Application of genomic evaluation to dairy cattle in New Zealand.

A hybrid method of estimating genomically enhanced breeding values (GEBV) that uses features of a single-step approach and traditional national estimated breeding value (EBV), based on pedigree, as the starting point was developed and assessed. The method uses deregressed EBV from the traditional EBV estimation procedures and a pedigree matrix that is augmented by a genomic relationship matrix based on a Euclidean distance (EDM) in a Gaussian kernel. Genotypes were obtained using the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). The pedigree information is restricted to animals with genotypes, as well as all of their ancestors, resulting in a system of equations that is considerably smaller than that of the national evaluation. Genome-wide association studies were used to identify regions of the genome that had high association with the traits in the New Zealand national breeding objective. The EDM were created for each selected region. The amount of variance accounted for by each region was estimated, and the variances, relative to the EDM excluding these areas, were used to create trait-specific weighted EDM that were used for the evaluations. The evaluation is done on the restricted data set and is a reversal of the deregression procedure using the augmented pedigree-based relationship matrix. The method was tested using data on 7,204 progeny-tested sires, in which the daughter records for the 3 youngest cohorts (i.e., validation data; n=1,410) were excluded. Evaluations were done for the 7 traits (3 production, 4 nonproduction) in the New Zealand national breeding objective. Regression of the traditional EBV based on daughter information on the GEBV for validation sires had an average slope of 0.99 (range 0.93 to 1.06); the average correlation between the EBV was 0.79 (range 0.56 to 0.84). The average slope and correlation for the previously used blended GEBV were 0.64 and 0.61, respectively. The method was applied to all genotyped animals that included approximately 13,000 genotyped males and 47,000 genotyped females and their ancestors. The correlation between the traditional EBV and GEBV of the proven bulls was 0.99; the correlations obtained from the previously used blended GEBV were 0.88 (no inflation adjustment) and 0.94 (following inflation adjustment). The values for the unproven bulls were 0.95 (parent average EBV and GEBV), 0.56 (blended GEBV, no inflation adjustment), and 0.88 (blended GEBV, following inflation adjustment). The use of trait-specific weighted EDM provided a 1 to 2% improvement in the accuracy of the genomic evaluations of the production traits and no improvement in the nonproduction traits. The hybrid method of estimating GEBV was found to be considerably less biased and generally more accurate than the previously used blended genomic breeding value.

Phenotypic associations between traits other than production and longevity in New Zealand dairy cattle.

A proportional hazards model was used to investigate the phenotypic effect of traits other than production (TOP) on true and functional longevity across purebred and crossbred Holstein-Friesian and Jersey dairy cattle in registered and commercial herds in New Zealand. The hazard function was described as the product of a baseline hazard function and the time-independent effects of age at first calving, heterosis, proportion of breed, period of last calving relative to herdmates, and TOP; a time-dependent effect of herd-year was also included. The influence of TOP on functional longevity was assessed by adjusting true longevity for the time-independent effects of production values as well as the time-dependent effects of deviation of milk, fat, and protein yield within contemporary group. All analyses were stratified by breed, and separate analyses were carried out for registered or commercial herds. All TOP were significantly related to true and functional longevity. Obvious differences existed in the relative influence of individual TOP on longevity in registered or commercial herds. Of the individual TOP describing the physical characteristics of the cow, the udder-related TOP exhibited the largest influence on functional longevity. Farmer opinion explained the largest proportion of variation in true and functional longevity among cows. In commercial herds, the risk of culling in cows with very low farmer opinion was 1.5 to 2.0 times that in cows with average or high farmer opinion.

Estimation of heritabilities and correlations associated with milk color traits.

The objective of this study was to estimate the genetic parameters associated with milk color traits of dairy cattle. The data consisted of test day records of 9516 first lactation dairy cows and the records of 6358 of these cows that went on to produce a second lactation. Friesians, Jerseys, and crossbred cows were included in the data. Test day records included measures of milk, fat, and protein as well as milk color measured as absorbance at 450 nm. From these measurements, fat color and beta-carotene yield were calculated. Analyses were performed both within and across breeds. Jerseys produced more beta-carotene than did Friesians, and milk and fat from Jerseys had more intense color. Lactation model estimates for the heritabilities of milk color traits ranged from 0.33 to 0.44 (across breed), 0.40 to 0.49 (Friesians), and 0.17 to 0.31 (Jerseys). In all analyses, the heritability estimates associated with beta-carotene yield were lower than the estimates associated with the color of milk or fat. Genetic correlations between beta-carotene yield and the production traits were positive, but genetic correlations between fat color and production traits were generally negative. Genetic correlations between milk color and milk and protein yields were negative, and the correlations with fat yield were close to zero.