BackgroundWhile autozygosity as a consequence of selection is well understood, there is limited information on the ability of different methods to measure true inbreeding. In the present study, a gene dropping simulation was performed and inbreeding estimates based on runs of homozygosity (ROH), pedigree, and the genomic relationship matrix were compared to true inbreeding. Inbreeding based on ROH was estimated using SNP1101, PLINK, and BCFtools software with different threshold parameters. The effects of different selection methods on ROH patterns were also compared. Furthermore, inbreeding coefficients were estimated in a sample of genotyped North American Holstein animals born from 1990 to 2016 using 50 k chip data and ROH patterns were assessed before and after genomic selection.ResultsUsing ROH with a minimum window size of 20 to 50 using SNP1101 provided the closest estimates to true inbreeding in simulation study. Pedigree inbreeding tended to underestimate true inbreeding, and results for genomic inbreeding varied depending on assumptions about base allele frequencies. Using an ROH approach also made it possible to assess the effect of population structure and selection on distribution of runs of autozygosity across the genome. In the simulation, the longest individual ROH and the largest average length of ROH were observed when selection was based on best linear unbiased prediction (BLUP), whereas genomic selection showed the largest number of small ROH compared to BLUP estimated breeding values (BLUP-EBV). In North American Holsteins, the average number of ROH segments of 1 Mb or more per individual increased from 57 in 1990 to 82 in 2016. The rate of increase in the last 5 years was almost double that of previous 5 year periods. Genomic selection results in less autozygosity per generation, but more per year given the reduced generation interval.ConclusionsThis study shows that existing software based on the measurement of ROH can accurately identify autozygosity across the genome, provided appropriate threshold parameters are used. Our results show how different selection strategies affect the distribution of ROH, and how the distribution of ROH has changed in the North American dairy cattle population over the last 25 years.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4453-z) contains supplementary material, which is available to authorized users.

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Recent studies demonstrated a high antioxidant capacity for pomegranate components due to their rich bioactive compounds, such as conjugated fatty acids and phenolics. The objective of the present study was, therefore, to assess whether pomegranate seed or pomegranate seed pulp (peel + seed) supplementation could be effective to improve antioxidant status, and hence metabolic profile and performance in periparturient dairy cows. After a 1-wk pretreatment period, Holstein cows (primiparous n = 12, multiparous n = 18) were assigned to 3 dietary treatments from 25 d before expected calving through 25 d postcalving. The dietary treatments included (1) control (CON); (2) diet supplemented with pomegranate seeds (PS; 400 g/cow per day); and (3) diet supplemented with pomegranate seed pulp (PSP; 400 g of seeds/cow per day + 1200 g of peels/cow per day). Compared with CON, supplementation with either PS or PSP had no effects on dry matter intake, rumen fermentation, and plasma concentrations of cholesterol, total protein, globulin, and aspartate amino transferase, but enhanced plasma total antioxidant activity, and lowered triacylglycerol, free fatty acids (FFA), and β-hydroxybutyrate at both pre-and postpartum periods. Plasma concentration of glucose, albumin, malondialdehyde (MDA) and blood superoxide dismutase (SOD) activity were not affected by dietary treatments at prepartum, whereas SOD activity increased and glucose, albumin, MDA, and FFAto-albumin ratio decreased by feeding both by-products at postpartum period. In contrast to PS, supplementing PSP resulted in a greater decrease in plasma glucose and triacylglycerol concentration and higher increase in SOD activity. Energy-and fat-corrected milk yields were higher in cows fed PSP diet compared with those fed CON or PS diets, but content of milk fat, protein, and lactose were similar across the dietary treatments. These findings indicated that dietary pomegranate byproducts supplementation, in particular PSP, could improve antioxidant status, which was associated with a decline in lipid oxidation (FFA and β-hydroxybutyrate) and peroxidation (MDA) and an enhancement in glucose utilization as well as fat-corrected milk yield.