Genome-wide and local pattern of linkage disequilibrium and persistence of phase for 3 Danish pig breeds

Background: The extent of linkage disequilibrium (LD) is of critical importance for genomic selection and marker assisted selection. The primary purpose of this study is to examine patterns of LD in three Danish pig breeds (Duroc, Landrace and Yorkshire); we also examine patterns of persistence of phase between the breeds. We quantify local LD by fitting a model relating LD to physical distance between markers in sliding windows, and use this to visualize how LD varies according to physical position. We use a similar method to examine local persistence of phase. Results: Average LD decay over distance for Duroc was significantly different from Landrace and Yorkshire, that showed similar patterns. Persistence of phase between Landrace and Yorkshire was much higher than between these breeds and Duroc. Local r(2) over the chromosomes showed more variation between breeds than average r(2) decay across whole genome. Also local persistence of phase was higher between Landrace and Yorkshire than between these breeds and Duroc. Conclusions: The results concerning genome-wide LD indicated that Duroc had old inbreeding, and confirmed the mixture history of Landrace and Yorkshire, which is also implied by the higher level of persistence of phase between Landrace and Yorkshire. The method to estimate and visualize local pattern of LD and persistence of phase provides insight into how these quantities vary along chromosomes and between breeds.