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Registro completo
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Biblioteca (s) : |
INIA La Estanzuela. |
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Fecha : |
29/09/2014 |
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Actualizado : |
25/10/2017 |
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Tipo de producción científica : |
Poster |
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Autor : |
BRANDARIZ, S.P.; GONZÁELZ-REYMÚNDEZ, A.; LADO, B.; QUINCKE, M.; VON ZITZEWITZ, J.; CASTRO, M.; MATUS, I.; DEL POZO, A.; GUTIÉRREZ, L. |
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Afiliación : |
BETTINA LADO LINDNER, Instituto Nacional de Investigación Agropecuaria (INIA), Uruguay; MARTIN CONRADO QUINCKE WALDEN, Instituto Nacional de Investigación Agropecuaria (INIA), Uruguay; JARISLAV RAMON VON ZITZEWITZ VON SALVIATI, Instituto Nacional de Investigación Agropecuaria (INIA), Uruguay; MARINA CASTRO DERENYI, Instituto Nacional de Investigación Agropecuaria (INIA), Uruguay. |
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Título : |
Effect of using imputed missing data on QTL detection on a wheat GWAS panel. |
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Fecha de publicación : |
2014 |
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Fuente / Imprenta : |
In: SEMINARIO INTERNACIONAL DE TRIGO, 2014, La Estanzuela, Colonia, UY. GERMÁN, S., et al. (Org.). 1914-2014, un siglo de mejoramiento de trigo en La Estanzuela: un valioso legado para el futuro: posters; resúmenes. La Estanzuela, Colonia, UY: INIA, 2014. |
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Páginas : |
p. 86. |
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Idioma : |
Inglés |
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Contenido : |
Molecular markers are an essential component of plant and animal breeding programs. One inexpensive way of obtaining molecular markers is through Next-Generation Sequencing (NGS). Genotyping-by-sequencing (GBS) is one of the NGS techniques which have been successfully used for complex genomes like wheat. A particularity of GBS is that it generates a lot of missing information which is generally imputed. Imputation is required for Genomic Prediction studies and several studies demonstrate its value. However, the effectiveness of missing data imputation for Genome-wide association (GWAS) studies has not been demonstrated. Data imputation for GWAS where one marker at a time is being studied could potentially create biased estimates. The aim of this study was to compare the effects of using either missing or imputed data for Quantitative Trait Loci (QTL) detection in a wheat GWAS pannel. A set of 384 advanced lines of wheat was included in this study consisting of 186 genotypes from INIA (Instituto Nacional de Investigación Agropecuaria) in Uruguay, 55 genotypes from INIA in Chile and 143 genotypes from CIMMYT (Centro Internacional de Mejoramiento de Maíz y Trigo). SNPs were obtained using the Tassel-GBS Pipeline. We excluded SNPs with more than 50 % missing data and SNPs with a minor allele frequency (MAF) more extreme than 10%. Sequence database available from the SyntheticxOpata map (synop) was used to construct the maps, obtaining a final data set with more than 18K SNPs. Missing data was handled in three different ways to create the SNP datasets used for QTL detection: 1) data not-imputed, 2) data imputed by the realized relationship matrix method multivariate normal expectation maximization (MVN-EM), and 3) data imputed by the mean. A number of QTL (either 25 or 50) with different heritability (0.2 and 0.7) were simulated on top of each dataset. The following mixed model was used to recover QTL: , where : phenotypic vector, : SNPs matrix, : unknown vector of allele effects to be estimated, : matrix that relates each measurement to population origin, : populations vector, : kinship matrix, : vector of random background polygenic effects, and : residual error. We used a liberal 0.01 significance level. The power to detect QTL was estimated for each dataset and differences among medians of QTL detection power among imputed datasets were studied using the Friedman test and non-parametric contrasts. For this purpose, methods of imputations were defined as treatments and simulation scenarios as blocks. The QTL detection power with the MVN-EM matrix was lower than with the mean imputed matrix or the no imputed matrix. No differences in QTL detection power were found between the mean imputed matrix or the no imputed matrix. Based on our results, imputing does not seem to improve QTL detection power. MenosMolecular markers are an essential component of plant and animal breeding programs. One inexpensive way of obtaining molecular markers is through Next-Generation Sequencing (NGS). Genotyping-by-sequencing (GBS) is one of the NGS techniques which have been successfully used for complex genomes like wheat. A particularity of GBS is that it generates a lot of missing information which is generally imputed. Imputation is required for Genomic Prediction studies and several studies demonstrate its value. However, the effectiveness of missing data imputation for Genome-wide association (GWAS) studies has not been demonstrated. Data imputation for GWAS where one marker at a time is being studied could potentially create biased estimates. The aim of this study was to compare the effects of using either missing or imputed data for Quantitative Trait Loci (QTL) detection in a wheat GWAS pannel. A set of 384 advanced lines of wheat was included in this study consisting of 186 genotypes from INIA (Instituto Nacional de Investigación Agropecuaria) in Uruguay, 55 genotypes from INIA in Chile and 143 genotypes from CIMMYT (Centro Internacional de Mejoramiento de Maíz y Trigo). SNPs were obtained using the Tassel-GBS Pipeline. We excluded SNPs with more than 50 % missing data and SNPs with a minor allele frequency (MAF) more extreme than 10%. Sequence database available from the SyntheticxOpata map (synop) was used to construct the maps, obtaining a final data set with more than 18K SNPs. Mi... Presentar Todo |
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Palabras claves : |
GBS; GENOMIC PREDICTION; GENOMIC WIDE ASSOCIATION; GENOTYPING BY SEQUENCING; GWAS; MARCADORES MOLECULARES; MULTIVARIATE NORMAL EXPECTATION MAXIMIZATION; MVN-EM; NEXT GENERATION SEQUENCING; NGS; QTL; QUANTITATIVE TRAIT LOCI DETECTION; SINGLE NUCLEOTIDE POLYMORPHISMS; SNPs; TRITICUM. |
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Thesagro : |
DETECCIÓN DE QTLS; MARCADORES MOLECULARES; TRIGO. |
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Asunto categoría : |
-- |
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Marc : |
LEADER 04260nam a2200433 a 4500
001 1050639
005 2017-10-25
008 2014 bl uuuu u00u1 u #d
100 1 $aBRANDARIZ, S.P.
245 $aEffect of using imputed missing data on QTL detection on a wheat GWAS panel.
260 $aIn: SEMINARIO INTERNACIONAL DE TRIGO, 2014, La Estanzuela, Colonia, UY. GERMÁN, S., et al. (Org.). 1914-2014, un siglo de mejoramiento de trigo en La Estanzuela: un valioso legado para el futuro: posters; resúmenes. La Estanzuela, Colonia, UY: INIA$c2014
300 $ap. 86.
520 $aMolecular markers are an essential component of plant and animal breeding programs. One inexpensive way of obtaining molecular markers is through Next-Generation Sequencing (NGS). Genotyping-by-sequencing (GBS) is one of the NGS techniques which have been successfully used for complex genomes like wheat. A particularity of GBS is that it generates a lot of missing information which is generally imputed. Imputation is required for Genomic Prediction studies and several studies demonstrate its value. However, the effectiveness of missing data imputation for Genome-wide association (GWAS) studies has not been demonstrated. Data imputation for GWAS where one marker at a time is being studied could potentially create biased estimates. The aim of this study was to compare the effects of using either missing or imputed data for Quantitative Trait Loci (QTL) detection in a wheat GWAS pannel. A set of 384 advanced lines of wheat was included in this study consisting of 186 genotypes from INIA (Instituto Nacional de Investigación Agropecuaria) in Uruguay, 55 genotypes from INIA in Chile and 143 genotypes from CIMMYT (Centro Internacional de Mejoramiento de Maíz y Trigo). SNPs were obtained using the Tassel-GBS Pipeline. We excluded SNPs with more than 50 % missing data and SNPs with a minor allele frequency (MAF) more extreme than 10%. Sequence database available from the SyntheticxOpata map (synop) was used to construct the maps, obtaining a final data set with more than 18K SNPs. Missing data was handled in three different ways to create the SNP datasets used for QTL detection: 1) data not-imputed, 2) data imputed by the realized relationship matrix method multivariate normal expectation maximization (MVN-EM), and 3) data imputed by the mean. A number of QTL (either 25 or 50) with different heritability (0.2 and 0.7) were simulated on top of each dataset. The following mixed model was used to recover QTL: , where : phenotypic vector, : SNPs matrix, : unknown vector of allele effects to be estimated, : matrix that relates each measurement to population origin, : populations vector, : kinship matrix, : vector of random background polygenic effects, and : residual error. We used a liberal 0.01 significance level. The power to detect QTL was estimated for each dataset and differences among medians of QTL detection power among imputed datasets were studied using the Friedman test and non-parametric contrasts. For this purpose, methods of imputations were defined as treatments and simulation scenarios as blocks. The QTL detection power with the MVN-EM matrix was lower than with the mean imputed matrix or the no imputed matrix. No differences in QTL detection power were found between the mean imputed matrix or the no imputed matrix. Based on our results, imputing does not seem to improve QTL detection power.
650 $aDETECCIÓN DE QTLS
650 $aMARCADORES MOLECULARES
650 $aTRIGO
653 $aGBS
653 $aGENOMIC PREDICTION
653 $aGENOMIC WIDE ASSOCIATION
653 $aGENOTYPING BY SEQUENCING
653 $aGWAS
653 $aMARCADORES MOLECULARES
653 $aMULTIVARIATE NORMAL EXPECTATION MAXIMIZATION
653 $aMVN-EM
653 $aNEXT GENERATION SEQUENCING
653 $aNGS
653 $aQTL
653 $aQUANTITATIVE TRAIT LOCI DETECTION
653 $aSINGLE NUCLEOTIDE POLYMORPHISMS
653 $aSNPs
653 $aTRITICUM
700 1 $aGONZÁELZ-REYMÚNDEZ, A.
700 1 $aLADO, B.
700 1 $aQUINCKE, M.
700 1 $aVON ZITZEWITZ, J.
700 1 $aCASTRO, M.
700 1 $aMATUS, I.
700 1 $aDEL POZO, A.
700 1 $aGUTIÉRREZ, L.
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Registro original : |
INIA La Estanzuela (LE) |
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Registro completo
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Biblioteca (s) : |
INIA La Estanzuela. |
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Fecha actual : |
09/09/2020 |
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Actualizado : |
05/09/2022 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Circulación / Nivel : |
Internacional - -- |
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Autor : |
RAEGAN HOEFLER; GONZALEZ-BARRIOS , P.; MADHAV BHATTA; NUNES, J.A.R.; BERRO, I.; NALIN, R.S.; BORGES, A.; COVARRUBIAS, E.; DIAZ-GARCIA, L.; QUINCKE, M.; GUTIERREZ, L. |
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Afiliación : |
HOEFLER, R., Department of Agronomy, University of Wisconsin?Madison, 1575 Linden Dr., Madison, WI, 53706, USA.; PABLO GONZALEZ-BARRIOS, Dpartment of Agronomy, University of Wisconsin?Madison, 1575 Linden Dr., Madison, WI, 53706, USA.; BHATTA, M., Department of Agronomy, University of Wisconsin?Madison, 1575 Linden Dr., Madison, WI, 53706, USA.; JOSE A. R. NUNES, Department of Agronomy, University of Wisconsin?Madison, 1575 Linden Dr., Madison, WI, 53706, USA.; INES BERRO, Department of Agronomy, University of Wisconsin–Madison, 1575 Linden Dr., Madison, WI, 53706, USA; RAFAEL S. NALIN, Department of Genetics, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, São Paulo, 131418-900, Brazil.; ALEJANDRA BORGES, Statistics Department, Facultad de Agronomía, Univesidad de la República, Garzón 780, Montevideo, Uruguay.; EDUARDO COVARRUBIAS, CGIAR Excellence in Breeding Platform (EiB), El Batan, Mexico International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico.; LUIS DIAZ-GARCIA, Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, 20676, Aguascalientes, Mexico.; MARTIN CONRADO QUINCKE WALDEN, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; LUCIA GUTIERREZ, Department of Agronomy, University of Wisconsin–Madison, 1575 Linden Dr., Madison, WI, 53706, USA. |
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Título : |
Do Spatial Designs Outperform Classic Experimental Designs?. |
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Fecha de publicación : |
2020 |
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Fuente / Imprenta : |
Journal of Agricultural, Biological, and Environmental Statistics, 1 December 2020, volume 25, number 4, pag.523-552, 1 December 2020. OPEN ACCESS. Doi: https://doi.org/10.1007/s13253-020-00406-2 |
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DOI : |
10.1007/s13253-020-00406-2 |
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Idioma : |
Inglés |
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Notas : |
Article history: Received 15 October 2019/Accepted 01 July 2020/Published 29 August 2020. This project was partially funded through a USDA_AFRI_NIFA_2018-67013-27620 award and by the Hatch Act Formula Fund WISO1984 and WIS03002. Additionally, JARN received funding from CAPES CAPES_PrInt_UFLA 88887.318846_2019-00 as Senior Visiting Professor at the University of Wisconsin-Madison. |
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Contenido : |
Controlling spatial variation in agricultural field trials is the most important step to compare treatments efficiently and accurately. Spatial variability can be controlled at the experimental design level with the assignment of treatments to experimental units and at the modeling level with the use of spatial corrections and other modeling strategies. The goal of this study was to compare the efficiency of methods used to control spatial variation in a wide range of scenarios using a simulation approach based on real wheat data. Specifically, classic and spatial experimental designs with and without a twodimensional autoregressive spatial correction were evaluated in scenarios that include differing experimental unit sizes, experiment sizes, relationships among genotypes, genotype by environment interaction levels, and trait heritabilities. Fully replicated designs outperformed partially and unreplicated designs in terms of accuracy; the alpha-lattice incomplete block design was best in all scenarios of the medium-sized experiments.
However, in terms of response to selection, partially replicated experiments that evaluate large population sizes were superior in most scenarios. The AR1×AR1 spatial correction had little benefit in most scenarios except for the medium-sized experiments with the largest experimental unit size and low GE. Overall, the results from this study provide a guide to researchers designing and analyzing large field experiments. Supplementary materials accompanying this paper appear online. MenosControlling spatial variation in agricultural field trials is the most important step to compare treatments efficiently and accurately. Spatial variability can be controlled at the experimental design level with the assignment of treatments to experimental units and at the modeling level with the use of spatial corrections and other modeling strategies. The goal of this study was to compare the efficiency of methods used to control spatial variation in a wide range of scenarios using a simulation approach based on real wheat data. Specifically, classic and spatial experimental designs with and without a twodimensional autoregressive spatial correction were evaluated in scenarios that include differing experimental unit sizes, experiment sizes, relationships among genotypes, genotype by environment interaction levels, and trait heritabilities. Fully replicated designs outperformed partially and unreplicated designs in terms of accuracy; the alpha-lattice incomplete block design was best in all scenarios of the medium-sized experiments.
However, in terms of response to selection, partially replicated experiments that evaluate large population sizes were superior in most scenarios. The AR1×AR1 spatial correction had little benefit in most scenarios except for the medium-sized experiments with the largest experimental unit size and low GE. Overall, the results from this study provide a guide to researchers designing and analyzing large field experiments. Supplementary materials ... Presentar Todo |
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Palabras claves : |
AUTOREGRESSIVE PROCESS; EXPERIMENTAL DESIGN; PREDICTION ACCURACY; RANDOMIZATION-BASED EXPERIMENTAL DESIGNS; RESPONSE TO SELECTION; SPATIAL CORRECTION. |
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Thesagro : |
DISENO EXPERIMENTAL. |
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Asunto categoría : |
-- |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/16700/1/JABES-2020.pdf
https://link.springer.com/content/pdf/10.1007/s13253-020-00406-2.pdf
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Marc : |
LEADER 03067naa a2200349 a 4500
001 1061304
005 2022-09-05
008 2020 bl uuuu u00u1 u #d
024 7 $a10.1007/s13253-020-00406-2$2DOI
100 1 $aRAEGAN HOEFLER
245 $aDo Spatial Designs Outperform Classic Experimental Designs?.$h[electronic resource]
260 $c2020
500 $aArticle history: Received 15 October 2019/Accepted 01 July 2020/Published 29 August 2020. This project was partially funded through a USDA_AFRI_NIFA_2018-67013-27620 award and by the Hatch Act Formula Fund WISO1984 and WIS03002. Additionally, JARN received funding from CAPES CAPES_PrInt_UFLA 88887.318846_2019-00 as Senior Visiting Professor at the University of Wisconsin-Madison.
520 $aControlling spatial variation in agricultural field trials is the most important step to compare treatments efficiently and accurately. Spatial variability can be controlled at the experimental design level with the assignment of treatments to experimental units and at the modeling level with the use of spatial corrections and other modeling strategies. The goal of this study was to compare the efficiency of methods used to control spatial variation in a wide range of scenarios using a simulation approach based on real wheat data. Specifically, classic and spatial experimental designs with and without a twodimensional autoregressive spatial correction were evaluated in scenarios that include differing experimental unit sizes, experiment sizes, relationships among genotypes, genotype by environment interaction levels, and trait heritabilities. Fully replicated designs outperformed partially and unreplicated designs in terms of accuracy; the alpha-lattice incomplete block design was best in all scenarios of the medium-sized experiments. However, in terms of response to selection, partially replicated experiments that evaluate large population sizes were superior in most scenarios. The AR1×AR1 spatial correction had little benefit in most scenarios except for the medium-sized experiments with the largest experimental unit size and low GE. Overall, the results from this study provide a guide to researchers designing and analyzing large field experiments. Supplementary materials accompanying this paper appear online.
650 $aDISENO EXPERIMENTAL
653 $aAUTOREGRESSIVE PROCESS
653 $aEXPERIMENTAL DESIGN
653 $aPREDICTION ACCURACY
653 $aRANDOMIZATION-BASED EXPERIMENTAL DESIGNS
653 $aRESPONSE TO SELECTION
653 $aSPATIAL CORRECTION
700 1 $aGONZALEZ-BARRIOS , P.
700 1 $aMADHAV BHATTA
700 1 $aNUNES, J.A.R.
700 1 $aBERRO, I.
700 1 $aNALIN, R.S.
700 1 $aBORGES, A.
700 1 $aCOVARRUBIAS, E.
700 1 $aDIAZ-GARCIA, L.
700 1 $aQUINCKE, M.
700 1 $aGUTIERREZ, L.
773 $tJournal of Agricultural, Biological, and Environmental Statistics, 1 December 2020, volume 25, number 4, pag.523-552, 1 December 2020. OPEN ACCESS. Doi: https://doi.org/10.1007/s13253-020-00406-2
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