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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. |
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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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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: |
LEADER 02353naa a2200337 a 4500
001 2058210
005 2024-02-06
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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Registro original: |
Embrapa Gado de Leite (CNPGL) |
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Registro Completo
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Biblioteca(s): |
Embrapa Meio-Norte. |
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Data corrente: |
14/06/2021 |
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Data da última atualização: |
10/08/2021 |
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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: |
NOBILE, F. O. de; HURTADO, A. C.; PRADO, R. de M.; SOUZA, H. A. de; ANUNCIAÇÃO, M. G.; PALARETT, L. F.; DEZEM, L. A. S. N. |
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Afiliação: |
FABIO OLIVIERI DE NOBILE, University Center of the Educational Foundation of Barretos/ UNESP; ALEXANDER CALERO HURTADO, FCAV/UNESP; RENATO DE MELLO PRADO, FCAV/UNESP; HENRIQUE ANTUNES DE SOUZA, CPAMN; MARIA GABRIELA ANUNCIAÇÃO, University Center of the Educational Foundation of Barretos/ UNESP; LUIZ FABIANO PALARETT, FCAV/UNESP; LETICIA ANE SIZUKI NOCITI DEZEM, University Center of the Educational Foundation of Barretos/ UNESP. |
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Título: |
A Novel Technology for Processing Urban Waste Compost as a Fast-Releasing Nitrogen Source to Improve Soil Properties and Broccoli and Lettuce Production. |
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Ano de publicação: |
2021 |
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Fonte/Imprenta: |
Waste and Biomass Valorization, Mar. 2021. |
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DOI: |
https://doi.org/10.1007/s12649-021-01415-z |
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Idioma: |
Inglês |
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Notas: |
Published online: 20 March 2021. |
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Conteúdo: |
This study evaluated nitrogen (N) mineralization dynamics in three soils after the addition of heat-treated urban waste amendments or urban waste compost (UWC). The effects of UWC and urea on soil properties and broccoli and lettuce production were compared. |
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Palavras-Chave: |
Processamento de composto; Resíduos. |
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Thesagro: |
Hortaliça; Produtividade. |
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Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/223750/1/Nobile2021-Article-ANovelTechnologyForProcessingU.pdf
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Marc: |
LEADER 01139naa a2200265 a 4500
001 2132291
005 2021-08-10
008 2021 bl uuuu u00u1 u #d
024 7 $ahttps://doi.org/10.1007/s12649-021-01415-z$2DOI
100 1 $aNOBILE, F. O. de
245 $aA Novel Technology for Processing Urban Waste Compost as a Fast-Releasing Nitrogen Source to Improve Soil Properties and Broccoli and Lettuce Production.$h[electronic resource]
260 $c2021
500 $aPublished online: 20 March 2021.
520 $aThis study evaluated nitrogen (N) mineralization dynamics in three soils after the addition of heat-treated urban waste amendments or urban waste compost (UWC). The effects of UWC and urea on soil properties and broccoli and lettuce production were compared.
650 $aHortaliça
650 $aProdutividade
653 $aProcessamento de composto
653 $aResíduos
700 1 $aHURTADO, A. C.
700 1 $aPRADO, R. de M.
700 1 $aSOUZA, H. A. de
700 1 $aANUNCIAÇÃO, M. G.
700 1 $aPALARETT, L. F.
700 1 $aDEZEM, L. A. S. N.
773 $tWaste and Biomass Valorization, Mar. 2021.
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