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 >or=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 x 10(-7), which was derived by a Bonferroni correction from a global alpha-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.
Ecke
Wolfgang
W
Department of Crop Sciences, Georg-August-University Göttingen, Von-Siebold-Str. 8, 37075, Göttingen, Germany. wecke@gwdg.de
Clemens
Rosemarie
R
Honsdorf
Nora
N
Becker
Heiko C
HC
D054458:Amplified Fragment Length Polymorphism Analysis; D029688:Brassica napus / Q000235:genetics* / Q000378:metabolism; D018556:Crops, Agricultural / Q000235:genetics; D005229:Fatty Acids, Monounsaturated / Q000378:metabolism; D005819:Genetic Markers; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D015810:Linkage Disequilibrium; D040641:Quantitative Trait Loci; D000074262:Rapeseed Oil; D011995:Recombination, Genetic
D005229:Fatty Acids, Monounsaturated; D005819:Genetic Markers; D000074262:Rapeseed Oil