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Registro Completo |
Biblioteca(s): |
Embrapa Café. |
Data corrente: |
19/01/2022 |
Data da última atualização: |
19/01/2022 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
Autoria: |
LIMA, L. P.; AZEVEDO, C. F.; RESENDE, M. D. V. de; NASCIMENTO, M.; SILVA, F. F. e. |
Afiliação: |
LEÍSA PIRES LIMA, UFV; CAMILA FERREIRA AZEVEDO, UFV; MARCOS DEON VILELA DE RESENDE, CNPCa; MOYSÉS NASCIMENTO, UFV; FABYANO FONSECA E SILVA, UFV. |
Título: |
Evaluation of Bayesian methods of genomic association via chromosomic regions using simulated data. |
Ano de publicação: |
2022 |
Fonte/Imprenta: |
Scientia Agricola, v. 79, n. 3, p. 1-10, 2022. |
Idioma: |
Inglês |
Conteúdo: |
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 greatest effects. Therefore, the objective of this work was to evaluate these approaches, in terms of efficiency in selecting and identifying markers or regions located within or close to genes associated with traits. This study also aimed to compare these methodologies with single-marker analyses. To accomplish this, simulated data were used in six scenarios, with SNPs allocated in non?overlapping genomic regions. Considering traits with oligogenic inheritance, WPPA criterion followed by %var and PPint criteria were shown to be superior, presenting higher values of detection power, capturing higher percentages of genetic variance and larger areas. For traits with polygenic inheritance, PPint and WPPA criteria were considered superior. Single?marker analyses identified SNPs associated only in oligogenic inheritance scenarios and was lower than the other criteria. MenosThe 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 greatest effects. Therefore, the objective of this work was to evaluate these approaches, in terms of efficiency in selecting and identifying markers or regions located within or close to genes associated with traits. This study also aimed to compare these methodologies with single-marker analyses. To accomplish this, simulated data were used in six scenarios, with SNPs allocated in non?overlapping genomic regions. Considering traits with oligogenic inheritance, WPPA criterion followed by %var and PPint criteria were shown to be superior, presenting higher values of detection power, capturing higher percentages of genetic variance and larger areas. For traits with polygenic inheritance, PPint and WPPA criteria were considered ... Mostrar Tudo |
Thesagro: |
Melhoramento Genético Vegetal; Método de Melhoramento. |
Thesaurus Nal: |
Genetic variance; Genomics; Molecular models; Plant breeding. |
Categoria do assunto: |
-- |
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/230380/1/evaluation-of-bayesian-methods.pdf
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Marc: |
LEADER 02367naa a2200241 a 4500 001 2139182 005 2022-01-19 008 2022 bl uuuu u00u1 u #d 100 1 $aLIMA, L. P. 245 $aEvaluation of Bayesian methods of genomic association via chromosomic regions using simulated data.$h[electronic resource] 260 $c2022 520 $aThe 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 greatest effects. Therefore, the objective of this work was to evaluate these approaches, in terms of efficiency in selecting and identifying markers or regions located within or close to genes associated with traits. This study also aimed to compare these methodologies with single-marker analyses. To accomplish this, simulated data were used in six scenarios, with SNPs allocated in non?overlapping genomic regions. Considering traits with oligogenic inheritance, WPPA criterion followed by %var and PPint criteria were shown to be superior, presenting higher values of detection power, capturing higher percentages of genetic variance and larger areas. For traits with polygenic inheritance, PPint and WPPA criteria were considered superior. Single?marker analyses identified SNPs associated only in oligogenic inheritance scenarios and was lower than the other criteria. 650 $aGenetic variance 650 $aGenomics 650 $aMolecular models 650 $aPlant breeding 650 $aMelhoramento Genético Vegetal 650 $aMétodo de Melhoramento 700 1 $aAZEVEDO, C. F. 700 1 $aRESENDE, M. D. V. de 700 1 $aNASCIMENTO, M. 700 1 $aSILVA, F. F. e 773 $tScientia Agricola$gv. 79, n. 3, p. 1-10, 2022.
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Registro original: |
Embrapa Café (CNPCa) |
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Biblioteca(s): |
Embrapa Gado de Leite. |
Data corrente: |
04/03/2015 |
Data da última atualização: |
05/02/2024 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
Circulação/Nível: |
B - 2 |
Autoria: |
KERN, E. L.; COBUCI, J. A.; COSTA, C. N.; BRACCINI NETO, J.; CAMPOS, G. S.; MCMANUS, C. M. |
Afiliação: |
ELISANDRA L. KERN, UFRGS; JAIME A. COBUCI, UFRGS; CLAUDIO NAPOLIS COSTA, CNPGL; JOSÉ BRACCINI NETO, UFRGS; GABRIEL S. CAMPOS, UFPEL; CONCEPTA M. MCMANUS, UNB; Instituto Nacional de Ciência e Tecnologia - Informação Genético-Sanitária da Pecuária Brasileira. |
Título: |
Genetic parameters for longevity measures in Brazilian Holstein cattle using linear and threshold models. |
Ano de publicação: |
2014 |
Fonte/Imprenta: |
Archiv fur Tierzucht, v. 57, n. 33, p. 1-12, 2014. |
Idioma: |
Inglês |
Conteúdo: |
The aim in this study was to estimate variance components and heritability of different longevity measures related to productive life and survival at a specified age, using linear and threshold models, to specify the more appropriate measure to express longevity in Brazilian Holstein cows. Production and reproduction records of Holstein cows were collected from 1991 to 2010, for cows born between 1987 and 2006. Variance components were obtained by restricted maximum likelihood (REML) for measures of productive life and a Bayesian analysis for survival measures. The heritability estimates for longevity measures ranged from 0.06 to 0.09, using the linear model and from 0.05 to 0.18 for traits using the threshold model. This suggests an inexpressive genetic gain using selection for these traits, whereas improvements in environmental factors which affect these animals may lead to greater phenotypic gains. Survival up to 48 months from first calving was the measureing point defined as the most appropriate to be included in future official genetic evaluations of Holstein cattle in Brazil. |
Palavras-Chave: |
Bayesian method; Productive life; REML method; Survival in herd. |
Categoria do assunto: |
G Melhoramento Genético |
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/doc/1010574/1/Genetic-parameters-for-longevity-measures-in-Brazilian-Holstein-cattle.pdf
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Marc: |
LEADER 01778naa a2200229 a 4500 001 2010574 005 2024-02-05 008 2014 bl uuuu u00u1 u #d 100 1 $aKERN, E. L. 245 $aGenetic parameters for longevity measures in Brazilian Holstein cattle using linear and threshold models.$h[electronic resource] 260 $c2014 520 $aThe aim in this study was to estimate variance components and heritability of different longevity measures related to productive life and survival at a specified age, using linear and threshold models, to specify the more appropriate measure to express longevity in Brazilian Holstein cows. Production and reproduction records of Holstein cows were collected from 1991 to 2010, for cows born between 1987 and 2006. Variance components were obtained by restricted maximum likelihood (REML) for measures of productive life and a Bayesian analysis for survival measures. The heritability estimates for longevity measures ranged from 0.06 to 0.09, using the linear model and from 0.05 to 0.18 for traits using the threshold model. This suggests an inexpressive genetic gain using selection for these traits, whereas improvements in environmental factors which affect these animals may lead to greater phenotypic gains. Survival up to 48 months from first calving was the measureing point defined as the most appropriate to be included in future official genetic evaluations of Holstein cattle in Brazil. 653 $aBayesian method 653 $aProductive life 653 $aREML method 653 $aSurvival in herd 700 1 $aCOBUCI, J. A. 700 1 $aCOSTA, C. N. 700 1 $aBRACCINI NETO, J. 700 1 $aCAMPOS, G. S. 700 1 $aMCMANUS, C. M. 773 $tArchiv fur Tierzucht$gv. 57, n. 33, p. 1-12, 2014.
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