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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha : |
11/12/2018 |
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Actualizado : |
11/12/2018 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
ZHANG, X.; LOURENCO, D.; AGUILAR, I.; LEGARRA, A.; MISZTAL, I. |
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Afiliación : |
XINYUE ZHANG, Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, United States; DANIELA LOURENCO, Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, United States; IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ANDRÉS LEGARRA, INRA (Institut National de la Recherche Agronomique); IGNACY MISZTAL, Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, United States. |
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Título : |
Weighting strategies for single-step genomic BLUP: An iterative approach for accurate calculation of GEBV and GWAS. |
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Fecha de publicación : |
2016 |
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Fuente / Imprenta : |
Frontiers in Genetics, 19 August 2016, Volume 7, Issue AUG, Article number 151. OPEN ACCESS |
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ISSN : |
1664-8021 |
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DOI : |
10.3389/fgene.2016.00151 |
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Idioma : |
Inglés |
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Notas : |
Article history: Received 15 May 2016 // Accepted 04 August 2016 // Published 19 August 2016.
Specialty section:
This article was submitted to Statistical Genetics and Methodology, a section of the journal Frontiers in Genetics. |
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Contenido : |
ABSTRACT.
Genomic Best Linear Unbiased Predictor (GBLUP) assumes equal variance for all single nucleotide polymorphisms (SNP). When traits are influenced by major SNP, Bayesian methods have the advantage of SNP selection. To overcome the limitation of GBLUP, unequal variance or weights for all SNP are applied in a method called weighted GBLUP (WGBLUP). If only a fraction of animals is genotyped, single-step WGBLUP (WssGBLUP) can be used. Default weights in WGBLUP or WssGBLUP are obtained iteratively based on single SNP effect squared (u2) and/or heterozygosity. When the weights are optimal, prediction accuracy, and ability to detect major SNP are maximized. The objective was to develop optimal weights for WGBLUP-based methods. We evaluated 5 new procedures that accounted for locus-specific or windows-specific variance to maximize accuracy of predicting genomic estimated breeding value (GEBV) and SNP effect. Simulated datasets consisted of phenotypes for 13,000 animals, including 1540 animals genotyped for 45,000 SNP. Scenarios with 5, 100, and 500 simulated quantitative trait loci (QTL) were considered. The 5 new procedures for SNP weighting were: (1) u2 plus a constant equal to the weight of the top SNP; (2) from a heavy-tailed distribution (similar to BayesA); (3) for every 20 SNP in a window along the whole genome, the largest effect (u2) among them; (4) the mean effect of every 20 SNP; and (5) the summation of every 20 SNP. Those methods were compared to the default WssGBLUP, GBLUP, BayesB, and BayesC. WssGBLUP methods were evaluated over 10 iterations. The accuracy of predicting GEBV was the correlation between true and estimated genomic breeding values for 300 genotyped animals from the last generation. The ability to detect the simulated QTL was also investigated. For most of the QTL scenarios, the accuracies obtained with all WssGBLUP procedures were higher compared to those from BayesB and BayesC, partly due to automatic inclusion of parent average in the former. Manhattan plots had higher resolution with 5 and 100 QTL. Using a common weight for a window of 20 SNP that sums or averages the SNP variance enhances accuracy of predicting GEBV and provides accurate estimation of marker effects.
© 2016 Zhang, Lourenco, Aguilar, Legarra and Misztal. MenosABSTRACT.
Genomic Best Linear Unbiased Predictor (GBLUP) assumes equal variance for all single nucleotide polymorphisms (SNP). When traits are influenced by major SNP, Bayesian methods have the advantage of SNP selection. To overcome the limitation of GBLUP, unequal variance or weights for all SNP are applied in a method called weighted GBLUP (WGBLUP). If only a fraction of animals is genotyped, single-step WGBLUP (WssGBLUP) can be used. Default weights in WGBLUP or WssGBLUP are obtained iteratively based on single SNP effect squared (u2) and/or heterozygosity. When the weights are optimal, prediction accuracy, and ability to detect major SNP are maximized. The objective was to develop optimal weights for WGBLUP-based methods. We evaluated 5 new procedures that accounted for locus-specific or windows-specific variance to maximize accuracy of predicting genomic estimated breeding value (GEBV) and SNP effect. Simulated datasets consisted of phenotypes for 13,000 animals, including 1540 animals genotyped for 45,000 SNP. Scenarios with 5, 100, and 500 simulated quantitative trait loci (QTL) were considered. The 5 new procedures for SNP weighting were: (1) u2 plus a constant equal to the weight of the top SNP; (2) from a heavy-tailed distribution (similar to BayesA); (3) for every 20 SNP in a window along the whole genome, the largest effect (u2) among them; (4) the mean effect of every 20 SNP; and (5) the summation of every 20 SNP. Those methods were compared to the default WssG... Presentar Todo |
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Palabras claves : |
BayesB; BayesC; GENOME-WIDE ASSOCIATION; SNP WINDOW; WssGBLUP. |
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Asunto categoría : |
-- |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/12161/1/fgene-07-00151.pdf
https://www.frontiersin.org/articles/10.3389/fgene.2016.00151/full
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Marc : |
LEADER 03310naa a2200265 a 4500
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022 $a1664-8021
024 7 $a10.3389/fgene.2016.00151$2DOI
100 1 $aZHANG, X.
245 $aWeighting strategies for single-step genomic BLUP$bAn iterative approach for accurate calculation of GEBV and GWAS.$h[electronic resource]
260 $c2016
500 $aArticle history: Received 15 May 2016 // Accepted 04 August 2016 // Published 19 August 2016. Specialty section: This article was submitted to Statistical Genetics and Methodology, a section of the journal Frontiers in Genetics.
520 $aABSTRACT. Genomic Best Linear Unbiased Predictor (GBLUP) assumes equal variance for all single nucleotide polymorphisms (SNP). When traits are influenced by major SNP, Bayesian methods have the advantage of SNP selection. To overcome the limitation of GBLUP, unequal variance or weights for all SNP are applied in a method called weighted GBLUP (WGBLUP). If only a fraction of animals is genotyped, single-step WGBLUP (WssGBLUP) can be used. Default weights in WGBLUP or WssGBLUP are obtained iteratively based on single SNP effect squared (u2) and/or heterozygosity. When the weights are optimal, prediction accuracy, and ability to detect major SNP are maximized. The objective was to develop optimal weights for WGBLUP-based methods. We evaluated 5 new procedures that accounted for locus-specific or windows-specific variance to maximize accuracy of predicting genomic estimated breeding value (GEBV) and SNP effect. Simulated datasets consisted of phenotypes for 13,000 animals, including 1540 animals genotyped for 45,000 SNP. Scenarios with 5, 100, and 500 simulated quantitative trait loci (QTL) were considered. The 5 new procedures for SNP weighting were: (1) u2 plus a constant equal to the weight of the top SNP; (2) from a heavy-tailed distribution (similar to BayesA); (3) for every 20 SNP in a window along the whole genome, the largest effect (u2) among them; (4) the mean effect of every 20 SNP; and (5) the summation of every 20 SNP. Those methods were compared to the default WssGBLUP, GBLUP, BayesB, and BayesC. WssGBLUP methods were evaluated over 10 iterations. The accuracy of predicting GEBV was the correlation between true and estimated genomic breeding values for 300 genotyped animals from the last generation. The ability to detect the simulated QTL was also investigated. For most of the QTL scenarios, the accuracies obtained with all WssGBLUP procedures were higher compared to those from BayesB and BayesC, partly due to automatic inclusion of parent average in the former. Manhattan plots had higher resolution with 5 and 100 QTL. Using a common weight for a window of 20 SNP that sums or averages the SNP variance enhances accuracy of predicting GEBV and provides accurate estimation of marker effects. © 2016 Zhang, Lourenco, Aguilar, Legarra and Misztal.
653 $aBayesB
653 $aBayesC
653 $aGENOME-WIDE ASSOCIATION
653 $aSNP WINDOW
653 $aWssGBLUP
700 1 $aLOURENCO, D.
700 1 $aAGUILAR, I.
700 1 $aLEGARRA, A.
700 1 $aMISZTAL, I.
773 $tFrontiers in Genetics, 19 August 2016, Volume 7, Issue AUG, Article number 151. OPEN ACCESS
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Registro original : |
INIA Las Brujas (LB) |
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Registro completo
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Biblioteca (s) : |
INIA Tacuarembó. |
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Fecha actual : |
21/02/2014 |
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Actualizado : |
30/06/2022 |
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Tipo de producción científica : |
Documentos |
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Autor : |
BENNADJI, Z.; ALFONSO, M.; NUÑEZ, P.; GONZALEZ, W.; LEMOS, J.; RODRIGUEZ, F. |
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Afiliación : |
ZOHRA BENNADJI SOUALHIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; MARCELO FABIAN ALFONSO DEL PINO, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; PABLO TABARE NUÑEZ RODRIGUEZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; CARLOS WILFREDO GONZALEZ BENAVIDEZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; JORGE DANIEL LEMOS LIMA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; FEDERICO GONZALO RODRIGUEZ ALBORNOZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
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Título : |
Evaluación del comportamiento productivo de procedencias de dos especies forestales multipropósito (ñandubay y pecan) en zona sur. |
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Fecha de publicación : |
2012 |
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Fuente / Imprenta : |
ln: Jornada Técnica. 26 de Abril de 2012, Maldonado, (UY) Benadji, Z. Diversificación de especies forestales en zona sur. Tacuarembó (Uruguay): INIA Tacuarembó, 2012. |
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Páginas : |
p. 35-42 |
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Serie : |
(INIA Serie Actividades de Difusión; 680) |
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Idioma : |
Español |
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Notas : |
Programa Nacional de Investigación en Producción Forestal. INIA Tacuarembó. Escuela Agraria Los Arrayanes, UTU. |
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Thesagro : |
CARYA ILLINOINENSIS; PROSOPIS AFFINIS. |
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Asunto categoría : |
K10 Producción forestal |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/1733/1/112935270412090812.pdf
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Marc : |
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245 $aEvaluación del comportamiento productivo de procedencias de dos especies forestales multipropósito (ñandubay y pecan) en zona sur.
260 $c2012
300 $ap. 35-42
490 $a(INIA Serie Actividades de Difusión; 680)
500 $aPrograma Nacional de Investigación en Producción Forestal. INIA Tacuarembó. Escuela Agraria Los Arrayanes, UTU.
650 $aCARYA ILLINOINENSIS
650 $aPROSOPIS AFFINIS
700 1 $aALFONSO, M.
700 1 $aNUÑEZ, P.
700 1 $aGONZALEZ, W.
700 1 $aLEMOS, J.
700 1 $aRODRIGUEZ, F.
773 $tln: Jornada Técnica. 26 de Abril de 2012, Maldonado, (UY) Benadji, Z. Diversificación de especies forestales en zona sur. Tacuarembó (Uruguay): INIA Tacuarembó, 2012.
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INIA Tacuarembó (TBO) |
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