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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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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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Avaliação genética do ganho de peso e conversão alimentar de coelhos da raça Nova Zelândia Branco criados em ambientes diferenciados - DOI: 10.4025/actascianimsci.v32i1.6262 Animal Sciences
Santos, Alexandre Leseur; UEM; Scapinello, Cláudio; UEM; Martins, Elias Nunes; UEM; Granzotto, Fernanda; UEM; Paula, Meybi Carneiro; UEM; Hidalgo, André Marubayashi; UEM.
O objetivo do presente trabalho foi avaliar se a seleção para conversão alimentar (CA) e ganho de peso (GP), com base no desempenho individual e ou coletivo dos láparos, pode produzir ganhos genéticos em progênies criadas coletivamente, e animais submetidos à avaliação no período de 50 a 70 dias de idade, utilizando inferência Bayesiana. Realizaram-se seis análises bicaráter. No teste de desempenho foi observado que as características ganho de peso e conversão alimentar em ambos os ambientes tiveram valores para herdabilidade que variam de 0,42 a 0,60. Tanto a correlação genética 0,44 a 0,68 (GP) e 0,23 a 0,56 (CA) como a fenotípica 0,30 (GP) e 0,17 (CA) foram positivas para a mesma característica quando avaliada nos dois ambientes, coletivo ou individual,...
Tipo: Pesquisa de Campo; Metodologia Palavras-chave: 5.04.02.00-5; Herdabilidade; Ganho de peso; Conversão alimentar; Correlação genética; Inferência bayesiana GENÉTICA E MELHORAMENTO DOS ANIMAIS DOMÉSTICOS Heritability; Weight gain; Feed conversion; Genetic correlation; Bayesian inference.
Ano: 2009 URL: http://periodicos.uem.br/ojs/index.php/ActaSciAnimSci/article/view/6262
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Bayesian AMMI applied to food-type soybean multi-environment trials Rev. Ciênc. Agron.
Freiria,Gustavo Henrique; Gonçalves,Leandro Simões Azeredo; Zeffa,Douglas Mariani; Lima,Wilmar Ferreira; Fonseca Júnior,Nelson da Silva; Prete,Cássio Egídio Cavenaghi; Fonseca,Inês Cristina de Batista.
ABSTRACT A complicating factor for the selection of plant strains is the influence of a genotype-environment (GE) interaction. The Bayesian approach is a tool to increase the efficiency of adaptability and stability methodologies. In this context, the objective of this study was to evaluate the linear and bi-linear parameters of the additive main effects and multiplicative interaction (AMMI) analysis using the Bayesian approach for selection of food-type soybean genotypes in multi-environment trials. The grain yields of five lipoxygenase-free lines intended for human consumption of from the soybean breeding program of the Londrina State University and two commercial standards (BRS 257 and BMX Potência RR) were evaluated in four counties of the State of...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Glycine max; Bayesian inference; Genotype - environment; Functional food; Grain yield.
Ano: 2020 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1806-66902020000400417
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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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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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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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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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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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Evaluation of Bayesian models for analysis of crude protein requirement for pigs of Brazilian Piau breed Scientia Agricola
Silva,Hugo Teixeira; Silva,Fabyano Fonseca e; Ferreira,Aloízio Soares; Veroneze,Renata; Lopes,Paulo Sávio.
ABSTRACT: We evaluated the inclusion of information on genetic relationship into the analysis of crude protein requirement in diets for pigs of Brazilian Piau breed, using Bayesian inference. The animals were assigned to treatments in a completely randomized design in factorial scheme 4 × 2 (crude protein levels × sex) with 12 repetitions per treatment. The evaluations were carried out in the initial, growing and finishing phases, and after slaughter. The traits evaluated were feed conversion (FC), backfat thickness (BF), daily weight gain (DWG), daily feed intake (DFI) and some carcass cuts. Three models were considered to evaluate the inclusion of information on genetic relationship into the analysis: Model I, a simple linear model; Model II, the same...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bayesian inference; Genetic relationship; Model selection; Performance.
Ano: 2019 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-90162019001300208
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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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Genotype by environment interaction in different birth seasons for weight at 240, 365 and 450 days of age in Tabapuã cattle R. Bras. Zootec.
Sousa Júnior,Severino Cavalcante de; Diaz,Iara Del Pilar Solar; Santos,Karina Rodrigues dos; Sousa,José Ernandes Rufino de; Sarmento,José Lindenberg Rocha; Martins Filho,Raimundo.
The objective of this study was to evaluate the effect of genotype by environment interaction (GEI) on the weight of Tabapuã cattle at 240 (W240), 365 (W365) and 450 (W450) days of age. In total, 35,732 records of 8,458 Tabapuã animals which were born in the state of Bahia, Brazil, from 1975 to 2001, from 167 sires and 3,707 dams, were used. Two birth seasons were tested as for the environment effect: the dry (D) and rainy (R) ones. The covariance components were obtained by a multiple-trait analysis using Bayesian inference, in which each trait was considered as being different in each season. Covariance components were estimated by software gibbs2f90. As for W240, the model was comprised of contemporary groups and cow age (in classes) as fixed effects;...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bayesian inference; Beef cattle; Genetic correlation; Multiple-trait analysis.
Ano: 2012 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982012001000005
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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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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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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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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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Inferences on the effects of selection for feed conversion over meat quality traits in broiler Scientia Agricola
Paiva,José Teodoro de; Mourão,Gerson Barreto; Ferraz,José Bento Sterman; Mattos,Elisângela Chicaroni; Michelan Filho,Tércio; Campos,Bárbara Machado; Eler,Joanir Pereira; Gaya,Leila de Genova.
ABSTRACT: The intense selection process for economic traits conducted by the poultry breeding programs has been caused several changes in broiler meat quality. A database belonging to a selection program of a broiler male line was used to estimate heritability and genetic correlations for feed conversion ratio and meat quality traits, which were: initial and final pH, lightness, drip loss, thawing loss and shear force. Two-trait analyses were performed and the components of co(variance) and genetic parameters were determined using the Bayesian approach and the GIBBS3F90 software. The heritability estimate found for feed conversion ratio (0.52) showed high influence of direct additive genetic effects on the expression of this trait; therefore, this trait is...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bayesian inference; Animal breeding; Genetic correlation; Indirect selection.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-90162018000200129
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Influence of genotype-environment interaction on the classification of Nellore bulls in Southern Brazil Animal Sciences
Bresolin, Tiago; Everling, Dionéia Magda; Rorato, Paulo Roberto Nogara; Braz, Camila Urbano; Breda, Fernanda Cristina.
The aim of this study was to assess the occurrence of genotype-environment interaction, as well as its effects on the magnitude of genetic parameters and the classification of Nellore breeding bulls for the trait adjusted weight at 205 days (W205) on Southern Brazil. The components of (co)variance were estimated by Bayesian inference, using a linear-linear animal model in a bi-trait analysis. The proposed model for the analyses considers as random the direct additive genetic and maternal effects and residual effects, and as fixed effects the contemporary groups, sex, season of birth and weighing, and calving age as covariable  (linear and quadratic effects). The a posteriori mean estimates of the direct heritabilities for W205 in the three States varied...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Beef cattle; Variance components; Genetic correlation; Bayesian inference; Genetic parameters..
Ano: 2015 URL: http://periodicos.uem.br/ojs/index.php/ActaSciAnimSci/article/view/23602
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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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Phylogenetic relationships between Bacillus species and related genera inferred from 16s rDNA sequences BJM
Wei Wang,Mi Sun.
Neigh-borjoining, maximum-parsimony, minimum-evolution, maximum-likelihood and Bayesian trees constructed based on 16S rDNA sequences of 181 type strains of Bacillus species and related taxa manifested nine phylogenetic groups. The phylogenetic analysis showed that Bacillus was not a monophyletic group. B. subtilis was in Group 1. Group 4, 6 and 8 respectively consisted of thermophiles, halophilic or halotolerant bacilli and alkaliphilic bacilli. Group 2, 4 and 8 consisting of Bacillus species and related genera demonstrated that the current taxonomic system did not agree well with the 16S rDNA evolutionary trees. The position of Caryophanaceae and Planococcaceae in Group 2 suggested that they might be transferred into Bacillaceae, and the heterogeneity of...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bacillus phylogeny; Bayesian inference; Evolutionary trees; 16S rDNA.
Ano: 2009 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822009000300013
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