Evaluation of genetic diversity and linkage disequilibrium in Korean-bred rice varieties using SSR markers
Background: In order to evaluate the variation among different rice types, the genetic diversity in a rice collection composed by 59 breeding lines, 23 landraces, 18 weedy rice lines, and 35 introduced lines that collected from countries worldwide was analyzed using 134 simple sequence repeat marker...
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Pontificia Universidad Católica de Valparaíso
2013
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oai:scielo:S0717-345820130005000112014-09-17Evaluation of genetic diversity and linkage disequilibrium in Korean-bred rice varieties using SSR markersWang,Xiao-QiangKwon,Soon-WookPark,Yong-Jin landraces linkage disequilibrium population structure rice simple sequence repeats Background: In order to evaluate the variation among different rice types, the genetic diversity in a rice collection composed by 59 breeding lines, 23 landraces, 18 weedy rice lines, and 35 introduced lines that collected from countries worldwide was analyzed using 134 simple sequence repeat markers. Results: In total, 1264 alleles were identified (average, 9.43 per locus). Rare alleles made up a large portion (58.4%) of the detected alleles, and 29 unique alleles associated with rice accessions were also discovered. A model-based structural analysis revealed the presence of three subpopulations. The genetic relationships revealed by the neighbour-joining tree method were fairly consistent with the structure-based membership assignments for most of the accessions. A total of 105 accessions (79.5%) showed a clear relationship to each cluster, while the remaining 27 accessions (20.5%) were categorized as admixtures. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide association mapping. The mean r² value for all intrachromosomal loci pairs was 0.1286. The LD between linked markers decreased with the genetic distance between pairs of linked loci. Conclusions: These results will provide an effective aid for future allele mining, association genetics, mapping and cloning gene(s), germplasm conservation, and improvement programs.info:eu-repo/semantics/openAccessPontificia Universidad Católica de ValparaísoElectronic Journal of Biotechnology v.16 n.5 20132013-09-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582013000500011en10.2225/vol16-issue5-fulltext-6 |
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Scielo Chile |
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Scielo Chile |
| language |
English |
| topic |
landraces linkage disequilibrium population structure rice simple sequence repeats |
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landraces linkage disequilibrium population structure rice simple sequence repeats Wang,Xiao-Qiang Kwon,Soon-Wook Park,Yong-Jin Evaluation of genetic diversity and linkage disequilibrium in Korean-bred rice varieties using SSR markers |
| description |
Background: In order to evaluate the variation among different rice types, the genetic diversity in a rice collection composed by 59 breeding lines, 23 landraces, 18 weedy rice lines, and 35 introduced lines that collected from countries worldwide was analyzed using 134 simple sequence repeat markers. Results: In total, 1264 alleles were identified (average, 9.43 per locus). Rare alleles made up a large portion (58.4%) of the detected alleles, and 29 unique alleles associated with rice accessions were also discovered. A model-based structural analysis revealed the presence of three subpopulations. The genetic relationships revealed by the neighbour-joining tree method were fairly consistent with the structure-based membership assignments for most of the accessions. A total of 105 accessions (79.5%) showed a clear relationship to each cluster, while the remaining 27 accessions (20.5%) were categorized as admixtures. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide association mapping. The mean r² value for all intrachromosomal loci pairs was 0.1286. The LD between linked markers decreased with the genetic distance between pairs of linked loci. Conclusions: These results will provide an effective aid for future allele mining, association genetics, mapping and cloning gene(s), germplasm conservation, and improvement programs. |
| author |
Wang,Xiao-Qiang Kwon,Soon-Wook Park,Yong-Jin |
| author_facet |
Wang,Xiao-Qiang Kwon,Soon-Wook Park,Yong-Jin |
| author_sort |
Wang,Xiao-Qiang |
| title |
Evaluation of genetic diversity and linkage disequilibrium in Korean-bred rice varieties using SSR markers |
| title_short |
Evaluation of genetic diversity and linkage disequilibrium in Korean-bred rice varieties using SSR markers |
| title_full |
Evaluation of genetic diversity and linkage disequilibrium in Korean-bred rice varieties using SSR markers |
| title_fullStr |
Evaluation of genetic diversity and linkage disequilibrium in Korean-bred rice varieties using SSR markers |
| title_full_unstemmed |
Evaluation of genetic diversity and linkage disequilibrium in Korean-bred rice varieties using SSR markers |
| title_sort |
evaluation of genetic diversity and linkage disequilibrium in korean-bred rice varieties using ssr markers |
| publisher |
Pontificia Universidad Católica de Valparaíso |
| publishDate |
2013 |
| url |
http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582013000500011 |
| work_keys_str_mv |
AT wangxiaoqiang evaluationofgeneticdiversityandlinkagedisequilibriuminkoreanbredricevarietiesusingssrmarkers AT kwonsoonwook evaluationofgeneticdiversityandlinkagedisequilibriuminkoreanbredricevarietiesusingssrmarkers AT parkyongjin evaluationofgeneticdiversityandlinkagedisequilibriuminkoreanbredricevarietiesusingssrmarkers |
| _version_ |
1718441880449974272 |