A.B. Bignardi

Random regression models using different functions to model test-day milk yield of Brazilian Holstein cows

We analyzed 152,145 test-day records from 7317 first lactations of Holstein cows recorded from 1995 to 2003. Our objective was to model variations in test-day milk yield during the first lactation of Holstein cows by random regression model (RRM), using various functions in order to obtain adequate and parsimonious models for the estimation of genetic parameters. Test-day milk yields were grouped into weekly classes of days in milk, ranging from 1 to 44 weeks. The contemporary groups were defined as herd-test-day. The analyses were performed using a single-trait RRM, including the direct additive, permanent environmental and residual random effects. In addition, contemporary group and linear and quadratic effects of the age of cow at calving were included as fixed effects. The mean trend of milk yield was modeled with a fourth-order orthogonal Legendre polynomial. The additive genetic and permanent environmental covariance functions were estimated by random regression on two parametric functions, Ali and Schaeffer and Wilmink, and on B-spline functions of days in milk. The covariance components and the genetic parameters were estimated by the restricted maximum likelihood method. Results from RRM parametric and B-spline functions were compared to RRM on Legendre polynomials and with a multi-trait analysis, using the same data set. Heritability estimates presented similar trends during mid-lactation (13 to 31 weeks) and between week 37 and the end of lactation, for all RRM. Heritabilities obtained by multi-trait analysis were of a lower magnitude than those estimated by RRM. The RRMs with a higher number of parameters were more useful to describe the genetic variation of test-day milk yield throughout the lactation. RRM using B-spline and Legendre polynomials as base functions appears to be the most adequate to describe the covariance structure of the data.

Genetic relationships among traits related to reproduction and growth of Nelore females

The objective of the study presented here was to analyze the genetic relationships among heifer pregnancy (HP), age at first calving (AFC), stayability (STAY), average annual productivity of the cow, in kilograms of weaned calf per cow per year (PRODAM), postweaning weight gain (PWG), and hip height (HH) of Nelore females from 12 Brazilian herds. (Co)variance components were obtained by six-trait animal model using Gibbs sampling. The posterior mean of the heritability estimates were 0.37, 0.18, 0.19, 0.16, 0.21, and 0.37 for HP, AFC, STAY, PRODAM, PWG, and HH, respectively. In general, the genetic correlations were strong between traits related to reproduction, for example, -0.85 between HP and AFC, and 0.94 between STAY and PRODAM. Weak genetic correlations were obtained between reproductive and growth traits (absolute values ranging from 0.02 to 0.30). Although weak, the genetic correlations between PWG and reproductive traits were favorable, whereas the genetic correlations between HH and reproductive traits were close to zero and slightly unfavorable for HP, AFC, and STAY. An increase of HH is therefore expected to have little or no negative effect on the reproductive performance of females. The posterior mean of genetic correlation between PWG and HH was moderate (0.50). On the basis of the heritability, genetic correlation estimates, and time to obtain data, HP and PRODAM seems to show the best potential as selection criteria to improve the productive and reproductive performance of Nelore females. In principle, it is possible to select for increased PWG without compromising the reproduction of Nelore females. However, selection for PWG may result in an increase of female HH as a correlated response, a fact that could increase management costs in advanced generations of selection. In the light of the results, all traits studied here can be used as selection criteria and there is no strong evidence of genetic antagonism among traits related to reproduction and growth of Nelore females.

Two-trait random regression model to estimate the genetic association of scrotal circumference with female reproductive performance in Nelore cattle.

In an attempt to determine when scrotal circumference (SC) could be a reasonable indicator of female reproductive performance, a series of two-trait random regression model (regression for SC on age at measurement) using Gibbs sampling was applied to field data of Nelore cattle raised in a tropical environment. The female traits evaluated were age at first calving (AFC), first calving interval (FCI), heifer pregnancy (HP), and stayability (STAY). The posterior means of heritability of female traits ranged from 0.15 for AFC to 0.46 for HP and were about 0.50 for SC. The posterior means of genetic correlations between SC and AFC, FCI, HP, STAY were up to -0.70, -0.25, 0.48, and 0.29, respectively. Genetically, SC could be a reasonable indicator of female puberty (e.g., HP) as long as it is measured at a young age (400-440 days). However, for female reproductive traits measured at an older age (e.g., STAY), SC is merely a modest or even poor indicator. The use of sire expected progeny differences for female reproductive traits will be more effective than the use of expected progeny differences for SC to improve the reproductive performance of female cattle.

Multi-trait linear reaction norm model to describe the pattern of phenotypic expression of some economic traits in beef cattle across a range of environments

The multi-trait reaction norm (MTRN) model was extended to beef cattle reared under tropical conditions with the following objectives: to compare multi-trait (MT) and MTRN models regarding the genetic parameters obtained; and to characterize G × E, the pattern of phenotypic expression, and the environmental sensitivity of animals for postweaning weight gain (PWG), scrotal circumference (SC), and annual average productivity of the cow (PRODAM). There was divergence in the estimates between the MT and MTRN models when the posterior probability intervals of additive genetic variances and heritability coefficients of PWG and PRODAM were analyzed. The MTRN model indicated an increase in heritability for PWG and PRODAM with improvement of the environmental conditions. For SC, heritability was practically the same, irrespective of the environmental conditions. The genetic correlations between the traits studied were low but varied over environments by the MTRN model. Considering genetic correlations obtained by the MTRN model for the same trait, lower estimates were obtained between extreme favorable and unfavorable environments. This finding suggest re-ranking of breeding values in different environments mainly for PWG and PRODAM. Thus, G × E is more important for PWG and PRODAM than for SC and should be included in the genetic evaluation of these traits. The traits PWG and PRODAM can be considered plastic traits, whereas SC is poorly plastic. The genetic trends in individual animal slopes indicate that the population is moving towards greater plasticity. This could be a matter of concern for breeders since greater plasticity seems to limit heritability and, consequently, the responses to selection.

Inbreeding depression in Zebu cattle traits

The productivity of herds may be negatively affected by inbreeding depression, and it is important to know how intense is this effect on the livestock performance. We performed a comprehensive analysis involving five Zebu breeds reared in Brazil to estimate inbreeding depression in productive and reproductive traits. Inbreeding depression was estimated for 13 traits by including the individual inbreeding rate as a linear covariate in the standard genetic evaluation models. For all breeds and for almost all traits (no effect was observed on gestation length), the performance of the animals was compromised by an increase in inbreeding. The average inbreeding depression was -0.222% and -0.859% per 1% of inbreeding for linear regression coefficients scaled on the percentage of mean (βm ) and standard deviation (βσ ), respectively. The means for βm (and βσ ) were -0.269% (-1.202%) for weight/growth traits and -0.174% (-0.546%) for reproductive traits. Hence, inbreeding depression is more pronounced in weight/growth traits than in reproductive traits. These findings highlight the need for the management of inbreeding in the respective breeding programmes of the breeds studied here.

Detrimental effect of selection for milk yield on genetic tolerance to heat stress in purebred Zebu cattle: Genetic parameters and trends

In an attempt to determine the possible detrimental effects of continuous selection for milk yield on the genetic tolerance of Zebu cattle to heat stress, genetic parameters and trends of the response to heat stress for 86,950 test-day (TD) milk yield records from 14,670 first lactations of purebred dairy Gir cows were estimated. A random regression model with regression on days in milk (DIM) and temperature-humidity index (THI) values was applied to the data. The most detrimental effect of THI on milk yield was observed in the stage of lactation with higher milk production, DIM 61 to 120 (-0.099kg/d per THI). Although modest variations were observed for the THI scale, a reduction in additive genetic variance as well as in permanent environmental and residual variance was observed with increasing THI values. The heritability estimates showed a slight increase with increasing THI values for any DIM. The correlations between additive genetic effects across the THI scale showed that, for most of the THI values, genotype by environment interactions due to heat stress were less important for the ranking of bulls. However, for extreme THI values, this type of genotype by environment interaction may lead to an important error in selection. As a result of the selection for milk yield practiced in the dairy Gir population for 3 decades, the genetic trend of cumulative milk yield was significantly positive for production in both high (51.81kg/yr) and low THI values (78.48kg/yr). However, the difference between the breeding values of animals at high and low THI may be considered alarming (355kg in 2011). The genetic trends observed for the regression coefficients related to general production level (intercept of the reaction norm) and specific ability to respond to heat stress (slope of the reaction norm) indicate that the dairy Gir population is heading toward a higher production level at the expense of lower tolerance to heat stress. These trends reflect the genetic antagonism between production and tolerance to heat stress demonstrated by the negative genetic correlation between these components (-0.23). Monitoring trends of the genetic component of heat stress would be a reasonable measure to avoid deterioration in one of the main traits of Zebu cattle (i.e., high tolerance to heat stress). On the basis of current genetic trends, the need for future genetic evaluation of dairy Zebu animals for tolerance to heat stress cannot be ruled out.

Genetic parameters for first lactation test-day milk flow in Holstein cows

Genetic parameters for test-day milk flow (TDMF) of 2175 first lactations of Holstein cows were estimated using multiple-trait and repeatability models. The models included the direct additive genetic effect as a random effect and contemporary group (defined as the year and month of test) and age of cow at calving (linear and quadratic effect) as fixed effects. For the repeatability model, in addition to the effects cited, the permanent environmental effect of the animal was also included as a random effect. Variance components were estimated using the restricted maximum likelihood method in single- and multiple-trait and repeatability analyses. The heritability estimates for TDMF ranged from 0.23 (TDMF 6) to 0.32 (TDMF 2 and TDMF 4) in single-trait analysis and from 0.28 (TDMF 7 and TDMF 10) to 0.37 (TDMF 4) in multiple-trait analysis. In general, higher heritabilities were observed at the beginning of lactation until the fourth month. Heritability estimated with the repeatability model was 0.27 and the coefficient of repeatability for first lactation TDMF was 0.66. The genetic correlations were positive and ranged from 0.72 (TDMF 1 and 10) to 0.97 (TDMF 4 and 5). The results indicate that milk flow should respond satisfactorily to selection, promoting rapid genetic gains because the estimated heritabilities were moderate to high. Higher genetic gains might be obtained if selection was performed in the TDMF 4. Both the repeatability model and the multiple-trait model are adequate for the genetic evaluation of animals in terms of milk flow, but the latter provides more accurate estimates of breeding values.

Estimates of genetic parameters for total milk yield over multiple ages in Brazilian Murrah buffaloes using different models.

The objective of this study was to estimate variance components and genetic parameters for accumulated 305-day milk yield (MY305) over multiple ages, from 24 to 120 months of age, applying random regression (RRM), repeatability (REP) and multi-trait (MT) models. A total of 4472 lactation records from 1882 buffaloes of the Murrah breed were utilized. The contemporary group (herd-year-calving season) and number of milkings (two levels) were considered as fixed effects in all models. For REP and RRM, additive genetic, permanent environmental and residual effects were included as random effects. MT considered the same random effects as did REP and RRM with the exception of permanent environmental effect. Residual variances were modeled by a step function with 1, 4, and 6 classes. The heritabilities estimated with RRM increased with age, ranging from 0.19 to 0.34, and were slightly higher than that obtained with the REP model. For the MT model, heritability estimates ranged from 0.20 (37 months of age) to 0.32 (94 months of age). The genetic correlation estimates for MY305 obtained by RRM (L23.res4) and MT models were very similar, and varied from 0.77 to 0.99 and from 0.77 to 0.99, respectively. The rank correlation between breeding values for MY305 at different ages predicted by REP, MT, and RRM were high. It seems that a linear and quadratic Legendre polynomial to model the additive genetic and animal permanent environmental effects, respectively, may be sufficient to explain more parsimoniously the changes in MY305 genetic variation with age.

Random regressions models to describe the genetic variation of milk yield over multiple parities in Buffaloes

Abstract The objectives of this study were to estimate (co)variance functions for additive genetic and permanent environmental effects, as well as the genetic parameters for milk yield over multiple parities, using random regressions models (RRM). Records of 4,757 complete lactations of Murrah breed buffaloes from 12 herds were analyzed. Ages at calving were between 2 and 11 years. The model included the additive genetic and permanent environmental random effects and the fixed effects of contemporary groups (herd, year and calving season) and milking frequency (1 or 2). A cubic regression on Legendre orthogonal polynomials of ages was used to model the mean trend. The additive genetic and permanent environmental effects were modeled by Legendre orthogonal polynomials. Residual variances were considered homogenous or heterogeneous, modeled through variance functions or step functions with 5, 7 or 10 classes. Results from Akaike’s and Schwarz’s Bayesian information criterion indicated that a RRM considering a third order polynomial for the additive genetic and permanent environmental effects and a step function with 5 classes for residual variances fitted best. Heritability estimates obtained by this model varied from 0.10 to 0.28. Genetic correlations were high between consecutive ages, but decreased when intervals between ages increased

Genetic variation of the weaning weight of beef cattle as a function of accumulated heat stress

The objective of this study was to identify the genetic variation in the weaning weight (WW) of beef cattle as a function of heat stress. The WWs were recorded at approximately 205 days of age in three Brazilian beef cattle populations: Nelore (93,616), Brangus (18,906) and Tropical Composite (62,679). In view of the cumulative nature of WW, the effect of heat stress was considered as the accumulation of temperature and humidity index units (ACTHI) from the animals birth to weaning. A reaction norm model was used to estimate the (co)variance components of WW across the ACTHI scale. The accumulation of THI units from birth to weaning negatively affected the WW. The definition of accumulated THI units as an environmental descriptor permitted to identify important genetic variation in the WW as a function of heat stress. As evidence of genotype by environment interaction, substantial heterogeneity was observed in the (co)variance components for WW across the environmental gradient. In this respect, the best animals in less stressful environments are not necessarily the best animals in more stressful environments. Furthermore, the response to selection for WW is expected to be lower in more stressful environments.