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| Registros recuperados : 94 | |
| 24. |  | ALENCAR; SILVA JUNIOR, O. B. da; TOGAWA, R. C.; COSTA, M.; REVERS, L. F.; PAPPAS JUNIOR, G. J. SNP discovery in apple cultivars using next generation sequencing. BMC Proceedings, v. 5, Suppl 7,p. P42, 2011. Edição dos resumos do IUFRO Tree Biotechnology Conference 2011: From Genomes to Integration, 2011, Arraial d Ajuda, Bahia.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 25. | | SILVA, P. I. T.; SILVA JUNIOR, O. B. da; RESENDE, L. V.; SOUSA, V. A. de; AGUIAR, A. V. de; GRATTAPAGLIA, D. A 3K Axiom SNP array from a transcriptomewide SNP resource sheds new light on the genetic diversity and structure of the iconic subtropical conifer tree Araucaria angustifolia (Bert.) Kuntze. PLoS ONE, v. 15, n. 8, e0230404, 2020.| Biblioteca(s): Embrapa Florestas; Embrapa Recursos Genéticos e Biotecnologia. |
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| 26. | | MARTINS, A. M.; SILVA JUNIOR, O. B. da; NOVAES, E.; PAPPAS, M. de C. R.; FARIA, D. A. de; SCHMUTZ, J.; GRATTAPAGLIA, D.; PAPPAS JUNIOR, G. J. Allelic BAC sequencing in the highly heterozygous Eucalyptus genome reveals microcollinearity with variable patterns of haplotype diversity due to the movement of transposons. In: IUFRO TREE BIOTECHNOLOGY CONFERENCE, 2009, Whislter. Abstracts. [S.l.]: IUFRO, 2009. p. 51| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 27. | | SILVA JUNIOR, O. B. da; TOGAWA, R. C.; NOVAES, E.; FARIA, D. A. de; PAPPAS JUNIOR, G. J.; MATIAS, K.; GRATTAPAGLIA, D. Assessment of predicted assay functionality of Eucalyptus SNP derived from large interspecific collections of ESTs. In: IUFRO TREE BIOTECHNOLOGY CONFERENCE, 2009, Whislter. Abstracts. [S.l.]: IUFRO, 2009. p-52| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 28. | | LIMA, B. M.; SILVA JUNIOR, O. B. da; FARIA, D. A.; MAMANI, E. M. C.; PAPPAS JUNIOR, G. J.; GRATTAPAGLIA, D. Assessment of SNPs for linkage mapping in Eucalyptus: construction of a consensus SNP/microsatellite map from two unrelated pedigrees. BMC Proceedings, v. 5, suppl, P31, 2012. (Open access) Edição do Proceedings IUFRO Tree Biotechnology Conference, Arraial d?Ajuda, 2011.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 29. | | PESSOA FILHO, M. A. C. de P.; SILVA, P. I. T.; RESENDE, L. V.; VIEIRA, E. A.; FALEIRO, F. G.; GRATTAPAGLIA, D.; SILVA JUNIOR, O. B. da. Application of the Axiom 3K SNP genotyping array in cassava breeding and genetics. In: PLANT AND ANIMAL GENOME CONFERENCE, 26., 2018, San Diego. Proceedings... Jersey City, NJ: Scherago International, 2018. PAG XXVI| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 30. | | PESSOA FILHO, M. A. C. de P.; SILVA, P. I. T.; RESENDE, L. V.; VIEIRA, E. A.; FALEIRO, F. G.; GRATTAPAGLIA, D.; SILVA JUNIOR, O. B. da. Application of the Axiom 3K SNP genotyping array in cassava breeding and genetics. In: PLANT AND ANIMAL GENOME CONFERENCE, 26., 2018, San Diego. Proceedings... Jersey City, NJ: Scherago International, 2018. PAG XXVI| Biblioteca(s): Embrapa Cerrados. |
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| 31. | | RESENDE, R. T.; TANNO, P.; SILVA JUNIOR, O. B. da; AGUIAR, A. V. de; SOUSA, V. A. de; SEBBENN, A.; GRATTAPAGLIA, D. Genetic analysis of growth curves of individual trees and country-wide provenances of Araucaria angustifolia shows huge potential for enhanced domestication, breeding and conservation of this iconic Brazilian conifer. Pesquisa Florestal Brasileira, Colombo, v. 39, (nesp), e201902043, 2019. p. 48. Edição especial dos resumos do IUFRO World Congress, 25., 2019, Curitiba.| Biblioteca(s): Embrapa Florestas; Embrapa Recursos Genéticos e Biotecnologia. |
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| 32. | | SILVA JUNIOR, O. B. da; ROSADO, T. B.; LAVIOLA, B. G.; PAPPAS, M. de C. R.; PAPPAS JUNIOR, G. J.; GRATTAPAGLIA, D. Genome-wide SNP discovery from a pooled sample of accessions of the biofuel plant Jatropha curcas based on whole-transcriptome illumina resequencing. In: IUFRO TREE BIOTECHNOLOGY CONFERENCE, 2011, Arraial D'Ajuda, Brazil. From genomes do integration and delivery: extended abstracts proceedings. Brasília, DF: Embrapa, 2011. p. 151-152.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 33. | | SILVA JUNIOR, O. B. da; ROSADO, T. B.; LAVIOLA, B. G.; PAPPAS, M. de C. R.; PAPPAS JUNIOR, G. J.; GRATTAPAGLIA, D. Genome-wide SNP discovery from a pooled sample of accessions of the biofuel plant Jatropha curcas based on whole-transcriptome illumina resequencing. In: IUFRO TREE BIOTECHNOLOGY CONFERENCE, 2011, Arraial D'Ajuda, Brazil. From genomes do integration and delivery: extended abstracts proceedings. Brasília, DF: Embrapa, 2011. p. 151-152.| Biblioteca(s): Embrapa Agroenergia. |
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| 34. | | RESENDE, R. T.; PIEPHO,H.-P.; ROSA, G. J. M.; SILVA JUNIOR, O. B. da; SILVA, F. F. e; RESENDE, M. D. V. de; GRATTAPAGLIA, D. Enviromics in breeding: applications and perspectives on envirotypic-assisted selection. Theoretical and Applied Genetics, v. 134, n. 1, 2021. p. 95-112.| Biblioteca(s): Embrapa Café; Embrapa Recursos Genéticos e Biotecnologia. |
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| 35. | | PESSOA FILHO, M. A. C. de P.; SOUZA SOBRINHO, F. de; FRAGOSO, R. da R.; SILVA JUNIOR, O. B. da; FERREIRA, M. E. A draft genome assembly for the forage grass Urochloa ruziziensis based on single-molecule real-time sequencing. In: BRAZILIAN BIOTECHNOLOGY CONGRESS, 7.; BIOTECHNOLOGY IBERO-AMERICAN CONGRESS, 2., 2018, Brasília, DF. Proceedings... Brasília, DF: SBBiotec, 2018.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 36. | | PESSOA FILHO, M. A. C. de P.; SOUZA SOBRINHO, F. de; FRAGOSO, R. da R.; SILVA JUNIOR, O. B. da; FERREIRA, M. E. A draft genome assembly for the forage grass Urochloa ruziziensis based on single-molecule real-time sequencing. In: BRAZILIAN BIOTECHNOLOGY CONGRESS, 7.; BIOTECHNOLOGY IBERO-AMERICAN CONGRESS, 2., 2018, Brasília, DF. Proceedings... Brasília, DF: SBBiotec, 2018.| Biblioteca(s): Embrapa Cerrados. |
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| 37. | | SILVA JUNIOR, O. B. da; PESSOA FILHO, M. A. C. de P.; SA, M. E. L.; DEAL, R.; RAGOUSSIS, I.; GRATTAPAGLIA, D.; RECH FILHO, E. L. Coupling in-depth genome annotations with genome editing technology for harnessing genomic variation to promote precision breeding in tropical soybean. In: BRAZILIAN BIOTECHNOLOGY CONGRESS, 7.; BIOTECHNOLOGY IBERO-AMERICAN CONGRESS, 2., 2018, Brasília, DF. Proceedings... Brasília, DF: SBBiotec, 2018.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 38. | | SILVA JUNIOR, O. B. da; PESSOA FILHO, M. A. C. de P.; SA, M. E. L.; DEAL, R.; RAGOUSSIS, I.; GRATTAPAGLIA, D.; RECH FILHO, E. L. Coupling in-depth genome annotations with genome editing technology for harnessing genomic variation to promote precision breeding in tropical soybean. In: BRAZILIAN BIOTECHNOLOGY CONGRESS, 7.; BIOTECHNOLOGY IBERO-AMERICAN CONGRESS, 2., 2018, Brasília, DF. Proceedings... Brasília, DF: SBBiotec, 2018.| Biblioteca(s): Embrapa Cerrados. |
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| 39. | | SILVA JUNIOR, O. B. da; RESENDE, L. V.; VIDAL, R. F.; BORDALLO, P. N.; SILVA, P. I. T.; MELO, D. S.; TOGAWA, R. C.; GRATTAPAGLIA, D. A chromosome-scale assembly of the cashew tree genome: leveraging the combined power of PacBio, DNA-Chromatin Proximity Ligation and SNP linkage maps. In: PLANT AND ANIMAL GENOME CONFERENCE, 25., 2017, San Diego. [Abstracts...]. San Diego, CA: [s.n.], 2017. W354.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 40. | | PESSOA FILHO, M. A. C. de P.; SOUZA SOBRINHO, F. de; FRAGOSO, R. da R.; SILVA JUNIOR, O. B. da; FERREIRA, M. E. A phased diploid genome assembly for the forage grass urochloa ruziziensis based on single-molecule real-time sequencing. In: PLANT AND ANIMAL GENOME CONFERENCE, 27., 2019, San Diego. Proceedings... Livingston, NJ: Scherago, 2019 Plant and Animal Genome XXVII Conference (PAG).| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| Registros recuperados : 94 | |
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Registro Completo
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Biblioteca(s): |
Embrapa Florestas; Embrapa Recursos Genéticos e Biotecnologia. |
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Data corrente: |
01/09/2020 |
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Data da última atualização: |
02/09/2020 |
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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: |
SILVA, P. I. T.; SILVA JUNIOR, O. B. da; RESENDE, L. V.; SOUSA, V. A. de; AGUIAR, A. V. de; GRATTAPAGLIA, D. |
|
Afiliação: |
PEDRO ITALO T. SILVA, UNB; ORZENIL BONFIM DA SILVA JUNIOR, Cenargen; LUCILEIDE V. RESENDE; VALDERES APARECIDA DE SOUSA, CNPF; ANANDA VIRGINIA DE AGUIAR, CNPF; DARIO GRATTAPAGLIA, Cenargen. |
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Título: |
A 3K Axiom SNP array from a transcriptomewide SNP resource sheds new light on the genetic diversity and structure of the iconic subtropical conifer tree Araucaria angustifolia (Bert.) Kuntze. |
|
Ano de publicação: |
2020 |
|
Fonte/Imprenta: |
PLoS ONE, v. 15, n. 8, e0230404, 2020. |
|
DOI: |
https://doi.org/10.1371/journal. pone.0230404 |
|
Idioma: |
Inglês |
|
Conteúdo: |
High-throughput SNP genotyping has become a precondition to move to higher precision and
wider genome coverage genetic analysis of natural and breeding populations of non-model
species. We developed a 44,318 annotated SNP catalog for Araucaria angustifolia, a grandiose subtropical conifer tree, one of the only two native Brazilian gymnosperms, critically endangered due to its valuable wood and seeds. Following transcriptome assembly and annotation,
SNPs were discovered from RNA-seq and pooled RAD-seq data. From the SNP catalog, an
Axiom® SNP array with 3,038 validated SNPs was developed and used to provide a comprehensive look at the genetic diversity and structure of 15 populations across the natural range of
the species. RNA-seq was a far superior source of SNPs when compared to RAD-seq in terms
of conversion rate to polymorphic markers on the array, likely due to the more efficient complexity reduction of the huge conifer genome. By matching microsatellite and SNP data on the
same set of A. angustifolia individuals, we show that SNPs reflect more precisely the actual
genome-wide patterns of genetic diversity and structure, challenging previous microsatellitebased assessments. Moreover, SNPs corroborated the known major north-south genetic
cline, but allowed a more accurate attribution to regional versus among-population differentiation, indicating the potential to select ancestry-informative markers. The availability of a public,
user-friendly 3K SNP array for A. angustifolia and a catalog of 44,318 SNPs predicted to provide ~29,000 informative SNPs across ~20,000 loci across the genome, will allow tackling still
unsettled questions on its evolutionary history, toward a more comprehensive picture of the origin, past dynamics and future trend of the species? genetic resources. Additionally, but not less
importantly, the SNP array described, unlocks the potential to adopt genomic prediction methods to accelerate the still very timid efforts of systematic tree breeding of A. angustifolia. MenosHigh-throughput SNP genotyping has become a precondition to move to higher precision and
wider genome coverage genetic analysis of natural and breeding populations of non-model
species. We developed a 44,318 annotated SNP catalog for Araucaria angustifolia, a grandiose subtropical conifer tree, one of the only two native Brazilian gymnosperms, critically endangered due to its valuable wood and seeds. Following transcriptome assembly and annotation,
SNPs were discovered from RNA-seq and pooled RAD-seq data. From the SNP catalog, an
Axiom® SNP array with 3,038 validated SNPs was developed and used to provide a comprehensive look at the genetic diversity and structure of 15 populations across the natural range of
the species. RNA-seq was a far superior source of SNPs when compared to RAD-seq in terms
of conversion rate to polymorphic markers on the array, likely due to the more efficient complexity reduction of the huge conifer genome. By matching microsatellite and SNP data on the
same set of A. angustifolia individuals, we show that SNPs reflect more precisely the actual
genome-wide patterns of genetic diversity and structure, challenging previous microsatellitebased assessments. Moreover, SNPs corroborated the known major north-south genetic
cline, but allowed a more accurate attribution to regional versus among-population differentiation, indicating the potential to select ancestry-informative markers. The availability of a public,
user-friendly 3K SNP array for A. angustif... Mostrar Tudo |
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Thesagro: |
Araucária Angustifólia. |
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Categoria do assunto: |
-- |
|
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/215688/1/journal.pone.0230404.pdf
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Marc: |
LEADER 02778naa a2200205 a 4500
001 2124667
005 2020-09-02
008 2020 bl uuuu u00u1 u #d
024 7 $ahttps://doi.org/10.1371/journal. pone.0230404$2DOI
100 1 $aSILVA, P. I. T.
245 $aA 3K Axiom SNP array from a transcriptomewide SNP resource sheds new light on the genetic diversity and structure of the iconic subtropical conifer tree Araucaria angustifolia (Bert.) Kuntze.$h[electronic resource]
260 $c2020
520 $aHigh-throughput SNP genotyping has become a precondition to move to higher precision and wider genome coverage genetic analysis of natural and breeding populations of non-model species. We developed a 44,318 annotated SNP catalog for Araucaria angustifolia, a grandiose subtropical conifer tree, one of the only two native Brazilian gymnosperms, critically endangered due to its valuable wood and seeds. Following transcriptome assembly and annotation, SNPs were discovered from RNA-seq and pooled RAD-seq data. From the SNP catalog, an Axiom® SNP array with 3,038 validated SNPs was developed and used to provide a comprehensive look at the genetic diversity and structure of 15 populations across the natural range of the species. RNA-seq was a far superior source of SNPs when compared to RAD-seq in terms of conversion rate to polymorphic markers on the array, likely due to the more efficient complexity reduction of the huge conifer genome. By matching microsatellite and SNP data on the same set of A. angustifolia individuals, we show that SNPs reflect more precisely the actual genome-wide patterns of genetic diversity and structure, challenging previous microsatellitebased assessments. Moreover, SNPs corroborated the known major north-south genetic cline, but allowed a more accurate attribution to regional versus among-population differentiation, indicating the potential to select ancestry-informative markers. The availability of a public, user-friendly 3K SNP array for A. angustifolia and a catalog of 44,318 SNPs predicted to provide ~29,000 informative SNPs across ~20,000 loci across the genome, will allow tackling still unsettled questions on its evolutionary history, toward a more comprehensive picture of the origin, past dynamics and future trend of the species? genetic resources. Additionally, but not less importantly, the SNP array described, unlocks the potential to adopt genomic prediction methods to accelerate the still very timid efforts of systematic tree breeding of A. angustifolia.
650 $aAraucária Angustifólia
700 1 $aSILVA JUNIOR, O. B. da
700 1 $aRESENDE, L. V.
700 1 $aSOUSA, V. A. de
700 1 $aAGUIAR, A. V. de
700 1 $aGRATTAPAGLIA, D.
773 $tPLoS ONE$gv. 15, n. 8, e0230404, 2020.
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