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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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Autoria: |
SILVA, P. I. T.; SILVA JUNIOR, O. B. da; RESENDE, L. V.; SOUSA, V. A. de; AGUIAR, A. V. de; GRATTAPAGLIA, D. |
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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. |
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Ano de publicação: |
2020 |
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Fonte/Imprenta: |
PLoS ONE, v. 15, n. 8, e0230404, 2020. |
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DOI: |
https://doi.org/10.1371/journal. pone.0230404 |
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Idioma: |
Inglês |
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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: |
-- |
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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.
Download
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Registro original: |
Embrapa Florestas (CNPF) |
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| Registros recuperados : 49 | |
| 1. |  | GIORDANO, L. B.; FERRAZ, E.; RESENDE, L. V.; ARAGÃO, F. A. S.; INOUE-NAGATA, A. K. Avaliação de linhagens de tomateiro para processamento industrial visando resistência a germinivírus. Horticultura Brasileira, Brasília, v. 21, n. 2, jul. 2003. Suplemento 2. Trabalho apresentado no 43º Congresso Brasileiro de Olericultura, 2003. Publicado também como resumo em: Horticultura Brasileira, Brasília, v. 21, n. 2, p. 350, jul. 2003. Suplemento 1.| Biblioteca(s): Embrapa Hortaliças. |
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| 2. | | TANNO, P.; SILVA JUNIOR, O. B. da; RESENDE, L. V.; SOUSA, V. A. de; GRATTAPAGLIA, D. A genotyping array of 3,400 Single Nucleotide Polymorphisms (SNPs) advances the genetic analysis of the iconic tree Araucaria angustifolia, showing that the natural populations ar e more differentiated than previously reported. Pesquisa Florestal Brasileira, Colombo, v. 39, (nesp), e201902043, 2019. p. 188. Edição especial dos resumos do IUFRO World Congress, 25., 2019, Curitiba.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Florestas. |
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| 4. | | FERRAZ, E.; RESENDE, L. V.; MARANHAO, E. A. A.; FRANCA, J. G. E.; GIORDANO, L. B. Evolucao da incidencia de tospoviroses em germoplasma de tomateiro para industria, em condicoes de campo, no Submedio Sao Francisco. Horticultura Brasileira, Brasilia, v.15, 1997. Resumo 100. Suplemento.| Biblioteca(s): Embrapa Hortaliças. |
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| 5. | | GRATTAPAGLIA, D.; SILVA JUNIOR, O. B. da; RESENDE, L. V.; SILVA, P. I. T. A five-species 50K Axiom SNP microarray allows high quality genotyping of coffee, cashew, cassava, brazilian pine and eucalyptus. In: PLANT AND ANIMAL GENOME CONFERENCE, 25., 2017, San Diego. [Abstracts...]. San Diego, CA: [s.n.], 2017.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 8. | | LAMEGO, F. P.; RESENDE, L. V.; DA-SILVA, P. R.; VIDAL, R. A.; NUNES, A. L. Distância genética e geográfica entre acessos de picão-preto suscetíveis e resistentes a herbicidas inibidores da acetolactato sintase. Pesquisa Agropecuária Brasileira, Brasília, DF, v. 41, n. 6, p. 963-968, jun. 2006 Título em inglês: Genetic and geographic distance among beggar-ticks accesses susceptible and resistant to acetolactate sintase herbicide inhibitors.| Biblioteca(s): Embrapa Unidades Centrais. |
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| 11. | | FRANÇA, E. M.; SILVA, C. F. da; SILVA, E. M. R. da; RESENDE, L. V.; SAGGIN JUNIOR, O. J. Influência do preparo do solo na comunidade de fungos micorrízicos arbusculares e na glomalina em área de cultivo sucessional. In: REUNIÃO BRASILEIRA DE FERTILIDADE DO SOLO E NUTRIÇÃO DE PLANTAS, 32.; REUNIÃO BRASILEIRA SOBRE MICORRIZAS, 16.; SIMPÓSIO BRASILEIRO DE MICROBIOLOGIA DO SOLO, 14.; REUNIÃO BRASILEIRA DE BIOLOGIA DO SOLO, 11., FERTBIO 2016. Goiânia. Rumo aos novos desafios: anais. Goiânia: UFG, 2016.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agrobiologia. |
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| 12. | | COSTA, E. M. R.; ANUNCIAÇÃO FILHO, C. J.; RESENDE, L. V.; SILVA, K. J. D. e; ANDRADE, M. C. Divergência genética entre acessos de feijão-caupi através de marcadores SSR. In: CONGRESSO NACIONAL DE FEIJÃO-CAUPI, 2., 2009, Belém, PA. Da agricultura de subsistência ao agronegócio: anais. Belém, PA: Embrapa Amazônia Oriental, 2009. p. 486-490. 1 CD-ROM. Autoria: DAMASCENO-SILVA, K. J. [i.e. SILVA, K. J. D. e]| Tipo: Artigo em Anais de Congresso / Nota Técnica |
| Biblioteca(s): Embrapa Meio-Norte. |
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| 13. | | SOARES, T. N.; CHAVES, L. J.; TELLES, M. P. de C.; DINIZ-FILHO, J. A. F.; RESENDE, L. V. Distribuição espacial da variabilidade genética intrapopulacional de Dipteryx alata. Pesquisa Agropecuária Brasileira, Brasília, DF, v. 43, n. 9, p. 1151-1158, set. 2008. Título em inglês: Spatial distribution of intrapopulational genetic variability in Dipteryx alata.| Biblioteca(s): Embrapa Unidades Centrais. |
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| 14. | | AMARAL, D. O. J. do; LIMA, M. M. de A.; RESENDE, L. V.; SILVA, M. V. da. Differential gene expression, induced by salicylic acid and fusarium oxysporum f. sp. lycopersici infection, in tomato. Pesquisa Agropecuária Brasileira, v. 43, n. 8, p. 1017-1023, ago., 2008.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: Internacional - A |
| Biblioteca(s): Embrapa Algodão; Embrapa Unidades Centrais. |
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| 15. | | RIBEIRO, S. G.; BEZERRA, I. C.; REZENDE, R. O.; LIMA, M. F.; RESENDE, L. V.; AVILA, A. C. de. New tomato geminiviruses in mixed infections in Brazil. IN: INTERNATIONAL WORKSHOP ON BEMISIA AND GEMINIVIRAL DISEASES, 2., 1998, San Juan, Puerto Rico. Program & abstracts... San Juan, 1998. p.P-63.| Biblioteca(s): Embrapa Hortaliças. |
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| 16. | | SANTOS, G. C.; VON PINHO, E. V. R.; ROSA, S. D. V. F. da; RESENDE, L. V.; FARRAPO, C. L. Qualidade fisiológica de sementes de Coffea arabica L. com diferentes graus de umidade e submetidas à diferentes métodos de secagem. In: CONGRESSO BRASILEIRO DE PESQUISA CAFEEIROAS, 35., 2009, Araxá. Anais...Brasília, DF: Embrapa Café, 2009.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Café. |
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| 17. | | SILVEIRA, F. Q. de P.; ROCHA, H. G. C.; LIMA, M. F.; RESENDE, L. V.; AVILA, A. C. de. A study of the diversity of whitefly-transmited geminivirus in the "submedio" of San Francisco Valley, Brazil. Fitopatologia Brasileira, Brasilia, v.23, p.312, ago. 1998. Resumo. Suplemento.| Biblioteca(s): Embrapa Hortaliças. |
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| 20. | | RIBEIRO, S. G.; BEZERRA, I. C.; REZENDE, R. O.; LIMA, M. F.; RESENDE, L. V.; AVILA, A. C. de. Three ner geminiviruses in tomato in the State of Pernambuco. Fitopatologia Brasileira, Brasilia, v.23, p.322, ago. 1998. Resumo. Suplemento.| Biblioteca(s): Embrapa Hortaliças. |
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| Registros recuperados : 49 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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