Assessment of the congruity of genetic relationships and variation revealed by individual- and bulked-samples-based approaches using RAPD and ISSR markers in Japanese turnip (Brassica rapa ssp. rapa) cultivars
To find out an efficient and accurate way to estimate the genetic relationship among cultivars having within-variety genetic variation by using different types of approaches, we compared among-varieties genetic similarity estimated based on individual samples and also on bulked population samples of...
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| Veröffentlicht in: | Breeding Science 2009, Vol.59(4), pp.447-452 |
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| creator | Wakui, K., Tokyo Univ. of Agriculture (Japan). Junior Coll Iwata, H Takahashi, Y Takahata, Y Fujigaki, J |
| description | To find out an efficient and accurate way to estimate the genetic relationship among cultivars having within-variety genetic variation by using different types of approaches, we compared among-varieties genetic similarity estimated based on individual samples and also on bulked population samples of six Japanese turnip (Brassica rapa ssp. rapa) cultivars using RAPD and ISSR markers. In both individual- and bulked-samples-based approaches, 37 individuals were sampled from each cultivar, amplified individually and also as bulked DNA, respectively. Genetic similarity matrices among six cultivars were estimated based on four similarity measures estimated with 125 or 124 polymorphic bands scored in the individual- or bulked-samples-based approach, respectively, and the correlations between the similarity matrices were calculated to evaluate the degree of agreement between matrices. Correlations between similarity matrices calculated based on individuals on the one hand and those calculated based on bulked samples on the other were also high and significant in all combinations of the four similarity measures. Use of computational analysis indicated that 6 to 8 individuals per cultivar were enough to accurately estimate similarity with the individual-based approach. |
| doi_str_mv | 10.1270/jsbbs.59.447 |
| format | Article |
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Junior Coll ; Iwata, H ; Takahashi, Y ; Takahata, Y ; Fujigaki, J</creator><creatorcontrib>Wakui, K., Tokyo Univ. of Agriculture (Japan). Junior Coll ; Iwata, H ; Takahashi, Y ; Takahata, Y ; Fujigaki, J</creatorcontrib><description>To find out an efficient and accurate way to estimate the genetic relationship among cultivars having within-variety genetic variation by using different types of approaches, we compared among-varieties genetic similarity estimated based on individual samples and also on bulked population samples of six Japanese turnip (Brassica rapa ssp. rapa) cultivars using RAPD and ISSR markers. In both individual- and bulked-samples-based approaches, 37 individuals were sampled from each cultivar, amplified individually and also as bulked DNA, respectively. Genetic similarity matrices among six cultivars were estimated based on four similarity measures estimated with 125 or 124 polymorphic bands scored in the individual- or bulked-samples-based approach, respectively, and the correlations between the similarity matrices were calculated to evaluate the degree of agreement between matrices. Correlations between similarity matrices calculated based on individuals on the one hand and those calculated based on bulked samples on the other were also high and significant in all combinations of the four similarity measures. Use of computational analysis indicated that 6 to 8 individuals per cultivar were enough to accurately estimate similarity with the individual-based approach.</description><identifier>ISSN: 1344-7610</identifier><identifier>EISSN: 1347-3735</identifier><identifier>DOI: 10.1270/jsbbs.59.447</identifier><language>eng</language><publisher>Tokyo: Japanese Society of Breeding</publisher><subject>BIOINFORMATICA ; BIOINFORMATICS ; BIOINFORMATIQUE ; BRASSICA CAMPESTRIS ; Brassica rapa ; Brassica rapa ssp. rapa ; Bulked-samples-based approach ; GENETIC MARKERS ; GENETIC VARIATION ; http://www.fao.org/aos/agrovoc#c_1062 ; http://www.fao.org/aos/agrovoc#c_15975 ; http://www.fao.org/aos/agrovoc#c_24030 ; http://www.fao.org/aos/agrovoc#c_36341 ; http://www.fao.org/aos/agrovoc#c_37958 ; Individual-based approach ; Inter-simple sequence repeat (ISSR) ; MARCADORES GENETICOS ; MARQUEUR GENETIQUE ; Random amplified polymorphic DNA (RAPD) ; RAPD ; VARIACION GENETICA ; VARIATION GENETIQUE</subject><ispartof>Breeding Science, 2009, Vol.59(4), pp.447-452</ispartof><rights>2009 by JAPANESE SOCIETY OF BREEDING</rights><rights>Copyright Japan Science and Technology Agency 2009</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c605t-e872d444da68bd8dd4d657116e49722dfde51cd12a99c3eaa6fb792da2a28f823</citedby><cites>FETCH-LOGICAL-c605t-e872d444da68bd8dd4d657116e49722dfde51cd12a99c3eaa6fb792da2a28f823</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,1881,4022,27922,27923,27924</link.rule.ids></links><search><creatorcontrib>Wakui, K., Tokyo Univ. of Agriculture (Japan). Junior Coll</creatorcontrib><creatorcontrib>Iwata, H</creatorcontrib><creatorcontrib>Takahashi, Y</creatorcontrib><creatorcontrib>Takahata, Y</creatorcontrib><creatorcontrib>Fujigaki, J</creatorcontrib><title>Assessment of the congruity of genetic relationships and variation revealed by individual- and bulked-samples-based approaches using RAPD and ISSR markers in Japanese turnip (Brassica rapa ssp. rapa) cultivars</title><title>Breeding Science</title><addtitle>Breeding Science</addtitle><description>To find out an efficient and accurate way to estimate the genetic relationship among cultivars having within-variety genetic variation by using different types of approaches, we compared among-varieties genetic similarity estimated based on individual samples and also on bulked population samples of six Japanese turnip (Brassica rapa ssp. rapa) cultivars using RAPD and ISSR markers. In both individual- and bulked-samples-based approaches, 37 individuals were sampled from each cultivar, amplified individually and also as bulked DNA, respectively. Genetic similarity matrices among six cultivars were estimated based on four similarity measures estimated with 125 or 124 polymorphic bands scored in the individual- or bulked-samples-based approach, respectively, and the correlations between the similarity matrices were calculated to evaluate the degree of agreement between matrices. Correlations between similarity matrices calculated based on individuals on the one hand and those calculated based on bulked samples on the other were also high and significant in all combinations of the four similarity measures. Use of computational analysis indicated that 6 to 8 individuals per cultivar were enough to accurately estimate similarity with the individual-based approach.</description><subject>BIOINFORMATICA</subject><subject>BIOINFORMATICS</subject><subject>BIOINFORMATIQUE</subject><subject>BRASSICA CAMPESTRIS</subject><subject>Brassica rapa</subject><subject>Brassica rapa ssp. rapa</subject><subject>Bulked-samples-based approach</subject><subject>GENETIC MARKERS</subject><subject>GENETIC VARIATION</subject><subject>http://www.fao.org/aos/agrovoc#c_1062</subject><subject>http://www.fao.org/aos/agrovoc#c_15975</subject><subject>http://www.fao.org/aos/agrovoc#c_24030</subject><subject>http://www.fao.org/aos/agrovoc#c_36341</subject><subject>http://www.fao.org/aos/agrovoc#c_37958</subject><subject>Individual-based approach</subject><subject>Inter-simple sequence repeat (ISSR)</subject><subject>MARCADORES GENETICOS</subject><subject>MARQUEUR GENETIQUE</subject><subject>Random amplified polymorphic DNA (RAPD)</subject><subject>RAPD</subject><subject>VARIACION GENETICA</subject><subject>VARIATION GENETIQUE</subject><issn>1344-7610</issn><issn>1347-3735</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><recordid>eNpdkVGL1DAQx4soeJ6--SoEBFG4rkmaNu3jenp6x4HHnT6HaTLtZq_b1ky7sB_Tb2SuK4eYh2SY-c2fmfyT5LXgKyE1_7iluqZVXq2U0k-SE5EpnWY6y58usUp1Ifjz5AXRlnOZc5WfJL_XREi0w35iQ8OmDTI79G2Y_XR4SLTY4-QtC9jB5IeeNn4kBr1jewh-ScXaHqFDx-oD873ze-9m6NKFqufuHl1KsBs7pLQGihyMYxjAbpDYTL5v2e365vOCX97d3bIdhHsMFLXYFYzQIyGb5tD7kb3_FIDIW2AhVhjRuFqiD8zO3eTjTPQyedZAR_jq73ua_Lz48uP8W3r9_evl-fo6tQXPpxRLLZ1SykFR1q50Trki10IUqCotpWsc5sI6IaGqbIYARVPrSjqQIMumlNlp8u6oG3f5NSNNZufJYtfFgYeZjBSyUlVZRPDtf-B2iNvE2YxQhdaaKy0idXakbBiIAjZmDD7-xMEIbh7cNYu7Jq9MdDfi6yO-pQlafIQhRLc6_Ac-XrHnsWY3EAz2UePNUaOBwUAbPJmrG8kFj6fIefYHasK91w</recordid><startdate>2009</startdate><enddate>2009</enddate><creator>Wakui, K., Tokyo Univ. of Agriculture (Japan). Junior Coll</creator><creator>Iwata, H</creator><creator>Takahashi, Y</creator><creator>Takahata, Y</creator><creator>Fujigaki, J</creator><general>Japanese Society of Breeding</general><general>Japan Science and Technology Agency</general><scope>FBQ</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope></search><sort><creationdate>2009</creationdate><title>Assessment of the congruity of genetic relationships and variation revealed by individual- and bulked-samples-based approaches using RAPD and ISSR markers in Japanese turnip (Brassica rapa ssp. rapa) cultivars</title><author>Wakui, K., Tokyo Univ. of Agriculture (Japan). Junior Coll ; Iwata, H ; Takahashi, Y ; Takahata, Y ; Fujigaki, J</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c605t-e872d444da68bd8dd4d657116e49722dfde51cd12a99c3eaa6fb792da2a28f823</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>BIOINFORMATICA</topic><topic>BIOINFORMATICS</topic><topic>BIOINFORMATIQUE</topic><topic>BRASSICA CAMPESTRIS</topic><topic>Brassica rapa</topic><topic>Brassica rapa ssp. rapa</topic><topic>Bulked-samples-based approach</topic><topic>GENETIC MARKERS</topic><topic>GENETIC VARIATION</topic><topic>http://www.fao.org/aos/agrovoc#c_1062</topic><topic>http://www.fao.org/aos/agrovoc#c_15975</topic><topic>http://www.fao.org/aos/agrovoc#c_24030</topic><topic>http://www.fao.org/aos/agrovoc#c_36341</topic><topic>http://www.fao.org/aos/agrovoc#c_37958</topic><topic>Individual-based approach</topic><topic>Inter-simple sequence repeat (ISSR)</topic><topic>MARCADORES GENETICOS</topic><topic>MARQUEUR GENETIQUE</topic><topic>Random amplified polymorphic DNA (RAPD)</topic><topic>RAPD</topic><topic>VARIACION GENETICA</topic><topic>VARIATION GENETIQUE</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wakui, K., Tokyo Univ. of Agriculture (Japan). Junior Coll</creatorcontrib><creatorcontrib>Iwata, H</creatorcontrib><creatorcontrib>Takahashi, Y</creatorcontrib><creatorcontrib>Takahata, Y</creatorcontrib><creatorcontrib>Fujigaki, J</creatorcontrib><collection>AGRIS</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><jtitle>Breeding Science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wakui, K., Tokyo Univ. of Agriculture (Japan). Junior Coll</au><au>Iwata, H</au><au>Takahashi, Y</au><au>Takahata, Y</au><au>Fujigaki, J</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Assessment of the congruity of genetic relationships and variation revealed by individual- and bulked-samples-based approaches using RAPD and ISSR markers in Japanese turnip (Brassica rapa ssp. rapa) cultivars</atitle><jtitle>Breeding Science</jtitle><addtitle>Breeding Science</addtitle><date>2009</date><risdate>2009</risdate><volume>59</volume><issue>4</issue><spage>447</spage><epage>452</epage><pages>447-452</pages><issn>1344-7610</issn><eissn>1347-3735</eissn><abstract>To find out an efficient and accurate way to estimate the genetic relationship among cultivars having within-variety genetic variation by using different types of approaches, we compared among-varieties genetic similarity estimated based on individual samples and also on bulked population samples of six Japanese turnip (Brassica rapa ssp. rapa) cultivars using RAPD and ISSR markers. In both individual- and bulked-samples-based approaches, 37 individuals were sampled from each cultivar, amplified individually and also as bulked DNA, respectively. Genetic similarity matrices among six cultivars were estimated based on four similarity measures estimated with 125 or 124 polymorphic bands scored in the individual- or bulked-samples-based approach, respectively, and the correlations between the similarity matrices were calculated to evaluate the degree of agreement between matrices. Correlations between similarity matrices calculated based on individuals on the one hand and those calculated based on bulked samples on the other were also high and significant in all combinations of the four similarity measures. Use of computational analysis indicated that 6 to 8 individuals per cultivar were enough to accurately estimate similarity with the individual-based approach.</abstract><cop>Tokyo</cop><pub>Japanese Society of Breeding</pub><doi>10.1270/jsbbs.59.447</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | BIOINFORMATICA BIOINFORMATICS BIOINFORMATIQUE BRASSICA CAMPESTRIS Brassica rapa Brassica rapa ssp. rapa Bulked-samples-based approach GENETIC MARKERS GENETIC VARIATION http://www.fao.org/aos/agrovoc#c_1062 http://www.fao.org/aos/agrovoc#c_15975 http://www.fao.org/aos/agrovoc#c_24030 http://www.fao.org/aos/agrovoc#c_36341 http://www.fao.org/aos/agrovoc#c_37958 Individual-based approach Inter-simple sequence repeat (ISSR) MARCADORES GENETICOS MARQUEUR GENETIQUE Random amplified polymorphic DNA (RAPD) RAPD VARIACION GENETICA VARIATION GENETIQUE |
| title | Assessment of the congruity of genetic relationships and variation revealed by individual- and bulked-samples-based approaches using RAPD and ISSR markers in Japanese turnip (Brassica rapa ssp. rapa) cultivars |
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