Linkage Disequilibrium and Persistence of Phase in Five Spanish Local Beef Cattle Breeds

Abstract Text:

We have used the BovineHD Genotyping BeadChip to obtain high density genotypes (>700,000 SNP after quality control) from 116 trios in five Spanish local beef cattle breeds. Linkage disequilibrium (LD) was measured through the r² statistic. Average r² for adjacent markers in the five breeds were very close, around 0.52, and decreased with increasing distance between markers, although in long distances some LD remained (0.07 and 0.05 for markers 200 kb and 1000 kb apart, respectively). At all distances the standard deviations were large and the shape of the distribution varied depending upon the marker distance. Average r² varied also between chromosomes. Pairwise correlations between the r’s estimated in two breeds at short distances (5 kb) was in the rank of 0.6 – 0.7. Similarly to r² estimates, this correlation decreased with increasing marker distance.

Keywords:

beef cattle

linkage disequilibrium

persistence of phase