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A comparison of regression methods based on dimensional reduction for genomic prediction. Repositório Alice
COSTA, J. A. da; AZEVEDO, C. F.; NASCIMENTO, M.; SILVA, F. F. e; RESENDE, M. D. V. de; NASCIMENTO, A. C. C..
multicollinearity and high dimensionality problems, making it impossible to obtain stable estimates through the traditional method of estimation based on ordinary least squares. To overcome such challenges, dimensionality reduction methods have been proposed, because of their simple theory and easy application. We compared three dimensionality reduction methods: Principal Components Regression (PCR), Partial Least Squares (PLS), and Independent Components Regression (ICR). An important step for dimensionality reduction and prediction is selecting the number of components, as it affects the linear combinations of the explanatory variables. The linear combinations are inserted into the model to predict the response based on a reduced number of parameters. We...
Tipo: Artigo de periódico Palavras-chave: Regression analysis; Genomics.
Ano: 2021 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1139234
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Adaptability and stability of cotton genotypes regarding fiber yield and quality traits. Repositório Alice
TEODORO, P. E.; FARIAS, F. J. C.; CARVALHO, L. P. de; RIBEIRO, L. P.; NASCIMENTO, M.; AZEVEDO, C. F.; CRUZ, C. D.; BHERING, L. L..
The performance of textile processes and the quality of the products depends on the several cotton (Gossypium hirsutum L.) fiber quality traits, such as micronaire index, fiber length, and fiber strength. This research aims to recommend cotton genotypes for the Brazilian Cerrado based on fiber yield and fiber quality traits. Nineteen cotton cultivar variety trials were performed in the 2013?2014 and 2014?2015 crop seasons. Each trial was conducted as a randomized complete block design with 12 treatments and four replications. The evaluated traits were fiber yield, fiber length, fiber strength, and micronaire. For each trait, a modified Lin and Binns method was used to recommend the best genotypes for all environments (favorable and unfavorable). This...
Tipo: Artigo de periódico Palavras-chave: Gossypium Hirsutum; Algodão; Fibra; Fiber quality; Micronaire; Cotton.
Ano: 2019 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1118672
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Bayesian model combining linkage and linkage disequilibrium analysis for low density-based genomic selection in animal breeding. Repositório Alice
SILVA, F. F.; JEREZ, E. A. Z.; RESENDE, M. D. V. de; VIANA, J. M. S.; AZEVEDO, C. F.; LOPES, P. S.; NASCIMENTO, M.; LIMA, R. O. de; GUIMARÃES, S. E. F..
We combined linkage (LA) and linkage disequilibrium (LDA) analyses (emerging the term ?LALDA?) for genomic selection (GS) purposes. The models were fitted to a simulated dataset and to a real data of feed conversion ratio in pigs. Firstly, the significant QTLs (quantitative trait locus) were identified through LA-based mixed models considering the QTL-genotypes as random effects by means of genotypic identity by descent matrix. This matrix was calculated at the positions of significant QTLs (based on LA) allowing to include the QTL-genotype effects additionally to SNP (single nucleotide polymorphism) markers (based on LDA) and additive polygenic effects in several GS models (Bayesian Ridge Regression ? BRR; Bayes A ? BA; Bayes B ? BB; Bayes C ? BC and...
Tipo: Artigo de periódico Palavras-chave: X.
Ano: 2018 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1093541
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Can cross-country genomic predictions be a reasonable strategy to support germplasm exchange? A case study with hydrogen cyanide in cassava. Repositório Alice
TORRES, L. G.; OLIVEIRA, E. J. de; OGBONNA, A. C.; BAUCHET, G. J.; MUELLER, L. A.; AZEVEDO, C. F.; SILVA, F. F.; SIMIQUELI, G. F.; RESENDE, M. D. V. de.
Genomic prediction (GP) offers great opportunities for accelerated genetic gains by optimizing the breeding pipeline. One of the key factors to be considered is how the training populations (TP) are composed in terms of genetic improvement, kinship/origin, and their impacts on GP. Hydrogen cyanide content (HCN) is a determinant trait to guide cassava?s products usage and processing. This work aimed to achieve the following objectives: (i) evaluate the feasibility of using cross-country (CC) GP between germplasm?s of Embrapa Mandioca e Fruticultura (Embrapa, Brazil) and The International Institute of Tropical Agriculture (IITA, Nigeria) for HCN; (ii) provide an assessment of population structure for the joint dataset; (iii) estimate the genetic parameters...
Tipo: Artigo de periódico Palavras-chave: Genoma; Germoplasma; Cianeto; Mandioca; Population structure; Breeding; Genomics; Hydrogen cyanide; Cassava.
Ano: 2021 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1139241
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Cassava yield traits predicted by genomic selection methods. Repositório Alice
ANDRADE, L. R. B. de; SOUSA, M. B. e; OLIVEIRA, E. J. de; RESENDE, M. D. V. de; AZEVEDO, C. F..
Genomic selection (GS) has been used to optimize genetic gains when phenotypic selection is considered costly and difficult to measure. The objective of this work was to evaluate the efficiency and consistency of GS prediction for cassava yield traits (Manihot esculenta Crantz) using different methods, taking into account the effect of population structure. BLUPs and deregressed BLUPs were obtained for 888 cassava accessions and evaluated for fresh root yield, dry root yield and dry matter content in roots in 21 trials conducted from 2011 to 2016. The deregressed BLUPs obtained for the accessions from a 48K single nucleotide polymorphism dataset were used for genomic predictions based on the BayesB, BLASSO, RR-BLUP, G-BLUP and RKHS methods. The accessions?...
Tipo: Artigo de periódico Palavras-chave: Genomic predictions; Heredity; Mandioca; Melhoramento Genético Vegetal; Plant breeding; Cassava.
Ano: 2019 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1115740
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Combined index of genomic prediction methods applied to productivity traits in rice. Repositório Alice
SUELA, M. M.; LIMA, L. P.; AZEVEDO, C. F.; RESENDE, M. D. V. de; NASCIMENTO, M.; SILVA, F. F. e.
A cultura do arroz tem grande importância nacional e mundial por ser um dos cereais mais produzidos e consumidos no mundo, caracterizando-se como o principal alimento de mais da metade da população mundial. Em função de sua importância alimentar, desenvolver métodos eficientes que visam a predição e a seleção de indivíduos geneticamente superiores, quanto a características da planta, é de extrema importância para os programas de melhoramento. Diante disso, o objetivo deste trabalho foi avaliar e comparar a eficiência do método Delta-p, G-BLUP, BayesCpi, BLASSO e o índice Delta-p/G-BLUP, índice Delta-p/BayesCpi e índice Delta-p/BLASSO, na estimação de valores genômicos e dos efeitos de marcadores SNPs (Single Nucleotide Polymorphisms) em dados fenotípicos...
Tipo: Artigo de periódico Palavras-chave: Predição genômica; Ganho genético; Genomic prediction; Genetic gain; Bayesian alphabet; Molecular bases; Regression; Índice de Seleção; Selection index.
Ano: 2019 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1110881
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Comparison of dimensionality reduction methods to predict genomic breeding values for carcass traits in pigs. Repositório Alice
AZEVEDO, C. F.; NASCIMENTO, M.; SILVA, F. F.; RESENDE, M. D. V. de; LOPES, P. S.; GUIMARÃES, S. E. F.; GLÓRIA, L. S..
A significant contribution of molecular genetics is the direct use of DNA information to identify genetically superior individuals. With this approach, genome-wide selection (GWS) can be used for this purpose. GWS consists of analyzing a large number of single nucleotide polymorphism markers widely distributed in the genome; however, because the number of markers is much larger than the number of genotyped individuals, and such markers are highly correlated, special statistical methods are widely required. Among these methods, independent component regression, principal component regression, partial least squares, and partial principal components stand out. Thus, the aim of this study was to propose an application of the methods of dimensionality reduction...
Tipo: Separatas Palavras-chave: Quadrados mínimos parciais; Componente de regressão independente; Componente principal de regressão; Componente principal parcial; Partial least squares; Independent component regression; Principal component regression; Partial principal component.
Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1030362
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Computação paralela aplicada à seleção genômica via inferência Bayesiana. Repositório Alice
LAGROTTA, M. R.; SILVA, F. F. e; RESENDE, M. D. V. de; NASCIMENTO, M.; DUARTE, D. A. S.; AZEVEDO, C. F.; MOTA, R. R..
Em seleção genômica (SG), o grande número de marcadores moleculares utilizados, bem como a demanda computacional dos modelos bayesianos, fundamentados nos algoritmos Monte Carlo Via Cadeias de Markov, faz com que as análises exijam semanas ou até meses de processamento. A computação paralela representa uma solução natural para este problema, visto que esta subdividi um algoritmo em várias tarefas independentes, as quais podem ser processadas em paralelo, reduzindo o tempo de processamento. Objetivou-se comparar a eficiência de processamento do método BayesCπ programado em paralelo com o seu algoritmo sequencial padrão. Duas estratégias de paralelização foram estudadas. A primeira envolveu a análise de múltiplas cadeias MCMC em paralelo, e a...
Tipo: Artigo de periódico Palavras-chave: Marcadores SNP; Regressão Bayesiana; Statistics; Genetic improvement.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1084055
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Desenvolvimento ponderal de rebanhos Nelore e Guzerá no estado do Rio Grande do Norte. Repositório Alice
MOURA, A. de A. A.; AZEVEDO, C. F.; LOBO, R. N. B.; MARTINS FILHO, R..
Um estudo foi conduzido com a finalidade de avaliar os efeitos de fatores de meio sobre os pesos ao nascer (PN) e aos 205 (P205), 365 (P365) e 550 dias de idade (P550) em animais Nelore e Guzerá, criados no estado do Rio Grande do Norte, entre 1977 e 1997. Foram utilizadas 3.116 informações de bezerros (2.017 Guzerá e 1.099 Nelore), provenientes de 14 propriedades. Por meio de análise de variância, avaliou-se modelos com os efeitos fixos da raça, propriedade dentro da raça, ano e mês de nascimento, sexo da cria, regime alimentar (somente a partir do desmame) e idade da vaca ao parto como covariável. As médias e erros-padrão para as variáveis PN, P205, P365 e P550 foram 29,1 ± 0,3 kg; 171,8 ± 2,3 kg; 246,6 ± 4,6 kg e 335,4 ± 5,8 kg para a raça Nelore e,...
Tipo: Anais e Proceedings de eventos Palavras-chave: Desenvolvimento ponderal.; Gado Nelore; Gado Guzerá..
Ano: 2002 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/903937
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Determination of optimal number of independent components in yield traits in rice. Repositório Alice
COSTA, J. A. da; AZEVEDO, C. F.; NASCIMENTO, M.; SILVA, F. F.; RESENDE, M. D. V. de; NASCIMENTO, A. C. C..
The principal component regression (PCR) and the independent component regression (ICR) are dimensionality reduction methods and extremely important in genomic prediction. These methods require the choice of the number of components to be inserted into the model. For PCR, there are formal criteria; however, for ICR, the adopted criterion chooses the number of independent components (ICs) associated to greater accuracy and requires high computational time. In this study, seven criteria based on the number of principal components (PCs) and methods of variable selection to guide this choice in ICR are proposed and evaluated in simulated and real data. For both datasets, the most efficient criterion and that drastically reduced computational time determined...
Tipo: Artigo de periódico Palavras-chave: Melhoramento Genético Vegetal; Produtividade; Arroz; Genomics; Plant breeding; Yields; Rice.
Ano: 2022 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1139185
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Divergência genética e índice de seleção via BLUP emacessos de algodoeiro para características tecnológicas da fibra. Repositório Alice
RESENDE, M. A. V. de; FREITAS, J. A. de; LANZA, M. A.; RESENDE, M. D. V. de; AZEVEDO, C. F..
As características tecnológicas da fibra do algodoeiro são determinantes da qualidade de seus produtos e de sua remuneração. Este trabalho objetivou estimar a divergência genética entre acessos de algodoeiro e ordenar os melhores, com base em um índice de seleção combinando todas essas características de interesse. Foram avaliados 248 acessos de algodoeiro, empregando-se análise multivariada (distância de Mahalanobis e agrupamento de Tocher) e índice de seleção baseado em rank médio via metodologia de modelos mistos (REML/BLUP). A análise de agrupamento de Tocher permitiu a estruturação populacional dos acessos, resumindo-os em 14 grupos divergentes. As acurácias seletivas foram altas para todas as características avaliadas, variando de 0,89 a 0,94,...
Tipo: Separatas Palavras-chave: Algodoeiro; Divergência genética; Melhoramento genético.; Fibra..
Ano: 2014 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1003335
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Estimating additive and dominance variances for complex traits in pigs combining genomic and pedigree information. Repositório Alice
COSTA, E. V.; DINIZ, D. B.; VERONEZE, R.; RESENDE, M. D. V. de; AZEVEDO, C. F.; GUIMARÃES, S. E. F.; SILVA, F. F.; LOPES, P. S..
Knowledge of dominance effects should improve genetic evaluations, provide the accurate selection of purebred animals, and enable better breeding strategies, including the exploitation of heterosis in crossbreeds. In this study, we combined genomic and pedigree data to study the relative importance of additive and dominance genetic variation in growth and carcass traits in an F2 pig population. Two GBLUP models were used, a model without a polygenic effect (ADM) and a model with a polygenic effect (ADMP). Additive effects played a greater role in the control of growth and carcass traits than did dominance effects. However, dominance effects were important for all traits, particularly in backfat thickness. The narrow-sense and broad-sense heritability...
Tipo: Separatas Palavras-chave: Melhoramento genético; Seleção genômica ampla; Métodos de seleção; Herdabilidade; Dominance; Genetic parameters; Polygenic effect; Piau pigs.
Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1021860
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Evaluation of a new additive-dominance genomic model and implications for quantitative genetics and genomic selection. Repositório Alice
MIRANDA, T. L. R.; RESENDE, M. D. V. de; AZEVEDO, C. F.; NUNES, A. C. P.; TAKAHASHI, E. K.; SIMIQUELI, G. F.; SILVA, F. F. e; ALVES, R. S..
The Fisher?s infinitesimal model is traditionally used in quantitative genetics and genomic selection, and it attributes most genetic variance to additive variance. Recently, the dominance maximization model was proposed and it prioritizes the dominance variance based on alternative parameterizations. In this model, the additive effects at the locus level are introduced into the model after the dominance variance is maximized. In this study, the new parameterizations of additive and dominance effects on quantitative genetics and genomic selection were evaluated and compared with the parameterizations traditionally applied using the genomic best linear unbiased prediction method. As the parametric relative magnitude of the additive and dominance effects...
Tipo: Artigo de periódico Palavras-chave: Melhoramento Genético Vegetal; Seleção Genética; Molecular models; Plant selection guides; Plant breeding.
Ano: 2022 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1139183
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Evaluation of Bayesian methods of genomic association via chromosomic regions using simulated data. Repositório Alice
LIMA, L. P.; AZEVEDO, C. F.; RESENDE, M. D. V. de; NASCIMENTO, M.; SILVA, F. F. e.
The development of efficient methods for genome-wide association studies (GWAS) between quantitative trait loci (QTL) and genetic values is extremely important to animal and plant breeding programs. Bayesian approaches that aim to select regions of single nucleotide polymorphisms (SNPs) proved to be efficient, indicating genes with important effects. Among the selection criteria for SNPs or regions, selection criterion by percentage of variance can be explained by genomic regions (%var), selection of tag SNPs, and selection based on the window posterior probability of association (WPPA). To also detect potentially associated regions, we proposed measuring posterior probability of the interval PPint), which aims to select regions based on the markers of...
Tipo: Artigo de periódico Palavras-chave: Método de Melhoramento; Melhoramento Genético Vegetal; Genomics; Molecular models; Genetic variance; Plant breeding.
Ano: 2022 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1139182
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Factor analysis applied to genome prediction for high-dimensional phenotypes in pigs. Repositório Alice
TEIXEIRA, F. R. F.; NASCIMENTO, M.; NASCIMENTO, A. C. C.; SILVA, F. F. e; CRUZ, C. D.; AZEVEDO, C. F.; PAIXÃO, D. M.; BARROSO, L. M. A.; VERARDO, L. L.; RESENDE, M. D. V. de; GUIMARÃES, S. E. F.; LOPES, P. S..
The aim of the present study was to propose and evaluate the use of factor analysis (FA) in obtaining latent variables (factors) that represent a set of pig traits simultaneously, for use in genome-wide selection (GWS) studies. We used crosses between outbred F2 populations of Brazilian Piau X commercial pigs. Data were obtained on 345 F2 pigs, genotyped for 237 SNPs, with 41 traits. FA allowed us to obtain four biologically interpretable factors: ?weight?, ?fat?, ?loin?, and ?performance?. These factors were used as dependent variables in multiple regression models of genomic selection (Bayes A, Bayes B, RR-BLUP, and Bayesian LASSO). The use of FA is presented as an interesting alternative to select individuals for multiple variables simultaneously in GWS...
Tipo: Artigo de periódico Palavras-chave: Genome enabled prediction; SNP effects; Análise multivariada.; Melhoramento genético animal; Estatística; Seleção genética.; Animal breeding; Multivariate analysis.
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1047516
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Genome wide selection in citrus breeding. Repositório Alice
GOIS, I. B.; BORÉM, A.; CRISTOFANI-YALY, M.; RESENDE, M. D. V. de; AZEVEDO, C. F.; BASTIANEL, M.; NOVELLI, V. M.; MACHADO, M. A..
Genome wide selection (GWS) is essential for the genetic improvement of perennial species such as Citrus because of its ability to increase gain per unit time and to enable the efficient selection of characteristics with low heritability. This study assessed GWS efficiency in a population of Citrus and compared it with selection based on phenotypic data. A total of 180 individual trees from a cross between Pera sweet orange (Citrus sinensis Osbeck) and Murcott tangor (Citrus sinensis Osbeck x Citrus reticulata Blanco) were evaluated for 10 characteristics related to fruit quality. The hybrids were genotyped using 5287 DArT_seqTM (diversity arrays technology) molecular markers and their effects on phenotypes were predicted using the random regression - best...
Tipo: Artigo de periódico Palavras-chave: Seleção precoce; DarT_seq; Selective accuracy; Molecular markers.; Fruta cítrica; Melhoramento vegetal; Marcador Molecular.; Citrus; Plant breeding; Early selection; Linkage disequilibrium..
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1072713
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Genome-wide association and regional heritability mapping of plant architecture, lodging and productivity in Phaseolus vulgaris. Repositório Alice
RESENDE, R. T.; RESENDE, M. D. V. de; AZEVEDO, C. F.; SILVA, F. F. e; MELO, L. C.; PEREIRA, H. S.; SOUZA, T. L. P. O. de; VALDISSER, P. A. M. R.; BRONDANI, C.; VIANELLO, R. P..
The availability of high-density molecular markers in common bean has allowed to explore the genetic basis of important complex agronomic traits with increased resolution. Genome-Wide Association Studies (GWAS) and Regional Heritability Mapping (RHM) are two analytical approaches for the detection of genetic variants. We carried out GWAS and RHM for plant architecture, lodging and productivity across two important growing environments in Brazil in a germplasm of 188 common bean varieties using DArTseq genotyping strategies. The coefficient of determination of G · E interaction (c2 int) was equal to 17, 21 and 41%, respectively for the traits architecture, lodging, and productivity. Trait heritabilities were estimated at 0.81 (architecture), 0.79 (lodging)...
Tipo: Artigo de periódico Palavras-chave: RHM QTL; GWAS QTL; DArTseq; Herdabilidade; Phaseolus Vulgaris; Feijão; Melhoramento Genético Vegetal; Heritability; Beans; Plant breeding.
Ano: 2018 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1095838
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Genomic prediction for additive and dominance effects of censored traits in pigs. Repositório Alice
SANTOS, V. S.; MARTINS FILHO, S.; RESENDE, M. D. V. de; AZEVEDO, C. F.; LOPES, P. S.; GUIMARÃES, S. E. F.; SILVA, F. F..
Age at the time of slaughter is a commonly used trait in animal breeding programs. Since studying this trait involves incomplete observations (censoring), analysis can be performed using survival models or modified linear models, for example, by sampling censored data from truncated normal distributions. For genomic selection, the greatest genetic gains can be achieved by including non-additive genetic effects like dominance. Thus, censored traits with effects on both survival models have not yet been studied under a genomic selection approach. We aimed to predict genomic values using the Cox model with dominance effects and compare these results with the linear model with and without censoring. Linear models were fitted via the maximum likelihood method....
Tipo: Artigo de periódico Palavras-chave: GBLUP; Modelo mixto; Censored data; Mixed model; Survival models; Porco; Suíno; Swine; Animal breeding.
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1072712
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Genomic prediction of lactation curves of Girolando cattle based on nonlinear mixed models. Repositório Alice
TEIXEIRA, F. R. F.; NASCIMENTO, M.; CECON, P. R.; CRUZ, C. D.; SILVA, F. F. e; NASCIMENTO, A. C. C.; AZEVEDO, C. F.; MARQUES, D. B. D.; SILVA, M. V. G. B.; CARNEIRO, A. P. S.; PAIXAO, D. M..
Knowledge of lactation curves in dairy cattle is essential for understanding the animal production in milk production systems. Genomic prediction of lactation curves represents the genetic pattern of milk production of the animals in the herd. In this context, we made genomic predictions of lactation curves through genome-wide selection (GWS) to characterize the genetic pattern of lactation traits in Girolando cattle based on parameters estimated by nonlinear mixed effects (NLME) models. Data of 1,822 milk control records from 226 Girolando animals genotyped for 37,673 single nucleotide polymorphisms were analyzed. Nine NLME models were compared to identify the equation with the best fit. The lactation traits estimated by the best model were submitted to...
Tipo: Artigo de periódico Palavras-chave: Previsão genômica; Bovino; Gado Leiteiro; Curva de Lactação; Heritability; Genome; Girolando.
Ano: 2021 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1133535
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Genomic prediction of leaf rust resistance to Arabica coffee using machine learning algorithms. Repositório Alice
SOUSA, I. C. de; NASCIMENTO, M.; SILVA, G. N.; NASCIMENTO, A. C. C.; CRUZ, C. D.; SILVA, F. F. e; ALMEIDA, D. P. de; PESTANA, K. N.; AZEVEDO, C. F.; ZAMBOLIM, L.; CAIXETA, E. T..
Genomic selection (GS) emphasizes the simultaneous prediction of the genetic effects of thousands of scattered markers over the genome. Several statistical methodologies have been used in GS for the prediction of genetic merit. In general, such methodologies require certain assumptions about the data, such as the normality of the distribution of phenotypic values. To circumvent the non-normality of phenotypic values, the literature suggests the use of Bayesian Generalized Linear Regression (GBLASSO). Another alternative is the models based on machine learning, represented by methodologies such as Artificial Neural Networks (ANN), Decision Trees (DT) and related possible refinements such as Bagging, Random Forest and Boosting. This study aimed to use DT and...
Tipo: Artigo de periódico Palavras-chave: Statistical learning; Hemileia Vastatrix; Plant breeding; Artificial intelligence.
Ano: 2020 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1125524
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