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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
Fecha : |
10/09/2014 |
Actualizado : |
15/10/2019 |
Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
Autor : |
WANG, H.; MISZTAL, I.; AGUILAR, I.; LEGARRA, A.; FERNANDO, R.L.; VITEZICA, Z.; OKIMOTO, R.; WING, T.; HAWKEN, R.; MUIR, W.M. |
Afiliación : |
IGNACIO AGUILAR GARCIA, Instituto Nacional de Investigación Agropecuaria (INIA), Uruguay. |
Título : |
Genome-wide association mapping including phenotypes from relatives without genotypes in a single-step (ssGWAS) for 6-week body weight in broiler chickens. |
Fecha de publicación : |
2014 |
Fuente / Imprenta : |
Frontiers in Genetics, 2014, v.5, p.1-10. OPEN ACCESS. |
ISSN : |
1664-8021 |
DOI : |
10.3389/fgene.2014.00134 |
Idioma : |
Inglés |
Notas : |
Article history: Received 03 March 2014 // Paper pending published 04 April 2014 // Accepted 25 April 2014 // Published online: 20 May 2014. |
Contenido : |
ABSTRACT.
The purpose of this study was to compare results obtained from various methodologies for genome-wide association studies, when applied to real data, in terms of number and commonality of regions identified and their genetic variance explained, computational speed, and possible pitfalls in interpretations of results. Methodologies include: two iteratively reweighted single-step genomic BLUP procedures (ssGWAS1 and ssGWAS2), a single-marker model (CGWAS), and BayesB. The ssGWAS methods utilize genomic breeding values (GEBVs) based on combined pedigree, genomic and phenotypic information, while CGWAS and BayesB only utilize phenotypes from genotyped animals or pseudo-phenotypes. In this study, ssGWAS was performed by converting GEBVs to SNP marker effects. Unequal variances for markers were incorporated for calculating weights into a new genomic relationship matrix. SNP weights were refined iteratively. The data was body weight at 6 weeks on 274,776 broiler chickens, of which 4553 were genotyped using a 60 k SNP chip. Comparison of genomic regions was based on genetic variances explained by local SNP regions (20 SNPs). After 3 iterations, the noise was greatly reduced for ssGWAS1 and results are similar to that of CGWAS, with 4 out of the top 10 regions in common. In contrast, for BayesB, the plot was dominated by a single region explaining 23.1% of the genetic variance. This same region was found by ssGWAS1 with the same rank, but the amount of genetic variation attributed to the region was only 3%. These findings emphasize the need for caution when comparing and interpreting results from various methods, and highlight that detected associations, and strength of association, strongly depends on methodologies and details of implementations. BayesB appears to overly shrink regions to zero, while overestimating the amount of genetic variation attributed to the remaining SNP effects. The real world is most likely a compromise between methods and remains to be determined.
© 2014 Wang, Misztal, Aguilar, Legarra, Fernando, Vitezica, Okimoto, Wing, Hawken and Muir. MenosABSTRACT.
The purpose of this study was to compare results obtained from various methodologies for genome-wide association studies, when applied to real data, in terms of number and commonality of regions identified and their genetic variance explained, computational speed, and possible pitfalls in interpretations of results. Methodologies include: two iteratively reweighted single-step genomic BLUP procedures (ssGWAS1 and ssGWAS2), a single-marker model (CGWAS), and BayesB. The ssGWAS methods utilize genomic breeding values (GEBVs) based on combined pedigree, genomic and phenotypic information, while CGWAS and BayesB only utilize phenotypes from genotyped animals or pseudo-phenotypes. In this study, ssGWAS was performed by converting GEBVs to SNP marker effects. Unequal variances for markers were incorporated for calculating weights into a new genomic relationship matrix. SNP weights were refined iteratively. The data was body weight at 6 weeks on 274,776 broiler chickens, of which 4553 were genotyped using a 60 k SNP chip. Comparison of genomic regions was based on genetic variances explained by local SNP regions (20 SNPs). After 3 iterations, the noise was greatly reduced for ssGWAS1 and results are similar to that of CGWAS, with 4 out of the top 10 regions in common. In contrast, for BayesB, the plot was dominated by a single region explaining 23.1% of the genetic variance. This same region was found by ssGWAS1 with the same rank, but the amount of genetic variation att... Presentar Todo |
Palabras claves : |
ASSOCIATION MAPPING; BayesB; BODY WEIGHT; BROILER CHICKEN; CARNE DE AVES; GENOME-WIDE ASSOCIATION; SsGWAS. |
Thesagro : |
ANIMALES DE CARNE; PESO CORPORAL; POLLO. |
Asunto categoría : |
L10 Genética y mejoramiento animal |
URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/3067/1/Aguilar-I.-2014-Frontiers-in-Genetics-v.5p.1-10.pdf
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Marc : |
LEADER 03333naa a2200385 a 4500 001 1050116 005 2019-10-15 008 2014 bl uuuu u00u1 u #d 022 $a1664-8021 024 7 $a10.3389/fgene.2014.00134$2DOI 100 1 $aWANG, H. 245 $aGenome-wide association mapping including phenotypes from relatives without genotypes in a single-step (ssGWAS) for 6-week body weight in broiler chickens.$h[electronic resource] 260 $c2014 500 $aArticle history: Received 03 March 2014 // Paper pending published 04 April 2014 // Accepted 25 April 2014 // Published online: 20 May 2014. 520 $aABSTRACT. The purpose of this study was to compare results obtained from various methodologies for genome-wide association studies, when applied to real data, in terms of number and commonality of regions identified and their genetic variance explained, computational speed, and possible pitfalls in interpretations of results. Methodologies include: two iteratively reweighted single-step genomic BLUP procedures (ssGWAS1 and ssGWAS2), a single-marker model (CGWAS), and BayesB. The ssGWAS methods utilize genomic breeding values (GEBVs) based on combined pedigree, genomic and phenotypic information, while CGWAS and BayesB only utilize phenotypes from genotyped animals or pseudo-phenotypes. In this study, ssGWAS was performed by converting GEBVs to SNP marker effects. Unequal variances for markers were incorporated for calculating weights into a new genomic relationship matrix. SNP weights were refined iteratively. The data was body weight at 6 weeks on 274,776 broiler chickens, of which 4553 were genotyped using a 60 k SNP chip. Comparison of genomic regions was based on genetic variances explained by local SNP regions (20 SNPs). After 3 iterations, the noise was greatly reduced for ssGWAS1 and results are similar to that of CGWAS, with 4 out of the top 10 regions in common. In contrast, for BayesB, the plot was dominated by a single region explaining 23.1% of the genetic variance. This same region was found by ssGWAS1 with the same rank, but the amount of genetic variation attributed to the region was only 3%. These findings emphasize the need for caution when comparing and interpreting results from various methods, and highlight that detected associations, and strength of association, strongly depends on methodologies and details of implementations. BayesB appears to overly shrink regions to zero, while overestimating the amount of genetic variation attributed to the remaining SNP effects. The real world is most likely a compromise between methods and remains to be determined. © 2014 Wang, Misztal, Aguilar, Legarra, Fernando, Vitezica, Okimoto, Wing, Hawken and Muir. 650 $aANIMALES DE CARNE 650 $aPESO CORPORAL 650 $aPOLLO 653 $aASSOCIATION MAPPING 653 $aBayesB 653 $aBODY WEIGHT 653 $aBROILER CHICKEN 653 $aCARNE DE AVES 653 $aGENOME-WIDE ASSOCIATION 653 $aSsGWAS 700 1 $aMISZTAL, I. 700 1 $aAGUILAR, I. 700 1 $aLEGARRA, A. 700 1 $aFERNANDO, R.L. 700 1 $aVITEZICA, Z. 700 1 $aOKIMOTO, R. 700 1 $aWING, T. 700 1 $aHAWKEN, R. 700 1 $aMUIR, W.M. 773 $tFrontiers in Genetics, 2014$gv.5, p.1-10. OPEN ACCESS.
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Registro original : |
INIA Las Brujas (LB) |
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Registros recuperados : 218 | |
201. | | ROMAN, L.; LA MANNA, A.; ACOSTA, Y.; MENDOZA, A.; AGUILAR, I.; MORALES-PIÑEYRUA, J.; PLA, M.; LAURA ASTIGARRAGA, L.; SARAVIA, C. Evaluación de medidas de mitigación del estrés por calor sobre las respuestas productivas de vacas lecheras de alta producción. In: Día de Campo: producción de forraje y leche en verano. La Estanzuela, Colonia, (Uruguay): INIA, 2013. p. 15. (Serie Actividades de Difusión; 705).Biblioteca(s): INIA La Estanzuela. |
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202. | | 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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203. | | PRAVIA, M.; NAVAJAS, E.; LEMA, O.; AGUILAR, I.; RAVAGNOLO, O.; BRITO, G.; CLARIGET, J.; PERAZA, P.; DE LOS SANTOS, J.; DALLA RIZZA, M.; MONTOSSI, F. Mejoramiento genético en eficiencia de conversión de alimento y características de canal: oportunidades a través del uso de la genómica. In: Congreso Asociación Uruguaya de Producción Animal (AUPA) (5º, 3-4 Dic. 2014, Montevideo, UY). Sede del evento: Facultad de Agronomía, Av. Garzón 780, Montevideo, Uruguay.Tipo: Trabajos en Congresos/Conferencias |
Biblioteca(s): INIA Tacuarembó. |
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204. | | RODRÍGUEZ NEIRA, J.D.; PERIPOLLI, E.; DE NEGREIROS M.P.M.; ESPIGOLAN, R.; LÓPEZ-CORREA R.; AGUILAR, I.; LOBO R.B.; BALDI, F. Prediction ability for growth and maternal traits using SNP arrays based on different marker densities in Nellore cattle using the ssGBLUP. Journal of Applied Genetics, 2022, Volume 63, Issue 2, pages 389-400. doi: https://doi.org/10.1007/s13353-022-00685-0 Article history: Received 26 September 2021; Revised 25 January 2022; Accepted 2 February 2022.
Corresponding author: Rodriguez Neira, J.D.; Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Universidade...Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
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205. | | NAVAJAS, E.; PRAVIA, M.I.; LEMA, O.M.; RAVAGNOLO, O.; AGUILAR, I.; BRITO, G.; CLARIGET, J.; DALLA RIZZA, M.; MONTOSSI, F. Selección genómica en eficiencia de conversión y calidad de canal de la raza Hereford en Uruguay. Anuario Hereford (Montevideo), p. 160-172, 2014.Biblioteca(s): INIA La Estanzuela. |
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206. | | TORO OSPINA, A.M.; AGUILAR, I.; VARGAS DE OLIVEIRA, M.H.; CRUZ DOS SANTOS CORREIA, L. E.; VERCESI FILHO, A. E.; ALBUQUERQUE, L.G.; JOSINEUDSON AUGUSTO II DE VASCONCELOS SILVA Assessing the accuracy of imputation in the Gyr breed using different SNP panels. Genome, 2021 Oct, Volume 64 , Issue 10, pag 893-899. Open Acces. Doi: https://doi.org/10.1139/gen-2020-0081 Article history: Received 22 May 2020./ Accepted 17 April 2021. Corresponding author: Alejandra Maria Toro Ospina (email: toroospina92@gmail.com)Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA La Estanzuela. |
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207. | | TONUSSI, R.L.; LONDOÑO-GIL, M.; DE OLIVEIRA SILVA, R.M.; MAGALHÃES, A.F.B.; AMORIM, S:T.; KLUSKA, S.; ESPIGOLAN, R.; PERIPOLLI, E.; PEREIRA, A.S.C.; LÔBO, R.B.; AGUILAR, I.; LOURENÇO, D.A.L.; BALDI, F. Accuracy of genomic breeding values and predictive ability for postweaning liveweight and age at first calving in a Nellore cattle population with missing sire information. Tropical Animal Health and Production, 2021, Volume 53, Issue 4, Article number 432. doi: https://doi.org/10.1007/s11250-021-02879-w Article history: Received 19 March 2021; Accepted 30 July 2021; Published online 10 August 2021.
Corresponding author: Londoño-Gil, M.; Grupo de Melhoramento Animal, Faculdade de Ciências Agrárias E Veterinárias, Universidade Estadual...Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
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208. | | CARDOSO, F. F.; YOKOO, M. J. I.; GULIAS-GOMES, C. C.; OLIVEIRA, M. M. DE; TEIXEIRA, B. B. M.; ROSO, V. M.; BRITO, F. V.; CAETANO, A. R.; AGUILAR, I. Avaliação genômica de touros Hereford e Braford. Bagé: Embrapa Pecuária Sul, 2012. 32 p. (Embrapa Pecuária Sul. Documentos, 127).Biblioteca(s): INIA Las Brujas. |
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209. | | CARDOSO, F. F.; GOMES, C.C.G.; SOLLERO, B. P.; OLIVEIRA, M. M.; ROSO, V. M.; PICCOLI, M. L.; HIGA, R. H.; YOKOO, M. J.; CAETANO, A. R.; AGUILAR, I. Genomic prediction for tick resistance in Braford and Hereford cattle. Journal of Animal Science, 2015. v. 95, p. 2693-2705. Published June 25, 2015 Article history: Received December 19, 2014 / Accepted April 6, 2015.Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
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210. | | 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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211. | | CARVALHO, F.E.; ESPIGOLAN, R.; BERTON, M.P.; NETO, J.B.S.; SILVA, R.P.; GRIGOLETTO, L.; SILVA, R.M.O.; FERRAZ, J.B.S.; ELER, J.P.; AGUILAR, I.; LÔBO, R.B.; BALDI, F. Genome-wide association study and predictive ability for growth traits in Nellore cattle. Livestock Science, January 2020, Volume 231, Article number 103861. OPEN ACCESS. Doi: https://doi.org/10.1016/j.livsci.2019.103861 Article history: Received 25 June 2019 / Revised 29 October 2019 / Accepted 4 November 2019 / Available online 6 November 2019.
Funding information: F.E. CARVALHO received a scholarship from Coordinating for the Improvement of Higher...Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
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212. | | TONUSSI, R.L.; SILVA, R.M.O.; MAGALHÃES, A.F.B.; PERIPOLLI , E.; OLIVIERI, B.F.; FEITOSA, F.L.B.; PEREIR, A.S.C.; LÔBO, R.B.; MAGNABOSCO, C.U.; AGUILAR, I.; BALDI, F. Impact of multiple sire mating system on the accuracy of genomic breeding value prediction in a beef cattle population under selection . [abstract 206]. Issue Section: Breeding and Genetics. Journal of Animal Science. 2017, Volume 95, Issue Supplement 4, Page 102. https://doi.org/10.2527/asasann.2017.206 Article history: Published 01 August 2017. --Tipo: Abstracts/Resúmenes |
Biblioteca(s): INIA Las Brujas. |
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213. | | NAVAJAS, E.; PRAVIA, M.I.; AGUIRRE, L.; MACEDO, F.; DE LA FUENTE, J.; MENDIOLA, B.; DEL PINO, M.L.; RAVAGNOLO, O.; LEMA, O.M.; PERAZA, P.; AGUILAR, I.; CARRAU, J.; CIAPPESONI, G. Tercer año de la evaluación de eficiencia de conversión de kiyú. Anuario Hereford (Montevideo), p. 182-186, 2016.Biblioteca(s): INIA La Estanzuela; INIA Treinta y Tres. |
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214. | | TONUSSI, R. L.; SILVA, R. M. D. O.; MAGALHÃES, A.F.B.; ESPIGOLAN, R.; PERIPOLLI, E.; OLIVIERI, B. F.; FEITOSA, F. L. B.; LEMOS, M. V. A.; BERTON, M. P.; CHIAIA, H. L. J.; PEREIRA, A. S. C.; LÔBO, R. B.; BEZERRA, L. A. F.; MAGNABOSCO, C. D. U.; LOURENÇO, D.A.L.; AGUILAR, I.; BALDI, F. Application of single step genomic BLUP under different uncertain paternity scenarios using simulated data. (Research article). PLoS ONE, September 2017, Volume 12, Issue 9, Article number e0181752. OPEN ACCESS. Article history: Received September 22, 2016 // Accepted July 6, 2017 // Published September 28, 2017.
Data Availability Statement: All relevant data are within the paper, its Supporting Information files, and in Figshare.
Funding: This...Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
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215. | | LEMOS, M.V.A.; CHIAIA, H.L.J.; BERTON, M.P.; FEITOSA, F.L.B.; ABOUJAOUD, C.; CAMARGO, G.M.F.; PEREIRA, A.S.C.; ALBUQUERQUE, L.G.; FERRINHO, A.M.; MUELLER, L.F.; MAZALLI, M.R.; FURLAN, J.J.M.; CARVALHEIRO, R.; GORDO, D.M.; TONUSSI, R.; ESPIGOLAN, R.; SILVA, R.M.O.; DE OLIVEIRA, H.N.; DUCKETT, S.; AGUILAR, I.; BALDI, F. Genome-wide association between single nucleotide polymorphisms with beef fatty acid profile in Nellore cattle using the single step procedure. BMC Genomics, 2016, v. 17:213. Received: 19 November 2015 / Accepted: 23 February 2016 /Published: 9 March 2016Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
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216. | | CHIAIA, H.L.J.; PERIPOLLI, E.; DE OLIVEIRA SILVA, R.M.; FEITOSA, F.L.B.; DE LEMOS, M.V.A.; BERTON, M.P.; OLIVIERI, B.F.; ESPIGOLAN, R.; TONUSSI, R.L.; GORDO, D.G.M.; DE ALBUQUERQUE, L.G.; DE OLIVEIRA, H.N.; FERRINHO, A.M.; MUELLER, L.F.; KLUSKA, S.; TONHATI, H.; PEREIRA, A.S.C.; AGUILAR, I.; BALDI, F. Genomic prediction ability for beef fatty acid profile in Nelore cattle using different pseudo-phenotypes. Journal of Applied Genetics, 1 November 2018, volume 59, Issue 4, pages 493-501. Article history: Received: 15 May 2018 // Revised: 28 August 2018 // Accepted: 17 September 2018.Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
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217. | | NAVAJAS, E.; VELAZCO, J.I.; SOTELO, J.; NOYA, H.; CASAL, A.; GIANOLA, D.; PERAZA, P.; BIELLI, A.; ITHURRALDE, J.; GENOVESE, P.; PÉREZ, R.; CANTALAPIEDRA, G.; AGUILAR, I.; LEMA, O.M.; RAVAGNOLO, O.; DEVINCENZI, T.; CARRACELAS, B.; DE SOUZA, G.; CIAPPESONI, G.; BRITO, G.; LUZARDO, S. Plataforma de Fenotipado intensivo - Kiyú. Anuario Hereford (Montevideo), 2020, p. 210-213.Biblioteca(s): INIA La Estanzuela; INIA Tacuarembó. |
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218. | | FEITOSA, F. L. B.; OLIVIERI, B. F.; ABOUJAOUDE, C.; PEREIRA, A. S. C.; DE LEMOS, M. V. A.; CHIAIA, H. L. J.; BERTON, M. P.; PERIPOLLI, E.; FERRINHO, A. M.; MUELLER, L. F.; MAZZALI, M. R.; DE ALBUQUERQUE, L. G.; DE OLIVERA, H. N.; TONHATI, H.; ESPIGOLAN, R.; TONUSSI, R. L.; DE OLIVIERA SILVA, R. M.; GORDO, D. G. M.; MAGALHAES, A. F. B.; AGUILAR, I.; BALDI, F. S. B. Genetic correlation estimates between beef fatty acid profile with meat and carcass traits in Nellore cattle finished in feedlot. Journal of Applied Genetics, 2017, 58 (1), 123-132. Article history: Received: 15 December 2015 /Revised: 10 March 2016 /Accepted: 5 July 2016 / Published Online: 30 July 2016Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
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Registros recuperados : 218 | |
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