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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
Fecha : |
23/05/2016 |
Actualizado : |
11/12/2018 |
Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
Autor : |
MASUDA, Y.; MISZTAL, I.; TSURUTA, S.; LEGARRA, A.; AGUILAR, I.; LOURENCO, D.A.L.; FRAGOMENI, B.O.; LAWLOR, T.J. |
Afiliación : |
Department of Animal and Dairy Science, University of Georgia; Department of Animal and Dairy Science, University of Georgia; Department of Animal and Dairy Science, University of Georgia; INRA (Institut National de la Recherche Agronomique); IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; Department of Animal and Dairy Science, University of Georgia; Department of Animal and Dairy Science, University of Georgia; Holstein Association USA Inc. |
Título : |
Implementation of genomic recursions in single-step genomic best linear unbiased predictor for US Holsteins with a large number of genotyped animals. |
Fecha de publicación : |
2016 |
Fuente / Imprenta : |
Journal of Dairy Science, 2016, v.99, no.3, p.1968-1974. OPEN ACCESS |
DOI : |
10.3168/jds.2015-10540 |
Idioma : |
Inglés |
Notas : |
OPEN ACCESS. Received 19 October 2015, Accepted 1 December 2015, Available online 21 January 2016 |
Contenido : |
ABSTRACT.
The objectives of this study were to develop and evaluate an efficient implementation in the computation of the inverse of genomic relationship matrix with the recursion algorithm, called the algorithm for proven and young (APY), in single-step genomic BLUP. We validated genomic predictions for young bulls with more than 500,000 genotyped animals in final score for US Holsteins. Phenotypic data included 11,626,576 final scores on 7,093,380 US Holstein cows, and genotypes were available for 569,404 animals. Daughter deviations for young bulls with no classified daughters in 2009, but at least 30 classified daughters in 2014 were computed using all the phenotypic data. Genomic predictions for the same bulls were calculated with single-step genomic BLUP using phenotypes up to 2009. We calculated the inverse of the genomic relationship matrix View the MathML source based on a direct inversion of genomic relationship matrix on a small subset of genotyped animals (core animals) and extended that information to noncore animals by recursion. We tested several sets of core animals including 9,406 bulls with at least 1 classified daughter, 9,406 bulls and 1,052 classified dams of bulls, 9,406 bulls and 7,422 classified cows, and random samples of 5,000 to 30,000 animals. Validation reliability was assessed by the coefficient of determination from regression of daughter deviation on genomic predictions for the predicted young bulls. The reliabilities were 0.39 with 5,000 randomly chosen core animals, 0.45 with the 9,406 bulls, and 7,422 cows as core animals, and 0.44 with the remaining sets. With phenotypes truncated in 2009 and the preconditioned conjugate gradient to solve mixed model equations, the number of rounds to convergence for core animals defined by bulls was 1,343; defined by bulls and cows, 2,066; and defined by 10,000 random animals, at most 1,629. With complete phenotype data, the number of rounds decreased to 858, 1,299, and at most 1,092, respectively. Setting up View the MathML source for 569,404 genotyped animals with 10,000 core animals took 1.3 h and 57 GB of memory. The validation reliability with APY reaches a plateau when the number of core animals is at least 10,000. Predictions with APY have little differences in reliability among definitions of core animals. Single-step genomic BLUP with APY is applicable to millions of genotyped animals.
© 2016, THE AUTHORS. Published by FASS and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/). MenosABSTRACT.
The objectives of this study were to develop and evaluate an efficient implementation in the computation of the inverse of genomic relationship matrix with the recursion algorithm, called the algorithm for proven and young (APY), in single-step genomic BLUP. We validated genomic predictions for young bulls with more than 500,000 genotyped animals in final score for US Holsteins. Phenotypic data included 11,626,576 final scores on 7,093,380 US Holstein cows, and genotypes were available for 569,404 animals. Daughter deviations for young bulls with no classified daughters in 2009, but at least 30 classified daughters in 2014 were computed using all the phenotypic data. Genomic predictions for the same bulls were calculated with single-step genomic BLUP using phenotypes up to 2009. We calculated the inverse of the genomic relationship matrix View the MathML source based on a direct inversion of genomic relationship matrix on a small subset of genotyped animals (core animals) and extended that information to noncore animals by recursion. We tested several sets of core animals including 9,406 bulls with at least 1 classified daughter, 9,406 bulls and 1,052 classified dams of bulls, 9,406 bulls and 7,422 classified cows, and random samples of 5,000 to 30,000 animals. Validation reliability was assessed by the coefficient of determination from regression of daughter deviation on genomic predictions for the predicted young bulls. The reliabilities were 0.39 with 5,000 rand... Presentar Todo |
Palabras claves : |
FINAL SCORE; GENOMIC EVALUATION; GENOMIC RELATIONSHIP MATRIX. |
Thesagro : |
SsGBLUP; TORO. |
Asunto categoría : |
-- |
URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/12160/1/1-s2.0-S0022030216000825-main.pdf
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Marc : |
LEADER 03610naa a2200289 a 4500 001 1054839 005 2018-12-11 008 2016 bl uuuu u00u1 u #d 024 7 $a10.3168/jds.2015-10540$2DOI 100 1 $aMASUDA, Y. 245 $aImplementation of genomic recursions in single-step genomic best linear unbiased predictor for US Holsteins with a large number of genotyped animals.$h[electronic resource] 260 $c2016 500 $aOPEN ACCESS. Received 19 October 2015, Accepted 1 December 2015, Available online 21 January 2016 520 $aABSTRACT. The objectives of this study were to develop and evaluate an efficient implementation in the computation of the inverse of genomic relationship matrix with the recursion algorithm, called the algorithm for proven and young (APY), in single-step genomic BLUP. We validated genomic predictions for young bulls with more than 500,000 genotyped animals in final score for US Holsteins. Phenotypic data included 11,626,576 final scores on 7,093,380 US Holstein cows, and genotypes were available for 569,404 animals. Daughter deviations for young bulls with no classified daughters in 2009, but at least 30 classified daughters in 2014 were computed using all the phenotypic data. Genomic predictions for the same bulls were calculated with single-step genomic BLUP using phenotypes up to 2009. We calculated the inverse of the genomic relationship matrix View the MathML source based on a direct inversion of genomic relationship matrix on a small subset of genotyped animals (core animals) and extended that information to noncore animals by recursion. We tested several sets of core animals including 9,406 bulls with at least 1 classified daughter, 9,406 bulls and 1,052 classified dams of bulls, 9,406 bulls and 7,422 classified cows, and random samples of 5,000 to 30,000 animals. Validation reliability was assessed by the coefficient of determination from regression of daughter deviation on genomic predictions for the predicted young bulls. The reliabilities were 0.39 with 5,000 randomly chosen core animals, 0.45 with the 9,406 bulls, and 7,422 cows as core animals, and 0.44 with the remaining sets. With phenotypes truncated in 2009 and the preconditioned conjugate gradient to solve mixed model equations, the number of rounds to convergence for core animals defined by bulls was 1,343; defined by bulls and cows, 2,066; and defined by 10,000 random animals, at most 1,629. With complete phenotype data, the number of rounds decreased to 858, 1,299, and at most 1,092, respectively. Setting up View the MathML source for 569,404 genotyped animals with 10,000 core animals took 1.3 h and 57 GB of memory. The validation reliability with APY reaches a plateau when the number of core animals is at least 10,000. Predictions with APY have little differences in reliability among definitions of core animals. Single-step genomic BLUP with APY is applicable to millions of genotyped animals. © 2016, THE AUTHORS. Published by FASS and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/). 650 $aSsGBLUP 650 $aTORO 653 $aFINAL SCORE 653 $aGENOMIC EVALUATION 653 $aGENOMIC RELATIONSHIP MATRIX 700 1 $aMISZTAL, I. 700 1 $aTSURUTA, S. 700 1 $aLEGARRA, A. 700 1 $aAGUILAR, I. 700 1 $aLOURENCO, D.A.L. 700 1 $aFRAGOMENI, B.O. 700 1 $aLAWLOR, T.J. 773 $tJournal of Dairy Science, 2016$gv.99, no.3, p.1968-1974. OPEN ACCESS
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4. | | MASUDA, Y.; AGUILAR, I.; TSURUTA, S.; MISZTAL, I. Acceleration of computations in AI REML for single-step GBLUP models. Volume Methods and Tools: Statistical methods - linear and nonlinear models (Posters), 703. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.703.Tipo: Trabajos en Congresos/Conferencias |
Biblioteca(s): INIA Las Brujas. |
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6. | | TSURUTA, S.; MISZTAL, I.; AGUILAR, I.; LAWLOR, T. J. Genome wide association study on cow mortality in three US regions. Volume Species Breeding: Dairy cattle (Posters), 805. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.805.Tipo: Trabajos en Congresos/Conferencias |
Biblioteca(s): INIA Las Brujas. |
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8. | | 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...Tipo: Trabajos en Congresos/Conferencias |
Biblioteca(s): INIA Las Brujas. |
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9. | | TSURUTA, S.; MISZTAL, I.; AGUILAR, I.; LAWLOR, T.J. Multiple-trait genomic evaluation of linear type traits using genomic and phenotypic data in US Holsteins. Journal of Dairy Science, 2011, v.94, no.8, p.4198-4204. OPEN ACCESS. Article history: Received February 9, 2011. / Accepted April 8, 2011.Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : A - 1 |
Biblioteca(s): INIA Las Brujas. |
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10. | | MASUDA, Y.; AGUILAR, I.; TSURUTA, S.; MISZTAL, I. Technical note: Acceleration of sparse operations for average-information REML analyses with supernodal methods and sparse-storage refinements. Journal of Animal Science, 2015, v. 93, p. 4670 - 4674. Published October 9, 2015 Article history: Received June 8, 2015.; Accepted August 7, 2015.
1. We acknowledge the work by François Guillaume in programming a hash function. We greatly appreciate the work of the two anonymous reviewers.
2. The AIREMLF90 program...Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
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11. | | 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.Tipo: Trabajos en Congresos/Conferencias |
Biblioteca(s): INIA Las Brujas. |
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12. | | GARCÍA, A.; AGUILAR, I.; LEGARRA, A.; MILLER, S.; TSURUTA, S.; MISZTAL, I.; LOURENCO, D. Accuracy of indirect predictions for large datasets based on prediction error covariance of SNP effects from single-step GBLUP. [abstract 22]. Issue Section: Animal Breeding and Genetics. Journal of Animal Science, 2020, Volume 98, Issue Supplement 4, Pages 6-7. doi: https://doi.org/10.1093/jas/skaa278.012 Article history: 30 November 2020.
ASAS Annual 2020 Meeting Abstracts.Tipo: Abstracts/Resúmenes |
Biblioteca(s): INIA Las Brujas. |
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14. | | LOURENCO, D; MISZTAL, I.; TSURUTA, S.; AGUILAR, I.; LAWLOR, T. J.; WELLER, J. I. Are evaluations on young genotyped dairy bulls benefiting from the past generations? [conference paper]. Volume Species Breeding: Dairy cattle, 297. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.297.Tipo: Trabajos en Congresos/Conferencias |
Biblioteca(s): INIA Las Brujas. |
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15. | | LOURENÇO, D. A. L.; MISZTAL, I.; TSURUTA, S.; FRAGOMENI, B.; AGUILAR, I.; MASUDA, Y.; MOSER, D. Direct and indirect genomic evaluations in beef cattle. Interbull Bulletin, 2015, v. 49, p.80 - 84.Tipo: Artículos Indexados |
Biblioteca(s): INIA Las Brujas. |
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16. | | AGUILAR, I.; TSURUTA, S.; MASUDA, Y.; LOURENCO, D.A.L.; LEGARRA, A.; MISZTAL, I. BLUPF90 suite of programs for animal breeding with focus on genomics. Volume Methods and Tools - Software, p. 751. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 11., Aotea Centre Auckland, New Zealand: WCGALP, ICAR, 11-16 feb 2018. 6 p.Tipo: Trabajos en Congresos/Conferencias |
Biblioteca(s): INIA Las Brujas. |
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17. | | GARCÍA, A.; AGUILAR, I.; LEGARRA, A.; TSURUTA, S.; MISZTAL, I.; LOURENCO, D. Correction: Theoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP (Genetics, selection, evolution : GSE (2022) 54:1 (66)). Genetics, Selection, Evolution : GSE, 2023, Volume 55, Issue 1, Pages 26. OPEN ACCESS. https://doi.org/10.1186/s12711-023-00799-x Article history: Published online 17 April 2023. -- Document: Erratum - Gold Open Access. -- The original article can be found online at https://doi.org/10.1186/s12711-022-00752-4Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
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18. | | MISZTAL, I.; TSURUTA, S.; AGUILAR, I.; LEGARRA, A.; VAN RADEN, P.M.; LAWLOR, T.J. Methods to approximate reliabilities in single-step genomic evaluation. Journal of Dairy Science, 2013, v.96, no.1, p.647-654. OPEN ACCESS. Article history: Received April 24, 2012. / Accepted September 18, 2012.Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : A - 1 |
Biblioteca(s): INIA Las Brujas. |
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19. | | AGUILAR, I.; MISZTAL, I.; JOHNSON, D.L.; LEGARRA, A.; TSURUTA, S.; LAWLOR, T.J. Hot topic: A unified approach to utilize phenotypic, full pedigree, and genomic information for genetic evaluation of Holstein final score. Journal of Dairy Science, 2010, v. 93, no. 2, p. 743-752. OPEN ACCESS Article history: Received September 14, 2009 / Accepted November 10, 2009 / Published in issue: February 2010.Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : A - 1 |
Biblioteca(s): INIA Las Brujas. |
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20. | | MISZTAL, I.; LOURENCO, D.; TSURUTA, S.; AGUILAR, I.; MASUDA, Y.; BERMANN, M.; CESARANI, A.; LEGARRA, A. How ssGBLUP became suitable for national dairy cattle evaluations. [668]. Part 37 - Bovine dairy - genetic evaluation methods. 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_668 2757-2760. Article history: Published online: February 9, 2023 -- Corresponding author: I. Misztal, email: ignacy@uga.eduTipo: Trabajos en Congresos/Conferencias |
Biblioteca(s): INIA Las Brujas. |
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Registros recuperados : 45 | |
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