Genetic analysis of milk production traits of polish black and white cattle using large-scale random regression test-day models

Genetic parameters for milk, fat, and protein yield and persistency in the first 3 lactations of Polish Black and White cattle were estimated. A multiple-lactation model was applied with random herd-test-day effect, fixed regressions for herd-year and age-season of calving, and random regressions for the additive genetic and permanent environmental effects. Three data sets with slightly different edits on minimal number of days in milk and the size of herd-year class were used. Each subset included more than 0.5 million test-day records and more than 58,000 cows. Estimates of covariance components and genetic parameters for each trait were obtained by Bayesian methods using the Gibbs sampler. Due to the large size and a good structure of the data, no differences in estimates were found when additional criteria for record selection were applied. More than 95% of the genetic variance for all traits and lactations was explained by the first 2 principal components, which were associated with the mean yield and lactation persistency. Heritabilities of 305-d milk yield in the first 3 lactations (0.18, 0.16, 0.17) were lower than those for fat (0.12, 0.11, 0.12) and protein (0.13, 0.14, 0.15). Estimates of daily heritabilities increased in general with days in milk for all traits and lactations, with no apparent abnormalities at the beginning or end of lactation. Genetic correlations between yields in different lactations ranged from 0.74 (fat yield in lactations 1 and 3) to 0.89 (milk yield in lactations 2 and 3). Persistency of lactation was defined as the linear regression coefficient of the lactation curve. Heritability of persistency increased with lactation number for all traits and genetic correlations between persistency in different lactations were smaller than those for 305d yield. Persistency was not genetically correlated with the total yield in lactation.     

Genetic parameters for tunisian holsteins using a test-day random regression model

Genetic parameters of milk, fat, and protein yields were estimated in the first 3 lactations for registered Tunisian Holsteins. Data included 140,187; 97,404; and 62,221 test-day production records collected on 22,538; 15,257; and 9,722 first-, second-, and third-parity cows, respectively. Records were of cows calving from 1992 to 2004 in 96 herds. (Co)variance components were estimated by Bayesian methods and a 3-trait-3-lactation random regression model. Gibbs sampling was used to obtain posterior distributions. The model included herd × test date, age × season of calving × stage of lactation [classes of 25 days in milk (DIM)], production sector × stage of lactation (classes of 5 DIM) as fixed effects, and random regression coefficients for additive genetic, permanent environmental, and herd-year of calving effects, which were defined as modified constant, linear, and quadratic Legendre coefficients. Heritability estimates for 305-d milk, fat and protein yields were moderate (0.12 to 0.18) and in the same range of parameters estimated in management systems with low to medium production levels. Heritabilities of test-day milk and protein yields for selected DIM were higher in the middle than at the beginning or the end of lactation. Inversely, heritabilities of fat yield were high at the peripheries of lactation. Genetic correlations among 305-d yield traits ranged from 0.50 to 0.86. The largest genetic correlation was observed between the first and second lactation, potentially due to the limited expression of genetic potential of superior cows in later lactations. Results suggested a lack of adaptation under the local management and climatic conditions. Results should be useful to implement a BLUP evaluation for the Tunisian cow population; however, results also indicated that further research focused on data quality might be needed.     

Comparison of random regression test-day models for Polish Black and White cattle

Test-day milk yields of first-lactation Black and White cows were used to select the model for routine genetic evaluation of dairy cattle in Poland. The population of Polish Black and White cows is characterized by small herd size, low level of production, and relatively early peak of lactation. Several random regression models for first-lactation milk yield were initially compared using the “percentage of squared bias” criterion and the correlations between true and predicted breeding values. Models with random herd-test-date effects, fixed age-season and herd-year curves, and random additive genetic and permanent environmental curves (Legendre polynomials of different orders were used for all regressions) were chosen for further studies. Additional comparisons included analyses of the residuals and shapes of variance curves in days in milk. The low production level and early peak of lactation of the breed required the use of Legendre polynomials of order 5 to describe age-season lactation curves. For the other curves, Legendre polynomials of order 3 satisfactorily described daily milk yield variation. Fitting third-order polynomials for the permanent environmental effect made it possible to adequately account for heterogeneous residual variance at different stages of lactation.     

Genetic parameters for a multiple-trait multiple-lactation random regression test-day model in Italian Holsteins

The objectives of this study were to estimate variance components for test-day milk, fat, and protein yields and average daily SCS in 3 subsets of Italian Holsteins using a multiple-trait, multiple-lactation random regression test-day animal model and to determine whether a genetic heterogeneous variance adjustment was necessary. Data were test-day yields of milk, fat, and protein and SCS (on a log₂ scale) from the first 3 lactations of Italian Holsteins collected from 1992 to 2002. The 3 subsets of data included 1) a random sample of Holsteins from all herds in Italy, 2) a random sample of Holsteins from herds using a minimum of 75% foreign sires, and 3) a random sample of Holsteins from herds using a maximum of 25% foreign sires. Estimations of variances and covariances for this model were achieved by Bayesian methods using the Gibbs sampler. Estimated 305-d genetic, permanent environmental, and residual variance was higher in herds using a minimum of 75% foreign sires compared with herds using a maximum of 25% foreign sires. Estimated average daily heritability of milk, fat, and protein yields did not differ among subsets. Heritability of SCS in the first lactation differed slightly among subsets and was estimated to be the highest in herds with a maximum of 25% foreign sire use (0.19 ± 0.01). Genetic correlations across lactations for milk, fat, and protein yields were similar among subsets. Genetic correlations across lactations for SCS were 0.03 to 0.08 higher in herds using a minimum of 75% or a maximum of 25% foreign sires, compared with herds randomly sampled from the entire population. Results indicate that adjustment for heterogeneous variance at the genetic level based on the percentage of foreign sire use should not be necessary with a multiple-trait random regression test-day animal model in Italy.     

Adjustment for heterogeneous covariance due to herd milk yield by transformation of test-day random regressions

A method of accounting for differences in covariance components of test-day milk records was developed based on transformation of regressions for random effects. Preliminary analysis indicated that genetic and nongenetic covariance structures differed by herd milk yield. Differences were found for phenotypic covariances and also for genetic, permanent environmental, and herd-time covariances. Heritabilities for test-day milk yield tended to be lower at the end and especially at the start of lactation; they also were higher (maximum of ∼25%) for high-yield herds and lower (maximum of 15%) for low-yield herds. Permanent environmental variances were on average 10% lower in high-yield herds. Relative herd-time variances were ∼10% at start of lactation and then began to decrease regardless of herd yield; high-yield herds increased in midlactation followed by another decrease, and medium-yield herds increased at the end of lactation. Regressors for random regression effects were transformed to adjust for heterogeneity of test-day yield covariances. Some animal reranking occurred because of this transformation of genetic and permanent environmental effects. When genetic correlations between environments were allowed to differ from 1, some additional animal re-ranking occurred. Correlations of variances of genetic and permanent-environmental regression solutions within herd, test-day, and milking frequency class with class mean milk yields were reduced with adjustment for heterogeneous covariance. The method suggests a number of innovative solutions to issues related to heterogeneous covariance structures, such as adjusted estimates in multibreed evaluation.     

Associations of breed and feeding management with milk production curves at herd level using a random regression test-day model

Earlier studies identified large between-herd variation in estimated lactation curve parameters from test-day milk yield and milk composition records collected in Ragusa province, Italy. The objective of this study was to identify sources of variation able to explain these between-herd differences in milk production curves, by estimating associations of animal breed (Holstein Friesian vs. Brown Swiss), feeding system [separate feeding (SF) vs. total mixed ration (TMR)], and TMR chemical composition on milk and milk components herd curves. Data recorded from 1992 through 2007 for test-day (TD) milk, fat, and protein yields from 1,287,019 records of 148,951 lactations of 51,489 cows in 427 herds were processed using a random regression TD model. Random herd curves (HCUR) for milk, fat, and protein yields were estimated from the model per herd, year, and parity (1, 2, and 3+) using 4-order Legendre polynomials. From March 2006 through December 2007, samples of TMR were collected every 3 mo from 37 farms in Ragusa province. Samples were analyzed for dry matter, ash, crude protein, soluble nitrogen, acid detergent lignin, neutral detergent fiber, acid detergent fiber, and starch. Traits used to describe milk production curves were peak, days in milk at peak, persistency, and mean. Association of feeding system and animal breed with HCUR traits was investigated using a general mixed model procedure. Association of TMR chemical composition with HCUR traits was investigated using multivariate analysis with regression and stepwise model selection. Results were consistent for all traits and parities. Feeding system was significantly associated with HCUR peak and mean, with higher values for TMR. Animal breed was significantly associated with HCUR persistency, with higher values for Brown Swiss herds. Furthermore, animal breed influenced HCUR peak and mean, with higher values for Holstein Friesian herds. Crude protein had the largest effect on HCUR peak and mean, whereas the interaction between crude protein and dry matter mainly affected persistency. When provided by a national evaluation system, HCUR can be used as an indicator of herd feeding management.     

Derivation and calculation of approximate reliabilities and daughter yield-deviations of a random regression test-day model for genetic evaluation of dairy cattle

Test-day milk, fat, protein yield, and somatic cell score (SCS) were analyzed separately using data from the first 3 lactations and a random regression model. Data used in the model were from Austria, Germany, and Luxembourg and from Holstein, Red, and Jersey dairy cattle. For reliability approximation, a multiple-trait effective daughter contribution (MTEDC) method was developed under general multiple trait models, including random regression test-day models, by extending the single-trait daughter equivalents concept. The MTEDC was applied to the very large dairy population, with about 15.5 million animals. The calculation of reliabilities required less computer memory than the corresponding iteration program and a significantly lower computing time equivalent to 24 rounds of iteration. A formula for daughter-yield deviations was derived for bulls under multiple-trait models. Reliability associated with daughter-yield deviations was approximated using the MTEDC method. Both the daughter-yield deviation formula and associated reliability method were verified in a simulation study using the random regression test-day model. Correlations of lactation daughter-yield deviations with estimated breeding values calculated from a routine genetic evaluation were 0.996 for all bulls and 0.95 for young bulls having only daughters with short lactations.     

Genetic parameters for milk production and persistency for Danish Holsteins estimated in random regression models using REML

(Co)variance components for milk, fat, and protein yield of 8075 first-parity Danish Holsteins (DH) were estimated in random regression models by REML. For all analyses, the fixed part of the model was held constant, whereas four different functions were applied to model the additive genetic effect and the permanent environment effect. Homogeneous residual variance was assumed throughout lactation. Univariate models were compared using a minimum of -2 ln(restricted likelihood) as the criterion for best fit. Heritabilities as a function of time were calculated from the estimated curve parameters from univariate analyses. Independent of the function applied and the trait in question, heritabilities were lowest in the beginning of the lactation. Heritabilities for persistency of fat yield were slightly higher than heritabilities for persistency of milk and protein yield. Genetic correlations between persistency and 305-d production were higher for protein and milk yield than for fat yield. Bivariate analyses between the production traits were carried out in sire models using the models with the best 3-parameter curve fit in the univariate analyses. Correlations between traits were calculated from covariance components for curve parameters estimated in bivariate analyses. Genetic correlations between milk and protein yield were higher than between milk and fat yield.     

Variance components for test-day milk, fat, and protein yield, and somatic cell score for analyzing management information

Test-day (TD) models are used in most countries to perform national genetic evaluations for dairy cattle. The TD models estimate lactation curves and their changes as well as variation in populations. Although potentially useful, little attention has been given to the application of TD models for management purposes. The potential of the TD model for management use depends on its ability to describe within- or between-herd variation that can be linked to specific management practices. The aim of this study was to estimate variance components for milk yield, milk component yields, and somatic cell score (SCS) of dairy cows in the Ragusa and Vicenza areas of Italy, such that the most relevant sources of variation can be identified for the development of management parameters. The available data set contained 1,080,637 TD records of 42,817 cows in 471 herds. Variance components were estimated with a multilactation, random-regression, TD animal model by using the software adopted by NRS for the Dutch national genetic evaluation. The model comprised 5 fixed effects [region × parity × days in milk (DIM), parity × year of calving × season of calving × DIM, parity × age at calving × year of calving, parity × calving interval × stage of pregnancy, and year of test × calendar week of test] and random herd × test date, regressions for herd lactation curve (HCUR), the animal additive genetic effect, and the permanent environmental effect by using fourth-order Legendre polynomials. The HCUR variances for milk and protein yields were highest around the time of peak yield (DIM 50 to 150), whereas for fat yield the HCUR variance was relatively constant throughout first lactation and decreased following the peak around 40 to 90 DIM for lactations 2 and 3. For SCS, the HCUR variances were relatively small compared with the genetic, permanent environmental, and residual variances. For all the traits except SCS, the variance explained by random herd × test date was much smaller than the HCUR variance, which indicates that the development of management parameters should focus on between-herd parameters during peak lactation for milk and milk components. For SCS, the within-herd variance was greater than the between-herd variance, suggesting that the focus should be on management parameters explaining variances at the cow level. The present study showed clear evidence for the benefits of using a random regression TD model for management decisions.     

Use of herd solutions from a random regression test-day model for diagnostic dairy herd management

In a random regression test-day model, environmental effects in addition to individual animal factors can be included and analyzed. Moreover, instead of herd-year classification of the management groups, the herd-test-day classification within the model better accounts for month-to-month short-term environmental variation in production and somatic cell count (SCC) traits. The herd management levels of milk yield (milk deviation from whole-country mean, kilograms/day), protein and fat concentration (protein and fat deviation, %), and SCC (SCC deviation, 1,000 cells/mL) are used in the dairy herd management Web application “Maitoisa” (in English, “Milky”). This management tool helps to recognize several management problems. For recognition of systematic patterns and single unusual test-days, a monthly time-trend analysis was developed to smooth the random fluctuations and display the yearly production pattern. In addition to analyzing single test-day deviations from the mean, modeled herd solutions assist users in identifying repeated phenomena and enable the forecasting of the management pattern for the subsequent year. The solutions are displayed either as tables or graphs plotted by calendar months. In addition to management effects of the farmer's own herd, he or she can request country or region percentiles to be displayed in the graphs. The Web service has been offered to farmers and dairy advisors since 2001, and it has proved to be a powerful tool for herd monitoring and planning.     

Random herd curves in a test-day model for milk, fat, and protein production of dairy cattle in The Netherlands

With random regression models, genetic parameters of test-day milk production records of dairy cattle can be estimated directly from the data. However, several researchers that used this method have reported unrealistically high variances at the borders of the lactation trajectory and low genetic correlations between beginning and end of lactation. Recently, it has been proposed to include herd-specific regression curves in the random regression model. The objective was to study the effect of including random herd curves on estimated genetic parameters. Genetic parameters were estimated with 2 models; both included random regressions for the additive genetic and permanent environmental effect, whereas the second model also included a random regression effect for herd x 2-yr period of calving. All random regressions were modeled with fourth-order Legendre polynomials. Bayesian techniques with Gibbs sampling were used to estimate all parameters. The data set comprised 857,255 test-day milk, fat, and protein records from lactations 1, 2, and 3 of 43,990 Holstein cows from 544 herds. Genetic variances estimated by the second model were lower in the first 100 d and at the end of the lactation, especially in lactations 2 and 3. Genetic correlations between d 50 and the end of lactation were around 0.25 higher in the second model and were consistent with studies where lactation stages are modeled as different traits. Subsequently, estimated heritabilities for persistency were up to 0.14 lower in the second model. It is suggested to include herd curves in a random regression model when estimating genetic parameters of test-day production traits in dairy cattle.     

Assessment of homogeneity vs. heterogeneity of residual variance in random regression test-day models in a Bayesian analysis

Test-day first-lactation milk yields from Holstein cows were analyzed with a set of random regression models based on Legendre polynomials of varying order on additive genetic and permanent environmental effects. Homogeneity and heterogeneity of residual variance, assuming three and 30 arbitrary measurement error classes of different length were considered. Unknown parameters were estimated within a Bayesian framework. Bayes factors and a checking function for the cross-validation predictive densities of the data were the tools chosen for selecting among competing models. Residual variances obtained from 30 arbitrary intervals were nearly constant between d 70 and 300 and tended to increase towards the extremes of the lactation, especially at the onset. In early lactation, the temporary measurement errors were found to be larger and highly variable. A high order of the regression submodels employed for modeling the permanent environmental deviations tended to strongly correct the heterogeneity of the residual variance. Accordingly, the assumption of homogeneity of residual variance was the most plausible specification under both comparison criteria when the number of random regression coefficients was set to five. Otherwise, the heterogeneity assumption, using three or 30 error classes, was better supported, depending on the criterion and on the order of the submodel fitted for the permanent environmental effect.     

Genetic line comparisons and genetic parameters for endoparasite infections and test-day milk production traits

Keeping dairy cows in grassland systems relies on detailed analyses of genetic resistance against endoparasite infections, including between- and within-breed genetic evaluations. The objectives of this study were (1) to compare different Black and White dairy cattle selection lines for endoparasite infections and (2) the estimation of genetic (co)variance components for endoparasite and test-day milk production traits within the Black and White cattle population. A total of 2,006 fecal samples were taken during 2 farm visits in summer and autumn 2015 from 1,166 cows kept in 17 small- and medium-scale organic and conventional German grassland farms. Fecal egg counts were determined for gastrointestinal nematodes (FEC-GIN) and flukes (FEC-FLU), and fecal larvae counts for the bovine lungworm Dictyocaulus viviparus (FLC-DV). The lowest values for gastrointestinal nematode infections were identified for genetic lines adopted to pasture-based production systems, especially selection lines from New Zealand. Heritabilities were low for FEC-GIN (0.05–0.06 ± 0.04) and FLC-DV (0.05 ± 0.04), but moderate for FEC-FLU (0.33 ± 0.06). Almost identical heritabilities were estimated for different endoparasite trait transformations (log-transformation, square root). The genetic correlation between FEC-GIN and FLC-DV was 1.00 ± 0.60, slightly negative between FEC-GIN and FEC-FLU (?0.10 ± 0.27), and close to zero between FLC-DV and FEC-FLU (0.03 ± 0.30). Random regression test-day models on a continuous time scale [days in milk (DIM)] were applied to estimate genetic relationships between endoparasite and longitudinal test-day production traits. Genetic correlations were negative between FEC-GIN and milk yield (MY) until DIM 85, and between FEC-FLU and MY until DIM 215. Genetic correlations between FLC-DV and MY were negative throughout lactation, indicating improved disease resistance for high-productivity cows. Genetic relationships between FEC-GIN and FEC-FLU with milk protein content were negative for all DIM. Apart from the very early and very late lactation stage, genetic correlations between FEC-GIN and milk fat content were negative, whereas they were positive for FEC-FLU. Genetic correlations between FEC-GIN and somatic cell score were positive, indicating similar genetic mechanisms for susceptibility to udder and endoparasite infections. The moderate heritabilities for FEC-FLU suggest inclusion of FEC-FLU into overall organic dairy cattle breeding goals to achieve long-term selection response for disease resistance.     

Relationship of test-day somatic cell score with test-day and lactation milk yields

To determine the relationship of test-day (TD) somatic cell score (SCS) to TD and lactation milk yields, 1,320,590 records from Holstein first and second calvings from 1995 through 2002 were examined. All lactations had recorded yield and SCS for at least the first 4 TD. Least square analyses were conducted for yields on TD 2 through 10 within herd and cow. The model included regressions on current TD SCS and mean SCS of all previous TD with separate estimates by parity; effects for parity and calving year were included as well as regression on days in milk on TD 1. Corresponding analyses were conducted without regression on current SCS. An analysis of lactation yield was performed with a similar model and regression on all TD SCS. The SCS was highest most often on TD 1 for parity 1 (22.5%) and on TD 10 for parity 2 (18.5%). Regression of TD milk yield on mean of previous TD SCS was highest during the latter half of lactation (maximum of -0.346 kg/SCS unit on TD 9) for parity 1 and during TD through 7 (maximum of -0.366 kg/SCS unit on TD 4) for parity 2. Regression of TD yield on current TD SCS tended to be larger for later lactation. Regression of lactation yield on TD SCS was negative and important for TD 1 through 6 for parity 1 and for all TD for parity 2. To minimize milk loss, mastitis control is most important immediately pre- and postcalving for parity 1 and throughout lactation for parity 2.     

Short communication: Genetic parameters of production traits in Chinese Holsteins using a random regression test-day model

The objective of this study was to estimate genetic parameters of production traits in the first 3 parities in Chinese Holsteins. Data were a random sample of complete herds (109,005 test-day records of 9,706 cows from 54 herds) extracted from the original data set, which included 362,304 test-day records of 30,942 Holstein cows from 105 herds. A test-day animal model with multiple-trait random regression and the Gibbs sampling method were used for parameter estimation. Regression curves were modeled using Legendre polynomials of order 4. The multiple-trait analysis included milk, fat, and protein yield, and somatic cell score (SCS). Average daily heritabilities ranged between 0.222 and 0.346 for the yield traits and between 0.092 and 0.187 for SCS. Heritabilities were higher in the third lactation for all traits. Within-parity genetic correlations were very high among the yield traits (>0.806) and were close to zero between SCS and yield traits, especially for first-parity cows. Results were similar to previous literature estimates from studies that used the same model as applied to this study. The estimates found in this study will be used to perform breeding value estimation for national genetic evaluations in Chinese Holsteins.     

Random regression test-day models with residuals following a Student's-t distribution

First-lactation milk yield test-day records of Canadian Holsteins were analyzed by single-trait random regression test-day models that assumed normal or Student's-t distribution for residuals. Objectives were to test the performance of the robust statistical models that use heavy-tailed distributions for the residual effect. Models fitted were: Gaussian, Student's-t, and Student's-t with fixed number of degrees of freedom (equal to 5, 15, 30, 100 or 1000) for the t distribution. Bayesian methods with Gibbs sampling were used to make inferences about overall model plausibility through Bayes factors, posterior means for covariance components, estimated breeding values for regression coefficients, solutions for permanent environmental regressions, and residuals of the models. Bayes factors favored Student's-t model with the posterior mean of degrees of freedom equal to 2.4 over all other models, indicating very strong departure from normality. Number of outliers in Student's-t model was reduced by 35% in comparison with the Gaussian model. Differences in covariance components for regression coefficients between models were small, and rankings of animals based on additive genetic merit for the first two regression coefficients (total yield and persistency) were similar. Results from the Gaussian and Student's-t models with fixed degrees of freedom become more alike (smaller departures from normality for Student's-t models) with increasing number of degrees of freedom for the t-distributions. For any pair of Student's-t models, the one with the smaller number of degrees of freedom for the t-distribution was shown to be superior. Similarly, number of outliers increased with increasing degrees of freedom for the t distribution.     

Random regression analysis of milk yield and milk composition in the first and second lactations of Murciano-Granadina goats

Records from the milk recording scheme of Spanish Murciano-Granadina goats were studied to estimate genetic (co)variance components and breeding values throughout the first and second lactations. The data used consisted of 49,696 monthly test-day records of milk (MY), protein (PY), fat (FY), and dry matter (DMY) yields from 5,163 goats, distributed in 20 herds, offspring of 2,086 does and 206 bucks. These records were analyzed by 2-trait random regression models (RRM) and a repeatability test-day model (RTDM). At the middle of lactation, heritability estimates for MY, DMY, and FY obtained with RTDM were larger than those estimated with RRM, and the opposite was true for PY. The RRM estimates of heritability for MY, FY, and PY were very similar throughout the trajectories of both lactations. Heritability estimates for DMY decreased through the lactation period. The genetic correlations between the first and second lactation records estimated for all traits by RRM were positive and ranged from 0.43 to 0.80 throughout the lactation curves. The correlation between BV estimated with RTDM and RRM was 0.742 for MY and 0.664 for DMY. The RRM could be a useful alternative to RTDM for the prediction of BV in this breed.     

Genetic parameters for test-day electrical conductivity of milk for first-lactation cows from random regression models

Electrical conductivity (EC) of milk has been introduced as an indicator trait for mastitis during the last few decades. The correlation of EC to mastitis, easy access to EC data, and the low cost of recording are properties that make EC a good indicator trait for mastitis. In this study, EC was measured daily during the lactation and available from 2101 first-lactation Holstein cows in 8 herds in the United States. Data were analyzed with an animal model that included herd-test-day, age at calving and days in milk (DIM) as fixed effects, and random additive genetic and permanent environmental effects. A repeatability model and 5 random regression (RR) models with increasing order of Legendre polynomials were used. The goodness of fit for the different models was evaluated based on several tests. Our results indicate that the best model was a RR model with a fourth-order Legendre polynomial for both additive genetic and permanent environmental effects. Heritability estimates obtained with this model were from 0.26 to 0.36. Due to the relatively high heritability obtained for EC of milk, EC might be a potential indicator trait to use in a breeding program designed to reduce the incidence of mastitis.     

Genetic parameters for test-day yield of milk, fat and protein in buffaloes estimated by random regression models

The test-day yields of milk, fat and protein were analysed from 1433 first lactations of buffaloes of the Murrah breed, daughters of 113 sires from 12 herds in the state of S?o Paulo, Brazil, born between 1985 and 2007. For the test-day yields, 10 monthly classes of lactation days were considered. The contemporary groups were defined as the herd-year-month of the test day. Random additive genetic, permanent environmental and residual effects were included in the model. The fixed effects considered were the contemporary group, number of milkings (1 or 2 milkings), linear and quadratic effects of the covariable cow age at calving and the mean lactation curve of the population (modelled by third-order Legendre orthogonal polynomials). The random additive genetic and permanent environmental effects were estimated by means of regression on third- to sixth-order Legendre orthogonal polynomials. The residual variances were modelled with a homogenous structure and various heterogeneous classes. According to the likelihood-ratio test, the best model for milk and fat production was that with four residual variance classes, while a third-order Legendre polynomial was best for the additive genetic effect for milk and fat yield, a fourth-order polynomial was best for the permanent environmental effect for milk production and a fifth-order polynomial was best for fat production. For protein yield, the best model was that with three residual variance classes and third- and fourth-order Legendre polynomials were best for the additive genetic and permanent environmental effects, respectively. The heritability estimates for the characteristics analysed were moderate, varying from 0·16±0·05 to 0·29±0·05 for milk yield, 0·20±0·05 to 0·30±0·08 for fat yield and 0·18±0·06 to 0·27±0·08 for protein yield. The estimates of the genetic correlations between the tests varied from 0·18±0·120 to 0·99±0·002; from 0·44±0·080 to 0·99±0·004; and from 0·41±0·080 to 0·99±0·004, for milk, fat and protein production, respectively, indicating that whatever the selection criterion used, indirect genetic gains can be expected throughout the lactation curve.     

Bivariate analysis of conception rates and test-day milk yields in Holsteins using a threshold-linear model with random regressions

The objective of this study was to estimate genetic correlations between conception rates (CR) and test-day (TD) milk yields in Holsteins for different days in milk (DIM) in small and large herds. The data included 217,213 first-parity service records of 94,984 cows in New York State between 1999 and 2003. The CR was defined as the outcome of a single insemination. Conception rate and TD milk were analyzed using a series of threshold-linear models with fixed effects that included herd-test-date for TD milk and herd-year for CR, age, service month, cubic regressions on DIM using Legendre polynomials and with random effects that included herd × sire interaction, sire additive genetic and permanent environments with quadratic random regressions on DIM, service sire for CR, and residual. Variance components were estimated using a Bayesian method via Gibbs sampling. Herds were categorized into small (≤80 cows) and large operations. Large herds produced a higher TD milk (34.0 vs. 30.8 kg), had lower CR (29.5 vs. 34.4%), began breeding earlier (75 vs. 92 d to first service), and had fewer days open (138 vs. 145 d). The average CR was 20% at 50 DIM, increased to about 38% at DIM 100, and then leveled off. Estimated genetic correlations between CR and TD milk stayed around −0.15 for small herds but changed from positive (0.3) at 60 DIM to negative (−0.3) at 120 DIM for large herds. Genetic correlations for CR between small and large herds were highest at 80 DIM and lowest at 140 DIM. The chi-square test showed that the frequency of service records was significantly different during a given week for 71% of large herds and for 15% of small herds, suggesting more timed artificial insemination services in large herds. For the top 15% of cows for milk, fertility peaked around 100 DIM in large herds and at around 100 and 170 DIM in small herds. It seems that optimum breeding practices in large herds of breeding cows earlier are already followed.