Genomic imputation and evaluation using high-density Holstein genotypes.

Genomic evaluations for 161,341 Holsteins were computed by using 311,725 of 777,962 markers on the Illumina BovineHD Genotyping BeadChip (HD). Initial edits with 1,741 HD genotypes from 5 breeds revealed that 636,967 markers were usable but that half were redundant. Holstein genotypes were from 1,510 animals with HD markers, 82,358 animals with 45,187 (50K) markers, 1,797 animals with 8,031 (8K) markers, 20,177 animals with 6,836 (6K) markers, 52,270 animals with 2,683 (3K) markers, and 3,229 nongenotyped dams (0K) with >90% of haplotypes imputable because they had 4 or more genotyped progeny. The Holstein HD genotypes were from 1,142 US, Canadian, British, and Italian sires, 196 other sires, 138 cows in a US Department of Agriculture research herd (Beltsville, MD), and 34 other females. Percentages of correctly imputed genotypes were tested by applying the programs findhap and FImpute to a simulated chromosome for an earlier population that had only 1,112 animals with HD genotypes and none with 8K genotypes. For each chip, 1% of the genotypes were missing and 0.02% were incorrect initially. After imputation of missing markers with findhap, percentages of genotypes correct were 99.9% from HD, 99.0% from 50K, 94.6% from 6K, 90.5% from 3K, and 93.5% from 0K. With FImpute, 99.96% were correct from HD, 99.3% from 50K, 94.7% from 6K, 91.1% from 3K, and 95.1% from 0K genotypes. Accuracy for the 3K and 6K genotypes further improved by approximately 2 percentage points if imputed first to 50K and then to HD instead of imputing all genotypes directly to HD. Evaluations were tested by using imputed actual genotypes and August 2008 phenotypes to predict deregressed evaluations of US bulls proven after August 2008. For 28 traits tested, the estimated genomic reliability averaged 61.1% when using 311,725 markers vs. 60.7% when using 45,187 markers vs. 29.6% from the traditional parent average. Squared correlations with future data were slightly greater for 16 traits and slightly less for 12 with HD than with 50K evaluations. The observed 0.4 percentage point average increase in reliability was less favorable than the 0.9 expected from simulation but was similar to actual gains from other HD studies. The largest HD and 50K marker effects were often located at very similar positions. The single-breed evaluation tested here and previous single-breed or multibreed evaluations have not produced large gains. Increasing the number of HD genotypes used for imputation above 1,074 did not improve the reliability of Holstein genomic evaluations.

Genetic analysis of return over feed in Canadian Holsteins.

The objective of this study was to investigate genetic merit of return over feed (ROF), which is a herd profit index defined by CanWest Dairy Herd Improvement as a difference between milk income and feed cost. A multiple-trait (MT) model and random regression model (RRM) were used. The traits analyzed in MT were rearing cost and ROF of the first three lactations. In RRM, a cumulative ROF was fitted as function of age and rearing cost was treated as a correlated trait. Variance components were estimated within a Bayesian framework by Gibbs sampling using a subsample of data. Breeding values were then estimated for 3 041 078 animals using records of 1 951 893 cows. Estimates of heritability for rearing cost from MT and RRM were 0.23 and 0.22, respectively. ROF per lactation and cumulative ROF were negatively correlated with rearing cost. Estimates of heritability of ROF through the first, second and third lactation from MT were 0.27, 0.10 and 0.08, respectively. Estimates of heritability of ROF from RRM increased with age and ranged from 0.08 through 0.31. Estimated breeding values (EBVs) for ROF from MT and RRM were moderately correlated with official EBV for production traits and the Canadian selection index (Lifetime Profit Index). Herd life EBV had -0.07 and 0.19 correlations with EBVs for ROF from MT and RRM, respectively. From both MT and RRM, small favorable correlations were reported between EBVs for ROF and for bone quality and angularity, whereas low unfavorable correlations were reported with EBV for udder depth, front end and chest width. Majority of correlations between EBVs for ROF and for reproduction traits were near 0, with the exception of EBV for gestation length, calf size and calving ease, where small favorable correlations were reported. The ROF is a good indicator of cow profitability despite the fact that it is a simplified profit index that does not account for animal-specific health and reproductive cost. However, because ROF does not account for differences in heritabilities between components of profit, ROF is not recommended to be used for direct selection for profit.

Relationship between reproduction traits and functional longevity in canadian dairy cattle.

The aim of this study was to use survival analysis to assess the relationship between reproduction traits and functional longevity of Canadian dairy cattle. Data consisted of 1,702,857; 67,470; and 33,190 Holstein, Ayrshire, and Jersey cows, respectively. Functional longevity was defined as the number of days from first calving to culling, death, or censoring; adjusted for the effect of milk yield. The reproduction traits included calving traits (calving ease, calf size, and calf survival) and female fertility traits (number of services, days from calving to first service, days from first service to conception, and days open). The statistical model was a Weibull proportional hazards model and included the fixed effects of stage of lactation, season of production, the annual change in herd size, and type of milk recording supervision, age at first calving, effects of milk, fat, and protein yields calculated as within herd-year-parity deviations for each reproduction trait. Herd-year-season of calving and sire were included as random effects. Analysis was performed separately for each reproductive trait. Significant associations between reproduction traits and longevity were observed in all breeds. Increased risk of culling was observed for cows that required hard pull, calved small calves, or dead calves. Moreover, cows that require more services per conception, a longer interval between first service to conception, an interval between calving to first service greater than 90 d, and increased days open were at greater risk of being culled.

Short communication: Modification of genetic evaluation of herd life from a three-trait to a five-trait model in Canadian dairy cattle.

The national genetic evaluation of herd life for Canadian dairy breeds was modified from a 3-trait to a 5-trait animal model. The genetic evaluation incorporates information from daughter survival (direct herd life) and information from conformation, fertility, and udder health traits that are related to longevity (indirect herd life). Genetic evaluations for direct herd life were based on cows' survival from first calving to 120 days in milk (DIM), from 120 to 240 DIM, from 240 DIM to second calving, survival to third calving, and survival to fourth calving, which were analyzed using a multiple-trait animal model. Sire evaluations obtained for each of the 5 survival traits were combined into an overall sire evaluation for direct herd life. Sire evaluations for indirect herd life were based on an index of sire evaluations for dairy strength, feet and legs, overall mammary, rump angle, somatic cell score, milking speed, nonreturn rate in cows, and interval from calving to first service. A multiple-trait sire model based on multiple-trait across-country evaluation methodology was used to combine direct and indirect genetic evaluations for herd life into an overall genetic evaluation for herd life. Sire evaluations for herd life were expressed as an estimated transmitting ability for the number of lactations. The transmitting ability represents expected differences among daughters for herd life; and the average herd life was set to 3 lactations.

Analysis of the relationship between somatic cell score and functional longevity in Canadian dairy cattle.

The aim of this study was to assess the level of somatic cell count (SCC) and to explore the impact of somatic cell score (SCS) on the functional longevity of Canadian dairy cattle by using a Weibull proportional hazards model. Data consisted of 1,911,428 cows from 15,970 herds sired by 7,826 sires for Holsteins, 80,977 cows in 2,036 herds from 1,153 sires for Ayrshires, and 53,114 cows in 1,372 herds from 1,758 sires for Jerseys. Functional longevity was defined as the number of days from the first calving to culling, death, or censoring. The test-day SCC was transformed to a linear score, and the resulting SCS were averaged within each lactation. The average SCS were grouped into 10 classes. The statistical model included the effects of stage of lactation; season of production; annual change in herd size; type of milk recording supervision; age at first calving; effects of milk, fat, and protein yields, calculated as within-herd-year-parity deviations; herd-year-season of calving; SCS class; and sire. The relative culling rate was calculated for animals in each SCS class after accounting for the aforementioned effects. The overall average SCC for Holsteins was 167,000 cells/mL, for Ayrshires was 155,000 cells/mL, and for the Jerseys was 212,000 cells/mL. In all breeds there were no appreciable differences in the relative risk of culling among classes of SCS breed averages (i.e., up to a SCS of 5). However, as the SCS increased beyond the breed average, the relative risk of cows being culled increased considerably. For instance, Holstein, Ayrshire, and Jersey cows with the highest classes of SCS had, respectively, a 4.95, 6.73, and 6.62 times greater risk of being culled than cows with average SCS.

Analysis of inbreeding and its relationship with functional longevity in Canadian dairy cattle.

The aim of this study was to assess the level of inbreeding and its relationship to the functional survival of Canadian dairy breeds by using a Weibull proportional hazard model. Data consisted of records from 72,385 cows in 1,505 herds from 2,499 sires for Jerseys, 112,723 cows in 1,482 herds from 2,926 sires for Ayrshires, and 1,977,311 cows in 17,182 herds from 8,261 sires for Holsteins. Longevity was defined as the number of days from first calving to culling, death, or censoring. Inbreeding coefficients (F) were grouped into 7 classes (F = 0, 0 < F < 3.125, 3.125 < or = F < 6.25, 6.25 < or = F <12.5, 12.5 < or = F < 18.25, 18.25 < or = F < 25.0, and F > or = 25.0%). The statistical model included the effects of stage of lactation, season of production, the annual change in herd size, type of milk recording supervision, age at first calving, effects of milk, fat, and protein yields calculated as within herd-year-parity deviations, herd-year-season of calving, inbreeding, and sire. The relative culling rate was calculated for animals in each class after accounting for the above-mentioned effects. A trend toward increased risk of culling among more inbred animals was observed for all breeds. Little difference in survival was observed for cows with 0 < F <12.5%. The relative risk ratios (relative to F = 0) for cows with inbreeding coefficients up to 12.5% were 1.19, 1.16, and 1.14 for Jersey, Ayrshire, and Holstein cows, respectively. Greater effects of inbreeding were seen, however, when F increased beyond 12.5%.

Relationship between type traits and longevity in Canadian Jerseys and Ayrshires using a Weibull proportional hazards model.

The aim of this study was to use a Weibull proportional hazards model to explore the impact of type traits on the functional survival of Canadian Jersey and Ayrshire cows. The data set consisted of 49,791 registered Jersey cows from 900 herds calving from 1985 to 2003. The corresponding figures for Ayrshire were 77,109 cows and 921 herds. Functional survival was defined as the number of days from first calving to culling, death, or censoring. Type information consisted of phenotypic type scores for 8 composite traits and 19 linear descriptive traits. The statistical model included the effects of stage of lactation; season of production; annual change in herd size; type of milk recording supervision; age at first calving; effects of milk, fat, and protein yields calculated as within herd-year-parity deviations; herd-year-season of calving; each type trait; and the animal's sire. Analysis was done one trait at a time for each of 27 type traits in each breed. The relative culling risk was calculated for animals in each class after accounting for the previously mentioned effects. Among the composite type traits with the greatest contribution to the likelihood function was final score followed by mammary system for Jersey breed, while in Ayrshire breed feet and legs was the second most important trait next to final score. Cows classified as Poor for final score in both breeds were >5 times more likely to be culled compared with the cows classified as Good Plus. In both breeds, cows classified as Poor for feet and legs were 5 times more likely to be culled than were cows classified as Excellent, and cows classified as Excellent for mammary system were >9 times more likely to survive than were cows classified as Poor.

Selection indices in Holstein cattle of various countries.

Fifteen countries, based on geographical representation, Interbull membership, and size of progeny testing programs, provided a brief description of national selection index and top bull listings from August 2003. Individual traits included in each selection index were grouped into 3 components as they related to production, durability, and health and reproduction. The relative emphasis for each component within the selection index, as well as the number of common bulls among top listings were compared across countries. Average relative emphasis for production, durability, and health and reproduction, across all countries, was 59.5, 28, and 12.5%, respectively. The main difference between selection indices in various countries was the relative emphasis on production. Overall, the Danish S-Index had the most balanced emphasis across the 3 components, with 34% on production, 29% on durability, and 37% on health and reproduction. Broadening of breeding goals through recent changes to selection indices decreased the similarities of top bull listings across the various countries, with a slightly greater commonality among sires of top bulls.

Genetic analysis of herd life in Canadian dairy cattle on a lactation basis using a Weibull proportional hazards model.

The objectives of this study were to identify the most important factors that influence functional survival and to estimate the genetic parameters of functional survival for Canadian dairy cattle. Data were obtained from lactation records extracted for the May 2002 genetic evaluation of Holstein, Jersey, and Ayrshire breeds that calved between July 1, 1985 and April 5, 2002. Analysis was performed using a Weibull proportional hazard model, and the baseline hazard function was defined on a lactation basis instead of the traditional analysis of the whole length of life. The statistical model included the effects of stage of lactation; season of production; the annual change in herd size; type of milk recording supervision; age at first calving; effects of milk, fat, and protein yields calculated within herd-year-parity deviations; and the random effects of herd-year-season of calving and sire. All effects fitted in the model had a significant effect on functional survival of cows in all breeds. Milk yield was by far the most important factor influencing survival, and the hazard increased as the milk production of the cows decreased. The hazard also increased as the fat content increased compared with the average group. Heifers that were older at calving were at higher risk of being culled, and expanding herds were at lower risk of being culled compared with stable herds. More culling was found in unsupervised herds than in supervised herds. The heritability values obtained were 0.14, 0.10, and 0.09 for Holstein, Jersey, and Ayrshire, respectively. Rank correlation between estimated breeding values (EBV) obtained from the current national genetic evaluation of direct herd life and the survival kit used in this study ranged from 0.65 to 0.87, depending on the number of daughters per sire. Estimated genetic trend obtained using the survival kit was overestimated.

Analysis of the relationship between type traits and functional survival in Canadian Holsteins using a Weibull proportional hazards model.

The aim of this study was to explore the impact of type traits on the functional survival of Canadian Holstein cows using a Weibull proportional hazards model. The data set consisted of 1,130,616 registered cows from 13,606 herds calving from 1985 to 2003. Functional survival was defined as the number of days from first calving to culling, death, or censoring. Type information consisted of phenotypic type scores for 8 composite traits (with 18 classes of each) and 23 linear descriptive traits (with 9 classes of each). The statistical model included the effects of stage of lactation, season of production, the annual change in herd size, type of milk recording supervision, age at first calving, effects of milk, fat and protein yields calculated within herd-year-parity deviations, herd-year-season of calving, each type trait, and the sire. Analysis was done one at a time for each of 31 type traits. The relative culling risk was calculated for animals in each class after accounting for the previously mentioned effects. Among the composite type traits with the greatest contribution to the likelihood function were final score, mammary system, and feet and legs, all having a strong relationship with functional survival. Cows with low scores for these traits had higher risk of culling compared with higher scores. For instance, cows classified as poor plus 1 vs. excellent plus 1 have a relative risk of culling 3.66 and 0.28, respectively. The corresponding figures for mammary system are 4.19 and 0.46 and for feet and legs are 2.34 and 0.50. Linear type traits with the greatest contribution to the likelihood function were fore udder attachment, udder texture, udder depth, rear udder attachment height, and rear udder attachment width. Stature and size had no strong relationship with functional survival.

Experience with a test-day model.

The Canadian Test-Day Model is a 12-trait random regression animal model in which traits are milk, fat, and protein test-day yields, and somatic cell scores on test days within each of first three lactations. Test-day records from later lactations are not used. Random regressions (genetic and permanent environmental) were based on Wilmink's three parameter function that includes an intercept, regression on days in milk, and regression on an exponential function to the power -0.05 times days in milk. The model was applied to over 22 million test-day records of over 1.4 million cows in seven dairy breeds for cows first calving since 1988. A theoretical comparison of test-day model to 305-d complete lactation animal model is given. Each animal in an analysis receives 36 additive genetic solutions (12 traits by three regression coefficients), and these are combined to give one estimated breeding value (EBV) for each of milk, fat, and protein yields, average daily somatic cell score and milk yield persistency (for bulls only). Correlation of yield EBV with previous 305-d lactation model EBV for bulls was 0.97 and for cows was 0.93 (Holsteins). A question is whether EBV for yield traits for each lactation should be combined into one overall EBV, and if so, what method to combine them. Implementation required development of new methods for approximation of reliabilities of EBV, inclusion of cows without test day records in analysis, but which were still alive and had progeny with test-day records, adjustments for heterogeneous herd-test date variances, and international comparisons. Efforts to inform the dairy industry about changes in EBV due to the model and recovering information needed to explain changes in specific animals' EBV are significant challenges. The Canadian dairy industry will require a year or more to become comfortable with the test-day model and to realize the impact it could have on selection decisions.

Impact of selection on components of variance and heritabilities of Canadian Holstein conformation traits.

Sire and error variance components and heritabilities were estimated for 26 conformation traits using linear type classifications of 175,693 daughters of 6681 Holstein sires in 21,869 herd-round-classifier subclasses. Estimates from first classifications during first lactations were contrasted with estimates from the same 175,693 females' most recent classification, which included reclassifications. Only cows that have their final classification raised a full category receive an official reclassification record; thus, heritability estimates from data that include these reclassification records may be biased. A total of 9420 (5.4%) of the first lactation, first classifications were replaced by reclassifications for the second analysis, which is current practice for official sire evaluations for Holsteins in Canada. Records, expressed as Snell's scores, were preadjusted for age within parity and stage of lactation at classification. Sire and error components of variance were estimated by Henderson's new method. When reclassifications replaced first classifications in the analysis, estimates of sire and error variances increased 7.2 and 11.1% respectively, as compared with the first lactation, first classification estimates. Heritabilities ranged from .07 for rear heel to .38 for stature and decreased by an average of 2.5% when first lactation, first classifications were replaced by reclassifications. Results indicate that the inclusion of reclassifications tends to bias heritabilities downward.

Estimation of genetic parameters for stayability in Canadian Holsteins.

Hazard functions were plotted and troughs were used to define stayability traits that best coincided with the time of culling decisions. Traits evaluated were stayability to 17, 30, 43, and 55 mo of productive life and stayability to 42, 54, 66, and 78 mo of total life. Holstein data from Record of Performance and supervised Dairy Herd Improvement and Dairy Herd Analysis Service testing programs formed two data sets with 243,348 and 118,362 daughters of 10,723 and 4,583 sires, respectively, and were used to estimate stayability heritabilities and correlations. Variance components were estimated by Henderson's new method using a model that included a fixed herd-year-season of first calving effect and random sire and error effects. Heritabilities for stayability to 17, 30, 43, and 55 mo of productive life were .025, .040, .039, and .033, respectively, for the Record of Performance data and .010, .017, .023, and .033, respectively, for the Dairy Herd Improvement-Dairy Herd Analysis Service supervised data. Heritability estimates for stayability to 42, 54, 66, and 78 mo of total life were .051, .040, .045, and .059, respectively, for the Dairy Herd Improvement-Dairy Herd Analysis Service supervised data. Genetic correlations among productive life traits were usually very high and approached unity. Genetic correlations among total life traits were lower and more variable. Most phenotypic correlations were moderately high but some were low. Stayability to 17 mo of productive life was concluded to be the best trait for incorporation into a selection program if evaluation of sires for longevity is desired.