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| Registros recuperados : 18 | |
| 1. |  | SANTOS, D. J.; BOISON, S. A.; UTSUNOMIYA, Y. T.; PEIXOTO, M. G. C. D.; TONHATI, H.; SÖLKNER, J.; SILVA, M. V. G. B. An approach to genomic analysis of longitudinal data using random regression In: WORLD CONGRESS ON GENETICS APPLIED TO LIVESTOCK PRODUCTION, 10., 2014, Vancouver. Proceedings... Champaign: ASAS, 2014. 3 p.| Biblioteca(s): Embrapa Gado de Leite. |
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| 2. | | GARCIA, J. F.; CARMO, A. S. DO; UTSUNOMIYA, Y. T.; NEVES, H. H. DE R.; CARVALHEIRO, R.; TASSELL, C. V.; SONSTEGARD, T. S.; SILVA, M. V. G. B. How bioinformatics enables livestock applied sciences in the genomic era. In: BRAZILIAN SYMPOSIUM ON BIOINFORMATICS, 2012, Heidelberg. Proceedings... Porto Alegre: Sociedade Brasileira e Computação, 2012.| Biblioteca(s): Embrapa Gado de Leite. |
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| 3. | | UTSUNOMIYA, Y. T.; MILANESI, M.; FORTES, M. R. S.; PORTO?NETO, L. R.; UTSUNOMIYA, A. T. H.; SILVA, M. V. G. B.; GARCIA, J. F.; AJMONE-MARSAN, P. Genomic clues of the evolutionary history of Bos indicus cattle. Animal Genetics, v. 50, n. 6, p. 557-568, 2019.| Biblioteca(s): Embrapa Gado de Leite. |
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| 4. | | PORTO NETO, L. R.; SONSTEGARD, T. S.; LIU, G.; BICKHART, D.; GONDRO, C.; SILVA, M. V. G. B.; UTSUNOMIYA, Y. T.; GARCIA, J. F.; VAN TASSELL, C. P. Genomic divergence of indicine and taurine cattle identified through high-density SNP gebotyping. In: ADSA-ASAS ANNUAL MEETINGS, 2013, Indianápolis, Indiana. Abstracts... Indianápolis: [s.n.], 2013.| Biblioteca(s): Embrapa Gado de Leite. |
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| 5. | | BOISON, S. A.; NEVES, H. H. R.; O'BRIEN, A. M. P.; UTSUNOMIYA, Y. T.; CARVALHEIRO, R.; SILVA, M. V. G. B.; SÖLKNER, J.; GARCIA, J. F. Imputation of non-genotyped individuals using genotyped progeny in Nellore, a Bos indicus cattle breed. Livestock Science, v. 166, p. 176-189, 2014.| Biblioteca(s): Embrapa Gado de Leite. |
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| 6. | | O'BRIEN, A. M. P.; MÉSZÁROS, G.; UTSUNOMIYA, Y. T.; SONSTEGARD, T. S.; GARCIA, J. F.; TASSEL, C. P. V.; CARVALHEIRO, R.; SILVA, M. V. G. B.; SÖLKNER, J. Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions. Livestock Science, v. 166, p. 121-132, 2014.| Biblioteca(s): Embrapa Gado de Leite. |
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| 7. | | O'BRIEN, A. M. P.; UTSUNOMIYA, Y. T.; MÉSZÁROS, G.; BICKHART, D. M.; LIU, G. E.; TASSEL, C. P. V.; SONSTEGARD, T. S.; SILVA, M. V. G. B.; GARCIA, J. F.; SÖLKNER, J. Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle. Genetics Selection Evolution, v. 46, n. 19, 2014. 14 p.| Biblioteca(s): Embrapa Gado de Leite. |
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| 8. | | MACHADO, M. A.; UTSUNOMIYA, A. T. H.; BOISON, S. A.; SANTOS, D. J. A. dos; UTSUNOMIYA, Y. T.; FONSECA, R. da; SÖLKNER, J.; GARCIA, J. F.; VERNEQUE, R. da S.; SILVA, M. V. G. B. Genome Wide Association Study for Calving Interval in Gyr Dairy Cattle. In: WORLD CONGRESS OF GENETICS APPLIED TO LIVESTOCK PRODUCTION, 10., 2014, Vancouver. Proceedings... Champaign: American Society of Animal Science, 2014. 3 p.| Biblioteca(s): Embrapa Gado de Leite. |
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| 9. | | UTSUNOMIYA, A. T. H.; BOISON, S. A.; SANTOS, D. J. A. dos; UTSUNOMIYA, Y. T.; MACHADO, M. A.; VERNEQUE, R. da S.; SÖLKNER, J.; GARCIA, J. F.; FONSECA, R. da; SILVA, M. V. G. B. Genome Wide Scan for Age at First Calving in Gyr Dairy Cattle. In: WORLD CONGRESS OF GENETICS APPLIED TO LIVESTOCK PRODUCTION, 10., 2014, Vancouver. Proceedings... Champaign: American Society of Animal Science, 2014. 3 p.| Biblioteca(s): Embrapa Gado de Leite. |
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| 10. | | PORTO-NETO, L. R.; SONSTEGARD, T. S.; LIU, G. E.; BICKHART, D. M.; SILVA, M. V. G. B.; MACHADO, M. A.; UTSUNOMIYA, Y. T.; GARCIA, J. F.; GONDRO, C.; VAN TASSELL, C. P. Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping. BMC Genomics, v. 14, article 876, 2013. Disponível em: http://www.biomedcentral.com/1471-2164/14/876| Biblioteca(s): Embrapa Gado de Leite. |
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| 11. | | UTSUNOMIYA, A. T. H.; SANTOS, D. J. A.; BOISON, S. A.; UTSUNOMIYA, Y. T.; MILANESI, M.; BICKHART, D. M.; AJMONE-MARSAN, P.; SOLKNER, J.; GARCIA, J. F.; FONSECA, R. da; SILVA, M. V. G. B. Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan. BMC Genomics, v. 17, article 705, 2016.| Biblioteca(s): Embrapa Gado de Leite. |
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| 12. | | NEVES, H. H.; CARVALHEIRO, R.; O'BRIEN, A. M.; UTSUNOMIYA, Y. T.; CARMO, A. S. do; SCHENKEL, F. S.; SÖLKNER, J.; MCEWAN, J. C.; VAN TASSELL, C. P.; COLE, J. B.; SILVA, M. V. G. B.; QUEIROZ, S. A.; SONSTEGARD, T. S.; GARCIA, J. F. Accuracy of genomic predictions in Bos indicus (Nellore) cattle. Genetics Selection Evolution, v. 46, article 17, 2014.| Biblioteca(s): Embrapa Gado de Leite. |
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| 13. | | BOISON, S. A.; UTSUNOMIYA, A. T. H.; SANTOS, D. J. A.; NEVES, H. H. R.; CARVALHEIRO, R.; MÉSZÁROS, G.; UTSUNOMIYA, Y. T.; CARMO, A. S. do; VERNEQUE, R. da S.; MACHADO, M. A.; PANETTO, J. C. do C.; GARCIA, J. F.; SÖLKNER, J.; SILVA, M. V. G. B. Accuracy of genomic predictions in Gyr (Bos indicus) dairy cattle. Journal of Dairy Science, v. 100, n. 7, p. 5479-5490, 2017.| Biblioteca(s): Embrapa Gado de Leite. |
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| 14. | | ZAVAREZ, L. B.; UTSUNOMIYA, Y. T.; CARMO, A. S.; NEVES, H. H.; CARVALHEIRO, R.; FERENCAKOVIC, M.; O'BRIEN, A. M. P.; CURIK, I.; COLE, J. B.; TASSELL, C. P. V.; SILVA, M. V. G. B.; SONSTEGARD, T. S.; SÖLKNER, J.; GARCIA, J. F. Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes. Frontiers in Genetics, v. 6, n. 5, p. 286-293, 2015.| Biblioteca(s): Embrapa Gado de Leite. |
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| 15. | | UTSUNOMIYA, Y. T.; CARMO, A. S. do; CARVALHEIRO, R.; NEVES, H. H. R.; MATOS, M. C.; ZAVAREZ, L. B.; O'BRIEN, A. M. P.; SÖLKNER, J.; McEWAN, J. C.; COLE, J. B.; TASSEL, C. P. V.; SCHENKEL, F. S.; SILVA, M. V. G. B.; PORTO NETO, L. R.; SONSTEGARD, T. S.; GARCIA, J. F. Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height. BMC Genetics, London, v. 14, article 52, 2013.| Biblioteca(s): Embrapa Gado de Leite. |
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| 16. | | UTSUNOMIYA, Y. T.; CARMO, A. S.; NEVES, H. H. R.; CARVALHEIRO, R.; MATOS, M. C.; ZAVAREZ, L. B.; ITO, P. K. R. K.; O'BRIEN, A. M. P.; SOLKNER, J.; PORTO-NETO, L. R.; SCHENKEL, F. S.; McEWAN, J.; COLE, J. B.; SILVA, M. V. G. B.; VAN TASSELL, C. P.; SONSTEGARD, T. S.; GARCIA, J. F. Genome-wide mapping of loci explaining variance in scrotal circumference in Nellore Cattle. Plos One v. 9, n. 2, p. 1-9, 2014.| Biblioteca(s): Embrapa Gado de Leite. |
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| 17. | | O'BRIEN, A. M. P.; HÖLLER, D.; BOISON, S. A.; MILANESI, M.; BOMBA, L.; UTSUNOMIYA, Y. T.; CARVALHEIRO, R.; NEVES, H. H. R.; SILVA, M. V. G. B.; VAN TASSEL, C. P.; SOSTENGARD, T. S.; MÉSZÁROS, G.; AJMONE-MARSAN, P.; GARCIA, J. F.; SÖLKNER, J. Low levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations. Genetics Selection Evolution, v. 47, article 31, 2015.| Biblioteca(s): Embrapa Gado de Leite. |
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| 18. | | SÖLKNER, J.; PEREZ O'BRIEN, A. M.; HÖLLER, D.; BOISON, S. A.; MILANESI, M.; BOMBA, L.; UTSUNOMIYA, Y. T.; CARVALHEIRO, R.; NEVES, H. H. R.; SILVA, M. V. G. B.; VAN TASSEL, C. P.; SOSTENGARD, T. S.; MÉSZÁROS, G.; AJMONE-MARSAN, P.; GARCIA, J. F. Zebuines kerngenom und taurine Mitochondrien: admixtur von Nelore, der größten brasilianischen rinderrasse. Nova Acta Leopoldina, NF 119, n. 404, p. 69-75, 2016.| Biblioteca(s): Embrapa Gado de Leite. |
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| Registros recuperados : 18 | |
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 | Acesso ao texto completo restrito à biblioteca da Embrapa Gado de Leite. Para informações adicionais entre em contato com cnpgl.biblioteca@embrapa.br. |
Registro Completo
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Biblioteca(s): |
Embrapa Gado de Leite. |
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Data corrente: |
07/12/2016 |
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Data da última atualização: |
06/02/2024 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
A - 1 |
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Autoria: |
UTSUNOMIYA, A. T. H.; SANTOS, D. J. A.; BOISON, S. A.; UTSUNOMIYA, Y. T.; MILANESI, M.; BICKHART, D. M.; AJMONE-MARSAN, P.; SOLKNER, J.; GARCIA, J. F.; FONSECA, R. da; SILVA, M. V. G. B. |
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Afiliação: |
Adam T. H. Utsunomiya, UNESP; Daniel J. A. Santos, UNESP; Solomon A. Boison, Nofima, Ås, Norway; Yuri T. Utsunomiya, UNESP; Marco Milanesi, UNESP; Derek M. Bickhart, ARS, USDA, Beltsville; Paolo Ajmone-Marsan, Università Cattolica del Sacro Cuore, Piacenza, Italy; Johann Sölkner, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria; José F. Garcia, UNESP / IAEA; Ricardo da Fonseca, UNESP; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL. |
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Título: |
Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan. |
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Ano de publicação: |
2016 |
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Fonte/Imprenta: |
BMC Genomics, v. 17, article 705, 2016. |
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DOI: |
https://doi.org/10.1186/s12864-016-3049-8 |
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Idioma: |
Inglês |
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Conteúdo: |
Background- Misassembly signatures, created by shuffling the order of sequences while assembling a genome, can be detected by the unexpected behavior of marker linkage disequilibrium (LD) decay. We developed a heuristic process to identify misassembly signatures, applied it to the bovine reference genome assembly (UMDv3.1) and presented the consequences of misassemblies in two case studies. Results -We identified 2,906 single nucleotide polymorphism (SNP) markers presenting unexpected LD decay behavior in 626 putative misassembled contigs, which comprised less than 1 % of the whole genome. Although this represents a small fraction of the reference sequence, these poorly assembled segments can lead to severe implications to local genome context. For instance, we showed that one of the misassembled regions mapped to the POLL locus, which affected the annotation of positional candidate genes in a GWAS case study for polledness in Nellore (Bos indicus beef cattle). Additionally, we found that poorly performing markers in imputation mapped to putative misassembled regions, and that correction of marker positions based on LD was capable to recover imputation accuracy. Conclusions - This heuristic approach can be useful to cross validate reference assemblies and to filter out markers located at low confidence genomic regions before conducting downstream analyses. |
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Palavras-Chave: |
GWAS; Imputation; Misassembly. |
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Thesagro: |
Bos Indicus; Bos Taurus. |
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Thesaurus NAL: |
Genome; linkage disequilibrium. |
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Categoria do assunto: |
L Ciência Animal e Produtos de Origem Animal |
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Marc: |
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001 2058210
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008 2016 bl uuuu u00u1 u #d
024 7 $ahttps://doi.org/10.1186/s12864-016-3049-8$2DOI
100 1 $aUTSUNOMIYA, A. T. H.
245 $aRevealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan.$h[electronic resource]
260 $c2016
520 $aBackground- Misassembly signatures, created by shuffling the order of sequences while assembling a genome, can be detected by the unexpected behavior of marker linkage disequilibrium (LD) decay. We developed a heuristic process to identify misassembly signatures, applied it to the bovine reference genome assembly (UMDv3.1) and presented the consequences of misassemblies in two case studies. Results -We identified 2,906 single nucleotide polymorphism (SNP) markers presenting unexpected LD decay behavior in 626 putative misassembled contigs, which comprised less than 1 % of the whole genome. Although this represents a small fraction of the reference sequence, these poorly assembled segments can lead to severe implications to local genome context. For instance, we showed that one of the misassembled regions mapped to the POLL locus, which affected the annotation of positional candidate genes in a GWAS case study for polledness in Nellore (Bos indicus beef cattle). Additionally, we found that poorly performing markers in imputation mapped to putative misassembled regions, and that correction of marker positions based on LD was capable to recover imputation accuracy. Conclusions - This heuristic approach can be useful to cross validate reference assemblies and to filter out markers located at low confidence genomic regions before conducting downstream analyses.
650 $aGenome
650 $alinkage disequilibrium
650 $aBos Indicus
650 $aBos Taurus
653 $aGWAS
653 $aImputation
653 $aMisassembly
700 1 $aSANTOS, D. J. A.
700 1 $aBOISON, S. A.
700 1 $aUTSUNOMIYA, Y. T.
700 1 $aMILANESI, M.
700 1 $aBICKHART, D. M.
700 1 $aAJMONE-MARSAN, P.
700 1 $aSOLKNER, J.
700 1 $aGARCIA, J. F.
700 1 $aFONSECA, R. da
700 1 $aSILVA, M. V. G. B.
773 $tBMC Genomics$gv. 17, article 705, 2016.
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