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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
Fecha : |
31/03/2021 |
Actualizado : |
31/03/2021 |
Tipo de producción científica : |
Trabajos en Congresos/Conferencias |
Autor : |
FORNERIS, N. S.; LEGARRA, A.; VITEZICA, Z. G.; TSURUTA, S.; AGUILAR, I.; CANTET, R.J.C.; MISZTAL, I. |
Afiliación : |
NATALIA S. FORNERIS, Department of Animal Science, University of Buenos Aires, Argentina; ANDRÉS LEGARRA, INRA, Castanet-Tolosan, France; ZULMA G VITEZICA, INRA, Castanet-Tolosan, France; SHOGO TSURUTA, University of Georgia, Athens, GA, USA; IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; RODOLFO J.C. CANTET, Department of Animal Science, University of Buenos Aires, Argentina; # CONICET, Argentina.; IGNACY MISZTAL, University of Georgia, Athens, GA, USA. |
Título : |
Quality control of genotypes using heritability estimates of gene content. |
Complemento del título : |
Volume Genetic Improvement Programs: Selection using molecular information (Posters), 471. |
Fecha de publicación : |
2014 |
Fuente / Imprenta : |
In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.471. |
Idioma : |
Inglés |
Contenido : |
ABSTRACT.
Quality control filtering of single nucleotide polymorphisms (SNP) is a key step when analyzing genomic data. Here, we present a practical method to identify poorly genotyped SNPs by detecting those for which gene content deviates from the pedigree-based expectation. This can be achieved by estimating the heritability of gene content at each marker, defined as the number of copies of a particular reference allele in a genotype of an animal (0, 1 or 2). The method uses Restricted Maximum Likelihood (REML) to estimate heritability of gene content at each SNP and also builds a likelihood ratio test statistic to test for zero error variance in genotyping. The proposed method is illustrated with a real dataset with genotypes from Illumina PorcineSNP60 chip. |
Palabras claves : |
Gene Content; Heritability; Likelihood Ratio; Quality Control. |
Asunto categoría : |
L10 Genética y mejoramiento animal |
URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/15444/1/Forneris-et-al.-2014.-WCGALP.pdf
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Marc : |
LEADER 01515nam a2200229 a 4500 001 1061920 005 2021-03-31 008 2014 bl uuuu u01u1 u #d 100 1 $aFORNERIS, N. S. 245 $aQuality control of genotypes using heritability estimates of gene content.$h[electronic resource] 260 $aIn: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.471.$c2014 520 $aABSTRACT. Quality control filtering of single nucleotide polymorphisms (SNP) is a key step when analyzing genomic data. Here, we present a practical method to identify poorly genotyped SNPs by detecting those for which gene content deviates from the pedigree-based expectation. This can be achieved by estimating the heritability of gene content at each marker, defined as the number of copies of a particular reference allele in a genotype of an animal (0, 1 or 2). The method uses Restricted Maximum Likelihood (REML) to estimate heritability of gene content at each SNP and also builds a likelihood ratio test statistic to test for zero error variance in genotyping. The proposed method is illustrated with a real dataset with genotypes from Illumina PorcineSNP60 chip. 653 $aGene Content 653 $aHeritability 653 $aLikelihood Ratio 653 $aQuality Control 700 1 $aLEGARRA, A. 700 1 $aVITEZICA, Z. G. 700 1 $aTSURUTA, S. 700 1 $aAGUILAR, I. 700 1 $aCANTET, R.J.C. 700 1 $aMISZTAL, I.
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Registros recuperados : 218 | |
161. | | ROSAS, J.E.; ALE, L.; REBOLLO, I.; SCHEFFEL, S.; AGUILAR, I.; MOLINA, F.; PÉREZ DE VIDA, F. Boosting INIA's Rice Breeding Program with molecular quantitative genetics approaches. [Abstract]. In: International Temperate Rice Conference (7., 2020, Pelotas, RS), Science & Innovation: feeding a world of 10 billion people: proceedings. Pelotas RS, Brasil, February 9-12, 2020. Brasília, DF : Embrapa, 2020.Tipo: Abstracts/Resúmenes |
Biblioteca(s): INIA Treinta y Tres. |
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162. | | BALMELLI, G.; SIMETO, S.; CASTILLO, A.; GASPARRI, P.; CABRERA, D.; AGUILAR, I.; QUEZADA, M.; DA SILVA, C.; GIORELLO, F. Breeding for resistance to Teratosphaeria nubilosa on Eucalyptus globulus. In: Pesquisa florestal brasileira = Brazilian journal of forestry research., v. 39, e201902043, Special issue, 2019. Colombo : Embrapa Florestas, 2019. Congreso IUFRO, 25., Curitiba, Brasil, 29 setiembre-05 octubre, 2019. Abstracts. p. 173Tipo: Abstracts/Resúmenes |
Biblioteca(s): INIA Tacuarembó. |
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163. | | BRUNES, L.C.; FARIA, C.U.D.; MAGNABOSCO, C.U.; LOBO, R.B.; PERIPOLLI, E.; AGUILAR, I.; BALDI, F. Genomic prediction ability and genetic parameters for residual feed intake calculated using different approaches and their associations with growth, reproductive, and carcass traits in Nellore cattle. Journal of Applied Genetics, 2023, Volume 64, Issue 1, Pages 159 - 167. doi: https://doi.org/10.1007/s13353-022-00734-8 Article history: Received 25 February 2022; Revised 3 September 2022; Accepted 26 October 2022; Published online 15 November 2022; Published February 2023. -- Corresponding author: Brunes, L.C.; Animal Performance Center, Embrapa...Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
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164. | | GRASSO, A.; GOLDBERG, V.; NAVAJAS, E.; IRIARTE, W.; GIMENO, D.; AGUILAR, I.; MEDRANO, J.F.; RINCÓN, G.; CIAPPESONI, G. Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale, Merino and Creole sheep. Genetics and Molecular Biology, 2014, v.37, n.2, p.389-395. Article history: Received: August 29, 2013 / Accepted: March 16, 2014.Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : B - 1 |
Biblioteca(s): INIA Las Brujas. |
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166. | | 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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167. | | RODRÍGUEZ, J.D.; PERIPOLLI, E.; LONDOÑO-GIL, M.; ESPIGOLAN, R.; LÔBO, R. B.; LÓPEZ-CORREA, R.; AGUILAR, I.; BALDI, F. Effect of minor allele frequency and density of single nucleotide polymorphism marker arrays on imputation performance and prediction ability using the single-step genomic Best Linear Unbiased Prediction in a simulated beef cattle population. Research paper. Animal Production Science. 2023, volume 63, issue 9, p. 844-852. https://doi.org/10.1071/AN21581 Article history: Submitted 1 December 2021, Accepted 1 March 2023, Published 4 April 2023. -- Correspondence to: Juan Diego Rodríguez,
Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrarias e Veterinárias, Departamento...Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
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168. | | 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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169. | | 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. |
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170. | | 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. |
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171. | | NEGRI, R.; AGUILAR, I.; FELTES, G. L.; MACHADO, J. D.; NETO, J. B.; COSTA-MAIA, F. M.; COBUCI, J. A. Inclusion of bioclimatic variables in genetic evaluations of dairy cattle.[Open Access]. Animal Bioscience [Asian-Australasian Journal of Animal Sciences], Volume 34, Issue 2, February 2021, Pages 163-171. Doi: https://doi.org/10.5713/ajas.19.0960 Article history: Submitted Dec 16, 2019 / Revised Mar 27, 2020 / Accepted Apr 28, 2020.
Corresponding Author: rn.negri@yahoo.comTipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : -- - -- |
Biblioteca(s): INIA Treinta y Tres. |
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172. | | RAVAGNOLO, O.; NAVAJAS, E.; AGUILAR, I.; CIAPPESONI, G.; LEMA, O.M.; MONTOSSI, F.; PERAZA, P.; DALLA RIZZA, M. Mejoramiento genético animal e importancia del banco de ADN. ln: INIA TACUAREMBÓ. UNIDAD DE BIOTECNOLOGÍA INIA. Jornada técnica. Jornada de Agrobiotecnología INIA, 15 NOVIEMBRE, Tacuarembó, Biotecnología para el sector productivo: situación actual y perspectivas. Tacuarembó (Uruguay): INIA, 2012. p. 4-7 (INIA Serie Actividades de Difusión; 702)Tipo: Actividades de Difusión |
Biblioteca(s): INIA Tacuarembó. |
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173. | | 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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174. | | 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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175. | | 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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176. | | 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. |
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177. | | 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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178. | | 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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179. | | Aguilar, I.; Pravia, M.I.; Ravagnolo, O.; Chiappesoni, G.; Mattos, M.; Ahlig, I.; Urioste, J.; Naya, H. Servicio de evaluación de reproductores Aberdeen Angus Las Brujas, Canelones (Uruguay): INIA, 2004. 23 pBiblioteca(s): INIA La Estanzuela. |
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180. | | LONDOÑO-GIL, M.; LÓPEZ-CORREA, R.; AGUILAR, I.; MAGNABOSCO, C.U.; HIDALGO, J.; BUSSIMAN, F.; BALDI, F.; LOURENCO, D. Strategies for genomic predictions of an indicine multi-breed population using single-step GBLUP. Journal of Animal Breeding and Genetics, 2024. https://doi.org/10.1111/jbg.12882 - [Early view] Article history: Received 22 March 2024, Revised 10 May 2024, Accepted 15 May 2024. -- Corresponding author: Londoño-Gil, M.; Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista Júlio de Mesquita Filho, Via de...Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
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Registros recuperados : 218 | |
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