Abundance of SSR Motifs and Development of Candidate Polymorphic SSR Markers (BARCSOYSSR_1.0) in Soybean
Simple sequence repeat (SSR) genetic markers, also referred to as microsatellites, function in map-based cloning and for marker-assisted selection in plant breeding. The objectives of this study were to determine the abundance of SSRs in the soybean genome and to develop and test soybean SSR markers...
Gespeichert in:
| Veröffentlicht in: | Crop science 2010-09, Vol.50 (5), p.1950-1960 |
|---|---|
| Hauptverfasser: | , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 1960 |
|---|---|
| container_issue | 5 |
| container_start_page | 1950 |
| container_title | Crop science |
| container_volume | 50 |
| creator | Song, Qijian Jia, Gaofeng Zhu, Youlin Grant, David Nelson, Rex T Hwang, Eun-Young Hyten, David L Cregan, Perry B |
| description | Simple sequence repeat (SSR) genetic markers, also referred to as microsatellites, function in map-based cloning and for marker-assisted selection in plant breeding. The objectives of this study were to determine the abundance of SSRs in the soybean genome and to develop and test soybean SSR markers to create a database of locus-specific markers with a high likelihood of polymorphism. A total of 210,990 SSRs with di-, tri-, and tetranucleotide repeats of five or more were identified in the soybean whole genome sequence (WGS) which included 61,458 SSRs consisting of repeat units of di- (≥10), tri- (≥8), and tetranucleotide (≥7). Among the 61,458 SSRs, (AT)n, (ATT)n and (AAAT)n were the most abundant motifs among di-, tri-, and tetranucleotide SSRs, respectively. After screening for a number of factors including locus-specificity using e-PCR, a soybean SSR database (BARCSOYSSR_1.0) with the genome position and primer sequences for 33,065 SSRs was created. To examine the likelihood that primers in the database would function to amplify locus-specific polymorphic products, 1034 primer sets were evaluated by amplifying DNAs of seven diverse Glycine max (L.) Merr. and one wild soybean (Glycine soja Siebold & Zucc.) genotypes. A total of 978 (94.6%) of the primer sets amplified a single polymerase chain reaction (PCR) product and 798 (77.2%) amplified polymorphic amplicons as determined by 4.5% agarose gel electrophoresis. The BARCSOYSSR1.0 SSR markers can be found in SoyBase (http://soybase.org; verified 21 June 2010) the USDA-ARS Soybean Genome Database. |
| doi_str_mv | 10.2135/cropsci2009.10.0607 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_journals_747847777</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2122112131</sourcerecordid><originalsourceid>FETCH-LOGICAL-c5047-c40d22e6bdbf472cf661287ff4ff6d25cf9de8f741a344ef3d7359be89695c4e3</originalsourceid><addsrcrecordid>eNqNkE2L1DAYx4MoOK5-Ag8GQdBDxyfv7XGsri6szDJ1QU8hTRO3a6epyYwy396UDuLRXAL_5_8CP4SeE1hTwsRbG8OUbE8BqnXWQIJ6gFaEM1GAFOwhWgEQUpCSfX2MnqR0DwCqUmKF7jbtcezMaB0OHjfNDn8Oh94nbMYOv3e_3BCmvRsP87XOWt-Zg8M3YTjtQ5zuertkTPzhYsKv3212dbP9ljVN1vAG9yNuwql1ZnyKHnkzJPfs_F-g28sPX-pPxfX241W9uS6sAK4Ky6Gj1Mm2az1X1HopCS2V99x72VFhfdW50itODOPcedYpJqrWlZWshOWOXaCXS-8Uw8-jSwd9H45xzJNacVVylV82scWUwaUUnddT7PcmnjQBPRPV_xCdtZloTr06V5tkzeBjxtanv1HKiORKyOy7XHy_-8Gd_qda101N6932pqmvZp3AefDFUuRN0OZ7zGO3DQXCgFRUSUXZH7oelP8</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>747847777</pqid></control><display><type>article</type><title>Abundance of SSR Motifs and Development of Candidate Polymorphic SSR Markers (BARCSOYSSR_1.0) in Soybean</title><source>Wiley Online Library - AutoHoldings Journals</source><source>Alma/SFX Local Collection</source><creator>Song, Qijian ; Jia, Gaofeng ; Zhu, Youlin ; Grant, David ; Nelson, Rex T ; Hwang, Eun-Young ; Hyten, David L ; Cregan, Perry B</creator><creatorcontrib>Song, Qijian ; Jia, Gaofeng ; Zhu, Youlin ; Grant, David ; Nelson, Rex T ; Hwang, Eun-Young ; Hyten, David L ; Cregan, Perry B</creatorcontrib><description>Simple sequence repeat (SSR) genetic markers, also referred to as microsatellites, function in map-based cloning and for marker-assisted selection in plant breeding. The objectives of this study were to determine the abundance of SSRs in the soybean genome and to develop and test soybean SSR markers to create a database of locus-specific markers with a high likelihood of polymorphism. A total of 210,990 SSRs with di-, tri-, and tetranucleotide repeats of five or more were identified in the soybean whole genome sequence (WGS) which included 61,458 SSRs consisting of repeat units of di- (≥10), tri- (≥8), and tetranucleotide (≥7). Among the 61,458 SSRs, (AT)n, (ATT)n and (AAAT)n were the most abundant motifs among di-, tri-, and tetranucleotide SSRs, respectively. After screening for a number of factors including locus-specificity using e-PCR, a soybean SSR database (BARCSOYSSR_1.0) with the genome position and primer sequences for 33,065 SSRs was created. To examine the likelihood that primers in the database would function to amplify locus-specific polymorphic products, 1034 primer sets were evaluated by amplifying DNAs of seven diverse Glycine max (L.) Merr. and one wild soybean (Glycine soja Siebold & Zucc.) genotypes. A total of 978 (94.6%) of the primer sets amplified a single polymerase chain reaction (PCR) product and 798 (77.2%) amplified polymorphic amplicons as determined by 4.5% agarose gel electrophoresis. The BARCSOYSSR1.0 SSR markers can be found in SoyBase (http://soybase.org; verified 21 June 2010) the USDA-ARS Soybean Genome Database.</description><identifier>ISSN: 0011-183X</identifier><identifier>EISSN: 1435-0653</identifier><identifier>DOI: 10.2135/cropsci2009.10.0607</identifier><identifier>CODEN: CRPSAY</identifier><language>eng</language><publisher>Madison: Crop Science Society of America</publisher><subject>Agronomy. Soil science and plant productions ; Biological and medical sciences ; Classical and quantitative genetics. Population genetics. Molecular genetics ; Cloning ; Crop science ; cultivars ; DNA primers ; Fundamental and applied biological sciences. Psychology ; gene banks ; Generalities. Genetics. Plant material ; Genetic markers ; genetic polymorphism ; Genetics and breeding of economic plants ; genome ; Genomics ; Genotypes ; Glycine max ; Glycine soja ; loci ; microsatellite repeats ; Molecular genetics ; molecular sequence data ; Plant breeding ; polymerase chain reaction ; Polymorphism ; Soybeans ; wild relatives</subject><ispartof>Crop science, 2010-09, Vol.50 (5), p.1950-1960</ispartof><rights>Crop Science Society of America</rights><rights>2015 INIST-CNRS</rights><rights>Copyright American Society of Agronomy Sep/Oct 2010</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5047-c40d22e6bdbf472cf661287ff4ff6d25cf9de8f741a344ef3d7359be89695c4e3</citedby><cites>FETCH-LOGICAL-c5047-c40d22e6bdbf472cf661287ff4ff6d25cf9de8f741a344ef3d7359be89695c4e3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.2135%2Fcropsci2009.10.0607$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.2135%2Fcropsci2009.10.0607$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>315,782,786,1419,27931,27932,45581,45582</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=23164756$$DView record in Pascal Francis$$Hfree_for_read</backlink></links><search><creatorcontrib>Song, Qijian</creatorcontrib><creatorcontrib>Jia, Gaofeng</creatorcontrib><creatorcontrib>Zhu, Youlin</creatorcontrib><creatorcontrib>Grant, David</creatorcontrib><creatorcontrib>Nelson, Rex T</creatorcontrib><creatorcontrib>Hwang, Eun-Young</creatorcontrib><creatorcontrib>Hyten, David L</creatorcontrib><creatorcontrib>Cregan, Perry B</creatorcontrib><title>Abundance of SSR Motifs and Development of Candidate Polymorphic SSR Markers (BARCSOYSSR_1.0) in Soybean</title><title>Crop science</title><description>Simple sequence repeat (SSR) genetic markers, also referred to as microsatellites, function in map-based cloning and for marker-assisted selection in plant breeding. The objectives of this study were to determine the abundance of SSRs in the soybean genome and to develop and test soybean SSR markers to create a database of locus-specific markers with a high likelihood of polymorphism. A total of 210,990 SSRs with di-, tri-, and tetranucleotide repeats of five or more were identified in the soybean whole genome sequence (WGS) which included 61,458 SSRs consisting of repeat units of di- (≥10), tri- (≥8), and tetranucleotide (≥7). Among the 61,458 SSRs, (AT)n, (ATT)n and (AAAT)n were the most abundant motifs among di-, tri-, and tetranucleotide SSRs, respectively. After screening for a number of factors including locus-specificity using e-PCR, a soybean SSR database (BARCSOYSSR_1.0) with the genome position and primer sequences for 33,065 SSRs was created. To examine the likelihood that primers in the database would function to amplify locus-specific polymorphic products, 1034 primer sets were evaluated by amplifying DNAs of seven diverse Glycine max (L.) Merr. and one wild soybean (Glycine soja Siebold & Zucc.) genotypes. A total of 978 (94.6%) of the primer sets amplified a single polymerase chain reaction (PCR) product and 798 (77.2%) amplified polymorphic amplicons as determined by 4.5% agarose gel electrophoresis. The BARCSOYSSR1.0 SSR markers can be found in SoyBase (http://soybase.org; verified 21 June 2010) the USDA-ARS Soybean Genome Database.</description><subject>Agronomy. Soil science and plant productions</subject><subject>Biological and medical sciences</subject><subject>Classical and quantitative genetics. Population genetics. Molecular genetics</subject><subject>Cloning</subject><subject>Crop science</subject><subject>cultivars</subject><subject>DNA primers</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>gene banks</subject><subject>Generalities. Genetics. Plant material</subject><subject>Genetic markers</subject><subject>genetic polymorphism</subject><subject>Genetics and breeding of economic plants</subject><subject>genome</subject><subject>Genomics</subject><subject>Genotypes</subject><subject>Glycine max</subject><subject>Glycine soja</subject><subject>loci</subject><subject>microsatellite repeats</subject><subject>Molecular genetics</subject><subject>molecular sequence data</subject><subject>Plant breeding</subject><subject>polymerase chain reaction</subject><subject>Polymorphism</subject><subject>Soybeans</subject><subject>wild relatives</subject><issn>0011-183X</issn><issn>1435-0653</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNqNkE2L1DAYx4MoOK5-Ag8GQdBDxyfv7XGsri6szDJ1QU8hTRO3a6epyYwy396UDuLRXAL_5_8CP4SeE1hTwsRbG8OUbE8BqnXWQIJ6gFaEM1GAFOwhWgEQUpCSfX2MnqR0DwCqUmKF7jbtcezMaB0OHjfNDn8Oh94nbMYOv3e_3BCmvRsP87XOWt-Zg8M3YTjtQ5zuertkTPzhYsKv3212dbP9ljVN1vAG9yNuwql1ZnyKHnkzJPfs_F-g28sPX-pPxfX241W9uS6sAK4Ky6Gj1Mm2az1X1HopCS2V99x72VFhfdW50itODOPcedYpJqrWlZWshOWOXaCXS-8Uw8-jSwd9H45xzJNacVVylV82scWUwaUUnddT7PcmnjQBPRPV_xCdtZloTr06V5tkzeBjxtanv1HKiORKyOy7XHy_-8Gd_qda101N6932pqmvZp3AefDFUuRN0OZ7zGO3DQXCgFRUSUXZH7oelP8</recordid><startdate>201009</startdate><enddate>201009</enddate><creator>Song, Qijian</creator><creator>Jia, Gaofeng</creator><creator>Zhu, Youlin</creator><creator>Grant, David</creator><creator>Nelson, Rex T</creator><creator>Hwang, Eun-Young</creator><creator>Hyten, David L</creator><creator>Cregan, Perry B</creator><general>Crop Science Society of America</general><general>American Society of Agronomy</general><scope>FBQ</scope><scope>IQODW</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X2</scope><scope>7XB</scope><scope>88I</scope><scope>8AF</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FK</scope><scope>8G5</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>HCIFZ</scope><scope>L6V</scope><scope>M0K</scope><scope>M2O</scope><scope>M2P</scope><scope>M7S</scope><scope>MBDVC</scope><scope>PATMY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>Q9U</scope><scope>R05</scope><scope>S0X</scope></search><sort><creationdate>201009</creationdate><title>Abundance of SSR Motifs and Development of Candidate Polymorphic SSR Markers (BARCSOYSSR_1.0) in Soybean</title><author>Song, Qijian ; Jia, Gaofeng ; Zhu, Youlin ; Grant, David ; Nelson, Rex T ; Hwang, Eun-Young ; Hyten, David L ; Cregan, Perry B</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5047-c40d22e6bdbf472cf661287ff4ff6d25cf9de8f741a344ef3d7359be89695c4e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Agronomy. Soil science and plant productions</topic><topic>Biological and medical sciences</topic><topic>Classical and quantitative genetics. Population genetics. Molecular genetics</topic><topic>Cloning</topic><topic>Crop science</topic><topic>cultivars</topic><topic>DNA primers</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>gene banks</topic><topic>Generalities. Genetics. Plant material</topic><topic>Genetic markers</topic><topic>genetic polymorphism</topic><topic>Genetics and breeding of economic plants</topic><topic>genome</topic><topic>Genomics</topic><topic>Genotypes</topic><topic>Glycine max</topic><topic>Glycine soja</topic><topic>loci</topic><topic>microsatellite repeats</topic><topic>Molecular genetics</topic><topic>molecular sequence data</topic><topic>Plant breeding</topic><topic>polymerase chain reaction</topic><topic>Polymorphism</topic><topic>Soybeans</topic><topic>wild relatives</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Song, Qijian</creatorcontrib><creatorcontrib>Jia, Gaofeng</creatorcontrib><creatorcontrib>Zhu, Youlin</creatorcontrib><creatorcontrib>Grant, David</creatorcontrib><creatorcontrib>Nelson, Rex T</creatorcontrib><creatorcontrib>Hwang, Eun-Young</creatorcontrib><creatorcontrib>Hyten, David L</creatorcontrib><creatorcontrib>Cregan, Perry B</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Agricultural Science Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Science Database (Alumni Edition)</collection><collection>STEM Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Engineering Collection</collection><collection>Agricultural Science Database</collection><collection>Research Library</collection><collection>Science Database</collection><collection>Engineering Database</collection><collection>Research Library (Corporate)</collection><collection>Environmental Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>ProQuest Central Basic</collection><collection>University of Michigan</collection><collection>SIRS Editorial</collection><jtitle>Crop science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Song, Qijian</au><au>Jia, Gaofeng</au><au>Zhu, Youlin</au><au>Grant, David</au><au>Nelson, Rex T</au><au>Hwang, Eun-Young</au><au>Hyten, David L</au><au>Cregan, Perry B</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Abundance of SSR Motifs and Development of Candidate Polymorphic SSR Markers (BARCSOYSSR_1.0) in Soybean</atitle><jtitle>Crop science</jtitle><date>2010-09</date><risdate>2010</risdate><volume>50</volume><issue>5</issue><spage>1950</spage><epage>1960</epage><pages>1950-1960</pages><issn>0011-183X</issn><eissn>1435-0653</eissn><coden>CRPSAY</coden><abstract>Simple sequence repeat (SSR) genetic markers, also referred to as microsatellites, function in map-based cloning and for marker-assisted selection in plant breeding. The objectives of this study were to determine the abundance of SSRs in the soybean genome and to develop and test soybean SSR markers to create a database of locus-specific markers with a high likelihood of polymorphism. A total of 210,990 SSRs with di-, tri-, and tetranucleotide repeats of five or more were identified in the soybean whole genome sequence (WGS) which included 61,458 SSRs consisting of repeat units of di- (≥10), tri- (≥8), and tetranucleotide (≥7). Among the 61,458 SSRs, (AT)n, (ATT)n and (AAAT)n were the most abundant motifs among di-, tri-, and tetranucleotide SSRs, respectively. After screening for a number of factors including locus-specificity using e-PCR, a soybean SSR database (BARCSOYSSR_1.0) with the genome position and primer sequences for 33,065 SSRs was created. To examine the likelihood that primers in the database would function to amplify locus-specific polymorphic products, 1034 primer sets were evaluated by amplifying DNAs of seven diverse Glycine max (L.) Merr. and one wild soybean (Glycine soja Siebold & Zucc.) genotypes. A total of 978 (94.6%) of the primer sets amplified a single polymerase chain reaction (PCR) product and 798 (77.2%) amplified polymorphic amplicons as determined by 4.5% agarose gel electrophoresis. The BARCSOYSSR1.0 SSR markers can be found in SoyBase (http://soybase.org; verified 21 June 2010) the USDA-ARS Soybean Genome Database.</abstract><cop>Madison</cop><pub>Crop Science Society of America</pub><doi>10.2135/cropsci2009.10.0607</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0011-183X |
| ispartof | Crop science, 2010-09, Vol.50 (5), p.1950-1960 |
| issn | 0011-183X 1435-0653 |
| language | eng |
| recordid | cdi_proquest_journals_747847777 |
| source | Wiley Online Library - AutoHoldings Journals; Alma/SFX Local Collection |
| subjects | Agronomy. Soil science and plant productions Biological and medical sciences Classical and quantitative genetics. Population genetics. Molecular genetics Cloning Crop science cultivars DNA primers Fundamental and applied biological sciences. Psychology gene banks Generalities. Genetics. Plant material Genetic markers genetic polymorphism Genetics and breeding of economic plants genome Genomics Genotypes Glycine max Glycine soja loci microsatellite repeats Molecular genetics molecular sequence data Plant breeding polymerase chain reaction Polymorphism Soybeans wild relatives |
| title | Abundance of SSR Motifs and Development of Candidate Polymorphic SSR Markers (BARCSOYSSR_1.0) in Soybean |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-05T04%3A43%3A30IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Abundance%20of%20SSR%20Motifs%20and%20Development%20of%20Candidate%20Polymorphic%20SSR%20Markers%20(BARCSOYSSR_1.0)%20in%20Soybean&rft.jtitle=Crop%20science&rft.au=Song,%20Qijian&rft.date=2010-09&rft.volume=50&rft.issue=5&rft.spage=1950&rft.epage=1960&rft.pages=1950-1960&rft.issn=0011-183X&rft.eissn=1435-0653&rft.coden=CRPSAY&rft_id=info:doi/10.2135/cropsci2009.10.0607&rft_dat=%3Cproquest_cross%3E2122112131%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=747847777&rft_id=info:pmid/&rfr_iscdi=true |