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Registro Completo |
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Biblioteca(s): |
Embrapa Cerrados. |
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Data corrente: |
11/04/2024 |
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Data da última atualização: |
11/04/2024 |
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Autoria: |
MIURA, T.; HUETE, A. R.; FERREIRA, L. G.; SANO, E. E. |
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Afiliação: |
TOMOAKI MIURA, UNIVERSITY OF HAWAII AT MĀNOA; ALFREDO R. HUETE, UNIVERSITY OF ARIZONA; LAERTE G. FERREIRA, UNIVERSIDADE FEDERAL DE GOIÁS; EDSON EYJI SANO, CPAC. |
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Título: |
An assessment of land cover dependencies of VI-biophysical relationships for regional extrapolations of ground LBA ecology measurements in Brazilian Cerrado |
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Ano de publicação: |
2004 |
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Fonte/Imprenta: |
In: CONFERÊNCIA CIENTÍFICA DO LBA, 3., 2004, Brasília, DF. Anais de trabalhos completos. Brasília, DF: LBA, 2004. |
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Páginas: |
1 p. |
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Idioma: |
Português |
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Conteúdo: |
The savanna in Brazil, locally known as “cerrado,” is the most intensely stressed biome with both natural environmental pressures and rapid/aggressive land conversions. Large-scale vegetation characterization of the biome is needed in order to improve our understanding of the human impact on carbon and other biogeochemical cycling and the prospect for sustainable land use in the Brazilian cerrado. One of the most common approaches for measuring or monitoring biophysical conditions is the empirical correlation of spectral vegetation indices (VIs) with such biophysical parameters as leaf area index (LAI), % green cover, and fraction of absorbed photosynthetically active radiation (fAPAR). Few studies, however, have been conducted to investigate the relationships of VIs with biophysical parameters for the Brazilian cerrado. In this study, we assessed VI-biophysical relationships and their land cover dependencies with the goal of deriving proper functional forms for cerrado using a hybrid, multi-layer canopy reflectance (CR) model. A range of cerrado physiognomies as well as converted pastures were measured for tissue optical and structural properties in the beginning of a dry period in 2002. The data were then used to contrain the CR model. The field sites included cerrado grassland, scrub cerrado, wooded cerrado, and cerrado woodland as undisturbed cerrado physiognomies, and pastures of various ages (from one to eight years old). VIs were computed from the model-simulated reflectance and correlated with the biophysical parameters of LAI and fAPAR to assess the relationships. The model-simulated data set showed observable trends where the data for cerrado grassland and scrub cerrado, for wooded cerrado and cerrado woodland, and for pastures formed different relationships. These results imply that the stratification of land cover types are necessary in order to accurately estimate LAI and fAPAR from the empirically-derived relationships, but the land cover classes do not have to follow conventional cerrado physiognomies, requiring only a few classes including grassy and woody cerrado, and pastures. MenosThe savanna in Brazil, locally known as “cerrado,” is the most intensely stressed biome with both natural environmental pressures and rapid/aggressive land conversions. Large-scale vegetation characterization of the biome is needed in order to improve our understanding of the human impact on carbon and other biogeochemical cycling and the prospect for sustainable land use in the Brazilian cerrado. One of the most common approaches for measuring or monitoring biophysical conditions is the empirical correlation of spectral vegetation indices (VIs) with such biophysical parameters as leaf area index (LAI), % green cover, and fraction of absorbed photosynthetically active radiation (fAPAR). Few studies, however, have been conducted to investigate the relationships of VIs with biophysical parameters for the Brazilian cerrado. In this study, we assessed VI-biophysical relationships and their land cover dependencies with the goal of deriving proper functional forms for cerrado using a hybrid, multi-layer canopy reflectance (CR) model. A range of cerrado physiognomies as well as converted pastures were measured for tissue optical and structural properties in the beginning of a dry period in 2002. The data were then used to contrain the CR model. The field sites included cerrado grassland, scrub cerrado, wooded cerrado, and cerrado woodland as undisturbed cerrado physiognomies, and pastures of various ages (from one to eight years old). VIs were computed from the model-simulated refl... Mostrar Tudo |
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Thesaurus Nal: |
Ecology; Land; Land cover; Savannas. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/doc/1163515/1/An-assessment-of-land-cover.pdf
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Marc: |
LEADER 02836nam a2200205 a 4500
001 2163515
005 2024-04-11
008 2004 bl uuuu u00u1 u #d
100 1 $aMIURA, T.
245 $aAn assessment of land cover dependencies of VI-biophysical relationships for regional extrapolations of ground LBA ecology measurements in Brazilian Cerrado$h[electronic resource]
260 $aIn: CONFERÊNCIA CIENTÍFICA DO LBA, 3., 2004, Brasília, DF. Anais de trabalhos completos. Brasília, DF: LBA$c2004
300 $a1 p.
520 $aThe savanna in Brazil, locally known as “cerrado,” is the most intensely stressed biome with both natural environmental pressures and rapid/aggressive land conversions. Large-scale vegetation characterization of the biome is needed in order to improve our understanding of the human impact on carbon and other biogeochemical cycling and the prospect for sustainable land use in the Brazilian cerrado. One of the most common approaches for measuring or monitoring biophysical conditions is the empirical correlation of spectral vegetation indices (VIs) with such biophysical parameters as leaf area index (LAI), % green cover, and fraction of absorbed photosynthetically active radiation (fAPAR). Few studies, however, have been conducted to investigate the relationships of VIs with biophysical parameters for the Brazilian cerrado. In this study, we assessed VI-biophysical relationships and their land cover dependencies with the goal of deriving proper functional forms for cerrado using a hybrid, multi-layer canopy reflectance (CR) model. A range of cerrado physiognomies as well as converted pastures were measured for tissue optical and structural properties in the beginning of a dry period in 2002. The data were then used to contrain the CR model. The field sites included cerrado grassland, scrub cerrado, wooded cerrado, and cerrado woodland as undisturbed cerrado physiognomies, and pastures of various ages (from one to eight years old). VIs were computed from the model-simulated reflectance and correlated with the biophysical parameters of LAI and fAPAR to assess the relationships. The model-simulated data set showed observable trends where the data for cerrado grassland and scrub cerrado, for wooded cerrado and cerrado woodland, and for pastures formed different relationships. These results imply that the stratification of land cover types are necessary in order to accurately estimate LAI and fAPAR from the empirically-derived relationships, but the land cover classes do not have to follow conventional cerrado physiognomies, requiring only a few classes including grassy and woody cerrado, and pastures.
650 $aEcology
650 $aLand
650 $aLand cover
650 $aSavannas
700 1 $aHUETE, A. R.
700 1 $aFERREIRA, L. G.
700 1 $aSANO, E. E.
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Registro original: |
Embrapa Cerrados (CPAC) |
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Registro Completo
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Biblioteca(s): |
Embrapa Gado de Corte. |
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Data corrente: |
27/12/2019 |
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Data da última atualização: |
27/12/2019 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
A - 2 |
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Autoria: |
MATIAS, F. I.; MEIRELES, K. G. X.; NAGAMATSU, S. T.; BARRIOS, S. C. L.; VALE, C. B. do; CARAZZOLLE, M. F.; FRITSCHE-NETO, R.; ENDELMAN, J. B. |
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Afiliação: |
Filipe Inácio Matias, Universidade de São Paulo - USP/ Escola Superior de Agricultura "Luiz de Queiroz" - ESALQ/Departamento de Genetica; KAREM GUIMARAES XAVIER MEIRELES, CNPGC; Sheila Tiemi Nagamatsu, Universiade Estadual de Campinas - UNICAMP/Departamento Genética e Evolução; SANZIO CARVALHO LIMA BARRIOS, CNPGC; Cacilda Borges do Valle, Colaboradora da Embrapa Gado de Corte; Marcelo Falsarella Carazzolle, Universiade Estadual de Campinas - UNICAMP/Departamento Genética e Evolução; Roberto Fritsche-Neto, Universidade de São Paulo - USP/ Escola Superior de Agricultura "Luiz de Queiroz" - ESALQ/Departamento de Genetica; Jeffrey B. Endelman, University of Wisconsin–Madison/Dep. Horticulture. |
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Título: |
Expected Genotype Quality and Diploidized Marker Data from Genotyping-by-Sequencing of Urocholoa spp. Tetraploids. |
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Ano de publicação: |
2019 |
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Fonte/Imprenta: |
The Plant Genome, v. 12, n. 3, november 2019. |
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Idioma: |
Português |
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Conteúdo: |
Although genotyping-by-sequencing (GBS) is a well-established marker technology in diploids, the development of best practices for tetraploid species is a topic of current research. We determined the theoretical relationship between read depth and the phred-scaled probability of genotype misclassification conditioned on the true genotype, which we call expected genotype quality (EGQ). If the GBS method has 0.5% allelic error, then 17 reads are needed to classify simplex tetraploids as heterozygous with 95% accuracy (EGQ = 13) vs. 61 reads to determine allele dosage. We developed an R script to convert tetraploid GBS data in variant call format (VCF) into diploidized genotype calls and applied it to 267 interspecific hybrids of the tetraploid forage grass Urochloa. When reads were aligned to a mock reference genome created from GBS data of the Urochloa brizantha (Hochst. ex A. Rich.) R. D. Webster cultivar Marandu, 25,678 biallelic single nucleotide polymorphism (SNPs) were discovered, compared with ~3000 SNPs when aligning to the closest true reference genomes, Setaria viridis (L.) P. Beauv. and S. italica (L.) P. Beauv. Crossvalidation revealed that missing genotypes were imputed by the random forest method with a median accuracy of 0.85 regardless of heterozygote frequency. Using the Urochloa spp. hybrids, we illustrated how filtering samples based only on genotype quality (GQ) creates genotype bias; a depth threshold based on EGQ is also needed regardless of whether genotypes are called using a diploidized or allele dosage model. MenosAlthough genotyping-by-sequencing (GBS) is a well-established marker technology in diploids, the development of best practices for tetraploid species is a topic of current research. We determined the theoretical relationship between read depth and the phred-scaled probability of genotype misclassification conditioned on the true genotype, which we call expected genotype quality (EGQ). If the GBS method has 0.5% allelic error, then 17 reads are needed to classify simplex tetraploids as heterozygous with 95% accuracy (EGQ = 13) vs. 61 reads to determine allele dosage. We developed an R script to convert tetraploid GBS data in variant call format (VCF) into diploidized genotype calls and applied it to 267 interspecific hybrids of the tetraploid forage grass Urochloa. When reads were aligned to a mock reference genome created from GBS data of the Urochloa brizantha (Hochst. ex A. Rich.) R. D. Webster cultivar Marandu, 25,678 biallelic single nucleotide polymorphism (SNPs) were discovered, compared with ~3000 SNPs when aligning to the closest true reference genomes, Setaria viridis (L.) P. Beauv. and S. italica (L.) P. Beauv. Crossvalidation revealed that missing genotypes were imputed by the random forest method with a median accuracy of 0.85 regardless of heterozygote frequency. Using the Urochloa spp. hybrids, we illustrated how filtering samples based only on genotype quality (GQ) creates genotype bias; a depth threshold based on EGQ is also needed regardless of whether genot... Mostrar Tudo |
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Palavras-Chave: |
Although genotyping-by-sequencing; Marker technology. |
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Thesaurus NAL: |
Genotype; Hybrids; Urochloa. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/207884/1/Expected-Genotype-Quality-and-Diploidized.pdf
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Marc: |
LEADER 02355naa a2200265 a 4500
001 2117777
005 2019-12-27
008 2019 bl uuuu u00u1 u #d
100 1 $aMATIAS, F. I.
245 $aExpected Genotype Quality and Diploidized Marker Data from Genotyping-by-Sequencing of Urocholoa spp. Tetraploids.$h[electronic resource]
260 $c2019
520 $aAlthough genotyping-by-sequencing (GBS) is a well-established marker technology in diploids, the development of best practices for tetraploid species is a topic of current research. We determined the theoretical relationship between read depth and the phred-scaled probability of genotype misclassification conditioned on the true genotype, which we call expected genotype quality (EGQ). If the GBS method has 0.5% allelic error, then 17 reads are needed to classify simplex tetraploids as heterozygous with 95% accuracy (EGQ = 13) vs. 61 reads to determine allele dosage. We developed an R script to convert tetraploid GBS data in variant call format (VCF) into diploidized genotype calls and applied it to 267 interspecific hybrids of the tetraploid forage grass Urochloa. When reads were aligned to a mock reference genome created from GBS data of the Urochloa brizantha (Hochst. ex A. Rich.) R. D. Webster cultivar Marandu, 25,678 biallelic single nucleotide polymorphism (SNPs) were discovered, compared with ~3000 SNPs when aligning to the closest true reference genomes, Setaria viridis (L.) P. Beauv. and S. italica (L.) P. Beauv. Crossvalidation revealed that missing genotypes were imputed by the random forest method with a median accuracy of 0.85 regardless of heterozygote frequency. Using the Urochloa spp. hybrids, we illustrated how filtering samples based only on genotype quality (GQ) creates genotype bias; a depth threshold based on EGQ is also needed regardless of whether genotypes are called using a diploidized or allele dosage model.
650 $aGenotype
650 $aHybrids
650 $aUrochloa
653 $aAlthough genotyping-by-sequencing
653 $aMarker technology
700 1 $aMEIRELES, K. G. X.
700 1 $aNAGAMATSU, S. T.
700 1 $aBARRIOS, S. C. L.
700 1 $aVALE, C. B. do
700 1 $aCARAZZOLLE, M. F.
700 1 $aFRITSCHE-NETO, R.
700 1 $aENDELMAN, J. B.
773 $tThe Plant Genome$gv. 12, n. 3, november 2019.
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Embrapa Gado de Corte (CNPGC) |
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