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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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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
Fecha actual : |
21/02/2014 |
Actualizado : |
04/10/2019 |
Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
Circulación / Nivel : |
Internacional - -- |
Autor : |
SORIA, L. A.; CORVA, P. M.; BRANDA, A.; SCHOR, A.; MELUCCI, L. M.; VILLARREAL, E. L.; MEZZADRA, C. A.; CANTET, R. J. C.; MIQUEL, M. C. |
Afiliación : |
LILIANA A. SORIA, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Argentina; PABLO M. CORVA, Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina; ANDREA BRANDA SICA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ALEJANDRO SCHOR, Facultad de Agronomia, Universidad de Buenos Aires, Argentina; LILIA M. MELUCCI, Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina; EDGARDO L. VILLARREAL, Instituto Nacional de Tecnología Agropecuaria, Balcarce, Argentina; CARLOS A. MEZZADRA, Instituto Nacional de Tecnología Agropecuaria, Balcarce, Argentina; RODOLFO J. C. CANTET, Facultad de Agronomía, Universidad de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; MARÍA C. MIQUEL, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Argentina. |
Título : |
Effect of three single-nucleotide polymorphisms in CAPN1 gene on beef tenderness (brief report). [Einfluss von drei Einzelnucleotidpolymorphismen im CAPN1 Gen
auf die Zartheit von Rindfleisch (Brief Report)]. |
Fecha de publicación : |
2009 |
Fuente / Imprenta : |
Archiv fur Tierzucht (Archives Animal Breeding), 2009, Volume 52, Issue 5, Pages 546-549. |
ISSN : |
0003-9438 |
DOI : |
10.5194/aab-52-546-2009 |
Idioma : |
Inglés |
Notas : |
Article history: Received 24 April 2008 / Accepted 18 April 2009 / Published 10 Oct 2009. |
Contenido : |
Abstract.
Meat tenderness is an important trait in beef cattle production, as consumers consider tenderness the most important attribute of beef palatability. There is ample evidence that post mortem proteolysis of myofibrillar proteins is responsible for the decline in shear force during storage. The bovine micromolar calcium-activated neutral protease (CAPN1) gene encodes the large subunit of μ-calpain, which is thought to be one of the most important enzymes involved in post mortem tenderization (KOOHMARAIE 1996). Three single-nucleotide polymorphisms (SNPs) on the CAPN1 gene (316, 530 and 4 751 markers) have been associated with tenderness in different cattle breeds (PAGE et al. 2002, PAGE et al. 2004, WHITE et al. 2005). A more recent study confirmed that markers 316 and 4 751 had an effect on beef tenderness (VAN EENENNAAM et al. 2007). The objective of this research was to determine the existence of polymorphisms and to assess the effect of the reported SNP in the bovine CAPN1 gene on tenderness from a sample of Angus and Brangus steers fattened on pasture. |
Palabras claves : |
MEAT; Meat tenderness. |
Asunto categoría : |
L01 Ganadería |
URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/13413/1/aab-52-546-2009.pdf
https://www.arch-anim-breed.net/52/546/2009/aab-52-546-2009.pdf
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Marc : |
LEADER 02101naa a2200277 a 4500 001 1012816 005 2019-10-04 008 2009 bl uuuu u00u1 u #d 022 $a0003-9438 024 7 $a10.5194/aab-52-546-2009$2DOI 100 1 $aSORIA, L. A. 245 $aEffect of three single-nucleotide polymorphisms in CAPN1 gene on beef tenderness (brief report). [Einfluss von drei Einzelnucleotidpolymorphismen im CAPN1 Gen auf die Zartheit von Rindfleisch (Brief Report)].$h[electronic resource] 260 $c2009 500 $aArticle history: Received 24 April 2008 / Accepted 18 April 2009 / Published 10 Oct 2009. 520 $aAbstract. Meat tenderness is an important trait in beef cattle production, as consumers consider tenderness the most important attribute of beef palatability. There is ample evidence that post mortem proteolysis of myofibrillar proteins is responsible for the decline in shear force during storage. The bovine micromolar calcium-activated neutral protease (CAPN1) gene encodes the large subunit of μ-calpain, which is thought to be one of the most important enzymes involved in post mortem tenderization (KOOHMARAIE 1996). Three single-nucleotide polymorphisms (SNPs) on the CAPN1 gene (316, 530 and 4 751 markers) have been associated with tenderness in different cattle breeds (PAGE et al. 2002, PAGE et al. 2004, WHITE et al. 2005). A more recent study confirmed that markers 316 and 4 751 had an effect on beef tenderness (VAN EENENNAAM et al. 2007). The objective of this research was to determine the existence of polymorphisms and to assess the effect of the reported SNP in the bovine CAPN1 gene on tenderness from a sample of Angus and Brangus steers fattened on pasture. 653 $aMEAT 653 $aMeat tenderness 700 1 $aCORVA, P. M. 700 1 $aBRANDA, A. 700 1 $aSCHOR, A. 700 1 $aMELUCCI, L. M. 700 1 $aVILLARREAL, E. L. 700 1 $aMEZZADRA, C. A. 700 1 $aCANTET, R. J. C. 700 1 $aMIQUEL, M. C. 773 $tArchiv fur Tierzucht (Archives Animal Breeding), 2009, Volume 52, Issue 5, Pages 546-549.
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