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 | Acesso ao texto completo restrito à biblioteca da Embrapa Gado de Leite. Para informações adicionais entre em contato com cnpgl.biblioteca@embrapa.br. |
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Registro Completo |
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Biblioteca(s): |
Embrapa Gado de Leite. |
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Data corrente: |
28/11/2014 |
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Data da última atualização: |
05/02/2024 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
O'BRIEN, A. M. P.; MÉSZÁROS, G.; UTSUNOMIYA, Y. T.; SONSTEGARD, T. S.; GARCIA, J. F.; TASSEL, C. P. V.; CARVALHEIRO, R.; SILVA, M. V. G. B.; SÖLKNER, J. |
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Afiliação: |
ANA M. PÉREZ O'BRIEN, University of Natural Resources and Life Sciences, Vienna; GÁBOR MÉSZÁROS, University of Natural Resources and Life Sciences, Vienna; YURI T. UTSUNOMIYA, UNESP; TAD S. SONSTEGARD, ARS-USDA, USA; JOSÉ F. GARCIA, UNESP; CURTIS P. VAN TASSEL, ARS-USDA, USA; ROBERTO CARVALHEIRO, GenSys Consultores Associados; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL; JOHANN SÖLKNER, University of Natural Resources and Life Sciences, Vienna. |
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Título: |
Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions. |
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Ano de publicação: |
2014 |
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Fonte/Imprenta: |
Livestock Science, v. 166, p. 121-132, 2014. |
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Idioma: |
Inglês |
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Conteúdo: |
Linkage disequilibrium (LD), the observed correlation between alleles at different loci in the genome, is a determinant parameter in many applications of molecular genetics. With the wider use of genomic technologies in animal breeding and animal genetics, it is worthwhile revising and improving the current knowledge and understanding of cattle LD. This study analyzes levels of LD assessed through the r2 measurement in seven breeds of cattle from both indicine (Bos indicus) and taurine (Bos taurus) (sub)species, genotyped with a high density panel (HD) of over 777,000 single nucleotide polymorphism (SNP) markers. Average levels of LD were assessed for inter-marker distances from 0 kb up to 10 Mb. Two more SNP panels were built in silico from the original genotypes to represent a lower density SNP chip including approximately 50,000 SNPs (50K) and a panel of 249,000 SNPs chosen to comply with specific minor allele frequency (MAF) distributions. The results show higher levels of LD than previously reported, especially at short inter-marker distances of less than 20 kb, assessed through the use of the higher density panel. Negligible impact of MAF changes in the estimation of r2 was observed, supporting the use of the HD panel for LD-based methodologies even when ascertainment bias in the choice of SNPs is suspected. The 50K SNP panel indicated lower levels of LD in the first 100 kb and highly unreliable LD estimates for distances shorter than 50 kb. Overall, lower levels of LD were observed for all indicine breeds as compared to taurine breeds, with larger differences assessed in the first 100 kb, suggesting the need for use of higher SNP densities in this (sub)species when applying LD-dependent methods, as compared to most taurine breeds. MenosLinkage disequilibrium (LD), the observed correlation between alleles at different loci in the genome, is a determinant parameter in many applications of molecular genetics. With the wider use of genomic technologies in animal breeding and animal genetics, it is worthwhile revising and improving the current knowledge and understanding of cattle LD. This study analyzes levels of LD assessed through the r2 measurement in seven breeds of cattle from both indicine (Bos indicus) and taurine (Bos taurus) (sub)species, genotyped with a high density panel (HD) of over 777,000 single nucleotide polymorphism (SNP) markers. Average levels of LD were assessed for inter-marker distances from 0 kb up to 10 Mb. Two more SNP panels were built in silico from the original genotypes to represent a lower density SNP chip including approximately 50,000 SNPs (50K) and a panel of 249,000 SNPs chosen to comply with specific minor allele frequency (MAF) distributions. The results show higher levels of LD than previously reported, especially at short inter-marker distances of less than 20 kb, assessed through the use of the higher density panel. Negligible impact of MAF changes in the estimation of r2 was observed, supporting the use of the HD panel for LD-based methodologies even when ascertainment bias in the choice of SNPs is suspected. The 50K SNP panel indicated lower levels of LD in the first 100 kb and highly unreliable LD estimates for distances shorter than 50 kb. Overall, lower levels of LD... Mostrar Tudo |
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Palavras-Chave: |
Indicine; Minor allele frequency. |
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Thesaurus Nal: |
cattle; linkage disequilibrium; taurine. |
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Categoria do assunto: |
L Ciência Animal e Produtos de Origem Animal |
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Marc: |
LEADER 02632naa a2200277 a 4500
001 2001105
005 2024-02-05
008 2014 bl uuuu u00u1 u #d
100 1 $aO'BRIEN, A. M. P.
245 $aLinkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions.$h[electronic resource]
260 $c2014
520 $aLinkage disequilibrium (LD), the observed correlation between alleles at different loci in the genome, is a determinant parameter in many applications of molecular genetics. With the wider use of genomic technologies in animal breeding and animal genetics, it is worthwhile revising and improving the current knowledge and understanding of cattle LD. This study analyzes levels of LD assessed through the r2 measurement in seven breeds of cattle from both indicine (Bos indicus) and taurine (Bos taurus) (sub)species, genotyped with a high density panel (HD) of over 777,000 single nucleotide polymorphism (SNP) markers. Average levels of LD were assessed for inter-marker distances from 0 kb up to 10 Mb. Two more SNP panels were built in silico from the original genotypes to represent a lower density SNP chip including approximately 50,000 SNPs (50K) and a panel of 249,000 SNPs chosen to comply with specific minor allele frequency (MAF) distributions. The results show higher levels of LD than previously reported, especially at short inter-marker distances of less than 20 kb, assessed through the use of the higher density panel. Negligible impact of MAF changes in the estimation of r2 was observed, supporting the use of the HD panel for LD-based methodologies even when ascertainment bias in the choice of SNPs is suspected. The 50K SNP panel indicated lower levels of LD in the first 100 kb and highly unreliable LD estimates for distances shorter than 50 kb. Overall, lower levels of LD were observed for all indicine breeds as compared to taurine breeds, with larger differences assessed in the first 100 kb, suggesting the need for use of higher SNP densities in this (sub)species when applying LD-dependent methods, as compared to most taurine breeds.
650 $acattle
650 $alinkage disequilibrium
650 $ataurine
653 $aIndicine
653 $aMinor allele frequency
700 1 $aMÉSZÁROS, G.
700 1 $aUTSUNOMIYA, Y. T.
700 1 $aSONSTEGARD, T. S.
700 1 $aGARCIA, J. F.
700 1 $aTASSEL, C. P. V.
700 1 $aCARVALHEIRO, R.
700 1 $aSILVA, M. V. G. B.
700 1 $aSÖLKNER, J.
773 $tLivestock Science$gv. 166, p. 121-132, 2014.
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Embrapa Gado de Leite (CNPGL) |
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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: |
05/09/2008 |
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Data da última atualização: |
05/09/2008 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
NADOLNY, H.; SILVA, V. L. da; NEVES, E. J. M.; CARPANEZZI, A. A.; BROWN, G. G. |
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Afiliação: |
Herlon Nadolny, Estudante Mestrado UFPR; Vagner L. da Silva, Estudante Mestrado UFPR; Edinelson José Maciel Neves, Embrapa Florestas; Antônio Aparecido Carpanezzi, Embrapa Florestas; George Gardner Brown, Embrapa Florestas. |
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Título: |
Soil macrofauna populations in tree plantations used to recover degraded pastures in the Atlantic Rainforest of Antonina, Paraná, Brazil. |
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Ano de publicação: |
2008 |
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Fonte/Imprenta: |
In: INTERNATIONAL COLLOQUIUM ON SOIL ZOOLOGY, 15; INTERNATIONAL COLLOQUIUM ON APTERYGOTA, 12., 2008, Curitiba. Biodiversity, conservation and sustainabele management of soil animal: abstracts. Colombo: Embrapa Florestas. Editors: George Gardner Brown; Klaus Dieter Sautter; Renato Marques; Amarildo Pasini. 1 CD-ROM. |
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Idioma: |
Inglês |
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Conteúdo: |
Large areas of the Atlantic coastal rainforest have been deforested in the past mainly for
agricultural purposes, especially cattle grazing. However, many of these areas are currently underutilized or degraded by overgrazing or intensive use. In the coastal region of Paraná, smallscale buffalo grazing has led to considerable local soil degradation and, with the abandonment of the pastures, the exotic Brachiaria sp. grass spreads and becomes a problem for the restoration of these pastures and for alternative uses, such as palmito (heart-of-palm), native forest regeneration or forestry activities. Therefore, to evaluate the potential of various native tree species in the restoration of these pastures, a trial was established in 2002 at a private reserve of the Sociedade de Proteção da Vida Silvestre (SPVS), near Antonina. The experiment was set up in 4 blocks with 3 replicates and 5 native species, planted in plots of 10 x 16 m. For the present study, two tree species were chosen, both legumes: ingá (Inga sp.) and capororoca (Myrsine sp.). The effect of these treatments on the soil fauna abundance and diversity was investigated using the standard TSBF method (25 x 25 cm blocks) but only in the top-soil horizon
(0-10 cm), due to a high water-table. Two samples were taken per plot, with a total of 18 samples in the Myrsine sp. and 14 in the Inga sp. Four earthworm species were found, two exotic megascolecids, Pontoscolex corethrurus (Müller, 1857), and another yet unidentified ocnerodrilid. Total macrofauna group diversity was higher in the Myrsine (11) than Inga (7) sp. plots, and total abundance was also slightly higher (644 vs. 483 indiv. m-2, respectively). Earthworms represented >80% of total abundance, and P. corethrurus predominated, representing 85% of all collected earthworms (973 individuals, including 33 cocoons). The other most abundant fauna were snails, beetles and Millipedes, representing each <10% of total abundance. Principle components and redundancy analyses showed a separation of the sample sites based mainly on soil moisture and earthworm (especially P. corethrurus) abundance, both of which tended to be larger in
Myrsine sp. plots. MenosLarge areas of the Atlantic coastal rainforest have been deforested in the past mainly for
agricultural purposes, especially cattle grazing. However, many of these areas are currently underutilized or degraded by overgrazing or intensive use. In the coastal region of Paraná, smallscale buffalo grazing has led to considerable local soil degradation and, with the abandonment of the pastures, the exotic Brachiaria sp. grass spreads and becomes a problem for the restoration of these pastures and for alternative uses, such as palmito (heart-of-palm), native forest regeneration or forestry activities. Therefore, to evaluate the potential of various native tree species in the restoration of these pastures, a trial was established in 2002 at a private reserve of the Sociedade de Proteção da Vida Silvestre (SPVS), near Antonina. The experiment was set up in 4 blocks with 3 replicates and 5 native species, planted in plots of 10 x 16 m. For the present study, two tree species were chosen, both legumes: ingá (Inga sp.) and capororoca (Myrsine sp.). The effect of these treatments on the soil fauna abundance and diversity was investigated using the standard TSBF method (25 x 25 cm blocks) but only in the top-soil horizon
(0-10 cm), due to a high water-table. Two samples were taken per plot, with a total of 18 samples in the Myrsine sp. and 14 in the Inga sp. Four earthworm species were found, two exotic megascolecids, Pontoscolex corethrurus (Müller, 1857), and another yet unidentified o... Mostrar Tudo |
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Palavras-Chave: |
Macrofauna; Pastagem degradada; Plantação florestal; Recuperação. |
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Thesagro: |
Solo. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 03149naa a2200229 a 4500
001 1314776
005 2008-09-05
008 2008 bl --- 0-- u #d
100 1 $aNADOLNY, H.
245 $aSoil macrofauna populations in tree plantations used to recover degraded pastures in the Atlantic Rainforest of Antonina, Paraná, Brazil.
260 $c2008
520 $aLarge areas of the Atlantic coastal rainforest have been deforested in the past mainly for agricultural purposes, especially cattle grazing. However, many of these areas are currently underutilized or degraded by overgrazing or intensive use. In the coastal region of Paraná, smallscale buffalo grazing has led to considerable local soil degradation and, with the abandonment of the pastures, the exotic Brachiaria sp. grass spreads and becomes a problem for the restoration of these pastures and for alternative uses, such as palmito (heart-of-palm), native forest regeneration or forestry activities. Therefore, to evaluate the potential of various native tree species in the restoration of these pastures, a trial was established in 2002 at a private reserve of the Sociedade de Proteção da Vida Silvestre (SPVS), near Antonina. The experiment was set up in 4 blocks with 3 replicates and 5 native species, planted in plots of 10 x 16 m. For the present study, two tree species were chosen, both legumes: ingá (Inga sp.) and capororoca (Myrsine sp.). The effect of these treatments on the soil fauna abundance and diversity was investigated using the standard TSBF method (25 x 25 cm blocks) but only in the top-soil horizon (0-10 cm), due to a high water-table. Two samples were taken per plot, with a total of 18 samples in the Myrsine sp. and 14 in the Inga sp. Four earthworm species were found, two exotic megascolecids, Pontoscolex corethrurus (Müller, 1857), and another yet unidentified ocnerodrilid. Total macrofauna group diversity was higher in the Myrsine (11) than Inga (7) sp. plots, and total abundance was also slightly higher (644 vs. 483 indiv. m-2, respectively). Earthworms represented >80% of total abundance, and P. corethrurus predominated, representing 85% of all collected earthworms (973 individuals, including 33 cocoons). The other most abundant fauna were snails, beetles and Millipedes, representing each <10% of total abundance. Principle components and redundancy analyses showed a separation of the sample sites based mainly on soil moisture and earthworm (especially P. corethrurus) abundance, both of which tended to be larger in Myrsine sp. plots.
650 $aSolo
653 $aMacrofauna
653 $aPastagem degradada
653 $aPlantação florestal
653 $aRecuperação
700 1 $aSILVA, V. L. da
700 1 $aNEVES, E. J. M.
700 1 $aCARPANEZZI, A. A.
700 1 $aBROWN, G. G.
773 $tIn: INTERNATIONAL COLLOQUIUM ON SOIL ZOOLOGY, 15; INTERNATIONAL COLLOQUIUM ON APTERYGOTA, 12., 2008, Curitiba. Biodiversity, conservation and sustainabele management of soil animal: abstracts. Colombo: Embrapa Florestas. Editors: George Gardner Brown; Klaus Dieter Sautter; Renato Marques; Amarildo Pasini. 1 CD-ROM.
Download
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