Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda
De novo construction of complete genetic linkage maps requires large mapping populations, large numbers of genetic markers, and efficient algorithms for ordering markers and evaluating order confidence. We constructed a complete genetic map of an individual loblolly pine (Pinus taeda L.) using ampli...
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| Veröffentlicht in: | Theoretical and applied genetics 1999-06, Vol.98 (8), p.1279-1292 |
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| creator | Remington, D.L Whetten, R.W Liu, B.H O'Malley, D.M |
| description | De novo construction of complete genetic linkage maps requires large mapping populations, large numbers of genetic markers, and efficient algorithms for ordering markers and evaluating order confidence. We constructed a complete genetic map of an individual loblolly pine (Pinus taeda L.) using amplified fragment length polymorphism (AFLP) markers segregating in haploid megagametophytes and PGRI mapping software. We generated 521 polymorphic fragments from 21 AFLP primer pairs. A total of 508 fragments mapped to 12 linkage groups, which is equal to the Pinus haploid chromosome number. Bootstrap locus order matrices and recombination matrices generated by PGRI were used to select 184 framework markers that could be ordered confidently. Order support was also evaluated using log likelihood criteria in MAPMAKER. Optimal marker orders from PGRI and MAPMAKER were identical, but the implied reliability of orders differed greatly. The framework map provides nearly complete coverage of the genome, estimated at approximately 1700 cM in length using a modified estimator. This map should provide a useful framework for merging existing loblolly pine maps and adding multiallelic markers as they become available. Map coverage with dominant markers in both linkage phases will make the map useful for subsequent quantitative trait locus mapping in families derived by self-pollination. |
| doi_str_mv | 10.1007/s001220051194 |
| format | Article |
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We constructed a complete genetic map of an individual loblolly pine (Pinus taeda L.) using amplified fragment length polymorphism (AFLP) markers segregating in haploid megagametophytes and PGRI mapping software. We generated 521 polymorphic fragments from 21 AFLP primer pairs. A total of 508 fragments mapped to 12 linkage groups, which is equal to the Pinus haploid chromosome number. Bootstrap locus order matrices and recombination matrices generated by PGRI were used to select 184 framework markers that could be ordered confidently. Order support was also evaluated using log likelihood criteria in MAPMAKER. Optimal marker orders from PGRI and MAPMAKER were identical, but the implied reliability of orders differed greatly. The framework map provides nearly complete coverage of the genome, estimated at approximately 1700 cM in length using a modified estimator. This map should provide a useful framework for merging existing loblolly pine maps and adding multiallelic markers as they become available. Map coverage with dominant markers in both linkage phases will make the map useful for subsequent quantitative trait locus mapping in families derived by self-pollination.</description><identifier>ISSN: 0040-5752</identifier><identifier>EISSN: 1432-2242</identifier><identifier>DOI: 10.1007/s001220051194</identifier><identifier>PMID: 12238515</identifier><identifier>CODEN: THAGA6</identifier><language>eng</language><publisher>Heidelberg: Springer</publisher><subject>alleles ; amplified fragment length polymorphism ; Biological and medical sciences ; Chromosome Mapping ; Classical genetics, quantitative genetics, hybrids ; computer analysis ; computer software ; DNA ; DNA primers ; framework markers ; Fundamental and applied biological sciences. Psychology ; Genes, Plant ; Genetic aspects ; Genetic Linkage ; genetic markers ; genetic recombination ; Genetics of eukaryotes. Biological and molecular evolution ; genome ; Genome, Plant ; Genomic libraries ; Genomics ; inheritance (genetics) ; linkage groups ; Lod Score ; mapmaker software ; Models, Genetic ; pgri software ; Physiological aspects ; Pine ; Pinus - genetics ; Pinus taeda ; Plant genetics ; Polymorphism, Genetic ; probability analysis ; Pteridophyta, spermatophyta ; Software ; Space life sciences ; Vegetals</subject><ispartof>Theoretical and applied genetics, 1999-06, Vol.98 (8), p.1279-1292</ispartof><rights>1999 INIST-CNRS</rights><rights>COPYRIGHT 1999 Springer</rights><rights>Springer-Verlag Berlin Heidelberg 1999</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c434t-65b98c9aedacf8afd305aeca633269c8b2732a686fc2f8571570ae6c69d35cb3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=1860251$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/12238515$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Remington, D.L</creatorcontrib><creatorcontrib>Whetten, R.W</creatorcontrib><creatorcontrib>Liu, B.H</creatorcontrib><creatorcontrib>O'Malley, D.M</creatorcontrib><title>Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda</title><title>Theoretical and applied genetics</title><addtitle>Theor Appl Genet</addtitle><description>De novo construction of complete genetic linkage maps requires large mapping populations, large numbers of genetic markers, and efficient algorithms for ordering markers and evaluating order confidence. We constructed a complete genetic map of an individual loblolly pine (Pinus taeda L.) using amplified fragment length polymorphism (AFLP) markers segregating in haploid megagametophytes and PGRI mapping software. We generated 521 polymorphic fragments from 21 AFLP primer pairs. A total of 508 fragments mapped to 12 linkage groups, which is equal to the Pinus haploid chromosome number. Bootstrap locus order matrices and recombination matrices generated by PGRI were used to select 184 framework markers that could be ordered confidently. Order support was also evaluated using log likelihood criteria in MAPMAKER. Optimal marker orders from PGRI and MAPMAKER were identical, but the implied reliability of orders differed greatly. The framework map provides nearly complete coverage of the genome, estimated at approximately 1700 cM in length using a modified estimator. This map should provide a useful framework for merging existing loblolly pine maps and adding multiallelic markers as they become available. Map coverage with dominant markers in both linkage phases will make the map useful for subsequent quantitative trait locus mapping in families derived by self-pollination.</description><subject>alleles</subject><subject>amplified fragment length polymorphism</subject><subject>Biological and medical sciences</subject><subject>Chromosome Mapping</subject><subject>Classical genetics, quantitative genetics, hybrids</subject><subject>computer analysis</subject><subject>computer software</subject><subject>DNA</subject><subject>DNA primers</subject><subject>framework markers</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genes, Plant</subject><subject>Genetic aspects</subject><subject>Genetic Linkage</subject><subject>genetic markers</subject><subject>genetic recombination</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>genome</subject><subject>Genome, Plant</subject><subject>Genomic libraries</subject><subject>Genomics</subject><subject>inheritance (genetics)</subject><subject>linkage groups</subject><subject>Lod Score</subject><subject>mapmaker software</subject><subject>Models, Genetic</subject><subject>pgri software</subject><subject>Physiological aspects</subject><subject>Pine</subject><subject>Pinus - genetics</subject><subject>Pinus taeda</subject><subject>Plant genetics</subject><subject>Polymorphism, Genetic</subject><subject>probability analysis</subject><subject>Pteridophyta, spermatophyta</subject><subject>Software</subject><subject>Space life sciences</subject><subject>Vegetals</subject><issn>0040-5752</issn><issn>1432-2242</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1999</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>eNqF0UFrFDEUB_AgFrtWj141iAgeRl-SSSZzXBarhYWWtuIxvM1mxikzyZpk1H57s-xC0UsP4RH4vcdL_oS8YvCRATSfEgDjHEAy1tZPyILVglec1_wpWQDUUMlG8lPyPKU7AOASxDNyWjqElkwuyPdV8CnH2eYheBo6ip4uz9dXtHfe5cHSCXf095B_UO8wjvfUhmk3uuz2IEyu3H-5iL2jg6dXg58Tzei2-IKcdDgm9_JYz8jt-efb1ddqffnlYrVcV7YWda6U3LTatvsO22nstgIkOotKCK5aqze8ERyVVp3lnZYNkw2gU1a1WyHtRpyR94exuxh-zi5lMw3JunFE78KcjGqlkFKLRyFruFRS8gLf_gfvwhx9eYPRtWzKUVDQhwPqcXRm8Db47P7kHueUzMXNtVkKYEJz3ehiq4O1MaQUXWd2cZgw3hsGZh-h-SfC4l8fF5g3k9s-6GNmBbw7AkwWxy6it0N6cFqVmFlhbw6sw2Cwj4V8u-FlLeCtYKL88F9BXana</recordid><startdate>19990601</startdate><enddate>19990601</enddate><creator>Remington, D.L</creator><creator>Whetten, R.W</creator><creator>Liu, B.H</creator><creator>O'Malley, D.M</creator><general>Springer</general><general>Springer Nature B.V</general><scope>FBQ</scope><scope>IQODW</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>ISR</scope><scope>3V.</scope><scope>7SS</scope><scope>7TK</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>19990601</creationdate><title>Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda</title><author>Remington, D.L ; Whetten, R.W ; Liu, B.H ; O'Malley, D.M</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c434t-65b98c9aedacf8afd305aeca633269c8b2732a686fc2f8571570ae6c69d35cb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1999</creationdate><topic>alleles</topic><topic>amplified fragment length polymorphism</topic><topic>Biological and medical sciences</topic><topic>Chromosome Mapping</topic><topic>Classical genetics, quantitative genetics, hybrids</topic><topic>computer analysis</topic><topic>computer software</topic><topic>DNA</topic><topic>DNA primers</topic><topic>framework markers</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genes, Plant</topic><topic>Genetic aspects</topic><topic>Genetic Linkage</topic><topic>genetic markers</topic><topic>genetic recombination</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>genome</topic><topic>Genome, Plant</topic><topic>Genomic libraries</topic><topic>Genomics</topic><topic>inheritance (genetics)</topic><topic>linkage groups</topic><topic>Lod Score</topic><topic>mapmaker software</topic><topic>Models, Genetic</topic><topic>pgri software</topic><topic>Physiological aspects</topic><topic>Pine</topic><topic>Pinus - genetics</topic><topic>Pinus taeda</topic><topic>Plant genetics</topic><topic>Polymorphism, Genetic</topic><topic>probability analysis</topic><topic>Pteridophyta, spermatophyta</topic><topic>Software</topic><topic>Space life sciences</topic><topic>Vegetals</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Remington, D.L</creatorcontrib><creatorcontrib>Whetten, R.W</creatorcontrib><creatorcontrib>Liu, B.H</creatorcontrib><creatorcontrib>O'Malley, D.M</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Theoretical and applied genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Remington, D.L</au><au>Whetten, R.W</au><au>Liu, B.H</au><au>O'Malley, D.M</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda</atitle><jtitle>Theoretical and applied genetics</jtitle><addtitle>Theor Appl Genet</addtitle><date>1999-06-01</date><risdate>1999</risdate><volume>98</volume><issue>8</issue><spage>1279</spage><epage>1292</epage><pages>1279-1292</pages><issn>0040-5752</issn><eissn>1432-2242</eissn><coden>THAGA6</coden><abstract>De novo construction of complete genetic linkage maps requires large mapping populations, large numbers of genetic markers, and efficient algorithms for ordering markers and evaluating order confidence. We constructed a complete genetic map of an individual loblolly pine (Pinus taeda L.) using amplified fragment length polymorphism (AFLP) markers segregating in haploid megagametophytes and PGRI mapping software. We generated 521 polymorphic fragments from 21 AFLP primer pairs. A total of 508 fragments mapped to 12 linkage groups, which is equal to the Pinus haploid chromosome number. Bootstrap locus order matrices and recombination matrices generated by PGRI were used to select 184 framework markers that could be ordered confidently. Order support was also evaluated using log likelihood criteria in MAPMAKER. Optimal marker orders from PGRI and MAPMAKER were identical, but the implied reliability of orders differed greatly. The framework map provides nearly complete coverage of the genome, estimated at approximately 1700 cM in length using a modified estimator. This map should provide a useful framework for merging existing loblolly pine maps and adding multiallelic markers as they become available. Map coverage with dominant markers in both linkage phases will make the map useful for subsequent quantitative trait locus mapping in families derived by self-pollination.</abstract><cop>Heidelberg</cop><cop>Berlin</cop><pub>Springer</pub><pmid>12238515</pmid><doi>10.1007/s001220051194</doi><tpages>14</tpages></addata></record> |
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| ispartof | Theoretical and applied genetics, 1999-06, Vol.98 (8), p.1279-1292 |
| issn | 0040-5752 1432-2242 |
| language | eng |
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| subjects | alleles amplified fragment length polymorphism Biological and medical sciences Chromosome Mapping Classical genetics, quantitative genetics, hybrids computer analysis computer software DNA DNA primers framework markers Fundamental and applied biological sciences. Psychology Genes, Plant Genetic aspects Genetic Linkage genetic markers genetic recombination Genetics of eukaryotes. Biological and molecular evolution genome Genome, Plant Genomic libraries Genomics inheritance (genetics) linkage groups Lod Score mapmaker software Models, Genetic pgri software Physiological aspects Pine Pinus - genetics Pinus taeda Plant genetics Polymorphism, Genetic probability analysis Pteridophyta, spermatophyta Software Space life sciences Vegetals |
| title | Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda |
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