A new approach to extending the wheat marker pool by anchored PCR amplification of compound SSRS
A study was undertaken to determine the utility in bread wheat of anchored PCR for the development of single locus SSR markers targeted at compound repeat motifs. In anchored PCR, microsatellite amplification is achieved using a single primer complementary to the flanking sequence, and one which anc...
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| Veröffentlicht in: | Theoretical and applied genetics 2004-02, Vol.108 (4), p.733-742 |
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| container_title | Theoretical and applied genetics |
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| creator | HAYDEN, M. J STEPHENSON, P LOGOJAN, A. M KHATKAR, D ROGERS, C KOEBNER, R. M. D SNAPE, J. W SHARP, P. J |
| description | A study was undertaken to determine the utility in bread wheat of anchored PCR for the development of single locus SSR markers targeted at compound repeat motifs. In anchored PCR, microsatellite amplification is achieved using a single primer complementary to the flanking sequence, and one which anchors to the repeat junction of the compound SSR. The recovery rate of useable markers was found to be similar (43%) to that reported for conventionally generated SSRs. Thus, anchored PCR can be used to reduce the costs of marker development, since it requires that only half the number of primers be synthesised. Where fluorescence-based platforms are used, marker deployment costs are lower, since only the anchoring primers need to be labelled. In addition, anchored PCR improves the recovery of useful markers, as it allows assays to be generated from microsatellite clones with repeat sequences located close to their ends, a situation where conventional PCR amplification fails as two flanking primers cannot be designed. Strategies to permit the large-scale development of compound SSR markers amplified by anchored PCR are discussed. |
| doi_str_mv | 10.1007/s00122-003-1480-0 |
| format | Article |
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J ; STEPHENSON, P ; LOGOJAN, A. M ; KHATKAR, D ; ROGERS, C ; KOEBNER, R. M. D ; SNAPE, J. W ; SHARP, P. J</creator><creatorcontrib>HAYDEN, M. J ; STEPHENSON, P ; LOGOJAN, A. M ; KHATKAR, D ; ROGERS, C ; KOEBNER, R. M. D ; SNAPE, J. W ; SHARP, P. J</creatorcontrib><description>A study was undertaken to determine the utility in bread wheat of anchored PCR for the development of single locus SSR markers targeted at compound repeat motifs. In anchored PCR, microsatellite amplification is achieved using a single primer complementary to the flanking sequence, and one which anchors to the repeat junction of the compound SSR. The recovery rate of useable markers was found to be similar (43%) to that reported for conventionally generated SSRs. Thus, anchored PCR can be used to reduce the costs of marker development, since it requires that only half the number of primers be synthesised. Where fluorescence-based platforms are used, marker deployment costs are lower, since only the anchoring primers need to be labelled. In addition, anchored PCR improves the recovery of useful markers, as it allows assays to be generated from microsatellite clones with repeat sequences located close to their ends, a situation where conventional PCR amplification fails as two flanking primers cannot be designed. Strategies to permit the large-scale development of compound SSR markers amplified by anchored PCR are discussed.</description><identifier>ISSN: 0040-5752</identifier><identifier>EISSN: 1432-2242</identifier><identifier>DOI: 10.1007/s00122-003-1480-0</identifier><identifier>PMID: 14598031</identifier><identifier>CODEN: THAGA6</identifier><language>eng</language><publisher>Heidelberg: Springer</publisher><subject>Agricultural research ; Alleles ; Biological and medical sciences ; Chromosome Mapping ; Classical genetics, quantitative genetics, hybrids ; DNA Primers ; Electrophoresis ; Fluorescence ; Fundamental and applied biological sciences. Psychology ; Genetic aspects ; Genetics ; Genetics of eukaryotes. Biological and molecular evolution ; Methods ; Microsatellites (Genetics) ; Minisatellite Repeats - genetics ; Plant genetic engineering ; Polymerase chain reaction ; Polymerase Chain Reaction - methods ; Production processes ; Pteridophyta, spermatophyta ; Silver Staining ; Triticeae ; Triticum - genetics ; Vegetals ; Wheat</subject><ispartof>Theoretical and applied genetics, 2004-02, Vol.108 (4), p.733-742</ispartof><rights>2004 INIST-CNRS</rights><rights>COPYRIGHT 2004 Springer</rights><rights>Springer-Verlag 2004</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c485t-ac60756461d8d39edf3eb21590fff63b02dbc18b9300c256a17b2b0bd8af773a3</citedby><cites>FETCH-LOGICAL-c485t-ac60756461d8d39edf3eb21590fff63b02dbc18b9300c256a17b2b0bd8af773a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27923,27924</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=15497210$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/14598031$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>HAYDEN, M. 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The recovery rate of useable markers was found to be similar (43%) to that reported for conventionally generated SSRs. Thus, anchored PCR can be used to reduce the costs of marker development, since it requires that only half the number of primers be synthesised. Where fluorescence-based platforms are used, marker deployment costs are lower, since only the anchoring primers need to be labelled. In addition, anchored PCR improves the recovery of useful markers, as it allows assays to be generated from microsatellite clones with repeat sequences located close to their ends, a situation where conventional PCR amplification fails as two flanking primers cannot be designed. Strategies to permit the large-scale development of compound SSR markers amplified by anchored PCR are discussed.</description><subject>Agricultural research</subject><subject>Alleles</subject><subject>Biological and medical sciences</subject><subject>Chromosome Mapping</subject><subject>Classical genetics, quantitative genetics, hybrids</subject><subject>DNA Primers</subject><subject>Electrophoresis</subject><subject>Fluorescence</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genetic aspects</subject><subject>Genetics</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Methods</subject><subject>Microsatellites (Genetics)</subject><subject>Minisatellite Repeats - genetics</subject><subject>Plant genetic engineering</subject><subject>Polymerase chain reaction</subject><subject>Polymerase Chain Reaction - methods</subject><subject>Production processes</subject><subject>Pteridophyta, spermatophyta</subject><subject>Silver Staining</subject><subject>Triticeae</subject><subject>Triticum - genetics</subject><subject>Vegetals</subject><subject>Wheat</subject><issn>0040-5752</issn><issn>1432-2242</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2004</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><recordid>eNqFkU2LFDEQhoMo7jj6A7xIEBQ8tFaSTid9HAY_FhaUGT3HfM702p20nW7W_fdmmIEFL57q8lRR7_sg9JLAewIgPmQAQmkFwCpSS6jgEVqRmtGK0po-RiuAGiouOL1Cz3K-BQDKgT1FV6TmrQRGVujnBkd_h_U4TknbI54T9n9mH10XD3g-enx39HrGg55--QmPKfXY3GMd7TFN3uFv2x3Ww9h3obN67lLEKWCbhjEt0eH9frd_jp4E3Wf_4jLX6Menj9-3X6qbr5-vt5ubytaSz5W2DQje1A1x0rHWu8C8oYS3EEJomAHqjCXStAzAUt5oIgw1YJzUQQim2Rq9Pd8tQX4vPs9q6LL1fa-jT0tWgjSS80b-FySiZaRhtICv_wFv0zLFEkJJIiWnDESB3p2hg-696qJNcS4FHvSSs7re79Sm4bWglJXi14icWTulnCcf1Dh1pdl7RUCdhKqzUFWEqpNQddp5dXliMYN3DxsXgwV4cwF0troPU3HT5QeO162gBNhfaUSmAw</recordid><startdate>20040201</startdate><enddate>20040201</enddate><creator>HAYDEN, M. 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J</au><au>STEPHENSON, P</au><au>LOGOJAN, A. M</au><au>KHATKAR, D</au><au>ROGERS, C</au><au>KOEBNER, R. M. D</au><au>SNAPE, J. W</au><au>SHARP, P. J</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A new approach to extending the wheat marker pool by anchored PCR amplification of compound SSRS</atitle><jtitle>Theoretical and applied genetics</jtitle><addtitle>Theor Appl Genet</addtitle><date>2004-02-01</date><risdate>2004</risdate><volume>108</volume><issue>4</issue><spage>733</spage><epage>742</epage><pages>733-742</pages><issn>0040-5752</issn><eissn>1432-2242</eissn><coden>THAGA6</coden><abstract>A study was undertaken to determine the utility in bread wheat of anchored PCR for the development of single locus SSR markers targeted at compound repeat motifs. In anchored PCR, microsatellite amplification is achieved using a single primer complementary to the flanking sequence, and one which anchors to the repeat junction of the compound SSR. The recovery rate of useable markers was found to be similar (43%) to that reported for conventionally generated SSRs. Thus, anchored PCR can be used to reduce the costs of marker development, since it requires that only half the number of primers be synthesised. Where fluorescence-based platforms are used, marker deployment costs are lower, since only the anchoring primers need to be labelled. In addition, anchored PCR improves the recovery of useful markers, as it allows assays to be generated from microsatellite clones with repeat sequences located close to their ends, a situation where conventional PCR amplification fails as two flanking primers cannot be designed. Strategies to permit the large-scale development of compound SSR markers amplified by anchored PCR are discussed.</abstract><cop>Heidelberg</cop><cop>Berlin</cop><pub>Springer</pub><pmid>14598031</pmid><doi>10.1007/s00122-003-1480-0</doi><tpages>10</tpages></addata></record> |
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| subjects | Agricultural research Alleles Biological and medical sciences Chromosome Mapping Classical genetics, quantitative genetics, hybrids DNA Primers Electrophoresis Fluorescence Fundamental and applied biological sciences. Psychology Genetic aspects Genetics Genetics of eukaryotes. Biological and molecular evolution Methods Microsatellites (Genetics) Minisatellite Repeats - genetics Plant genetic engineering Polymerase chain reaction Polymerase Chain Reaction - methods Production processes Pteridophyta, spermatophyta Silver Staining Triticeae Triticum - genetics Vegetals Wheat |
| title | A new approach to extending the wheat marker pool by anchored PCR amplification of compound SSRS |
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