Quantitative Trait Locus (QTL) Isogenic Recombinant Analysis: A Method for High-Resolution Mapping of QTL Within a Single Population
In the quest for fine mapping quantitative trait loci (QTL) at a subcentimorgan scale, several methods that involve the construction of inbred lines and the generation of large progenies of such inbred lines have been developed (Complex Trait Consortium 2003). Here we present an alternative method t...
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| Veröffentlicht in: | Genetics (Austin) 2005-11, Vol.171 (3), p.1341-1352 |
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| creator | Peleman, Johan D Wye, Crispin Zethof, Jan Sorensen, Anker P Verbakel, Henk van Oeveren, Jan Gerats, Tom van der Voort, Jeroen Rouppe |
| description | In the quest for fine mapping quantitative trait loci (QTL) at a subcentimorgan scale, several methods that involve the construction of inbred lines and the generation of large progenies of such inbred lines have been developed (Complex Trait Consortium 2003). Here we present an alternative method that significantly speeds up QTL fine mapping by using one segregating population. As a first step, a rough mapping analysis is performed on a small part of the population. Once the QTL have been mapped to a chromosomal interval by standard procedures, a large population of 1000 plants or more is analyzed with markers flanking the defined QTL to select QTL isogenic recombinants (QIRs). QIRs bear a recombination event in the QTL interval of interest, while other QTL have the same homozygous genotype. Only these QIRs are subsequently phenotyped to fine map the QTL. By focusing at an early stage on the informative individuals in the population only, the efforts in population genotyping and phenotyping are significantly reduced as compared to prior methods. The principles of this approach are demonstrated by fine mapping an erucic acid QTL of rapeseed at a subcentimorgan scale. |
| doi_str_mv | 10.1534/genetics.105.045963 |
| format | Article |
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Here we present an alternative method that significantly speeds up QTL fine mapping by using one segregating population. As a first step, a rough mapping analysis is performed on a small part of the population. Once the QTL have been mapped to a chromosomal interval by standard procedures, a large population of 1000 plants or more is analyzed with markers flanking the defined QTL to select QTL isogenic recombinants (QIRs). QIRs bear a recombination event in the QTL interval of interest, while other QTL have the same homozygous genotype. Only these QIRs are subsequently phenotyped to fine map the QTL. By focusing at an early stage on the informative individuals in the population only, the efforts in population genotyping and phenotyping are significantly reduced as compared to prior methods. The principles of this approach are demonstrated by fine mapping an erucic acid QTL of rapeseed at a subcentimorgan scale.</description><identifier>ISSN: 0016-6731</identifier><identifier>ISSN: 1943-2631</identifier><identifier>EISSN: 1943-2631</identifier><identifier>DOI: 10.1534/genetics.105.045963</identifier><identifier>PMID: 16085696</identifier><identifier>CODEN: GENTAE</identifier><language>eng</language><publisher>United States: Genetics Soc America</publisher><subject>Brassica rapa ; Brassica rapa - genetics ; Brassica rapa - metabolism ; Chromosome Mapping - statistics & numerical data ; Erucic Acids - metabolism ; Genetic Markers ; Genetics ; Genetics, Population - statistics & numerical data ; Genomics ; Investigations ; Methods ; Population ; Quantitative Trait Loci ; Recombination, Genetic ; Sample Size</subject><ispartof>Genetics (Austin), 2005-11, Vol.171 (3), p.1341-1352</ispartof><rights>Copyright Genetics Society of America Nov 2005</rights><rights>Copyright © 2005 by the Genetics Society of America 2005</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c524t-1c43f4fde6b062e97b35e8372dbc0fe63c754ea8e90ed208acb4e67a207891d23</citedby><cites>FETCH-LOGICAL-c524t-1c43f4fde6b062e97b35e8372dbc0fe63c754ea8e90ed208acb4e67a207891d23</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,776,780,881,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16085696$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Peleman, Johan D</creatorcontrib><creatorcontrib>Wye, Crispin</creatorcontrib><creatorcontrib>Zethof, Jan</creatorcontrib><creatorcontrib>Sorensen, Anker P</creatorcontrib><creatorcontrib>Verbakel, Henk</creatorcontrib><creatorcontrib>van Oeveren, Jan</creatorcontrib><creatorcontrib>Gerats, Tom</creatorcontrib><creatorcontrib>van der Voort, Jeroen Rouppe</creatorcontrib><title>Quantitative Trait Locus (QTL) Isogenic Recombinant Analysis: A Method for High-Resolution Mapping of QTL Within a Single Population</title><title>Genetics (Austin)</title><addtitle>Genetics</addtitle><description>In the quest for fine mapping quantitative trait loci (QTL) at a subcentimorgan scale, several methods that involve the construction of inbred lines and the generation of large progenies of such inbred lines have been developed (Complex Trait Consortium 2003). Here we present an alternative method that significantly speeds up QTL fine mapping by using one segregating population. As a first step, a rough mapping analysis is performed on a small part of the population. Once the QTL have been mapped to a chromosomal interval by standard procedures, a large population of 1000 plants or more is analyzed with markers flanking the defined QTL to select QTL isogenic recombinants (QIRs). QIRs bear a recombination event in the QTL interval of interest, while other QTL have the same homozygous genotype. Only these QIRs are subsequently phenotyped to fine map the QTL. By focusing at an early stage on the informative individuals in the population only, the efforts in population genotyping and phenotyping are significantly reduced as compared to prior methods. The principles of this approach are demonstrated by fine mapping an erucic acid QTL of rapeseed at a subcentimorgan scale.</description><subject>Brassica rapa</subject><subject>Brassica rapa - genetics</subject><subject>Brassica rapa - metabolism</subject><subject>Chromosome Mapping - statistics & numerical data</subject><subject>Erucic Acids - metabolism</subject><subject>Genetic Markers</subject><subject>Genetics</subject><subject>Genetics, Population - statistics & numerical data</subject><subject>Genomics</subject><subject>Investigations</subject><subject>Methods</subject><subject>Population</subject><subject>Quantitative Trait Loci</subject><subject>Recombination, Genetic</subject><subject>Sample Size</subject><issn>0016-6731</issn><issn>1943-2631</issn><issn>1943-2631</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNqFkktv1DAUhSMEokPhFyAhiwWPRQa_Y7NAGlVAK00FLYNYWo5zM-MqiYfY6ah7fjiuZnhuurrSvd89fpxTFE8JnhPB-Js1DJC8i3OCxRxzoSW7V8yI5qykkpH7xQxjIktZMXJUPIrxCmMstVAPiyMisRJSy1nx42KyQ_LJJn8NaDVan9AyuCmiVxer5Wt0FkM-xzt0CS70tR8yjRaD7W6ij2_RAp1D2oQGtWFEp369KS8hhm5KPgzo3G63flij0KKshb75tPEDsuhLbnaAPoft1Nlb8nHxoLVdhCeHelx8_fB-dXJaLj99PDtZLEsnKE8lcZy1vG1A1lhS0FXNBChW0aZ2uAXJXCU4WAUaQ0Oxsq7mICtLcaU0aSg7Lt7tdbdT3UPjYEij7cx29L0db0yw3vw7GfzGrMO1IVxIRVUWeHEQGMP3CWIyvY8Ous4OEKZopFKUV4LdCRItNGZM3g1WhFFFqgw-_w-8CtOYjYiGEk6wZlJniO0hN4YYR2h_v41gcxsa8ys0uSHMPjR569nf3_Jn55CSDLzcA5vs8M6PYGJvuy7jxOx2u3xHwwxhnLCfakbOOA</recordid><startdate>20051101</startdate><enddate>20051101</enddate><creator>Peleman, Johan D</creator><creator>Wye, Crispin</creator><creator>Zethof, Jan</creator><creator>Sorensen, Anker P</creator><creator>Verbakel, Henk</creator><creator>van Oeveren, Jan</creator><creator>Gerats, Tom</creator><creator>van der Voort, Jeroen Rouppe</creator><general>Genetics Soc America</general><general>Genetics Society of America</general><general>Copyright © 2005 by the Genetics Society of America</general><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>3V.</scope><scope>4T-</scope><scope>4U-</scope><scope>7QP</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</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>GUQSH</scope><scope>HCIFZ</scope><scope>K9-</scope><scope>K9.</scope><scope>LK8</scope><scope>M0K</scope><scope>M0R</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M2P</scope><scope>M7N</scope><scope>M7P</scope><scope>MBDVC</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20051101</creationdate><title>Quantitative Trait Locus (QTL) Isogenic Recombinant Analysis: A Method for High-Resolution Mapping of QTL Within a Single Population</title><author>Peleman, Johan D ; Wye, Crispin ; Zethof, Jan ; Sorensen, Anker P ; Verbakel, Henk ; van Oeveren, Jan ; Gerats, Tom ; van der Voort, Jeroen Rouppe</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c524t-1c43f4fde6b062e97b35e8372dbc0fe63c754ea8e90ed208acb4e67a207891d23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Brassica rapa</topic><topic>Brassica rapa - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genetics (Austin)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Peleman, Johan D</au><au>Wye, Crispin</au><au>Zethof, Jan</au><au>Sorensen, Anker P</au><au>Verbakel, Henk</au><au>van Oeveren, Jan</au><au>Gerats, Tom</au><au>van der Voort, Jeroen Rouppe</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Quantitative Trait Locus (QTL) Isogenic Recombinant Analysis: A Method for High-Resolution Mapping of QTL Within a Single Population</atitle><jtitle>Genetics (Austin)</jtitle><addtitle>Genetics</addtitle><date>2005-11-01</date><risdate>2005</risdate><volume>171</volume><issue>3</issue><spage>1341</spage><epage>1352</epage><pages>1341-1352</pages><issn>0016-6731</issn><issn>1943-2631</issn><eissn>1943-2631</eissn><coden>GENTAE</coden><abstract>In the quest for fine mapping quantitative trait loci (QTL) at a subcentimorgan scale, several methods that involve the construction of inbred lines and the generation of large progenies of such inbred lines have been developed (Complex Trait Consortium 2003). Here we present an alternative method that significantly speeds up QTL fine mapping by using one segregating population. As a first step, a rough mapping analysis is performed on a small part of the population. Once the QTL have been mapped to a chromosomal interval by standard procedures, a large population of 1000 plants or more is analyzed with markers flanking the defined QTL to select QTL isogenic recombinants (QIRs). QIRs bear a recombination event in the QTL interval of interest, while other QTL have the same homozygous genotype. Only these QIRs are subsequently phenotyped to fine map the QTL. By focusing at an early stage on the informative individuals in the population only, the efforts in population genotyping and phenotyping are significantly reduced as compared to prior methods. 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| identifier | ISSN: 0016-6731 |
| ispartof | Genetics (Austin), 2005-11, Vol.171 (3), p.1341-1352 |
| issn | 0016-6731 1943-2631 1943-2631 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_1456828 |
| source | Oxford University Press Journals All Titles (1996-Current); MEDLINE; EZB-FREE-00999 freely available EZB journals; Alma/SFX Local Collection |
| subjects | Brassica rapa Brassica rapa - genetics Brassica rapa - metabolism Chromosome Mapping - statistics & numerical data Erucic Acids - metabolism Genetic Markers Genetics Genetics, Population - statistics & numerical data Genomics Investigations Methods Population Quantitative Trait Loci Recombination, Genetic Sample Size |
| title | Quantitative Trait Locus (QTL) Isogenic Recombinant Analysis: A Method for High-Resolution Mapping of QTL Within a Single Population |
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