Study of Genomic Structure and Signatures of Recent Positive Selection in Cattle

We used DNA samples of 810 German Holstein–Friesian cattle genotyped by the Illumina Bovine SNP50K BeadChip to analyze linkage disequilibrium (LD) structure. A panel of 40’854 (75.65%) markers was included into the final analysis. The pair-wise r statistic of SNPs apart up to 5Mbp across the genome was estimated. A mean value of r =0.30 ± 0.32 was observed in pair-wise distances of <25 Kb and it dropped to 0.20 ± 0.24 at 50 to 75 Kb, which is nearly the average inter-marker space in this study. The proportion of SNPs in useful LD was 26% for the distance of 50 and 75 Kb between SNPs. We found a lower level of LD for SNP pairs at the distance ≤100 Kb than previously thought. Analysis revealed 712 haplo-blocks spanning 4.6 % of the genome. Mean and median block length were estimated as 164. ± 117.1 and 144 Kb, respectively. Analysis of effective population size based on the direct estimates of recombination rates from SNP data showed a decline in effective population size to 103 up to ~4 generation ago. The impact of allele frequency in analyzing genome-wide LD was also explored in this study. The observations revealed that minimizing the allele frequency difference between SNPs, reduces the influence of frequency on r estimates. This study presents a second generation of LD map statistics for the Holstein genome which has four times higher resolution compared to the maps available so far. 2 nd Chapter LD Pattern 29