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.
This study aimed to investigate the genetic variability of conception rate (CR) and non-return rate (NR) in Iranian dairy cows under heat stress conditions. A total of 34,304 records of CR, and NR at 45 days (NR45) and 90 days (NR90) after the first insemination, from 21,405 Holstein cows were included in this study. The weather records were obtained from seven meteorological stations located at a distance of less than 70 km from the farms. Temperature-Humidity Index (THI) was determined for each record on the insemination day. The statistical models for CR, NR45, and NR90 included the fixed effects of herd-yearseason, parity, milk yield, and THI. Genetic components were estimated using an animal model and fitting random regression models on THI based on the Bayesian method. Results showed similar decreasing trends for CR, NR45, and NR90 when increasing the THI levels. The additive genetic variance of heat tolerance for CR, NR45, and NR90 were 0.008 ± 0.0004, 0.0262 ± 0.007, and 0.0254 ± 0.006, respectively. The additive genetic variance of heat tolerance increased directly with THI, and therefore, our findings indicate that a combined selection using heat tolerance can be considered for genetic evaluation of reproduction traits under heat stress conditions.
Extensively grazed cattle are often mustered only once a year. Therefore, birthdates are typically unknown or inaccurate. Birthdates would be useful for deriving important traits (growth rate; calving interval), breed registrations, and making management decisions. Epigenetic clocks use methylation of DNA to predict an individual’s age. An epigenetic clock for cattle could provide a solution to the challenges of industry birthdate recording. Here we derived the first epigenetic clock for tropically adapted cattle using portable sequencing devices from tail hair, a tissue which is widely used in industry for genotyping. Cattle (n = 66) with ages ranging from 0.35 to 15.7 years were sequenced using Oxford Nanopore Technologies MinION and methylation was called at CpG sites across the genome. Sites were then filtered and used to calculate a covariance relationship matrix based on methylation state. Best linear unbiased prediction was used with 10-fold cross validation to predict age. A second methylation relationship matrix was also calculated that contained sites associated with genes used in the dog and human epigenetic clocks. The correlation between predicted age and actual age was 0.71 for all sites and 0.60 for dog and human gene epigenetic clock sites. The mean absolute deviation was 1.4 years for animals aged less than 3 years of age, and 1.5 years for animals aged 3–10 years. This is the first reported epigenetic clock using industry relevant samples in cattle.
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