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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. |
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Fecha : |
16/03/2020 |
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Actualizado : |
10/08/2020 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
AGUILAR, I.; FERNÁNDEZ, E.N.; BLASCO, A.; RAVAGNOLO, O.; LEGARRA, A. |
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Afiliación : |
IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; EDUARDO N. FERNÁNDEZ, Cátedra de Mejora y Conservación de Recursos Genéticos e Instituto de Investigación sobre Producción Agropecuaria, Ambiente y Salud, Facultad de Ciencias Agrarias, UNLZ, Buenos Aires, Argentina; AGUSTÍN BLASCO, Institute for Animal Science and Technology, Universitat Politècnica de València, València, Spain; OLGA RAVAGNOLO GUMILA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ANDRÉS LEGARRA, UMR GenPhySE, INRA Toulouse, Castanet Tolosan, France. |
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Título : |
Effects of ignoring inbreeding in model-based accuracy for BLUP and SSGBLUP. |
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Fecha de publicación : |
2020 |
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Fuente / Imprenta : |
Journal of Animal Breeding and Genetics, 1 July 2020, Volume 137, Issue 4, pp. 356-364. Doi: https://doi.org/10.1111/jbg.12470 |
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ISSN : |
0931-2668 |
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DOI : |
10.1111/jbg.12470 |
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Idioma : |
Inglés |
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Notas : |
Article history: Received: 22 August 2019 / Revised: 10 December 2019 / Accepted: 11 January 2020 / First published:20 February 2020
Corresponding author: Aguilar, I.; email:iaguilar@inia.org.uy
Funding information: FEDER; INRA; Universidad Nacional de Lomas de Zamora; European Unions' Horizon 2020 Research & Innovation Programme, Grant/Award Number: N°772787 |
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Contenido : |
ABSTRACT.
Model-based accuracy, defined as the theoretical correlation between true and estimated breeding value, can be obtained for each individual as a function of its prediction error variance (PEV) and inbreeding coefficient F, in BLUP, GBLUP and SSGBLUP genetic evaluations. However, for computational convenience, inbreeding is often ignored in two places. First, in the computation of reliability = 1-PEV/(1 + F). Second, in the set-up, using Henderson's rules, of the inverse of the pedigree-based relationship matrix A. Both approximations have an effect in the computation of model-based accuracy and result in wrong values. In this work, first we present a reminder of the theory and extend it to SSGBLUP. Second, we quantify the error of ignoring inbreeding with real data in three scenarios: BLUP evaluation and SSGBLUP in Uruguayan dairy cattle, and BLUP evaluations in a line of rabbit closed for >40 generations with steady increase of inbreeding up to an average of 0.30. We show that ignoring inbreeding in the set-up of the A-inverse is equivalent to assume that non-inbred animals are actually inbred. This results in an increase of apparent PEV that is negligible for dairy cattle but considerable for rabbit. Ignoring inbreeding in reliability = 1-PEV/(1 + F) leads to underestimation of reliability for BLUP evaluations, and this underestimation is very large for rabbit. For SSGBLUP in dairy cattle, it leads to both underestimation and overestimation of reliability, both for genotyped and non-genotyped animals. We strongly recommend to include inbreeding both in the set-up of A-inverse and in the computation of reliability from PEVs.
© 2020 Blackwell Verlag GmbH MenosABSTRACT.
Model-based accuracy, defined as the theoretical correlation between true and estimated breeding value, can be obtained for each individual as a function of its prediction error variance (PEV) and inbreeding coefficient F, in BLUP, GBLUP and SSGBLUP genetic evaluations. However, for computational convenience, inbreeding is often ignored in two places. First, in the computation of reliability = 1-PEV/(1 + F). Second, in the set-up, using Henderson's rules, of the inverse of the pedigree-based relationship matrix A. Both approximations have an effect in the computation of model-based accuracy and result in wrong values. In this work, first we present a reminder of the theory and extend it to SSGBLUP. Second, we quantify the error of ignoring inbreeding with real data in three scenarios: BLUP evaluation and SSGBLUP in Uruguayan dairy cattle, and BLUP evaluations in a line of rabbit closed for >40 generations with steady increase of inbreeding up to an average of 0.30. We show that ignoring inbreeding in the set-up of the A-inverse is equivalent to assume that non-inbred animals are actually inbred. This results in an increase of apparent PEV that is negligible for dairy cattle but considerable for rabbit. Ignoring inbreeding in reliability = 1-PEV/(1 + F) leads to underestimation of reliability for BLUP evaluations, and this underestimation is very large for rabbit. For SSGBLUP in dairy cattle, it leads to both underestimation and overestimation of reliability, both f... Presentar Todo |
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Palabras claves : |
BREEDING; Genomic predictions; GENOMICS. |
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Asunto categoría : |
L10 Genética y mejoramiento animal |
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Marc : |
LEADER 02789naa a2200241 a 4500
001 1060921
005 2020-08-10
008 2020 bl uuuu u00u1 u #d
022 $a0931-2668
024 7 $a10.1111/jbg.12470$2DOI
100 1 $aAGUILAR, I.
245 $aEffects of ignoring inbreeding in model-based accuracy for BLUP and SSGBLUP.$h[electronic resource]
260 $c2020
500 $aArticle history: Received: 22 August 2019 / Revised: 10 December 2019 / Accepted: 11 January 2020 / First published:20 February 2020 Corresponding author: Aguilar, I.; email:iaguilar@inia.org.uy Funding information: FEDER; INRA; Universidad Nacional de Lomas de Zamora; European Unions' Horizon 2020 Research & Innovation Programme, Grant/Award Number: N°772787
520 $aABSTRACT. Model-based accuracy, defined as the theoretical correlation between true and estimated breeding value, can be obtained for each individual as a function of its prediction error variance (PEV) and inbreeding coefficient F, in BLUP, GBLUP and SSGBLUP genetic evaluations. However, for computational convenience, inbreeding is often ignored in two places. First, in the computation of reliability = 1-PEV/(1 + F). Second, in the set-up, using Henderson's rules, of the inverse of the pedigree-based relationship matrix A. Both approximations have an effect in the computation of model-based accuracy and result in wrong values. In this work, first we present a reminder of the theory and extend it to SSGBLUP. Second, we quantify the error of ignoring inbreeding with real data in three scenarios: BLUP evaluation and SSGBLUP in Uruguayan dairy cattle, and BLUP evaluations in a line of rabbit closed for >40 generations with steady increase of inbreeding up to an average of 0.30. We show that ignoring inbreeding in the set-up of the A-inverse is equivalent to assume that non-inbred animals are actually inbred. This results in an increase of apparent PEV that is negligible for dairy cattle but considerable for rabbit. Ignoring inbreeding in reliability = 1-PEV/(1 + F) leads to underestimation of reliability for BLUP evaluations, and this underestimation is very large for rabbit. For SSGBLUP in dairy cattle, it leads to both underestimation and overestimation of reliability, both for genotyped and non-genotyped animals. We strongly recommend to include inbreeding both in the set-up of A-inverse and in the computation of reliability from PEVs. © 2020 Blackwell Verlag GmbH
653 $aBREEDING
653 $aGenomic predictions
653 $aGENOMICS
700 1 $aFERNÁNDEZ, E.N.
700 1 $aBLASCO, A.
700 1 $aRAVAGNOLO, O.
700 1 $aLEGARRA, A.
773 $tJournal of Animal Breeding and Genetics, 1 July 2020, Volume 137, Issue 4, pp. 356-364. Doi: https://doi.org/10.1111/jbg.12470
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| 84. |  | CIAPPESONI, G.; RAVAGNOLO, O.; GIMENO, D.; MONTOSSI, F.; DE BARBIERI, I. Estimation of genetic parameters and genetic trends for wool production and quality for the Uruguayan Merino. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 8., Belo Horizonte, Minas Gerais, Brazil, August 13-18, 2006, p. 05.04. Acknowledgements: This work would not have been possible without the support of ARU (Asociación Rural del Uruguay) and SCMAU (Association of the Uruguayan Merino Breeders of Uruguay).| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 86. | | MARTÍNEZ, G.; LÓPEZ, R.; MACEDO, F.; LEMA, O.M.; RAVAGNOLO, O. Fixed environmental effects and connectedness of the genetic evaluation of the Limousin breed in Uruguay. [Fixed environmental effects and connectedness of the genetic evaluation of the Limousin breed in Uruguay]. Agrociencia Uruguay, 2020, v. 24, n. 1, Epub 01-Jun-2020. Doi: http://dx.doi.org/10.31285/agro.24.141 Article history: Received 17 Oct 2019 // Accepted 02 Apr 2020 // Published 15 May 2020.
Martinez-Boggio G, López R, Macedo F, Lema M, Ravagnolo O. Fixed environmental effects and connectedness of the genetic evaluation of the Limousin...| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Treinta y Tres. |
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| 87. | | RAVAGNOLO, O.; BRITO, G.; AGUILAR, I.; CIAPPESONI, G.; LEMA, O.M. Genetic parameters for ultrasound live traits in pasture fed Angus cattle. Volume Session:Species breeding: Beef cattle breeding - Poster Sessions, 0617. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 9., Leipzig, Germany, August 1-6, 2010. p. 0617. Acknowledgements: The authors thank the Uruguayan Aberdeen Angus Breed Association, ARU and the University of Agronomy for their collaboration during the last years. This work could not have been possible without financing and technical...| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 88. | | CORREA, D.; LEMA, O.M.; RAVAGNOLO, O.; CLARIGET, J.M.; LUZARDO, S.; BRITO, G. Effects of differences in level of post-weaning nutrition and in sire expected progeny differences for ribeye area on retail cuts yield in Hereford steers. Animal Production Science, 2020, 61(2), p. 172-178. DOI: https://doi.org/10.1071/AN19604 Article history: Received 25 October 2019, accepted 25 September 2020, published online 15 October 2020. Acknowledgements: The authors would like to thank INIA Uruguay for the funding which made this study possible. We would also like to...| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Tacuarembó; INIA Treinta y Tres. |
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| 89. | | AGUILAR, I.; FERNÁNDEZ, E.N.; BLASCO, A.; RAVAGNOLO, O.; LEGARRA, A. Effects of ignoring inbreeding in model-based accuracy for BLUP and SSGBLUP. Journal of Animal Breeding and Genetics, 1 July 2020, Volume 137, Issue 4, pp. 356-364. Doi: https://doi.org/10.1111/jbg.12470 Article history: Received: 22 August 2019 / Revised: 10 December 2019 / Accepted: 11 January 2020 / First published:20 February 2020
Corresponding author: Aguilar, I.; email:iaguilar@inia.org.uy
Funding information: FEDER; INRA;...| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
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| 97. | | CIAPPESONI, G.; GIMENO, D.; RAVAGNOLO, O.; DE BARBIERI, I.; MONTOSSI, F.; GRATTAROLA, M.; MEDEROS, A. Evaluación genética del núcleo fundacional: caracterización de los animales que se entregan. ln: INIA Tacuarembó. Unidad Experimental Glencoe. Proyecto Merino Fino del Uruguay: sexta distribución de carneros generados en el núcleo fundacional de merino fino de la Unidad Experimental Glencoe, INIA Tacuarembó, 1999 - 2005. 16 diciembre, Glencoe, Paysandú, 2005. Tacuarembó (Uruguay): INIA, 2005. p. 49-74 (INIA Serie Actividades de Difusión ; 439)| Biblioteca(s): INIA Tacuarembó. |
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| 100. | | CIAPPESONI, G.; GIMENO, D.; RAVAGNOLO, O.; DE BARBIERI, I.; AGUILAR, I.; MONTOSSI, F.; GRATTAROLA, M. Evaluación genética preliminar del Núcleo Fundacional Merino Fino: análisis combinado población Merino fino - generación 2003. ln: INIA Tacuarembó. Sociedad Criadores Merino Australiano del Uruguay. SUL. Proyecto Merino Fino del Uruguay: quinta distribución de carneros generados en el núcleo fundacional de merino fino de la Unidad Experimental Glencoe, INIA Tacuarembó, 1999 - 2004. Glencoe, Paysandú, 10 diciembre, 2004. Tacuarembó (Uruguay): INIA, 2004. p. 69-83 (INIA Serie Actividades de Difusión ; 392)| Biblioteca(s): INIA Tacuarembó. |
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