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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 : |
12/11/2015 |
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Actualizado : |
02/12/2015 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
FRAGOMENI, B.O.; LOURENCO, D.A.L.; TSURUTA, S.; MASUDA, Y.; AGUILAR, I.; MISZTAL, I. |
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Afiliación : |
IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
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Título : |
Use of genomic recursions and algorithm for proven and young animals for single-step genomic BLUP analyses - a simulation study. |
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Fecha de publicación : |
2015 |
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Fuente / Imprenta : |
Journal of Animal Breeding and Genetics, 2015, v.132, no.5, p. 340-345. |
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ISSN : |
0931-2668 |
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DOI : |
10.1111/jbg.12161 |
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Idioma : |
Inglés |
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Contenido : |
ABSTRACT.
The purpose of this study was to examine accuracy of genomic selection via single-step genomic BLUP (ssGBLUP) when the direct inverse of the genomic relationship matrix (G) is replaced by an approximation of G1 based on recursions for young genotyped animals conditioned on a subset of proven animals, termed algorithm for proven and young animals
(APY). With the efficient implementation, this algorithm has a cubic cost with proven animals and linear with young animals. Ten duplicate data sets mimicking a dairy cattle population were simulated. In a first scenario, genomic information for 20k genotyped bulls, divided in 7k proven and 13k young bulls, was generated for each replicate. In a second scenario, 5k genotyped cows with phenotypes were included in the analysis as young animals. Accuracies (average for the 10 replicates) in regular EBV were 0.72 and 0.34 for proven and young animals, respectively.
When genomic information was included, they increased to 0.75 and 0.50. No differences between genomic EBV (GEBV) obtained with the regular G1 and the approximated G1 via the recursive method were observed. In the second scenario, accuracies in GEBV (0.76, 0.51 and 0.59 for proven bulls, young males and young females, respectively)
were also higher than those in EBV (0.72, 0.35 and 0.49). Again, no differences between GEBV with regular G1 and with recursions were observed. With the recursive algorithm, the number of iterations to achieve convergence was reduced from 227 to 206 in the first scenario and from 232 to 209 in the second scenario. Cows can be treated as young animals in APY without reducing the accuracy. The proposed algorithm can be implemented to reduce computing costs and to overcome current limitations on the number of genotyped animals in the ssGBLUP method.
© 2015 Blackwell Verlag GmbH MenosABSTRACT.
The purpose of this study was to examine accuracy of genomic selection via single-step genomic BLUP (ssGBLUP) when the direct inverse of the genomic relationship matrix (G) is replaced by an approximation of G1 based on recursions for young genotyped animals conditioned on a subset of proven animals, termed algorithm for proven and young animals
(APY). With the efficient implementation, this algorithm has a cubic cost with proven animals and linear with young animals. Ten duplicate data sets mimicking a dairy cattle population were simulated. In a first scenario, genomic information for 20k genotyped bulls, divided in 7k proven and 13k young bulls, was generated for each replicate. In a second scenario, 5k genotyped cows with phenotypes were included in the analysis as young animals. Accuracies (average for the 10 replicates) in regular EBV were 0.72 and 0.34 for proven and young animals, respectively.
When genomic information was included, they increased to 0.75 and 0.50. No differences between genomic EBV (GEBV) obtained with the regular G1 and the approximated G1 via the recursive method were observed. In the second scenario, accuracies in GEBV (0.76, 0.51 and 0.59 for proven bulls, young males and young females, respectively)
were also higher than those in EBV (0.72, 0.35 and 0.49). Again, no differences between GEBV with regular G1 and with recursions were observed. With the recursive algorithm, the number of iterations to achieve convergence was reduced from... Presentar Todo |
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Palabras claves : |
GENETIC EVALUATION; GENOMIC SELECTION; SINGLE-STEP METHOD. |
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Thesagro : |
MEJORAMIENTO GENETICO ANIMAL. |
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Asunto categoría : |
L10 Genética y mejoramiento animal |
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Marc : |
LEADER 02627naa a2200253 a 4500
001 1053862
005 2015-12-02
008 2015 bl uuuu u00u1 u #d
022 $a0931-2668
024 7 $a10.1111/jbg.12161$2DOI
100 1 $aFRAGOMENI, B.O.
245 $aUse of genomic recursions and algorithm for proven and young animals for single-step genomic BLUP analyses - a simulation study.
260 $c2015
520 $aABSTRACT. The purpose of this study was to examine accuracy of genomic selection via single-step genomic BLUP (ssGBLUP) when the direct inverse of the genomic relationship matrix (G) is replaced by an approximation of G1 based on recursions for young genotyped animals conditioned on a subset of proven animals, termed algorithm for proven and young animals (APY). With the efficient implementation, this algorithm has a cubic cost with proven animals and linear with young animals. Ten duplicate data sets mimicking a dairy cattle population were simulated. In a first scenario, genomic information for 20k genotyped bulls, divided in 7k proven and 13k young bulls, was generated for each replicate. In a second scenario, 5k genotyped cows with phenotypes were included in the analysis as young animals. Accuracies (average for the 10 replicates) in regular EBV were 0.72 and 0.34 for proven and young animals, respectively. When genomic information was included, they increased to 0.75 and 0.50. No differences between genomic EBV (GEBV) obtained with the regular G1 and the approximated G1 via the recursive method were observed. In the second scenario, accuracies in GEBV (0.76, 0.51 and 0.59 for proven bulls, young males and young females, respectively) were also higher than those in EBV (0.72, 0.35 and 0.49). Again, no differences between GEBV with regular G1 and with recursions were observed. With the recursive algorithm, the number of iterations to achieve convergence was reduced from 227 to 206 in the first scenario and from 232 to 209 in the second scenario. Cows can be treated as young animals in APY without reducing the accuracy. The proposed algorithm can be implemented to reduce computing costs and to overcome current limitations on the number of genotyped animals in the ssGBLUP method. © 2015 Blackwell Verlag GmbH
650 $aMEJORAMIENTO GENETICO ANIMAL
653 $aGENETIC EVALUATION
653 $aGENOMIC SELECTION
653 $aSINGLE-STEP METHOD
700 1 $aLOURENCO, D.A.L.
700 1 $aTSURUTA, S.
700 1 $aMASUDA, Y.
700 1 $aAGUILAR, I.
700 1 $aMISZTAL, I.
773 $tJournal of Animal Breeding and Genetics, 2015$gv.132, no.5, p. 340-345.
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INIA Las Brujas (LB) |
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| Registros recuperados : 17 | |
| 1. |  | 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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| 2. | | 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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| 3. | | 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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| 4. | | MACEDO, F.; CHRISTENSEN, O. F.; ASTRUC, J.M.; AGUILAR, I.; MASUDA, Y.; LEGARRA, A. Bias and accuracy of dairy sheep evaluations using BLUP and SSGBLUP with metafounders and unknown parent groups. Genetics, Selection, Evolution : GSE, 12 August 2020, Volume 52, Issue 1, Page 47. OPEN ACCESS. DOI: https://doi.org/10.1186/s12711-020-00567-1 Article history: Received 03 March 2020; Accepted 04 August 2020; Published 12 August 2020.| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
|  |
| 5. | | 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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| 6. | | AGUILAR, I.; LEGARRA, A.; CARDOSO, F.; MASUDA, Y.; LOURENCO, D.; MISZTAL, I. Frequentist p-values for large-scale-single step genome-wide association, with an application to birth weight in American Angus cattle. (Short Communication) Genetics Selection Evolution, 20 June 2019, v. 51, Issue 1, Article number 28. OPEN ACCESS. Article history: Received: 3 January 2019 // Accepted: 27 May 2019 // Published Online: 20 June 2019.
Funding text: This study was partially funded by the American Angus Association (St. Joseph, MO) and by Agriculture and Food Research...| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
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| 7. | | 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.edu| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 8. | | LOURENCO, D.; TSURUTA, S.; AGUILAR, I.; MASUDA, Y.; BERMANN, M.; LEGARRA, A.; MISZTAL, I. Recent updates in the BLUPF90 software suite. [366]. Part 19 - Methods and tools: software and computing strategies. 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_366 1530-1533. Article history: Published online: February 9, 2023. -- Corresponding author: D. Lourenco, email: danilino@uga.edu| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 9. | | LOURENCO, D.; LEGARRA, A.; TSURUTA, S.; MASUDA, Y.; AGUILAR, I.; MISZTAL, I. Single-step genomic evaluations from theory to practice: using snp chips and sequence data in blupf90. Genes, July 2020. Volume 11, Issue 7, Article number 790, Pages 1-32. Open Access. Doi: https://doi.org/10.3390/genes11070790 Article history: Received: 19 June 2020 / Revised: 3 July 2020 / Accepted: 6 July 2020 / Published: 14 July 2020.
(This article belongs to the Special Issue Genomic Prediction Methods for Sequencing Data):...| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
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| 10. | | FRAGOMENI, B.O.; LOURENCO, D.A.L.; TSURUTA, S.; MASUDA, Y.; AGUILAR, I.; MISZTAL, I. Use of genomic recursions and algorithm for proven and young animals for single-step genomic BLUP analyses - a simulation study. Journal of Animal Breeding and Genetics, 2015, v.132, no.5, p. 340-345.| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
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| 11. | | MISZTAL, I.; FRAGOMENI, B.; LOURENÇO, D. A. L.; TSURUTA, S.; MASUDA, Y.; AGUILAR, I.; LEGARRA, A.; LAWLOR, T. J. Efficient inversion of genomic relationship matrix by the Algorithm for Proven and Young (APY). Interbull Bulletin, 2015, v. 49, p. 111-116.| Tipo: Artículos Indexados |
| Biblioteca(s): INIA Las Brujas. |
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| 12. | | MASUDA, Y.; MISZTAL, I.; TSURUTA, S.; LEGARRA, A.; AGUILAR, I.; LOURENCO, D.A.L.; FRAGOMENI, B.O.; LAWLOR, T.J. Implementation of genomic recursions in single-step genomic best linear unbiased predictor for US Holsteins with a large number of genotyped animals. Journal of Dairy Science, 2016, v.99, no.3, p.1968-1974. OPEN ACCESS OPEN ACCESS. Received 19 October 2015, Accepted 1 December 2015, Available online 21 January 2016| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
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| 13. | | FRAGOMENI, B.O.; LOURENCO, D.A.L.; TSURUTA, S.; MASUDA, Y.; AGUILAR, I.; LEGARRA, A.; LAWLOR, T.J.; MIZTAL, I. Hot topic: Use of genomic recursions in single-step genomic best linear unbiased predictor (BLUP) with a large number of genotypes. Journal of Dairy Science, 2015, v.98, no.6, p.4090-4094. OPEN ACCESS. Article history: Received November 18, 2014 / Accepted March 13, 2015 / Published online: April 8, 2015.| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
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| 14. | | LOURENCO, D.; TSURUTA, S.; FRAGOMENI, B.; MASUDA, Y.; AGUILAR, I.; LEGARRA, A.; MILLER, S.; MOSER, D.; MISZTAL, I. Single-step genomic BLUP for national beef cattle evaluation in US: from initial developments to final implementation. Volume Species - Bovine (beef) 1, 495. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 11., Aotea Centre Auckland, New Zealand: WCGALP, ICAR, 11-16 feb 2018.| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 15. | | MASUDA, Y.; MISZTAL, I.; TSURUTA, S.; LOURENÇO, D. A. L.; FRAGOMENI, B.; LEGARRA, A.; AGUILAR, I.; LAWLOR, T. J. Single-step genomic evaluations with 570K genotyped animals in US Holsteins. Interbull Bulletin, 2015, v. 49, p. 85-89.| Tipo: Artículos Indexados |
| Biblioteca(s): INIA Las Brujas. |
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| 16. | | MASUDA, Y; MISZTAL, I.; LEGARRA, A.; TSURUTA, S.; LOURENCO, D.A.L.; FRAGOMENI, B.O.; AGUILAR, I. Technical note: Avoiding the direct inversion of the numerator relationship matrix for genotyped animals in single-step genomic best linear unbiased prediction solved with the preconditioned conjugate gradient. Journal of Animal Science, 2017, v. 95(1): 49-52. Article history: Received: July 05, 2016; Accepted: Aug 16, 2016; Published: February 2, 2017.
This research was partially funded by the United States Department of Agriculture?s National Institute of Food and Agriculture (Agriculture and...| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
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| 17. | | LOURENCO, D. A. L.; TSURUTA, S.; FRAGOMENI, B. O.; MASUDA, Y.; AGUILAR, I.; LEGARRA, A.; BERTRAND, J. K.; AMEN, T. S.; WANG. L.; MOSER, D. W.; MISZTAL, I. Genetic evaluation using single-step genomic best linear unbiased predictor in American Angus.(*) Journal of Animal Science, 2015, v. 93, p. 2653-2662. Published June 25, 2015. OPEN ACCESS. (*) This study was partially funded by the American Angus Association (St. Joseph, MO), Zoetis (Kalamazoo, MI), and Agriculture and Food Research Initiative Competitive Grants no. 2015-67015-22936 from the U.S. Department of Agriculture?s...| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
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| Registros recuperados : 17 | |
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