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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
Esconder MarcMostrar Marc Completo |
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Registro original: |
Embrapa Florestas (CNPF) |
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Biblioteca |
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URL |
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| Registros recuperados : 49 | |
| 41. |  | RESENDE, L. V.; BRONDANI, R.; MELO, D. B.; TELLES, M. P. C.; BORBA, T. C. O.; SOARES, T. N.; SILVA JUNIOR, N. J. Isolamento e caracterização de regiões microssatélites em Hypostomus gymnorhyncus. In: CONGRESSO BRASILEIRO DE GENÉTICA, 54., 2008, Salvador. Resumos... Salvador: SBG, 2008. p. 93.| Biblioteca(s): Embrapa Arroz e Feijão. |
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| 42. | | TELLES, M. P. C.; RESENDE, L. V.; BRONDANI, R. P. V.; COLLEVATTI, R. G.; COSTA, M. C.; SILVA JÚNIOR, N. J. Isolation and characterization of microsatellite markers in the armored catfish Hypostomus gymnorhynchus (Loricariidae). Genetics and Molecular Research, Ribeirão Preto, v. 9, n. 3, p. 1770-1774, 2010.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 1 |
| Biblioteca(s): Embrapa Arroz e Feijão. |
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| 43. | | SOARES, T. N.; RESENDE, L. V.; MELO, D. B.; BRONDANI, R. P. V.; TELLES, M. P. C.; BORBA, T. C. O.; CHAVES, L. J. Sequenciamento "shotgun" para o desenvolvimento de marcadores SSR em Dipteryx alata Vogel. In: CONGRESSO BRASILEIRO DE GENÉTICA, 54., 2008, Salvador. Resumos... Salvador: SBG, 2008. p. 27.| Biblioteca(s): Embrapa Arroz e Feijão. |
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| 44. | | SOUZA, D. C. de; OSSANI, P. C.; COSTA, A. S.; GUERRA, T. S.; ARAÚJO, A. L.; RESENDE, F. V.; RESENDE, L. V. Selection of experimental strawberry clones for fruit appearance attributes. Pesquisa Agropecuária Brasileira, v. 56, e02560, 2021. Título em português: Seleção de clones experimentais de morangueiro quanto aos atributos de aparência do fruto.| Tipo: Artigo em Periódico Indexado |
| Biblioteca(s): Embrapa Hortaliças. |
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| 46. | | MAGNABOSCO, C. de U.; RESENDE, L. V.; TELLES, M. P. de C.; TROVO, J. B. de F.; VASCONCELLOS, B. de F. e; JOSAHKIANS, L. A.; SAINZ, R. D. Relações polimorfismo de locos STR com características de crescimento e carcaça em bovinos da raça nelore. In: REUNIÃO ANUAL DA SOCIEDADE BRASILEIRA DE ZOOTECNIA, 43., 2006, João Pessoa. Anais... João Pessoa: SBZ; UFPB, 2006. 1 CD-ROM.| Biblioteca(s): Embrapa Cerrados. |
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| 47. | | SAMARTINI, C. Q.; RESENDE, L. V.; TECHIO, V. H.; BRAZ, G. T.; SILVA, L. F. L. e; RESENDE, K. F. M. de. Número cromossômico e conteúdo de DNA nuclear em espécies do gênero Amaranthus (Amaranthaceae). Pesquisa Agropecuária Brasileira, Brasília, DF, v. 51, n. 8, p. 998-1001, ago. 2016. Notas científicas.
Título em inglês: Chromosome number and nuclear DNA content of species of the genus Amaranthus (Amaranthaceae).| Biblioteca(s): Embrapa Unidades Centrais. |
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| 48. | | GOUVEIA, F. O.; RESENDE, L. V.; MELO, D. B.; BRONDANI, R. P. V.; CHAVES, L. J.; LIMA, J. S.; SANTANA, L. L.; TELLES, M. P. C.; SOARES, T. N. Isolamento e caracterização de marcadores microssatélites do genoma de Dipteryx alata Vogel. In: CONGRESSO BRASILEIRO DE GENÉTICA, 55., 2009, Águas de Lindóia, SP. Resumos... Ribeirão Preto: Sociedade Brasileira de Genética, 2009. p. 126.| Biblioteca(s): Embrapa Arroz e Feijão. |
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| 49. | | SOARES, T. N.; TELLES, M. P. C.; RESENDE, L. V.; SILVEIRA, L.; JÁCOMO, A. T. A.; MORATO, R. G.; DINIZ-FILHO, J. A. F.; EIZIRIK, E.; BRONDANI, R. P. V.; BRONDANI, C. Paternity testing and behavioral ecology: a case study of jaguars (Panthera onca) in Emas National Park, Central Brazil. Genetics and Molecular Biology, v. 29, n. 4, p. 735-740, 2006.| Tipo: Artigo em Periódico Indexado |
| Biblioteca(s): Embrapa Arroz e Feijão. |
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| Registros recuperados : 49 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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