A Set of SCAR Markers Efficiently Differentiating Hybrid Rice
Molecular markers have been widely used in crop genetic improvement, seed test and genetic mapping. Of which, sequence characterized amplified region (SCAR) markers are particularly popular for its diversity, stable reproducibility, and suitability for analyzing large number of samples. In this stud...
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| Veröffentlicht in: | Rice science 2012-03, Vol.19 (1), p.14-20 |
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| creator | LI, Shu-jing XIE, Hong-wei QIAN, Ming-juan CHEN, Guang-hui LI, Shao-qing ZHU, Ying-guo |
| description | Molecular markers have been widely used in crop genetic improvement, seed test and genetic mapping. Of which, sequence characterized amplified region (SCAR) markers are particularly popular for its diversity, stable reproducibility, and suitability for analyzing large number of samples. In this study, 500 random amplified polymorphic DNA (RAPD) primers were tested, and a set of SCAR markers comprising 37 pairs of loci-specific primers were developed from the DNA fragments ranging from 300 to 1000 bp which correspond to the stable, distinctive RAPD banding patterns. Using these SCAR markers, 59 hybrid rice combinations were assessed and distinguished into 58 subgroups at the similarity coefficient of 0.97 in a genetic clustering tree based on the allele diversities of the SCAR markers. Furthermore, 13 hybrid rice combinations were reassayed with 40 randomly selected simple sequence repeat (SSR) markers to evaluate the effectiveness of these SCAR markers. SSR markers produced similar results to SCAR markers as the 13 hybrid rice combinations were completely separated at the similarity coefficient of 0.91 in the clustering tree established from SSR patterns. Taken together, SCAR markers prove to be effective tools for identifying and differentiating hybrid rice combinations. |
| doi_str_mv | 10.1016/S1672-6308(12)60015-8 |
| format | Article |
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Of which, sequence characterized amplified region (SCAR) markers are particularly popular for its diversity, stable reproducibility, and suitability for analyzing large number of samples. In this study, 500 random amplified polymorphic DNA (RAPD) primers were tested, and a set of SCAR markers comprising 37 pairs of loci-specific primers were developed from the DNA fragments ranging from 300 to 1000 bp which correspond to the stable, distinctive RAPD banding patterns. Using these SCAR markers, 59 hybrid rice combinations were assessed and distinguished into 58 subgroups at the similarity coefficient of 0.97 in a genetic clustering tree based on the allele diversities of the SCAR markers. Furthermore, 13 hybrid rice combinations were reassayed with 40 randomly selected simple sequence repeat (SSR) markers to evaluate the effectiveness of these SCAR markers. SSR markers produced similar results to SCAR markers as the 13 hybrid rice combinations were completely separated at the similarity coefficient of 0.91 in the clustering tree established from SSR patterns. Taken together, SCAR markers prove to be effective tools for identifying and differentiating hybrid rice combinations.</description><identifier>ISSN: 1672-6308</identifier><identifier>EISSN: 1876-4762</identifier><identifier>DOI: 10.1016/S1672-6308(12)60015-8</identifier><language>eng</language><publisher>Elsevier B.V</publisher><subject>alleles ; chromosome mapping ; crops ; DNA ; genetic improvement ; genetic markers ; hybrid rice ; hybrids ; microsatellite repeats ; molecular marker ; random amplified polymorphic DNA technique ; rice ; SCAR标记 ; seeds ; sequence characterized amplified region ; SSR标记 ; trees ; variety identification ; 作物遗传改良 ; 分子标记 ; 杂交水稻 ; 杂交稻组合 ; 等位基因多样性 ; 随机扩增多态性DNA</subject><ispartof>Rice science, 2012-03, Vol.19 (1), p.14-20</ispartof><rights>2012 China National Rice Research Institute</rights><rights>Copyright © Wanfang Data Co. Ltd. All Rights Reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c395t-e5371d441ff399b35e70304ec6a80236b4beb85c21a946e4f360dcc0530edd1f3</citedby><cites>FETCH-LOGICAL-c395t-e5371d441ff399b35e70304ec6a80236b4beb85c21a946e4f360dcc0530edd1f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://image.cqvip.com/vip1000/qk/84241A/84241A.jpg</thumbnail><link.rule.ids>315,781,785,27929,27930</link.rule.ids></links><search><creatorcontrib>LI, Shu-jing</creatorcontrib><creatorcontrib>XIE, Hong-wei</creatorcontrib><creatorcontrib>QIAN, Ming-juan</creatorcontrib><creatorcontrib>CHEN, Guang-hui</creatorcontrib><creatorcontrib>LI, Shao-qing</creatorcontrib><creatorcontrib>ZHU, Ying-guo</creatorcontrib><title>A Set of SCAR Markers Efficiently Differentiating Hybrid Rice</title><title>Rice science</title><addtitle>Rice science</addtitle><description>Molecular markers have been widely used in crop genetic improvement, seed test and genetic mapping. Of which, sequence characterized amplified region (SCAR) markers are particularly popular for its diversity, stable reproducibility, and suitability for analyzing large number of samples. In this study, 500 random amplified polymorphic DNA (RAPD) primers were tested, and a set of SCAR markers comprising 37 pairs of loci-specific primers were developed from the DNA fragments ranging from 300 to 1000 bp which correspond to the stable, distinctive RAPD banding patterns. Using these SCAR markers, 59 hybrid rice combinations were assessed and distinguished into 58 subgroups at the similarity coefficient of 0.97 in a genetic clustering tree based on the allele diversities of the SCAR markers. Furthermore, 13 hybrid rice combinations were reassayed with 40 randomly selected simple sequence repeat (SSR) markers to evaluate the effectiveness of these SCAR markers. SSR markers produced similar results to SCAR markers as the 13 hybrid rice combinations were completely separated at the similarity coefficient of 0.91 in the clustering tree established from SSR patterns. Taken together, SCAR markers prove to be effective tools for identifying and differentiating hybrid rice combinations.</description><subject>alleles</subject><subject>chromosome mapping</subject><subject>crops</subject><subject>DNA</subject><subject>genetic improvement</subject><subject>genetic markers</subject><subject>hybrid rice</subject><subject>hybrids</subject><subject>microsatellite repeats</subject><subject>molecular marker</subject><subject>random amplified polymorphic DNA technique</subject><subject>rice</subject><subject>SCAR标记</subject><subject>seeds</subject><subject>sequence characterized amplified region</subject><subject>SSR标记</subject><subject>trees</subject><subject>variety identification</subject><subject>作物遗传改良</subject><subject>分子标记</subject><subject>杂交水稻</subject><subject>杂交稻组合</subject><subject>等位基因多样性</subject><subject>随机扩增多态性DNA</subject><issn>1672-6308</issn><issn>1876-4762</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><recordid>eNqFkN9LwzAQgIsoOKd_gljfFKlemjRpH0TGnE5QhM09hzS91ExtNanK_OvN3PRVCNzBffcjXxTtEzglQPjZlHCRJpxCfkTSYw5AsiTfiHokFzxhgqebIf9FtqMd7-cAnHEoetH5IJ5iF7cmng4Hk_hOuSd0Ph4ZY7XFpntexJfWGHQht6qzTR2PF6WzVTyxGnejLaOePe6tYz-aXY0ehuPk9v76Zji4TTQtsi7BjApSMUaMoUVR0gwFUGCoucohpbxkJZZ5plOiCsaRGcqh0hoyClhVxNB-dLKa-6kao5paztt314SN8qv21WLelRJTIOEB0EBnK1q71nuHRr46-6LcQhKQS2Pyx5hc6pAkxKUxmYe-g1WfUa1UtbNezqZhJgv1PCepCMTFisDw2Q-LTvqlJY2Vdag7WbX23x2H69se26Z-Cz7_jmMpFEQIQb8BGA-FRg</recordid><startdate>20120301</startdate><enddate>20120301</enddate><creator>LI, Shu-jing</creator><creator>XIE, Hong-wei</creator><creator>QIAN, Ming-juan</creator><creator>CHEN, Guang-hui</creator><creator>LI, Shao-qing</creator><creator>ZHU, Ying-guo</creator><general>Elsevier B.V</general><general>Key Laboratory for Research and Utilization of Heterosis in Indica Rice. Ministry of Agriculture</general><general>College of Life Sciences,Wuhan University, Wuhan 430072, China%College of Plant Science, Hunan Agricultural University, Changsha 410128, China</general><general>Bangbu Medical College, Bangbu 233030, China%State Key Laboratory of Hybrid Rice</general><general>Engineering Research Center for Plant Biotechology and Germplasm Utilization of Ministry of Education</general><general>College of Life Sciences,Wuhan University, Wuhan 430072, China</general><general>State Key Laboratory of Hybrid Rice</general><scope>2RA</scope><scope>92L</scope><scope>CQIGP</scope><scope>W95</scope><scope>~WA</scope><scope>FBQ</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>2B.</scope><scope>4A8</scope><scope>92I</scope><scope>93N</scope><scope>PSX</scope><scope>TCJ</scope></search><sort><creationdate>20120301</creationdate><title>A Set of SCAR Markers Efficiently Differentiating Hybrid Rice</title><author>LI, Shu-jing ; XIE, Hong-wei ; QIAN, Ming-juan ; CHEN, Guang-hui ; LI, Shao-qing ; ZHU, Ying-guo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c395t-e5371d441ff399b35e70304ec6a80236b4beb85c21a946e4f360dcc0530edd1f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>alleles</topic><topic>chromosome mapping</topic><topic>crops</topic><topic>DNA</topic><topic>genetic improvement</topic><topic>genetic markers</topic><topic>hybrid rice</topic><topic>hybrids</topic><topic>microsatellite repeats</topic><topic>molecular marker</topic><topic>random amplified polymorphic DNA technique</topic><topic>rice</topic><topic>SCAR标记</topic><topic>seeds</topic><topic>sequence characterized amplified region</topic><topic>SSR标记</topic><topic>trees</topic><topic>variety identification</topic><topic>作物遗传改良</topic><topic>分子标记</topic><topic>杂交水稻</topic><topic>杂交稻组合</topic><topic>等位基因多样性</topic><topic>随机扩增多态性DNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>LI, Shu-jing</creatorcontrib><creatorcontrib>XIE, Hong-wei</creatorcontrib><creatorcontrib>QIAN, Ming-juan</creatorcontrib><creatorcontrib>CHEN, Guang-hui</creatorcontrib><creatorcontrib>LI, Shao-qing</creatorcontrib><creatorcontrib>ZHU, Ying-guo</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>CrossRef</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>Rice science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>LI, Shu-jing</au><au>XIE, Hong-wei</au><au>QIAN, Ming-juan</au><au>CHEN, Guang-hui</au><au>LI, Shao-qing</au><au>ZHU, Ying-guo</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A Set of SCAR Markers Efficiently Differentiating Hybrid Rice</atitle><jtitle>Rice science</jtitle><addtitle>Rice science</addtitle><date>2012-03-01</date><risdate>2012</risdate><volume>19</volume><issue>1</issue><spage>14</spage><epage>20</epage><pages>14-20</pages><issn>1672-6308</issn><eissn>1876-4762</eissn><abstract>Molecular markers have been widely used in crop genetic improvement, seed test and genetic mapping. Of which, sequence characterized amplified region (SCAR) markers are particularly popular for its diversity, stable reproducibility, and suitability for analyzing large number of samples. In this study, 500 random amplified polymorphic DNA (RAPD) primers were tested, and a set of SCAR markers comprising 37 pairs of loci-specific primers were developed from the DNA fragments ranging from 300 to 1000 bp which correspond to the stable, distinctive RAPD banding patterns. Using these SCAR markers, 59 hybrid rice combinations were assessed and distinguished into 58 subgroups at the similarity coefficient of 0.97 in a genetic clustering tree based on the allele diversities of the SCAR markers. Furthermore, 13 hybrid rice combinations were reassayed with 40 randomly selected simple sequence repeat (SSR) markers to evaluate the effectiveness of these SCAR markers. SSR markers produced similar results to SCAR markers as the 13 hybrid rice combinations were completely separated at the similarity coefficient of 0.91 in the clustering tree established from SSR patterns. Taken together, SCAR markers prove to be effective tools for identifying and differentiating hybrid rice combinations.</abstract><pub>Elsevier B.V</pub><doi>10.1016/S1672-6308(12)60015-8</doi><tpages>7</tpages></addata></record> |
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| subjects | alleles chromosome mapping crops DNA genetic improvement genetic markers hybrid rice hybrids microsatellite repeats molecular marker random amplified polymorphic DNA technique rice SCAR标记 seeds sequence characterized amplified region SSR标记 trees variety identification 作物遗传改良 分子标记 杂交水稻 杂交稻组合 等位基因多样性 随机扩增多态性DNA |
| title | A Set of SCAR Markers Efficiently Differentiating Hybrid Rice |
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