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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha : |
31/03/2021 |
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Actualizado : |
31/03/2021 |
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Tipo de producción científica : |
Trabajos en Congresos/Conferencias |
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Autor : |
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. |
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Afiliación : |
IGNACY MISZTAL, University of Georgia, Athens, GA, USA; H. WANG, Genus PIC, Hendersonville, TN; IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ANDRÉS LEGARRA, INRA, Toulouse, France; S. TSURUTA, University of Georgia, Athens, GA, USA; D.A.L. LOURENCO, University of Georgia, Athens, GA, USA; B. O. FRAGOMENI, University of Georgia, Athens, GA, USA; X. ZHANG, University of Georgia, Athens, GA, USA; W. M. MUIR, Purdue University, West Lafayette, IN, USA; H. H. CHENG, Cobb-Vantress Inc., Siloam Springs, AR, USA; R. OKIMOTO, Cobb-Vantress Inc., Siloam Springs, AR, USA; T. WING, Cobb-Vantress Inc., Siloam Springs, AR, USA; R. R. HAWKEN, Cobb-Vantress Inc., Siloam Springs, AR, USA; B. ZUMBACH, Cobb-Vantress Inc., Siloam Springs, AR, USA; R. FERNANDO, Department of Animal Science, Iowa State University, Ames, IA, USA. |
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Título : |
GWAS using ssGBLUP. |
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Complemento del título : |
Volume Species Breeding: Poultry, 325. |
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Fecha de publicación : |
2014 |
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Fuente / Imprenta : |
In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.325. |
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Idioma : |
Inglés |
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Contenido : |
ABSTRACT.
This study aimed to compare results of genome-wide associations obtained from various methodologies for GWAS when applied to two lines of broiler chicken. Each line contained >250k birds with 3 traits and 5k SNP60k genotypes. Methods included single-step GWAS, single marker model and BayesB. Mannhattan plots were based on variances of 20-SNP segments, as shorter segments produced noisy plots. Only a few segments explained >1 % of the additive variance. One segment explained >20% variance in BayesB but 3% with ssGWAS and <1% with a single marker model. In two lines, no major segment overlapped for any trait. When analyses used slices of generations (1-3,2-4,3-5,1-5), variances for the same segment varied greatly. The plots were more distinct with a new data set that included >16k genotypes, but no segment explained >1% of the variance. Strength of associations strongly depends on methodologies and details of implementations. |
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Palabras claves : |
GWAS; SNP variance; SsGBLUP. |
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Asunto categoría : |
L10 Genética y mejoramiento animal |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/15454/1/Misztal-et-al.-2014.WCGALP.pdf
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Marc : |
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100 1 $aMISZTAL, I.
245 $aGWAS using ssGBLUP.$h[electronic resource]
260 $aIn: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.325.$c2014
520 $aABSTRACT. This study aimed to compare results of genome-wide associations obtained from various methodologies for GWAS when applied to two lines of broiler chicken. Each line contained >250k birds with 3 traits and 5k SNP60k genotypes. Methods included single-step GWAS, single marker model and BayesB. Mannhattan plots were based on variances of 20-SNP segments, as shorter segments produced noisy plots. Only a few segments explained >1 % of the additive variance. One segment explained >20% variance in BayesB but 3% with ssGWAS and <1% with a single marker model. In two lines, no major segment overlapped for any trait. When analyses used slices of generations (1-3,2-4,3-5,1-5), variances for the same segment varied greatly. The plots were more distinct with a new data set that included >16k genotypes, but no segment explained >1% of the variance. Strength of associations strongly depends on methodologies and details of implementations.
653 $aGWAS
653 $aSNP variance
653 $aSsGBLUP
700 1 $aWANG, H.
700 1 $aAGUILAR, I.
700 1 $aLEGARRA, A.
700 1 $aTSURUTA, S.
700 1 $aLOURENCO, D.
700 1 $aFRAGOMENI, B. O.
700 1 $aZHANG, X.
700 1 $aMUIR, W. M.
700 1 $aCHENG, H. H.
700 1 $aOKIMOTO, R.
700 1 $aWING, T.
700 1 $aHAWKEN, R. R.
700 1 $aZUMBACH, B.
700 1 $aFERNANDO, R.
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INIA Las Brujas (LB) |
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| Registros recuperados : 9 | |
| 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. | | 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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| 3. | | 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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| 4. | | 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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| 5. | | 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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| 6. | | 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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| 7. | | 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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| 8. | | 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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| 9. | | 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 : 9 | |
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