| |
|
|
|
Registro Completo |
|
Biblioteca(s): |
Embrapa Amapá; Embrapa Amazônia Oriental; Embrapa Florestas. |
|
Data corrente: |
26/10/2001 |
|
Data da última atualização: |
12/12/2016 |
|
Tipo da produção científica: |
Artigo em Periódico Indexado |
|
Autoria: |
FARIAS NETO, J. T. de; RESENDE, M. D. V. de. |
|
Afiliação: |
JOAO TOME DE FARIAS NETO, CPATU; MARCOS DEON VILELA DE RESENDE, CNPF. |
|
Título: |
Aplicação da metodologia de modelos mistos (REML/BLUP) na estimação de componentes de variância e predição de valores genéticos em pupunheira (Bactris gasipaes). |
|
Ano de publicação: |
2001 |
|
Fonte/Imprenta: |
Revista Brasileira de Fruticultura, Jaboticabal, v. 23, n. 2, p. 320-324, ago. 2001. |
|
Descrição Física: |
il. |
|
Idioma: |
Português |
|
Conteúdo: |
O trabalho objetivou a estimacao de componentes de variancia, herdabilidade e predicao de valores geneticos para varios caracteres em teste de progenies de pupunheira, bem como a comparacao entre os procedimentos REML/BLUP e analise de variancia no processo de estimacao. |
|
Palavras-Chave: |
Componente de variancia; Espécie perene; Genetica quantitativa; Herdabilidade; Modelo linear; Modelos lineares; Predição de variável aleatória; Tamanho efetivo; Variabilidade genética; Variaveis aleatorias. |
|
Thesagro: |
Bactris Gasipaes; Método Estatístico; Pupunha; Teste de Progênie. |
|
Thesaurus Nal: |
linear models; quantitative genetics. |
|
Categoria do assunto: |
-- |
|
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/38236/1/RevistaBrasileiraFruticultura-1.pdf
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/28229/1/7974.pdf
|
|
Marc: |
LEADER 01374naa a2200337 a 4500
001 1403865
005 2016-12-12
008 2001 bl uuuu u00u1 u #d
100 1 $aFARIAS NETO, J. T. de
245 $aAplicação da metodologia de modelos mistos (REML/BLUP) na estimação de componentes de variância e predição de valores genéticos em pupunheira (Bactris gasipaes).
260 $c2001
300 $cil.
520 $aO trabalho objetivou a estimacao de componentes de variancia, herdabilidade e predicao de valores geneticos para varios caracteres em teste de progenies de pupunheira, bem como a comparacao entre os procedimentos REML/BLUP e analise de variancia no processo de estimacao.
650 $alinear models
650 $aquantitative genetics
650 $aBactris Gasipaes
650 $aMétodo Estatístico
650 $aPupunha
650 $aTeste de Progênie
653 $aComponente de variancia
653 $aEspécie perene
653 $aGenetica quantitativa
653 $aHerdabilidade
653 $aModelo linear
653 $aModelos lineares
653 $aPredição de variável aleatória
653 $aTamanho efetivo
653 $aVariabilidade genética
653 $aVariaveis aleatorias
700 1 $aRESENDE, M. D. V. de
773 $tRevista Brasileira de Fruticultura, Jaboticabal$gv. 23, n. 2, p. 320-324, ago. 2001.
Download
Esconder MarcMostrar Marc Completo |
|
Registro original: |
Embrapa Amazônia Oriental (CPATU) |
|
|
Biblioteca |
ID |
Origem |
Tipo/Formato |
Classificação |
Cutter |
Registro |
Volume |
Status |
URL |
Voltar
|
|
|
Registro Completo
|
Biblioteca(s): |
Embrapa Gado de Corte. |
|
Data corrente: |
27/12/2019 |
|
Data da última atualização: |
27/12/2019 |
|
Tipo da produção científica: |
Artigo em Periódico Indexado |
|
Circulação/Nível: |
A - 2 |
|
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. |
|
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. |
|
Título: |
Expected Genotype Quality and Diploidized Marker Data from Genotyping-by-Sequencing of Urocholoa spp. Tetraploids. |
|
Ano de publicação: |
2019 |
|
Fonte/Imprenta: |
The Plant Genome, v. 12, n. 3, november 2019. |
|
Idioma: |
Português |
|
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 |
|
Palavras-Chave: |
Although genotyping-by-sequencing; Marker technology. |
|
Thesaurus NAL: |
Genotype; Hybrids; Urochloa. |
|
Categoria do assunto: |
-- |
|
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/207884/1/Expected-Genotype-Quality-and-Diploidized.pdf
|
|
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.
Download
Esconder MarcMostrar Marc Completo |
|
Registro original: |
Embrapa Gado de Corte (CNPGC) |
|
|
Biblioteca |
ID |
Origem |
Tipo/Formato |
Classificação |
Cutter |
Registro |
Volume |
Status |
Fechar
|
| Nenhum registro encontrado para a expressão de busca informada. |
|
|
