S. Brotherstone

Estimating variance components for test day milk records by restricted maximum likelihood with a random regression animal model

Variance components for weekly averages of daily milk yield were estimated by restricted maximum likelihood (REML) using a random regression animal model. Additive genetic (σ2a) and permanent environmental (σ2pe) covariances were modelled with orthogonal polynomial regressions of varying order, while residual variance (σ2e) was assumed to be constant for yields in all or some weeks of lactation. The data comprised records of 488 first lactation Holstein–Friesian cows in one herd. The results indicate that the log likelihood increased as the order of polynomial regression in both the fixed and random part of the model increased from 3 to 5. However, only the first three eigenvalues of the additive covariance coefficient matrix were greater than zero in all models. Estimates of σ2a and σ2pe did not show any trend due to the increase in the order of the covariance function. Additive genetic variance declined from about 9 kg2 in week 4 to 6 kg2 in week 10 and increased linearly afterwards to peak at about 16 kg2 in week 35. Permanent environmental variance was relatively constant at about 12 kg2 in the first 35 weeks of lactation for most models. Estimates of residual variance (σ2e) in all stages of lactation declined as the order of fit of the other variance components increased and depended on the assumption about variation in measurement error across lactation. When assumed constant throughout lactation, σ2e was estimated as 3.2, 2.8 and 2.6 kg2 for the quadratic, cubic and quartic models, respectively.

Genetic correlations between linear type traits, food intake, live weight and condition score in Holstein Friesian dairy cattle

Variance components were estimated from an animal model using a restricted maximum likelihood procedure which allowed for unequal design matrices and missing observations (VCE). Data sets containing: (i) 15 275 records of linear type classifications on heifers, (ii) 3399 live weight and condition scores measured at calving and (iii) 1157 records of yield, dry-matter intake, average live weight and condition score during the first 26 weeks of lactation; were analysed jointly. Heritability estimates for dry-matter intake, live weight and condition score in the largest data set were 0·44, 0·44 and 0·35 respectively and the genetic correlation between condition score and the yield traits ranged from −0·29 to −0·46. The genetic correlation between milk yield and average live weight was negative (−0·09) but after adjusting for the genetic variation in condition score this correlation was positive (0·29). Genetic correlations between live weight and stature, chest width, body depth and rump width were consistently high (0·52 to 0·64; 0·75 to 0·86; 0·59 to 0·81; 0·56 to 0·74, respectively). Chest width and body depth were little to moderately correlated with dry-matter intake (0·25 to 0·28 and 0·20 to 0·34 respectively), and angularity (−0·47 to −0·77) and chest width (0·32 to 0·73) appeared to be good predictors of condition score. These correlations showed that (i) the relative value of live weight compared with food intake capacity determines the optimum direction of selection for stature, chest width, body depth and angularity, and consequently the optimum size of the dairy cow, and that (ii) live weight, condition score and food intake can be predicted from the type traits with little loss in accuracy. A restricted index which maintains condition score at its current level was predicted to reduce overall (economic) genetic gain by 5%.

Fit of standard models of the lactation curve to weekly records of milk production of cows in a single herd

Abstract Five standard lactation curve models (incomplete gamma, inverse polynomial, polynomial, exponential and mixed log) were used to predict a typical dairy cow lactation derived as the average daily milk yield of 325 complete first lactation Holstein–Friesian cows in one herd. All but one of these models were fitted to the lactation records of 488 individual cows to determine how well they predict the phenotype of each animals daily milk production. Accuracy was assessed by the correlation between observed and predicted yield, the magnitude and distribution of the residuals by lactation stage, and the proportion of individual lactations that were well predicted. All models tested predicted the pattern of mean herd lactation well, with little difference in fit. The residuals were mostly non-random, however, with serial correlations indicating biased predictions of yield at certain stages of lactation. The correlation between observed and predicted individual cows daily milk yields, however, ranged from 0.0 to 0.99 for all models. For some individual lactations, the difference between observed and predicted daily milk yield in certain weeks was as high as 5 kg. The models tested did equally well in predicting typical lactations, which peaked between weeks 6 and 9, and equally poorly in predicting non-typical lactations. The proportion of individual lactations accurately predicted in any group of cows therefore depends mainly on the number whose production follows the typical lactation pattern.

Genetic modelling of daily milk yield using orthogonal polynomials and parametric curves

Random regression models have been advocated for the analysis of test day records in dairy cattle. The effectiveness of a random regression analysis depends on the function used to model the data. To investigate functions suitable for the analysis of daily milk yield, test day milk yields of 7860 first lactation Holstein Friesian cows were analysed using random regression models involving three types of curves. Each analysis fitted the same curve to model overall trends through a fixed regression and random deviations due to animals. Curves included orthogonal polynomials, fitted to order 3 (quadratic), 4 (cubic) and 5 (quartic), respectively, a three-parameter parametric curve and a five-parameter parametric curve. Sets of random regression coefficients were fitted to model both animals’ genetic effects and permanent environmental effects. Temporary measurement errors were assumed independently but heterogeneously distributed, and assigned to one of 12 classes. Results showed that the measurement error variances were generally lowest around peak lactation, and higher at the beginning and end of lactation. Parametric curves yielded the highest likelihoods, but produced negative genetic associations between yield in early lactation and later lactation yields, while positive genetic correlations across the entire lactation were estimated with all models involving orthogonal polynomials. The fit of models using orthogonal polynomials to model test day yield was improved by including higher order fixed regressions.

Genetic evaluation of dairy bulls for energy balance traits using random regression

Current selection objectives for dairy cattle breeding may be favouring cows that are genetically predisposed to mobilize body tissue. This may have consequences for fertility since cows may resume reproductive activity only once the nadir of negative energy balance (NEB) has passed. In this study, we repeatedly measured food intake, live weight, milk yield and condition score of Holstein cattle in their first lactation. They were given either a high concentrate or low concentrate diet and were either selected or control animals for genetic merit for kg milk fat plus milk protein. Orthogonal polynomials were used to model each trait over time and random regression techniques allowed curves to vary between animals at both the genetic and the permanent environmental levels. Breeding values for bulls were calculated for each trait for each day of lactation. Estimates of genetic merit for energy balance were calculated from combined breeding values for either (1) food intake and milk yield output, or (2) live weight and condition-score changes. When estimated from daily fluxes of energy calculated from food intake and milk output, the average genetic merit of bulls for energy balance was approximately -15 MJ/day in early lactation. It became positive at about day 40 and rose to +18 MJ/day at approximately day 150. When estimated from body energy state changes the NEB in early lactation was also -15 MJ/day. It became positive at about day 80 and then rose to a peak of +10 MJ/day. The difference between the two methods may arise either because of the contribution of food wastage to intake measures or through inadequate predictions of body lipid from equations using live weight and condition score or a combination of both. Body energy mobilized in early lactation was not fully recovered until day 200 of lactation. The results suggest that energy balance may be estimated from changes in body energy state that can be calculated from body weight and condition score. Since body weight can be predicted from linear type measures, it may be possible to calculate breeding values for energy balance from national evaluations for production and type. Energy balance may be more suitable as a breeding objective than persistency.

Heterogeneity of variance amongst herds for milk production

Estimates were obtained of the variability among herds of dairy cattle of the standard deviation (s.d.) and coefficient of variation (CV) of milk, fat and protein yield. For fat yield, for example, the mean s.d. within herds for heifers was about 30 kg, the s.d. among herds was 5·2 kg and the mean and s.d. of CV were 0·15 and 0·026, respectively. Correlations of both s.d. and CV were high between both heifers and cows in the same herd and year and between heifers or cows in the same herd in successive years, showing that variability was consistent over time and over age groups.Ways of correcting for the heterogeneity of variance for use in cow index calculations are suggested; because CVs are heterogeneous, simple log transformation is not sufficient.

Genetic and phenotypic correlations between linear type traits and production traits in Holstein-Friesian dairy cattle

First lactation production and linear type records of 72 559Holstein-Friesian cows, calving from 1982 to 1989, were analysed by multivariate restricted maximum likelihood, using a sire model. The data comprised offspring of 1066 randomly used sires, and 91 proven i.e. widely used bulls. All phenotypic correlations between the type traits and the yield traits were small, but moderate genetic correlations were obtained between milk, fat and protein yield and angularity (~—0·43) and between the yield traits and udder depth (~0·44), indicating that higher yielding heifers are more angular and have deeper udders. The heritabilities of the type traits were in line with previous analyses, but those for milk, fat and protein yield were rather high at 0·47, 0·52 and 0·45 respectively

Genetics of tuberculosis in Irish Holstein-Friesian dairy herds

Information is lacking on genetic parameters for tuberculosis (TB) susceptibility in dairy cattle. Mycobacterium bovis is the principal agent of tuberculosis in cattle. The objective of this study was to quantify the genetic variation present among Irish Holstein-Friesian dairy herds in their susceptibility to M. bovis infection. A total of 15,182 cow and 8,104 heifer single intradermal comparative tuberculin test (SICTT, a test for M. bovis exposure and presumed infection) records from November 1, 2002, to October 31, 2005, were available for inclusion in the analysis. Data on observed carcass TB lesions from abattoirs were also available for inclusion in the analysis. The only animals retained were those present in a herd during episodes in which at least 2 animals showed evidence of infection; this ensured a high likelihood of exposure to M. bovis. Linear animal models, and sire and animal threshold models were used to estimate the variance components for susceptibility to M. bovis-purified protein derivative (PPD) responsiveness and confirmed M. bovis infection. The heritability estimates from the threshold sire models were biased upward because the relatedness between dam-daughter pairs was ignored. The threshold animal model produced heritability estimates of 0.14 in cows and 0.12 in heifers for susceptibility to M. bovis-PPD responsiveness, and 0.18 in cows for confirmed M. bovis infection susceptibility. Therefore, exploitable genetic variation exists among Irish dairy cows for susceptibility to M. bovis infection. Sire rankings from the linear and threshold animal models were similar, indicating that either model could be used for the analysis of susceptibility to M. bovis-PPD responsiveness. A favorable genetic correlation close to unity was observed between susceptibility to confirmed M. bovis infection and M. bovis-PPD responsiveness, indicating that direct selection for resistance to M. bovis-PPD responsiveness will indirectly reduce susceptibility to confirmed M. bovis infection. Data from the national TB eradication program could be used routinely to estimate breeding values for susceptibility to M. bovis infection.

Effect of gestation stage on milk yield and composition in Holstein Friesian dairy cattle

The effect of gestation stage on daily milk production and composition was investigated using first lactation weekly test day records of 325 Holstein Friesian cows in one herd. Gestation stage had a significant effect (P < 0.05) on all traits, accounting for 1.38 to 1.69% reduction in total sum of squares for yield traits and less than 0.4% reduction in total sum of squares for content traits. Decline in daily yield due to pregnancy began from the first month of gestation and increased non-linearly to about 3.0, 0.08, 0.12 and 0.14 kg/day respectively for milk, fat, protein and lactose yield in the 8th month of gestation, corresponding to 7–12% of the mean daily yield. There was little change in protein and lactose content but fat content increased significantly from the 6th month of gestation. A significant interaction between gestation stage and lactation stage was observed, indicating that the adverse effect of pregnancy was higher in mid lactation than in late lactation. Lactation milk, fat, protein and lactose yield was estimated to decline by 21, 1.5, 0.9 and 1.4 kg respectively for cows that were pregnant for three months during lactation. If pregnant for eight months, corresponding losses were 207, 8.1, 8.7 and 10.7 kg respectively due directly to the effect of pregnancy.

Evidence of genetic resistance of cattle to infection with Mycobacterium bovis.

Anecdotal evidence points to genetic variation in resistance of cattle to infection with Mycobacterium bovis, the causative agent of bovine tuberculosis (BTB), and published experimental evidence in deer and cattle suggests significant genetic variation in resistance and reactivity to diagnostic tests. However, such genetic variation has not been properly quantified in the United Kingdom dairy cattle population; it is possible that it exists and may be a factor influencing the occurrence of BTB. Using models based on the outcome of the process of diagnosis (ultimate fate models) and on the outcome of a single stage of diagnosis (continuation ratio models, herd test-date models), this study shows that there is heritable variation in individual cow susceptibility to BTB, and that selection for milk yield is unlikely to have contributed to the current epidemic. Results demonstrate that genetics could play an important role in controlling BTB by reducing both the incidence and the severity of herd breakdowns.