Linkage disequilibrium and haplotype block structure in Limousin, Simmental and native Polish Red cattle

- Differences in level of LD were found between commercial and native breeds.
- Shorter haplotype block structure in Polish Red than in both commercial breeds.
- Population history and breeding schemes may influence patterns of LD.

The aim of this study was to characterize in detail linkage disequilibrium (LD) decay and haplotype block structures in genomes of commercial Limousin (LM, n=201) and Simmental (SM, n=106) cattle and refer this data to the characteristics found in native unselected Polish Red (PR, n=299) cattle. A panel of 40,158 (LM), 40,117 (SM) and 42,118 (PR) high quality SNP (single nucleotide polymorphism) markers from Illumina BovineSNP50 v2 BeadChip were utilized for the LD analysis based on the pairwise r2 statistic of SNPs at a distance up to 5 Mb. The lower average r2 of 0.27 was observed in RP cattle at a short distance up to 25 kb when compared to two other studied breeds (0.3 in both LM and SM). The minimum average values of r2 (0.01) were observed at the distances of 1500-3000 kb in LM and 3000-5000 kb in SM. In PR cattle LD persisted similarly as in SM cattle and the minimum average values of r2 (0.02) were observed at a distance of 3000-5000 kb. The effects of minor allelic frequency threshold on the extent of LD was also evaluated by applying three different minimum MAF levels (0.05, 0.1 and 0.2). A total of 828 (LM), 667 (SM) and 761 (PR) haplotype block structures spanning 89,781 kb (LM), 72,582 kb (SM) and 70,647 kb (PR) of the genome were detected. In total, 7.92% (LM), 6.43% (SM) and 6.52% (PR) of all SNPs formed blocks with a range of 2-15 SNPs per block in LM and SM breeds and 2-16 SNPs per block in PR cattle. Mean block lengths were slightly lower in RP cattle than in two other breeds and were estimated as 108.4±99 kb, 108.8±97 kb and 92.8±87 for LM, SM and PR respectively. For all studied breeds chromosome 1 showed the longest haplotype block structures in the genome, having 66 blocks spanning 8120 kb in LM, 57 blocks spanning 6754 kb in SM and 59 blocks spanning 5920 kb in PR. The results showed slightly faster LD decay in Polish Red cattle (especially at short distances) than in two other breeds and shorter haplotype block structures which may result from population demographic history, overall genetic diversity as well as extensive breeding applied in this breed.