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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha : |
16/08/2022 |
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Actualizado : |
27/04/2023 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
MCWHORTER, T.M.; BERMANN, M.; GARCIA, A.L.S.; LEGARRA, A.; AGUILAR, I.; MISZTAL, I.; LOURENCO, D. |
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Afiliación : |
TAYLOR M. MCWHORTER, Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, USA; MATIAS BERMANN, Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, USA; ANDRE L. S. GARCIA, Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, USA; ANDRÉS LEGARRA, UMR GenPhySE, Institut National de la Recherche Agronomique, Castanet- Tolosan, France; IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; IGNACY MISZTAL, Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, USA; DANIELA LOURENCO, Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, USA. |
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Título : |
Implication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP. |
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Fecha de publicación : |
2023 |
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Fuente / Imprenta : |
Journal of Animal Breeding and Genetics, 2023, volume 140, issue 1, pp. 60-78. OPEN ACCESS. doi: https://doi.org/10.1111/jbg.12734 |
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ISSN : |
0931-2668; eISSN: 1439-0388 |
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DOI : |
10.1111/jbg.12734 |
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Idioma : |
Inglés |
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Notas : |
Article history: Received 18 March 2019; Revised 15 July 2019; Accepted: 29 July 2019; First published 10 August 2022.
Correspondence: McWhorter, T.M.; Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States; email:taylor.mcwhorter@uga.edu --
This study was partially funded by Agriculture and Food Research Initiative Competitive Grant no. 2020?67015?31030 from the U.S. Department of Agriculture, Australian Government's National Institute of Food and Agriculture (Washington, DC). -- This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. License Creative Commons: https://creativecommons.org/licenses/by-nc-nd/4.0/ |
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Contenido : |
ABSTRACT.- Single-step genomic BLUP (ssGBLUP) relies on the combination of the genomic ((Formula presented.)) and pedigree relationship matrices for all ((Formula presented.)) and genotyped ((Formula presented.)) animals. The procedure ensures (Formula presented.) and (Formula presented.) are compatible so that both matrices refer to the same genetic base (?tuning?). Then (Formula presented.) is combined with a proportion of (Formula presented.) (?blending?) to avoid singularity problems and to account for the polygenic component not accounted for by markers. This computational procedure has been implemented in the reverse order (blending before tuning) following the sequential research developments. However, blending before tuning may result in less optimal tuning because the blended matrix already contains a proportion of (Formula presented.). In this study, the impact of ?tuning before blending? was compared with ?blending before tuning? on genomic estimated breeding values (GEBV), single nucleotide polymorphism (SNP) effects and indirect predictions (IP) from ssGBLUP using American Angus Association and Holstein Association USA, Inc. data. Two slightly different tuning methods were used; one that adjusts the mean diagonals and off-diagonals of (Formula presented.) to be similar to those in (Formula presented.) and another one that adjusts based on the average difference between all elements of (Formula presented.) and (Formula presented.). Over 6 million Angus growth records and 5.9 million Holstein udder depth records were available. Genomic information was available on 51,478 Angus and 105,116 Holstein animals. Average realized relationship estimates among groups of animals were similar across scenarios. Scatterplots show that GEBV, SNP effects and IP did not noticeably change for all animals in the evaluation regardless of the order of computations and when using blending parameter of 0.05. Formulas were derived to determine the blending parameter that maximizes changes in the genomic relationship matrix and GEBV when changing the order of blending and tuning. Algebraically, the change is maximized when the blending parameter is equal to 0.5. Overall, tuning (Formula presented.) before blending, regardless of blending parameter used, had a negligible impact on genomic predictions and SNP effects in this study. © 2022 The Authors. Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd. MenosABSTRACT.- Single-step genomic BLUP (ssGBLUP) relies on the combination of the genomic ((Formula presented.)) and pedigree relationship matrices for all ((Formula presented.)) and genotyped ((Formula presented.)) animals. The procedure ensures (Formula presented.) and (Formula presented.) are compatible so that both matrices refer to the same genetic base (?tuning?). Then (Formula presented.) is combined with a proportion of (Formula presented.) (?blending?) to avoid singularity problems and to account for the polygenic component not accounted for by markers. This computational procedure has been implemented in the reverse order (blending before tuning) following the sequential research developments. However, blending before tuning may result in less optimal tuning because the blended matrix already contains a proportion of (Formula presented.). In this study, the impact of ?tuning before blending? was compared with ?blending before tuning? on genomic estimated breeding values (GEBV), single nucleotide polymorphism (SNP) effects and indirect predictions (IP) from ssGBLUP using American Angus Association and Holstein Association USA, Inc. data. Two slightly different tuning methods were used; one that adjusts the mean diagonals and off-diagonals of (Formula presented.) to be similar to those in (Formula presented.) and another one that adjusts based on the average difference between all elements of (Formula presented.) and (Formula presented.). Over 6 million Angus growth rec... Presentar Todo |
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Palabras claves : |
Genetic base; Indirect predictions; Residual polygenic effect; Scaling of genomic matrices; Single-step genomic best linear unbiased prediction. |
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Asunto categoría : |
L10 Genética y mejoramiento animal |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/16748/1/J-Animal-Breeding-Genetics-2022-McWhorter-Implication-of-the-order-of-blending-and-tuning-when-computing-the-genomic.pdf
https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/jbg.12734?download=true
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Marc : |
LEADER 04321naa a2200289 a 4500
001 1063528
005 2023-04-27
008 2023 bl uuuu u00u1 u #d
022 $a0931-2668; eISSN: 1439-0388
024 7 $a10.1111/jbg.12734$2DOI
100 1 $aMCWHORTER, T.M.
245 $aImplication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP.$h[electronic resource]
260 $c2023
500 $aArticle history: Received 18 March 2019; Revised 15 July 2019; Accepted: 29 July 2019; First published 10 August 2022. Correspondence: McWhorter, T.M.; Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States; email:taylor.mcwhorter@uga.edu -- This study was partially funded by Agriculture and Food Research Initiative Competitive Grant no. 2020?67015?31030 from the U.S. Department of Agriculture, Australian Government's National Institute of Food and Agriculture (Washington, DC). -- This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. License Creative Commons: https://creativecommons.org/licenses/by-nc-nd/4.0/
520 $aABSTRACT.- Single-step genomic BLUP (ssGBLUP) relies on the combination of the genomic ((Formula presented.)) and pedigree relationship matrices for all ((Formula presented.)) and genotyped ((Formula presented.)) animals. The procedure ensures (Formula presented.) and (Formula presented.) are compatible so that both matrices refer to the same genetic base (?tuning?). Then (Formula presented.) is combined with a proportion of (Formula presented.) (?blending?) to avoid singularity problems and to account for the polygenic component not accounted for by markers. This computational procedure has been implemented in the reverse order (blending before tuning) following the sequential research developments. However, blending before tuning may result in less optimal tuning because the blended matrix already contains a proportion of (Formula presented.). In this study, the impact of ?tuning before blending? was compared with ?blending before tuning? on genomic estimated breeding values (GEBV), single nucleotide polymorphism (SNP) effects and indirect predictions (IP) from ssGBLUP using American Angus Association and Holstein Association USA, Inc. data. Two slightly different tuning methods were used; one that adjusts the mean diagonals and off-diagonals of (Formula presented.) to be similar to those in (Formula presented.) and another one that adjusts based on the average difference between all elements of (Formula presented.) and (Formula presented.). Over 6 million Angus growth records and 5.9 million Holstein udder depth records were available. Genomic information was available on 51,478 Angus and 105,116 Holstein animals. Average realized relationship estimates among groups of animals were similar across scenarios. Scatterplots show that GEBV, SNP effects and IP did not noticeably change for all animals in the evaluation regardless of the order of computations and when using blending parameter of 0.05. Formulas were derived to determine the blending parameter that maximizes changes in the genomic relationship matrix and GEBV when changing the order of blending and tuning. Algebraically, the change is maximized when the blending parameter is equal to 0.5. Overall, tuning (Formula presented.) before blending, regardless of blending parameter used, had a negligible impact on genomic predictions and SNP effects in this study. © 2022 The Authors. Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd.
653 $aGenetic base
653 $aIndirect predictions
653 $aResidual polygenic effect
653 $aScaling of genomic matrices
653 $aSingle-step genomic best linear unbiased prediction
700 1 $aBERMANN, M.
700 1 $aGARCIA, A.L.S.
700 1 $aLEGARRA, A.
700 1 $aAGUILAR, I.
700 1 $aMISZTAL, I.
700 1 $aLOURENCO, D.
773 $tJournal of Animal Breeding and Genetics, 2023, volume 140, issue 1, pp. 60-78. OPEN ACCESS. doi: https://doi.org/10.1111/jbg.12734
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| 3. |  | ALZUGARAY, R. Avispita del lotus I. Actualización de información tecnológica sobre pasturas sembradas In: RESTAINO, E.; INDARTE, E. (Eds.). Pasturas y Producción Animal en Areas de Ganadería Intensiva Montevideo (Uruguay): INIA, 1997. p. 43-47 (INIA Serie Técnica ; 15)| Tipo: Capítulo en Libro Técnico-Científico |
| Biblioteca(s): INIA La Estanzuela; INIA Las Brujas; INIA Tacuarembó. |
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| 5. | | Alzugaray, R. Control químico de Isocas ln: Jornada Cultivos de Invierno, 1990 abr 26 : La Estanzuela [Memorias]. Montevideo (Uruguay): CIAAB, 1990. p1-5 (sic) Jornada Cultivos de Invierno (CIAAB)| Biblioteca(s): INIA La Estanzuela. |
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| 8. | | Alzugaray, R. Manejo de insectos ln: Rebuffo, M., ed; Risso, D.F., ed; Restaino, E., ed. Tecnología en alfalfa. Montevideo: INIA, 2000. p. 115-123 Boletín de Divulgación| Biblioteca(s): INIA La Estanzuela. |
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| 14. | | ALZUGARAY, R.; ÁVILA, S. Acerca de los cascarudos negros Revista INIA, 2006, no. 9, p. 21-23 Los Ing. Agr. Enrique Deambrosi (INIA Treinta y Tres) y Hernán Zorrilla (Asesor privado) aportaron sus observaciones de la zafra 2005-2006.| Tipo: Artículos en Revistas Agropecuarias |
| Biblioteca(s): INIA La Estanzuela; INIA Las Brujas; INIA Tacuarembó; INIA Treinta y Tres. |
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| 17. | | ALZUGARAY, R.; CASCO, M. Métodos de control de pulgones. In:REUNIÓN TÉCNICA (2013, LA ESTANZUELA, COLONIA, UY): el éxito productivo de una pastura con leguminosas perennes comienza en su implantación.La Estanzuela, Colonia: INIA, 2013. p. 11-12. (Serie Actividades de Difusión ; 711).| Tipo: Actividades de Difusión |
| Biblioteca(s): INIA La Estanzuela. |
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| 18. | | ALZUGARAY, R.; RIBEIRO, A. Insectos en pasturas In: ZERBINO, M.S.; RIBEIRO,A. (Eds.). Manejo de plagas en pasturas y cultivos. Montevideo (Uruguay): INIA, 2000. p. 13-30 (INIA Serie Técnica ; 112)| Tipo: Capítulo en Libro Técnico-Científico |
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