Influence of genetic differences in merit of mates on sire evaluation

Effect of nonrandomness of bulls' mates on daughter milk yield was examined from first lactation records of cows with birth dates in 1965 and later. Results were based on 67,081 Ayrshire, 77,633 Brown Swiss, 241,486 Guernsey, 1,433,761 Holstein, 291,201 Jersey, and 10,465 Milking Shorthorn records. Extent of assortative mating was examined. Correlations between sire Predicted Difference and dam (mate) Cow Index for individual years ranged from -.08 to .20. Correlations for all records within herd-year (.00 to .02) indicated essentially no assortative mating for milk yield for any breed except Ayrshire. For Ayrshires, negative assortative mating was indicated by a correlation of -.07. Within-sire regressions of daughter milk yield deviated from contemporary average (which had been adjusted for average Predicted Difference of contemporaries' sires) on dam Cow Index (merit of mates) by breed were .84 to 1.08. Expected regression was 1.00. Effect of merit of mates on sire evaluation was determined by comparing evaluations from standardized yield with those from standardized yield minus dam Cow Index. Correlations between evaluations for 4233 Ayrshire, 5275 Brown Swiss, 13,742 Guernsey, 32,572 Holstein, 13,688 Jersey, and 1240 Milking Shorthorn bulls rounded to 1.00 except for Milking Shorthorns (.99); average absolute differences in evaluations were 9 to 16 kg, and maximum differences were 49 to 118 kg. Adding an adjustment to Sire Summaries to account for nonrandomness of mates would do little to increase accuracy.     

Genetic evaluation of lactation persistency for five breeds of dairy cattle

Cows with high lactation persistency tend to produce less milk than expected at the beginning of lactation and more than expected at the end. Best prediction of lactation persistency is calculated as a function of trait-specific standard lactation curves and linear regressions of test-day deviations on days in milk. Because regression coefficients are deviations from a tipping point selected to make yield and lactation persistency phenotypically uncorrelated it should be possible to use 305-d actual yield and lactation persistency to predict yield for lactations with later endpoints. The objectives of this study were to calculate (co)variance components and breeding values for best predictions of lactation persistency of milk (PM), fat (PF), protein (PP), and somatic cell score (PSCS) in breeds other than Holstein, and to demonstrate the calculation of prediction equations for 400-d actual milk yield. Data included lactations from Ayrshire, Brown Swiss, Guernsey (GU), Jersey (JE), and Milking Shorthorn (MS) cows calving since 1997. The number of sires evaluated ranged from 86 (MS) to 3,192 (JE), and mean sire estimated breeding value for PM ranged from 0.001 (Ayrshire) to 0.10 (Brown Swiss); mean estimated breeding value for PSCS ranged from −0.01 (MS) to −0.043 (JE). Heritabilities were generally highest for PM (0.09 to 0.15) and lowest for PSCS (0.03 to 0.06), with PF and PP having intermediate values (0.07 to 0.13). Repeatabilities varied considerably between breeds, ranging from 0.08 (PSCS in GU, JE, and MS) to 0.28 (PM in GU). Genetic correlations of PM, PF, and PP with PSCS were moderate and favorable (negative), indicating that increasing lactation persistency of yield traits is associated with decreases in lactation persistency of SCS, as expected. Genetic correlations among yield and lactation persistency were low to moderate and ranged from −0.55 (PP in GU) to 0.40 (PP in MS). Prediction equations for 400-d milk yield were calculated for each breed by regression of both 305-d yield and 305-d yield and lactation persistency on 400-d yield. Goodness-of-fit was very good for both models, but the addition of lactation persistency to the model significantly improved fit in all cases. Routine genetic evaluations for lactation persistency, as well as the development of prediction equations for several lactation end-points, may provide producers with tools to better manage their herds.     

Composition of milks of dairy cattle. I. Protein, lactose, and fat contents and distribution of protein fraction.

Milks from commercial dairy herds in Southeastern Pennsylvania were analyzed for total protein, casein, whey protein, beta-lactoglobulin, nonprotein nitrogen, and lactose contents. Data for fat contents and milk yields were from Dairy Herd Improvement Association records for the same lactation. Milk samples were from a single milking of healthy cows (151) in midlactation. Since the remainder of the milk was returned to the bulk milk of the farm, the data represent market milk composition. The data were grouped and analyzed by breed and beta-lactoglobulin phenotype; there were 18 to 33 cows per breed. In true protein percentage, the breeds ranked: Jersey 4.07 plus or minus .49, Brown Swiss 3.84 plus or minus .47, Guernsey 3.56 plus or minus .53, Ayrshire 3.30 plus or minus .52, Milking Shorthorn 3.17 plus or minus .47, Holstein 3.07 plus or minus .43. Breeds differed in all other components and in milk yield. Brown Swiss ranked highest in yield of protein. Only whey protein and beta-lactoglobulin contents were influenced by the beta-lactoglobulin genotype with beta-lactoglobulin A greater than AB greater than B in whey protein content.     

Growth and reproduction characteristics of purebred and crossbred dairy cattle in first lactation

Breed additive, maternal, and heterozygotic effects on 11 monthly postpartum body weights, average size, weight gain, age at first calving, and days open were estimated by linear regression analyses from records of 680 purebred and crossbred animals. Calving year, age, and milk yield were significant environmental effects. Positive regressions of age on body weights indicated late calving cows were heaviest postpartum and had most days open. Negative regressions of milk yield on weight gain and postpartum weight showed greatest losses of weight associated with highest yields. There were breed differences in growth; purebreds highest to lowest were Brown Swiss, Holstein, Red Dane, Jersey, and Ayrshire and for weight gain, Brown Swiss, Ayrshire, and for weight gain, Brown Swiss, Ayrshire, Jersey, Holsteins, and Red Dane. Crosses were superior to purebreds in these traits. Additive effects of Holstein were greater than Ayrshire, Jersey, and Red Dane for postpartum body weights and average size. All constants for heterozygotic effect combinations were significant for postpartum weights and average size. Heterozygosity effects increased in magnitude with advancing lactation. Generally, age at first calving and postpartum interval to conception reflected little heterozygotic or maternal effects. There was some indication of breed differences in mean and additive effects for age at first calving.     

Genetic polymorphism of the epithelial mucin, PAS-I, in milk samples from the major dairy breeds.

Genetic polymorphism in a mucin of the human milk fat globule arises from variable numbers of a tandemly repeated amino acid sequence. As a consequence, the gene from each parent expresses a variable-sized protein. This is manifest on SDS gels in the form of either one or, more often, two protein bands, which differ among individuals in mobility. Evidence of such polymorphism in the bovine mucin, PAS-I, was first obtained from Holstein milk samples. The objective of this study was to evaluate the other major dairy breeds for polymorphism of their PAS-I. Milk samples from individual Jerseys, Guernseys, Ayrshires, and Brown Swiss were analyzed by SDS-PAGE. Bands of the mucin varying in number and mobility were seen in samples from all four breeds. In three of the breeds (Ayrshire, Brown Swiss, and Jersey), there was evidence that two alleles for PAS-I may have become predominant, possibly through degeneration in the structure of their tandem repeats, one that gives rise to a faster moving mucin (relative molecular weight 170,000) and the other to a slower form (relative molecular weight 200,000). In contrast, the PAS-I band patterns on SDS gels for both Guernseys and Holsteins were characterized in nearly 50% of samples by two close bands near the 205,000-molecular weight marker. This pattern was never seen in the other three breeds. The findings suggest a genetic kinship among the Ayrshire, Brown Swiss, and Jersey, on the one hand, and between the Holstein and Guernsey, on the other.     

Marker selection and genomic prediction of economically important traits using imputed high-density genotypes for 5 breeds of dairy cattle

Marker sets used in US dairy genomic predictions were previously expanded by including high-density (HD) or sequence markers with the largest effects for Holstein breed only. Other non-Holstein breeds lacked enough HD genotyped animals to be used as a reference population at that time, and thus were not included in the genomic prediction. Recently, numbers of non-Holstein breeds genotyped using HD panels reached an acceptable level for imputation and marker selection, allowing HD genomic prediction and HD marker selection for Holstein plus 4 other breeds. Genotypes for 351,461 Holsteins, 347,570 Jerseys, 42,346 Brown Swiss, 9,364 Ayrshires (including Red dairy cattle), and 4,599 Guernseys were imputed to the HD marker list that included 643,059 SNP. The separate HD reference populations included Illumina BovineHD (San Diego, CA) genotypes for 4,012 Holsteins, 407 Jerseys, 181 Brown Swiss, 527 Ayrshires, and 147 Guernseys. The 643,059 variants included the HD SNP and all 79,254 (80K) genetic markers and QTL used in routine national genomic evaluations. Before imputation, approximately 91 to 97% of genotypes were unknown for each breed; after imputation, 1.1% of Holstein, 3.2% of Jersey, 6.7% of Brown Swiss, 4.8% of Ayrshire, and 4.2% of Guernsey alleles remained unknown due to lower density haplotypes that had no matching HD haplotype. The higher remaining missing rates in non-Holstein breeds are mainly due to fewer HD genotyped animals in the imputation reference populations. Allele effects for up to 39 traits were estimated separately within each breed using phenotypic reference populations that included up to 6,157 Jersey males and 110,130 Jersey females. Correlations of HD with 80K genomic predictions for young animals averaged 0.986, 0.989, 0.985, 0.992, and 0.978 for Jersey, Ayrshire, Brown Swiss, Guernsey, and Holstein breeds, respectively. Correlations were highest for yield traits (about 0.991) and lowest for foot angle and rear legs–side view (0.981and 0.982, respectively). Some HD effects were more than twice as large as the largest 80K SNP effect, and HD markers had larger effects than nearby 80K markers for many breed-trait combinations. Previous studies selected and included markers with large effects for Holstein traits; the newly selected HD markers should also improve non-Holstein and crossbred genomic predictions and were added to official US genomic predictions in April 2020.     

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.     

Relationships Between Sires and Sons for Evaluations from First,All, and Later Records

January 1984 Modified Contemporary Comparison sire evaluations for first, all, and later records were used to create sire-son pairs in five dairy breeds. Each evaluation for each bull included 10 or more daughters. Regressions of son on sire for evaluations for first, all, or later records exceeded the expectation of .5 and were most divergent for Jerseys and Brown Swiss. Regressions and coefficients of determination were generally highest when sire's evaluation based on all records predicted sons’ evaluations from first, all, or later records. Regression of son on sire for difference in evaluations (later minus first) was positive in all breeds, ranging from .08 to .10, and was significant for all breeds except Brown Swiss. Coefficients of determination were low (.01 to .02). Both regression of son on sire for difference and coefficient of determination increased with son's Repeatability, with a regression of .33 and a coefficient of determination of .09 for sons over 99% Repeatability, Regressions for 8,055 Holsteins with evaluations for sires and maternal grandsires on those ancestors were .46 to .54 for sires and .25 to .31 for maternal grandsires. Regressions of son's evaluation on pedigree index were .94 for first, 1.05 for all, and 1.12 for later lactations.     

Type trait (co)variance components for five dairy breeds

(Co)variance components were estimated for final score and 14 or 15 linear type traits for the Ayrshire, Brown Swiss, Guernsey, Jersey, and Milking Shorthorn breeds. Appraisals from 1995 or later were used. New estimates were calculated to accommodate changes in scoring of traits and because of a change from multiplicative to additive adjustment for age and lactation stage. The adjustment method was changed for better support of the adjustment for heterogeneous variance within iteration, which was implemented in 2002. The largest changes in heritability were an increase of 0.10 for rump angle for Milking Shorthorns and a decrease of 0.11 for udder depth for Jerseys. The new estimates of (co)variance components should provide improved accuracy of type evaluations, particularly for traits that have had variance changes over time.     

Phenotypic and genetic relationship between linear functional type traits and milk yield for five breeds

Lactation records of cows first calving between 18 and 35 mo were combined with linear type ratings assigned during the same lactation if before 43 mo. Phenotypic relationships were examined between final score and 13 type appraisal traits and first lactation milk yield from 2935 Ayrshire, 3154 Brown Swiss, 13,110 Guernsey, 50,422 Jersey, and 924 Milking Shorthorn records. Most phenotypic correlations between type and milk yield were low. Linear correlations of final score with first lactation milk yield were .18 to .38. Of the linear functional type traits, correlations with first lactation yield had greatest absolute values for dairy character (.19 to .53), udder depth (-.26 to -.30), and rear udder width (.20 to .31). Multiple correlations of all type appraisal traits with first lactation milk yield ranged from .41 to .59. Herd-year-season components of variance averaged 25% for type traits. Herd-year-season with sire interaction averaged 4%. Heritability estimates for final score from paternal half-sib analysis were from .11 to .21. Heritability estimates for linear traits ranged from .01 to .37. Genetic correlation between milk and final score was positive for Guernseys (.25) and Jerseys (.21). Genetic correlations between yield and most linear type traits were low to moderate except for dairy character (.53 to .77).     

Multibreed genomic evaluations using purebred Holsteins, Jerseys, and Brown Swiss

Multibreed models are currently used in traditional US Department of Agriculture (USDA) dairy cattle genetic evaluations of yield and health traits, but within-breed models are used in genomic evaluations. Multibreed genomic models were developed and tested using the 19,686 genotyped bulls and cows included in the official August 2009 USDA genomic evaluation. The data were divided into training and validation sets. The training data set comprised bulls that were daughter proven and cows that had records as of November 2004, totaling 5,331Holstein, 1,361 Jersey, and 506 Brown Swiss. The validation data set had 2,508Holstein, 413 Jersey, and 185 Brown Swiss bulls that were unproven (no daughter information) in November 2004 and proven by August 2009. A common set of 43,385 single nucleotide polymorphisms (SNP) was used for all breeds. Three methods of multibreed evaluation were investigated. Method 1 estimated SNP effects separately within breed and then applied those breed-specific SNP estimates to the other breeds. Method 2 estimated a common set of SNP effects from combined genotypes and phenotypes of all breeds. Method 3 solved for correlated SNP effects within each breed estimated jointly using a multitrait model where breeds were treated as different traits. Across-breed genomic predicted transmitting ability (GPTA) and within-breed GPTA were compared using regressions to predict the deregressed validation data. Method 1 worked poorly, and coefficients of determination (R(2)) were much lower using training data from a different breed to estimate SNP effects. Correlations between direct genomic values computed using training data from different breeds were less than 30% and sometimes negative. Across-breed GPTA from method 2had higher R(2) values than parent average alone but typically produced lower R(2) values than the within-breed GPTA. The across-breed R(2) exceeded the within-breed R(2) for a few traits in the Brown Swiss breed, probably because information from the other breeds compensated for the small numbers of Brown Swiss training animals. Correlations between within-breed GPTA and across-breed GPTA ranged from 0.91 to 0.93. The multibreed GPTA from method 3 were significantly better than the current within-breed GPTA, and adjusted R(2) for protein yield (the only trait tested for method 3) were highest of all methods for all breeds. However, method 3 increased the adjusted R(2) by only 0.01 for Holsteins, ≤0.01 for Jerseys, and 0.01 for Brown Swiss compared with within-breed predictions.     

Genomic characterization of autozygosity and recent inbreeding trends in all major breeds of US dairy cattle

Maintaining a genetically diverse dairy cattle population is critical to preserving adaptability to future breeding goals and avoiding declines in fitness. This study characterized the genomic landscape of autozygosity and assessed trends in genetic diversity in 5 breeds of US dairy cattle. We analyzed a sizable genomic data set containing 4,173,679 pedigreed and genotyped animals of the Ayrshire, Brown Swiss, Guernsey, Holstein, and Jersey breeds. Runs of homozygosity (ROH) of 2 Mb or longer in length were identified in each animal. The within-breed means for number and the combined length of ROH were highest in Jerseys (62.66 ± 8.29 ROH and 426.24 ± 83.40 Mb, respectively; mean ± SD) and lowest in Ayrshires (37.24 ± 8.27 ROH and 265.05 ± 85.00 Mb, respectively). Short ROH were the most abundant, but moderate to large ROH made up the largest proportion of genome autozygosity in all breeds. In addition, we identified ROH islands in each breed. This revealed selection patterns for milk production, productive life, health, and reproduction in most breeds and evidence for parallel selective pressure for loci on chromosome 6 between Ayrshire and Brown Swiss and for loci on chromosome 20 between Holstein and Jersey. We calculated inbreeding coefficients using 3 different approaches, pedigree-based (F_PED), marker-based using a genomic relationship matrix (F_GRM), and segment-based using ROH (F_ROH). The average inbreeding coefficient ranged from 0.06 in Ayrshires and Brown Swiss to 0.08 in Jerseys and Holsteins using F_PED, from 0.22 in Holsteins to 0.29 in Guernsey and Jerseys using F_GRM, and from 0.11 in Ayrshires to 0.17 in Jerseys using F_ROH. In addition, the effective population size at past generations (5–100 generations ago), the yearly rate of inbreeding, and the effective population size in 3 recent periods (2000–2009, 2010–2014, and 2015–2018) were determined in each breed to ascertain current and historical trends of genetic diversity. We found a historical trend of decreasing effective population size in the last 100 generations in all breeds and breed differences in the effect of the recent implementation of genomic selection on inbreeding accumulation.     

Factors associated with colostral specific gravity in dairy cows

The objectives of this study were to identify factors associated with colostral specific gravity in dairy cows, as measured by a commercially available hydrometer (Colostrometer). Colostral specific gravity was measured in 1085 first-milking colostrum samples from 608 dairy cows of four breeds on a single farm during a 5-yr period. Effects of breed, lactation number, and month and year of calving on colostral specific gravity were determined, as were correlations between colostral specific gravity, nonlactating period length, and 305-d yields of milk, protein, and fat. For 75 multiparous Holstein cows, relationships between colostral specific gravity, colostral IgG1, protein, and fat concentrations, and season of calving were determined. Colostral specific gravity values were lower for Brown Swiss and Ayrshire cows than for Jersey and Holstein cows, and lower for cows entering first or second lactation than third or later lactations. Month of calving markedly affected colostral specific gravity values, with highest values occurring in autumn and lowest values in summer. In multiparous Holstein cows, colostral specific gravity was more strongly correlated with colostral protein concentration (r = 0.76) than IgG1 concentration (r = 0.53), and colostral protein concentration varied seasonally (higher in autumn than summer). Our results demonstrate that colostral specific gravity more closely reflects colostral protein concentration than IgG1 concentration and is markedly influenced by month of calving. These results highlight potential limitations of using colostral specific gravity as an indicator of IgG1 concentration.     

Changes of evaluation for natural-service sampled bulls brought into artificial insemination

United States Department of Agriculture Sire Summary files were used to select bulls with a published Modified Contemporary Comparison sire evaluation prior to entry into artificial insemination. Canadian bulls were not included. Of the Brown Swiss, Guernsey, Holstein, and Jersey bulls that entered artificial insemination since 1974, 28 Brown Swiss, 19 Guernseys, 298 Holsteins, and 45 Jerseys (4 to 12%) had natural service evaluations. Of these bulls, 10 Guernseys, 154 Holsteins, and 28 Jerseys had an increase of Repeatability of 30% or more after entering artificial insemination. Evaluations for bulls just prior to their entering artificial insemination were compared with their most recent evaluations through July 1983. Average Repeatabilities for evaluations of bulls just prior to their entering artificial insemination were 32% for Guernseys, 32% for Holsteins, and 31% for Jerseys and 88, 90, and 87% for their most recent evaluations. Average Predicted Differences prior to entering artificial insemination were 305 kg for Guernseys, 394 kg for Holsteins, and 452 kg for Jerseys for milk and 11, 10, and 16 kg for fat. Most recent average Predicted Differences were 268, 380, and 532 kg for milk and 7, 10, and 18 kg for fat. Predicted Differences of natural service bulls were not overevaluated regardless of number of herds for sampling or year of entry into artificial insemination. Artificial insemination organizations can continue to acquire bulls with natural service evaluations calculated with the Modified Contemporary Comparison and be confident that these Predicted Differences are not overestimated.     

Timeliness and effectiveness of progeny testing through artificial insemination

Progeny-test (PT) programs of US artificial-insemination (AI) organizations were examined to determine timeliness of sampling, PT daughter distribution, rate of return of PT bulls to widespread service, and genetic merit of PT bulls compared with AI-proven and natural-service (NS) bulls. Bull age at semen release and at birth and calving of PT daughters was documented by breed (Ayrshire, Brown Swiss, Guernsey, Holstein, Jersey, and Milking Shorthorn) for bulls that entered AI service since 1960. Mean Holstein bull age at semen release (16 mo) changed little over time, but standard deviations (SD) decreased from 4.0 mo during the 1960s to 2.4 mo during the 1990s. Most Holstein bulls (80%) had semen released by 18 mo. Mean age of Holstein bulls at birth and calving of PT daughters during the 1990s was 29 and 56 mo, respectively (a decline of 4 mo from the 1960s); SD decreased from 6 to 3 mo. Bulls of other breeds usually were older at birth and calving of PT daughters, and SD were larger. Mean Holstein bull age when 80% of PT daughters had been born declined from 36 mo during the 1960s to 31 mo during the early 1990s; for other breeds, bulls showed the same trend but at older ages. Mean Holstein bull age when 80% of PT daughters had calved declined from 65 mo during the 1960s to 59 mo during the 1990s; for other breeds, bulls were older. Percentage of herds with PT daughters has increased over time. For Holsteins, herds with five or more usable first-parity records that had PT daughters with usable records increased from 15% during 1965 to 61% during 1998; percentage of herds with from 1 to 19% PT records increased from 11 to 38%, and percentage of herds with >50% PT daughters increased from 1 to 5%. Percentage of Holstein PT bulls returned to AI service declined to about 12% for bulls with PT entry around 1990; for other breeds, 12 to 23% of most recent PT bulls were returned to service. Percentage of milking daughters that had records usable for genetic evaluation that were sired by PT bulls increased steadily from 10 to 18%, whereas percentage of daughters with usable records that were sired by NS bulls declined from 14 to 7%. Milk yield of daughters of AI-proven bulls was 107 to 200 kg greater than for daughters of PT bulls and 366 to 444 kg greater than for daughters of NS bulls for all years. More extensive and rapid sampling and increased selection intensity of PT programs have led to more rapid genetic progress. More extensive use of AI could increase US producer income by millions of dollars annually.     

Analysis of the relationship between workability traits and functional longevity in Canadian dairy breeds

The aim of this study was to assess the effect of workability traits like milking speed and temperament on functional longevity of Canadian dairy cattle using a Weibull proportional hazards model. First-lactation data consisted of the following: 1,728,289 and 2,426,123 Holstein cows for milking temperament and milking speed, respectively, from 18,401 herds and sired by 8,248 sires; 39,618 and 60,121 Jersey cows for milking temperament and milking speed, respectively, from 1,845 herds and sired by 2,413 sires; and 54,391 and 94,847 Ayrshire cows for milking temperament and milking speed, respectively, from 1,316 herds and sired by 2,779 sires. Functional longevity was defined as the number of days from the first calving to culling, death, or censoring adjusted for production. Milking temperament and milking speed were recorded on a 1- to 5-point scale from very nervous to very calm and from very slow to very fast, respectively. 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; sire; and milking temperament or milking speed class. The relative culling rate was calculated for animals in each milking temperament or milking speed class after accounting for the above-mentioned effects. The study showed that there was a statistically significant association between workability traits and functional longevity. Very nervous cows were 26, 23, and 46% more likely to be culled than very calm cows in Holstein, Ayrshire, and Jersey breeds, respectively. Similarly, very slow milkers were 36, 33, and 28% more likely to be culled than average milkers in Holstein, Ayrshire, and Jersey breeds, respectively. Additionally, very fast milkers were 11, 13, and 15% more likely to be culled than average milkers in Holstein, Ayrshire, and Jersey breeds, respectively. Producers might want to avoid consequences associated with the fast milkers such as udder health problems.     

Economic merit of crossbred and purebred US dairy cattle

Heterosis and breed differences were estimated for milk yield traits, somatic cell score (SCS), and productive life (PL), a measure of longevity. Yield trait data were from 10,442 crossbreds and 140,421 purebreds born since 1990 in 572 herds. Productive life data were from 41,131 crossbred cows and 726,344 purebreds born from 1960 through 1991. The model for test-day yields and SCS included effects of herd-year-season, age, lactation stage, regression on sire's predicted transmitting ability, additive breed effects, heterosis, and recombination. The model for PL included herd-year-season, breed effects, and general heterosis. All effects were assumed to be additive, but estimates of heterosis were converted to a percentage of the parent breed average for reporting. Estimates of general heterosis were 3.4% for milk yield, 4.4% for fat yield, and 4.1% for protein yield. A coefficient of general recombination was derived for multiple-breed crosses, but recombination effects were not well estimated and small gains, not losses, were observed for yield traits in later generations. Heterosis for SCS was not significant. Estimated heterosis for PL was 1.2% of mean productive life and remained constant across the range of birth years. Protein yield of Brown Swiss x Holstein crossbreds (0.94 kg/d) equaled protein yield of purebred Holsteins. Fat yields of Jersey x Holstein and Brown Swiss x Holstein crossbreds (1.14 and 1.13 kg/d, respectively) slightly exceeded that of Holsteins (1.12 kg/d). With cheese yield pricing and with all traits considered, profit from these crosses exceeded that of Holsteins for matings at breed bases. For elite matings, Holsteins were favored because the range of evaluations is smaller and genetic progress is slower in breeds other than Holstein, in part because fewer bulls are sampled. A combined national evaluation of data for all breeds and crossbreds may be desirable but would require an extensive programming effort. Animals should receive credit for heterosis when considered as mates for another breed.     

Phenotypic analysis of pregnancy effect on milk, fat, and protein yields of Canadian Ayrshire, Jersey, Brown Swiss, and Guernsey breeds

Pregnancy has a negative impact on milk production in dairy cattle. Estimates of the effects of pregnancy are required in genetic evaluation models. Test-day records of Ayrshire, Jersey, Brown Swiss, and Guernsey breeds were analyzed phenotypically for the effect of pregnancy using 4 different models. Milk, fat, and protein yields were analyzed separately. The first model used a fourth-order Legendre polynomial regression on days in milk within classes of 10 d open. The second model fitted stage of pregnancy within days open classes to investigate the possible interaction between lactation stage and gestation stage. The third model included a fourth-order Legendre polynomial regression on days pregnant. In the fourth model, test-day records were divided into stage of pregnancy classes. Given that the effect of pregnancy was significant for all models, and that the adjusted R-squared values were consistent across the models, implying that the models for each trait fitted equally well within breeds, models were therefore compared based on the practicality of the results. Analysis of the first model indicated that milk production for cows with ≤180 d open tended to have low yields in the last part of lactation. Cows with longer days open, however, had proportionally higher milk yield throughout lactation, suggesting a possible confounding effect of production level with days open effects. Results from the analysis involving the second model illustrated that there was no apparent interaction between lactation stage and gestation stage. Results from the third and fourth models showed that milk and fat yields began to decline after about 4 mo of pregnancy for all breeds, and protein yield began to decline after about 2 mo of pregnancy for all breeds. A lack of records during the final 60 d of pregnancy (the typical dry period) severely limited the third model, as pregnancy effects could not be estimated accurately. This problem was lessened, however, with the fourth (stage of pregnancy) model, because test-day records for cows ≥210 d pregnant were grouped together, allowing for a moderate number of test-day records in the final class of days pregnant. Because the stage of pregnancy model showed a decline in production that increased as gestation progressed, and because there was not a lack of test-day records at the end of pregnancy, the fourth model provided the most realistic estimate of the effect of pregnancy on milk production. Further investigation is needed into the incorporation of stage of pregnancy effects into genetic evaluations.     

Animal model evaluation of dairy goats for milk, fat, and protein yields with crossbred animals included

Genetic evaluation of dairy goats was extended to include evaluation of protein yield and evaluation of Oberhasli and experimental breeds. Diverse genetic background of parents of crossbred animals can be accounted for with an animal model that includes all relationships. The animal model system implemented for dairy goats differed from the one for dairy cattle in that all breeds were processed simultaneously and evaluations of relatives included data from does without a first lactation record and from later herds for does that changed herds. Unknown parent groups were defined for each breed except Oberhasli, which was grouped with the Alpine breed because of small population size. Management groups were 2-mo seasons with separate groups for first and later lactations. Management groups with fewer than five lactation records were combined with other groups until five lactations were included or the management group was 10-mo long. Evaluations for milk and fat were computed for 141,003 animals: 80,227 does with lactation records, 34,294 dams without records, and 26,482 bucks. About 70% of animals had protein evaluations. Genetic trend in 1984 for the five breeds with largest population sizes ranged from 3.8 to 5.2 kg/yr for milk yield.     

Genome-wide association for milk production traits and somatic cell score in different lactation stages of Ayrshire,Holstein, and Jersey dairy cattle

We performed genome-wide association analyses for milk, fat, and protein yields and somatic cell score based on lactation stages in the first 3 parities of Canadian Ayrshire, Holstein, and Jersey cattle. The genome-wide association analyses were performed considering 3 different lactation stages for each trait and parity: from 5 to 95, from 96 to 215, and from 216 to 305 d in milk. Effects of single nucleotide polymorphisms (SNP) for each lactation stage, trait, parity, and breed were estimated by back-solving the direct breeding values estimated using the genomic best linear unbiased predictor and single-trait random regression test-day models containing only the fixed population average curve and the random genomic curves. To identify important genomic regions related to the analyzed lactation stages, traits, parities and breeds, moving windows (SNP-by-SNP) of 20 adjacent SNP explaining more than 0.30% of total genetic variance were selected for further analyses of candidate genes. A lower number of genomic windows with a relatively higher proportion of the explained genetic variance was found in the Holstein breed compared with the Ayrshire and Jersey breeds. Genomic regions associated with the analyzed traits were located on 12, 8, and 15 chromosomes for the Ayrshire, Holstein, and Jersey breeds, respectively. Especially for the Holstein breed, many of the identified candidate genes supported previous reports in the literature. However, well-known genes with major effects on milk production traits (e.g., diacylglycerol O-acyltransferase 1) showed contrasting results among lactation stages, traits, and parities of different breeds. Therefore, our results suggest evidence of differential sets of candidate genes underlying the phenotypic expression of the analyzed traits across breeds, parities, and lactation stages. Further functional studies are needed to validate our findings in independent populations.