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Extent and structure of linkage disequilibrium in canola quality winter rapeseed (Brassica napus L.)
Linkage disequilibrium was investigated in canola quality winter rapeseed to analyze (1) the prospects for whole-genome association analyses and (2) the impact of the recent breeding history of rapeseed on linkage disequilibrium. A total of 845 mapped AFLP markers with allele frequencies ≥0.1 were u...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
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Springer-Verlag
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820662/ https://www.ncbi.nlm.nih.gov/pubmed/19953219 http://dx.doi.org/10.1007/s00122-009-1221-0 |
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author | Ecke, Wolfgang Clemens, Rosemarie Honsdorf, Nora Becker, Heiko C. |
author_facet | Ecke, Wolfgang Clemens, Rosemarie Honsdorf, Nora Becker, Heiko C. |
author_sort | Ecke, Wolfgang |
collection | PubMed |
description | Linkage disequilibrium was investigated in canola quality winter rapeseed to analyze (1) the prospects for whole-genome association analyses and (2) the impact of the recent breeding history of rapeseed on linkage disequilibrium. A total of 845 mapped AFLP markers with allele frequencies ≥0.1 were used for the analysis of linkage disequilibrium in a population of 85 canola quality winter rapeseed genotypes. A low overall level of linkage disequilibrium was found with a mean r (2) of only 0.027 over all 356,590 possible marker pairs. At a significance threshold of P = 2.8 × 10(−7), which was derived by a Bonferroni correction from a global α-level of 0.1, only 0.78% of the marker pairs were in significant linkage disequilibrium. Among physically linked marker pairs, the level of linkage disequilibrium was about five times higher with more than 10% of marker pairs in significant linkage disequilibrium. Linkage disequilibrium decayed rapidly with distance between linked markers with high levels of linkage disequilibrium extending only for about 2 cM. Owing to the rapid decay of linkage disequilibrium with distance association analyses in canola quality rapeseed will have a significantly higher resolution than QTL analyses in segregating populations by interval mapping, but much larger number of markers will be necessary to cover the whole genome. A major impact of the recent breeding history of rapeseed on linkage disequilibrium could not be observed. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00122-009-1221-0) contains supplementary material, which is available to authorized users. |
format | Text |
id | pubmed-2820662 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Springer-Verlag |
record_format | MEDLINE/PubMed |
spelling | pubmed-28206622010-02-19 Extent and structure of linkage disequilibrium in canola quality winter rapeseed (Brassica napus L.) Ecke, Wolfgang Clemens, Rosemarie Honsdorf, Nora Becker, Heiko C. Theor Appl Genet Original Paper Linkage disequilibrium was investigated in canola quality winter rapeseed to analyze (1) the prospects for whole-genome association analyses and (2) the impact of the recent breeding history of rapeseed on linkage disequilibrium. A total of 845 mapped AFLP markers with allele frequencies ≥0.1 were used for the analysis of linkage disequilibrium in a population of 85 canola quality winter rapeseed genotypes. A low overall level of linkage disequilibrium was found with a mean r (2) of only 0.027 over all 356,590 possible marker pairs. At a significance threshold of P = 2.8 × 10(−7), which was derived by a Bonferroni correction from a global α-level of 0.1, only 0.78% of the marker pairs were in significant linkage disequilibrium. Among physically linked marker pairs, the level of linkage disequilibrium was about five times higher with more than 10% of marker pairs in significant linkage disequilibrium. Linkage disequilibrium decayed rapidly with distance between linked markers with high levels of linkage disequilibrium extending only for about 2 cM. Owing to the rapid decay of linkage disequilibrium with distance association analyses in canola quality rapeseed will have a significantly higher resolution than QTL analyses in segregating populations by interval mapping, but much larger number of markers will be necessary to cover the whole genome. A major impact of the recent breeding history of rapeseed on linkage disequilibrium could not be observed. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00122-009-1221-0) contains supplementary material, which is available to authorized users. Springer-Verlag 2009-12-02 2010 /pmc/articles/PMC2820662/ /pubmed/19953219 http://dx.doi.org/10.1007/s00122-009-1221-0 Text en © The Author(s) 2009 https://creativecommons.org/licenses/by-nc/4.0/ This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. |
spellingShingle | Original Paper Ecke, Wolfgang Clemens, Rosemarie Honsdorf, Nora Becker, Heiko C. Extent and structure of linkage disequilibrium in canola quality winter rapeseed (Brassica napus L.) |
title | Extent and structure of linkage disequilibrium in canola quality winter rapeseed (Brassica napus L.) |
title_full | Extent and structure of linkage disequilibrium in canola quality winter rapeseed (Brassica napus L.) |
title_fullStr | Extent and structure of linkage disequilibrium in canola quality winter rapeseed (Brassica napus L.) |
title_full_unstemmed | Extent and structure of linkage disequilibrium in canola quality winter rapeseed (Brassica napus L.) |
title_short | Extent and structure of linkage disequilibrium in canola quality winter rapeseed (Brassica napus L.) |
title_sort | extent and structure of linkage disequilibrium in canola quality winter rapeseed (brassica napus l.) |
topic | Original Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820662/ https://www.ncbi.nlm.nih.gov/pubmed/19953219 http://dx.doi.org/10.1007/s00122-009-1221-0 |
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