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Registro completo
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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
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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.
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INIA Las Brujas (LB) |
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Registros recuperados : 45 | |
41. | | 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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42. | | 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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43. | | 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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44. | | 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. |
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45. | | 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 : 45 | |
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