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 | Acesso ao texto completo restrito à biblioteca da Embrapa Recursos Genéticos e Biotecnologia. Para informações adicionais entre em contato com cenargen.biblioteca@embrapa.br. |
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Biblioteca(s): |
Embrapa Recursos Genéticos e Biotecnologia. |
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Data corrente: |
19/02/2013 |
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Data da última atualização: |
06/03/2023 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
PETROLI, C. D.; SANSALONI, C. P; CARLING, J.; STEANE, D. A.; VAILLANCOURT, R. E.; MYBURG, A. M.; SILVA JUNIOR, O. B. da; PAPPAS JUNIOR, G. J.; KILIAN, A.; GRATTAPAGLIA, D. |
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Afiliação: |
CESAR D. PETROLI, UnB; CAROLINA P. SANSALONI, UnB; JASON CARLING, Diversity Arrays Technology Pty Ltd., Yarralumla, Australia; DOROTHY A. STEANE, University of Tasmania, Hobart, Tasmania, Australia; RENE E. VAILLANCOURT, University of Tasmania, Hobart, Tasmania, Australia; ALEXANDER A. MYBURG, University of Pretoria, Pretoria, South Africa; ORZENIL BONFIM DA SILVA JUNIOR, CENARGEN; GEORGIOS JOANNIS PAPPAS JUNIOR, CENARGEN; ANDRZEJ KILIAN, Diversity Arrays Technology Pty Ltd., Yarralumla, Australia; DARIO GRATTAPAGLIA, CENARGEN. |
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Título: |
Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome. |
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Ano de publicação: |
2012 |
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Fonte/Imprenta: |
PLoS ONE, v. 7, n. 9, set. 2012. |
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Idioma: |
Inglês |
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Conteúdo: |
Diversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference genome is yet available to allow such detailed characterization. MenosDiversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in pla... Mostrar Tudo |
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Palavras-Chave: |
Caracterização genómica; Dart genotyping; Genoma do Eucalipto; Microsatellite genotyping. |
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Thesagro: |
Genoma. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 02933naa a2200289 a 4500
001 1949877
005 2023-03-06
008 2012 bl uuuu u00u1 u #d
100 1 $aPETROLI, C. D.
245 $aGenomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome.$h[electronic resource]
260 $c2012
520 $aDiversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference genome is yet available to allow such detailed characterization.
650 $aGenoma
653 $aCaracterização genómica
653 $aDart genotyping
653 $aGenoma do Eucalipto
653 $aMicrosatellite genotyping
700 1 $aSANSALONI, C. P
700 1 $aCARLING, J.
700 1 $aSTEANE, D. A.
700 1 $aVAILLANCOURT, R. E.
700 1 $aMYBURG, A. M.
700 1 $aSILVA JUNIOR, O. B. da
700 1 $aPAPPAS JUNIOR, G. J.
700 1 $aKILIAN, A.
700 1 $aGRATTAPAGLIA, D.
773 $tPLoS ONE$gv. 7, n. 9, set. 2012.
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Embrapa Recursos Genéticos e Biotecnologia (CENARGEN) |
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Registro Completo
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Biblioteca(s): |
Embrapa Soja. |
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Data corrente: |
11/02/2009 |
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Data da última atualização: |
25/11/2009 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
SOSA-GÓMEZ, D. R.; BINNECK, E.; MARIN, S. R. R. |
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Afiliação: |
Daniel Ricardo Sosa Gómez, CNPSo; Eliseu Binneck, CNPSo; Silvana Regina Rockenbach Marin, CNPSo. |
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Título: |
New PCR method to study the intergenic spacer (IGS) region of Nomuraea rileyi (Farlow) Samson. |
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Ano de publicação: |
2008 |
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Fonte/Imprenta: |
In: ANNUAL MEETING OF THE SOCIETY FOR INVERTEBRATE PATHOLOGY, 41.; INTERNATIONAL CONFERENCE ON BACILLUS THURINGIENSIS, 9., 2008, Warwick. Abstracts... Warwick: Society Invertebrate Pathology, 2008 |
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Idioma: |
Inglês |
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Conteúdo: |
The variability in the IGS region of the rDNA gene complex has proven useful in the development of PCR primers for strain identification. However, the lack of information on this region in Nomuraea rileyi ha precluded the development of specific primers for PCR amplification. Also, due to the high variability in this region, amplification is not possible with universal primers. Thus, to obtain sequences of the IGS region a new approach was used, a combination of IGS primer with 10-mer oligonucleotides (OD11 or E04, Operon Technologies) were used. The amplification products were visualized by agarose gel electrophoresis. DNA bands were selected for comparison between IGS-10 mer primer product amplification and DNA bands produced by 10-mer amplification. When DNA products were absent in the RAPO amplification and present in the combination IGS-10 mer amplification, these products were gel-purified, ligated into the plasmid vector TOPO TA (lnvitrogen), and amplified in DH10 B Escherichia coli cells. The DNA obtained from positive clones were subjected to Sanger sequencing. The obtained sequences ranged from 681 to 1,025 bases. Comparisons among isolates obtained from the same geographic region suggest that this technique could be used to develop strain specific primers for Nomuraea rileyi. |
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Thesagro: |
Entomologia; Nomuraea Rileyi. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 01951naa a2200169 a 4500
001 1471519
005 2009-11-25
008 2008 bl --- 0-- u #d
100 1 $aSOSA-GÓMEZ, D. R.
245 $aNew PCR method to study the intergenic spacer (IGS) region of Nomuraea rileyi (Farlow) Samson.
260 $c2008
520 $aThe variability in the IGS region of the rDNA gene complex has proven useful in the development of PCR primers for strain identification. However, the lack of information on this region in Nomuraea rileyi ha precluded the development of specific primers for PCR amplification. Also, due to the high variability in this region, amplification is not possible with universal primers. Thus, to obtain sequences of the IGS region a new approach was used, a combination of IGS primer with 10-mer oligonucleotides (OD11 or E04, Operon Technologies) were used. The amplification products were visualized by agarose gel electrophoresis. DNA bands were selected for comparison between IGS-10 mer primer product amplification and DNA bands produced by 10-mer amplification. When DNA products were absent in the RAPO amplification and present in the combination IGS-10 mer amplification, these products were gel-purified, ligated into the plasmid vector TOPO TA (lnvitrogen), and amplified in DH10 B Escherichia coli cells. The DNA obtained from positive clones were subjected to Sanger sequencing. The obtained sequences ranged from 681 to 1,025 bases. Comparisons among isolates obtained from the same geographic region suggest that this technique could be used to develop strain specific primers for Nomuraea rileyi.
650 $aEntomologia
650 $aNomuraea Rileyi
700 1 $aBINNECK, E.
700 1 $aMARIN, S. R. R.
773 $tIn: ANNUAL MEETING OF THE SOCIETY FOR INVERTEBRATE PATHOLOGY, 41.; INTERNATIONAL CONFERENCE ON BACILLUS THURINGIENSIS, 9., 2008, Warwick. Abstracts... Warwick: Society Invertebrate Pathology, 2008
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Embrapa Soja (CNPSO) |
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