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Controlling inbreeding in livestock populations is of great importance because excess relatedness among animals leads to a rapid loss of genetic variation and to adverse phenotypical effects associated with an inbreeding depression. Recent advances in genotyping technology have made it possible to study inbreeding at a molecular level by the analysis of genome-wide single nucleotide polymorphism panels. In this study, we used BovineSNP50 assay (Illumina) to estimate genomic inbreeding coefficient in 298 Holstein cattle by the analysis of the genome portion in runs of homozygosity (F) or using genomic relationship matrix (F), and compared this data with conventional pedigree-based inbreeding coefficients (F). Weak or moderate Spearman's rank correlations were observed between F and F which depended on the ROH length categories used for calculations and inclusion of animals with different number of complete generations registered in pedigrees. The highest correlations were observed when using ROH with lengths over 8 Mb (0.334). The correlations tended to increase as pedigree depth increased, and were the highest for animals with seven complete generations of pedigree data. F correlated poorly with pedigree-based estimates, which suggests that ROH-based inbreeding coefficients better reflect recent relatedness among animals. [ABSTRACT FROM AUTHOR]

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 r 2 statistic of SNPs at a distance up to 5 Mb. The lower average r 2 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 r 2 (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 r 2 (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. [ABSTRACT FROM AUTHOR]

The study is aimed at identifying selection footprints within the genome of Limousin cattle. With the use of Extended Haplotype Homozygosity test, supplemented with correction for variation in recombination rates across the genome, we created map of selection footprints and detected 173 significant (p < 0.01) core haplotypes being potentially under positive selection. Within these regions, a number of candidate genes associated inter alia with skeletal muscle growth ( GDF15, BMP7, BMP4 and TGFB3) or postmortem proteolysis and meat maturation ( CAPN1 and CAPN5) were annotated. Noticeable clusters of selection footprints were detected on chromosomes 1, 4, 8 and 14, which are known to carry several quantitative trait loci for growth traits and meat quality. The study provides information about the genes and metabolic pathways potentially modified under the influence of directional selection, aimed at improving beef production characteristics in Limousin cattle. [ABSTRACT FROM AUTHOR]

• Differences in level of LD were found between breeds representing different horse types. • Breeds representing the same horse type showed similar trends of historical N e. • Longer haplotype block structure was found in Arabian breed than in native horse breeds. • Population history and breeding schemes may influence patterns of LD. This study was conducted to investigate linkage disequilibrium (LD), historical effective population size (N e) and haplotype block structures in genomes of highly selected Polish Arabian (AR; n=124) horses and conserved horse breeds derived from Polish native breeds, in particular, Malopolski (MLP; n=56), Sokolski (SOK; n=107), Sztumski (SZTUM; n=69), Hucul (HC; n=116) and Polish Konik (KN; n=99) horses, based on single nucleotide polymorphisms (SNPs) from the Neogen Equine Community BeadChip assay (Illumina, San Diego, CA). LD analysis was performed based on the pairwise r2 statistic of SNPs at a distance up to 5Mb. At a short distance, up to 100kb, the lower average r2 was observed in SOK (0.09) and SZTUM (0.10) breeds, representing draft horse type, and the highest average r2 was observed in AR (0.19) and MLP (0.17) breeds, representing light horse type. At a distance of 4-5Mb, the average values of r2 were 0.03 for HC and KN, 0.02 for AR and MLP and 0.01 for SOK and SZTUM. About 100 generations ago, effective population size (N e) ranged from 518 (SOK) to 310 (AR) and five generations ago from 85 (SOK) to 40 (HC). A total of 6,162 (AR), 5,792 (MLP), 5,744 (HC), 5,429 (KN), 5,542 (SOK) and 4,848 (SZTUM) haplotype block structures, spanning 656.2Mb (AR), 439.4Mb (MLP), 381.2Mb (HC), 344.3 (KN), 206.7 (SOK) and 171.0Mb (SZTUM) of the genome were detected. Mean block lengths were estimated as 106.5±138kb, 75.9±120kb, 66.4±109kb, 63.4±109kb, 37.3±80kb and 35.3±81kb for AR, MLP, HC, KN, SOK and SZTUM, respectively. A visible similarity in the decay of LD across the genome, as well as in trends of historical N e, were found for breeds representing the same horse type. Differences in the span of haplotype block structures were found between AR and Polish native horse breeds, which may reflect different demographic population histories and differences in intensity of selection. [ABSTRACT FROM AUTHOR]