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

Genetic evaluations for resistance to bovine tuberculosis (bTB) were calculated based on British national data including individual animal tuberculin skin test results, postmortem examination (presence of bTB lesions and bacteriological culture for Mycobacterium bovis), animal movement and location information, production history, and pedigree records. Holstein cows with identified sires in herds with bTB breakdowns (new herd incidents) occurring between the years 2000 and 2014 were considered. In the first instance, cows with a positive reaction to the skin test and a positive postmortem examination were defined as infected. Values of 0 and 1 were assigned to healthy and infected animal records, respectively. Data were analyzed with mixed models. Linear and logit function heritability estimates were 0.092 and 0.172, respectively. In subsequent analyses, breakdowns were split into 2-mo intervals to better model time of exposure and infection in the contemporary group. Intervals with at least one infected individual were retained and multiple intervals within the same breakdown were included. Healthy animal records were assigned values of 0, and infected records a value of 1 in the interval of infection and values reflecting a diminishing probability of infection in the preceding intervals. Heritability and repeatability estimates were 0.115 and 0.699, respectively. Reliabilities and across time stability of the genetic evaluation were improved with the interval model. Subsequently, 2 more definitions of "infected" were analyzed with the interval model: (1) all positive skin test reactors regardless of postmortem examination, and (2) all positive skin test reactors plus nonreactors with positive postmortem examination. Estimated heritability was 0.085 and 0.089, respectively; corresponding repeatability estimates were 0.701 and 0.697. Genetic evaluation reliabilities and across time stability did not change. Correlations of genetic evaluations for bTB with other traits in the current breeding goal were mostly not different from zero. Correlation with the UK Profitable Lifetime Index was moderate, significant, and favorable. Results demonstrated the feasibility of a national genetic evaluation for bTB resistance. Selection for enhanced resistance will have a positive effect on profitability and no antagonistic effects on current breeding goal traits. Official genetic evaluations are now based on the interval model and the last bTB trait definition.

Somatic cell count (SCO data collected on individual cows since 1991 were obtained from National Milk Records. Following validation genetic and phenotypic parameters were estimated from the lactation average SCCfor 63 424 Holstein/Friesian (HOD, 7966 Ayrshire (AYR) and 14 509 Jersey (JER) animals. The first three lactations were included in the analyses. The heritabilities (h 2 ) for first lactation log SCC (LSCC) were 0-11 (s.e. 0-01), 0-12 (s.e. 0-02) and 0-09 (s.e. 0-03) for the HOL, ]ER and AYR breeds respectively. Estimates for herd sire interaction (c 2 ) effects ranged from 0-01 to 0-02. Analysis of the first three lactations with a repeatability model produced similar h 2 and c 2 estimates. Permanent environment estimates ranged from 0-21 to 0-25. Heritabilities of individual test day LSCC ranged from 0-04 (s.e. 0-02) to 0-10 (s.e. 0-03). Genetic correlations between SCC and milk, fat and protein yield for the HOL breed were 0-06 (s.e. 0-05), 0-14 (s.e. 0-06) and 0-09 (s.e. 0-06) respectively. Genetic evaluations were obtained for 666 595 and 9136 animals for Holsteins and Ayrshires, providing evaluations on 13 525 and 1713 bulls respectively in each breed. The range of LSCC predicted transmitting abilities (PTA) was ±25% although the proportion of bulls with reliability >0-50 was low at 0-17 and 0-05 for HOL and AYR respectively.The correlations between the LSCC PTAs for HOL bulls with at least 50 daughters and their genetic evaluations for linear type were essentially zero for body and some udder traits. Significant negative correlations were obtained for a number of traits including foot angle (-0-14), fore-udder attachment (-0-19) and udder depth (-0-19) and a positive correlation for teat length (0-15). SCC evaluations will be implemented by the Animal Data Centre. Reliabilities will be lower than production because of the lower h 2 for SCC and the lower progeny group size since only 0-80 of recorded cows have SCC records.

Background This study aimed to determine the association between the lameness advantage genetic index and four outcomes: sole haemorrhage (SH), sole ulcers (SU), white line lesions (WL), and lameness during mobility scoring. Methods We enrolled 2352 Holstein cows from four predominantly housed dairy herds in the UK. Cows were mobility scored and foot lesions recorded at four time points from before calving to late lactation. Cows were genotyped and genetic indexes were assigned to each cow following national genetic evaluations. Lameness records and genetic indexes were matched for 2107 cows. Four separate multivariable logistic regression models, which included farm and parity as covariables, were used to quantify the association between the lameness advantage index and whether animals were affected by SH, SU, WL, or lameness. Results The odds ratios (95% confidence intervals) for one‐point increases in the lameness advantage index were 0.79 (0.72–0.86), 0.68 (0.59–0.78), 0.94 (0.84–1.04), and 0.82 (0.74–0.91) for SH, SU, WL, and lameness, respectively. The same trends were present when the sire's lameness advantage index was evaluated in place of the animal's own, although the strength of this association was generally weaker. Conclusion The lameness advantage index is associated with SH, SU, and lameness, therefore selection on the lameness advantage index could be considered in herds aiming to reduce lameness. Where genomic testing of heifers is not conducted, sire lameness advantage index may still be effective to reduce SH and SU incidence.

Countries, which import a significant amount of semen, embryos and animals, are faced with the problem of how properly to evaluate the animals in the national evaluation system when information on the foreign parents is generally missing. Additional problems arise when the foreign parents obtain an evaluation, usually on the basis of progeny, in the country of import with the result that there are two published evaluations for the animals in question. This paper presents a post-iterative method of incorporating foreign information into home country evaluations. The foreign information is initially converted to the same scale and base as in the home country using procedures recommended by the International Bull Evaluation Service. The method consists essentially of calculating a combined evaluation for animals with home and foreign information as a weighted average of yield deviations, parent averages and progeny contributions from the foreign and home countries. The combined evaluations are used to adjust the evaluations of progeny on the basis of formulae derived from the usual mixed model equations. The same principles were used to combine reliabilities from the respective home and foreign reliabilities. The results from the application of the method to the United Kingdom (UK) Holstein Friesian population are presented. There was re-ranking of both bulls and cows, especially foreign bulls with few UK daughters.