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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha : |
29/09/2014 |
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Actualizado : |
15/10/2019 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
WANG, H.; MISZTAL, I.; AGUILAR, I.; LEGARRA, A.; MUIR, W.M. |
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Afiliación : |
IGNACIO AGUILAR GARCIA, Instituto Nacional de Investigación Agropecuaria (INIA), Uruguay. |
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Título : |
Genome-wide association mapping including phenotypes from relatives without genotypes. |
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Fecha de publicación : |
2012 |
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Fuente / Imprenta : |
Genetics Research, 2012, v.94, no.2, p.73-83. OPEN ACCESS. |
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ISSN : |
0016-6723 |
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DOI : |
10.1017/S0016672312000274 |
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Idioma : |
Inglés |
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Notas : |
Article history: Received 19 September 2011 / Revised 8 December 2011 and 9 March 2012. / Accepted 13 March 2012. |
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Contenido : |
ABSTRACT.
A common problem for genome-wide association analysis (GWAS) is lack of power for detection of quantitative trait loci (QTLs) and precision for fine mapping. Here, we present a statistical method, termed single-step GBLUP (ssGBLUP), which increases both power and precision without increasing genotyping costs by taking advantage of phenotypes from other related and unrelated subjects. The procedure achieves these goals by blending traditional pedigree relationships with those derived from genetic markers, and by conversion of estimated breeding values (EBVs) to marker effects and weights. Additionally, the application of mixed model approaches allow for both simple and complex analyses that involve multiple traits and confounding factors, such as environmental, epigenetic or maternal environmental effects. Efficiency of the method was examined using simulations with 15 800 subjects, of which 1500 were genotyped. Thirty QTLs were simulated across genome and assumed heritability was 05. Comparisons included ssGBLUP applied directly to phenotypes, BayesB and classical GWAS (CGWAS) with deregressed proofs. An average accuracy of prediction 089 was obtained by ssGBLUP after one iteration, which was 001 higher than by BayesB. Power and precision for GWAS applications were evaluated by the correlation between true QTL effects and the sum of m adjacent single nucleotide polymorphism (SNP) effects. The highest correlations were 082 and 074 for ssGBLUP and CGWAS with m=8, and 083 for BayesB with m=16. Standard deviations of the correlations across replicates were several times higher in BayesB than in ssGBLUP. The ssGBLUP method with marker weights is faster, more accurate and easier to implement for GWAS applications without computing pseudo-data.
© Cambridge University Press 2012. MenosABSTRACT.
A common problem for genome-wide association analysis (GWAS) is lack of power for detection of quantitative trait loci (QTLs) and precision for fine mapping. Here, we present a statistical method, termed single-step GBLUP (ssGBLUP), which increases both power and precision without increasing genotyping costs by taking advantage of phenotypes from other related and unrelated subjects. The procedure achieves these goals by blending traditional pedigree relationships with those derived from genetic markers, and by conversion of estimated breeding values (EBVs) to marker effects and weights. Additionally, the application of mixed model approaches allow for both simple and complex analyses that involve multiple traits and confounding factors, such as environmental, epigenetic or maternal environmental effects. Efficiency of the method was examined using simulations with 15 800 subjects, of which 1500 were genotyped. Thirty QTLs were simulated across genome and assumed heritability was 05. Comparisons included ssGBLUP applied directly to phenotypes, BayesB and classical GWAS (CGWAS) with deregressed proofs. An average accuracy of prediction 089 was obtained by ssGBLUP after one iteration, which was 001 higher than by BayesB. Power and precision for GWAS applications were evaluated by the correlation between true QTL effects and the sum of m adjacent single nucleotide polymorphism (SNP) effects. The highest correlations were 082 and 074 for ssGBLUP and CGWAS with m=8, an... Presentar Todo |
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Thesagro : |
ANIMALES; CRIA; FENOTIPOS; GENOTIPO; MARCADORES GENÉTICOS; MEJORAMIENTO GENÉTICO ANIMAL. |
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Asunto categoría : |
L10 Genética y mejoramiento animal |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/3348/1/Aguilar-I.-2012.-Genet.Res.Camb.-v.942-p.73-83.pdf
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Marc : |
LEADER 02696naa a2200277 a 4500
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008 2012 bl uuuu u00u1 u #d
022 $a0016-6723
024 7 $a10.1017/S0016672312000274$2DOI
100 1 $aWANG, H.
245 $aGenome-wide association mapping including phenotypes from relatives without genotypes.$h[electronic resource]
260 $c2012
500 $aArticle history: Received 19 September 2011 / Revised 8 December 2011 and 9 March 2012. / Accepted 13 March 2012.
520 $aABSTRACT. A common problem for genome-wide association analysis (GWAS) is lack of power for detection of quantitative trait loci (QTLs) and precision for fine mapping. Here, we present a statistical method, termed single-step GBLUP (ssGBLUP), which increases both power and precision without increasing genotyping costs by taking advantage of phenotypes from other related and unrelated subjects. The procedure achieves these goals by blending traditional pedigree relationships with those derived from genetic markers, and by conversion of estimated breeding values (EBVs) to marker effects and weights. Additionally, the application of mixed model approaches allow for both simple and complex analyses that involve multiple traits and confounding factors, such as environmental, epigenetic or maternal environmental effects. Efficiency of the method was examined using simulations with 15 800 subjects, of which 1500 were genotyped. Thirty QTLs were simulated across genome and assumed heritability was 05. Comparisons included ssGBLUP applied directly to phenotypes, BayesB and classical GWAS (CGWAS) with deregressed proofs. An average accuracy of prediction 089 was obtained by ssGBLUP after one iteration, which was 001 higher than by BayesB. Power and precision for GWAS applications were evaluated by the correlation between true QTL effects and the sum of m adjacent single nucleotide polymorphism (SNP) effects. The highest correlations were 082 and 074 for ssGBLUP and CGWAS with m=8, and 083 for BayesB with m=16. Standard deviations of the correlations across replicates were several times higher in BayesB than in ssGBLUP. The ssGBLUP method with marker weights is faster, more accurate and easier to implement for GWAS applications without computing pseudo-data. © Cambridge University Press 2012.
650 $aANIMALES
650 $aCRIA
650 $aFENOTIPOS
650 $aGENOTIPO
650 $aMARCADORES GENÉTICOS
650 $aMEJORAMIENTO GENÉTICO ANIMAL
700 1 $aMISZTAL, I.
700 1 $aAGUILAR, I.
700 1 $aLEGARRA, A.
700 1 $aMUIR, W.M.
773 $tGenetics Research, 2012$gv.94, no.2, p.73-83. 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 La Estanzuela; INIA Tacuarembó. |
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Fecha actual : |
21/02/2014 |
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Actualizado : |
16/06/2021 |
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Tipo de producción científica : |
Documentos |
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Autor : |
CAVESTANY, D. |
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Afiliación : |
DANIEL CAVESTANY BOCKING, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
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Título : |
Manejo reproductivo de la vaca lechera. |
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Fecha de publicación : |
1994 |
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Fuente / Imprenta : |
In: INIA La Estanzuela. Programa Nacional de Lechería. Jornada sobre presentación de resultados experimentales: ejercicio 1993. Colonia (UY): INIA La Estanzuela, 1994. |
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Páginas : |
p. 35-43 |
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Serie : |
(INIA Serie Actividades de Difusión; 21) |
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Idioma : |
Español |
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Thesagro : |
REPRODUCCION DIRIGIDA; SINCRONIZACION DEL CELO; VACAS LECHERAS. |
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Asunto categoría : |
-- |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/7361/1/UY.INIA.SAD.1994.n.21.pdf;#page=37
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Marc : |
LEADER 00607naa a2200169 a 4500
001 1047146
005 2021-06-16
008 1994 bl uuuu u00u1 u #d
100 1 $aCAVESTANY, D.
245 $aManejo reproductivo de la vaca lechera.
260 $c1994
300 $ap. 35-43
490 $a(INIA Serie Actividades de Difusión; 21)
650 $aREPRODUCCION DIRIGIDA
650 $aSINCRONIZACION DEL CELO
650 $aVACAS LECHERAS
773 $tIn: INIA La Estanzuela. Programa Nacional de Lechería. Jornada sobre presentación de resultados experimentales: ejercicio 1993. Colonia (UY): INIA La Estanzuela, 1994.
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