Extent and structure of linkage disequilibrium in canola quality winter rapeseed (Brassica napus L.)

Abstract

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.

Fig. 1

Relationship between marker distance and linkage disequilibrium. a Number of marker pairs at different distances. b Average linkage disequilibrium and fraction of marker pairs in significant LD at different distances. Distances between markers of physically linked pairs are given as recombination rates determined in the mapping population and rounded to full percentages. Average linkage disequilibrium is presented as the mean r ² of all linked marker pairs at a given recombination rate

Fig. 2

LD maps of individual linkage groups of the genetic map. a LD map of linkage group N1. b Segment of the LD map of linkage group N5. Below the diagonal the level of linkage disequilibrium between individual marker pairs is indicated, above the diagonal the significance level of the linkage disequilibrium (P = 2.8 × 10⁻⁷, P = 1.4 × 10⁻⁷, not significant). Groups of co-segregating markers are framed in green