Mapeamento de marcas moleculares e identificação de QTL com base em desequilíbrio de fase gamética

Detalhes bibliográficos
Autor(a) principal: Silva, Admilson da Costa e
Data de Publicação: 2008
Tipo de documento: Dissertação
Idioma: por
Título da fonte: LOCUS Repositório Institucional da UFV
Texto Completo: http://locus.ufv.br/handle/123456789/4665
Resumo: In the study of genetic linkage between two marker loci or between markers and a QTL it is usually necessary to have appropriate designed populations (experimental populations). However, for some species such designed populations could be hard to obtain. In this scenario, the linkage disequilibrium (LD) has been used to build genetic map and to identify QTL. In this work, we used simulation to evaluate the efficiency of LD to construct genetic maps (LD-genetic map) of molecular markers as well as to map QTL (LD-QTL mapping) in non- structured families of outbreed populations. As for the LD- genetic map study, we designed genomes with high saturation level (markers apart from each other less than 5 cM), and random saturation level (markers apart from each other ranging from 0 to 20 cM), five linkage groups and 20 markers per linkage group. We simulated compounds of second generation with 200 and 1000 individuals, derived from the mating of two parental populations of size 200, under four levels (1.0, 0.9, 0.8 and 0.7) of difference in the frequency of each marker (marker-frequency difference) between parental populations. These compounds were used to obtain the sampled genomes, which were compared with the designed genomes to measure the efficiency of LD to construct genetic map. In the LD-QTL mapping study, we adopted, with slightly modifications, the steps to obtain the designed genome and the compounds as described above. We designed genomes with ten linkage groups, each with 20 markers, but for linkage group 1 which had just five markers. We distributed 200 genes controlling quantitative traits along the ten linkage groups. However, only the linkage group 1 had a major QTL along with 19 minor genes. All other linkage groups had 20 minor genes each. In the LD-QTL mapping study, for the detection, estimation of substitution effects and of dominance, we idealized three quantitative traits, each being affected by a major QTL. The trait yield (g/ear) had a QTL with positive dominance; the trait expansion capacity (mL/g) had a QTL with bidirectional dominance; and the trait relative liquid growth (%) had a QTL with negative dominance. We used the method of single marker analysis base on regression to model the QTL effects. The analyses of power for QTL identification and substitution effect estimation were done by linear regression. On the other hand, the analysis of dominance effect was done by polynomial regression with the quadratic term included in the model. In the LD-genetic map study the linkage groups were satisfactory recovered, with only few exceptions. The bias in recovering the designed genome increased with the decreasing of the marker- frequency difference between parental populations from 1.0 to 0.7. Based on the percentage of correct ordered markers in the genome, we found that the LD-genetic map was efficient, with correct ordering of markers superior to 86%. Our results support that the most efficient population for LD-genetic map was the one equivalent to an F2 intercross population. With respect to the QTL detection, in general, the power of detection was satisfactory, independent of the quantitative trait simulated. The results of effect substitution of marker revealed that markers closer to the QTL had bigger effects. The detections of dominance effects were efficient only on the compounds from the mating of parental populations with marker-frequency difference superior than 0.9 and sample size of 1.000. The results of dominance direction analyses on the markers for the trait yield were efficient in determining the direction of dominance of QTL, with few exceptions where complete dominance was present. For the trait expansion capacity, the specification of which markers had positive or negative effect was not possible because of the bidirectional nature of the simulated dominance effects. For the trait liquid growth the estimated effects of dominance at markers often revealed the correct dominance effects direction of the QTL. It is important to point out that the results of our LD-QTL mapping study were based on traits in which the phenotypic variance explained by the QTL is between 10 and 30% of the total phenotypic variance.
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spelling Silva, Admilson da Costa ehttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4717648E6Cruz, Cosme Damiãohttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4788274A6Silva, Fabyano Fonseca ehttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4766260Z2Viana, José Marcelo Sorianohttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4786170D5Guimarães, Cláudia Teixeirahttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4782346A3Magalhães, Jurandir Vieira dehttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4782698J92015-03-26T13:42:01Z2008-07-212015-03-26T13:42:01Z2008-03-26SILVA, Admilson da Costa e. Constructing genetic map and indentifying QTL based on linkage disequilibrium. 2008. 83 f. Dissertação (Mestrado em Genética animal; Genética molecular e de microrganismos; Genética quantitativa; Genética vegetal; Me) - Universidade Federal de Viçosa, Viçosa, 2008.http://locus.ufv.br/handle/123456789/4665In the study of genetic linkage between two marker loci or between markers and a QTL it is usually necessary to have appropriate designed populations (experimental populations). However, for some species such designed populations could be hard to obtain. In this scenario, the linkage disequilibrium (LD) has been used to build genetic map and to identify QTL. In this work, we used simulation to evaluate the efficiency of LD to construct genetic maps (LD-genetic map) of molecular markers as well as to map QTL (LD-QTL mapping) in non- structured families of outbreed populations. As for the LD- genetic map study, we designed genomes with high saturation level (markers apart from each other less than 5 cM), and random saturation level (markers apart from each other ranging from 0 to 20 cM), five linkage groups and 20 markers per linkage group. We simulated compounds of second generation with 200 and 1000 individuals, derived from the mating of two parental populations of size 200, under four levels (1.0, 0.9, 0.8 and 0.7) of difference in the frequency of each marker (marker-frequency difference) between parental populations. These compounds were used to obtain the sampled genomes, which were compared with the designed genomes to measure the efficiency of LD to construct genetic map. In the LD-QTL mapping study, we adopted, with slightly modifications, the steps to obtain the designed genome and the compounds as described above. We designed genomes with ten linkage groups, each with 20 markers, but for linkage group 1 which had just five markers. We distributed 200 genes controlling quantitative traits along the ten linkage groups. However, only the linkage group 1 had a major QTL along with 19 minor genes. All other linkage groups had 20 minor genes each. In the LD-QTL mapping study, for the detection, estimation of substitution effects and of dominance, we idealized three quantitative traits, each being affected by a major QTL. The trait yield (g/ear) had a QTL with positive dominance; the trait expansion capacity (mL/g) had a QTL with bidirectional dominance; and the trait relative liquid growth (%) had a QTL with negative dominance. We used the method of single marker analysis base on regression to model the QTL effects. The analyses of power for QTL identification and substitution effect estimation were done by linear regression. On the other hand, the analysis of dominance effect was done by polynomial regression with the quadratic term included in the model. In the LD-genetic map study the linkage groups were satisfactory recovered, with only few exceptions. The bias in recovering the designed genome increased with the decreasing of the marker- frequency difference between parental populations from 1.0 to 0.7. Based on the percentage of correct ordered markers in the genome, we found that the LD-genetic map was efficient, with correct ordering of markers superior to 86%. Our results support that the most efficient population for LD-genetic map was the one equivalent to an F2 intercross population. With respect to the QTL detection, in general, the power of detection was satisfactory, independent of the quantitative trait simulated. The results of effect substitution of marker revealed that markers closer to the QTL had bigger effects. The detections of dominance effects were efficient only on the compounds from the mating of parental populations with marker-frequency difference superior than 0.9 and sample size of 1.000. The results of dominance direction analyses on the markers for the trait yield were efficient in determining the direction of dominance of QTL, with few exceptions where complete dominance was present. For the trait expansion capacity, the specification of which markers had positive or negative effect was not possible because of the bidirectional nature of the simulated dominance effects. For the trait liquid growth the estimated effects of dominance at markers often revealed the correct dominance effects direction of the QTL. It is important to point out that the results of our LD-QTL mapping study were based on traits in which the phenotypic variance explained by the QTL is between 10 and 30% of the total phenotypic variance.No estudo de ligação entre dois locos marcadores e análise de QTL é preciso realizar cruzamentos apropriados para o mapeamento das populações. No entanto, a realização de cruzamentos pode ser difícil em algumas espécies. Nestes casos, tem-se utilizado desequilíbrio de ligação (LD) ou de fase gamética. Este trabalho, realizado por meio de simulação de dados, teve como objetivos avaliar a eficiência do mapeamento de marcas moleculares e identificar o QTL em populações não-endogâmicas e não-estruturadas em famílias, com base em desequilíbrio de fase gamética. Para o mapeamento de marcas moleculares foram simulados genomas com nível de saturação alto (distância menor que 5 cM) e aleatório (distância entre 0 e 20 cM), cinco grupos de ligação e 20 marcas por grupo. Para obtenção dos genomas amostrais foram simulados compostos de segunda geração, com 1.000 e 200 indivíduos, derivados do cruzamento entre duas populações parentais, com tamanho 200, sob quatro níveis (1,0, 0,9, 0,8 e 0,7) de diferença mínima de freqüência de mesma marca entre os genitores. A partir dos genomas amostrais foi avaliada a eficiência de recuperação dos genomas paramétricos. Na detecção de QTL, seguiu-se o mesmo processo para simulação dos genomas e dos compostos, porém com algumas particularidades. Foram simulados genomas com dez grupos de ligação, devendo ser ressaltado que em cada genoma somente o grupo de ligação 1 foi simulado com cinco locos marcadores. Nestes grupos também foram distribuídos 200 genes controladores de características quantitativas. Porém, somente no grupo de ligação 1 foram alocados QTL e 19 genes de efeito menor. Em cada um dos demais grupos de ligação foram alocados mais 20 genes de efeito menor. Na análise de QTL, incluindo detecção e estimação dos efeitos de substituição e desvios de dominância, foram idealizadas três características quantitativas, com um QTL controlando cada característica. As características foram: produção (g/espiga), com direção de dominância positiva; capacidade de expansão (ml/g), com direção de dominância bidirecional; e crescimento líquido relativo (%), com direção de dominância negativa. Neste trabalho, foi empregado o método das marcas simples com base em análise de regressão. A avaliação do poder de detecção de QTL e os efeitos de substituição foram obtidos por regressão linear, enquanto os efeitos de dominância foram obtidos por regressão polinomial, incluindo o termo quadrático. No mapeamento de marcas moleculares, verificou-se que os grupos de ligação foram recuperados de forma satisfatória, com algumas exceções. Maior viés na recuperação dos genomas paramétricos foi verificado à medida que se diminuiu a diferença de freqüência de mesma marca entre os genitores de 1,0 para 0,7. Com base no porcentual de marcas ordenadas corretamente o mapeamento foi eficiente, apresentando valores superiores a 86%. Diante dos resultados obtidos concluiu-se que a população mais eficiente para o mapeamento é a equivalente a uma F2. Quanto à detecção de QTL, de modo geral, o poder de detecção foi satisfatório, independentemente do caráter idealizado. A análise do efeito de substituição de marca revelou maior magnitude de efeito para as marcas mais próximas ao QTL. Em relação ao teste de dominância nos locos marcadores, foi verificada eficiência na detecção de dominância apenas nos compostos obtidos do cruzamento entre genitores com diferença de freqüência de mesma marca maior ou igual a 0,9 e com tamanho de amostra igual 1.000. Avaliando o sinal do efeito de dominância, para a característica produção, verificou-se que os efeitos estimados nos locos marcadores foram consistentes em revelar a direção de dominância no loco do QTL, com algumas exceções quando dominância completa. Para característica capacidade de expansão, em virtude de ter sido considerada sob direção de dominância bidirecional, não foi possível a determinação de quais marcas têm efeito positivo ou negativo. Para a característica crescimento líquido relativo, as estimativas dos efeitos de dominância nos marcadores revelaram, quase sem exceção, a direção de dominância no loco do QTL. É importante ressaltar que os resultados obtidos neste trabalho, para o mapeamento de QTL, são válidos para QTLs que expliquem entre 10 e 30% a variação fenotípica do caráter.Conselho Nacional de Desenvolvimento Científico e Tecnológicoapplication/pdfporUniversidade Federal de ViçosaMestrado em Genética e MelhoramentoUFVBRGenética animal; Genética molecular e de microrganismos; Genética quantitativa; Genética vegetal; MeDesequilíbrio de ligação gênicaMarcador co-dominanteSimulaçãoGene linkage disequilibriumCo-dominant markerSimulationCNPQ::CIENCIAS BIOLOGICAS::GENETICA::GENETICA QUANTITATIVAMapeamento de marcas moleculares e identificação de QTL com base em desequilíbrio de fase gaméticaConstructing genetic map and indentifying QTL based on linkage disequilibriuminfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisinfo:eu-repo/semantics/openAccessreponame:LOCUS Repositório Institucional da UFVinstname:Universidade Federal de Viçosa (UFV)instacron:UFVORIGINALtexto completo.pdfapplication/pdf338043https://locus.ufv.br//bitstream/123456789/4665/1/texto%20completo.pdfa834b14ee2a313c551703de0f053cc4dMD51TEXTtexto completo.pdf.txttexto completo.pdf.txtExtracted texttext/plain145917https://locus.ufv.br//bitstream/123456789/4665/2/texto%20completo.pdf.txt942c2cceab0b03c892ec9abfa0e94686MD52THUMBNAILtexto completo.pdf.jpgtexto completo.pdf.jpgIM Thumbnailimage/jpeg3611https://locus.ufv.br//bitstream/123456789/4665/3/texto%20completo.pdf.jpg4e58421bcde74e88f4179edfcb9e35abMD53123456789/46652016-04-10 23:11:22.245oai:locus.ufv.br:123456789/4665Repositório InstitucionalPUBhttps://www.locus.ufv.br/oai/requestfabiojreis@ufv.bropendoar:21452016-04-11T02:11:22LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)false
dc.title.por.fl_str_mv Mapeamento de marcas moleculares e identificação de QTL com base em desequilíbrio de fase gamética
dc.title.alternative.eng.fl_str_mv Constructing genetic map and indentifying QTL based on linkage disequilibrium
title Mapeamento de marcas moleculares e identificação de QTL com base em desequilíbrio de fase gamética
spellingShingle Mapeamento de marcas moleculares e identificação de QTL com base em desequilíbrio de fase gamética
Silva, Admilson da Costa e
Desequilíbrio de ligação gênica
Marcador co-dominante
Simulação
Gene linkage disequilibrium
Co-dominant marker
Simulation
CNPQ::CIENCIAS BIOLOGICAS::GENETICA::GENETICA QUANTITATIVA
title_short Mapeamento de marcas moleculares e identificação de QTL com base em desequilíbrio de fase gamética
title_full Mapeamento de marcas moleculares e identificação de QTL com base em desequilíbrio de fase gamética
title_fullStr Mapeamento de marcas moleculares e identificação de QTL com base em desequilíbrio de fase gamética
title_full_unstemmed Mapeamento de marcas moleculares e identificação de QTL com base em desequilíbrio de fase gamética
title_sort Mapeamento de marcas moleculares e identificação de QTL com base em desequilíbrio de fase gamética
author Silva, Admilson da Costa e
author_facet Silva, Admilson da Costa e
author_role author
dc.contributor.authorLattes.por.fl_str_mv http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4717648E6
dc.contributor.author.fl_str_mv Silva, Admilson da Costa e
dc.contributor.advisor-co1.fl_str_mv Cruz, Cosme Damião
dc.contributor.advisor-co1Lattes.fl_str_mv http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4788274A6
dc.contributor.advisor-co2.fl_str_mv Silva, Fabyano Fonseca e
dc.contributor.advisor-co2Lattes.fl_str_mv http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4766260Z2
dc.contributor.advisor1.fl_str_mv Viana, José Marcelo Soriano
dc.contributor.advisor1Lattes.fl_str_mv http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4786170D5
dc.contributor.referee1.fl_str_mv Guimarães, Cláudia Teixeira
dc.contributor.referee1Lattes.fl_str_mv http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4782346A3
dc.contributor.referee2.fl_str_mv Magalhães, Jurandir Vieira de
dc.contributor.referee2Lattes.fl_str_mv http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4782698J9
contributor_str_mv Cruz, Cosme Damião
Silva, Fabyano Fonseca e
Viana, José Marcelo Soriano
Guimarães, Cláudia Teixeira
Magalhães, Jurandir Vieira de
dc.subject.por.fl_str_mv Desequilíbrio de ligação gênica
Marcador co-dominante
Simulação
topic Desequilíbrio de ligação gênica
Marcador co-dominante
Simulação
Gene linkage disequilibrium
Co-dominant marker
Simulation
CNPQ::CIENCIAS BIOLOGICAS::GENETICA::GENETICA QUANTITATIVA
dc.subject.eng.fl_str_mv Gene linkage disequilibrium
Co-dominant marker
Simulation
dc.subject.cnpq.fl_str_mv CNPQ::CIENCIAS BIOLOGICAS::GENETICA::GENETICA QUANTITATIVA
description In the study of genetic linkage between two marker loci or between markers and a QTL it is usually necessary to have appropriate designed populations (experimental populations). However, for some species such designed populations could be hard to obtain. In this scenario, the linkage disequilibrium (LD) has been used to build genetic map and to identify QTL. In this work, we used simulation to evaluate the efficiency of LD to construct genetic maps (LD-genetic map) of molecular markers as well as to map QTL (LD-QTL mapping) in non- structured families of outbreed populations. As for the LD- genetic map study, we designed genomes with high saturation level (markers apart from each other less than 5 cM), and random saturation level (markers apart from each other ranging from 0 to 20 cM), five linkage groups and 20 markers per linkage group. We simulated compounds of second generation with 200 and 1000 individuals, derived from the mating of two parental populations of size 200, under four levels (1.0, 0.9, 0.8 and 0.7) of difference in the frequency of each marker (marker-frequency difference) between parental populations. These compounds were used to obtain the sampled genomes, which were compared with the designed genomes to measure the efficiency of LD to construct genetic map. In the LD-QTL mapping study, we adopted, with slightly modifications, the steps to obtain the designed genome and the compounds as described above. We designed genomes with ten linkage groups, each with 20 markers, but for linkage group 1 which had just five markers. We distributed 200 genes controlling quantitative traits along the ten linkage groups. However, only the linkage group 1 had a major QTL along with 19 minor genes. All other linkage groups had 20 minor genes each. In the LD-QTL mapping study, for the detection, estimation of substitution effects and of dominance, we idealized three quantitative traits, each being affected by a major QTL. The trait yield (g/ear) had a QTL with positive dominance; the trait expansion capacity (mL/g) had a QTL with bidirectional dominance; and the trait relative liquid growth (%) had a QTL with negative dominance. We used the method of single marker analysis base on regression to model the QTL effects. The analyses of power for QTL identification and substitution effect estimation were done by linear regression. On the other hand, the analysis of dominance effect was done by polynomial regression with the quadratic term included in the model. In the LD-genetic map study the linkage groups were satisfactory recovered, with only few exceptions. The bias in recovering the designed genome increased with the decreasing of the marker- frequency difference between parental populations from 1.0 to 0.7. Based on the percentage of correct ordered markers in the genome, we found that the LD-genetic map was efficient, with correct ordering of markers superior to 86%. Our results support that the most efficient population for LD-genetic map was the one equivalent to an F2 intercross population. With respect to the QTL detection, in general, the power of detection was satisfactory, independent of the quantitative trait simulated. The results of effect substitution of marker revealed that markers closer to the QTL had bigger effects. The detections of dominance effects were efficient only on the compounds from the mating of parental populations with marker-frequency difference superior than 0.9 and sample size of 1.000. The results of dominance direction analyses on the markers for the trait yield were efficient in determining the direction of dominance of QTL, with few exceptions where complete dominance was present. For the trait expansion capacity, the specification of which markers had positive or negative effect was not possible because of the bidirectional nature of the simulated dominance effects. For the trait liquid growth the estimated effects of dominance at markers often revealed the correct dominance effects direction of the QTL. It is important to point out that the results of our LD-QTL mapping study were based on traits in which the phenotypic variance explained by the QTL is between 10 and 30% of the total phenotypic variance.
publishDate 2008
dc.date.available.fl_str_mv 2008-07-21
2015-03-26T13:42:01Z
dc.date.issued.fl_str_mv 2008-03-26
dc.date.accessioned.fl_str_mv 2015-03-26T13:42:01Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/masterThesis
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dc.identifier.citation.fl_str_mv SILVA, Admilson da Costa e. Constructing genetic map and indentifying QTL based on linkage disequilibrium. 2008. 83 f. Dissertação (Mestrado em Genética animal; Genética molecular e de microrganismos; Genética quantitativa; Genética vegetal; Me) - Universidade Federal de Viçosa, Viçosa, 2008.
dc.identifier.uri.fl_str_mv http://locus.ufv.br/handle/123456789/4665
identifier_str_mv SILVA, Admilson da Costa e. Constructing genetic map and indentifying QTL based on linkage disequilibrium. 2008. 83 f. Dissertação (Mestrado em Genética animal; Genética molecular e de microrganismos; Genética quantitativa; Genética vegetal; Me) - Universidade Federal de Viçosa, Viçosa, 2008.
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dc.publisher.country.fl_str_mv BR
dc.publisher.department.fl_str_mv Genética animal; Genética molecular e de microrganismos; Genética quantitativa; Genética vegetal; Me
publisher.none.fl_str_mv Universidade Federal de Viçosa
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