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Análisis bayesiano de modelos lineales - bilineales. Colegio de Postgraduados
Hernández Jarquín, Juan Diego.
El análisis de tablas de doble entrada es una herramienta estadística que se presenta en diversos campos de investigación; por ejemplo, en fitomejoramiento uno de los principales objetivos es evaluar la adaptabilidad y estabilidad genotípica en la selección de los padres para el siguiente ciclo de mejoramiento. Generalmente, este proceso se ve afectado por la presencia de la interacción Genotipo x Ambiente (GE). Bajo el enfoque clásico, para el estudio de la interacción se consideran modelos parsimoniosos como el AMMI ó el SREG y se obtienen estimaciones puntuales mediante Mínimos Cuadrados Ordinarios (MCO) por lo que no es trivial la construcción de intervalos de confianza y el diseño de pruebas de hipótesis. En este trabajo se propone una modelación...
Palavras-chave: Distribución von Mises-Fisher; Inferencia bayesiana; Fitomejoramiento; Tablas de doble entrada con interacción; Términos bilineales de interacción; Bayesian inference; Bilinear interaction terms; Plant breeding; Two-way tables with interaction; Von mises fisher distribution; Estadística; Doctorado.
Ano: 2012 URL: http://hdl.handle.net/10521/676
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Series de tiempo con múltiples puntos de cambio y observaciones censuradas Colegio de Postgraduados
Castro Montoya, René.
Debido a factores externos a las variables de inter´es, una serie de tiempo puede presentar cambios en la estructura del modelo o en algunos par´ametros, y debido a l´ımitaciones en los instrumentos de medici´on puede presentar tambi´en censura en las observaciones. Por ejem- plo, cuando se monitorean contaminantes del aire, como pueden ser hidrocarburos arom´aticos (PAHs), mon´oxido de carbono (CO), di´oxido de sulfuro (S O2 ), etc., las series de tiempo ob- servadas pueden tener mediciones censuradas y cambios en la estructura del modelo. En esta tesis se propone un modelo bayesiano para series de tiempo con un n´ umero desconocido de puntos de cambio y con algunas observaciones censuradas, donde cada segmento es un proceso autoregresivo de...
Tipo: Tesis Palavras-chave: Imputación múltiple; Inferencia bayesiana; Algoritmo de Metrópolis; Algoritmo de cadenas de Markov Monte Carlo con saltos reversibles; Doctorado; Estadística; Multiple imputation; Bayesian inference; Metropolis algorithm; Reversible jump Markov chain Monte Carlo algorithm.
Ano: 2009 URL: http://hdl.handle.net/10521/1396
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Series de tiempo con múltiples puntos de cambio y observaciones censuradas Colegio de Postgraduados
Castro Montoya, René.
Debido a factores externos a las variables de inter´es, una serie de tiempo puede presentar cambios en la estructura del modelo o en algunos par´ametros, y debido a l´ımitaciones en los instrumentos de medici´on puede presentar tambi´en censura en las observaciones. Por ejem- plo, cuando se monitorean contaminantes del aire, como pueden ser hidrocarburos arom´aticos (PAHs), mon´oxido de carbono (CO), di´oxido de sulfuro (S O2 ), etc., las series de tiempo ob- servadas pueden tener mediciones censuradas y cambios en la estructura del modelo. En esta tesis se propone un modelo bayesiano para series de tiempo con un n´ umero desconocido de puntos de cambio y con algunas observaciones censuradas, donde cada segmento es un proceso autoregresivo de...
Tipo: Tesis Palavras-chave: Imputación múltiple; Inferencia bayesiana; Algoritmo de Metrópolis; Algoritmo de cadenas de Markov Monte Carlo con saltos reversibles Multiple imputation; Bayesian inference; Metropolis algorithm; Reversible jump Markov chain Monte Carlo algorithm.
Ano: 2012 URL: http://hdl.handle.net/10521/1067
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Comparison of breeding value prediction for two traits in a Nellore-Angus crossbred population using different Bayesian modeling methodologies Genet. Mol. Biol.
Hanna,Lauren L. Hulsman; Garrick,Dorian J.; Gill,Clare A.; Herring,Andy D.; Sanders,James O.; Riley,David G..
The objectives of this study were to 1) compare four models for breeding value prediction using genomic or pedigree information and 2) evaluate the impact of fixed effects that account for family structure. Comparisons were made in a Nellore-Angus population comprising F2, F3 and half-siblings to embryo transfer F2 calves with records for overall temperament at weaning (TEMP; n = 769) and Warner-Bratzler shear force (WBSF; n = 387). After quality control, there were 34,913 whole genome SNP markers remaining. Bayesian methods employed were BayesB ( π = 0.995 or 0.997 for WBSF or TEMP, respectively) and BayesC (π = 0 and π), where π is the ideal proportion of markers not included. Direct genomic values (DGV) from single trait Bayesian analyses were compared...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bayesian inference; Crossbred cattle; Genomic prediction; Model comparison.
Ano: 2014 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572014000500005
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Phylogeny of the Serrasalmidae (Characiformes) based on mitochondrial DNA sequences Genet. Mol. Biol.
Ortí,Guillermo; Sivasundar,Arjun; Dietz,Kelly; Jégu,Michel.
Previous studies based on DNA sequences of mitochondrial (mt) rRNA genes showed three main groups within the subfamily Serrasalminae: (1) a "pacu" clade of herbivores (Colossoma, Mylossoma, Piaractus); (2) the "Myleus" clade (Myleus, Mylesinus, Tometes, Ossubtus); and (3) the "piranha" clade (Serrasalmus, Pygocentrus, Pygopristis, Pristobrycon, Catoprion, Metynnis). The genus Acnodon was placed as the sister taxon of clade (2+3). However, poor resolution within each clade was obtained due to low levels of variation among rRNA gene sequences. Complete sequences of the hypervariable mtDNA control region for a total of 45 taxa, and additional sequences of 12S and 16S rRNA from a total of 74 taxa representing all genera in the family are now presented to...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Piranhas; Pacus; D-loop; Phylogeny; Bayesian inference.
Ano: 2008 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000200030
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Bayesian inference on field data for genetic parameters for some reproductive and related traits of Nellore cattle (Bos indicus) Genet. Mol. Biol.
Faria,Carina Ubirajara de; Magnabosco,Cláudio de Ulhôa; Reyes,Arcadio de los; Lôbo,Raysildo Barbosa; Bezerra,Luiz Antônio Framartino; Sainz,Roberto Daniel.
We used Gibbs sampling in single and two-trait animal models to estimate genetic parameters for some reproductive and related traits of Nellore cattle (Bos indicus). Female traits were age at first calving (AFC), cumulative productivity (CP) and adult weight (AW). For males, scrotal circumferences at 365 and 450 days of age were analyzed. Gibbs sampling using the ‘Multiple Trait using Gibbs Sampling under Animal Model’ (MTGSAM) program of Van Tassel and Van Vleck was used to estimate the (co)variance components of the traits and conduct genetic analyses. Heritabilities were AFC = 0.26, AW = 0.36 and CP = 0.25 under the single-trait animal model. The mean, mode and median estimates for genetic parameters obtained from the marginal posterior distributions...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bayesian inference; Genetic parameters; Heritabilities; Nellore cattle; Reproductive traits.
Ano: 2007 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000300008
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ITS2 variability of Biomphalaria (Mollusca, Planorbidae) species from the Paranapanema Valley (São Paulo State, Brazil): diversity patterns, population structure, and phylogenetic relationships Genet. Mol. Biol.
Tuan,Roseli; Santos,Priscila dos.
The ribosomal DNA internal transcribed spacer 2 (ITS2) has been shown to be a useful genetic marker for species identification and phylogenetic reconstruction in the genus of freshwater snails Biomphalaria (Preston 1910). Additionally, ITS2 studies in Biomphalaria have uncovered significant intra-specific genetic variability suggesting the presence of cryptic species complexes. We obtained ITS2 sequences for the Biomphalaria species B. glabrata, B. tenagophila, B. occidentalis and B. peregrina from the Paranapanema Valley (São Paulo State, Brazil) and compared them with a comprehensive set of published Biomphalaria ITS2 sequences using Bayesian inference of phylogeny. Analysis of the resulting trees showed that the newly obtained B. glabrata sequences did...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bayesian inference; Biomphalaria; DNA sequences; Internal transcribed spacer 2 (ITS2); Ribosomal DNA.
Ano: 2007 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000100024
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Bayesian inference in a quantitative genetic study of growth traits in Nelore cattle (Bos indicus) Genet. Mol. Biol.
Faria,Carina Ubirajara de; Magnabosco,Cláudio de Ulhôa; Reyes,Arcadio de los; Lôbo,Raysildo Barbosa; Bezerra,Luiz Antônio Framartino; Sainz,Roberto Daniel.
The objective of this study was to estimate (co)variance components and genetic parameters for weights (W) and scrotal circumferences (SC) at 365 and 450 days of age, of Nelore (Bos indicus) cattle, using Bayesian inference in single and multiple-trait animal models. The fitted linear models included, besides the animal and residual random effects, the contemporary group (herd-year-season-sex-management group) and age-of-dam as "fixed effects". The analyses were carried out using a Gibbs sampler implemented through the MTGSAM program. The heritabilities (in parentheses) obtained fitting single-trait models were W365 (0.49), W450 (0.52), SC365 (0.68) and SC450 (0.66). Estimates of means, modes and medians for genetic parameters obtained from marginal...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bayesian inference; Growth traits; Genetic parameters.
Ano: 2007 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000400007
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Genotype by environment interaction in Nelore cattle from five Brazilian states Genet. Mol. Biol.
Diaz,Iara Del Pilar Solar; Oliveira,Henrique Nunes de; Bezerra,Luis Antônio Framartino; Lôbo,Raysildo Barbosa.
Records from 75,941 Nelore cattle were used to determine the importance of genotype by environment interaction (GEI) in five Brazilian states. (Co)variance components were estimated by single-trait analysis (with yearling weight, W450, considered to be the same trait in all states) and multiple-trait analysis (with the record from each state considered to be a different trait). The direct heritability estimates for yearling weight were 0.51, 0.39, 0.44, 0.37 and 0.41 in the states of Goiás, Mato Grosso, São Paulo, Mato Grosso do Sul and Minas Gerais, respectively. The across-state genetic correlation estimates between Goiás and Mato Grosso, Goiás and Minas Gerais, São Paulo and Minas Gerais, and Mato Grosso do Sul and Minas Gerais ranged from 0.67 to 0.75....
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bayesian inference; Beef cattle; Genetic correlation.
Ano: 2011 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572011000300012
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Shellfish monitoring for lipophilic phycotoxins in France, recommendation for an updated sampling strategy ArchiMer
Thebault, Anne; Arnich, Nathalie; Belin, Catherine; Neaud-masson, Nadine.
In France, the sampling strategy for the official monitoring of lipophilic phycotoxins in bivalve shellfish relies on the definition of risk areas and high risk periods, during which a systematic weekly analysis of toxins in shellfish is performed. Since 2010, high risk periods are defined as follows: the occurrence of one result above the European regulatory limit (160 μg equivalent okadaic acid/kg shellfish) over the last 3 years leads to that month being considered a high risk period. This definition was established according to a statistical analysis of the official monitoring results for the period 2003-2008, based on the mouse bioassay (MBA) as the official analytical method. As of the 1st January 2010, the MBA has been replaced by LC-MS/MS. In 2014,...
Tipo: Text Palavras-chave: Monitoring; Shellfish; Lipophilic phycotoxins; Bayesian inference.
Ano: 2014 URL: http://archimer.ifremer.fr/doc/00393/50470/51205.pdf
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Relationships of the haematophagous marine snail Colubraria (Rachiglossa: Colubrariidae), within the neogastropod phylogenetic framework ArchiMer
Oliverio, Marco; Modica, Maria Vittoria.
The gastropod genus Colubraria includes marine shallow-water species from tropical, subtropical, and temperate rocky coral environments. At least six species are known to feed on fish blood. Although there is general consensus in placing Colubraria in the Neogastropoda, the actual relationships and the systematic position of Colubraria and related genera are unknown. This is partly the consequence of the lack of a clear phylogenetic framework for the Neogastropoda. This study attempts to propose a phylogenetic framework for the Neogastropoda, by testing: (1) a preliminary phylogenetic arrangement for a large number of recognized neogastropod families; (2) the position of Colubraria within the neogastropods; and (3) the relationships of Colubraria within...
Tipo: Text Palavras-chave: Bayesian inference; Buccinoidea; Cancellarioidea; Conoidea; Maximum Likelihood; Muricoidea; Neogastropoda; Phylogeny; Radula; Systematics.
Ano: 2010 URL: https://archimer.ifremer.fr/doc/00207/31804/30216.pdf
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Geoglossomycetes cl. nov., Geoglossales ord. nov. and taxa above class rank in the Ascomycota Tree of Life Naturalis
Schoch, C.L.; Wang, Z.; Townsend, J.P.; Spatafora, J.W..
Featuring a high level of taxon sampling across Ascomycota, we evaluate a multi-gene phylogeny and propose a novel order and class in Ascomycota. We describe two new taxa, Geoglossomycetes and Geoglossales, to host three earth tongue genera: Geoglossum, Trichoglossum and Sarcoleotia as a lineage of ‘Leotiomyceta’. Correspondingly, we confirm that these genera are not closely related to the genera Neolecta, Mitrula, Cudonia, Microglossum, Thuemenidum, Spathularia and Bryoglossum, all of which have been previously placed within the Geoglossaceae. We also propose a non-hierarchical system for naming well-resolved nodes, such as ‘Saccharomyceta’, ‘Dothideomyceta’, and ‘Sordariomyceta’ for supraordinal nodes, within the current phylogeny, acting as rankless...
Tipo: Article / Letter to the editor Palavras-chave: Bayesian inference; Hybrid classification; Maximum likelihood.
Ano: 2009 URL: http://www.repository.naturalis.nl/record/532418
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Variance components for body weight in Japanese quails (Coturnix japonica) Rev. Bras. Ciênc. Avic.
Resende,RO; Martins,EN; Georg,PC; Paiva,E; Conti,ACM; Santos,AI; Sakaguti,ES; Murakami,AE.
The objective of this study was to estimate the variance components for body weight in Japanese quails by Bayesian procedures. The body weight at hatch (BWH) and at 7 (BW07), 14 (BW14), 21 (BW21) and 28 days of age (BW28) of 3,520 quails was recorded from August 2001 to June 2002. A multiple-trait animal model with additive genetic, maternal environment and residual effects was implemented by Gibbs sampling methodology. A single Gibbs sampling with 80,000 rounds was generated by the program MTGSAM (Multiple Trait Gibbs Sampling in Animal Model). Normal and inverted Wishart distributions were used as prior distributions for the random effects and the variance components, respectively. Variance components were estimated based on the 500 samples that were...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bayesian inference; Heritability; Maternal environment.
Ano: 2005 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-635X2005000100004
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Bayesian analysis for comparison of nonlinear regression model parameters: an application to ruminal degradability data R. Bras. Zootec.
Rossi,Robson Marcelo; Martins,Elias Nunes; Guedes,Terezinha Aparecida; Jobim,Clóves Cabreira.
This paper shows the Bayesian approach as an alternative to the classical analysis of nonlinear models for ruminal degradation data. The data set was obtained from a Latin square experimental design, established for testing the ruminal degradation of dry matter, crude protein and fiber in neutral detergent of three silages: elephant grass (Pennisetum purpureum Schum) with bacterial inoculant or enzyme-bacterial inoculant and corn silage (Zea mays L.). The incubation times were 0, 2, 6, 12, 24, 48, 72 and 96 hours. The parameter estimates of the equations fitted by both methods showed small differences, but by the Bayesian approach it was possible to compare the estimates correctly, that does not happen with the frequentist methodology because it is much...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bayesian inference; Degradability; Nonlinear models.
Ano: 2010 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982010000200027
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Addressing scope of inference for global genetic evaluation of livestock R. Bras. Zootec.
Tempelman,Robert John.
Genetic evaluations should become more accurate with the advent of whole genome selection (WGS) based on high density SNP panels. The use of WGS should then accelerate genetic gains for production traits given likely decreases in generation interval due to the greater intent to select more animals based just on their genotypes rather than phenotypes. However, past and current genetic evaluations may not generally connect well to the intended scope of inference. For example, estimating haplotype effects from the data of a single reference population does not bode well for the use of WGS in other diverse environments since the scope of inference is too narrow; conversely, WGS based on estimates, for example, derived from daughter yield deviations of dairy...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bayesian inference; Genotype by environment interaction; Heterogeneous variances; Mixed effects models; Multiple traits; Random effects.
Ano: 2010 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982010001300029
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Hierarchical Bayesian models for genotype × environment estimates in post-weaning gain of Hereford bovine via reaction norms R. Bras. Zootec.
Cardoso,Leandro Lunardini; Braccini Neto,José; Cardoso,Fernando Flores; Cobuci,Jaime Araújo; Biassus,Igor de Oliveira; Barcellos,Júlio Otávio Jardim.
It was evaluated statistical models with different assumptions to define the one that best describes the presence of genotype × environment interaction on adjusted post-weaning weight gain (PWG345) of Hereford cattle, through the study of reactions norms to the environment, obtained by random regression using a Bayesian approach. Four reaction norms hierarchical models (RNHM) were used through the INTERGEN program. The RNHM K uses the solutions of contemporary groups previously estimated by the standard animal model (AM) and considers them as environmental level for predicting the reaction norms and the RNHM S, which jointly estimate these two sets of unknowns. For both models, two versions were considered, one with a homogeneous (hm) and another with a...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Adaptability; Bayesian inference; Environmental sensitivity; Genetic evaluation; Random regression.
Ano: 2011 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982011000200009
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Estimates of covariance components for hygienic behavior in Africanized honeybees (Apis mellifera) R. Bras. Zootec.
Costa-Maia,Fabiana Martins; Toledo,Vagner de Alencar Arnaut de; Martins,Elias Nunes; Lino-Lourenço,Daniela Andressa; Sereia,Maria Josiane; Oliveira,Carlos Antonio Lopes de; Faquinello,Patrícia; Halak,André Luiz.
Genetic and phenotypic parameters considering the genetic effect on hygienic behavior of queen and workers from 40 Africanized honeybees colonies were estimated separately. Maternal origin of queens was controlled whereas the paternal was unknown, and different groups of workers were considered in three seasons, October 2006, April 2007 and August 2007, but with the same queen. Colonies were 21 honey producers and 19 royal jelly producers. After the method of freezing capped brood, hygienic behavior was determined by the ratio between the number of dead capped brood removed at 24, 48 and 72 hours and the total number of capped brood at zero hour. Data was submitted to single and three traits analyses using Bayesian inference. Estimates of direct...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Africanized honeybee queens; Bayesian inference; Genetic correlation; Heritability; Maternal effect; Removal of dead capped brood.
Ano: 2011 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982011000900010
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Genetic parameters and relationships between heifers rebreeding and hip height in Nellore cattle R. Bras. Zootec.
Boligon,Arione Augusti; Albuquerque,Lucia Galvão de.
The objective of this study was to estimate heritability and verify the genetic correlations between heifers subsequent rebreeding with weaning hip height (WHH) and yearling hip height (YHH), using Bayesian inference. The (co)variance components and genetic parameters were estimated using an animal nonlinear (threshold) model for subsequent rebreeding and an animal linear model for WHH and YHH. The animal model included the contemporary group as the systematic effect and direct additive genetic and residual effects as random effects. Genetic maternal and maternal permanent environment effects were also considered in the model for WHH. Covariables considered were: rest period (linear effect), for subsequent rebreeding; animal age at measurement and age of...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bayesian inference; Beef cattle; Heritability; Reproductive trait.
Ano: 2012 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982012000300017
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Heteroskedasticity for weaning weight of Charolais-Zebu crossbred calves R. Bras. Zootec.
Toral,Fábio Luiz Buranelo; Torres Júnior,Roberto Augusto de Almeida; Lopes,Paulo Sávio; Cardoso,Fernando Flores; Silva,Luiz Otávio Campos da.
The objective of the present study was to analyze models with genetic and/or residual heteroskedasticity for genetic evaluation of the weaning weight of Charolais-Zebu crossbred calves. Weaning weight data from 56,965 crossbred calves were analyzed using animal models with different combinations of genetic and residual heteroskedasticity and/or homoskedasticity. The inference on a posteriori distributions of genetic parameters were by the Monte Carlo method via Markov chains. The model with genetic and residual heteroskedasticity was the best fit on the data. Groups of animals with different genetic compositions, expressed as percentages of Charolais-Zebu breed alleles and individual and maternal heterozygosis, had different genetic variances. These...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Animal breeding; Bayesian inference; Canchim; Crossbreeding; Selection.
Ano: 2012 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982012000500013
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Reaction norms models in the adjusted weight at 550 days of age for Polled Nellore cattle in Northeast Brazil R. Bras. Zootec.
Ambrosini,Diego Pagung; Carneiro,Paulo Luiz Souza; Braccini Neto,José; Martins Filho,Raimundo; Amaral,Rosimira dos Santos; Cardoso,Fernando Flores; Malhado,Carlos Henrique Mendes.
The objective of this study was to evaluate the genotype-environment interaction (GEI) in the body weight adjusted to 550 days of age (W550) of Polled Nellore cattle raised in Northeastern Brazil using reaction norms (RN) models. Hierarchical RN models included fixed effects for age of cow (linear and quadratic) and random effects for contemporary groups (CG) and additive genetic RN level and slope. Four RN hierarchical models (RNHM) were used. The RNHM2S uses the solutions of contemporary groups estimated by the standard animal model (AM) and considers them as environmental level for predicting the reaction norms and the RNHM1S, which jointly estimate these two sets of unknowns. Two versions were considered for both models, one with a homogeneous (Hm) and...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bayesian inference; Environmental gradient; Genetic value; Random regression; Zebu cattle.
Ano: 2014 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982014000700351
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