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| 4. |  | LEGARRA, A.; AGUILAR, I.; COLLEAU, J.J. Short communication: Methods to compute genomic inbreeding for ungenotyped individuals. Journal of Dairy Science, April 2020, Volume 103, Issue 4, Pages 3363-3367. Doi: https://doi.org/10.3168/jds.2019-17750 Article history: Received October 15, 2019. / Accepted December 18, 2019.
Corresponding author: A. Legarra - email: andres.legarra@inra.fr
This study was partially funded by the INRA (Paris, France) SELGEN funding metaprogram (Project...| Biblioteca(s): INIA Las Brujas. |
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| 5. | | LEGARRA, A.; AGUILAR, I.; MISZTAL, I. Single step methods with a view towards poultry breeding. Volume Species Breeding: Poultry, 324. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.324. Acknowledgements: This work has been financed by X-Gen and GenSSeq actions from SelGen metaprogram (INRA).| Biblioteca(s): INIA Las Brujas. |
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| 9. | | AGUILAR, I.; MISZTAL, I.; LEGARRA, A.; TSURUTA, S. Efficient computations of genomic relationship matrix and other matrices used in the single-step evaluation. Volume Methods and tools: Software and bioinformatics - Lecture Sessions, 0768. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 9., Leipzig, Germany, August 1-6, 2010. p. 0768. Acknowledgments: This study was partially funded by the Holstein Association USA Inc. and by AFRI grants 2009-65205-05665 and 2010-65205-20366 from the USDA NIFA Animal Genome Program. The authors thank P.M. VanRaden from Animal...| Biblioteca(s): INIA Las Brujas. |
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| 10. | | BERMANN, M.; MISZTAL, I.; LOURENCO, D.; AGUILAR, I.; LEGARRA, A. Definition of reliabilities for models with metafounders. [289] Part 17 - Challenges - improving genomic prediction. In: Proceedings of the World Congress on Genetics Applied to Livestock Production (WCGALP), 12., Rotterdam, the Netherlands, 3-8 July 2022. doi: https://doi.org/10.3920/978-90-8686-940-4_289 1217-1220. Article history: Published online: February 9, 2023. -- Corresponding author: A. Legarra, email: andres.legarra@inrae.fr -- Acknowledgment: This work received financing from European Unions' Horizon 2020 Research & Innovation Programme,...| Biblioteca(s): INIA Las Brujas. |
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| 14. | | AGUILAR, I.; MISZTAL, I.; TSURUTA, S.; LEGARRA, A.; WANG, H. PREGSF90 - POSTGSF90: Computational tools for the implementation of single-step genomic selection and genome-wide association with ungenotyped individuals in BLUPF90 programs. Volume Methods and Tools: Statistical and genomic tools for mapping QTL and genes (Posters), 680. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.680.| Biblioteca(s): INIA Las Brujas. |
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| 15. | | BERMANN, M.; AGUILAR, I.; LOURENCO , D.; MISZTAL, I.; LEGARRA, A. Reliabilities of estimated breeding values in models with metafounders. Research article. Genetics, Selection, Evolution : GSE, 2023, volume55, issue 1, article 6. OPEN ACCESS. doi: https://doi.org/10.1186/s12711-023-00778-2 Article history: Received 29 June 2022; Accepted 04 January 2023; Published 23 January 2023. -- Corresponding author: Matias Bermann, Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA, email: mbermann@uga.edu...| Biblioteca(s): INIA Las Brujas. |
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| 17. | | ZHANG, X.; LOURENCO, D.; MISZTAL, I.; AGUILAR, I.; LEGARRA, A. Weighted single-step genomic BLUP: an iterative approach for accurate calculation of GEBV and GWAS. Volume Methods and Tools: Statistical and genomic tools for mapping QTL and genes (Posters), 681. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.681.| Biblioteca(s): INIA Las Brujas. |
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| 18. | | ZHANG, X.; LOURENCO, D.; AGUILAR, I.; LEGARRA, A.; MISZTAL, I. Weighting strategies for single-step genomic BLUP: An iterative approach for accurate calculation of GEBV and GWAS. Frontiers in Genetics, 19 August 2016, Volume 7, Issue AUG, Article number 151. OPEN ACCESS 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.| Biblioteca(s): INIA Las Brujas. |
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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 actual : |
04/10/2014 |
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Actualizado : |
10/02/2020 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Circulación / Nivel : |
A - 2 |
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Autor : |
AGUILAR, I.; MISZTAL, I.; LEGARRA, A.; TSURUTA, S. |
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Afiliación : |
IGNACIO AGUILAR GARCIA, Instituto Nacional de Investigación Agropecuaria (INIA), Uruguay. |
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Título : |
Efficient computation of the genomic relationship matrix and other matrices used in single-step evaluation. |
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Fecha de publicación : |
2011 |
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Fuente / Imprenta : |
Journal of Animal Breeding and Genetics, 2011, v.128, no.6, p.422-428. |
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ISSN : |
0931-2668 |
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DOI : |
10.1111/j.1439-0388.2010.00912.x |
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Idioma : |
Inglés |
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Contenido : |
ABSTRACT.
Genomic evaluations can be calculated using a unified procedure that combines phenotypic, pedigree and genomic information. Implementation of such a procedure requires the inverse of the relationship matrix based on pedigree and genomic relationships. The objective of this study was to investigate efficient computing options to create relationship matrices based on genomic markers and pedigree information as well as their inverses. SNP maker information was simulated for a panel of 40K SNPs, with the number of genotyped animals up to 30000. Matrix multiplication in the computation of the genomic relationship was by a simple 'do' loop, by two optimized versions of the loop, and by a specific matrix multiplication subroutine. Inversion was by a generalized inverse algorithm and by a LAPACK subroutine. With the most efficient choices and parallel processing, creation of matrices for 30000 animals would take a few hours. Matrices required to implement a unified approach can be computed efficiently. Optimizations can be either by modifications of existing code or by the use of efficient automatic optimizations provided by open source or third-party libraries.
© 2011 Blackwell Verlag GmbH. |
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Thesagro : |
MEJORAMIENTO GENÉTICO ANIMAL; MODELOS MATEMÁTICOS; SELECCIÓN GENÓMICA. |
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Asunto categoría : |
L10 Genética y mejoramiento animal |
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Marc : |
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260 $c2011
520 $aABSTRACT. Genomic evaluations can be calculated using a unified procedure that combines phenotypic, pedigree and genomic information. Implementation of such a procedure requires the inverse of the relationship matrix based on pedigree and genomic relationships. The objective of this study was to investigate efficient computing options to create relationship matrices based on genomic markers and pedigree information as well as their inverses. SNP maker information was simulated for a panel of 40K SNPs, with the number of genotyped animals up to 30000. Matrix multiplication in the computation of the genomic relationship was by a simple 'do' loop, by two optimized versions of the loop, and by a specific matrix multiplication subroutine. Inversion was by a generalized inverse algorithm and by a LAPACK subroutine. With the most efficient choices and parallel processing, creation of matrices for 30000 animals would take a few hours. Matrices required to implement a unified approach can be computed efficiently. Optimizations can be either by modifications of existing code or by the use of efficient automatic optimizations provided by open source or third-party libraries. © 2011 Blackwell Verlag GmbH.
650 $aMEJORAMIENTO GENÉTICO ANIMAL
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773 $tJournal of Animal Breeding and Genetics, 2011$gv.128, no.6, p.422-428.
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