Evaluation of AFLP in beta
AFLP markers were evaluated for their usefulness in the genetic analysis of sugarbeet and wild Beta species. Accessions of ten different sugarbeet breeding lines and five wild beets were screened using 256 primer combinations. Of the 11 309 bands investigated, 96.4% were polymorphic among the access...
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| Veröffentlicht in: | Theoretical and applied genetics 1999-05, Vol.98 (6/7), p.845-852 |
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| creator | Hansen, M Kraft, T Christiansson, M Nilsson, N.O |
| description | AFLP markers were evaluated for their usefulness in the genetic analysis of sugarbeet and wild Beta species. Accessions of ten different sugarbeet breeding lines and five wild beets were screened using 256 primer combinations. Of the 11 309 bands investigated, 96.4% were polymorphic among the accessions. A strong positive correlation was found between the number of polymorphisms and AT content of the selective bases of the primer combinations. Random subsets of primer combinations were used to produce genetic distance trees. Permutation tests showed that, for the wild beets, 500 AFLP bands sufficed to obtain the best topology of the tree with a probability at any given node of more than 99%. Ten times as many bands were necessary to obtain support values of the same order of magnitude for the sugarbeet lines. The reproducibility of AFLP for seven primer combinations was investigated by repeated analysis of all steps from DNA isolation to data scoring. For 5088 comparisons, the overall reproducibility was 97.6%. Robustness to genotyping errors was investigated by including an artificial F(1) (1:1 DNA mixture) of two sugarbeet lines in the screen for polymorphisms. For the 3160 cases of polymorphism between the two lines, 0.2% genotyping errors were found. The general reliability and usefulness of AFLP markers are discussed in relation to the results obtained. |
| doi_str_mv | 10.1007/s001220051143 |
| format | Article |
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Accessions of ten different sugarbeet breeding lines and five wild beets were screened using 256 primer combinations. Of the 11 309 bands investigated, 96.4% were polymorphic among the accessions. A strong positive correlation was found between the number of polymorphisms and AT content of the selective bases of the primer combinations. Random subsets of primer combinations were used to produce genetic distance trees. Permutation tests showed that, for the wild beets, 500 AFLP bands sufficed to obtain the best topology of the tree with a probability at any given node of more than 99%. Ten times as many bands were necessary to obtain support values of the same order of magnitude for the sugarbeet lines. The reproducibility of AFLP for seven primer combinations was investigated by repeated analysis of all steps from DNA isolation to data scoring. For 5088 comparisons, the overall reproducibility was 97.6%. Robustness to genotyping errors was investigated by including an artificial F(1) (1:1 DNA mixture) of two sugarbeet lines in the screen for polymorphisms. For the 3160 cases of polymorphism between the two lines, 0.2% genotyping errors were found. The general reliability and usefulness of AFLP markers are discussed in relation to the results obtained.</description><identifier>ISSN: 0040-5752</identifier><identifier>EISSN: 1432-2242</identifier><identifier>DOI: 10.1007/s001220051143</identifier><identifier>CODEN: THAGA6</identifier><language>eng</language><publisher>Heidelberg: Springer</publisher><subject>amplified fragment length polymorphism ; Analysis ; Beta ; beta patula ; Beta procumbens ; Beta vulgaris ; Beta vulgaris subsp. maritima ; Beta vulgaris subsp. vulgaris ; beta webbiana ; biochemical techniques ; Biological and medical sciences ; Classical genetics, quantitative genetics, hybrids ; DNA ; DNA primers ; Flowers & plants ; Fundamental and applied biological sciences. Psychology ; Genetic aspects ; genetic distance ; Genetic markers ; genetic polymorphism ; Genetic polymorphisms ; Genetic screening ; Genetics of eukaryotes. Biological and molecular evolution ; genotype ; genotyping ; identification ; Kinases ; lines ; phylogeny ; Plant genetics ; Polymorphism ; Pteridophyta, spermatophyta ; Reproducibility ; Sugar beet ; Vegetals ; wild relatives</subject><ispartof>Theoretical and applied genetics, 1999-05, Vol.98 (6/7), p.845-852</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-c412t-e21432d76c7eaffa0b567ffdd34ef64222a00137226a0310de70daff6dba50d73</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=1794002$$DView record in Pascal Francis$$Hfree_for_read</backlink></links><search><creatorcontrib>Hansen, M</creatorcontrib><creatorcontrib>Kraft, T</creatorcontrib><creatorcontrib>Christiansson, M</creatorcontrib><creatorcontrib>Nilsson, N.O</creatorcontrib><title>Evaluation of AFLP in beta</title><title>Theoretical and applied genetics</title><description>AFLP markers were evaluated for their usefulness in the genetic analysis of sugarbeet and wild Beta species. Accessions of ten different sugarbeet breeding lines and five wild beets were screened using 256 primer combinations. Of the 11 309 bands investigated, 96.4% were polymorphic among the accessions. A strong positive correlation was found between the number of polymorphisms and AT content of the selective bases of the primer combinations. Random subsets of primer combinations were used to produce genetic distance trees. Permutation tests showed that, for the wild beets, 500 AFLP bands sufficed to obtain the best topology of the tree with a probability at any given node of more than 99%. Ten times as many bands were necessary to obtain support values of the same order of magnitude for the sugarbeet lines. The reproducibility of AFLP for seven primer combinations was investigated by repeated analysis of all steps from DNA isolation to data scoring. For 5088 comparisons, the overall reproducibility was 97.6%. Robustness to genotyping errors was investigated by including an artificial F(1) (1:1 DNA mixture) of two sugarbeet lines in the screen for polymorphisms. For the 3160 cases of polymorphism between the two lines, 0.2% genotyping errors were found. The general reliability and usefulness of AFLP markers are discussed in relation to the results obtained.</description><subject>amplified fragment length polymorphism</subject><subject>Analysis</subject><subject>Beta</subject><subject>beta patula</subject><subject>Beta procumbens</subject><subject>Beta vulgaris</subject><subject>Beta vulgaris subsp. maritima</subject><subject>Beta vulgaris subsp. vulgaris</subject><subject>beta webbiana</subject><subject>biochemical techniques</subject><subject>Biological and medical sciences</subject><subject>Classical genetics, quantitative genetics, hybrids</subject><subject>DNA</subject><subject>DNA primers</subject><subject>Flowers & plants</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genetic aspects</subject><subject>genetic distance</subject><subject>Genetic markers</subject><subject>genetic polymorphism</subject><subject>Genetic polymorphisms</subject><subject>Genetic screening</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>genotype</subject><subject>genotyping</subject><subject>identification</subject><subject>Kinases</subject><subject>lines</subject><subject>phylogeny</subject><subject>Plant genetics</subject><subject>Polymorphism</subject><subject>Pteridophyta, spermatophyta</subject><subject>Reproducibility</subject><subject>Sugar beet</subject><subject>Vegetals</subject><subject>wild relatives</subject><issn>0040-5752</issn><issn>1432-2242</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1999</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp90UFLwzAUB_AgCs7p0YsXh4jiofrymjTtcYxNBwPFuXN4a5PR0bWzaUW_vSkbiB685F1-ee-fF8bOOdxzAPXgADgigORchAes508MEAUesh6AgEAqicfsxLk1AKCEsMcuxh9UtNTkVTmo7GA4mb0M8nKwNA2dsiNLhTNn-9pni8n4bfQUzJ4fp6PhLEgFxyYw2M3JVJQqQ9YSLGWkrM2yUBgbCUQknytUiBFByCEzCjIPo2xJEjIV9tntru-2rt5b4xq9yV1qioJKU7VOJ1HMVSyl8PLmX8kVyo56ePUHrqu2Lv0rdCykin3kDt3t0IoKo_MyrcrGfDYrap3T0_mrHoY-d4wxdhmDnU3ryrnaWL2t8w3VX5qD7pavfy3f--t9AHIpFbamMs3dzyWVCP8Dnl3umKVK06r2ZDFHPxUw4XGUiPAbSxqHgA</recordid><startdate>19990501</startdate><enddate>19990501</enddate><creator>Hansen, M</creator><creator>Kraft, T</creator><creator>Christiansson, M</creator><creator>Nilsson, N.O</creator><general>Springer</general><general>Springer Nature B.V</general><scope>FBQ</scope><scope>IQODW</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></search><sort><creationdate>19990501</creationdate><title>Evaluation of AFLP in beta</title><author>Hansen, M ; Kraft, T ; Christiansson, M ; Nilsson, N.O</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c412t-e21432d76c7eaffa0b567ffdd34ef64222a00137226a0310de70daff6dba50d73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1999</creationdate><topic>amplified fragment length polymorphism</topic><topic>Analysis</topic><topic>Beta</topic><topic>beta patula</topic><topic>Beta procumbens</topic><topic>Beta vulgaris</topic><topic>Beta vulgaris subsp. maritima</topic><topic>Beta vulgaris subsp. vulgaris</topic><topic>beta webbiana</topic><topic>biochemical techniques</topic><topic>Biological and medical sciences</topic><topic>Classical genetics, quantitative genetics, hybrids</topic><topic>DNA</topic><topic>DNA primers</topic><topic>Flowers & plants</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genetic aspects</topic><topic>genetic distance</topic><topic>Genetic markers</topic><topic>genetic polymorphism</topic><topic>Genetic polymorphisms</topic><topic>Genetic screening</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>genotype</topic><topic>genotyping</topic><topic>identification</topic><topic>Kinases</topic><topic>lines</topic><topic>phylogeny</topic><topic>Plant genetics</topic><topic>Polymorphism</topic><topic>Pteridophyta, spermatophyta</topic><topic>Reproducibility</topic><topic>Sugar beet</topic><topic>Vegetals</topic><topic>wild relatives</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hansen, M</creatorcontrib><creatorcontrib>Kraft, T</creatorcontrib><creatorcontrib>Christiansson, M</creatorcontrib><creatorcontrib>Nilsson, N.O</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</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><jtitle>Theoretical and applied genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hansen, M</au><au>Kraft, T</au><au>Christiansson, M</au><au>Nilsson, N.O</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Evaluation of AFLP in beta</atitle><jtitle>Theoretical and applied genetics</jtitle><date>1999-05-01</date><risdate>1999</risdate><volume>98</volume><issue>6/7</issue><spage>845</spage><epage>852</epage><pages>845-852</pages><issn>0040-5752</issn><eissn>1432-2242</eissn><coden>THAGA6</coden><abstract>AFLP markers were evaluated for their usefulness in the genetic analysis of sugarbeet and wild Beta species. Accessions of ten different sugarbeet breeding lines and five wild beets were screened using 256 primer combinations. Of the 11 309 bands investigated, 96.4% were polymorphic among the accessions. A strong positive correlation was found between the number of polymorphisms and AT content of the selective bases of the primer combinations. Random subsets of primer combinations were used to produce genetic distance trees. Permutation tests showed that, for the wild beets, 500 AFLP bands sufficed to obtain the best topology of the tree with a probability at any given node of more than 99%. Ten times as many bands were necessary to obtain support values of the same order of magnitude for the sugarbeet lines. The reproducibility of AFLP for seven primer combinations was investigated by repeated analysis of all steps from DNA isolation to data scoring. For 5088 comparisons, the overall reproducibility was 97.6%. Robustness to genotyping errors was investigated by including an artificial F(1) (1:1 DNA mixture) of two sugarbeet lines in the screen for polymorphisms. For the 3160 cases of polymorphism between the two lines, 0.2% genotyping errors were found. The general reliability and usefulness of AFLP markers are discussed in relation to the results obtained.</abstract><cop>Heidelberg</cop><cop>Berlin</cop><pub>Springer</pub><doi>10.1007/s001220051143</doi><tpages>8</tpages></addata></record> |
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| subjects | amplified fragment length polymorphism Analysis Beta beta patula Beta procumbens Beta vulgaris Beta vulgaris subsp. maritima Beta vulgaris subsp. vulgaris beta webbiana biochemical techniques Biological and medical sciences Classical genetics, quantitative genetics, hybrids DNA DNA primers Flowers & plants Fundamental and applied biological sciences. Psychology Genetic aspects genetic distance Genetic markers genetic polymorphism Genetic polymorphisms Genetic screening Genetics of eukaryotes. Biological and molecular evolution genotype genotyping identification Kinases lines phylogeny Plant genetics Polymorphism Pteridophyta, spermatophyta Reproducibility Sugar beet Vegetals wild relatives |
| title | Evaluation of AFLP in beta |
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