Changes in genetic trends in US dairy cattle since the implementation of genomic selection.

Genomic selection increases accuracy and decreases generation interval, accelerating genetic changes in populations. Assumptions of genetic improvement must be addressed to quantify the magnitude and direction of change. Genetic trends of US dairy cattle breeds were examined to determine the genetic gain since the implementation of genomic evaluations in 2009. Inbreeding levels and generation intervals were also investigated. Breeds included Ayrshire, Brown Swiss, Guernsey, Holstein (HO), and Jersey (JE), which were characterized by the evaluation breed the animal received. Mean genomic predicted breeding values (PBV¯) were analyzed per year to calculate genetic trends for bulls and cows. The data set contained 154,008 bulls and 33,022,242 cows born since 1975. Breakpoints were estimated using linear regression, and nonlinear regression was used to fit the piecewise model for the small sample number in some years. Generation intervals and inbreeding levels were also investigated since 1975. Milk, fat, and protein yields, somatic cell score, productive life, daughter pregnancy rate, and livability PBV¯ were documented. In 2017, 100% of bulls in this data set were genotyped. The percentage of genotyped cows has increased 23 percentage points since 2010. Overall, production traits have increased steadily over time, as expected. The HO and JE breeds have benefited most from genomics, with up to 192% increase in genetic gain since 2009. Due to the low number of observations, trends for Ayrshire, Brown Swiss, and Guernsey are difficult to infer from. Trends in fertility are most substantial; particularly, most breeds are trending downwards and daughter pregnancy rate for JE has been decreasing steadily since 1975 for bulls and cows. Levels of genomic inbreeding are increasing in HO bulls and cows. In 2017, genomic inbreeding levels were 12.7% for bulls and 7.9% for cows. A suggestion to control this is to include the genomic inbreeding coefficient with a negative weight to the selection index of bulls with high future genomic inbreeding levels. For sires of bulls, the current generation intervals are 2.2 yr in HO, 3.2 in JE, 4.4 in Brown Swiss, 5.1 in Ayrshire, and 4.3 in Guernsey. The number of colored breed bulls in the United States is currently at an extremely low level, and this number will only increase with a market incentive or additional breed association involvement. Increased education and extension could be beneficial to increase knowledge about inbreeding levels, use of genomics and genetic improvement, and genetic diversity in the genomic selection era.

Multiple-trait random regression modeling of feed efficiency in US Holsteins.

Residual feed intake (RFI) and feed saved (FS) are important feed efficiency traits that have been increasingly considered in genetic improvement programs. Future sustainability of these genetic evaluations will depend upon greater flexibility to accommodate sparsely recorded dry matter intake (DMI) records on many more cows, especially from commercial environments. Recent multiple-trait random regression (MTRR) modeling developments have facilitated days in milk (DIM)-specific inferences on RFI and FS, particularly in modeling the effect of change in metabolic body weight (MBW). The MTRR analyses, using daily data on the core traits of DMI, MBW, and milk energy (MilkE), were conducted separately for 2,532 primiparous and 2,379 multiparous US Holstein cows from 50 to 200 DIM. Estimated MTRR variance components were used to derive genetic RFI and FS and DIM-specific genetic partial regressions of DMI on MBW, MilkE, and change in MBW. Estimated daily heritabilities of RFI and FS varied across lactation for both primiparous (0.05-0.07 and 0.11-0.17, respectively) and multiparous (0.03-0.13 and 0.10-0.17, respectively) cows. Genetic correlations of RFI across DIM varied (>0.05) widely compared with FS (>0.54) within either parity class. Heritability estimates based on average lactation-wise measures were substantially larger than daily heritabilities, ranging from 0.17 to 0.25 for RFI and from 0.35 to 0.41 for FS. The partial genetic regression coefficients of DMI on MBW (0.11 to 0.16 kg/kg0.75 for primiparous and 0.12 to 0.14 kg/kg0.75 for multiparous cows) and of DMI on MilkE (0.45 to 0.68 kg/Mcal for primiparous and 0.36 to 0.61 kg/Mcal for multiparous cows) also varied across lactation. In spite of the computational challenges encountered with MTRR, the model potentially facilitates an efficient strategy for harnessing more data involving a wide variety of data recording scenarios for genetic evaluations on feed efficiency.

Symposium review: Development, implementation, and perspectives of health evaluations in the United States.

The rate at which new traits are being developed is increasing, leading to an expanding number of evaluations provided to dairy producers, especially for functional traits. This review will discuss the development and implementation of genetic evaluations for direct health traits in the United States, as well as potential future developments. Beginning in April 2018, routine official genomic evaluations for 6 direct health traits in Holsteins were made available to US producers from the Council on Dairy Cattle Breeding (Bowie, MD). Traits include resistance to milk fever, displaced abomasum, ketosis, clinical mastitis, metritis, and retained placenta. These health traits were included in net merit indices beginning in August 2018, with a total weight of approximately 2%. Previously, improvement of cow health was primarily made through changes to management practices or genetic selection on indicator traits, such as somatic cell score, productive life, or livability. Widespread genomic testing now allows for accelerated improvement of traits with low heritabilities such as health; however, phenotypes remain essential to the success of genomic evaluations. Establishment and maintenance of data pipelines is a critical component of health trait evaluations, as well as appropriate data quality control standards. Data standardization is a necessary process when multiple data sources are involved. Model refinement continues, including implementation of variance adjustments beginning with the April 2019 evaluation. Mastitis evaluations are submitted to Interbull along with somatic cell score for international validation and evaluation of udder health. Additional areas of research include evaluation of other breeds for direct health traits, use of multiple-trait models, and evaluations for additional functional traits such as calf health and feed efficiency. Future developments will require new and continued cooperation among numerous industry stakeholders. There is more information available than ever before with which to make better selection decisions; however, this also makes it increasingly important to provide accurate and unbiased information.

Estimates of genetic variance and variance of predicted genetic merits using pedigree or genomic relationship matrices in six Brown Swiss cattle populations for different traits.

The amount of variance captured in genetic estimations may depend on whether a pedigree-based or genomic relationship matrix is used. The purpose of this study was to investigate the genetic variance as well as the variance of predicted genetic merits (PGM) using pedigree-based or genomic relationship matrices in Brown Swiss cattle. We examined a range of traits in six populations amounting to 173 population-trait combinations. A main aim was to determine how using different relationship matrices affect variance estimation. We calculated ratios between different types of estimates and analysed the impact of trait heritability and population size. The genetic variances estimated by REML using a genomic relationship matrix were always smaller than the variances that were similarly estimated using a pedigree-based relationship matrix. The variances from the genomic relationship matrix became closer to estimates from a pedigree relationship matrix as heritability and population size increased. In contrast, variances of predicted genetic merits obtained using a genomic relationship matrix were mostly larger than variances of genetic merit predicted using pedigree-based relationship matrix. The ratio of the genomic to pedigree-based PGM variances decreased as heritability and population size rose. The increased variance among predicted genetic merits is important for animal breeding because this is one of the factors influencing genetic progress.

Impact of type traits on functional herd life of Quebec Holsteins assessed by survival analysis.

Survival analysis was used to study the effects of composite and descriptive linear type traits on functional herd life of Quebec Holsteins. Functional herd life was defined as the length of life from first calving to death, culling, or censoring, and was adjusted for 305-d milk production. The dataset contained information from 331,105 cows from Quebec province calving for the first time between 1981 and 1995; 58% of the records had type information. Weibull models were fitted to analyze the data. The hazard function was described as the product of a baseline hazard function and the time-independent effects of age at first calving and type, and the time-dependent effects of year of calving, stage of lactation x lactation number, annual change in herd size, 305-d milk production, and herd-year (random). Analyses were done one at a time for each type trait. The strongest relationships between survival and composite type traits were found for final score, mammary system, and feet and legs. Among the linear type traits, the highest impact on functional herd life was found for traits related to the udder.

Genetic analysis of herd life in Quebec Holsteins using Weibull models.

Survival analysis methodologies were used to study herd life in Canadian Holstein cows. Herd life was defined as true herd life or the length of time between first calving and censoring. True herd life adjusted for 305-d milk production was defined as functional herd life. Lifetime record (censored or completed) were from 331,147 Holstein cows registered in the Programme d'Analyse des Troupeaux Laitiers du Québec (PATLQ) that calved for the first time between March 1, 1981 and March 31, 1995. The Weibull (proportional hazards) model used to analyze true herd life and functional herd life contained a Weibull baseline hazard function and the time-dependent effects of year of first calving, lactation number by stage of lactation, annual change in herd size and herd-year (random), and the time-independent effects of the milk recording option (supervised or not) and age at first calving. The model for functional herd life included also the time-dependent effect of herd-year-parity class of 305-d milk production. Genetic differences between sires with regard to the hazard function of their daughters was clearly demonstrated. The hazard rate followed a different pattern in later lactations, particularly in the first 240 d in milk. Older age at first calving was found to be associated with higher risks of culling. Changes in herd size had a small impact on the hazard function of animals. The hazard decreased as production of the cow increased. Heritability in the log scale was 0.09 for true herd life and 0.08 for functional herd life, but when heritability was expressed on the original scale, the estimates for the two traits were 0.19 and 0.15, respectively. The difference in the median survival between a bull with an estimated transmitting ability of 0.6 and another bull with an estimated transmitting ability of 1.3 was 690 d or 1.7 lactations. Rank correlations between the official estimated transmitting abilities for true herd life and functional herd life and those obtained in this study were 0.62 and 0.66, respectively.

Correlations of neutrophil phagocytosis for proven bulls with traits of economic importance of their daughters.

Neutrophil phagocytic parameters, measured on 25 AI Canadian Holstein bulls, were investigated for evidence of association with production and type traits, SCC, and survival of dairy cows. An animal model and REML methodologies were used to evaluate the bulls for their neutrophil potential phagocytic activity and capacity. A total of 42,103 first lactation records, collected from 1985 through 1993 for 2919 Quebec dairy herds, were used to obtain EBV for SCC and log SCC for 697 sires. From the same population of cows, 32,900 lactation records were used to calculate EBV for survival after first lactation for 338 sires. Correlations of EBV for SCC and log SCC with all other traits were not significant. Official Canadian ETA for type traits related to the mammary system tended to be positively correlated with phagocytosis parameters. Official Canadian ETA for production traits tended to be negatively correlated. The ETA for milk protein had a significant negative correlation with potential phagocytic activity. Survival after first lactation was significantly associated with ETA for dairy character, milk fat, and fat percentage.