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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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INIA Las Brujas (LB) |
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| 141. |  | MACEDO, I.; CASTILLO, J.; SALDAIN, N.E.; MARTÍNEZ, S.; BERMÚDEZ, R.; AYALA, W.; HERNANDEZ, J.; TERRA, J.A. Rotaciones arroceras: resultados productivos en las primeras tres zafras. ln: [JORNADA ANUAL] ARROZ-SOJA, 2015, Treinta y Tres, UY. Resultados experimentales 2014-2015. Treinta y Tres: INIA, 2015. Cap. 6, p.1-3. (INIA Serie Actividades de Difusión; 748)| Biblioteca(s): INIA Tacuarembó; INIA Treinta y Tres. |
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| 143. | | BAO, L.; GINELLA, J.; CADENAZZI, M.; CASTIGLIONI, E.A.; MARTÍNEZ, S.; CASALES, L.; CARABALLO, M.P.; LABORDA, A.; SIMO, M. Spider assemblages associated with different crop stages of irrigated rice agroecosystems form eastern Uruguay. Biodiversity Data Journal, 6: e24974 Article history: Received: 12 Mar 2018. Accepted: 24 Apr 2018. Published: 3 May 2018.| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Treinta y Tres. |
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| 145. | | REBOLLO, I.; SCHEFFEL, S.; BLANCO, P.H.; MOLINA, F.; MARTÍNEZ, S.; CARRACELAS, G.; AGUILAR, I.; PÉREZ DE VIDA, F.; ROSAS, J.E. Consolidating twenty-three years of historical data from an irrigated subtropical rice breeding program in Uruguay. Crop Science, 2023. https://doi.org/10.1002/csc2.20955 - [Article in Press]. Article history: First published 15 March 2023. -- Corresponding author: jrosas@inia.org.uy --| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
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| 146. | | BONNECARRERE, V.; GARAYCOCHEA, S.; GUTIERREZ, L.; ROSAS, J.E.; BERBERIAN, N.; FERNÁNDEZ, S.; MARTÍNEZ, S.; PÉREZ DE VIDA, F.; BLANCO, P.H. Avances de resultados del proyecto mapeo asociativo para la identificación de marcadores asociados a rendimiento, calidad y resistencia a enfermedades In: PROGRAMA NACIONAL PRODUCCIÓN DE ARROZ; JORNADA ANUAL ARROZ-SOJA, 2013, INIA TREINTA Y TRES, UY. Arroz-soja: resultados experimentales 2012-2013. Treinta y Tres: INIA, 2013. "cap. 6; p. 22-24" (INIA Serie Actividades de Difusión ; 713)| Biblioteca(s): INIA Tacuarembó; INIA Treinta y Tres. |
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| 147. | | BONNECARRERE, M.; ROSAS, J.; DIEZ, M.; CASTILLO, A.; GARAYCOCHEA, S.; MARTÍNEZ, S.; PÉREZ DE VIDA, F.; SALDAIN, N.E.; BLANCO, P.H. La Biotecnología en el campo: el ejemplo del arroz. ln: Jornada técnica, VI Jornada de agrobiotecnología. INIA Las Brujas, 20 de octubre de 2012 Conocimiento intensivo para el sector productivo: situación actual y perspectivas. Canelones (UY): INIA, 2012. 19-22 (Serie Actividades de Difusión; 698)| Tipo: Actividades de Difusión |
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| 148. | | BLANCO, P.H.; PÉREZ DE VIDA, F.; MOLINA, F.; LAVECCHIA, A.; MARCHESI, C.; BONNECARRERE, V.; MARTINEZ, S.; SILVERA, W.; ROSAS, J.E.; ARISMENDI, G.; CASALES, L.; ESCALANTE, F. Comentarios generales sobre la evaluación interna de cultivares. ln: INIA TREINTA Y TRES. Arroz : Resultados experimentales 2010-2011. Treinta y Tres (Uruguay): INIA, 2011. C. 6 p. 3-5. (INIA Serie Actividades de Difusión; 651)| Biblioteca(s): INIA Treinta y Tres. |
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| 149. | | ROSAS, J.E.; MARTÍNEZ, S.; BONNECARRERE, M.; PÉREZ DE VIDA, F.; BLANCO, P.H.; MALOSETTI, M.; JANNINK, J.L.; GUTIÉRREZ, L. Comparison of phenotyping methods for resistance to stem rot and aggregated sheath spot in rice. Crop Science, 2016, v. 56, no. 4, p. 1619-1627. Open Access Article history: Published June 15, 2016.| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
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| 150. | | ROSAS, J.E.; BONNECARRERE, V.; MARTÍNEZ, S.; PÉREZ DE VIDA, F.; BLANCO, P.H.; QUERO, G.; FERNANDEZ, S.; GARAYCOCHEA, S.; JANNINK, J.L.; GUTIÉRREZ, L. GWAS for resistance to stem rot and aggregated sheath spot in advanced temperate rice (Oryza sativa L.) germplasm. [Poster]. In: International Conference on Quantitative Genetics, (5o., 2016, Madison)| Biblioteca(s): INIA Treinta y Tres. |
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| 151. | | ROSAS, J.E.; MARTÍNEZ, S.; BONNECARRERE, V.; PÉREZ DE VIDA, F.; BLANCO, P.H.; FERNANDEZ, S.; GARAYCOCHEA, S.; JANNINK, J.L.; GUTIERREZ, L. GWAS for resistance to stem rot and aggregated sheath spot of rice advanced breeding lines. [Poster]. In: International Symposium on Rice Functional Genomics, (14o., 2016, Montpellier),| Biblioteca(s): INIA Treinta y Tres. |
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| 152. | | ROSAS, J.E.; MARTÍNEZ, S.; BONNECARRERE, V.; BLANCO, P.H.; PÉREZ DE VIDA, F.; GERMAN, S.; JANNINK, J.L.; GUTIÉRREZ, L. Herramientas bioestadísticas para mejoramiento de la resistencia genética a enfermedades del tallo en arroz. In: INIA (Instituto Nacional de Investigación Agropecuaria); INIA Las Brujas; Biotecnología. Jornada de Agrobiotecnología, X. Encuentro Nacional de REDBIO, II. Jornada técnica. Las Brujas, Canelones (UY): INIA, 2017. p. 9-12. (Serie Actividades de Difusión; 780)| Biblioteca(s): INIA Las Brujas. |
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| 153. | | ROSAS, J.E.; MARTÍNEZ, S.; BONNECARRERE, V.; BLANCO, P.H.; PÉREZ DE VIDA, F.; GERMAN, S.; JANNINK, J.L.; GUTIÉRREZ, L. Evaluación de nuevos métodos de selección para resistencia a enfermedades del tallo y la vaina en arroz. In: Zorrilla, G.; Martínez, S.; Saravia, H. (Eds.) Arroz 2017. Montevideo (UY): INIA, 2017. p. 31-34. (INIA Serie Técnica; 233)| Tipo: Capítulo en Libro Técnico-Científico |
| Biblioteca(s): INIA Treinta y Tres. |
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| 154. | | ROSAS, J.E.; BONNECARRERE, V.; MARTÍNEZ, S.; PÉREZ DE VIDA, F.; BLANCO, P.H.; QUERO, G.; FERNANDEZ, S.; GARAYCOCHEA, S.; JANNINK, J.; GUTIERREZ, L. Mapeo asociativo de la resistencia a enfermedades del tallo y la vaina en germoplasma avanzado de arroz. 2 - SIMPOSIOS "MEJORAMIENTO GENÉTICO POR RESISTENCIA A ENFERMEDADES E INTERACCIONES PLANTA-PATÓGENO" In: JOURNAL OF BASIC & APPLIED GENETICS, 2016, Vol.27, Iss. 1 (Supp.). XVI LATIN AMERICAN CONGRESS OF GENETICS, IV CONGRESS OF THE URUGUAYAN SOCIETY OF GENETICS, XLIX ANNUAL MEETING OF THE GENETICS SOCIETY OF CHILE, XLV ARGENTINE CONGRESS OF GENETICS, 9-12 October 2016. PROCEEDINGS. Montevideo (Uruguay): SAG, 2016. p. 61| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 155. | | BONNECARRERE, M.; QUERO, G.; ROSAS, J.E.; FERNANDEZ, S.; GARAYCOCHEA, S.; MARTÍNEZ, S.; PÉREZ DE VIDA, F.; BLANCO, P.H.; BERBERIAN, N.; GUTIERREZ, L. Marcadores moleculares identificados en el Proyecto "Mapeo asociativo para asistir el mejoramiento genético de arroz". In: JORNADA TÉCNICA, VIII JORNADA DE AGROBIOTECNOLOGÍA. INIA LAS BRUJAS, 30 DE OCTUBRE DE 2014. UNIDAD DE BIOTECNOLOGÍA. Montevideo (Uruguay): INIA, 2014. 5-6 (Actividades de Difusión; 741)| Biblioteca(s): INIA Las Brujas. |
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| 156. | | BONNECARRERE, V.; QUERO, G.; ROSAS, J.; FERNÁNDEZ, S.; GARAYCOCHEA, S.; MARTINEZ, S.; PÉREZ DE VIDA, F.; BLANCO, P.H.; BERDERIAN, N.; GUTIERREZ, L. Marcadores moleculares identificados en el proyecto mapeo asociativo para asistir el mejoramiento por calidad del grano. En: INIA TREINTA Y TRES. Arroz-Soja:Resultados Experimentales 2013-2014. Treinta y Tres (UY): INIA Treinta y Tres. cap. 6. p. 24-26 (INIA Serie Actividades de Difusión; 735)| Biblioteca(s): INIA Treinta y Tres. |
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| 157. | | MACEDO, I.; CASTILLO, J.; SALDAIN, N.E.; MARTÍNEZ, S.; AYALA, W.; HERNANDEZ, J.; SERRON, N.; BORDAGORRI, P.; ZORRILLA DE SAN MARTÍN, G.; TERRA, J.A. Nuevas rotaciones arroceras: primeros datos de productividad Arroz, 2016, v.16, no. 88, p. 34-39.| Tipo: Artículos en Revistas Agropecuarias |
| Biblioteca(s): INIA Treinta y Tres. |
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| 158. | | MOLINA, F.; BLANCO, P.H.; DE LA PAVA, K. LOAIZA; VILLALBA, M.; VARGAS, J.; MARTÍNEZ, S.; ESCALANTE, F.; PÉREZ DE VIDA, F. Nuevos cultivares Clearfield. In: Terra, J. A.; Martínez, S.; Saravia, H. (Eds.) Arroz 2019. Montevideo (UY): INIA, 2019. p. 77-80. (INIA Serie Técnica; 250)| Tipo: Capítulo en Libro Técnico-Científico |
| Biblioteca(s): INIA Treinta y Tres. |
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| 159. | | TERRA, J.A.; FERNÁNDEZ, A.; CANTOU, G.; MARTÍNEZ, S.; CASTILLO, J.; MACEDO, I.; FERRANDO, L.; IRISARRI, P.; CARRASCO-LETELIER, L.; PÉREZ-PARADA, A.; ROEL, A. Integrated rice-pasture systems sustainability in Uruguay.* Panel: Plant component. In: IV International Symposium on Integrated Crop-livestock Systems; Bento Gonçalves (RS), Brazil, November 7-11, 2023. Conference Proceedings, Volume 1. pp.61-65. * Part of Project: Evaluation of the environmental sustainability of rice production systems, funded by ANII. -- Junto al IV ICLS se realizó el III Congresso Brasileiro de Sistemas Integrados de Produção Agropecuária y el VII Encontro de...| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 160. | | SALVADOR-MONTOYA, C. A.; ELÍAS, S. G.; POPOFF, O. F.; ROBLEDO, G. L.; URCELAY, C.; GÓES-NETO, A.; MARTÍNEZ, S.; DRECHSLER-SANTOS, E. R. Neotropical studies on Hymenochaetaceae: Unveiling the diversity and endemicity of Phellinotus. Journal of Fungi, 22 february 2022, vol. 8 (3) art.216. OPEN ACCESS. Doi: https://doi.org/10.3390/jof8030216 Article history: Received: 15 January 2022 / Revised: 12 February 2022 / Accepted: 17 February 2022 / Published: 22 February 2022| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Treinta y Tres. |
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| Registros recuperados : 171 | |
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