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