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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha : |
16/09/2014 |
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Actualizado : |
23/10/2019 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
MISZTAL, I.; TSURUTA, S.; AGUILAR, I.; LEGARRA, A.; VAN RADEN, P.M.; LAWLOR, T.J. |
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Afiliación : |
IGNACIO AGUILAR GARCIA, Instituto Nacional de Investigación Agropecuaria (INIA), Uruguay. |
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Título : |
Methods to approximate reliabilities in single-step genomic evaluation. |
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Fecha de publicación : |
2013 |
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Fuente / Imprenta : |
Journal of Dairy Science, 2013, v.96, no.1, p.647-654. OPEN ACCESS. |
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ISSN : |
0022-0302 |
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DOI : |
10.3168/jds.2012-5656 |
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Idioma : |
Inglés |
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Notas : |
Article history: Received April 24, 2012. / Accepted September 18, 2012. |
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Contenido : |
ABSTRACT.
Reliability of predictions from single-step genomic BLUP (ssGBLUP) can be calculated by matrix inversion, but that is not feasible for large data sets. Two methods of approximating reliability were developed based on the decomposition of a function of reliability into contributions from records, pedigrees, and genotypes. Those contributions can be expressed in record or daughter equivalents. The first approximation method involved inversion of a matrix that contains inverses of the genomic relationship matrix and the pedigree relationship matrix for genotyped animals. The second approximation method involved only the diagonal elements of those inverses. The 2 approximation methods were tested with a simulated data set. The correlations between ssGBLUP and approximated contributions from genomic information were 0.92 for the first approximation method and 0.56 for the second approximation method; contributions were inflated by 62 and 258%, respectively. The respective correlations for reliabilities were 0.98 and 0.72. After empirical correction for inflation, those correlations increased to 0.99 and 0.89. Approximations of reliabilities of predictions by ssGBLUP are accurate and computationally feasible for populations with up to 100,000 genotyped animals. A critical part of the approximations is quality control of information from single nucleotide polymorphisms and proper scaling of the genomic relationship matrix.
© 2013 American Dairy Science Association. |
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Thesagro : |
GENETICA ANIMAL; MEJORAMIENTO GENETICO ANIMAL; MÉTODOS ESTADÍSTICOS. |
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Asunto categoría : |
L10 Genética y mejoramiento animal |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/3143/1/Aguilar-J.-2013.-Jr.Dairy-Sci.-v.961-p.647-654.pdf
http://www.journalofdairyscience.org/article/S0022-0302(12)00802-8/pdf
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Marc : |
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245 $aMethods to approximate reliabilities in single-step genomic evaluation.$h[electronic resource]
260 $c2013
500 $aArticle history: Received April 24, 2012. / Accepted September 18, 2012.
520 $aABSTRACT. Reliability of predictions from single-step genomic BLUP (ssGBLUP) can be calculated by matrix inversion, but that is not feasible for large data sets. Two methods of approximating reliability were developed based on the decomposition of a function of reliability into contributions from records, pedigrees, and genotypes. Those contributions can be expressed in record or daughter equivalents. The first approximation method involved inversion of a matrix that contains inverses of the genomic relationship matrix and the pedigree relationship matrix for genotyped animals. The second approximation method involved only the diagonal elements of those inverses. The 2 approximation methods were tested with a simulated data set. The correlations between ssGBLUP and approximated contributions from genomic information were 0.92 for the first approximation method and 0.56 for the second approximation method; contributions were inflated by 62 and 258%, respectively. The respective correlations for reliabilities were 0.98 and 0.72. After empirical correction for inflation, those correlations increased to 0.99 and 0.89. Approximations of reliabilities of predictions by ssGBLUP are accurate and computationally feasible for populations with up to 100,000 genotyped animals. A critical part of the approximations is quality control of information from single nucleotide polymorphisms and proper scaling of the genomic relationship matrix. © 2013 American Dairy Science Association.
650 $aGENETICA ANIMAL
650 $aMEJORAMIENTO GENETICO ANIMAL
650 $aMÉTODOS ESTADÍSTICOS
700 1 $aTSURUTA, S.
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773 $tJournal of Dairy Science, 2013$gv.96, no.1, p.647-654. OPEN ACCESS.
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INIA Las Brujas (LB) |
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| Registros recuperados : 45 | |
| 21. |  | TSURUTA, S.; AGUILAR, I.; MISZTAL, I.; LEGARRA, A.; LAWLOR, T. J. Multiple trait genetic evaluation of linear type traits using genomic and phenotypic data in US Holsteins. Volume Genetic improvement programmes: Selection using molecular information - Poster Sessions, 0489. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 9., Leipzig, Germany, August 1-6, 2010. p. 0489.| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 23. | | 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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| 24. | | 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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| 25. | | MISZTAL, I.; AGUILAR, I.; TSURUTA, S.; SÁNCHEZ, J.P.; ZUMBACH, B. Studies on heat stress in dairy cattle and pigs. Volume Special topics: Animal breeding and the environmental challenges - Lecture Sessions, 0625. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 9., Leipzig, Germany, August 1-6, 2010. p. 0625.| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 26. | | LOURENCO, D.A.L.; MISZTAL, I.; WANG, H.; AGUILAR, I.; TSURUTA, S.; BERTRAND, J.K. Prediction accuracy for a simulated maternally affected trait of beef cattle using different genomic evaluation models. Journal of Animal Science, 2013, v.91, no.9, p.4090-4098. Article history: Published online July 26, 2013.
This study was partially funded by the American Angus Association (St. Joseph, MO) and the USDA Agriculture and Food Research Initiative (Grant no. 2009-65205-05665 from the USDA National...| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : A - 2 |
| Biblioteca(s): INIA Las Brujas. |
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| 27. | | GARCÍA, A.; AGUILAR, I.; LEGARRA, A.; TSURUTA, S.; MISZTAL, I.; LOURENCO, D. Theoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP. Genetics, Selection, Evolution : GSE, 2022, Volume 54, Issue 1, Pages 66. OPEN ACCESS. doi: https://doi.org/10.1186/s12711-022-00752-4 Article history: Received 22 March 2022; Accepted 23 August 2022; Published 27 September 2022.| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - 1 |
| Biblioteca(s): INIA Las Brujas. |
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| 28. | | MISZTAL, I.; AGUILAR, I.; LEGARRA, A.; JOHNSON, D.; TSURUTA, S.; LAWLOR, T. J. A unified approach to utilize phenotypic, full pedigree, and genomic information for genetic evaluation. Volume Methods and tools: Software and bioinformatics - Lecture Sessions, 0050. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 9., Leipzig, Germany, August 1-6, 2010. p. 0050. Acknowledgements: This study was partially funded by the Holstein Association, Smithfield Premium Genetics, and AFRI grants 2009-65205-05665 and 2010-65205-20366 from the USDA NIFA Animal Genome Program.| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 29. | | 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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| 30. | | AGUILAR, I.; MISZTAL, I.; JOHNSON, D. L.; LEGARRA, A.; TSURUTA, S.; LAWLOR, T. J. Uso de información genómica en evaluaciones genéticas. Agrociencia Uruguay, 2010, v. 14, no. 3, p. 43-47. Agrociencia, Nro especial: Congreso Asociación Uruguaya de Producción Animal, 3., 4-5 Noviembre 2010, Montevideo, UY: INIA, Facultad de Agronomía, SMVU.| Tipo: Artículos en Revistas Indexadas Nacionales | Circulación / Nivel : B - 5 |
| Biblioteca(s): INIA Las Brujas. |
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| 31. | | 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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| 32. | | LOURENCO, D.A.L.; MISZTAL, I.; TSURUTA, S.; AGUILAR, I.; LAWLOR, T.J.; FORNI, S.; WELLER, J.I. Are evaluations on young genotyped animals benefiting from the past generations?. Journal of Dairy Science, 2014, v.97, no.6, p.3930-3942. OPEN ACCESS Article history: Received November 26, 2013. // Accepted February 11, 2014. OPEN ACCESS| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : A - 1 |
| Biblioteca(s): INIA Las Brujas. |
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| 33. | | CHEN, C. Y.; MISZTAL, I.; AGUILAR, I.; TSURUTA, S.; MEUWISSEN, T.; AGGREY, S. E.; MUIR, W. M. Genome wide marker assisted selection in chicken: making the most of all data, pedigree, phenotypic, and genomic in a simple one step procedure. Volume Genetic improvement programmes: Selection using molecular information - Lecture Sessions, 0288. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 9., Leipzig, Germany, August 1-6, 2010. p. 0288. Acknowledgements: The authors thank Cobb-Vantress for access to data for this study. This study was partially funded by the Holstein Association, Smithfield Premium Genetics, and by AFRI grants 2009-65205-05665 and 2010-65205-20366 from...| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 34. | | 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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| 35. | | LOURENCO, D.A.L.; MISZTAL, I.; TSURUTA, S.; AGUILAR, I.; EZRA, E.; RON, M.; SHIRAK, A.; WELLER, J.I. Methods for genomic evaluation of a relatively small genotyped dairy population and effect of genotyped cow information in multiparity analyses. Journal of Dairy Science, 2014, v.97, no.3, p.1742-1752. OPEN ACCESS. Article history: Received September 10, 2013. / Accepted December 6, 2013.| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : A - 1 |
| Biblioteca(s): INIA Las Brujas. |
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| 36. | | 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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| 37. | | 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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| 38. | | FORNERIS, N. S.; LEGARRA, A.; VITEZICA, Z. G.; TSURUTA, S.; AGUILAR, I.; MISZTAL, I.; CANTET, R. J. C. Quality control of genotypes using heritability estimates of gene content at the marker. Genetics, 2015, v. 199, p. 675-681. OPEN ACCESS. Manuscript received September 26, 2014; accepted for publication December 18, 2014; published Early Online January 6, 2015.| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
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| 39. | | FORNERIS, N. S.; LEGARRA, A.; VITEZICA, Z. G.; TSURUTA, S.; AGUILAR, I.; CANTET, R.J.C.; MISZTAL, I. Quality control of genotypes using heritability estimates of gene content. Volume Genetic Improvement Programs: Selection using molecular information (Posters), 471. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.471.| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 40. | | 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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| Registros recuperados : 45 | |
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