Efficiency of QTL mapping based on least squares, maximum likelihood, and Bayesian approaches under high marker density

Detalhes bibliográficos
Autor(a) principal: Jan, Hikmat Ullah
Data de Publicação: 2016
Tipo de documento: Tese
Idioma: eng
Título da fonte: LOCUS Repositório Institucional da UFV
Texto Completo: http://www.locus.ufv.br/handle/123456789/7521
Resumo: Previous studies on quantitative trait loci (QTL) mapping efficiency assumed few QTLs of higher effect, no minor genes, and low marker density. This study assessed the efficiency of the least squares, maximum likelihood, and Bayesian approaches for QTL mapping assuming high single nucleotide polymorphism (SNP) density, zero to three QTLs and eight or nine minor genes per chromosome, and low proportion of the phenotypic variance explained by each QTL. We simulated 50 samples of 400 F2 individuals, which were genotyped for 1,000 SNPs (average density of one SNP/centiMorgan) and phenotyped for three traits controlled by 12 QTLs and 88 minor genes. The genes were randomly distributed in the regions covered by the SNPs along 10 chromosomes. The heritabilities were 0.3 and 0.7, and the sample sizes were 200 and 400. The least squares and maximum likelihood approaches were equivalent. The QTL mapping efficiency was not influenced by the degree of dominance but it was affected by heritability, sample size, marker density, and QTL effect. The Bayesian analysis showed greater power of QTL detection, mapping precision, and number of false- positives compared to the least squares and maximum likelihood approaches. The most important factor affecting the QTL mapping efficiency is the QTL effect.
id UFV_514cabba525a7ee511951845b178f80b
oai_identifier_str oai:locus.ufv.br:123456789/7521
network_acronym_str UFV
network_name_str LOCUS Repositório Institucional da UFV
repository_id_str 2145
spelling Efficiency of QTL mapping based on least squares, maximum likelihood, and Bayesian approaches under high marker densityEficiência de mapeamento de QTL com base nas abordagens de quadrados mínimos, de máxima verossimilhança e Bayesiana, sob alta densidade de marcadoresGenética vegetalGenética quantitativaBiologia molecularMarcadores molecularesGenética QuantitativaPrevious studies on quantitative trait loci (QTL) mapping efficiency assumed few QTLs of higher effect, no minor genes, and low marker density. This study assessed the efficiency of the least squares, maximum likelihood, and Bayesian approaches for QTL mapping assuming high single nucleotide polymorphism (SNP) density, zero to three QTLs and eight or nine minor genes per chromosome, and low proportion of the phenotypic variance explained by each QTL. We simulated 50 samples of 400 F2 individuals, which were genotyped for 1,000 SNPs (average density of one SNP/centiMorgan) and phenotyped for three traits controlled by 12 QTLs and 88 minor genes. The genes were randomly distributed in the regions covered by the SNPs along 10 chromosomes. The heritabilities were 0.3 and 0.7, and the sample sizes were 200 and 400. The least squares and maximum likelihood approaches were equivalent. The QTL mapping efficiency was not influenced by the degree of dominance but it was affected by heritability, sample size, marker density, and QTL effect. The Bayesian analysis showed greater power of QTL detection, mapping precision, and number of false- positives compared to the least squares and maximum likelihood approaches. The most important factor affecting the QTL mapping efficiency is the QTL effect.Os principais estudos sobre eficiência de mapeamento de locos determinantes de caracteres quantitativos (QTLs) assumiram poucos QTLs de efeito maior, nenhum gene de efeito menor, e reduzida densidade de marcadores moleculares. Este estudo avaliou a eficiência das análises de quadrados mínimos (regressão), de máxima verossimilhança e Bayesiana para o mapeamento de QTLs, assumindo alta densidade de polimorfismos de nucleotídeo único (SNPs), zero a três QTLs e oito ou nove genes de efeitos menores em cada cromossomo, e reduzida proporção da variância fenotípica explicada por cada QTL (reduzida herdabilidade de QTL). Foram também avaliadas a influência do grau de dominância, da herdabilidade, do tamanho amostral, da densidade de marcadores e do efeito de QTL, e as conseqüências do ajuste de modelo aditivo-dominante na ausência de dominância, no mapeamento de QTLs. Foram simuladas 50 amostras de 400 indivíduos F2, os quais foram genotipados em relação a 1000 SNPs (densidade média de um SNP a cada centimorgan) e fenotipados para três caracteres apresentando distintos graus de dominância (dominância unidirecional positiva, dominância bidirecional e ausência de dominância). Para cada característica foi assumido controle por 12 QTLs e 88 genes de efeito menor, distribuídos nas regiões cromossômicas cobertas pelos SNPs (10 cromossomos). As herdabilidade foram 0.3 e 0.7 e os tamanhos amostrais foram 200 e 400. As análises de máxima verossimilhança e de regressão foram equivalentes quanto à eficiência. O mapeamento de QTL não é influenciado pelo grau de dominância, mas é afetado pela herdabilidade, pelo tamanho amostral, pela densidade de marcas e pelo efeito de QTL. A análise Bayesiana apresentou maior poder de detecção de QTLs, maior precisão de mapeamento, e maior número de falso-positivos em comparação às análises de máxima verossimilhança e de regressão. O fator que mais afeta o mapeamento de QTLs é o efeito do QTL.Conselho Nacional de Desenvolvimento Científico e TecnológicoUniversidade Federal de ViçosaViana, José Marcelo Sorianohttp://lattes.cnpq.br/6124903488002317Silva, Fabyano Fonseca eLima, Rodrigo Oliveira deJan, Hikmat Ullah2016-04-20T08:36:57Z2016-04-20T08:36:57Z2016-02-19info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/doctoralThesisapplication/pdfJAN, Hikmat Ullah. Efficiency of QTL mapping based on least squares, maximum likelihood, and Bayesian approaches under high marker density. 2016. 33 f. Tese (Doutorado em Genética e Melhoramento) - Universidade Federal de Viçosa, Viçosa. 2016.http://www.locus.ufv.br/handle/123456789/7521enginfo:eu-repo/semantics/openAccessreponame:LOCUS Repositório Institucional da UFVinstname:Universidade Federal de Viçosa (UFV)instacron:UFV2017-08-01T16:53:39Zoai:locus.ufv.br:123456789/7521Repositório InstitucionalPUBhttps://www.locus.ufv.br/oai/requestfabiojreis@ufv.bropendoar:21452017-08-01T16:53:39LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)false
dc.title.none.fl_str_mv Efficiency of QTL mapping based on least squares, maximum likelihood, and Bayesian approaches under high marker density
Eficiência de mapeamento de QTL com base nas abordagens de quadrados mínimos, de máxima verossimilhança e Bayesiana, sob alta densidade de marcadores
title Efficiency of QTL mapping based on least squares, maximum likelihood, and Bayesian approaches under high marker density
spellingShingle Efficiency of QTL mapping based on least squares, maximum likelihood, and Bayesian approaches under high marker density
Jan, Hikmat Ullah
Genética vegetal
Genética quantitativa
Biologia molecular
Marcadores moleculares
Genética Quantitativa
title_short Efficiency of QTL mapping based on least squares, maximum likelihood, and Bayesian approaches under high marker density
title_full Efficiency of QTL mapping based on least squares, maximum likelihood, and Bayesian approaches under high marker density
title_fullStr Efficiency of QTL mapping based on least squares, maximum likelihood, and Bayesian approaches under high marker density
title_full_unstemmed Efficiency of QTL mapping based on least squares, maximum likelihood, and Bayesian approaches under high marker density
title_sort Efficiency of QTL mapping based on least squares, maximum likelihood, and Bayesian approaches under high marker density
author Jan, Hikmat Ullah
author_facet Jan, Hikmat Ullah
author_role author
dc.contributor.none.fl_str_mv Viana, José Marcelo Soriano
http://lattes.cnpq.br/6124903488002317
Silva, Fabyano Fonseca e
Lima, Rodrigo Oliveira de
dc.contributor.author.fl_str_mv Jan, Hikmat Ullah
dc.subject.por.fl_str_mv Genética vegetal
Genética quantitativa
Biologia molecular
Marcadores moleculares
Genética Quantitativa
topic Genética vegetal
Genética quantitativa
Biologia molecular
Marcadores moleculares
Genética Quantitativa
description Previous studies on quantitative trait loci (QTL) mapping efficiency assumed few QTLs of higher effect, no minor genes, and low marker density. This study assessed the efficiency of the least squares, maximum likelihood, and Bayesian approaches for QTL mapping assuming high single nucleotide polymorphism (SNP) density, zero to three QTLs and eight or nine minor genes per chromosome, and low proportion of the phenotypic variance explained by each QTL. We simulated 50 samples of 400 F2 individuals, which were genotyped for 1,000 SNPs (average density of one SNP/centiMorgan) and phenotyped for three traits controlled by 12 QTLs and 88 minor genes. The genes were randomly distributed in the regions covered by the SNPs along 10 chromosomes. The heritabilities were 0.3 and 0.7, and the sample sizes were 200 and 400. The least squares and maximum likelihood approaches were equivalent. The QTL mapping efficiency was not influenced by the degree of dominance but it was affected by heritability, sample size, marker density, and QTL effect. The Bayesian analysis showed greater power of QTL detection, mapping precision, and number of false- positives compared to the least squares and maximum likelihood approaches. The most important factor affecting the QTL mapping efficiency is the QTL effect.
publishDate 2016
dc.date.none.fl_str_mv 2016-04-20T08:36:57Z
2016-04-20T08:36:57Z
2016-02-19
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/doctoralThesis
format doctoralThesis
status_str publishedVersion
dc.identifier.uri.fl_str_mv JAN, Hikmat Ullah. Efficiency of QTL mapping based on least squares, maximum likelihood, and Bayesian approaches under high marker density. 2016. 33 f. Tese (Doutorado em Genética e Melhoramento) - Universidade Federal de Viçosa, Viçosa. 2016.
http://www.locus.ufv.br/handle/123456789/7521
identifier_str_mv JAN, Hikmat Ullah. Efficiency of QTL mapping based on least squares, maximum likelihood, and Bayesian approaches under high marker density. 2016. 33 f. Tese (Doutorado em Genética e Melhoramento) - Universidade Federal de Viçosa, Viçosa. 2016.
url http://www.locus.ufv.br/handle/123456789/7521
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Universidade Federal de Viçosa
publisher.none.fl_str_mv Universidade Federal de Viçosa
dc.source.none.fl_str_mv reponame:LOCUS Repositório Institucional da UFV
instname:Universidade Federal de Viçosa (UFV)
instacron:UFV
instname_str Universidade Federal de Viçosa (UFV)
instacron_str UFV
institution UFV
reponame_str LOCUS Repositório Institucional da UFV
collection LOCUS Repositório Institucional da UFV
repository.name.fl_str_mv LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)
repository.mail.fl_str_mv fabiojreis@ufv.br
_version_ 1822610583310041088

Registros relacionados