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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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Origem |
Tipo/Formato |
Classificação |
Cutter |
Registro |
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Registro Completo
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Biblioteca(s): |
Embrapa Milho e Sorgo. |
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Data corrente: |
09/05/2018 |
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Data da última atualização: |
09/05/2018 |
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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: |
MENEZES, C. B. de; LIMA, G. M.; MARUCCI, R. C.; BERNARDINO, K. C.; SANTOS, C. V. dos; JÚLIO, M. P. M.; SCHAFFERT, R. E. |
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Afiliação: |
CICERO BESERRA DE MENEZES, CNPMS; Geisiane Matos Lima; Rosangela Cristina Marucci; Karine Costa Bernardino; Crislene Vieira dos Santos; Marcos Paulo Mingote Júlio; ROBERT EUGENE SCHAFFERT, CNPMS. |
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Título: |
Evaluation of grain sorghum hybrids for aluminum tolerance in nutrient solution. |
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Ano de publicação: |
2018 |
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Fonte/Imprenta: |
Acta Scientiarum. Agronomy, Maringá, v. 40, p. 1-6, 2018. |
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DOI: |
10.4025/actasciagron.v40i1.35304 |
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Idioma: |
Inglês |
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Conteúdo: |
Sorghum (Sorghum bicolor L. Moench) is one of the most important cereal crops in the world. In Brazil, the acreage of grain sorghum during off-season is quite expansive. Most of this area is the Cerrado, a Brazilian biome that is similar to a Savannah and is characterized by high acidity and soluble aluminum at toxic levels for plants. The aluminum acts as a limiting factor in achieving high yields. The purpose of this work was to phenotype sorghum hybrids for aluminum tolerance. Eighteen hybrids were evaluated in a nutrient solution containing {0} or {27} μM Al3+. The work was carried out in a growth chamber at the Embrapa Maize and Sorghum, from April 4 to May 30, 2014. The lines ATF 13B (susceptible) and ATF 14B (tolerant) were used as check cultivars. Based on the Net Root Growth after 120 hours (NRG120), Net Root Growth (NRG168) after 168 hours and Relative Net Root Growth after 168 hours (RNRG168), it was possible to distinguish tolerant hybrids from susceptible ones. The high aluminum saturation reduced root growth by 70%. The hybrids BRS 310 and BRS 373 were tolerant to aluminum stress under nutrient solution. The hybrid BRS 330 was clustered in an intermediate group, with an approximately 50% root growth reduction. The other hybrids were susceptible with significant root reduction. |
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Thesagro: |
Acidez do Solo; Melhoramento Vegetal; Sorghum Bicolor. |
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Categoria do assunto: |
F Plantas e Produtos de Origem Vegetal |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/176541/1/Evaluation-grain-1.pdf
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Marc: |
LEADER 02052naa a2200241 a 4500
001 2091291
005 2018-05-09
008 2018 bl uuuu u00u1 u #d
024 7 $a10.4025/actasciagron.v40i1.35304$2DOI
100 1 $aMENEZES, C. B. de
245 $aEvaluation of grain sorghum hybrids for aluminum tolerance in nutrient solution.$h[electronic resource]
260 $c2018
520 $aSorghum (Sorghum bicolor L. Moench) is one of the most important cereal crops in the world. In Brazil, the acreage of grain sorghum during off-season is quite expansive. Most of this area is the Cerrado, a Brazilian biome that is similar to a Savannah and is characterized by high acidity and soluble aluminum at toxic levels for plants. The aluminum acts as a limiting factor in achieving high yields. The purpose of this work was to phenotype sorghum hybrids for aluminum tolerance. Eighteen hybrids were evaluated in a nutrient solution containing {0} or {27} μM Al3+. The work was carried out in a growth chamber at the Embrapa Maize and Sorghum, from April 4 to May 30, 2014. The lines ATF 13B (susceptible) and ATF 14B (tolerant) were used as check cultivars. Based on the Net Root Growth after 120 hours (NRG120), Net Root Growth (NRG168) after 168 hours and Relative Net Root Growth after 168 hours (RNRG168), it was possible to distinguish tolerant hybrids from susceptible ones. The high aluminum saturation reduced root growth by 70%. The hybrids BRS 310 and BRS 373 were tolerant to aluminum stress under nutrient solution. The hybrid BRS 330 was clustered in an intermediate group, with an approximately 50% root growth reduction. The other hybrids were susceptible with significant root reduction.
650 $aAcidez do Solo
650 $aMelhoramento Vegetal
650 $aSorghum Bicolor
700 1 $aLIMA, G. M.
700 1 $aMARUCCI, R. C.
700 1 $aBERNARDINO, K. C.
700 1 $aSANTOS, C. V. dos
700 1 $aJÚLIO, M. P. M.
700 1 $aSCHAFFERT, R. E.
773 $tActa Scientiarum. Agronomy, Maringá$gv. 40, p. 1-6, 2018.
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Registro original: |
Embrapa Milho e Sorgo (CNPMS) |
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