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| Registros recuperados : 70 | |
| 21. |  | FRITSCHE-NETO, R.; MIRANDA, G. V.; DELIMA, R. O.; SOUZA, L. V. de; SILVA, J. da. Herança de caracteres associados à eficiência de utilização do fósforo em milho. Pesquisa Agropecuária Brasileira, Brasília, DF, v. 45, n. 5, p. 465-471, mai. 2010.| Biblioteca(s): Embrapa Mandioca e Fruticultura; Embrapa Unidades Centrais. |
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| 26. | | SANT'ANA, G. C.; LANES, E. C. M. de; MIRANDA, G. V.; FERREIRA, J. L.; BOREM, A.; FRITSCHE-NETO, R. Análise da diversidade genética entre acessos de milho tolerantes a baixos níveis de nitrogênio e fósforo utilizando marcadores moleculares microssatélites. In: CONGRESSO BRASILEIRO DE MELHORAMENTO DE PLANTAS, 7., 2013, Uberlândia. Variedade melhorada: a força da nossa agricultura: anais. Viçosa, MG: SBMP, 2013. p. 138-141. 1 CD-ROM.| Biblioteca(s): Embrapa Pecuária Sul. |
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| 27. | | SOUZA, V. Q. de; PEREIRA, A. da S.; SILVA, G. O. da; FRITSCHE NETO, R.; OLIVEIRA, A. C. de. Consistency of two stability analysis methods in potatoes. Ciência Rural, Santa Maria, RS, v. 37, n.3, p. 656-661, mai./jun. 2007.| Biblioteca(s): Embrapa Hortaliças. |
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| 28. | | SILVA, G. O.; PEREIRA, A. da S.; SOUZA, V. Q.; CARVALHO, F. I. F.; FRITSCHE NETO, R. Correlações entre caracteres de aparência e rendimento e análise de trilha para aparência de batata. Bragantia, Lavras, v. 66, n. 3, p. 381-388, set. 2007.| Biblioteca(s): Embrapa Hortaliças. |
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| 29. | | SILVA, G. O. da; SOUZA, V. Q. de; PEREIRA, A. da S.; CARVALHO, F. I. F. de; FRITSCHE NETO, R. Early generation selection for tuber appearance affects potato yield components. Crop Breeding and Applied Biotechnology, Viçosa, MG, v. 6, n. 1, p. 73-78, Mar. 2006.| Biblioteca(s): Embrapa Arroz e Feijão. |
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| 31. | | FRITSCHE NETO, R.; PEREIRA, A. da S.; RASEIRA, M. do C. B.; SILVA, G. O.; SOUZA, V. Q. Métodos de avaliação de pólen e influência do ácido giberélico em cruzamentos de batata. Ciência e Agrotecnologia, Lavras, v. 32, n. 2, p. 469-473, fev. 2008.| Biblioteca(s): Embrapa Clima Temperado; Embrapa Hortaliças. |
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| 32. | | FRITSCHE-NETO, R.; DOVALE, J. C.; LANES, É. C. M. de; RESENDE, M. D. V. de; MIRANDA, G. V. Genome-wide selection for tropical maize root traits under conditions of nitrogen and phosphorus stress. Acta Scientiarum. Agronomy, Maringá, v. 34, n. 4, p. 389-395, Oct./Dec. 2012.| Biblioteca(s): Embrapa Florestas. |
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| 34. | | TREVISAN, R.; FRANZON, R. C.; FRITSCHE NETO, R.; GONÇALVES, R. da S.; GONÇALVES, E. D.; ANTUNES, L. E. C. Enraizamento de estacas herbáceas de mirtilo: influência da lesão na base e do ácido indolbutírico. Ciência e Agrotecnologia, Lavras, v. 32, p. 402-406, 2008.| Biblioteca(s): Embrapa Clima Temperado; Embrapa Uva e Vinho. |
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| 35. | | FRITSCHE NETO, R.; SOUZA, V. Q. de; PEREIRA, A. da S.; SILVA, G. O. da; GARCIA, S. M. Estimate of cross efficiency of potato parents. Crop Breeding and Applied Biotechnology, Londrina, v. 6, n. 3, p. 242-249, June 2006.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 36. | | SILVA, G. O. da; PEREIRA, A. da S.; SOUZA, V. Q. de; CARVALHO, F. I. F. de; FRITSCHE NETO, R. Estimativa de capacidades de combinação em gerações iniciais de seleção de batata. Horticultura Brasileira, Brasília, DF, v. 27, n. 3, p. 275-279, jul./set. 2009.| Biblioteca(s): Embrapa Hortaliças. |
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| 39. | | BATISTA, L. G.; CARVALHO, H. F.; GRANATO, I. S. C.; CAIXETA, D. S.; GUIMARAES, L. J. M.; FRITSCHE-NETO, R. Relação entre caracteres agronômicos e produtividade de grãos em híbridos de milho. In: CONGRESSO NACIONAL DE MILHO E SORGO, 29., 2012, Águas de Lindóia. Diversidade e inovações na era dos transgênicos: resumos expandidos. Campinas: Instituto Agronômico; Sete Lagoas: Associação Brasileira de Milho e Sorgo, 2012. p. 2558-2562. 1 CD-ROM.| Biblioteca(s): Embrapa Milho e Sorgo. |
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| Registros recuperados : 70 | |
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Registro Completo
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Biblioteca(s): |
Embrapa Gado de Corte. |
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Data corrente: |
27/12/2019 |
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Data da última atualização: |
27/12/2019 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
A - 2 |
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Autoria: |
MATIAS, F. I.; MEIRELES, K. G. X.; NAGAMATSU, S. T.; BARRIOS, S. C. L.; VALE, C. B. do; CARAZZOLLE, M. F.; FRITSCHE-NETO, R.; ENDELMAN, J. B. |
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Afiliação: |
Filipe Inácio Matias, Universidade de São Paulo - USP/ Escola Superior de Agricultura "Luiz de Queiroz" - ESALQ/Departamento de Genetica; KAREM GUIMARAES XAVIER MEIRELES, CNPGC; Sheila Tiemi Nagamatsu, Universiade Estadual de Campinas - UNICAMP/Departamento Genética e Evolução; SANZIO CARVALHO LIMA BARRIOS, CNPGC; Cacilda Borges do Valle, Colaboradora da Embrapa Gado de Corte; Marcelo Falsarella Carazzolle, Universiade Estadual de Campinas - UNICAMP/Departamento Genética e Evolução; Roberto Fritsche-Neto, Universidade de São Paulo - USP/ Escola Superior de Agricultura "Luiz de Queiroz" - ESALQ/Departamento de Genetica; Jeffrey B. Endelman, University of Wisconsin–Madison/Dep. Horticulture. |
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Título: |
Expected Genotype Quality and Diploidized Marker Data from Genotyping-by-Sequencing of Urocholoa spp. Tetraploids. |
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Ano de publicação: |
2019 |
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Fonte/Imprenta: |
The Plant Genome, v. 12, n. 3, november 2019. |
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Idioma: |
Português |
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Conteúdo: |
Although genotyping-by-sequencing (GBS) is a well-established marker technology in diploids, the development of best practices for tetraploid species is a topic of current research. We determined the theoretical relationship between read depth and the phred-scaled probability of genotype misclassification conditioned on the true genotype, which we call expected genotype quality (EGQ). If the GBS method has 0.5% allelic error, then 17 reads are needed to classify simplex tetraploids as heterozygous with 95% accuracy (EGQ = 13) vs. 61 reads to determine allele dosage. We developed an R script to convert tetraploid GBS data in variant call format (VCF) into diploidized genotype calls and applied it to 267 interspecific hybrids of the tetraploid forage grass Urochloa. When reads were aligned to a mock reference genome created from GBS data of the Urochloa brizantha (Hochst. ex A. Rich.) R. D. Webster cultivar Marandu, 25,678 biallelic single nucleotide polymorphism (SNPs) were discovered, compared with ~3000 SNPs when aligning to the closest true reference genomes, Setaria viridis (L.) P. Beauv. and S. italica (L.) P. Beauv. Crossvalidation revealed that missing genotypes were imputed by the random forest method with a median accuracy of 0.85 regardless of heterozygote frequency. Using the Urochloa spp. hybrids, we illustrated how filtering samples based only on genotype quality (GQ) creates genotype bias; a depth threshold based on EGQ is also needed regardless of whether genotypes are called using a diploidized or allele dosage model. MenosAlthough genotyping-by-sequencing (GBS) is a well-established marker technology in diploids, the development of best practices for tetraploid species is a topic of current research. We determined the theoretical relationship between read depth and the phred-scaled probability of genotype misclassification conditioned on the true genotype, which we call expected genotype quality (EGQ). If the GBS method has 0.5% allelic error, then 17 reads are needed to classify simplex tetraploids as heterozygous with 95% accuracy (EGQ = 13) vs. 61 reads to determine allele dosage. We developed an R script to convert tetraploid GBS data in variant call format (VCF) into diploidized genotype calls and applied it to 267 interspecific hybrids of the tetraploid forage grass Urochloa. When reads were aligned to a mock reference genome created from GBS data of the Urochloa brizantha (Hochst. ex A. Rich.) R. D. Webster cultivar Marandu, 25,678 biallelic single nucleotide polymorphism (SNPs) were discovered, compared with ~3000 SNPs when aligning to the closest true reference genomes, Setaria viridis (L.) P. Beauv. and S. italica (L.) P. Beauv. Crossvalidation revealed that missing genotypes were imputed by the random forest method with a median accuracy of 0.85 regardless of heterozygote frequency. Using the Urochloa spp. hybrids, we illustrated how filtering samples based only on genotype quality (GQ) creates genotype bias; a depth threshold based on EGQ is also needed regardless of whether genot... Mostrar Tudo |
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Palavras-Chave: |
Although genotyping-by-sequencing; Marker technology. |
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Thesaurus NAL: |
Genotype; Hybrids; Urochloa. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/207884/1/Expected-Genotype-Quality-and-Diploidized.pdf
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Marc: |
LEADER 02355naa a2200265 a 4500
001 2117777
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008 2019 bl uuuu u00u1 u #d
100 1 $aMATIAS, F. I.
245 $aExpected Genotype Quality and Diploidized Marker Data from Genotyping-by-Sequencing of Urocholoa spp. Tetraploids.$h[electronic resource]
260 $c2019
520 $aAlthough genotyping-by-sequencing (GBS) is a well-established marker technology in diploids, the development of best practices for tetraploid species is a topic of current research. We determined the theoretical relationship between read depth and the phred-scaled probability of genotype misclassification conditioned on the true genotype, which we call expected genotype quality (EGQ). If the GBS method has 0.5% allelic error, then 17 reads are needed to classify simplex tetraploids as heterozygous with 95% accuracy (EGQ = 13) vs. 61 reads to determine allele dosage. We developed an R script to convert tetraploid GBS data in variant call format (VCF) into diploidized genotype calls and applied it to 267 interspecific hybrids of the tetraploid forage grass Urochloa. When reads were aligned to a mock reference genome created from GBS data of the Urochloa brizantha (Hochst. ex A. Rich.) R. D. Webster cultivar Marandu, 25,678 biallelic single nucleotide polymorphism (SNPs) were discovered, compared with ~3000 SNPs when aligning to the closest true reference genomes, Setaria viridis (L.) P. Beauv. and S. italica (L.) P. Beauv. Crossvalidation revealed that missing genotypes were imputed by the random forest method with a median accuracy of 0.85 regardless of heterozygote frequency. Using the Urochloa spp. hybrids, we illustrated how filtering samples based only on genotype quality (GQ) creates genotype bias; a depth threshold based on EGQ is also needed regardless of whether genotypes are called using a diploidized or allele dosage model.
650 $aGenotype
650 $aHybrids
650 $aUrochloa
653 $aAlthough genotyping-by-sequencing
653 $aMarker technology
700 1 $aMEIRELES, K. G. X.
700 1 $aNAGAMATSU, S. T.
700 1 $aBARRIOS, S. C. L.
700 1 $aVALE, C. B. do
700 1 $aCARAZZOLLE, M. F.
700 1 $aFRITSCHE-NETO, R.
700 1 $aENDELMAN, J. B.
773 $tThe Plant Genome$gv. 12, n. 3, november 2019.
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Embrapa Gado de Corte (CNPGC) |
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