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Candidate mutations used to aid the prediction of genetic merit for female reproductive traits in tropical beef cattle R. Bras. Zootec.
Fortes,Marina Rufino Salinas; Enculescu,Charmaine; Porto Neto,Laercio R.; Lehnert,Sigrid A.; McCulloch,Russell; Hayes,Ben.
ABSTRACT In this study, we aimed to provide a wet laboratory validation for a set of single nucleotide polymorphisms (SNP), which had been identified as candidate functional variants in silico. Genotyping for candidate SNP was performed in Brahman and Tropical Composite cattle. After quality control, 29 SNP were first investigated individually for their association with female reproductive traits and then used as a panel for genomic predictions. The reproductive traits studied were age at first corpus luteum (AGECL; days), post-partum anoestrus interval (PPAI; days), and a binary trait that described if the cow had ovulated before weaning the first calf or not (PW, 0-1). Single nucleotide polymorphisms in six genes (FOXA2, TRAF4, IRF2, IRF1, BPTF, and...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Anoestrus; BayesR; Candidate genes; Genomic prediction; Heifer puberty.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982018000100412
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Combined index of genomic prediction methods applied to productivity Ciência Rural
Suela,Matheus Massariol; Lima,Leísa Pires; Azevedo,Camila Ferreira; Resende,Marcos Deon Vilela de; Nascimento,Moysés; Silva,Fabyano Fonseca e.
ABSTRACT: Rice cultivation has great national and global importance, being one of the most produced and consumed cereals in the world and the primary food for more than half of the world’s population. Because of its importance as food, developing efficient methods to select and predict genetically superior individuals in reference to plant traits is of extreme importance for breeding programs. The objective of this research was to evaluate and compare the efficiency of the Delta-p, G-BLUP (Genomic Best Linear Unbiased Predictor), BayesCpi, BLASSO (Bayesian Least Absolute Shrinkage and Selection Operator), Delta-p/G-BLUP index, Delta-p/BayesCpi index, and Delta-p/BLASSO index in the estimation of genomic values and the effects of single nucleotide...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Genomic prediction; Selection index; Genetic gain.
Ano: 2019 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-84782019000600404
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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 em periódico indexado (ALICE) 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 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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New accuracy estimators for genomic selection with application in a cassava (Manihot esculenta) breeding program. Repositório Alice
AZEVEDO, C. F.; RESENDE, M. D. V. de; SILVA, F. F.; VIANA, J. M. S.; VALENTE, M. S. F.; RESENDE JUNIOR, M. F. R.; OLIVEIRA, E. J. de.
ABSTRACT. Genomic selection is the main force driving applied breeding programs and accuracy is the main measure for evaluating its efficiency. The traditional estimator (TE) of experimental accuracy is not fully adequate. This study proposes and evaluates the performance and efficiency of two new accuracy estimators, called regularized estimator (RE) and hybrid estimator (HE), which were applied to a practical cassava breeding program and also to simulated data. The simulation study considered two individual narrow sense heritability levels and two genetic architectures for traits. TE, RE, and HE were compared under four validation procedures: without validation (WV), independent validation, ten-fold validation through jacknife allowing different markers,...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Seleção genômica; Genomic prediction; Accuracy estimator; Cross-validation; Manihot esculenta; Mandioca; Melhoramento vegetal; Cassava; Plant breeding.
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1072711
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New insights into genomic selection through population-based non-parametric prediction methods. Repositório Alice
LIMA L. P.; AZEVEDO, C. F.; RESENDE, M. D. V. de; SILVA, F. F. e; SUELA, M. M.; NASCIMENTO, M.; VIANA, J. M. S..
Genome-wide selection (GWS) is based on a large number of markers widely distributed throughout the genome. Genome-wide selection provides for the estimation of the effect of each molecular marker on the phenotype, thereby allowing for the capture of all genes affecting the quantitative traits of interest. The main statistical tools applied to GWS are based on random regression or dimensionality reduction methods. In this study a new non-parametric method, called Delta-p was proposed, which was then compared to the Genomic Best Linear Unbiased Predictor (G-BLUP) method. Furthermore, a new selection index combining the genetic values obtained by the G-BLUP and Delta-p, named Delta-p/G-BLUP methods, was proposed. The efficiency of the proposed methods was...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Genomic prediction; Genetic gain; Asian rice; Oryza Sativa; Arroz; Selection index.
Ano: 2019 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1110406
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New insights into genomic selection through population-based non-parametric prediction methods Scientia Agricola
Lima,Leísa Pires; Azevedo,Camila Ferreira; Resende,Marcos Deon Vilela de; Silva,Fabyano Fonseca e; Suela,Matheus Massariol; Nascimento,Moysés; Viana,José Marcelo Soriano.
ABSTRACT: Genome-wide selection (GWS) is based on a large number of markers widely distributed throughout the genome. Genome-wide selection provides for the estimation of the effect of each molecular marker on the phenotype, thereby allowing for the capture of all genes affecting the quantitative traits of interest. The main statistical tools applied to GWS are based on random regression or dimensionality reduction methods. In this study a new non-parametric method, called Delta-p was proposed, which was then compared to the Genomic Best Linear Unbiased Predictor (G-BLUP) method. Furthermore, a new selection index combining the genetic values obtained by the G-BLUP and Delta-p, named Delta-p/G-BLUP methods, was proposed. The efficiency of the proposed...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Genomic prediction; Selection index; Genetic gain; Asian rice.
Ano: 2019 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-90162019001400290
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The optimal number of partial least squares components in genomic selection for pork pH Ciência Rural
Silveira,Fernanda Gomes da; Duarte,Darlene Ana Souza; Chaves,Lucas Monteiro; Silva,Fabyano Fonseca e; Filho,Ivan Carvalho; Duarte,Marcio de Souza; Lopes,Paulo Sávio; Guimarães,Simone Eliza Facioni.
ABSTRACT: The main application of genomic selection (GS) is the early identification of genetically superior animals for traits difficult-to-measure or lately evaluated, such as meat pH (measured after slaughter). Because the number of markers in GS is generally larger than the number of genotyped animals and these markers are highly correlated owing to linkage disequilibrium, statistical methods based on dimensionality reduction have been proposed. Among them, the partial least squares (PLS) technique stands out, because of its simplicity and high predictive accuracy. However, choosing the optimal number of components remains a relevant issue for PLS applications. Thus, we applied PLS (and principal component and traditional multiple regression)...
Tipo: Info:eu-repo/semantics/article Palavras-chave: SNP; Genomic prediction; Meat quality.
Ano: 2017 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-84782017000100652
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Triple categorical regression for genomic selection: application to cassava breeding. Repositório Alice
LIMA, L. P.; AZEVEDO, C. F.; RESENDE, M. D. V. de; SILVA, F. F. e; VIANA, J. M. S.; OLIVEIRA, E. J. de.
Genome-wide selection (GWS) is currently a technique of great importance in plant breeding, since it improves efficiency of genetic evaluations by increasing genetic gains. The process is based on genomic estimated breeding values (GEBVs) obtained through phenotypic and dense marker genomic information. In this context, GEBVs of N individuals are calculated through appropriate models, which estimate the effect of each marker on phenotypes, allowing the early identification of genetically superior individuals. However, GWS leads to statistical challenges, due to high dimensionality and multicollinearity problems. These challenges require the use of statistical methods to approach the regularization of the estimation process. Therefore, we aimed to propose a...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: G-BLUP; BLASSO; Genomic prediction; Genomic heritability; Quantitative genetics theory; Molecular markers; Herdabilidade genômica; Predição genômica; Genética quantitativa; Ridge; Marcador Molecular; Prediction.
Ano: 2019 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1110879
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Triple categorical regression for genomic selection: application to cassava breeding Scientia Agricola
Lima,Leísa Pires; Azevedo,Camila Ferreira; Resende,Marcos Deon Vilela de; Silva,Fabyano Fonseca e; Viana,José Marcelo Soriano; Oliveira,Eder Jorge de.
ABSTRACT: Genome-wide selection (GWS) is currently a technique of great importance in plant breeding, since it improves efficiency of genetic evaluations by increasing genetic gains. The process is based on genomic estimated breeding values (GEBVs) obtained through phenotypic and dense marker genomic information. In this context, GEBVs of N individuals are calculated through appropriate models, which estimate the effect of each marker on phenotypes, allowing the early identification of genetically superior individuals. However, GWS leads to statistical challenges, due to high dimensionality and multicollinearity problems. These challenges require the use of statistical methods to approach the regularization of the estimation process. Therefore, we aimed to...
Tipo: Info:eu-repo/semantics/article Palavras-chave: G-BLUP; BLASSO; Genomic prediction; Genomic heritability.
Ano: 2019 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-90162019001500368
Registros recuperados: 10
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