Martinho de Almeida e Silva

Inferring causal phenotype networks using structural equation models

Phenotypic traits may exert causal effects between them. For example, on the one hand, high yield in dairy cows may increase the liability to certain diseases and, on the other hand, the incidence of a disease may affect yield negatively. Likewise, the transcriptome may be a function of the reproductive status in mammals and the latter may depend on other physiological variables. Knowledge of phenotype networks describing such interrelationships can be used to predict the behavior of complex systems, e.g. biological pathways underlying complex traits such as diseases, growth and reproduction. Structural Equation Models (SEM) can be used to study recursive and simultaneous relationships among phenotypes in multivariate systems such as genetical genomics, system biology, and multiple trait models in quantitative genetics. Hence, SEM can produce an interpretation of relationships among traits which differs from that obtained with traditional multiple trait models, in which all relationships are represented by symmetric linear associations among random variables, such as covariances and correlations. In this review, we discuss the application of SEM and related techniques for the study of multiple phenotypes. Two basic scenarios are considered, one pertaining to genetical genomics studies, in which QTL or molecular marker information is used to facilitate causal inference, and another related to quantitative genetic analysis in livestock, in which only phenotypic and pedigree information is available. Advantages and limitations of SEM compared to traditional approaches commonly used for the analysis of multiple traits, as well as some indication of future research in this area are presented in a concluding section.

Efeito da ractopamina e de métodos de formulação de dietas sobre o desempenho e as características de carcaça de suínos machos castrados em terminação

An experiment was conduced with the objective of evaluating the effects of diet formulation methods and supplementation of ractopamine (RAC) on the performance and carcass characteristics of finishing barrows. Sixty commercial hybrid swines were used, distributed in a randomized experimental block design, in a 2 x 3 factorial arrangment, with two levels of RAC and three methods of diet formulation. Supplementation with RAC improved the final weight, daily weight gain (DWG) and feed conversion (FC) of the finishing barrows. Addition of RAC improved also the carcass characteristics by reducing the backfat thickness in point P1 and increase daily lean meat deposition rate. Diets formulated based in the concept of ideal protein or by the increase of soybean meal provided better results on FC, but did not influence significantly daily feed intake, DWG and carcass characteristics. Finishing barrows supplemented with RAC during 21 or 28 days showed better performance and carcass quality. Diets formulated to attend the levels of digestible lysine by the inclusion of L-lysine HCL with the adjustment of other amino acids for ideal protein relation (ideal protein) or by the greater inclusion of soybean meal (increase of CP) provided better results of feed conversion in finishing borrows supplemented with RAC during 28 days.

Searching for recursive causal structures in multivariate quantitative genetics mixed models.

Biology is characterized by complex interactions between phenotypes, such as recursive and simultaneous relationships between substrates and enzymes in biochemical systems. Structural equation models (SEMs) can be used to study such relationships in multivariate analyses, e.g., with multiple traits in a quantitative genetics context. Nonetheless, the number of different recursive causal structures that can be used for fitting a SEM to multivariate data can be huge, even when only a few traits are considered. In recent applications of SEMs in mixed-model quantitative genetics settings, causal structures were preselected on the basis of prior biological knowledge alone. Therefore, the wide range of possible causal structures has not been properly explored. Alternatively, causal structure spaces can be explored using algorithms that, using data-driven evidence, can search for structures that are compatible with the joint distribution of the variables under study. However, the search cannot be performed directly on the joint distribution of the phenotypes as it is possibly confounded by genetic covariance among traits. In this article we propose to search for recursive causal structures among phenotypes using the inductive causation (IC) algorithm after adjusting the data for genetic effects. A standard multiple-trait model is fitted using Bayesian methods to obtain a posterior covariance matrix of phenotypes conditional to unobservable additive genetic effects, which is then used as input for the IC algorithm. As an illustrative example, the proposed methodology was applied to simulated data related to multiple traits measured on a set of inbred lines.

Lactation curve in Guzera breed

The objectives of this work were to identify the mathematical functions that better fitted the milk production of Guzera breed cows, to evaluate the effects of the environmental factors on the lactation curve format and to estimate the genetic parameters for the milk production and for the dependable components of the lactation curve format. A total of 1130 lactations from 583 Guzera breed cows, daughters of 165 bulls, with production over the period from 1983 to 1997 were used. The models y = a n e -cn, y = a - cn + ln (n), y=a -cn e y =a e-c n were the ones that best fitted the milk production of the cows. By the analysis of variance, it was observed that the effects of cow herd, calving year and cow age at calving influenced the total milk production, initial milk production and milk decline production rate characteristics. The coefficients of heritability and repeatability estimates were obtained by means of one and two characteristic analyses. The animal selection, based only on the of the lactation curve format, would be of low efficiency.

Efeito dos Níveis de Cantaxantina na Dieta Sobre o Desempenho e Qualidade dos Ovos de Poedeiras Comerciais

The objective of this study was to evaluate the effects of cantaxantina levels on performance and egg yolk color. Three hundred and eighty four Hisex laying 65-week old hens were randomized allocated in a block design with six treatments (0, 12, 24, 26, 48 and 60 ppm of cantaxantina , and eight replications of eight birds per pen, during eight weeks. The egg color analysis was determined using the Roche fan colorimeter. The best egg yolk color (14.3) during the first 14 days of essay were reached at 5.43 days of receiving diets with 60 ppm of cataxantina. During the total period, egg yolk color increased quadratically (p .05).

Avaliação do crescimento de bovinos jovens da raça Tabapuã, por meio de análises de funções de covariâncias

Restricted maximum likelihood (REML) estimates of additive and residual variances and covariances for birth weight and adjusted weights at 120, 205, 240, 365, 420 e 550 days of age were used to estimate growth covariance functions (CFs) of Tabapua beef calves. Data were observed on 41,415 animals born from 1975 to 1997 and raised under pasture conditions. Estimation of CFs is a very useful tool to analyze beef cattle growth. It was possible to estimate covariance between any pair of ages and the analyses of eigenfunctions associated with the eigenvalues of coefficients matrix of CFs showed that the growth curves of Tabapua calves could be easily changed by selection. Weaning stress, compensatory growth and selection of animals in the final period caused changes on (co)variance trajectories. Therefore only CFs of more complex order were able to estimate values near to REML estimates. However, high order Legendre polynomials drew sharp waves on variances trajectories at the period edges, witch does not have a coherently biological reason.

Exigência de lisina para codornas japonesas em postura

Three hundred 49-days old Japanese female quails, averaging 138.0g, were used to estimate the requirement of digestible lysine level for Japanese quail in completely randomized block design with five replicates of ten females per experimental unit. The treatment consisted six levels of digestible lysine (0.80, 0.90, 1.00, 1.10, 1.20 and 1.30%) and the analyzed traits were rate of egg production (%), egg weight (g), egg mass (g of eggs/quail/day), feed intake (g), feed consumption: weight gain ratio (g of diet/g of eggs), final body weight (g) and shell percentage (%). No signicant effect of treatments on final body weight (g) was observed, but there was quadratic effect for egg production (%), egg mass (g of eggs/quail/day) and feed consumption: gain diet (g of diet/g of eggs) and linear effect on shell egg (%) and feed intake (g). The estimated requirements of digestible lysine for laying Japanese quail was 1.117% of the diet, corresponding to a daily intake of 254 mg of digestible lysine.

Exigência de metionina mais cistina para codornas japonesas em postura

Three hundred and sixty 45-days old female quails, averaging 137.0 g, were used during four experimental periods of 28 days each. A completely randomized block design, with six replicates and ten females per experimental unit, was used to study the digestible methionine plus cystine requirement and the best digestible methionine plus cystine: digestible lysine ratio (0.60, 0.65, 0.70, 0.75, 0.80 and 0.85), on the rate of eggs production (%), egg weight (g), eggs mass (g of eggs/quail/day), feed intake (g), feed consumption: weight gain ratio (g of diet/g of eggs), body weight (g) and shell percentage (%). No significant effect of treatments on feed consumption: gain diet (g of diet/g of eggs). Quadratic effects were observed for final body weight (g), egg production (%), egg weight (g), egg mass (g of eggs/quail/day) and shell egg (%), and for feed intake (g) the effect was linear. The estimated digestible methionine plus cystine requirement was .727%, for a daily intake of 164 mg of digestible methionine plus cystine, and the best estimated digestible methionine plus cystine: digestible lysine ratio for laying Japanese quails was .80.Three hundred and sixty 45-days old female quails, averaging 137.0 g, were used during four experimental periods of 28 days each. A completely randomized block design, with six replicates and ten females per experimental unit, was used to study the digestible methionine plus cystine requirement and the best digestible methionine plus cystine: digestible lysine ratio (0.60, 0.65, 0.70, 0.75, 0.80 and 0.85), on the rate of eggs production (%), egg weight (g), eggs mass (g of eggs/quail/day), feed intake (g), feed consumption: weight gain ratio (g of diet/g of eggs), body weight (g) and shell percentage (%). No significant effect of treatments on feed consumption: gain diet (g of diet/g of eggs). Quadratic effects were observed for final body weight (g), egg production (%), egg weight (g), egg mass (g of eggs/quail/day) and shell egg (%), and for feed intake (g) the effect was linear. The estimated digestible methionine plus cystine requirement was .727%, for a daily intake of 164 mg of digestible methionine plus cystine, and the best estimated digestible methionine plus cystine: digestible lysine ratio for laying Japanese quails was .80.

Exigência de metionina mais cistina para codornas japonesas em crescimento

Five hundred and forty 7-days old female quails, averaging 21.50 g, were used during 35 days. A completely randomized blocks design with five replicates and 18 females per experimental unity was used to study the effect of six digestible methionine plus cystine: digestible lysine ratios (0.48, 0.53, 0.58, 0.63, 0.68 and 0.75) on the traits evaluated during the growing period. Final weight (g), weight gain (g), feed intake (g), feed conversion (g/g), feather rate (%), chemical composition (%) (dry matter, water, crude protein and ether extract) and body protein and fat deposition (g). The effect of the amino acids on feed intake (g), feed conversion (g/g), feather rate (%), chemical composition (%) (dry matter, water, crud protein and ether extract) and protein deposition was quadratic and the effect on final body weight (g) and weight gain (g) was linear. The best estimated digestible methionine plus cystine: digestible lysine ratio was .66 and the estimated digestible methionine plus cystine requirement for growing Japanese quail was .758%, for a intake of 91.43 mg of digestible methionine plus cystine intake.

Fatores genéticos e de meio na produção de leite de caprinos leiteiros

The objectives of this study were to evaluate the influence of environmental factors on milk production from dairy goats raised in the Brazilian Southeast and to estimate genetic parameters for this trait through least squares. The data originated from seven farms and three breeds (Alpine Brown, Saanen and Toggenburg). Milk yields obtained from 1,336 lactations were initially fitted to a diphasic function, whereby total milk production (TMP) was estimated. The overall mean and standard error for TMP were 635.31±39.75 kg. A significant year x kidding season interaction was observed. In all three kidding seasons a quadratic yearly trend of PLT was observed: it increased from 1986 until mid-1990, decreasing thereafter. Age of maximum PLT was estimated as 46.65 months. Alpine Brown was superior to Saanen in some farms, the opposite occurring in others, but both showed higher PLT values than Toggenburg. Estimated heritability and repeatability coefficients were 0.296±0.079 and 0.227±0.033, respectively. These results show low reliability due to the small number of observations or to inconsistent PLT estimates obtained through the biphasic function. Since PLT is a sex-limited trait, it is suggested the use of progeny tests as the most efficient selection method for bucks and artificial insemination for spreading the selected genetic material.