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Registro Completo |
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Biblioteca(s): |
Embrapa Milho e Sorgo. |
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Data corrente: |
18/09/2020 |
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Data da última atualização: |
20/12/2020 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
OLIVEIRA, A. A. de; GUIMARAES, L. J. M.; GUIMARÃES, C. T.; GUIMARAES, P. E. de O.; PINTO, M. de O.; PASTINA, M. M.; MARGARIDO, G. R. A. |
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Afiliação: |
Amanda Avelar de Oliveira, Escola Superior de Agricultura "Luiz de Queiroz"; LAURO JOSE MOREIRA GUIMARAES, CNPMS; CLAUDIA TEIXEIRA GUIMARAES, CNPMS; PAULO EVARISTO DE O GUIMARAES, CNPMS; MARCOS DE OLIVEIRA PINTO, CNPMS; MARIA MARTA PASTINA, CNPMS; Gabriel Rodrigues Alves Margarido, Escola Superior de Agricultura "Luiz de Queiroz". |
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Título: |
Single nucleotide polymorphism calling and imputation strategies for cost-effective genotyping in a tropical maize breeding program. |
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Ano de publicação: |
2020 |
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Fonte/Imprenta: |
Crop Science, v. 60, n. 6, p. 3066-3082, 2020. |
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DOI: |
10.1002/csc2.20255 |
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Idioma: |
Inglês |
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Conteúdo: |
Genotyping-by-sequencing (GBS) datasets typically feature high rates of missingness and heterozygote undercalling, prompting the use of data imputation. We compared the accuracy of four imputation methods?NPUTE, Beagle, knearest neighbors imputation (KNNI), and fast inbreed line library imputation (FILLIN)?using GBS data of maize (Zea mays L.) inbred lines, genotyped using different multiplexing levels. Two strategies for SNP-calling and genotype imputation were evaluated. First, only lines genotyped through 96-plex were used for single nucleotide polymorphism (SNP) discovery, whereas both 96- and 384-plex were simultaneously used in the second strategy. In the first genotype imputation strategy, only the 96-plex lines were imputed, then the remaining lines were appended (96-plex-imputed plus 384-plex) and then imputed. In the second imputation strategy, we jointly imputed both datasets. We also investigated the impacts of including heterozygous genotypes and distinct rates of missing genotypes per locus. The different SNP-calling strategies and percentage of missing data did not substantially affect the imputation accuracy. However, the different imputation strategies showed a substantial effect. Generally, imputations were less accurate for heterozygotes. The scenario 96-plex-imputed plus 384-plex showed accuracies similar to the 96-plex scenario. Beagle and NPUTE produced the highest accuracies. Our results indicate that combining SNP-calling and imputation strategies can enhance genotyping in a cost-effective manner, resulting in higher imputation accuracies. MenosGenotyping-by-sequencing (GBS) datasets typically feature high rates of missingness and heterozygote undercalling, prompting the use of data imputation. We compared the accuracy of four imputation methods?NPUTE, Beagle, knearest neighbors imputation (KNNI), and fast inbreed line library imputation (FILLIN)?using GBS data of maize (Zea mays L.) inbred lines, genotyped using different multiplexing levels. Two strategies for SNP-calling and genotype imputation were evaluated. First, only lines genotyped through 96-plex were used for single nucleotide polymorphism (SNP) discovery, whereas both 96- and 384-plex were simultaneously used in the second strategy. In the first genotype imputation strategy, only the 96-plex lines were imputed, then the remaining lines were appended (96-plex-imputed plus 384-plex) and then imputed. In the second imputation strategy, we jointly imputed both datasets. We also investigated the impacts of including heterozygous genotypes and distinct rates of missing genotypes per locus. The different SNP-calling strategies and percentage of missing data did not substantially affect the imputation accuracy. However, the different imputation strategies showed a substantial effect. Generally, imputations were less accurate for heterozygotes. The scenario 96-plex-imputed plus 384-plex showed accuracies similar to the 96-plex scenario. Beagle and NPUTE produced the highest accuracies. Our results indicate that combining SNP-calling and imputation strategies can... Mostrar Tudo |
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Palavras-Chave: |
Genotipagem; Imputação. |
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Thesagro: |
Genética Vegetal; Genótipo; Melhoramento Genético Vegetal; Milho; Polimorfismo; Seleção Genótipa. |
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Categoria do assunto: |
G Melhoramento Genético |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/217686/1/Single-nucleotide-polymorphism.pdf
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Marc: |
LEADER 02517naa a2200301 a 4500
001 2125019
005 2020-12-20
008 2020 bl uuuu u00u1 u #d
024 7 $a10.1002/csc2.20255$2DOI
100 1 $aOLIVEIRA, A. A. de
245 $aSingle nucleotide polymorphism calling and imputation strategies for cost-effective genotyping in a tropical maize breeding program.$h[electronic resource]
260 $c2020
520 $aGenotyping-by-sequencing (GBS) datasets typically feature high rates of missingness and heterozygote undercalling, prompting the use of data imputation. We compared the accuracy of four imputation methods?NPUTE, Beagle, knearest neighbors imputation (KNNI), and fast inbreed line library imputation (FILLIN)?using GBS data of maize (Zea mays L.) inbred lines, genotyped using different multiplexing levels. Two strategies for SNP-calling and genotype imputation were evaluated. First, only lines genotyped through 96-plex were used for single nucleotide polymorphism (SNP) discovery, whereas both 96- and 384-plex were simultaneously used in the second strategy. In the first genotype imputation strategy, only the 96-plex lines were imputed, then the remaining lines were appended (96-plex-imputed plus 384-plex) and then imputed. In the second imputation strategy, we jointly imputed both datasets. We also investigated the impacts of including heterozygous genotypes and distinct rates of missing genotypes per locus. The different SNP-calling strategies and percentage of missing data did not substantially affect the imputation accuracy. However, the different imputation strategies showed a substantial effect. Generally, imputations were less accurate for heterozygotes. The scenario 96-plex-imputed plus 384-plex showed accuracies similar to the 96-plex scenario. Beagle and NPUTE produced the highest accuracies. Our results indicate that combining SNP-calling and imputation strategies can enhance genotyping in a cost-effective manner, resulting in higher imputation accuracies.
650 $aGenética Vegetal
650 $aGenótipo
650 $aMelhoramento Genético Vegetal
650 $aMilho
650 $aPolimorfismo
650 $aSeleção Genótipa
653 $aGenotipagem
653 $aImputação
700 1 $aGUIMARAES, L. J. M.
700 1 $aGUIMARÃES, C. T.
700 1 $aGUIMARAES, P. E. de O.
700 1 $aPINTO, M. de O.
700 1 $aPASTINA, M. M.
700 1 $aMARGARIDO, G. R. A.
773 $tCrop Science$gv. 60, n. 6, p. 3066-3082, 2020.
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Registro original: |
Embrapa Milho e Sorgo (CNPMS) |
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Registro Completo
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Biblioteca(s): |
Embrapa Amazônia Ocidental. |
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Data corrente: |
13/09/2023 |
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Data da última atualização: |
04/10/2023 |
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Autoria: |
TEIXEIRA, W. G.; PASCHOAL, W. H.; RODRIGUES, M. do R. L.; MACEDO, J. L. V. de; CARVALHO FILHO, A. de; LUMBRERAS, J. F.; NEVES, M. L. S. das; SHINZATO, E. |
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Afiliação: |
WENCESLAU GERALDES TEIXEIRA, CNPS; WILLER HERMETO PASCHOAL, SECRETARIA DA EDUCAÇÃO DO ESTADO DO AMAZONAS; MARIA DO ROSARIO LOBATO RODRIGUES, CPAA; JEFERSON LUIS VASCONCELOS DE MACEDO, CPAA; AMAURY DE CARVALHO FILHO, CNPS; JOSE FRANCISCO LUMBRERAS, CNPS; MATHEUS LEAL SOARES DAS NEVES, BOLSISTA CNPS; EDGAR SHINZATO, SERVIÇO GEOLÓGICO DO BRASIL. |
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Título: |
Nota técnica - mapa de reconhecimento dos solos de parte da área do município de Parintins-AM - Escala 1:100.000. |
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Ano de publicação: |
2023 |
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Fonte/Imprenta: |
Rio de Janeiro: Embrapa Solos, 2023. |
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Páginas: |
Não paginado. |
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Idioma: |
Português |
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Conteúdo: |
Esta Nota Técnica apresenta as áreas (ha) e estima os percentuais de cada unidade de mapeamento (UM), assim como os nomes dos solos componentes na legenda original e atualizada. O mapa está disponível para download em PDF e no formato SIG (shapefile) no Portal de Dados do PronaSolos e do Geoinfo - Embrapa Solos. |
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Palavras-Chave: |
Amazonas; Parintins. |
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Thesagro: |
Solo. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/doc/1156649/1/Nt-Mapa-Solos-Parintins.pdf
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Marc: |
LEADER 01043nam a2200241 a 4500
001 2156649
005 2023-10-04
008 2023 bl uuuu u0uu1 u #d
100 1 $aTEIXEIRA, W. G.
245 $aNota técnica - mapa de reconhecimento dos solos de parte da área do município de Parintins-AM - Escala 1$b100.000.$h[electronic resource]
260 $aRio de Janeiro: Embrapa Solos$c2023
300 $aNão paginado.
520 $aEsta Nota Técnica apresenta as áreas (ha) e estima os percentuais de cada unidade de mapeamento (UM), assim como os nomes dos solos componentes na legenda original e atualizada. O mapa está disponível para download em PDF e no formato SIG (shapefile) no Portal de Dados do PronaSolos e do Geoinfo - Embrapa Solos.
650 $aSolo
653 $aAmazonas
653 $aParintins
700 1 $aPASCHOAL, W. H.
700 1 $aRODRIGUES, M. do R. L.
700 1 $aMACEDO, J. L. V. de
700 1 $aCARVALHO FILHO, A. de
700 1 $aLUMBRERAS, J. F.
700 1 $aNEVES, M. L. S. das
700 1 $aSHINZATO, E.
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Registro original: |
Embrapa Amazônia Ocidental (CPAA) |
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