Navegando por Autor "Junqueira, Vinícius Silva"
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Item Contemporary groups in the genetic evaluation of Nellore cattle using Bayesian inference(Pesquisa Agropecuária Brasileira, 2017-08) Silva, Delvan Alves da; Silva, Fabyano Fonseca e; Ventura, Henrique Torres; Junqueira, Vinícius Silva; Silva, Alessandra Alves da; Mota, Rodrigo Reis; Lopes, Paulo SávioThe objective of this work was to evaluate the criteria for the formation of contemporary groups (CGs) in the genetic evaluation of body weight at weaning in Nellore cattle. A total of 713,474 records from 3,066 herds located in Midwestern and Northern Brazil were used. Data were obtained from the genealogical registry of zebu breeds of the Brazilian association of zebu breeders. Data structures were defined based on the number of standard deviations (SDs) for outlier removal (±2.0, ±2.5, ±3.0, and ±3.5) and on the minimal number of animals per CG (3, 7, and 15). Genetic evaluation was performed with an animal model using Bayesian inference. Data structures with ±3.5 SDs and CG with at least 15 animals presented the highest additive genetic variance (82.65±2.93), and those with ±2.0 SDs and CG with at least 3 animals showed the lowest one (60.23±1.96). The proper formation of CGs results in better-quality data archives, allowing to obtain more trustable estimates for the genetic parameters. Better selection responses are obtained when the following criteria are adopted for the removal of outliers: 2.5, 3.0, and 3.5 standard deviations and a minimum of 15 animals per contemporary group.Item Genomic information for breed determination, multibreed evaluation, and estimation of variance components in large populations(Universidade Federal de Viçosa, 2018-06-04) Junqueira, Vinícius Silva; Lopes, Paulo Sávio; http://lattes.cnpq.br/4686677580216927The knowledge on breed composition is of major importance under design of breeding schemes. With this respect, the estimation of such parameters must be as accurately as possible. Currently, most of genetic evaluation programs has been predicting breed composition based on pedigree datasets; but, such estimations only accounts for the expected (allele frequency) contributions across ancestors After the development and establishment of single nucleotide polymorphism (SNP) genotyping platforms on the last decade, an interest in genetic diversity studies has arisen and especially the study of individuals’ origin. The objective of the present study was to evaluate the minimum required number of ancestry informative markers necessary to differentiate Hereford, Nelore, Brahman and Braford breeds genotyped with 777 K Illumina Bovine HD Bead Chip. In addition, we also compared the effects of different panels size on breed composition inference under different AIMs methods. To that, it was used the high-density Illumina Bovine HD BeadChip with more than 777 K SNPs to elucidate the structure of Hereford, Nelore, Brahman and Braford populations. Three different ancestry informative marker methods were used to distinguish such populations. Additionally, random marker selection was considered. Admixture software was used to infer breed composition using very low-density SNP panels assembled with AIMs. Our results suggest that is possible to assign individuals to populations with high confidence using less than 8 SNP markers selected per breed. Although millions of SNP markers have been identified, only few of them are needed to accurately infer ancestry in a cost-effective manner. Pedigree information is by nature incomplete and commonly not well established simply because many of the true genetic ties existent between individuals are not a priori known or they can be even wrong. Genomic era brought new opportunities when calculating relationships between individuals. The challenge under genomic approaches is the correct definition of genetic base by the use of pedigree and genomic data. Genetic base may change as more individuals are included and are inadequately defined if populations are genetically structured. Metafounder concept relies on the definition of pseudo-individuals that describes some level of within and/or across genetic relationship between base population. The purpose of this study was to evaluate metafounder theory to estimate breeding values and the predictive ability under a single-step approach for a multibreed population. Three different scenarios were adopted to estimate variance components and to compute breeding values: pedigree-based model, single- step GBLUP and single-step GBLUP with addition of metafounders. A total of 28 different metafounders were included in the ssGBLUP+metafounder model. In general, it was possible to note that genomic models were able to greater ability to predict the future performance. Among genomic models, the inclusion of metafounder information could increment even more the predictive ability under cross-validation approach. Restricted maximum likelihood (REML) is a popular method for parameter estimation. Because it uses the mixed model equations, it is resistant to selection bias and efficient implementations are currently available. When genomic information is available, two versions of REML may be applicable. When only genotyped animals have phenotypes, genomic REML can be applied with a genomic relationship matrix. When only a fraction of animals is genotyped, a single-step REML is applicable. In general, it is of interest to include many genotyped animals in parameter estimation and into evaluations, to account for genomic selection or pre- selection. The aim of this study was to investigate to what extent generations truncation affects estimates for a simulated population under selection.The use of less generations reduced the ability of pedigree-based model in estimating the benchmark heritability (0.30). The decrease in heritabilities based on genomic information was less than using only pedigree relationships. Genomic models provided greater correlations than pedigree-based model; on average 25 points. Single-step genomic models do not require a deeper pedigree relationship to estimate reliable variance components and breeding values. The use of APY algorithm does not affect the estimation of variance components. An extra of 2 ungenotyped generations are sufficient to compute reliable variance components; as well as breeding values and accuracies.Item Impact of embryo transfer phenotypic records on large-scale beef cattle genetic evaluations(Revista Brasileira de Zootecnia, 2018-06) Junqueira, Vinícius Silva; Lopes, Paulo Sávio; Resende, Marcos Deon Vilela de; Silva, Fabyano Fonseca e; Lourenço, Daniela Andressa Lino; Yokoo, Marcos Jun Iti; Cardoso, Fernando FloresWe aimed to evaluate the impact of using embryo transfer (ET) information on weaning weight estimated breeding values (EBV) and its accuracy. Data from Hereford and Braford cattle, raised under extensive conditions in Southern Brazil, were used. A model that included ET information in addition to maternal (genetic and permanent environmental) effects as a function of foster dams was compared to a model without ET information. Accuracy of both bulls and calves increased due to inclusion of ET records in 0.04 and 0.12 points, respectively. In general, the inclusion of ET records provided a greater amount of phenotypic variance and most accurate EBV for sires and progeny. The results obtained in this study encourage the use of ET phenotypic records in large-scale genetic evaluation programs, especially for bulls that have most of their progeny coming from ET. Most of the Brazilian genetic evaluation programs do not use phenotypic records of ET animals. Therefore, breeding values are predicted based only on parentage average, which implies in underestimated accuracies. Considering that ET has been widely used in Brazil and that such information improves genetic predictions, we suggest modifying the traditional adopted models by considering ET information in the Brazilian genetic evaluations.Item Qualidade das informações de parentesco na avaliação genética de bovinos de corte(Universidade Federal de Viçosa, 2014-07-25) Junqueira, Vinícius Silva; Cardoso, Fernando Flores; http://lattes.cnpq.br/5739317705056424; Silva, Fabyano Fonseca e; http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4766260Z2; Lopes, Paulo Sávio; http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4783377H1; http://lattes.cnpq.br/4686677580216927; Silva, Marcos Vinicius Gualberto Barbosa da; http://lattes.cnpq.br/6353954532527478O objetivo desse estudo foi verificar o reflexo da qualidade das informações de parentesco sobre as estimativas de parâmetros genéticos e acurácias das predições de valor genética Dessa forma, foi avaliada a qualidade dessas informações ao realizar correções no pedigree baseadas em marcadores do tipo SNPs. Os componentes de variância foram estimados sob enforque Bayesiano por amostragem de Gibbs. A avaliação da correta definição de parentesco foi realizada utilizando-se informações de marcadores SNPs de 3.591 indivíduos em uma população constituída de 12.668 animais. Os conflitos mendelianos entre as marcas da progênie e dos pais foram utilizados como critério de avaliação de parentesco. Dessa forma, foram realizadas 460 mudanças no pedigree, dentre os quais 54% possuíam um touro ou vaca identificado. Foi observado que, em média, novos relacionamentos genéticos foram definidos com 75 marcas em conflito, enquanto que a rejeição do parentesco foi realizada com 2.700 marcas. O uso do programa Molecular Coancestry para inferência de parentesco a partir de informações de marcadores moleculares proporcionou a definição de 2.174 novos relacionamentos de meio-irmãos. Foi possível observar que as correções de parentesco proporcionaram aumento da acurácia média dos valores genéticos preditos. O aumento na qualidade das informações de pedigree proporcionou a estimação de herdabilidade de maior magnitude (0,22 i 0,0286), sugerindo a possibilidade de seleção direta para a resistência a carrapatos. Foi utilizada uma estratégia de validação cruzada pelo método K-médias e também de forma aleatória, no qual cinco grupos de treinamento foram formados. Os resultados da validação cruzada indicam que maior qualidade nos relacionamentos do pedigree proporcionam maior valor de acurácia. O peso padronizado aos 205 dias foi utilizado para avaliar a inclusão de informações de filhos de reprodutores múltiplos (RM) e de animais oriundos de biotécnicas da reprodução (TEF). Foram avaliadas três estratégias de inclusão dessas informações: grupos genéticos (GG), método hierárquico bayesiano (HIER) e matriz da média dos numeradores dos coeficientes de parentesco (ANRM). O critério de informação da deviance (DIC) foi utilizado como avaliador da qualidade de ajuste e sugeriu que a estratégia HIER proporcionou melhor ajuste ao considerar as informações de RM. Entretanto, o método ANRM apresentou melhor ajuste ao incluir informações dos animais TEF. A inclusão das informações de animais TEF foi realizada pelo uso da informação da receptora para estimação do efeito genético materno e de ambiente permanente materno. Não foi observada diferença estatística nas estimativas de componentes de variância e de parâmetros genéticos ao considerar informações de animais TEF, porém os valores genéticos preditos apresentaram maior magnitude. As correlações de Spearman entre os valores genéticos foram de elevadas magnitudes para os animais fundadores, animais com certeza no parentesco e para os fiIhos de RM. Entretanto, o uso das informações dos animais TEF modificou de forma significativa as predições dos valores genéticos. O uso de metodologias adequadas para incluir a informação de animais com incerteza de paternidade e animais oriundos de transferência de embriões e fertilização in vitro proporcionam a predição de valores genéticos mais acurados e auxiliam em maiores taxas de ganho genético.