Assessment of inbreeding depression in a Guzerat dairy herd: Effects of individual increase in inbreeding coefficients on production and reproduction

Influences of inbreeding on daily milk yield (DMY), age at first calving (AFC), and calving intervals (CI) were determined on a highly inbred zebu dairy subpopulation of the Guzerat breed. Variance components were estimated using animal models in single-trait analyses. Two approaches were employed to estimate inbreeding depression: using individual increase in inbreeding coefficients or using inbreeding coefficients as possible covariates included in the statistical models. The pedigree file included 9,915 animals, of which 9,055 were inbred, with an average inbreeding coefficient of 15.2%. The maximum inbreeding coefficient observed was 49.45%, and the average inbreeding for the females still in the herd during the analysis was 26.42%. Heritability estimates were 0.27 for DMY and 0.38 for AFC. The genetic variance ratio estimated with the random regression model for CI ranged around 0.10. Increased inbreeding caused poorer performance in DMY, AFC, and CI. However, some of the cows with the highest milk yield were among the highly inbred animals in this subpopulation. Individual increase in inbreeding used as a covariate in the statistical models accounted for inbreeding depression while avoiding overestimation that may result when fitting inbreeding coefficients.

Testicular traits as selection criteria for young Nellore bulls

The objective of this study was to evaluate the possible use of biometric testicular traits as selection criteria for young Nellore bulls using Bayesian inference to estimate heritability coefficients and genetic correlations. Multitrait analysis was performed including 17,211 records of scrotal circumference obtained during andrological assessment (SCAND) and 15,313 records of testicular volume and shape. In addition, 50,809 records of scrotal circumference at 18 mo (SC18), used as an anchor trait, were analyzed. The (co) variance components and breeding values were estimated by Gibbs sampling using the Gibbs2F90 program under an animal model that included contemporary groups as fixed effects, age of the animal as a linear covariate, and direct additive genetic effects as random effects. Heritabilities of 0.42, 0.43, 0.31, 0.20, 0.04, 0.16, 0.15, and 0.10 were obtained for SC18, SCAND, testicular volume, testicular shape, minor defects, major defects, total defects, and satisfactory andrological evaluation, respectively. The genetic correlations between SC18 and the other traits were 0.84 (SCAND), 0.75 (testicular shape), 0.44 (testicular volume), -0.23 (minor defects), -0.16 (major defects), -0.24 (total defects), and 0.56 (satisfactory andrological evaluation). Genetic correlations of 0.94 and 0.52 were obtained between SCAND and testicular volume and shape, respectively, and of 0.52 between testicular volume and testicular shape. In addition to favorable genetic parameter estimates, SC18 was found to be the most advantageous testicular trait due to its easy measurement before andrological assessment of the animals, even though the utilization of biometric testicular traits as selection criteria was also found to be possible. In conclusion, SC18 and biometric testicular traits can be adopted as a selection criterion to improve the fertility of young Nellore bulls.

Performance of balanced two-stage empirical predictors of realized cluster latent values from finite populations: A simulation study

Predictors of random effects are usually based on the popular mixed effects (ME) model developed under the assumption that the sample is obtained from a conceptual infinite population; such predictors are employed even when the actual population is finite. Two alternatives that incorporate the finite nature of the population are obtained from the superpopulation model proposed by Scott and Smith (1969. Estimation in multi-stage surveys. J. Amer. Statist. Assoc. 64, 830-840) or from the finite population mixed model recently proposed by Stanek and Singer (2004. Predicting random effects from finite population clustered samples with response error. J. Amer. Statist. Assoc. 99, 1119-1130). Predictors derived under the latter model with the additional assumptions that all variance components are known and that within-cluster variances are equal have smaller mean squared error (MSE) than the competitors based on either the ME or Scott and Smith`s models. As population variances are rarely known, we propose method of moment estimators to obtain empirical predictors and conduct a simulation study to evaluate their performance. The results suggest that the finite population mixed model empirical predictor is more stable than its competitors since, in terms of MSE, it is either the best or the second best and when second best, its performance lies within acceptable limits. When both cluster and unit intra-class correlation coefficients are very high (e.g., 0.95 or more), the performance of the empirical predictors derived under the three models is similar. (c) 2007 Elsevier B.V. All rights reserved.

Estimation of Parameters in Random Effect Models with Incidence Matrix Uncertainty

Random effect models have been widely applied in many fields of research. However, models with uncertain design matrices for random effects have been little investigated before. In some applications with such problems, an expectation method has been used for simplicity. This method does not include the extra information of uncertainty in the design matrix is not included. The closed solution for this problem is generally difficult to attain. We therefore propose an two-step algorithm for estimating the parameters, especially the variance components in the model. The implementation is based on Monte Carlo approximation and a Newton-Raphson-based EM algorithm. As an example, a simulated genetics dataset was analyzed. The results showed that the proportion of the total variance explained by the random effects was accurately estimated, which was highly underestimated by the expectation method. By introducing heuristic search and optimization methods, the algorithm can possibly be developed to infer the 'model-based' best design matrix and the corresponding best estimates.

O crescimento da empresa: uma análise da variabilidade das taxas de crescimento

Esta pesquisa investigou a variabilidade da taxa de crescimento das empresas, associando-a a grupos de fatores como os associados ao ramo de negócios, ao período ou ano em que se observa o crescimento, ao país e, finalmente, o grupo de fatores associado à empresa individual de forma idiossincrática. O trabalho inspirou-se na linha de pesquisa de componentes de variância do desempenho financeiro em estratégia usando o crescimento como variável dependente. Os achados indicam que a firma individual é a responsável pela maior parte da variância observada nas taxas de crescimento. País e ano também são fontes de variação relevantes. O ramo de negócios no qual a firma está inserida, contudo, tem uma pequena relevância na explicação da variabilidade. O trabalho usou a base de dados Compustat Global como fonte principal. Os resultados têm implicações tanto para a gestão de empresas ao nível corporativo como para a criação de políticas de desenvolvimento e crescimento. Esta pesquisa fez uma avaliação de uma amostra internacional para poder avaliar o efeito país, mas abre espaço para vários outros estudos mais profundos, com maior foco na realidade brasileira.

Earnings dynamics and inequality in Venezuela: 1995-1997

In this paper, we decompose the variance of logarithmic monthly earnings of prime age males into its permanent and transitory components, using a five-wave rotating panel from the Venezuelan “Encuesta de Hogares por Muestreo” from 1995 to 1997. As far as we know, this is the first time a variance components model is estimated for a developing country. We test several specifications and find that an error component model with individual random effects and first order serially correlated errors fits the data well. In the simplest model, around 22% of earnings variance is explained by the variance of permanent component, 77% by purely stochastic variation and the remaining 1% by serial correlation. These results contrast with studies from industrial countries where the permanent component is predominant. The permanent component is usually interpreted as the results of productivity characteristics of individuals whereas the transitory component is due to stochastic perturbations such as job and/or price instability, among others. Our findings may be due to the timing of the panel when occurred precisely during macroeconomic turmoil resulting from a severe financial crisis. The findings suggest that earnings instability is an important source of inequality in a region characterized by high inequality and macroeconomic instability.

Minimizing inter-genotypic competition effects to predict genetic values and selection in forestry genetic tests

The effect of competition is an important source of variation in breeding experiments. This study aimed to compare the selection of plants of open-pollinated families of Eucalyptus with and without the use of competition covariables. Genetic values were determined for each family and tree and for the traits height, diameter at breast height and timber volume in a randomized block design, resulting in the variance components, genetic parameters, selection gains, effective size and selection coincidence, with and without the use of covariables. Intergenotypic competition is an important factor of environmental variation. The use of competition covariables generally reduces the estimates of variance components and influences genetic gains in the studied traits. Intergenotypic competition biases the selection of open-pollinated eucalypt progenies, and can result in an erroneous choice of superior genotypes; the inclusion of covariables in the model reduces this influence.

Componentes da variância em caracteres agronômicos de acerola

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estimates of genetic parameters for visual scores and daily weight gain in Brangus animals

(Co) variance components were estimated for visual scores of conformation (CY), early finishing (PY) and muscling (MY) at 550 days of age (yearling), average daily gain from weaning to yearling (GWY), conformation (CW), early finishing (PW) and muscling (MW) scores at weaning, and average daily gain from birth to weaning (GBW) in animals forming the Brazilian Brangus breed born between 1986 and 2002 from the livestock files of GenSys Consultants Associados S/C Ltda. The data set contained 53 683; 45 136; 52 937; 56 471; 24 531; 21 166; 24 006 and 25 419 records for CW, PW, MW, GBW, CY, PY, MY and GWY, respectively. Data were analyzed by the restricted maximum likelihood method using single-and two-trait animal models. Direct heritability estimates obtained by single-trait analysis were 0.12, 0.14, 0.13 and 0.14 for CY, PY and MY scores and GWY, respectively. A positive association was observed between the same visual scores at weaning and yearling, with correlations ranging from 0.64 to 0.94. Estimated correlations between GBW and weaning and yearling scores ranged from 0.60 to 0.77. The genetic correlation between GBW and GWY was low (0.10), whereas correlations of 0.55, 0.37 and 0.47 were observed between GWY and CY, PY and MY, respectively. Moreover, GWY showed a weak correlation with CW (0.10), PW (-0.08) and MW (-0.03) scores. These results indicate that selection of the traits that was studied would result in a small response. In addition, selection based on average daily gain may have an indirect effect on visual scores as the correlations between GWY and visual scores were generally strong.

Genetic parameters for body weight, carcass chemical composition and yield in a broiler-layer cross developed for QTL mapping

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estimativa de parâmetros genéticos da habilidade de permanência aos 48, 60 e 72 meses de idade em vacas da raça Caracu

Objetivou-se estimar a herdabilidade da característica habilidade de permanência (HP) em um rebanho de bovinos da raça Caracu visando sua utilização como critério de seleção. A característica em estudo foi definida como a probabilidade de a vaca estar presente no rebanho aos 48 (HP48), aos 60 (HP60) e aos 72 (HP72) meses, desde que possuíssem registros de pelo menos duas lactações nas específicas idades. Observações binárias, com zero (0 = fracasso) e um (1 = sucesso) foram designadas aos animais. Para análise da HP, foram utilizados dados de 5.487, 4.947 e 4.308 animais aos 48, 60 e 72 meses, respectivamente. Os componentes de variância e as herdabilidades foram estimados mediante inferência Bayesiana, via amostragem de Gibbs, pelo programa MTGSAM - threshold, utilizando-se um modelo touro. Foram utilizadas como variáveis explanatórias grupo de contemporâneos, classe de produção de leite na primeira lactação, classe de idade ao primeiro parto e sua interação. As análises forneceram estimativas médias de herdabilidade iguais a 0,28 ± 0,07 para HP48, 0,27 ± 0,07 para HP60 e 0,23 ± 0,07 para HP72. Os resultados evidenciaram que a característica HP apresentou variação aditiva em todas as idades estudadas e, portanto, pode ser empregada como critério de seleção para longevidade produtiva.

Modelagem e estimação de parâmetros genéticos e fenotípicos para pesos do nascimento à seleção (378 dias) de machos Nelore

Genetic parameters for weights (17, 942 records), obtained in intervals of 60 days, from the birth to selection (378 days of age), of 2,582 males of the Nellore breed was estimated in univariate analyses by the Maximum Restricted Likelihood method. The models of analysis models included the fixed effects of contemporary groups, month of birth, mother age and age when the weights were collected as covariate. Three models differing in random effects were tested: the model 1 (M1) was adjusted for the direct and maternal addictive genetic effects and maternal permanent environment; in model 2 (M2) the maternal genetic effect was excluded; and the model 3 (M3) was only adjusted for the direct addictive genetic effect. The test of likelihood (LRT) detected significant differences, for all the ages, of M2 and M1 in relation to the simple model (M3), evidencing the importance of the maternal effects. Except for the birth weight (0.40), low values (0.05 to 0.12) of h(2) were found for M1 and M2 until 8 months of age and, after this period, reasonable increase could be observed, reaching 0.28 until 13 months of age. The estimates of the total variance fraction, due to the effect of maternal permanent environment, were high and practically became unaffected between the models 1 and 2. Maternal effects, not necessarily decomposed (in genetic addictive and permanent environment), affected the Nellore males growth. Models that contemplate maternal effects, besides the genetic addictive direct effects, are more realistic to describe the trajectory of the variances in the initial phases of growth of Nelore male calves.

Estimates of genetic correlations between days to calving and reproductive and weight traits in Nelore cattle

Data comprising 53,181 calving records were analyzed to estimate the genetic correlation between days to calving (DC), and days to first calving (DFC), and the following traits: scrotal circumference (SC), age at first calving (AFC), and weight adjusted for 550 d of age (W550) in a Nelore herd. (Co)variance components were estimated using the REML method fitting bivariate animal models. The fixed effects considered for DC were contemporary group, month of last calving, and age at breeding season (linear and quadratic effects). Contemporary groups were composed by herd, year, season, and management group at birth; herd and management group at weaning; herd, season, and management group at mating; and sex of calf and mating type (multiple sires, single sire, or AI). In DFC analysis, the same fixed effects were considered excluding the month of last calving. For DC, a repeatability animal model was applied. Noncalvers were not considered in analyses because an attempt to include them, attributing a penalty, did not improve the identification of genetic differences between animals. Heritability estimates ranged from 0.04 to 0.06 for DC, from 0.06 to 0.13 for DFC, from 0.42 to 0.44 for SC, from 0.06 to 0.08 for AFC, and was 0.30 for W550. The genetic correlation estimated between DC and SC was low and negative (-0.10), between DC and AFC was high and positive (0.76), and between DC and W550 was almost null (0.07). Similar results were found for genetic correlation estimates between DFC and SC (-0.14), AFC (0.94), and W550 (-0.02). The genetic correlation estimates indicate that the use of DC in the selection of beef cattle may promote favorable correlated responses to age at first mating and, consequently, higher gains in sexual precocity can be expected.

Genetic aspects of productive and reproductive traits in a Murrah buffalo herd in São Paulo, Brazil

This study investigated genetic trends of some productive and reproductive traits in a herd of Murrah buffalo raised in São Paulo, Brazil. Variance components for milk production (Mr), length of lactation (LL), calving interval (CI) and age of first calving (AFC) were estimated by che restricted maximum likelihood method, using an animal model. Estimated heritability values were 0.38; 0.01; 0.10 and 0.20 for MP, LL, CI and AFC, respectively. Estimated repeatability values were 0.50, 0.13 and 0.20 for MP, LL and CI, respectively. Means of predicted breeding values for cows, dams and sires according to calving year and the genetic correlations were presented.