ABSTRACT: BACKGROUND: The success of marker assisted selection depends<br />on the amount of linkage disequilibrium (LD) across the genome. To<br />implement marker assisted selection in the swine breeding industry,<br />information about extent and degree of LD is essential. The objective<br />of this study is to estimate LD in four US breeds of pigs (Duroc,<br />Hampshire, Landrace, and Yorkshire) and subsequently calculate persistence<br />of phase among them using a 60k SNP panel. In addition, we report<br />LD when using only a fraction of the available markers, to estimate<br />persistence of LD over distance. RESULTS: Average r2 between adjacent<br />SNP across all chromosomes was 0.36 for Landrace, 0.39 for Yorkshire,<br />0.44 for Hampshire and 0.46 for Duroc. For markers 1 Mb apart, r2<br />ranged from 0.15 for Landrace to 0.20 for Hampshire. Reducing the<br />marker panel to 10% of its original density, average r2 ranged between<br />0.20 for Landrace to 0.25 for Duroc. We also estimated persistence<br />of phase as a measure of prediction reliability of markers in one<br />breed by those in another and found that markers less than 10 kb<br />apart could be predicted with a maximal accuracy of 0.92 for Landrace<br />with Yorkshire. CONCLUSIONS: Our estimates of LD, although in good<br />agreement with previous reports, are more comprehensive and based<br />on a larger panel of markers. Our estimates also confirmed earlier<br />findings reporting higher LD in pigs than in American Holstein cattle,<br />especially at increasing marker distances (>1 Mb). High average LD<br />(r2>0.4) between adjacent SNP found in this study is an important<br />precursor for the implementation of marker assisted selection within<br />a livestock species. Results of this study are relevant to the US<br />purebred pig industry and critical for the design of programs of<br />whole genome marker assisted evaluation and selection. In addition,<br />results indicate that a more cost efficient implementation of marker<br />assisted selection using low density panels with genotype imputation,<br />would be feasible for these breeds.
Badke, Y. M., Bates, R. O., Ernst, C. W., Schwab, C., & Steibel, J. P. (2012). Estimation of linkage disequilibrium in four US pig breeds. BMC Genomics, 13(1). https://doi.org/10.1186/1471-2164-13-24