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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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Biblioteca |
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 | Acesso ao texto completo restrito à biblioteca da Embrapa Florestas. Para informações adicionais entre em contato com cnpf.biblioteca@embrapa.br. |
Registro Completo
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Biblioteca(s): |
Embrapa Florestas. |
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Data corrente: |
26/11/2013 |
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Data da última atualização: |
18/02/2015 |
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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: |
CARDOSO, D. J.; LACERDA, A. E. B. de; ROSOT, M. A. D.; GARRASTAZU, M. C.; LIMA, R. T. |
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Afiliação: |
DENISE JETON CARDOSO, CNPF; ANDRE EDUARDO BISCAIA DE LACERDA, CNPF; MARIA AUGUSTA DOETZER ROSOT, CNPF; MARILICE CORDEIRO GARRASTAZU, CNPF; RENATO TEIXEIRA LIMA, VALOR FLORESTAL. |
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Título: |
Influence of spacing regimes on the development of loblolly pine (Pinus taeda L.) in Southern Brazil. |
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Ano de publicação: |
2013 |
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Fonte/Imprenta: |
Forest Ecology and Management, n. 310, p. 761-769, 2013. |
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Idioma: |
Inglês |
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Conteúdo: |
The economic potential of loblolly pine has long been recognized due to the ability to achieve growth levels in commercial plantations that far exceed their expected natural growth. Interest in this species is on the rise as the potential for increased production is becoming more feasible in Brazil and particularly in the US. As production increases and cultural treatments are adopted, understanding long-term outcomes based on similar practices are essential for managers. Long-term spacing studies using a variety of initial densities for different tree species show that initial density has little effect on total wood yield for cycles longer than 20 years. On the other hand, initial density has important implications when considering the intended product and its respective value as well as the overall costs of cultural treatments. This paper reports the 24-year growth of Pinus taeda – loblolly pine – in Southern Brazil in response to five cultural regimes. Five initial spacing regimes (2.5 1.2, 2.5 2.0, 2.5 2.8, 2.5 3.6 and 2.5 4.4 m) combined with cultural procedures generally used in commercial stands were studied. Dendrometric variables analyzed include diameter at breast height (dbh), average and dominant height, site index (SI), basal area, volume per tree and per hectare, and assortment volume; variables were tested using analysis of variance and Tukey test. The results indicate a final lower dbh average in denser spacing regimes but no significant difference in relation to volume per hectare and stand basal area at the end of the 24 year cycle. Our results demonstrate that it is possible to obtain the same volume per hectare, on average 385.7 m3 ha1, at the age of harvesting by combining different initial spacings with thinning intensities. The mean annual increment (MAI) was analyzed by reconstructing growth (volume) using the software Pisapro. The simulations showed that MAI has a positive correlation with initial spacing in which the densest spacing obtained a MAI approximately 45% higher than the widest treatment. The results provide managers with long-term data that can be used in forest management planning, e.g. by allowing companies to adjust their operations depending on the costs of planting, maintenance and other cultural treatments. The results also point out that depending on the aim of the production, initial spacing and thinning can be adjusted to meet target product specifications (e.g. larger dbh, lack of knots). MenosThe economic potential of loblolly pine has long been recognized due to the ability to achieve growth levels in commercial plantations that far exceed their expected natural growth. Interest in this species is on the rise as the potential for increased production is becoming more feasible in Brazil and particularly in the US. As production increases and cultural treatments are adopted, understanding long-term outcomes based on similar practices are essential for managers. Long-term spacing studies using a variety of initial densities for different tree species show that initial density has little effect on total wood yield for cycles longer than 20 years. On the other hand, initial density has important implications when considering the intended product and its respective value as well as the overall costs of cultural treatments. This paper reports the 24-year growth of Pinus taeda – loblolly pine – in Southern Brazil in response to five cultural regimes. Five initial spacing regimes (2.5 1.2, 2.5 2.0, 2.5 2.8, 2.5 3.6 and 2.5 4.4 m) combined with cultural procedures generally used in commercial stands were studied. Dendrometric variables analyzed include diameter at breast height (dbh), average and dominant height, site index (SI), basal area, volume per tree and per hectare, and assortment volume; variables were tested using analysis of variance and Tukey test. The results indicate a final lower dbh average in denser spacing regimes but no significant difference in relatio... Mostrar Tudo |
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Palavras-Chave: |
Brasil; Espécie exótica; Espécie florestal. |
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Thesagro: |
Densidade de Plantio; Pinus Taeda. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 03175naa a2200229 a 4500
001 1972136
005 2015-02-18
008 2013 bl uuuu u00u1 u #d
100 1 $aCARDOSO, D. J.
245 $aInfluence of spacing regimes on the development of loblolly pine (Pinus taeda L.) in Southern Brazil.$h[electronic resource]
260 $c2013
520 $aThe economic potential of loblolly pine has long been recognized due to the ability to achieve growth levels in commercial plantations that far exceed their expected natural growth. Interest in this species is on the rise as the potential for increased production is becoming more feasible in Brazil and particularly in the US. As production increases and cultural treatments are adopted, understanding long-term outcomes based on similar practices are essential for managers. Long-term spacing studies using a variety of initial densities for different tree species show that initial density has little effect on total wood yield for cycles longer than 20 years. On the other hand, initial density has important implications when considering the intended product and its respective value as well as the overall costs of cultural treatments. This paper reports the 24-year growth of Pinus taeda – loblolly pine – in Southern Brazil in response to five cultural regimes. Five initial spacing regimes (2.5 1.2, 2.5 2.0, 2.5 2.8, 2.5 3.6 and 2.5 4.4 m) combined with cultural procedures generally used in commercial stands were studied. Dendrometric variables analyzed include diameter at breast height (dbh), average and dominant height, site index (SI), basal area, volume per tree and per hectare, and assortment volume; variables were tested using analysis of variance and Tukey test. The results indicate a final lower dbh average in denser spacing regimes but no significant difference in relation to volume per hectare and stand basal area at the end of the 24 year cycle. Our results demonstrate that it is possible to obtain the same volume per hectare, on average 385.7 m3 ha1, at the age of harvesting by combining different initial spacings with thinning intensities. The mean annual increment (MAI) was analyzed by reconstructing growth (volume) using the software Pisapro. The simulations showed that MAI has a positive correlation with initial spacing in which the densest spacing obtained a MAI approximately 45% higher than the widest treatment. The results provide managers with long-term data that can be used in forest management planning, e.g. by allowing companies to adjust their operations depending on the costs of planting, maintenance and other cultural treatments. The results also point out that depending on the aim of the production, initial spacing and thinning can be adjusted to meet target product specifications (e.g. larger dbh, lack of knots).
650 $aDensidade de Plantio
650 $aPinus Taeda
653 $aBrasil
653 $aEspécie exótica
653 $aEspécie florestal
700 1 $aLACERDA, A. E. B. de
700 1 $aROSOT, M. A. D.
700 1 $aGARRASTAZU, M. C.
700 1 $aLIMA, R. T.
773 $tForest Ecology and Management$gn. 310, p. 761-769, 2013.
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