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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 : |
09/11/2017 |
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Actualizado : |
25/11/2019 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
MASUDA, Y; MISZTAL, I.; LEGARRA, A.; TSURUTA, S.; LOURENCO, D.A.L.; FRAGOMENI, B.O.; AGUILAR, I. |
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Afiliación : |
Y. MASUDA, Department of Animal and Dairy Science, University of Georgia; I. MISZTAL, Department of Animal and Dairy Science, University of Georgia; A. LEGARRA, INRA (Institut National de la Recherche Agronomique); S. TSURUTA, Department of Animal and Dairy Science, University of Georgia; D.A.L. LOURENCO, Department of Animal and Dairy Science, University of Georgia; B.O. FRAGOMENI, Department of Animal and Dairy Science, University of Georgia; IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
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Título : |
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. |
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Fecha de publicación : |
2017 |
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Fuente / Imprenta : |
Journal of Animal Science, 2017, v. 95(1): 49-52. |
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DOI : |
10.2527/jas.2016.0699 |
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Idioma : |
Inglés |
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Notas : |
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 Food Research Initiative competitive grant 2015-67015-22936). |
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Contenido : |
ABSTRACT.
This paper evaluates an efficient implementation to multiply the inverse of a numerator relationship matrix for genotyped animals () by a vector (q). The computation is required for solving mixed model equations in single-step genomic BLUP (ssGBLUP) with the preconditioned conjugate gradient (PCG). The inverse can be decomposed into sparse matrices that are blocks of the sparse inverse of a numerator relationship matrix (A−1) including genotyped animals and their ancestors. The elements of A−1 were rapidly calculated with the Henderson?s rule and stored as sparse matrices in memory. Implementation of was by a series of sparse matrix?vector multiplications. Diagonal elements of , which were required as preconditioners in PCG, were approximated with a Monte Carlo method using 1,000 samples. The efficient implementation of was compared with explicit inversion of A22 with 3 data sets including about 15,000, 81,000, and 570,000 genotyped animals selected from populations with 213,000, 8.2 million, and 10.7 million pedigree animals, respectively. The explicit inversion required 1.8 GB, 49 GB, and 2,415 GB (estimated) of memory, respectively, and 42 s, 56 min, and 13.5 d (estimated), respectively, for the computations. The efficient implementation required <1 MB, 2.9 GB, and 2.3 GB of memory, respectively, and <1 sec, 3 min, and 5 min, respectively, for setting up. Only <1 sec was required for the multiplication in each PCG iteration for any data sets. When the equations in ssGBLUP are solved with the PCG algorithm, is no longer a limiting factor in the computations.
Copyright © 2016. American Society of Animal Science. MenosABSTRACT.
This paper evaluates an efficient implementation to multiply the inverse of a numerator relationship matrix for genotyped animals () by a vector (q). The computation is required for solving mixed model equations in single-step genomic BLUP (ssGBLUP) with the preconditioned conjugate gradient (PCG). The inverse can be decomposed into sparse matrices that are blocks of the sparse inverse of a numerator relationship matrix (A−1) including genotyped animals and their ancestors. The elements of A−1 were rapidly calculated with the Henderson?s rule and stored as sparse matrices in memory. Implementation of was by a series of sparse matrix?vector multiplications. Diagonal elements of , which were required as preconditioners in PCG, were approximated with a Monte Carlo method using 1,000 samples. The efficient implementation of was compared with explicit inversion of A22 with 3 data sets including about 15,000, 81,000, and 570,000 genotyped animals selected from populations with 213,000, 8.2 million, and 10.7 million pedigree animals, respectively. The explicit inversion required 1.8 GB, 49 GB, and 2,415 GB (estimated) of memory, respectively, and 42 s, 56 min, and 13.5 d (estimated), respectively, for the computations. The efficient implementation required <1 MB, 2.9 GB, and 2.3 GB of memory, respectively, and <1 sec, 3 min, and 5 min, respectively, for setting up. Only <1 sec was required for the multiplication in each PCG iteration for any data sets. When t... Presentar Todo |
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Palabras claves : |
COMPUTATION; GENOMIC SELECTION; INVERSION; NUMERATOR RELATIONSHIP MATRIX; PRECONDITIONED CONJUGATE GRADIENT; SPARSE MATRIX. |
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Asunto categoría : |
-- |
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Marc : |
LEADER 02919naa a2200289 a 4500
001 1057743
005 2019-11-25
008 2017 bl uuuu u00u1 u #d
024 7 $a10.2527/jas.2016.0699$2DOI
100 1 $aMASUDA, Y
245 $aTechnical note$bAvoiding 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.$h[electronic resource]
260 $c2017
500 $aArticle 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 Food Research Initiative competitive grant 2015-67015-22936).
520 $aABSTRACT. This paper evaluates an efficient implementation to multiply the inverse of a numerator relationship matrix for genotyped animals () by a vector (q). The computation is required for solving mixed model equations in single-step genomic BLUP (ssGBLUP) with the preconditioned conjugate gradient (PCG). The inverse can be decomposed into sparse matrices that are blocks of the sparse inverse of a numerator relationship matrix (A−1) including genotyped animals and their ancestors. The elements of A−1 were rapidly calculated with the Henderson?s rule and stored as sparse matrices in memory. Implementation of was by a series of sparse matrix?vector multiplications. Diagonal elements of , which were required as preconditioners in PCG, were approximated with a Monte Carlo method using 1,000 samples. The efficient implementation of was compared with explicit inversion of A22 with 3 data sets including about 15,000, 81,000, and 570,000 genotyped animals selected from populations with 213,000, 8.2 million, and 10.7 million pedigree animals, respectively. The explicit inversion required 1.8 GB, 49 GB, and 2,415 GB (estimated) of memory, respectively, and 42 s, 56 min, and 13.5 d (estimated), respectively, for the computations. The efficient implementation required <1 MB, 2.9 GB, and 2.3 GB of memory, respectively, and <1 sec, 3 min, and 5 min, respectively, for setting up. Only <1 sec was required for the multiplication in each PCG iteration for any data sets. When the equations in ssGBLUP are solved with the PCG algorithm, is no longer a limiting factor in the computations. Copyright © 2016. American Society of Animal Science.
653 $aCOMPUTATION
653 $aGENOMIC SELECTION
653 $aINVERSION
653 $aNUMERATOR RELATIONSHIP MATRIX
653 $aPRECONDITIONED CONJUGATE GRADIENT
653 $aSPARSE MATRIX
700 1 $aMISZTAL, I.
700 1 $aLEGARRA, A.
700 1 $aTSURUTA, S.
700 1 $aLOURENCO, D.A.L.
700 1 $aFRAGOMENI, B.O.
700 1 $aAGUILAR, I.
773 $tJournal of Animal Science, 2017$gv. 95(1): 49-52.
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INIA Las Brujas (LB) |
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| Registros recuperados : 13 | |
| 1. |  | FRAGOMENI, B.O.; MISZTAL, I.; LOURENCO, D.L.; AGUILAR, I.; OKIMOTO, R.; MUIR, W.M. Changes in variance explained by top SNP windows over generations for three traits in broiler chicken Frontiers in Genetics, 2014, v.5, no.Oct., Article number 332. OPEN ACCESS. Article history: Published 01 October 2014.| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : B - 2 |
| Biblioteca(s): INIA Las Brujas. |
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| 2. | | 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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| 3. | | 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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| 4. | | LOURENCO, D.A.L.; FRAGOMENI, B.O.; TSURUTA, S.; AGUILAR, I.; ZUMBACH, B.; HAWKEN, R.J.; LEGARRA, A.; MISZTAL, I. Accuracy of estimated breeding values with genomic information on males, females, or both: An example on broiler chicken. Genetics Selection Evolution, 2015, v. 242, p. 47-56. OPEN ACCESS. Article history: Received: 14 October 2014 / Accepted: 22 June 2015 / Published: 02 July 2015.| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
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| 5. | | 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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| 6. | | 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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| 7. | | 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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| 8. | | 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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| 9. | | 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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| 10. | | 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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| 11. | | 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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| 12. | | LOURENCO, D.A.L.; FRAGOMENI, B.O.; BRADFORD, H.L.; MENEZES I.R.; FERRAZ, J.B.S.; AGUILAR, I.; MISZTAL, I. Implications of SNP weighting on single-step genomic predictions for different reference population sizes. Journal of Animal Breeding and Genetics, 2017, v. 134 (6), p. 463-471. Article history: Received: 28 February 2017 / Accepted: 19 July 2017.
This study was partially funded by the American Angus Association (St. Joseph, MO), Zoetis (Kalamazoo, MI) and by Agriculture and Food Research Initiative Competitive...| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
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| 13. | | MISZTAL, I.; WANG, H.; AGUILAR, I.; LEGARRA, A.; TSURUTA, S.; LOURENCO, D.; FRAGOMENI, B. O.; ZHANG, X.; MUIR, W. M.; CHENG, H. H.; OKIMOTO, R.; WING, T.; HAWKEN, R. R.; ZUMBACH, B.; FERNANDO, R. GWAS using ssGBLUP. Volume Species Breeding: Poultry, 325. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.325.| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| Registros recuperados : 13 | |
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