|
|
Registro completo
|
Biblioteca (s) : |
INIA Las Brujas. |
Fecha : |
21/02/2014 |
Actualizado : |
18/12/2018 |
Tipo de producción científica : |
Artículos Indexados |
Autor : |
MASUDA, Y.; MISZTAL, I.; TSURUTA, S.; LOURENÇO, D. A. L.; FRAGOMENI, B.; LEGARRA, A.; AGUILAR, I.; LAWLOR, T. J. |
Afiliación : |
IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
Título : |
Single-step genomic evaluations with 570K genotyped animals in US Holsteins. |
Fecha de publicación : |
2015 |
Fuente / Imprenta : |
Interbull Bulletin, 2015, v. 49, p. 85-89. |
Idioma : |
Inglés |
Contenido : |
ABSTRACT.
The objectives of this study were to implement and evaluate the ?Algorithm for proven and Young? (APY) for inversion of the genomic relationship matrix (G) in single-step genomic BLUP (ssGBLUP). Phenotypic data included 11,626,576 final scores on 7,093,380 US Holsteins and genotypes were available for 569,404 animals. Daughter deviations for young genotyped bulls with no classified daughters in 2009 but with at least 30 classified daughters in 2014 were computed using BLUP with all the phenotypes and pedigrees. Genomic predictions (GEBV) were obtained by ssGBLUP using phenotypes up to 2009. We calculated the G inverse with APY based on genomic recursions on a subset of ?base? animals. We tested several subsets including 9,406 bulls with at least 1 daughter, 9,046 bulls and 1052 dams, 9,046 bulls and 7,422 classified cows, and random samples of 5,000, 10,000, 15,000, 20,000, and 30,000 animals. Validation reliability was calculated as R2 with a linear regression of daughter deviations on GEBV for young genotyped bulls. The reliabilities were 0.39 with 5,000 randomly chosen base-animals, 0.45 with base-animals including bulls and cows, and 0.44 with the remaining subsets. Setting up the G inverse for all the genotypes with 10,000 base-animals took 1.3 hours and 57GB of memory. Genomic predictions with G inverse are accurate when the number of base animals is at least 10,000. Single-step genomic BLUP using the G inverse via APY is applicable to populations with a large number of genotyped animals. MenosABSTRACT.
The objectives of this study were to implement and evaluate the ?Algorithm for proven and Young? (APY) for inversion of the genomic relationship matrix (G) in single-step genomic BLUP (ssGBLUP). Phenotypic data included 11,626,576 final scores on 7,093,380 US Holsteins and genotypes were available for 569,404 animals. Daughter deviations for young genotyped bulls with no classified daughters in 2009 but with at least 30 classified daughters in 2014 were computed using BLUP with all the phenotypes and pedigrees. Genomic predictions (GEBV) were obtained by ssGBLUP using phenotypes up to 2009. We calculated the G inverse with APY based on genomic recursions on a subset of ?base? animals. We tested several subsets including 9,406 bulls with at least 1 daughter, 9,046 bulls and 1052 dams, 9,046 bulls and 7,422 classified cows, and random samples of 5,000, 10,000, 15,000, 20,000, and 30,000 animals. Validation reliability was calculated as R2 with a linear regression of daughter deviations on GEBV for young genotyped bulls. The reliabilities were 0.39 with 5,000 randomly chosen base-animals, 0.45 with base-animals including bulls and cows, and 0.44 with the remaining subsets. Setting up the G inverse for all the genotypes with 10,000 base-animals took 1.3 hours and 57GB of memory. Genomic predictions with G inverse are accurate when the number of base animals is at least 10,000. Single-step genomic BLUP using the G inverse via APY is applicable to populations with a lar... Presentar Todo |
Palabras claves : |
APY; SSGBLUP; VALIDATION. |
Asunto categoría : |
-- |
URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/12203/1/1382-2378-1-PB.pdf
|
Marc : |
LEADER 02171naa a2200241 a 4500 001 1012457 005 2018-12-18 008 2015 bl uuuu u00u1 u #d 100 1 $aMASUDA, Y. 245 $aSingle-step genomic evaluations with 570K genotyped animals in US Holsteins.$h[electronic resource] 260 $c2015 520 $aABSTRACT. The objectives of this study were to implement and evaluate the ?Algorithm for proven and Young? (APY) for inversion of the genomic relationship matrix (G) in single-step genomic BLUP (ssGBLUP). Phenotypic data included 11,626,576 final scores on 7,093,380 US Holsteins and genotypes were available for 569,404 animals. Daughter deviations for young genotyped bulls with no classified daughters in 2009 but with at least 30 classified daughters in 2014 were computed using BLUP with all the phenotypes and pedigrees. Genomic predictions (GEBV) were obtained by ssGBLUP using phenotypes up to 2009. We calculated the G inverse with APY based on genomic recursions on a subset of ?base? animals. We tested several subsets including 9,406 bulls with at least 1 daughter, 9,046 bulls and 1052 dams, 9,046 bulls and 7,422 classified cows, and random samples of 5,000, 10,000, 15,000, 20,000, and 30,000 animals. Validation reliability was calculated as R2 with a linear regression of daughter deviations on GEBV for young genotyped bulls. The reliabilities were 0.39 with 5,000 randomly chosen base-animals, 0.45 with base-animals including bulls and cows, and 0.44 with the remaining subsets. Setting up the G inverse for all the genotypes with 10,000 base-animals took 1.3 hours and 57GB of memory. Genomic predictions with G inverse are accurate when the number of base animals is at least 10,000. Single-step genomic BLUP using the G inverse via APY is applicable to populations with a large number of genotyped animals. 653 $aAPY 653 $aSSGBLUP 653 $aVALIDATION 700 1 $aMISZTAL, I. 700 1 $aTSURUTA, S. 700 1 $aLOURENÇO, D. A. L. 700 1 $aFRAGOMENI, B. 700 1 $aLEGARRA, A. 700 1 $aAGUILAR, I. 700 1 $aLAWLOR, T. J. 773 $tInterbull Bulletin, 2015$gv. 49, p. 85-89.
Descargar
Esconder MarcPresentar Marc Completo |
Registro original : |
INIA Las Brujas (LB) |
|
Biblioteca
|
Identificación
|
Origen
|
Tipo / Formato
|
Clasificación
|
Cutter
|
Registro
|
Volumen
|
Estado
|
Volver
|
|
Registros recuperados : 81 | |
61. | | 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. |
| |
63. | | 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. |
| |
64. | | 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. |
| |
65. | | 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. |
| |
66. | | 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 ACCESSTipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : A - 1 |
Biblioteca(s): INIA Las Brujas. |
| |
67. | | 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. |
| |
68. | | 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. |
| |
69. | | 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. |
| |
70. | | 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 2016Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
| |
71. | | MCWHORTER, T.M.; BERMANN, M.; GARCIA, A.L.S.; LEGARRA, A.; AGUILAR, I.; MISZTAL, I.; LOURENCO, D. Implication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP. Journal of Animal Breeding and Genetics, 2023, volume 140, issue 1, pp. 60-78. OPEN ACCESS. doi: https://doi.org/10.1111/jbg.12734 Article history: Received 18 March 2019; Revised 15 July 2019; Accepted: 29 July 2019; First published 10 August 2022.
Correspondence: McWhorter, T.M.; Department of Animal and Dairy Science, University of Georgia, Athens, GA, United...Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
| |
72. | | 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. |
| |
73. | | 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. |
| |
74. | | 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. |
| |
75. | | 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. |
| |
76. | | 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. |
| |
77. | | 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. |
| |
78. | | WANG, H.; MISZTAL, I.; AGUILAR, I.; LEGARRA, A.; FERNANDO, R.L.; VITEZICA, Z.; OKIMOTO, R.; WING, T.; HAWKEN, R.; MUIR, W.M. Genome-wide association mapping including phenotypes from relatives without genotypes in a single-step (ssGWAS) for 6-week body weight in broiler chickens. Frontiers in Genetics, 2014, v.5, p.1-10. OPEN ACCESS. Article history: Received 03 March 2014 // Paper pending published 04 April 2014 // Accepted 25 April 2014 // Published online: 20 May 2014.Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : B - 2 |
Biblioteca(s): INIA Las Brujas. |
| |
79. | | CHEN, C.Y.; MISZTAL, I.; AGUILAR, I.; TSURUTA, S.; MEUWISSEN, T.H.E.; AGGREY, S.E.; WING, T.; MUIR, W.M. Genome-wide marker-assisted selection combining all pedigree phenotypic information with genotypic data in one step: An example using broiler chickens. Journal of Animal Science, 2011, v.89, no.1, p.23-28. Article history: Received April 9, 2010 / Accepted September 22, 2010.Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : A - 1 |
Biblioteca(s): INIA Las Brujas. |
| |
80. | | 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. |
| |
Registros recuperados : 81 | |
|
Expresión de búsqueda válido. Check! |
|
|