The effects of increased pedigree inbreeding in dairy cattle populations have been well documented and result in a negative impact on profitability. Recent advances in genotyping technology have allowed researchers to move beyond pedigree analysis and study inbreeding at a molecular level. In this study, 5,853 animals were genotyped for 54,001 single nucleotide polymorphisms (SNP); 2,913 cows had phenotypic records including a single lactation for milk yield (from either lactation 1, 2, 3, or 4), reproductive performance, and linear type conformation. After removing SNP with poor call rates, low minor allele frequencies, and departure from Hardy-Weinberg equilibrium, 33,025 SNP remained for analyses. Three measures of genomic inbreeding were evaluated: percent homozygosity (FPH), inbreeding calculated from runs of homozygosity (FROH), and inbreeding derived from a genomic relationship matrix (FGRM). Average FPH was 60.5±1.1%, average FROH was 3.8±2.1%, and average FGRM was 20.8±2.3%, where animals with larger values for each of the genomic inbreeding indices were considered more inbred. Decreases in total milk yield to 205d postpartum of 53, 20, and 47kg per 1% increase in FPH, FROH, and FGRM, respectively, were observed. Increases in days open per 1% increase in FPH (1.76 d), FROH (1.72 d), and FGRM (1.06 d) were also noted, as well as increases in maternal calving difficulty (0.09, 0.03, and 0.04 on a 5-point scale for FPH, FROH, and FGRM, respectively). Several linear type traits, such as strength (-0.40, -0.11, and -0.19), rear legs rear view (-0.35, -0.16, and -0.14), front teat placement (0.35, 0.25, 0.18), and teat length (-0.24, -0.14, and -0.13) were also affected by increases in FPH, FROH, and FGRM, respectively. Overall, increases in each measure of genomic inbreeding in this study were associated with negative effects on production and reproductive ability in dairy cows.
Genetic evaluation of sires for functional longevity of their daughters based on survival analysis has been implemented in the populations of Braunvieh, Simmental, and Holstein cattle in Switzerland. A Weibull mixed sire-maternal grandsire survival model was used to estimate breeding values of sires with data on cows that calved since April 1, 1980. Data on Braunvieh and Simmental cows included about 1.1 million records, data on Holstein cows comprised about 220,000 records. Data contained approximately 20 to 24% right-censored records and 6 to 9% left-truncated records. Besides the random sire and maternal grandsire effects, the model included effects of herd-year-season, age at first calving, parity, stage of lactation, alpine pasturing (Braunvieh and Simmental), and relative milk yield and relative fat and protein percentage within herd to account for culling for production. Heritability of functional longevity, estimated on a subset of data including approximately 150,000 animals, were 0.181, 0.198, and 0.184 for Braunvieh, Simmental, and Holstein, respectively. Breeding values were estimated for all sires with at least six daughters or three granddaughters in the data. Breeding values of sires are expressed in months of functional productive life and published in sire catalogs along with breeding values for production traits.
In March 2016, Zoetis Genetics offered the first commercially available evaluation for wellness traits of Holstein dairy cattle. Phenotypic data on health events, pedigree, and genotypes were collected directly from producers upon obtaining their permission. Among all recorded health events, 6 traits were chosen to be included in the evaluation: mastitis, metritis, retained placenta, displaced abomasum, ketosis, and lameness. Each trait was defined as a binary event, having a value of 1 if a cow has been recorded with a disorder at any point during the lactation and zero otherwise. The number of phenotypic records ranged from 1.8 million for ketosis to 4.1 million for mastitis. Over 14 million pedigree records and 114,216 genotypes were included in the evaluation. All traits were analyzed using univariate threshold animal model with repeated observations, including fixed effect of parity and random effects of herd by year by season of calving, animal, and permanent environment. A total of 45,425 single nucleotide polymorphisms were used in the genomic analyses. Animals genotyped with low-density chips were imputed to the required number of single nucleotide polymorphisms. All analyses were based on the single-step genomic BLUP, a method that combines phenotype, pedigree, and genotype information. Predicted transmitting abilities were expressed in percentage points as a difference from the average estimated probability of a disorder in the base population. Reliabilities of breeding values were obtained by approximation based on partitioning of a function of reliability into contributions from records, pedigree, and genotypes. Reliabilities of genomic predicted transmitting abilities for young genotyped and pedigreed females without recorded health events had average values between 50.2% (displaced abomasum) and 51.9% (mastitis). Genomic predictions for wellness traits can provide new information about an animal's genetic potential for health and new selection tools for dairy wellness improvement.
Reducing calf morbidity and mortality is important for attaining financial sustainability and improving animal welfare on commercial dairy operations. Zoetis (Kalamazoo, MI) has developed genomic predictions for calf wellness traits in Holsteins that include calf respiratory disease (RESP; recorded between 0 and 365 d of age), calf scours (DIAR; recorded between 2 and 50 d of age), and calf livability (DEAD; recorded between 2 and 365 d of age). Phenotype and pedigree data were from commercial dairies and provided directly by producers upon obtaining their permission. The number of records ranged from 741,484 for DIAR to 1,926,261 for DEAD. The number of genotyped animals was 325,025. All traits were analyzed using a univariate threshold animal model including fixed effect of year of birth × calving season × region, and random effects of herd × year of birth and animal. A total of 45,425 SNP were used in genomic analyses. Animals genotyped with low-density chips were imputed to the required number of SNP. All analyses were conducted using single-step genomic BLUP implementing the "algorithm for proven and young" (APY) animals designed to accommodate very large numbers of genotypes. Estimated heritabilities were 0.042, 0.045, and 0.060 for RESP, DIAR, and DEAD, respectively. The genomic predicted transmitting abilities ranged between −8.0 and 24.0, −11.5 and 28.5, and −6.5 to 22.8 for RESP, DIAR, and DEAD, respectively. Reliabilities of breeding values were obtained by approximation based on partitioning of a function of reliability into contributions from records, pedigree, and genotypes, where the genotype contribution was approximated using the diagonal value of the genomic relationship matrix. The average reliabilities for the genotyped animals were 41.9, 42.6, and 47.3% for RESP, DIAR, and DEAD, respectively. Estimated genomic predicted transmitting abilities and reliabilities were approximately normally distributed for all analyzed traits. Approximated genetic correlations of calf wellness with Zoetis dairy wellness traits and traits included in the US national genetic evaluation were low to moderate. The results indicate that direct evaluation of calf wellness traits under a genomic threshold model is feasible and offers predictions with average reliabilities comparable to other lowly heritable traits. Genetic selection for calf wellness traits presents a compelling opportunity for dairy producers to help manage herd replacement costs and improve overall profitability.
An analysis of productive life of Swiss Brown cattle was performed using a mixed survival model based on Cox regression. Data included 52,862 daughters of 297 sires. The length of productive life was observed from May 1, 1985 through August 15, 1995. Records on cows that were still alive in the end of study (32.4%) were treated as censored. The probability of being culled (hazard) was defined as a product of a baseline hazard function and a function of explanatory variables. In addition to sire effects, the model included effects of age at first calving and the time-dependent variables herd by year, lactation number, stage of lactation, and milk production within the herd to account for culling because of low production. Solutions for fixed effects indicated a higher probability of being culled for primiparous cows, for cows in the end stage of lactation, and for cows with low production. The impact of censoring on the accuracy of estimation was investigated by computing the rank correlations between the estimated transmitting abilities (ETA) of sires using a simplified model from uncensored data (reference) and the ETA from several different data files with an increased proportion of censored records. The rank correlations among sire ETA decreased as number of daughters per sire decreased and as the proportion of censored records increased. The maximum number of censored records that is acceptable to obtain accurate results is 30 to 40%. The acceptable proportion of censored records would be higher if the reference ETA were obtained on a larger data file using daughters of old sires.
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