Overview of progeny-test programs of artificial-insemination organizations in the United States

Characteristics of progeny-test (PT) programs of artificial insemination (AI) organizations in the United States were examined for changes since 1960. Mean number of bulls that were progeny tested annually by major AI organizations during the mid 1990s was 11 for Ayrshires, 24 for Brown Swiss, 21 for Guernseys, 1261 for Holsteins, 112 for Jerseys, and 3 for Milking Shorthorns. Mean parent age at progeny-test (PT) bull birth decreased except for Milking Shorthorns; mean age of maternal grandsire at bull birth decreased for Holsteins and Jerseys but increased for other breeds. For Holsteins, mean ancestor ages at PT bull birth were 85 mo for sires, 47 mo for dams, and 136 mo for maternal grandsires during the mid 1990s. Percentage of PT bulls that resulted from embryo transfer increased to 78% for Brown Swiss and 80% for Holsteins by 1999. Inbreeding in PT bulls increased over time and ranged from 3.8% for Brown Swiss to 6.4% for Jerseys (5.6% for Holsteins) during the mid 1990s. Mean numbers of daughters and herds per PT bull generally declined except for Holsteins, which increased during the early 1990s to 61 daughters and 44 herds. Mean number of states in which PT daughters are located increased; for Holstein PT bulls during 1994, 22% of daughters were in California, 13% in Wisconsin, 12% in New York, and 10% in Pennsylvania and Minnesota. Percentage of first-lactation cows that were PT daughters increased and ranged from 6% for Milking Shorthorns to 22% for Ayrshires (14% for Holsteins) during 1998. Percentage of PT daughters that were registered declined and was 19% for Holsteins and around 80% for other breeds.     

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.     

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.     

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.     

Short communication: Use of young bulls in the United States

The availability of genomic evaluations since 2008 has resulted in many changes to dairy cattle breeding programs. One such change has been the increased contribution of young bulls (0.8 to 3.9 yr old) to those programs. The increased use of young bulls was investigated using pedigree data and breeding records obtained from the US national dairy database (Beltsville, MD). The adoption of genotyping was so rapid that by 2009, >90% of all Holstein artificial insemination (AI) service sires and 86% of Jersey AI service sires were genotyped, regardless of age. The percentage of sons sired by young bulls increased by 49 percentage points (10% in 2008 compared with 59% in 2012) due to the onset of genomic evaluations for Holsteins and by 46 percentage points for Jerseys (11 and 57%, respectively). When limiting these data to sons retained for breeding purposes through AI, the increase was even more dramatic, increasing approximately 80 percentage points from 2008 to 2012 for both Holsteins and Jerseys (1, 5, 28, 52, and 81% for Holsteins and 3, 4, 43, 46, and 82% for Jerseys from 2008 through 2012). From US breeding records from 2007 through 2012, 24,580,793 Holstein and 1,494,095 Jersey breedings were examined. Young bulls accounted for 28% and 25% of Holstein and Jersey breedings in 2007, respectively. These percentages increased to 51% of Holstein and 52% of Jersey breedings in 2012, representing 23- and 27-percentage-unit increases, respectively. Matings to genotyped young bulls have rapidly increased while the use of nongenotyped bulls has diminished since the onset of genomics. Mean sire age for Holstein male progeny born in 2012 was 2.7 yr younger than males born in 2006, and 1.3 yr younger for females; corresponding values for Jerseys were 2.3 and 0.9 yr. Holstein male offspring had an increase of 281 kg between 2006 and 2012, compared with 197 kg between 2000 and 2006 for parent averages (PA) for milk, an increase of 84 kg between the 2 periods. Jersey male offspring had an increase of 49 kg between the 2 periods. To demonstrate the economic impact of the differential use of young bulls, herds were grouped by the frequency of their use of young bulls, and average PTA for milk and net merit for cows that were bred in 2003 through 2012 were calculated. In 2012, herds using >75% young bulls created offspring that had a PA of +52 kg for milk and +$58 net merit compared with herds using no young bulls. Jersey herds using >75% young bulls created offspring that had a PA of +142 kg for milk and +$63 for net merit compared with herds using no young bulls. Use of young bulls has greatly reduced the generation interval and improved the rate of genetic gain since the implementation of genomic evaluations.     

The genomic evaluation system in the United States: past, present, future

Implementation of genomic evaluation has caused profound changes in dairy cattle breeding. All young bulls bought by major artificial insemination organizations now are selected based on such evaluation. Evaluation reliability can reach approximately 75% for yield traits, which is adequate for marketing semen of 2-yr-old bulls. Shortened generation interval from using genomic evaluations is the most important factor in increasing the rate of genetic improvement. Genomic evaluations are based on 42,503 single nucleotide polymorphisms (SNP) genotyped with technology that became available in 2007. The first unofficial USDA genomic evaluations were released in 2008 and became official for Holsteins, Jerseys, and Brown Swiss in 2009. Evaluation accuracy has increased steadily from including additional bulls with genotypes and traditional evaluations (predictor animals). Some of that increase occurs automatically as young genotyped bulls receive a progeny test evaluation at 5 yr of age. Cow contribution to evaluation accuracy is increased by decreasing mean and variance of their evaluations so that they are similar to bull evaluations. Integration of US and Canadian genotype databases was critical to achieving acceptable initial accuracy and continues to benefit both countries. Genotype exchange with other countries added predictor bulls for Brown Swiss. In 2010, a low-density chip with 2,900 SNP and a high-density chip with 777,962 SNP were released. The low-density chip has increased greatly the number of animals genotyped and is expected to replace microsatellites in parentage verification. The high-density chip can increase evaluation accuracy by better tracking of loci responsible for genetic differences. To integrate information from chips of various densities, a method to impute missing genotypes was developed based on splitting each genotype into its maternal and paternal haplotypes and tracing their inheritance through the pedigree. The same method is used to impute genotypes of nongenotyped dams based on genotyped progeny and mates. Reliability of resulting evaluations is discounted to reflect errors inherent in the process. Further increases in evaluation accuracy are expected because of added predictor animals and more SNP. The large population of existing genotypes can be used to evaluate new traits; however, phenotypic observations must be obtained for enough animals to allow estimation of SNP effects with sufficient accuracy for application to the general population.     

Harmful recessive effects on fertility detected by absence of homozygous haplotypes

Five new recessive defects were discovered in Holsteins, Jerseys, and Brown Swiss by examining haplotypes that had a high population frequency but were never homozygous. The method required genotypes only from apparently normal individuals and not from affected embryos. Genotypes from the BovineSNP50 BeadChip (Illumina, San Diego, CA) were examined for 58,453 Holsteins, 5,288 Jerseys, and 1,991 Brown Swiss with genotypes in the North American database. Haplotypes with a length of ≤75 markers were obtained. Eleven candidate haplotypes were identified, with the earliest carrier born before 1980; 7 to 90 homozygous haplotypes were expected, but none were observed in the genomic data. Expected numbers were calculated using either the actual mating pattern or assuming random mating. Probability of observing no homozygotes ranged from 0.0002 for 7 to 10⁻⁴⁵ for 90 expected homozygotes. Phenotypic effects were confirmed for 5 of the 11 candidate haplotypes using 14,911,387 Holstein, 830,391 Jersey, and 68,443 Brown Swiss records for conception rate. Estimated effect for interaction of carrier service sire with carrier maternal grandsire ranged from −3.0 to −3.7 percentage points, which was slightly smaller than the −3.9 to −4.6 percentage points expected for lethal recessives but slightly larger than estimated effects for previously known lethal alleles of −2.5 percentage points for brachyspina and −2.9 percentage points for complex vertebral malformation. Conception rate was coded as a success only if the gestation went to term or the cow was confirmed to be pregnant. Estimated effect of carrier interaction for stillbirth rate based on 10,876,597 Holstein and 25,456 Jersey records was small. Thus, lethal effects may include conception, gestation, and stillbirth losses. Carrier frequency has been >20% for many years for the confirmed defect in Jerseys and is currently 16% for the defect in Brown Swiss. The 3 defects discovered in Holsteins have carrier frequencies of 2.7 to 6.4% in the current population. For previously known defects, map locations and lack of homozygotes were consistent with the literature and lethal recessive inheritance, but numbers of expected homozygotes for some were small because of low frequency. Very large genotypic and phenotypic data sets allow efficient detection of smaller and less frequent effects. Haplotype tests can help breeders avoid carrier matings for such defects and reduce future frequencies.     

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.     

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.     

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.     

Effects of breed and region on longevity traits through five years of age in Brown Swiss, Holstein, and Jersey cows in the United States

The objective of this study was to assess breed, and breed × region interactions for several longevity-related traits, measured up to 5 yr of age in Brown Swiss, Holstein, and Jersey cows in 7 regions of the United States. Data were analyzed using logistic, poisson, and linear models, and survival analyses. The traits were stayability (yes/no survived to 5 yr of age), number of completed lactations, days lived, herd-life, and days in milk (DIM) to 5 yr of age. Probable lifetime DIM were also estimated using data from the first 5 yr of age of the cows. Herd-life was defined as the days lived up to 5 yr of age minus the age at first calving. Days in milk consisted of herd-life up to 5 yr of age minus the dry periods. Three data files were analyzed: herds with one breed of cows, herds with Holstein and Brown Swiss, and herds with Holstein and Jersey cows. Breed × region interaction was usually significant, with larger effects for the southern regions. Jerseys obtained largest values for the ratio of DIM to days lived, and for the number of completed lactations to 5 yr of age. Brown Swiss had the largest probabilities of surviving to 5 yr of age (stayabilities) in all regions. For the other traits, the results for Brown Swiss were inconsistent, but usually the cows of this breed had shorter herd-life and DIM to 5 yr of age than Holsteins. Brown Swiss cows were expected to have more total DIM in their lifetime in the Southeast than Holsteins. Survival analysis gave the most readily interpretable information, although the linear, poisson, and logistic analyses answered slightly different questions. Adjustment for herd size did not modify the results.     

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.     

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.     

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.     

Selection of single-nucleotide polymorphisms and quality of genotypes used in genomic evaluation of dairy cattle in the United States and Canada

Nearly 57,000 single-nucleotide polymorphisms (SNP) genotyped with the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA) were investigated to determine usefulness of the associated SNP for genomic prediction. Genotypes were obtained for 12,591 bulls and cows, and SNP were selected based on 5,503 bulls with genotypes from a larger set of SNP. The following SNP were deleted: 6,572 that were monomorphic, 3,213 with scoring problems (primarily because of poor definition of clusters and excess number of clusters), and 3,649 with a minor allele frequency of <2%. Number of SNP for each minor allele frequency class (≥2%) was fairly uniform (777 to 1,004). For 5 contiguous SNP assigned to chromosome 7, no bulls were heterozygous, which indicated that those SNP are actually on the nonpseudoautosomal portion of the X chromosome. Another 178 SNP that were not assigned to a chromosome but that had many fewer heterozygotes than expected were also assigned to the X chromosome. Existence of Hardy-Weinberg equilibrium was investigated by comparing observed with expected heterozygosity. For 11 SNP, the observed percentage of heterozygous individuals differed from the expected by >15%; therefore, those SNP were deleted. For 2,628 SNP, the genotype at another SNP was highly correlated (i.e., genotypes were identical for >99.5% of bulls), and those were deleted. After edits, 40,874 SNP remained. A parent-progeny conflict was declared when the genotypes were alternate homozygotes. Mean number of conflicts was 2.3 when pedigree was correct and 2,411 when it was incorrect. The sire was genotyped for >93% of animals. Maternal grandsire genotype was similarly checked; however, because alternate homozygotes could be valid, a conflict threshold of 16% was used to indicate a need for further investigation. Genotyping consistency was investigated for 21 bulls genotyped twice with differences primarily from SNP that were not scored in one of the genotypes. Concordance for readable SNP was extremely high (99.96-100%). Thousands of SNP that were polymorphic in Holsteins were monomorphic in Jerseys or Brown Swiss, which indicated that breed-specific SNP sets are required or that all breeds need to be considered in the SNP selection process. Genotypes from the Illumina BovineSNP50 BeadChip are of high accuracy and provide the basis for genomic evaluations in the United States and Canada.     

Statistical evaluation of factors and interactions affecting dairy herd improvement milk urea nitrogen in commercial midwest dairy herds

In this study, 400,729 Dairy Herd Improvement (DHI) records collected on 77,178 cows in 692 Midwest herds over 29 mo (January 1999 to May 2001) were used to analyze milk urea nitrogen (MUN) as collected the day of the test in 6 breeds. Records of Holsteins, Jerseys, and Brown Swiss were subjected to stepwise backward elimination analysis with a model including parity (primiparous vs. multiparous cows), sample type (morning vs. evening), milking frequency (2× vs. 3× [Holstein only]), season (winter, spring, summer, and fall), yield of fat-corrected milk (FCM) classified into 1 of 3 FCM categories (FCMc) and all possible higher-order interactions. Results indicated that FCMc contributed to test-day MUN variation in multiparous, but not primiparous, Holsteins. Sample type and season were significant in both parity groups; milking frequency was not significant, but milking frequency × season and milking frequency × FCMc were significant in both parity groups. The nature of these interactions differed for each parity group. For Jersey and Brown Swiss data analyzed by sample type separately, parity was not significant but tended to interact with FCMc, whereas season, FCMc, and season × FCMc were generally significant. Mean test-day MUN was 12.7, 14.6, and 14.4 mg/dL, with 24, 45, and 42% of records above 14.5 mg/dL in Holsteins, Jerseys, and Brown Swiss in single-breed herds, respectively. In Holsteins, MUN peaked at 7 to 10 d in milk (DIM), declined until 28 to 35 DIM, and rose again thereafter. In primiparous Holsteins, MUN did not change with FCM ≤42 kg/d, but for higher FCM yield, MUN declined linearly by 0.05 mg/dL per kilogram of FCM. In multiparous Holsteins, MUN increased by 0.06 and 0.03 mg/dL per kilogram of FCM as FCM yield increased from 5 to 29 and from 30 to 59 kg/d, respectively, but decreased by 0.06 mg/dL as FCM yield increased from 60 to 85 kg/d. The use of adjustment coefficients may facilitate interpretation of test-day MUN on commercial herds. Research should focus on the biological significance of the pattern of change in MUN the first few weeks postpartum and the drop in MUN in unusually high-producing cows.     

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.     

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).     

Genomic inbreeding and relationships among Holsteins, Jerseys, and Brown Swiss

Genomic measures of relationship and inbreeding within and across breeds were compared with pedigree measures using genotypes for 43,385 loci of 25,219 Holsteins, 3,068 Jerseys, and 872 Brown Swiss. Adjustment factors allow genomic and pedigree relationships to match more closely within breeds and in multibreed populations and were estimated using means and regressions of genomic on pedigree relationships and allele frequencies in base populations. Correlations of genomic relationships with pedigree inbreeding were higher within each breed when an allele frequency of 0.5, rather than base population frequencies, was used, whereas correlations of average genomic relationships with average pedigree relationships and also reliabilities of genomic evaluations were higher using base population frequencies. Allele frequencies differed in the 3 breeds and were correlated by 0.65 to 0.67 when estimated from genotyped animals compared with 0.72 to 0.74 when estimated from breed base populations. The largest difference in allele frequency was between Holstein and the other breeds on chromosome Bos taurus autosome 4 near a gene affecting appearance of white skin patches (vitiligo) in humans. Each animal's breed composition was predicted very accurately with a standard deviation of <3% using regressions on genotypes at all loci or less accurately with a standard deviation of <6% using subsets of loci. Genomic future inbreeding (half an animal's mean genomic relationship to current animals of the same breed) was correlated by 0.75 to 0.94 with expected future inbreeding (half the average pedigree relationship). Correlations of both were slightly higher with parent averages than with genomic evaluations for net merit of young Holstein bulls. Thus, rates of increase in genomic and pedigree inbreeding per generation should be slightly reduced with genomic selection, in agreement with previous simulations. Genomic inbreeding and future inbreeding have been provided with individual genomic predictions since 2008. New methods to adjust pedigree and genomic relationship matrices so that they match may provide an improved basis for multibreed genomic evaluation. Positive definite matrices can be obtained by adjusting pedigree relationships for covariances among base animals within breed, whereas adjusting genomic relationships to match pedigree relationships can introduce negative eigenvalues. Pedigree relationship matrices ignore common ancestry shared by base animals within breed and may not approximate genomic relationships well in multibreed populations.     

Crossbred and purebred dairy cattle in warm and cool seasons

This study was to determine if breed groups ranked differently in warm (May to August) and cool (November to February) seasons of calving and to determine if heterosis was more important in the warm season. A total of 719 records of cows in first lactation in four herds in the southeastern United States were used. Breeds were Holsteins, Brown Swiss, and Jerseys and the crosses among them. Milk and milk fat yields were greater in the cool season than in the warm season. Holsteins exceeded other breeds for milk and milk fat yield in both seasons, but their superiority was less among cows calving from May through August. Days open were longer for Holsteins, particularly in the warm season. In the cool season only the 3/4 Holstein X 1/4 Swiss group exceeded Holsteins for milk, but two groups--1/2 Holsteins X 1/2 Swiss and 5/8 Holstein X 1/4 Swiss-1/8 Jersey--were higher in the warm season. In the cool season three crossbred groups--1) 1/2 Holstein X 1/2 Swiss (Holstein sires), 2) 3/4 Holstein X 1/4 Swiss, and 3) 1/2 Holstein X 1/4 Swiss-1/4 Jersey--had greater milk fat yields than Holsteins, and a fourth--1/2 Holstein X 1/2 Jersey--yielded an equal amount. In the warm season six of the eight crossbred groups had greater milk fat yields than Holsteins. More crossbreds exceeded Holsteins in the warm than in the cool season, suggesting interactions for yields. There was slightly more heterosis in warm than in cool seasons for all traits.