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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha : |
10/09/2014 |
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Actualizado : |
09/10/2019 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
LOURENCO, D.A.L.; MISZTAL, I.; TSURUTA, S.; AGUILAR, I.; LAWLOR, T.J.; FORNI, S.; WELLER, J.I. |
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Afiliación : |
IGNACIO AGUILAR GARCIA, Instituto Nacional de Investigación Agropecuaria (INIA), Uruguay. |
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Título : |
Are evaluations on young genotyped animals benefiting from the past generations?. |
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Fecha de publicación : |
2014 |
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Fuente / Imprenta : |
Journal of Dairy Science, 2014, v.97, no.6, p.3930-3942. OPEN ACCESS |
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ISSN : |
0022-0302 |
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DOI : |
10.3168/jds.2013-7769 |
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Idioma : |
Inglés |
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Notas : |
Article history: Received November 26, 2013. // Accepted February 11, 2014. OPEN ACCESS |
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Contenido : |
ABSTRACT.
Data sets of US Holsteins, Israeli Holsteins, and pigs from PIC (a Genus company, Hendersonville, TN) were used to evaluate the effect of different numbers of generations on ability to predict genomic breeding values of young genotyped animals. The influence of including only 2 generations of ancestors (A2) or all ancestors (Af) was also investigated. A total of 34,506 US Holsteins, 1,305 Israeli Holsteins, and 5,236 pigs were genotyped. The evaluations were computed by traditional BLUP and single-step genomic BLUP, and computing performance was assessed for the latter method. For the 2 Holstein data sets, coefficients of determination (R2) and regression (?) of deregressed evaluations from a full data set with records up to 2011 on estimated breeding values and genomic estimated breeding values from the truncated data sets were computed. The thresholds for data deletion were set by intervals of 5 yr, based on the average generation interval in dairy cattle. For the PIC data set, correlations between corrected phenotypes and estimated or genomic estimated breeding values were used to evaluate predictive ability on young animals born in 2010 and 2011. The reduced data set contained data up to 2009, and the thresholds were set based on an average generation interval of 3 yr. The number of generations that could be deleted without a reduction in accuracy depended on data structure and trait. For US Holsteins, removing 3 and 4 generations of data did not reduce accuracy of evaluations for final score in Af and A2 scenarios, respectively. For Israeli Holsteins, the accuracies for milk, fat, and protein yields were the highest when only phenotypes recorded in 2000 and later were included and full pedigrees were applied. Of the 135 Israeli bulls with genotypes (validation set) and daughter records only in the complete data set, 38 and 97 were sons of Israeli and foreign bulls, respectively. Although more phenotypic data increased the prediction accuracy for sons of Israeli bulls, the reverse was true for sons of foreign bulls. Also, more phenotypic data caused large inflation of genomic estimated breeding values for sons of foreign bulls, whereas the opposite was true with the deletion of all but the most recent phenotypic data. Results for protein and fat percentage were different from those for milk, fat, and protein yields; however, relatively, the changes in coefficients of determination and regression were smaller for percentage traits. For PIC data set, removing data from up to 5 generations did not erode predictive ability for genotyped animals for the 2 reproductive traits used in validation. Given the data used in this study, truncating old data reduces computation requirements but does not decrease the accuracy. For small populations that include local and imported animals, truncation may be beneficial for one group of animals and detrimental to another group. MenosABSTRACT.
Data sets of US Holsteins, Israeli Holsteins, and pigs from PIC (a Genus company, Hendersonville, TN) were used to evaluate the effect of different numbers of generations on ability to predict genomic breeding values of young genotyped animals. The influence of including only 2 generations of ancestors (A2) or all ancestors (Af) was also investigated. A total of 34,506 US Holsteins, 1,305 Israeli Holsteins, and 5,236 pigs were genotyped. The evaluations were computed by traditional BLUP and single-step genomic BLUP, and computing performance was assessed for the latter method. For the 2 Holstein data sets, coefficients of determination (R2) and regression (?) of deregressed evaluations from a full data set with records up to 2011 on estimated breeding values and genomic estimated breeding values from the truncated data sets were computed. The thresholds for data deletion were set by intervals of 5 yr, based on the average generation interval in dairy cattle. For the PIC data set, correlations between corrected phenotypes and estimated or genomic estimated breeding values were used to evaluate predictive ability on young animals born in 2010 and 2011. The reduced data set contained data up to 2009, and the thresholds were set based on an average generation interval of 3 yr. The number of generations that could be deleted without a reduction in accuracy depended on data structure and trait. For US Holsteins, removing 3 and 4 generations of data did not reduce accura... Presentar Todo |
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Palabras claves : |
DAIRY CATTLE; GENOMIC SELECTION; PEDIGREE DEPTH; SINGLE-STEP GENOMIC BLUP. |
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Thesagro : |
BLUP; GANADO DE LECHE; SELECCIÓN GENÓMICA. |
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Asunto categoría : |
L10 Genética y mejoramiento animal |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/3064/1/Aguilar-I.-2014-Jr.Dairy-Sci.-v.976-p.3930-3942.pdf
https://www.journalofdairyscience.org/article/S0022-0302(14)00225-2/pdf
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Marc : |
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008 2014 bl uuuu u00u1 u #d
022 $a0022-0302
024 7 $a10.3168/jds.2013-7769$2DOI
100 1 $aLOURENCO, D.A.L.
245 $aAre evaluations on young genotyped animals benefiting from the past generations?.$h[electronic resource]
260 $c2014
500 $aArticle history: Received November 26, 2013. // Accepted February 11, 2014. OPEN ACCESS
520 $aABSTRACT. Data sets of US Holsteins, Israeli Holsteins, and pigs from PIC (a Genus company, Hendersonville, TN) were used to evaluate the effect of different numbers of generations on ability to predict genomic breeding values of young genotyped animals. The influence of including only 2 generations of ancestors (A2) or all ancestors (Af) was also investigated. A total of 34,506 US Holsteins, 1,305 Israeli Holsteins, and 5,236 pigs were genotyped. The evaluations were computed by traditional BLUP and single-step genomic BLUP, and computing performance was assessed for the latter method. For the 2 Holstein data sets, coefficients of determination (R2) and regression (?) of deregressed evaluations from a full data set with records up to 2011 on estimated breeding values and genomic estimated breeding values from the truncated data sets were computed. The thresholds for data deletion were set by intervals of 5 yr, based on the average generation interval in dairy cattle. For the PIC data set, correlations between corrected phenotypes and estimated or genomic estimated breeding values were used to evaluate predictive ability on young animals born in 2010 and 2011. The reduced data set contained data up to 2009, and the thresholds were set based on an average generation interval of 3 yr. The number of generations that could be deleted without a reduction in accuracy depended on data structure and trait. For US Holsteins, removing 3 and 4 generations of data did not reduce accuracy of evaluations for final score in Af and A2 scenarios, respectively. For Israeli Holsteins, the accuracies for milk, fat, and protein yields were the highest when only phenotypes recorded in 2000 and later were included and full pedigrees were applied. Of the 135 Israeli bulls with genotypes (validation set) and daughter records only in the complete data set, 38 and 97 were sons of Israeli and foreign bulls, respectively. Although more phenotypic data increased the prediction accuracy for sons of Israeli bulls, the reverse was true for sons of foreign bulls. Also, more phenotypic data caused large inflation of genomic estimated breeding values for sons of foreign bulls, whereas the opposite was true with the deletion of all but the most recent phenotypic data. Results for protein and fat percentage were different from those for milk, fat, and protein yields; however, relatively, the changes in coefficients of determination and regression were smaller for percentage traits. For PIC data set, removing data from up to 5 generations did not erode predictive ability for genotyped animals for the 2 reproductive traits used in validation. Given the data used in this study, truncating old data reduces computation requirements but does not decrease the accuracy. For small populations that include local and imported animals, truncation may be beneficial for one group of animals and detrimental to another group.
650 $aBLUP
650 $aGANADO DE LECHE
650 $aSELECCIÓN GENÓMICA
653 $aDAIRY CATTLE
653 $aGENOMIC SELECTION
653 $aPEDIGREE DEPTH
653 $aSINGLE-STEP GENOMIC BLUP
700 1 $aMISZTAL, I.
700 1 $aTSURUTA, S.
700 1 $aAGUILAR, I.
700 1 $aLAWLOR, T.J.
700 1 $aFORNI, S.
700 1 $aWELLER, J.I.
773 $tJournal of Dairy Science, 2014$gv.97, no.6, p.3930-3942. OPEN ACCESS
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INIA Las Brujas (LB) |
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| Registros recuperados : 34 | |
| 1. |  | 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,...| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 2. | | 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...| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
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| 3. | | 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.| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 4. | | 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.| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : A - 2 |
| Biblioteca(s): INIA Las Brujas. |
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| 5. | | 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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| 6. | | 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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| 7. | | 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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| 8. | | 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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| 9. | | 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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| 10. | | 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/s12711-022-00752-4| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
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| 11. | | MISZTAL, I.; AGUILAR, I.; LOURENCO, D.; MA, L.; STEIBEL, J.P. Emerging issues in genomic selection. Animal Genetics and Genomics. Journal of Animal Science, June 2021, Volume 99, Issue 61, skab092. OPEN ACCESS. Doi: https://doi.org/10.1093/jas/skab092 Article history: Received 23 January 2021; Accepted 26 March 2021; Advance Access publication March 27, 2021.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License...| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
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| 12. | | 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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| 13. | | 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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| 14. | | 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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| 15. | | 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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| 16. | | 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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| 17. | | 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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| 18. | | 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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| 19. | | 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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| 20. | | 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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| Registros recuperados : 34 | |
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