Second Generation of High Resolution Haplotype Block Structure in the Cattle Genome

In a second generation of high resolution haplotype block and LD analysis in the Cattle genome, 503 samples from 20 different breeds where genotyped with the BovineHD Beadchip, which interrogates 777,000 SNPs. The analysis focused on chromosomes 1, 6, 14, and 25, containing 46492, 35512, 24774, and 12931 SNPs, respectively. Haplotype blocks were estimated based on r². In summary, the average maximum number of markers per block was 68.79. The mean block size varied from 7.81 to 13.25 kb across breeds (with a mean block size of 10.25 kb over all breeds) and an average of 4.65 markers per block. The analysis also includes: linkage disequilibrium within and between breeds, breeds differentiation based on haplotype sharing and haplotype block boundary discordances, and effective population size estimations.