Legume Anchor Markers Link Syntenic Regions Between Phaseolus vulgaris, Lotus japonicus, Medicago truncatula and Arachis
We have previously described a bioinformatics pipeline identifying comparative anchor-tagged sequence (CATS) loci, combined with design of intron-spanning primers. The derived anchor markers defining the linkage position of homologous genes are essential for evaluating genome conservation among rela...
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| Veröffentlicht in: | Genetics (Austin) 2008-08, Vol.179 (4), p.2299-2312 |
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| creator | Hougaard, Birgit Kristine Madsen, Lene Heegaard Sandal, Niels de Carvalho Moretzsohn, Marcio Fredslund, Jakob Schauser, Leif Nielsen, Anna Marie Rohde, Trine Sato, Shusei Tabata, Satoshi Bertioli, David John Stougaard, Jens |
| description | We have previously described a bioinformatics pipeline identifying comparative anchor-tagged sequence (CATS) loci, combined with design of intron-spanning primers. The derived anchor markers defining the linkage position of homologous genes are essential for evaluating genome conservation among related species and facilitate transfer of genetic and genome information between species. Here we validate this global approach in the common bean and in the AA genome complement of the allotetraploid peanut. We present the successful conversion of approximately 50% of the bioinformatics-defined primers into legume anchor markers in bean and diploid Arachis species. One hundred and four new loci representing single-copy genes were added to the existing bean map. These new legume anchor-marker loci enabled the alignment of genetic linkage maps through corresponding genes and provided an estimate of the extent of synteny and collinearity. Extensive macrosynteny between Lotus and bean was uncovered on 8 of the 11 bean chromosomes and large blocks of macrosynteny were also found between bean and Medicago. This suggests that anchor markers can facilitate a better understanding of the genes and genetics of important traits in crops with largely uncharacterized genomes using genetic and genome information from related model plants. |
| doi_str_mv | 10.1534/genetics.108.090084 |
| format | Article |
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The derived anchor markers defining the linkage position of homologous genes are essential for evaluating genome conservation among related species and facilitate transfer of genetic and genome information between species. Here we validate this global approach in the common bean and in the AA genome complement of the allotetraploid peanut. We present the successful conversion of approximately 50% of the bioinformatics-defined primers into legume anchor markers in bean and diploid Arachis species. One hundred and four new loci representing single-copy genes were added to the existing bean map. These new legume anchor-marker loci enabled the alignment of genetic linkage maps through corresponding genes and provided an estimate of the extent of synteny and collinearity. Extensive macrosynteny between Lotus and bean was uncovered on 8 of the 11 bean chromosomes and large blocks of macrosynteny were also found between bean and Medicago. This suggests that anchor markers can facilitate a better understanding of the genes and genetics of important traits in crops with largely uncharacterized genomes using genetic and genome information from related model plants.</description><identifier>ISSN: 0016-6731</identifier><identifier>ISSN: 1943-2631</identifier><identifier>EISSN: 1943-2631</identifier><identifier>DOI: 10.1534/genetics.108.090084</identifier><identifier>PMID: 18689902</identifier><identifier>CODEN: GENTAE</identifier><language>eng</language><publisher>United States: Genetics Soc America</publisher><subject>Arachis - genetics ; Dietary fiber ; Genetic Linkage ; Genetic Markers ; Genome, Plant ; Genomics ; Investigations ; Legumes ; Lotus - genetics ; Medicago truncatula - genetics ; Phaseolus - genetics ; Synteny</subject><ispartof>Genetics (Austin), 2008-08, Vol.179 (4), p.2299-2312</ispartof><rights>Copyright Genetics Society of America Aug 2008</rights><rights>Copyright © 2008 by the Genetics Society of America</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c528t-82bff69af7d635aba09dce1043eca2b3ef8425281575558efbd89cba363531dc3</citedby><cites>FETCH-LOGICAL-c528t-82bff69af7d635aba09dce1043eca2b3ef8425281575558efbd89cba363531dc3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,776,780,881,27903,27904</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18689902$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hougaard, Birgit Kristine</creatorcontrib><creatorcontrib>Madsen, Lene Heegaard</creatorcontrib><creatorcontrib>Sandal, Niels</creatorcontrib><creatorcontrib>de Carvalho Moretzsohn, Marcio</creatorcontrib><creatorcontrib>Fredslund, Jakob</creatorcontrib><creatorcontrib>Schauser, Leif</creatorcontrib><creatorcontrib>Nielsen, Anna Marie</creatorcontrib><creatorcontrib>Rohde, Trine</creatorcontrib><creatorcontrib>Sato, Shusei</creatorcontrib><creatorcontrib>Tabata, Satoshi</creatorcontrib><creatorcontrib>Bertioli, David John</creatorcontrib><creatorcontrib>Stougaard, Jens</creatorcontrib><title>Legume Anchor Markers Link Syntenic Regions Between Phaseolus vulgaris, Lotus japonicus, Medicago truncatula and Arachis</title><title>Genetics (Austin)</title><addtitle>Genetics</addtitle><description>We have previously described a bioinformatics pipeline identifying comparative anchor-tagged sequence (CATS) loci, combined with design of intron-spanning primers. The derived anchor markers defining the linkage position of homologous genes are essential for evaluating genome conservation among related species and facilitate transfer of genetic and genome information between species. Here we validate this global approach in the common bean and in the AA genome complement of the allotetraploid peanut. We present the successful conversion of approximately 50% of the bioinformatics-defined primers into legume anchor markers in bean and diploid Arachis species. One hundred and four new loci representing single-copy genes were added to the existing bean map. These new legume anchor-marker loci enabled the alignment of genetic linkage maps through corresponding genes and provided an estimate of the extent of synteny and collinearity. Extensive macrosynteny between Lotus and bean was uncovered on 8 of the 11 bean chromosomes and large blocks of macrosynteny were also found between bean and Medicago. This suggests that anchor markers can facilitate a better understanding of the genes and genetics of important traits in crops with largely uncharacterized genomes using genetic and genome information from related model plants.</description><subject>Arachis - genetics</subject><subject>Dietary fiber</subject><subject>Genetic Linkage</subject><subject>Genetic Markers</subject><subject>Genome, Plant</subject><subject>Genomics</subject><subject>Investigations</subject><subject>Legumes</subject><subject>Lotus - genetics</subject><subject>Medicago truncatula - genetics</subject><subject>Phaseolus - genetics</subject><subject>Synteny</subject><issn>0016-6731</issn><issn>1943-2631</issn><issn>1943-2631</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><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>eNpdkUuP0zAUhSMEYsrAL0BCFgvYkOJXUnuDVEa8pI5APNaW49wk7iR2seMJ8-_xqOW5urrX3zny0SmKxwSvScX4yx4czNbENcFijSXGgt8pVkRyVtKakbvFCmNSl_WGkbPiQYx7jHEtK3G_OCOiFlJiuip-7KBPE6CtM4MP6FKHKwgR7ay7Ql9u3AzOGvQZeutdRK9hXgAc-jToCH5MEV2nsdfBxhdo5-e87_XBZ0XKh0tordG9R3NIzug5jRpp16Jt0Gaw8WFxr9NjhEeneV58e_vm68X7cvfx3YeL7a40FRVzKWjTdbXU3aatWaUbjWVrgGDOwGjaMOgEp5kk1aaqKgFd0wppGs0yzUhr2Hnx6uh7SM0EWevmoEd1CHbS4UZ5bdW_L84OqvfXilakxlJmg2cng-C_J4izmmw0MI7agU9R1ZJzSgTP4NP_wL1PweVwihJOWCX5rRs7Qib4GAN0v39CsLqtVf2qNR-EOtaaVU_-DvFHc-oxA8-PwGD7YbEBVJz0OGacqGVZyEYqrijNcX4CPbSw9Q</recordid><startdate>20080801</startdate><enddate>20080801</enddate><creator>Hougaard, Birgit Kristine</creator><creator>Madsen, Lene Heegaard</creator><creator>Sandal, Niels</creator><creator>de Carvalho Moretzsohn, Marcio</creator><creator>Fredslund, Jakob</creator><creator>Schauser, Leif</creator><creator>Nielsen, Anna Marie</creator><creator>Rohde, Trine</creator><creator>Sato, Shusei</creator><creator>Tabata, Satoshi</creator><creator>Bertioli, David John</creator><creator>Stougaard, Jens</creator><general>Genetics Soc America</general><general>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>20080801</creationdate><title>Legume Anchor Markers Link Syntenic Regions Between Phaseolus vulgaris, Lotus japonicus, Medicago truncatula and Arachis</title><author>Hougaard, Birgit Kristine ; Madsen, Lene Heegaard ; Sandal, Niels ; de Carvalho Moretzsohn, Marcio ; Fredslund, Jakob ; Schauser, Leif ; Nielsen, Anna Marie ; Rohde, Trine ; Sato, Shusei ; Tabata, Satoshi ; Bertioli, David John ; Stougaard, Jens</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c528t-82bff69af7d635aba09dce1043eca2b3ef8425281575558efbd89cba363531dc3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Arachis - 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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>Hougaard, Birgit Kristine</au><au>Madsen, Lene Heegaard</au><au>Sandal, Niels</au><au>de Carvalho Moretzsohn, Marcio</au><au>Fredslund, Jakob</au><au>Schauser, Leif</au><au>Nielsen, Anna Marie</au><au>Rohde, Trine</au><au>Sato, Shusei</au><au>Tabata, Satoshi</au><au>Bertioli, David John</au><au>Stougaard, Jens</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Legume Anchor Markers Link Syntenic Regions Between Phaseolus vulgaris, Lotus japonicus, Medicago truncatula and Arachis</atitle><jtitle>Genetics (Austin)</jtitle><addtitle>Genetics</addtitle><date>2008-08-01</date><risdate>2008</risdate><volume>179</volume><issue>4</issue><spage>2299</spage><epage>2312</epage><pages>2299-2312</pages><issn>0016-6731</issn><issn>1943-2631</issn><eissn>1943-2631</eissn><coden>GENTAE</coden><abstract>We have previously described a bioinformatics pipeline identifying comparative anchor-tagged sequence (CATS) loci, combined with design of intron-spanning primers. The derived anchor markers defining the linkage position of homologous genes are essential for evaluating genome conservation among related species and facilitate transfer of genetic and genome information between species. Here we validate this global approach in the common bean and in the AA genome complement of the allotetraploid peanut. We present the successful conversion of approximately 50% of the bioinformatics-defined primers into legume anchor markers in bean and diploid Arachis species. One hundred and four new loci representing single-copy genes were added to the existing bean map. These new legume anchor-marker loci enabled the alignment of genetic linkage maps through corresponding genes and provided an estimate of the extent of synteny and collinearity. Extensive macrosynteny between Lotus and bean was uncovered on 8 of the 11 bean chromosomes and large blocks of macrosynteny were also found between bean and Medicago. This suggests that anchor markers can facilitate a better understanding of the genes and genetics of important traits in crops with largely uncharacterized genomes using genetic and genome information from related model plants.</abstract><cop>United States</cop><pub>Genetics Soc America</pub><pmid>18689902</pmid><doi>10.1534/genetics.108.090084</doi><tpages>14</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Genetics (Austin), 2008-08, Vol.179 (4), p.2299-2312 |
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Oxford University Press Journals All Titles (1996-Current); Alma/SFX Local Collection |
| subjects | Arachis - genetics Dietary fiber Genetic Linkage Genetic Markers Genome, Plant Genomics Investigations Legumes Lotus - genetics Medicago truncatula - genetics Phaseolus - genetics Synteny |
| title | Legume Anchor Markers Link Syntenic Regions Between Phaseolus vulgaris, Lotus japonicus, Medicago truncatula and Arachis |
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