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Registro Completo |
Biblioteca(s): |
Embrapa Agricultura Digital; Embrapa Gado de Corte; Embrapa Recursos Genéticos e Biotecnologia. |
Data corrente: |
26/11/2015 |
Data da última atualização: |
29/03/2016 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
Autoria: |
SILVA, J. M. da; GIACHETTO, P. F.; SILVA, L. O. C. da; CINTRA, L. C.; PAIVA, S. R.; CAETANO, A. R.; YAMAGISHI, M. E. B. |
Afiliação: |
JOAQUIM MANOEL DA SILVA, Faculdade de Ciências Agrárias, Biológicas e Sociais Aplicadas, Universidade do Estado de Mato Grosso (UNEMAT), Nova Xavantina, Mato Grosso, Bra; POLIANA FERNANDA GIACHETTO, CNPTIA; LUIZ OTAVIO CAMPOS DA SILVA, CNPGC; LEANDRO CARRIJO CINTRA, CNPTIA; SAMUEL REZENDE PAIVA, SRI; ALEXANDRE RODRIGUES CAETANO, CENARGEN; MICHEL EDUARDO BELEZA YAMAGISHI, CNPTIA. |
Título: |
Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle. |
Ano de publicação: |
2015 |
Fonte/Imprenta: |
PLoS ONE, v. 10, n. 8, p. 1-18, 2015 |
Idioma: |
Inglês Português |
Conteúdo: |
High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus) samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production. |
Palavras-Chave: |
Genotypes; Nelore; Polimorfismo de nucleotídeo único; Sequenciamento de DNA. |
Thesagro: |
Bos Indicus; Gado de corte. |
Thesaurus Nal: |
Cattle; Sequence analysis; Single nucleotide polymorphism. |
Categoria do assunto: |
-- |
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/134042/1/journal.pone.0136035.pdf
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/137040/1/Genomic-variants-Silva.pdf
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Marc: |
LEADER 02316naa a2200301 a 4500 001 2029638 005 2016-03-29 008 2015 bl uuuu u00u1 u #d 100 1 $aSILVA, J. M. da 245 $aGenomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.$h[electronic resource] 260 $c2015 520 $aHigh density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus) samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production. 650 $aCattle 650 $aSequence analysis 650 $aSingle nucleotide polymorphism 650 $aBos Indicus 650 $aGado de corte 653 $aGenotypes 653 $aNelore 653 $aPolimorfismo de nucleotídeo único 653 $aSequenciamento de DNA 700 1 $aGIACHETTO, P. F. 700 1 $aSILVA, L. O. C. da 700 1 $aCINTRA, L. C. 700 1 $aPAIVA, S. R. 700 1 $aCAETANO, A. R. 700 1 $aYAMAGISHI, M. E. B. 773 $tPLoS ONE$gv. 10, n. 8, p. 1-18, 2015
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Embrapa Gado de Corte (CNPGC) |
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1. | | MAYORGA, L. F. S. P.; BHERING, R. C. C.; MEDEIROS, L. C. C.; SILVA, E. L. F.; NÓBREGA, Y. C.; RANGEL, M. C. V.; FONSECA, L. A.; ROSSI JUNIOR, J. L. Valores hematológicos e bioquímicos de pinguins-de-Magalhães em reabilitação no Espírito santo, Sudeste do Brasil. Pesquisa Veterinária Brasileira, Brasília, DF, v. 36 (supl. 1), p. 58-68, jun. 2016.Biblioteca(s): Embrapa Unidades Centrais. |
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