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.     

Genomic evaluation,breed identification,and discovery of a haplotype affecting fertility for Ayrshire dairy cattle

Genomic evaluations of dairy cattle in the United States have been available for Brown Swiss, Holsteins, and Jerseys since 2009. As of January 2013, 1,023 Ayrshires had genotypes in the North American database. Evaluation accuracy was assessed using genomic evaluations based on 646 bulls with 2008 traditional evaluations to predict daughter performance of up to 180 bulls in 2012. Mean gain in reliability over parent average for all traits was 8.2 percentage points. The highest gains were for protein yield (16.9 percentage points), milk yield (16.6 percentage points), and stature (16.2 percentage points). Twelve single nucleotide polymorphisms were useful for Ayrshire breed determination. Fewer breed-determining SNP were available for Ayrshires than for Holsteins, Jerseys, and Brown Swiss because of the similarity of Ayrshires and Holsteins. A haplotype that affects fertility was identified on chromosome 17 and traces back in the genotyped population to the bull Selwood Betty’s Commander (born in 1953). The haplotype carrier frequency for genotyped Ayrshires was 26.1%. Sire conception rate was decreased by 4.3 ± 2.5 percentage points for carriers of the haplotype as determined by 618 matings of carrier sire by carrier maternal grandsire. Genomic evaluations for Ayrshires were officially implemented in the United States in April 2013.     

Trend of age at first calving

Mean ages at first calving were computed from over 6 million cow records from 1960 through 1982 for six breeds. Average Jerseys first calved at 26.18 mo compared with 28.75 mo for Ayrshires. Other breed means were intermediate: Holsteins, 27.52 mo; Guernseys, 27.72 mo; Brown Swiss, 28.04 mo; and Milking Shorthorns, 28.11 mo. Mean age at first calving in 1982 was .16 to .32 mo less than for all data. Standard deviations of annual mean ages were similar and ranged from 3.23 to 3.67 mo for the 138 breed-year means. Frequency distributions for calving ages were skewed to the left. Cows born from January through March were about .5 mo older at first calving than those born in August and September for most breeds. Annual means did not show a significant trend although all breeds had highest means around 1976 and regressions of age on year of -.075 to -.111 mo per year for 1976 through 1982. Heifer fertility as indicated by age at first calving did not appear to change over 23 yr.     

Trends in calving ages and calving intervals for dairy cattle breeds in the United States

Trends since 1980 for calving age and calving interval, 2 factors that influence herd life, were examined by parity for 5 breeds of US dairy cattle. Calving data were from cows with records that passed edits for USDA genetic evaluations and were in herds that remained on Dairy Herd Improvement test. First-calf heifers calved at progressively younger ages over time, but the age decline was less for later parities because of longer calving intervals. Breed differences for calving age were evident for all parities; current mean age at first calving ranged from 24 mo for Jerseys to 28 mo for Ayrshires. Mean calving age across all parities declined over time for all breeds, primarily because of increased turnover rate, and ranged from 48 mo for Holsteins to 54 mo for Ayrshires. Across parity, annual increase in calving interval was reasonably consistent (0.90 to 1.07 d/yr) for all breeds except Jersey (0.49 d/yr). Within parity, regressions of calving interval on year were generally similar to overall breed trend. Breed means for first calving interval across time ranged from 390 d for Jerseys to 407 d for Brown Swiss.     

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.     

Modified Contemporary and Herdmate Comparisons in Sire Summary

The influence of various factors on differences in sire evaluation from herdmate comparison and modified contemporary comparison methodology was examined. The average Predicted Difference for milk of bulls with 10 or more daughters changed —8, 33, 13, —20, and —8 kg in Ayrshires, Brown Swiss, Guernseys, Holsteins, and Jerseys; standard deviations of change ranged from 76 to 118 kg. The population from which the bulls were selected (pedigree group means) accounted for 49 to 73% of the change. Genetic average of herdmates’ sires accounted for 26 to 39% of the change. For bulls with repeatabilities of over 80%, the genetic average of herd-mates’ sires accounted for 41 to 83%. New repeatabilities averaged 1.6 to 1.9 less than those from the old method but were more variable. Correlations of Predicted Difference for milk by modified contemporary comparison with information from daughters added after the October, 1974 summary were from .04 to .15 higher than Predicted Differences by herdmate comparison. The Predicted Difference by modified contemporary comparison had the greatest advantage over that from the herdmate comparison when bulls had small numbers of daughters. Correlation of Predicted Difference by modified contemporary comparison with additional daughter information was .13 higher than that of the herdmate comparison when fewer than 10 daughters were in the summary and was only .04 higher when more than 100 daughters were in the summary.     

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 and environmental factors that affect gestation length in dairy cattle

Genetic and environmental factors that might affect gestation length (GL) were investigated. Data included information from >11 million parturitions from 1999 through 2006 for 7 US dairy breeds. Effects examined were year, herd-year, month, and age within parity of conception; parturition code (sex and multiple-birth status); lactation length and standardized milk yield of cow; service sire; cow sire; and cow. All effects were fixed except for service sire, cow sire, and cow. Mean GL for heifers and cows, respectively, were 277.8 and 279.4 d for Holsteins, 278.4 and 280.0 d for Jerseys, 279.3 and 281.1 d for Milking Shorthorns, 281.6 and 281.7 d for Ayrshires, 284.8 and 285.7 d for Guernseys, and 287.2 and 287.5 d for Brown Swiss. Estimated standard deviations of GL were greatly affected by data restrictions but generally were approximately 5 to 6 d. Year effects on GL were extremely small, but month effects were moderate. For Holstein cows, GL was 2.0 d shorter for October conceptions than for January and February conceptions; 4.7 and 5.6 d shorter for multiple births of the same sex than for single-birth females and males, respectively; 0.8 d longer for lactations of ≤250 d than for lactations of ≥501 d; and 0.6 d shorter for standardized yield of ≤8,000 kg than for yield of ≥14,001 kg. Estimates for GL heritability from parities 2 to 5 were 33 to 36% for service sire and 7 to 12% for cow sire; corresponding estimates from parity 1 were 46 to 47% and 10 to 12%. Estimates of genetic correlations between effects of service sire and cow sire on GL were 0.70 to 0.85 for Brown Swiss, Holsteins, and Jerseys, which indicates that those traits likely are controlled by many of the same genes and can be used to evaluate each other. More accurate prediction of calving dates can help dairy producers to meet management requirements of pregnant animals and to administer better health care during high-risk phases of animals’ lives. However, intentional selection for either shorter or longer GL is not recommended without consideration of its possible effect on other dependent traits (e.g., calving ease and stillbirth).     

Impact of genetic merit for milk somatic cell score of sires and maternal grandsires on herd life of their daughters

A retrospective study of the impact of the estimated breeding values of sires and maternal grandsires for somatic cell score (SCS) on productive life (PL) of Holsteins and Jerseys was conducted. Data included records from 2,626,425 Holstein and 142,725 Jersey cows. The sires and maternal grandsires of cows were required to have been available through artificial insemination and to have predicted transmitting ability (PTA) SCS evaluations based on 35 or more daughters. A weighted function (WPTA) of sire and maternal grandsire PTA for SCS was used: (sire PTA + 0.5 maternal grandsire PTA)/1.5. The 3 dependent variables were PL, frequency of cows culled for mastitis, and first-lactation SCS. The model included effects of herd, birth year, and WPTA (WPTA was categorized into groups: <2.70, 2.70 to 2.79, …, 3.20 to 3.29, ≥3.30). For analysis of first-lactation SCS, calving year and calving month were substituted for birth year. Differences among WPTA groups were highly significant: as WPTA increased, PL decreased, whereas percentage culled for mastitis and first-lactation SCS increased. The range in PL from lowest to highest WPTA was 5.07 mo for Holsteins and 4.73 mo for Jerseys. Corresponding differences for percentage culled for mastitis were 7.0 and 5.6% and for SCS were 0.95 and 1.04 (for Holsteins and Jerseys, respectively). Although phenotypic studies suggest that cows with extremely low SCS were less resistant to mastitis, our results showed consistent improvements in PL, percentage culled for mastitis, and SCS of daughters when bulls were chosen for low PTA SCS.     

Comparisons of Holsteins with Brown Swiss and Jersey cows on the same farm for age at first calving and first calving interval

Our objective was to evaluate breed differences for heat-stress resistance as reflected by age at first calving and first calving interval. We examined the effect of geographic location and birth season on age at first calving, and geographic location and first calving season on first calving interval on Holsteins and Jerseys, and Holsteins and Brown Swiss located on the same farm. We defined 7 regions within the United States: Northwest, Central north, Northeast, Central, Central south, Southwest, and Southeast, and analyzed 7 individual states: Ohio, Wisconsin, Oregon, California, Arizona, Texas, and Florida. Brown Swiss were older than Holsteins at first calving (833 +/- 2.4 vs. 806 +/- 2.0 d in regions, and 830 +/- 3.1 vs. 803 +/- 2.4 d in states), but Holsteins and Brown Swiss did not differ for first calving interval. Jerseys were younger than Holsteins at first calving and had shorter first calving intervals. In data from individual states, Holsteins housed with Brown Swiss were older at first calving than were Holsteins housed with Jerseys (800 +/- 2.7 vs. 780 +/- 2.5 d). Holsteins housed with one breed or the other were analyzed as a separate data set, and referred to as "type of Holstein." The interaction of "type of Holstein" with first calving season was highly significant for first calving interval. Geographic location and season effects were smaller for Jerseys than for Holsteins; thus, Jerseys showed evidence of heat-stress resistance with respect to Holsteins. Management modified age at first calving in Holsteins to more nearly match that of the other breed. Longer calving intervals might be partly due to voluntary waiting period to breed the cows.     

Survival rates and productive herd life of dairy cattle in the United States

Survival rates and productive herd life were examined for 13.8 million US dairy cows that calved from January 1, 1980, through March 2, 2005. Cows that left the herd for dairy purposes or were from herds that discontinued Dairy Herd Improvement testing were excluded from any calculations to prevent underestimation of population longevity. Mean lactation length for cows without subsequently recorded lactations ranged from 205 to 235 d across breed-parity subsets and were 4 to 29 d longer for parities 2 through 7 than for parity 1. Mean survival rates were 73% to parity 2; 50% to parity 3; 32% to parity 4; and 19, 10, 5, and 2% to parities 5 through 8, respectively. The mean number of parities for Holsteins declined from 3.2 for those first calving in 1980 to 2.8 for those first calving in 1994. Mean numbers of parities for other breeds first calving in 1994 were 2.9 for Ayrshires and Brown Swiss, 2.4 for Guernseys, and 3.2 for Jerseys. Breed means for productive herd life (through parity 8) ranged from 28 to 36 mo. All regressions of mean number of parities or mean productive herd life on year were negative. The trend for decline of many of those indicators of longevity slowed or ended after the early 1990s. Between 31 (Jersey) and 39% (Guernsey) of herds were made up of first-calf heifers.     

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.     

Mating programs including genomic relationships and dominance effects

Computerized mating programs using genomic information are needed by breed associations, artificial-insemination organizations, and on-farm software providers, but such software is already challenged by the size of the relationship matrix. As of October 2012, over 230,000 Holsteins obtained genomic predictions in North America. Efficient methods of storing, computing, and transferring genomic relationships from a central database to customers via a web query were developed for approximately 165,000 genotyped cows and the subset of 1,518 bulls whose semen was available for purchase at that time. This study, utilizing 3 breeds, investigated differences in sire selection, methods of assigning mates, the use of genomic or pedigree relationships, and the effect of including dominance effects in a mating program. For both Jerseys and Holsteins, selection and mating programs were tested using the top 50 marketed bulls for genomic and traditional lifetime net merit as well as 50 randomly selected bulls. The 500 youngest genotyped cows in the largest herd in each breed were assigned mates of the same breed with limits of 10 cows per bull and 1 bull per cow (only 79 cows and 8 bulls for Brown Swiss). A dominance variance of 4.1 and 3.7% was estimated for Holsteins and Jerseys using 45,187 markers and management group deviation for milk yield. Sire selection was identified as the most important component of improving expected progeny value, followed by managing inbreeding and then inclusion of dominance. The respective percentage gains for milk yield in this study were 64, 27, and 9, for Holsteins and 73, 20, and 7 for Jerseys. The linear programming method of assigning a mate outperformed sequential selection by reducing genomic or pedigree inbreeding by 0.86 to 1.06 and 0.93 to 1.41, respectively. Use of genomic over pedigree relationship information provided a larger decrease in expected progeny inbreeding and thus greater expected progeny value. Based on lifetime net merit, the economic value of using genomic relationships was >$3 million per year for Holsteins when applied to all genotyped females, assuming that each will provide 1 replacement. Previous mating programs required transferring only a pedigree file to customers, but better service is possible by incorporating genomic relationships, more precise mate allocation, and dominance effects. Economic benefits will continue to grow as more females are genotyped.     

Differences in modified contemporary comparison sire evaluations from first and later lactations by breed

Sire evaluations from three sets of daughter records, first records only (first), later records after firsts (later), and all records (all) by Modified Contemporary Comparison procedures were used to examine differences in first and later lactation evaluations by breed. January 1984 evaluations for milk for 767 Ayrshires, 3,175 Guernsey, 29,498 Holstein, 3,530 Jersey, and 984 Brown Swiss bulls with 10 or more daughters in each set were used. Average differences between evaluations (later minus first) were 36, 0, 6, 35, and 35 kg milk for Ayrshire, Guernsey, Holstein, Jersey, and Brown Swiss bulls. Standard deviations of the difference were 114, 94, 142, 91, and 134 kg, showing considerable sire-to-sire variation in difference. Correlations between evaluations based on first and later records were .84 to .86 for all breeds except .92 for Jerseys. Percent of first lactations culled was correlated .20, .18, .16, .16, and .19 with difference for Ayrshire, Guernsey, Holstein, Jersey, and Brown Swiss, indicating that culling produced larger differences between evaluations for first and later lactations in favor of later evaluations. Prediction of sire evaluation from later records was enhanced by knowledge of sire's age in addition to first evaluation for Guernsey, Holstein and Jersey sires. In these breeds, for a constant first evaluation, and percent culled in first lactation, younger bulls had higher evaluations from later records. This study showed important differences between evaluations from first and later records for all breeds.     

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.     

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.     

Differences among methods to validate genomic evaluations for dairy cattle

Two methods of testing predictions from genomic evaluations were investigated. Data used were from the August 2006 and April 2010 official USDA genetic evaluations of dairy cattle. The training data set consisted of both cows and bulls that were proven (had own or daughter information) as of August 2006 and included 8,022, 1,959, and 1,056 Holsteins, Jerseys, and Brown Swiss, respectively. The validation data set consisted of bulls that were unproven as of August 2006 and were proven by April 2010 with 2,653, 411, and 132 Holsteins, Jerseys, and Brown Swiss for the production traits. Method 1 used the training animal's predicted transmitting ability (PTA) from August of 2006. Method 2 used the training animal's April 2010 PTA to estimate single nucleotide polymorphism effects. Both methods were tested using several regressions with the same validation animals. In both cases, the validation animals were tested using the deregressed April 2010 PTA. All traits that had genomic evaluations from the official USDA April 2010 genetic evaluations were tested. Results included bias, differences from expected regressions (calculated using selection intensities), and the coefficients of determination. The genomic information increased the predictive ability for most of the traits in all of the breeds. The 2 methods of testing resulted in some differences that would affect interpretation of results. The coefficient of determination was higher for all traits using method 2. This was the expected result as the data were not independent because evaluations of the validation bulls contributed to their sires’ evaluations. The regression coefficients from method 2 were often higher than the regression coefficients from method 1. Many traits had regression coefficients that were higher than 2 standard deviations from the expected regressions when using method 2. This was partially due to the lack of independence of the training and validation data sets. Most traits did have some level of bias in the prediction equations, regardless of breed. The use of method 1 made it possible to evaluate the increased accuracy in proven first-crop bull evaluations by using genomic information. Proven first-crop bulls had an increase in accuracy from the addition of genomic information. It is advised to use method 1 for validation of genomic evaluations.     

Technical note: adjustment of traditional cow evaluations to improve accuracy of genomic predictions

Genomic evaluations are calculated using deregressed predicted transmitting abilities (PTA) from traditional evaluations to estimate effects of single nucleotide polymorphisms. The direct genomic value (sum of an animal's marker effects) should be consistent with traditional PTA, which is the case for bulls. However, traditional PTA of yield traits (milk, fat, and protein) for genotyped cows are higher than their direct genomic values. To ensure that characteristics of cow PTA for yield traits were more similar to those for bull PTA, mean and variance of cow Mendelian sampling (PTA minus parent average) were adjusted to be similar to those of bulls. The same adjustments were used for all genotyped cows in a breed. To determine gains in reliabilities, predictions were made for bulls with August 2010 evaluations that did not have traditional evaluations in August 2006. By adjusting cow PTA and parent averages of genotyped animals, Holstein and Jersey regressions of August 2010 deregressed PTA on genomic evaluations based on August 2006 data became closer to 1 for the adjusted predictor population compared with the unadjusted predictor population. Evaluation bias was decreased for Holsteins when the predictor population was adjusted. Mean gain in reliability over parent average increased 3.5 percentage points across yield traits for Holsteins and 0.9 percentage points for Jerseys when the predictor population was adjusted. The accuracy of genomic evaluations for Holsteins and Jerseys was increased through better use of information from cows.     

Progeny testing and selection intensity for Holstein bulls in different countries

International Bull Evaluation Service (Interbull) Holstein evaluations from February 1995 through February 2003 were used to determine characteristics of progeny testing for Holstein bulls in Australia, Canada, Denmark, France, Germany, Italy, New Zealand, Sweden, The Netherlands, and the United States. The decision to graduate a bull from progeny test (PT) was assumed to have been made based on the second Interbull evaluation, and graduation was defined as the addition of 200 daughters in the period 2.5 to 4.5 yr later. Mean bull age at PT decision varied across countries by 12 mo. Mean numbers of herds and daughters ranged from 39 to 111 and 54 to 144, respectively. Countries with higher requirements for official evaluations generally had more herds and daughters but older bulls at PT decision. Mean estimated breeding values for yield traits of sires of tested bulls were most similar across countries for fat, differing by only 6.4 kg. The four countries highest for sire protein differed only by 1 kg; however, the range was 12 kg. Percentages of bulls graduated ranged from 4.4 to 14.7 across countries. Selection intensities (standardized selection differentials) tended to be about 1.0 for yield traits. Selection intensities for somatic cell score were generally unfavorable, reflecting selection for negatively correlated yield traits. Reflecting variation in national breeding goals, selection intensities for stature were positive for most countries and highly negative for New Zealand. Selection intensity for fore udder was generally the lowest among the traits examined. All but one country showed positive selection for udder support. These statistics permit comparison of the components of PT programs across country, illustrating possible opportunities for improvement.     

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.