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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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INIA La Estanzuela (LE) |
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 | Acceso al texto completo restringido a Biblioteca INIA Las Brujas. Por información adicional contacte bibliolb@inia.org.uy. |
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Registro completo
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Biblioteca (s) : |
INIA Las Brujas; INIA Treinta y Tres. |
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Fecha actual : |
12/11/2015 |
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Actualizado : |
09/10/2019 |
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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 : |
MARCAIDA, M.; ASSENG, S.; EWERT, F.; BASSU, S.; DURAND, J.L.; LI, T.; MARTRE, P.; ADAM, M.; AGGARWAL, P.K.; ANGULO, C.; BARON, C.; BASSO, B.; BERTUZZI, P.; BIERNATH, C.; BOOGAARD, H.; BOOTE, K.J.; BOUMAN, B.; BREGAGLIO, S.; BRISSON, N.; BUIS, S.; CAMMARANO, D.; CHALLINOR, A.J.; CONFALONIERI, R.; CONIJN, J.G.; CORBEELS, M.; DERYNG, D.; DE SANCTIS, G.; DOLTRA, J.; FUMOTO, T.; GAYDON, D.; GAYLER, S.; GOLDBERG, R.; GRANT, R.F.; GRASSINI, P.; HATFIELD, J.L.; HASEGAWA, T.; HENG, L.; HOEK, S.; HOOKER, J.; HUNT, L.A.; INGWERSEN, J.; IZAURRALDE, R.C.; JONGSCHAAP, R.E.E.; JONES, J.W.; KEMANIAN, R.A.; KERSEBAUM, K.C.; KIM, S.-H.; LIZASO, J.; MÜLLER, C.; NAKAGAWA, H.; NARESH KUMAR, S.; NENDEL, C.; O'LEARY, G.J.; OLESEN, J.E.; ORIOL, P.; OSBORNE, T.M.; PALOSUO, T.; PRAVIA, V.; PRIESACK, E.; RIPOCHE, D.; ROSENZWEIG, C.; RUANE, A.C.; RUGET, F.; SAU, F.; SEMENOV, M.A.; SHCHERBAK, I.; SINGH, B.; SINGH, U.; SOO, H.K.; STEDUTO, P.; STÖCKLE, C.; STRATONOVITCH, P.; STRECK, T.; SUPIT, I.; TANG, L.; TAO, F.; TEIXEIRA, E.I.; THORBURN, P.; TIMLIN, D.; TRAVASSO, M.; RÖTTER, R.P.; WAHA, K.; WALLACH, D.; WHITE, J.W.; WILKENS, P.; WILLIAMS, J.R.; WOLF, J.; YIN, X.; YOSHIDA, H.; ZHANG, Z.; ZHU, Y. |
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Afiliación : |
MARIA VIRGINIA PRAVIA NIN, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
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Título : |
A statistical analysis of three ensembles of crop model responses to temperature and CO2 concentration. |
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Fecha de publicación : |
2015 |
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Fuente / Imprenta : |
Agricultural and Forest Meteorology, 2015, v.214-215, p. 483-493. |
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ISSN : |
0168-1923 |
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DOI : |
10.1016/j.agrformet.2015.09.013 |
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Idioma : |
Inglés |
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Notas : |
Article history: Received 6 March 2015 / Received in revised form 29 July 2015 / Accepted 20 September 2015 / Available online 1 October 2015. |
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Contenido : |
ABSTRACT.
Ensembles of process-based crop models are increasingly used to simulate crop growth for scenariosof temperature and/or precipitation changes corresponding to different projections of atmospheric CO2concentrations. This approach generates large datasets with thousands of simulated crop yield data. Suchdatasets potentially provide new information but it is difficult to summarize them in a useful way due totheir structural complexities. An associated issue is that it is not straightforward to compare crops and tointerpolate the results to alternative climate scenarios not initially included in the simulation protocols.Here we demonstrate that statistical models based on random-coefficient regressions are able to emulateensembles of process-based crop models. An important advantage of the proposed statistical models isthat they can interpolate between temperature levels and between CO2concentration levels, and canthus be used to calculate temperature and [CO2] thresholds leading to yield loss or yield gain, without re-running the original complex crop models. Our approach is illustrated with three yield datasets simulatedby 19 maize models, 26 wheat models, and 13 rice models. Several statistical models are fitted to thesedatasets, and are then used to analyze the variability of the yield response to [CO2] and temperature.Based on our results, we show that, for wheat, a [CO2] increase is likely to outweigh the negative effectof a temperature increase of +2◦C in the considered sites. Compared to wheat, required levels of [CO2]increase are much higher for maize, and intermediate for rice. For all crops, uncertainties in simulatingclimate change impacts increase more with temperature than with elevated [CO2].
© 2015 Elsevier B.V. All rights reserved. MenosABSTRACT.
Ensembles of process-based crop models are increasingly used to simulate crop growth for scenariosof temperature and/or precipitation changes corresponding to different projections of atmospheric CO2concentrations. This approach generates large datasets with thousands of simulated crop yield data. Suchdatasets potentially provide new information but it is difficult to summarize them in a useful way due totheir structural complexities. An associated issue is that it is not straightforward to compare crops and tointerpolate the results to alternative climate scenarios not initially included in the simulation protocols.Here we demonstrate that statistical models based on random-coefficient regressions are able to emulateensembles of process-based crop models. An important advantage of the proposed statistical models isthat they can interpolate between temperature levels and between CO2concentration levels, and canthus be used to calculate temperature and [CO2] thresholds leading to yield loss or yield gain, without re-running the original complex crop models. Our approach is illustrated with three yield datasets simulatedby 19 maize models, 26 wheat models, and 13 rice models. Several statistical models are fitted to thesedatasets, and are then used to analyze the variability of the yield response to [CO2] and temperature.Based on our results, we show that, for wheat, a [CO2] increase is likely to outweigh the negative effectof a temperature increase of +2◦C in... Presentar Todo |
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Palabras claves : |
Climate change; CROP MODEL; Emulator; MAIZE; Meta-model; MODELIZACIÓN DE LOS CULTIVOS; RICE; Statistical model; WHEAT; Yield. |
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Thesagro : |
ARROZ; CAMBIO CLIMÁTICO; MAÍZ; MODELOS ESTADISTICOS; TRIGO. |
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Asunto categoría : |
A50 Investigación agraria |
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Marc : |
LEADER 05363naa a2201417 a 4500
001 1053856
005 2019-10-09
008 2015 bl uuuu u00u1 u #d
022 $a0168-1923
024 7 $a10.1016/j.agrformet.2015.09.013$2DOI
100 1 $aMARCAIDA, M.
245 $aA statistical analysis of three ensembles of crop model responses to temperature and CO2 concentration.
260 $c2015
500 $aArticle history: Received 6 March 2015 / Received in revised form 29 July 2015 / Accepted 20 September 2015 / Available online 1 October 2015.
520 $aABSTRACT. Ensembles of process-based crop models are increasingly used to simulate crop growth for scenariosof temperature and/or precipitation changes corresponding to different projections of atmospheric CO2concentrations. This approach generates large datasets with thousands of simulated crop yield data. Suchdatasets potentially provide new information but it is difficult to summarize them in a useful way due totheir structural complexities. An associated issue is that it is not straightforward to compare crops and tointerpolate the results to alternative climate scenarios not initially included in the simulation protocols.Here we demonstrate that statistical models based on random-coefficient regressions are able to emulateensembles of process-based crop models. An important advantage of the proposed statistical models isthat they can interpolate between temperature levels and between CO2concentration levels, and canthus be used to calculate temperature and [CO2] thresholds leading to yield loss or yield gain, without re-running the original complex crop models. Our approach is illustrated with three yield datasets simulatedby 19 maize models, 26 wheat models, and 13 rice models. Several statistical models are fitted to thesedatasets, and are then used to analyze the variability of the yield response to [CO2] and temperature.Based on our results, we show that, for wheat, a [CO2] increase is likely to outweigh the negative effectof a temperature increase of +2◦C in the considered sites. Compared to wheat, required levels of [CO2]increase are much higher for maize, and intermediate for rice. For all crops, uncertainties in simulatingclimate change impacts increase more with temperature than with elevated [CO2]. © 2015 Elsevier B.V. All rights reserved.
650 $aARROZ
650 $aCAMBIO CLIMÁTICO
650 $aMAÍZ
650 $aMODELOS ESTADISTICOS
650 $aTRIGO
653 $aClimate change
653 $aCROP MODEL
653 $aEmulator
653 $aMAIZE
653 $aMeta-model
653 $aMODELIZACIÓN DE LOS CULTIVOS
653 $aRICE
653 $aStatistical model
653 $aWHEAT
653 $aYield
700 1 $aASSENG, S.
700 1 $aEWERT, F.
700 1 $aBASSU, S.
700 1 $aDURAND, J.L.
700 1 $aLI, T.
700 1 $aMARTRE, P.
700 1 $aADAM, M.
700 1 $aAGGARWAL, P.K.
700 1 $aANGULO, C.
700 1 $aBARON, C.
700 1 $aBASSO, B.
700 1 $aBERTUZZI, P.
700 1 $aBIERNATH, C.
700 1 $aBOOGAARD, H.
700 1 $aBOOTE, K.J.
700 1 $aBOUMAN, B.
700 1 $aBREGAGLIO, S.
700 1 $aBRISSON, N.
700 1 $aBUIS, S.
700 1 $aCAMMARANO, D.
700 1 $aCHALLINOR, A.J.
700 1 $aCONFALONIERI, R.
700 1 $aCONIJN, J.G.
700 1 $aCORBEELS, M.
700 1 $aDERYNG, D.
700 1 $aDE SANCTIS, G.
700 1 $aDOLTRA, J.
700 1 $aFUMOTO, T.
700 1 $aGAYDON, D.
700 1 $aGAYLER, S.
700 1 $aGOLDBERG, R.
700 1 $aGRANT, R.F.
700 1 $aGRASSINI, P.
700 1 $aHATFIELD, J.L.
700 1 $aHASEGAWA, T.
700 1 $aHENG, L.
700 1 $aHOEK, S.
700 1 $aHOOKER, J.
700 1 $aHUNT, L.A.
700 1 $aINGWERSEN, J.
700 1 $aIZAURRALDE, R.C.
700 1 $aJONGSCHAAP, R.E.E.
700 1 $aJONES, J.W.
700 1 $aKEMANIAN, R.A.
700 1 $aKERSEBAUM, K.C.
700 1 $aKIM, S.-H.
700 1 $aLIZASO, J.
700 1 $aMÜLLER, C.
700 1 $aNAKAGAWA, H.
700 1 $aNARESH KUMAR, S.
700 1 $aNENDEL, C.
700 1 $aO'LEARY, G.J.
700 1 $aOLESEN, J.E.
700 1 $aORIOL, P.
700 1 $aOSBORNE, T.M.
700 1 $aPALOSUO, T.
700 1 $aPRAVIA, V.
700 1 $aPRIESACK, E.
700 1 $aRIPOCHE, D.
700 1 $aROSENZWEIG, C.
700 1 $aRUANE, A.C.
700 1 $aRUGET, F.
700 1 $aSAU, F.
700 1 $aSEMENOV, M.A.
700 1 $aSHCHERBAK, I.
700 1 $aSINGH, B.
700 1 $aSINGH, U.
700 1 $aSOO, H.K.
700 1 $aSTEDUTO, P.
700 1 $aSTÖCKLE, C.
700 1 $aSTRATONOVITCH, P.
700 1 $aSTRECK, T.
700 1 $aSUPIT, I.
700 1 $aTANG, L.
700 1 $aTAO, F.
700 1 $aTEIXEIRA, E.I.
700 1 $aTHORBURN, P.
700 1 $aTIMLIN, D.
700 1 $aTRAVASSO, M.
700 1 $aRÖTTER, R.P.
700 1 $aWAHA, K.
700 1 $aWALLACH, D.
700 1 $aWHITE, J.W.
700 1 $aWILKENS, P.
700 1 $aWILLIAMS, J.R.
700 1 $aWOLF, J.
700 1 $aYIN, X.
700 1 $aYOSHIDA, H.
700 1 $aZHANG, Z.
700 1 $aZHU, Y.
773 $tAgricultural and Forest Meteorology, 2015$gv.214-215, p. 483-493.
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