Biometrical analysis and selection of tetraploid progenies of Panicum maximum using mixed model methods

The objectives of this work were to estimate the genetic and phenotypic parameters and to predict the genetic and genotypic values of the selection candidates obtained from intraspecific crosses in Panicum maximum as well as the performance of the hybrid progeny of the existing and projected crosses. Seventy-nine intraspecific hybrids obtained from artificial crosses among five apomictic and three sexual autotetraploid individuals were evaluated in a clonal test with two replications and ten plants per plot. Green matter yield, total and leaf dry matter yields and leaf percentage were evaluated in five cuts per year during three years. Genetic parameters were estimated and breeding and genotypic values were predicted using the restricted maximum likelihood/best linear unbiased prediction procedure (REML/BLUP). The dominant genetic variance was estimated by adjusting the effect of full-sib families. Low magnitude individual narrow sense heritabilities (0.02-0.05), individual broad sense heritabilities (0.14-0.20) and repeatability measured on an individual basis (0.15-0.21) were obtained. Dominance effects for all evaluated characteristics indicated that breeding strategies that explore heterosis must be adopted. Less than 5% increase in the parameter repeatability was obtained for a three-year evaluation period and may be the criterion to determine the maximum number of years of evaluation to be adopted, without compromising gain per cycle of selection. The identification of hybrid candidates for future cultivars and of those that can be incorporated into the breeding program was based on the genotypic and breeding values, respectively. The prediction of the performance of the hybrid progeny, based on the breeding values of the progenitors, permitted the identification of the best crosses and indicated the best parents to use in crosses.

A bivariate regression model for matched paired survival data: local influence and residual analysis

The use of bivariate distributions plays a fundamental role in survival and reliability studies. In this paper, we consider a location scale model for bivariate survival times based on the proposal of a copula to model the dependence of bivariate survival data. For the proposed model, we consider inferential procedures based on maximum likelihood. Gains in efficiency from bivariate models are also examined in the censored data setting. For different parameter settings, sample sizes and censoring percentages, various simulation studies are performed and compared to the performance of the bivariate regression model for matched paired survival data. Sensitivity analysis methods such as local and total influence are presented and derived under three perturbation schemes. The martingale marginal and the deviance marginal residual measures are used to check the adequacy of the model. Furthermore, we propose a new measure which we call modified deviance component residual. The methodology in the paper is illustrated on a lifetime data set for kidney patients.

Genetic and environmental heterogeneity of residual variance of weight traits in Nellore beef cattle

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

Estimation of variance components and prediction of breeding values in rubber tree breeding using the REML/BLUP procedure

The present paper deals with estimation of variance components, prediction of breeding values and selection in a population of rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Müell.-Arg.] from Rio Branco, State of Acre, Brazil. The REML/BLUP (restricted maximum likelihood/best linear unbiased prediction) procedure was applied. For this purpose, 37 rubber tree families were obtained and assessed in a randomized complete block design, with three unbalanced replications. The field trial was carried out at the Experimental Station of UNESP, located in Selvíria, State of Mato Grosso do Sul, Brazil. The quantitative traits evaluated were: girth (G), bark thickness (BT), number of latex vessel rings (NR), and plant height (PH). Given the unbalanced condition of the progeny test, the REML/BLUP procedure was used for estimation. The narrow-sense individual heritability estimates were 0.43 for G, 0.18 for BT, 0.01 for NR, and 0.51 for PH. Two selection strategies were adopted: one short-term (ST - selection intensity of 8.85%) and the other long-term (LT - selection intensity of 26.56%). For G, the estimated genetic gains in relation to the population average were 26.80% and 17.94%, respectively, according to the ST and LT strategies. The effective population sizes were 22.35 and 46.03, respectively. The LT and ST strategies maintained 45.80% and 28.24%, respectively, of the original genetic diversity represented in the progeny test. So, it can be inferred that this population has potential for both breeding and ex situ genetic conservation as a supplier of genetic material for advanced rubber tree breeding programs. Copyright by the Brazilian Society of Genetics.

Test-day model for milk yield of dairy buffaloes in colombia

The test-day model is the preferred method for genetic evaluations in dairy cattle. For this study, 28372 test-day records of 1220 lactations from 1997 to 2009 were used. The (co)variance components for milk in test-day were estimated using a Uni and multiple-traits repeated animal model with the Restricted Maximum Likelihood method (REML). The Contemporary Group (herd, year, and season of parity) and the age of parity (linear and quadratic) fixed effects, and the additive genetic, permanent environmental, and residual random effects were included in the model. The heritabilities ranged between 0.06 and 0.45 during lactation. The genetic correlations were greater than 0.93. In conclusion, the test-day model is appropriate for the genetic evaluation of dairy buffaloes in Colombia.

Associações genéticas entre características reprodutivas em bovinos da raça Guzerá

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

Interação genótipo-ambiente para a produção de leite em bubalinos no Brasil e na Colômbia

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

Seleção de famílias e progênies de irmãos completos de cana-de-açúcar para atributos tecnológicos e de produção pelo método de REML/BLUP

The objective of this study was to assess families and highlight the superior progenies of sugarcane originating from 38 biparental crosses for the following attributes: tons of cane per hectare (TCH), tons of biomass per hectare (TBIOH), brix (% cane juice), fiber content, purity, pol and total recoverable sugar (TRS). The data were analyzed by mixed model REML / BLUP in the REML (Restricted Maximum Likelihood) allowed us to estimate genetic parameters and BLUP (best linear unbiased prediction) to predict the additive and genotypic values. The best family for the attributes TCH and TBIOH was 41, whose parents are cultivars IACSP022019 x CTC9. In individual selection for TCH, the plant number 3 of Block 2, the crossing 78, showed the best results. To TBIOH the plant number 33, Block 1, family 41, showed the best results. Families 40, 41, 43, 68, 69, 79, 91, 92 and 147, were higher for the variables brix, pol, purity, and ATR, where as 85 families, 147, 148, 149, 161, 163, 177, 178, 179, and 183 were higher for fiber. The family 147 whose parents are IACSP042286 x IACSP963055, showed three progenies ranked among the top ten for both brix, and for fiber, which identifies the combination as a potential source of progenies for bioenergy production.

Estudo do peso metabólico e índice de Kleiber na estimação de parâmetros genéticos de características ponderais em uma população de bovinos de raça brahman

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Análise genética da produção in vitro de embriões em bovinos Guzerá

O objetivo dessa pesquisa foi avaliar aspectos genéticos que relacionados à produção in vitro de embriões na raça Guzerá. O primeiro estudo focou na estimação de (co) variâncias genéticas e fenotípicas em características relacionadas a produção de embriões e na detecção de possível associação com a idade ao primeiro parto (AFC). Foi detectada baixa e média herdabilidade para características relacionadas à produção de oócitos e embriões. Houve fraca associação genética entre características ligadas a reprodução artificial e a idade ao primeiro parto. O segundo estudo avaliou tendências genéticas e de endogamia em uma população Guzerá no Brasil. Doadoras e embriões produzidos in vitro foram considerados como duas subpopulações de forma a realizar comparações acerca das diferenças de variação anual genética e do coeficiente de endogamia. A tendência anual do coeficiente de endogamia (F) foi superior para a população geral, sendo detectado efeito quadrático. No entanto, a média de F para a sub- população de embriões foi maior do que na população geral e das doadoras. Foi observado ganho genético anual superior para a idade ao primeiro parto e para a produção de leite (305 dias) entre embriões produzidos in vitro do que entre doadoras ou entre a população geral. O terceiro estudo examinou os efeitos do coeficiente de endogamia da doadora, do reprodutor (usado na fertilização in vitro) e dos embriões sobre resultados de produção in vitro de embriões na raça Guzerá. Foi detectado efeito da endogamia da doadora e dos embriões sobre as características estudadas. O quarto (e último) estudo foi elaborado para comparar a adequação de modelos mistos lineares e generalizados sob método de Máxima Verossimilhança Restrita (REML) e sua adequação a variáveis discretas. Quatro modelos hierárquicos assumindo diferentes distribuições para dados de contagem encontrados no banco. Inferência foi realizada com base em diagnósticos de resíduo e comparação de razões entre componentes de variância para os modelos em cada variável. Modelos Poisson superaram tanto o modelo linear (com e sem transformação da variável) quanto binomial negativo à qualidade do ajuste e capacidade preditiva, apesar de claras diferenças observadas na distribuição das variáveis. Entre os modelos testados, a pior qualidade de ajuste foi obtida para o modelo linear mediante transformação logarítmica (Log10 X +1) da variável resposta.

Estimates of genetic trend for carcass traits in a commercial broiler line

Data from the slaughter of 24,001 chickens that were part of a selection program for the production of commercial broilers were used to estimate genetic trend for absolute carcass (CW), breast meat (BRW), and leg (LW) weights, and relative carcass (CY), breast meat (BRY), and leg (LY) weights. The components of (co) variance and breeding values of individuals were obtained by the restricted maximum likelihood method applied to animal models. The relationship matrix was composed of 132,442 birds. The models included as random effects, maternal additive genetic and permanent environmental for CW, BRW, LW, CY, and BRY, and only maternal permanent environmental for LY, besides the direct additive genetic and residual effects, and as fixed effects, hatch week, parents' mating group and sex. The estimates of genetic trend were obtained by average regression of breeding value on generation, and the average genetic trend was estimated by regression coefficients. The genetic trends for CW (+ 6.0336 g/generation), BRW (+ 3.6723 g/generation), LW (+ 1.5846 g/generation), CY (+ 0.1195%/generation), and BRY (+ 0.1388%/generation) were positive, and they were in accordance with the objectives of the selection program for these traits. The genetic trend for LY(-0.0019%/generation) was negative, possibly due to the strong emphasis on selection for BRY and the negative correlations between these two traits.

A note on the likelihood and moments of the skew-normal distribution

In this paper an alternative approach to the one in Henze (1986) is proposed for deriving the odd moments of the skew-normal distribution considered in Azzalini (1985). The approach is based on a Pascal type triangle, which seems to greatly simplify moments computation. Moreover, it is shown that the likelihood equation for estimating the asymmetry parameter in such model is generated as orthogonal functions to the sample vector. As a consequence, conditions for a unique solution of the likelihood equation are established, which seem to hold in more general setting.

On estimation and influence diagnostics for zero-inflated negative binomial regression models

The zero-inflated negative binomial model is used to account for overdispersion detected in data that are initially analyzed under the zero-Inflated Poisson model A frequentist analysis a jackknife estimator and a non-parametric bootstrap for parameter estimation of zero-inflated negative binomial regression models are considered In addition an EM-type algorithm is developed for performing maximum likelihood estimation Then the appropriate matrices for assessing local influence on the parameter estimates under different perturbation schemes and some ways to perform global influence analysis are derived In order to study departures from the error assumption as well as the presence of outliers residual analysis based on the standardized Pearson residuals is discussed The relevance of the approach is illustrated with a real data set where It is shown that zero-inflated negative binomial regression models seems to fit the data better than the Poisson counterpart (C) 2010 Elsevier B V All rights reserved

Random regression models to estimate test-day milk yield genetic parameters Holstein cows in Southeastern Brazil

A total of 152,145 weekly test-day milk yield records from 7317 first lactations of Holstein cows distributed in 93 herds in southeastern Brazil were analyzed. Test-day milk yields were classified into 44 weekly classes of DIM. The contemporary groups were defined as herd-year-week of test-day. The model included direct additive genetic, permanent environmental and residual effects as random and fixed effects of contemporary group and age of cow at calving as covariable, linear and quadratic effects. Mean trends were modeled by a cubic regression on orthogonal polynomials of DIM. Additive genetic and permanent environmental random effects were estimated by random regression on orthogonal Legendre polynomials. Residual variances were modeled using third to seventh-order variance functions or a step function with 1, 6,13,17 and 44 variance classes. Results from Akaike`s and Schwarz`s Bayesian information criterion suggested that a model considering a 7th-order Legendre polynomial for additive effect, a 12th-order polynomial for permanent environment effect and a step function with 6 classes for residual variances, fitted best. However, a parsimonious model, with a 6th-order Legendre polynomial for additive effects and a 7th-order polynomial for permanent environmental effects, yielded very similar genetic parameter estimates. (C) 2008 Elsevier B.V. All rights reserved.

Likelihood-based estimation of the regression model with scrambled responses

A significant problem in the collection of responses to potentially sensitive questions, such as relating to illegal, immoral or embarrassing activities, is non-sampling error due to refusal to respond or false responses. Eichhorn & Hayre (1983) suggested the use of scrambled responses to reduce this form of bias. This paper considers a linear regression model in which the dependent variable is unobserved but for which the sum or product with a scrambling random variable of known distribution, is known. The performance of two likelihood-based estimators is investigated, namely of a Bayesian estimator achieved through a Markov chain Monte Carlo (MCMC) sampling scheme, and a classical maximum-likelihood estimator. These two estimators and an estimator suggested by Singh, Joarder & King (1996) are compared. Monte Carlo results show that the Bayesian estimator outperforms the classical estimators in almost all cases, and the relative performance of the Bayesian estimator improves as the responses become more scrambled.