| |
|
|
|
Registro Completo |
|
Biblioteca(s): |
Embrapa Semiárido. |
|
Data corrente: |
13/02/2012 |
|
Data da última atualização: |
06/06/2023 |
|
Tipo da produção científica: |
Resumo em Anais de Congresso |
|
Autoria: |
FREITAS, A. C.; MIRANDA, T. D.; BARBOSA, M. A. G.; FERREIRA, M. A. S. V. |
|
Afiliação: |
A. C. FREITAS, UnB; T. D. MIRANDA, UnB; MARIA ANGELICA GUIMARAES BARBOSA, CPATSA; M. A. S. V. FERREIRA, UnB. |
|
Título: |
Limite de detecção de Xanthomonas campestris pv. viticola por nested-PCR em frutos assintomáticos de videiras. |
|
Ano de publicação: |
2011 |
|
Fonte/Imprenta: |
Tropical Plant Pathology, Brasília, DF, v. 36, 2011. |
|
Páginas: |
p. 1039. |
|
Descrição Física: |
1 CD-ROM. |
|
Idioma: |
Português |
|
Notas: |
Suplemento. Edição dos Resumos do 44 Congresso Brasileiro de Fitopatologia, Bento Gonçalves, ago. 2011. |
|
Conteúdo: |
O cancro bacteriano da videira causado por Xanthomonas campestris pv. viticola é responsável por grandes prejuízos ao cultivo da videira no Vale do Submédio São Francisco. Diante da preocupação com a disseminação do patógeno, este estudo teve como objetivo determinar o limite mínimo de detecção da bactéria por nested-PCR. Dois experimentos foram realizados com frutos das variedades comerciais Crimson e Moscatel, desinfestados e inoculados artificialmente através de pulverizações com suspensões bacterianas de diferentes concentrações (102 a 108 ufc/ml), com duas repetições (de 100-120g) para cada tratamento. Os frutos foram depositados em bandejas de isopor e mantidos por 24 h à temperatura ambiente para secagem. As amostras foram lavadas em 100 ml de água estéril em agitador por 1 h e 30 min a 200 rpm. Em seguida, foram retiradas alíquotas de 1 ml que foram centrifugadas por 15 minutos a 13.200 rpm, descartando-se o sobrenadante. O sedimento foi ressuspendido em 50 μl de água estéril. Com essas amostras foi realizada a nested-PCR, sendo o primeiro ciclo com os iniciadores RST2/Xcv3R, cujo produto foi diluído em água a 1:50 e assim realizado o segundo ciclo com os iniciadores Xcv1F/Xcv3R. O limite de detecção de X. campestris pv. viticola por nested-PCR em frutos inoculados variou de 102 a 103 ufc/ml. |
|
Palavras-Chave: |
Cancro bacteriano da videira; Vale do Submédio São Francisco; Xanthomonas campestris pv. |
|
Thesagro: |
Doença; Uva; Vitis Vinifera. |
|
Thesaurus Nal: |
Grapes. |
|
Categoria do assunto: |
H Saúde e Patologia |
|
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/53953/1/Angelica4-2011.pdf
|
|
Marc: |
LEADER 02219nam a2200253 a 4500
001 1915227
005 2023-06-06
008 2011 bl uuuu u00u1 u #d
100 1 $aFREITAS, A. C.
245 $aLimite de detecção de Xanthomonas campestris pv. viticola por nested-PCR em frutos assintomáticos de videiras.
260 $aTropical Plant Pathology, Brasília, DF, v. 36$c2011
300 $ap. 1039.$c1 CD-ROM.
500 $aSuplemento. Edição dos Resumos do 44 Congresso Brasileiro de Fitopatologia, Bento Gonçalves, ago. 2011.
520 $aO cancro bacteriano da videira causado por Xanthomonas campestris pv. viticola é responsável por grandes prejuízos ao cultivo da videira no Vale do Submédio São Francisco. Diante da preocupação com a disseminação do patógeno, este estudo teve como objetivo determinar o limite mínimo de detecção da bactéria por nested-PCR. Dois experimentos foram realizados com frutos das variedades comerciais Crimson e Moscatel, desinfestados e inoculados artificialmente através de pulverizações com suspensões bacterianas de diferentes concentrações (102 a 108 ufc/ml), com duas repetições (de 100-120g) para cada tratamento. Os frutos foram depositados em bandejas de isopor e mantidos por 24 h à temperatura ambiente para secagem. As amostras foram lavadas em 100 ml de água estéril em agitador por 1 h e 30 min a 200 rpm. Em seguida, foram retiradas alíquotas de 1 ml que foram centrifugadas por 15 minutos a 13.200 rpm, descartando-se o sobrenadante. O sedimento foi ressuspendido em 50 μl de água estéril. Com essas amostras foi realizada a nested-PCR, sendo o primeiro ciclo com os iniciadores RST2/Xcv3R, cujo produto foi diluído em água a 1:50 e assim realizado o segundo ciclo com os iniciadores Xcv1F/Xcv3R. O limite de detecção de X. campestris pv. viticola por nested-PCR em frutos inoculados variou de 102 a 103 ufc/ml.
650 $aGrapes
650 $aDoença
650 $aUva
650 $aVitis Vinifera
653 $aCancro bacteriano da videira
653 $aVale do Submédio São Francisco
653 $aXanthomonas campestris pv
700 1 $aMIRANDA, T. D.
700 1 $aBARBOSA, M. A. G.
700 1 $aFERREIRA, M. A. S. V.
Download
Esconder MarcMostrar Marc Completo |
|
Registro original: |
Embrapa Semiárido (CPATSA) |
|
|
Biblioteca |
ID |
Origem |
Tipo/Formato |
Classificação |
Cutter |
Registro |
Volume |
Status |
URL |
Voltar
|
|
|
Registro Completo
|
Biblioteca(s): |
Embrapa Gado de Leite. |
|
Data corrente: |
15/02/2016 |
|
Data da última atualização: |
06/02/2024 |
|
Tipo da produção científica: |
Artigo em Periódico Indexado |
|
Circulação/Nível: |
A - 1 |
|
Autoria: |
BOISON, S. A.; SANTOS, D. J. A.; UTSONOMIYA, A. H. T.; CARVALHEIRO, R.; NEVES, H. H. R.; O'BRIEN, A. M. P.; GARCIA, J. F.; SÖLKNER, J.; SILVA, M. V. G. B. |
|
Afiliação: |
S. A. Boison, University of Natural Resources and Life Sciences, Vienna, Austria; D. J. A. Santos, UNESP; A. H. T. Utsunomiya, UNESP; R. Carvalheiro, UNESP; H. H. R. Neves, UNESP; A. M. Perez O'Brien, University of Natural Resources and Life Sciences, Vienna, Aústria; J. F. Garcia, UNESP; J. Sölkner, University of Natural Resources and Life Sciences, Vienna, Aústria; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL. |
|
Título: |
Strategies for single nucleotide polymorphism (SNP) genotyping to enhance genotype imputation in Gyr (Bos indicus) dairy cattle: Comparison of commercially available SNP chips. |
|
Ano de publicação: |
2015 |
|
Fonte/Imprenta: |
Journal of Dairy Science, v. 98, n. 7, p. 4969-4989, 2015. |
|
Idioma: |
Português |
|
Conteúdo: |
Genotype imputation is widely used as a cost-effective strategy in genomic evaluation of cattle. Key determinants of imputation accuracies, such as linkage disequilibrium patterns, marker densities, and ascertainment bias, differ between Bos indicus and Bos taurus breeds. Consequently, there is a need to investigate effectiveness of genotype imputation in indicine breeds. Thus, the objective of the study was to investigate strategies and factors affecting the accuracy of genotype imputation in Gyr (Bos indicus) dairy cattle. Four imputation scenarios were studied using 471 sires and 1,644 dams genotyped on Illumina BovineHD (HD-777K; San Diego, CA) and BovineSNP50 (50K) chips, respectively. Scenarios were based on which reference high-density single nucleotide polymorphism (SNP) panel (HDP) should be adopted [HD-777K, 50K, and GeneSeek GGP-75Ki (Lincoln, NE)]. Depending on the scenario, validation animals had their genotypes masked for one of the lower-density panels: Illumina (3K, 7K, and 50K) and GeneSeek (SGGP-20Ki and GGP-75Ki). We randomly selected 171 sires as reference and 300 as validation for all the scenarios. Additionally, all sires were used as reference and the 1,644 dams were imputed for validation. Genotypes of 98 individuals with 4 and more offspring were completely masked and imputed. Imputation algorithms FImpute and Beagle v3.3 and v4 were used. Imputation accuracies were measured using the correlation and allelic correct rate. FImpute resulted in highest accuracies, whereas Beagle 3.3 gave the least-accurate imputations. Accuracies evaluated as correlation (allelic correct rate) ranged from 0.910 (0.942) to 0.961 (0.974) using 50K as HDP and with 3K (7K) as low-density panels. With GGP-75Ki as HDP, accuracies were moderate for 3K, 7K, and 50K, but high for SGGP-20Ki. The use of HD-777K as HDP resulted in accuracies of 0.888 (3K), 0.941 (7K), 0.980 (SGGP-20Ki), 0.982 (50K), and 0.993 (GGP-75Ki). Ungenotyped individuals were imputed with an average accuracy of 0.970. The average top 5 kinship coefficients between reference and imputed individuals was a strong predictor of imputation accuracy. FImpute was faster and used less memory than Beagle v4. Beagle v4 outperformed Beagle v3.3 in accuracy and speed of computation. A genotyping strategy that uses the HD-777K SNP chip as a reference panel and SGGP-20Ki as the lower-density SNP panel should be adopted as accuracy was high and similar to that of the 50K. However, the effect of using imputed HD-777K genotypes from the SGGP-20Ki on genomic evaluation is yet to be studied. MenosGenotype imputation is widely used as a cost-effective strategy in genomic evaluation of cattle. Key determinants of imputation accuracies, such as linkage disequilibrium patterns, marker densities, and ascertainment bias, differ between Bos indicus and Bos taurus breeds. Consequently, there is a need to investigate effectiveness of genotype imputation in indicine breeds. Thus, the objective of the study was to investigate strategies and factors affecting the accuracy of genotype imputation in Gyr (Bos indicus) dairy cattle. Four imputation scenarios were studied using 471 sires and 1,644 dams genotyped on Illumina BovineHD (HD-777K; San Diego, CA) and BovineSNP50 (50K) chips, respectively. Scenarios were based on which reference high-density single nucleotide polymorphism (SNP) panel (HDP) should be adopted [HD-777K, 50K, and GeneSeek GGP-75Ki (Lincoln, NE)]. Depending on the scenario, validation animals had their genotypes masked for one of the lower-density panels: Illumina (3K, 7K, and 50K) and GeneSeek (SGGP-20Ki and GGP-75Ki). We randomly selected 171 sires as reference and 300 as validation for all the scenarios. Additionally, all sires were used as reference and the 1,644 dams were imputed for validation. Genotypes of 98 individuals with 4 and more offspring were completely masked and imputed. Imputation algorithms FImpute and Beagle v3.3 and v4 were used. Imputation accuracies were measured using the correlation and allelic correct rate. FImpute resulted in highest ... Mostrar Tudo |
|
Palavras-Chave: |
FImpute; Gyr; Imputation. |
|
Thesaurus NAL: |
Beagle. |
|
Categoria do assunto: |
L Ciência Animal e Produtos de Origem Animal |
|
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/138978/1/Cnpgl-2015-JDairySci-Strategies.pdf
|
|
Marc: |
LEADER 03421naa a2200265 a 4500
001 2036928
005 2024-02-06
008 2015 bl uuuu u00u1 u #d
100 1 $aBOISON, S. A.
245 $aStrategies for single nucleotide polymorphism (SNP) genotyping to enhance genotype imputation in Gyr (Bos indicus) dairy cattle$bComparison of commercially available SNP chips.$h[electronic resource]
260 $c2015
520 $aGenotype imputation is widely used as a cost-effective strategy in genomic evaluation of cattle. Key determinants of imputation accuracies, such as linkage disequilibrium patterns, marker densities, and ascertainment bias, differ between Bos indicus and Bos taurus breeds. Consequently, there is a need to investigate effectiveness of genotype imputation in indicine breeds. Thus, the objective of the study was to investigate strategies and factors affecting the accuracy of genotype imputation in Gyr (Bos indicus) dairy cattle. Four imputation scenarios were studied using 471 sires and 1,644 dams genotyped on Illumina BovineHD (HD-777K; San Diego, CA) and BovineSNP50 (50K) chips, respectively. Scenarios were based on which reference high-density single nucleotide polymorphism (SNP) panel (HDP) should be adopted [HD-777K, 50K, and GeneSeek GGP-75Ki (Lincoln, NE)]. Depending on the scenario, validation animals had their genotypes masked for one of the lower-density panels: Illumina (3K, 7K, and 50K) and GeneSeek (SGGP-20Ki and GGP-75Ki). We randomly selected 171 sires as reference and 300 as validation for all the scenarios. Additionally, all sires were used as reference and the 1,644 dams were imputed for validation. Genotypes of 98 individuals with 4 and more offspring were completely masked and imputed. Imputation algorithms FImpute and Beagle v3.3 and v4 were used. Imputation accuracies were measured using the correlation and allelic correct rate. FImpute resulted in highest accuracies, whereas Beagle 3.3 gave the least-accurate imputations. Accuracies evaluated as correlation (allelic correct rate) ranged from 0.910 (0.942) to 0.961 (0.974) using 50K as HDP and with 3K (7K) as low-density panels. With GGP-75Ki as HDP, accuracies were moderate for 3K, 7K, and 50K, but high for SGGP-20Ki. The use of HD-777K as HDP resulted in accuracies of 0.888 (3K), 0.941 (7K), 0.980 (SGGP-20Ki), 0.982 (50K), and 0.993 (GGP-75Ki). Ungenotyped individuals were imputed with an average accuracy of 0.970. The average top 5 kinship coefficients between reference and imputed individuals was a strong predictor of imputation accuracy. FImpute was faster and used less memory than Beagle v4. Beagle v4 outperformed Beagle v3.3 in accuracy and speed of computation. A genotyping strategy that uses the HD-777K SNP chip as a reference panel and SGGP-20Ki as the lower-density SNP panel should be adopted as accuracy was high and similar to that of the 50K. However, the effect of using imputed HD-777K genotypes from the SGGP-20Ki on genomic evaluation is yet to be studied.
650 $aBeagle
653 $aFImpute
653 $aGyr
653 $aImputation
700 1 $aSANTOS, D. J. A.
700 1 $aUTSONOMIYA, A. H. T.
700 1 $aCARVALHEIRO, R.
700 1 $aNEVES, H. H. R.
700 1 $aO'BRIEN, A. M. P.
700 1 $aGARCIA, J. F.
700 1 $aSÖLKNER, J.
700 1 $aSILVA, M. V. G. B.
773 $tJournal of Dairy Science$gv. 98, n. 7, p. 4969-4989, 2015.
Download
Esconder MarcMostrar Marc Completo |
|
Registro original: |
Embrapa Gado de Leite (CNPGL) |
|
|
Biblioteca |
ID |
Origem |
Tipo/Formato |
Classificação |
Cutter |
Registro |
Volume |
Status |
Fechar
|
| Nenhum registro encontrado para a expressão de busca informada. |
|
|
