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Registro Completo |
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Biblioteca(s): |
Embrapa Unidades Centrais. |
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Data corrente: |
16/08/2001 |
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Data da última atualização: |
27/09/2004 |
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Autoria: |
SILVEIRA JUNIOR, P.; PINHEIRO, J. E. P.; ZONTA, E. P.; GONCALVES, I. M. G. |
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Título: |
Modelo de Crescimento Sazonal em Animais Provenientes de Testes de Progenie. |
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Ano de publicação: |
1993 |
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Fonte/Imprenta: |
Pesquisa Agropecuaria Brasileira, Brasilia, v.28, n.9, p.1065-1076,set.1993 |
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Idioma: |
Português |
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Conteúdo: |
A curva de desenvolvimento ponderal de bovinos Hereford e Charolês, provenientes de testes de progenie de bovinos de corte, efetuados pelo Instituto de Pesquisas Zootecnicas "Francisco Osorio", da Secretaria da Agricultura do Estado do Rio Grande do Sul, foi ajustada pelo modelo Brody para a raiz cubica do peso com um componente periodico adicional. As estimativas preliminares dos parametros, para dar inicio ao processo iterativo, foram obtidas atraves de um metodo que e, também, apresentado. Devido a heterogeneidade de variancias dos pesos entre as pesagens, foi utilizada a transformacao raiz cubica, que, alem de homogeneizar a variancia, facilitou o tratamento teorico do modelo. |
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Palavras-Chave: |
bovinos de corte; componente periodico; modelo Brody. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/AI-SEDE/20558/1/pab11_set_93.pdf
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Marc: |
LEADER 01271naa a2200193 a 4500
001 1105470
005 2004-09-27
008 1993 bl uuuu u00u1 u #d
100 1 $aSILVEIRA JUNIOR, P.
245 $aModelo de Crescimento Sazonal em Animais Provenientes de Testes de Progenie.
260 $c1993
520 $aA curva de desenvolvimento ponderal de bovinos Hereford e Charolês, provenientes de testes de progenie de bovinos de corte, efetuados pelo Instituto de Pesquisas Zootecnicas "Francisco Osorio", da Secretaria da Agricultura do Estado do Rio Grande do Sul, foi ajustada pelo modelo Brody para a raiz cubica do peso com um componente periodico adicional. As estimativas preliminares dos parametros, para dar inicio ao processo iterativo, foram obtidas atraves de um metodo que e, também, apresentado. Devido a heterogeneidade de variancias dos pesos entre as pesagens, foi utilizada a transformacao raiz cubica, que, alem de homogeneizar a variancia, facilitou o tratamento teorico do modelo.
653 $abovinos de corte
653 $acomponente periodico
653 $amodelo Brody
700 1 $aPINHEIRO, J. E. P.
700 1 $aZONTA, E. P.
700 1 $aGONCALVES, I. M. G.
773 $tPesquisa Agropecuaria Brasileira, Brasilia$gv.28, n.9, p.1065-1076,set.1993
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Registro original: |
Embrapa Unidades Centrais (AI-SEDE) |
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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
005 2019-12-27
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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