Evaluación genómica en ganado Holstein Colombiano, usando genotipos imputados a densidad media

Autores:: Zambrano, Juan C.
Echeverri Zuluaga, José Julián
López Herrera, Albeiro

Tipo de recurso:: Article of journal

Fecha de publicación:: 2019

Institución:: Universidad de Córdoba

Repositorio:: Repositorio Institucional Unicórdoba

Idioma:: spa

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dc.title.spa.fl_str_mv	Evaluación genómica en ganado Holstein Colombiano, usando genotipos imputados a densidad media
dc.title.translated.eng.fl_str_mv	Genomic Evaluation of Colombian Holstein Cattle Using Imputed Genotypes at Medium Density
title	Evaluación genómica en ganado Holstein Colombiano, usando genotipos imputados a densidad media
spellingShingle	Evaluación genómica en ganado Holstein Colombiano, usando genotipos imputados a densidad media Genotyping genomic selection single nucleotide polymorphism Genotipificación polimorfismo de nucleótido simple selección genómica
title_short	Evaluación genómica en ganado Holstein Colombiano, usando genotipos imputados a densidad media
title_full	Evaluación genómica en ganado Holstein Colombiano, usando genotipos imputados a densidad media
title_fullStr	Evaluación genómica en ganado Holstein Colombiano, usando genotipos imputados a densidad media
title_full_unstemmed	Evaluación genómica en ganado Holstein Colombiano, usando genotipos imputados a densidad media
title_sort	Evaluación genómica en ganado Holstein Colombiano, usando genotipos imputados a densidad media
dc.creator.fl_str_mv	Zambrano, Juan C. Echeverri Zuluaga, José Julián López Herrera, Albeiro
dc.contributor.author.spa.fl_str_mv	Zambrano, Juan C. Echeverri Zuluaga, José Julián López Herrera, Albeiro
dc.subject.eng.fl_str_mv	Genotyping genomic selection single nucleotide polymorphism
topic	Genotyping genomic selection single nucleotide polymorphism Genotipificación polimorfismo de nucleótido simple selección genómica
dc.subject.spa.fl_str_mv	Genotipificación polimorfismo de nucleótido simple selección genómica
publishDate	2019
dc.date.accessioned.none.fl_str_mv	2019-04-11 00:00:00 2022-07-01T21:01:15Z
dc.date.available.none.fl_str_mv	2019-04-11 00:00:00 2022-07-01T21:01:15Z
dc.date.issued.none.fl_str_mv	2019-04-11
dc.type.spa.fl_str_mv	Artículo de revista
dc.type.eng.fl_str_mv	Journal article
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dc.relation.references.spa.fl_str_mv	Goddard ME, Hayes BJ. Genomic Selection. J Anim Breed Genet. 2007; 124(6):323-330. https://doi.org/10.1111/j.1439-0388.2007.00702.x Wang L, Zhu G, Johnson W, Kher M. Three new approaches to genomic selection. Plant Breeding. 2018;137(5):673–681. https://doi.org/10.1111/pbr.12640 Meuwissen TH, Hayes BJ, Goddard ME: Prediction of total genetic value using genome-wide dense marker maps. Genetics. 2001; 157(4):1819–1829. https://www.ncbi.nlm.nih.gov/pubmed/11290733 Boichard D, Chung H, Dassonneville R, David X, Eggen A, Fritz S. et al. Design of a bovine low-density SNP array optimized for imputation. PLoS ONE. 2012; 7(3):e34130. https://doi.org/10.1371/journal.pone.0034130 Weng Z, Zhang Z, Ding X, Fu W, Ma P, Wang C, Zhang Q. Application of imputation methods to genomic selection in Chinese Holstein cattle. J Anim Sci Biotechnol. 2012, 3(1):6. https://doi.org/10.1186/2049-1891-3-6 Khatkar MS, Moser G, Hayes BJ, Raadsma HW. Strategies and utility of imputed SNP genotypes for genomic analysis in dairy cattle. BMC Genomics. 2012; 13(1):538. https://doi.org/10.1186/1471-2164-13-538 Schefers J, Weigel KA. Genomic selection in dairy cattle: Integration of DNA testing into breeding programs. Anim Front. 2012; 12(1):4-9. https://doi.org/10.2527/af.2011-0032 Huang YJ, Hickey JM, Cleveland MA, Maltecca C. Assessment of alternative genotyping strategies to maximize imputation accuracy at minimal cost. Genet Sel Evol. 2012; 44(1):25. https://doi.org/10.1186/1297-9686-44-25 Scheet P, Stephens M. A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet. 2006; 78(4):629-644. https://doi.org/10.1086/502802 Browning BL, Browning SR. A unified approach to genotype imputation and haplotype phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet. 2009; 84(2):210-223. https://doi.org/10.1016/j.ajhg.2009.01.005 Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 2009; 5(6):e1000529. https://doi.org/10.1371/journal.pgen.1000529 VanRaden PM, Null DJ, Sargolzaei M, Wiggans GR, Tooker ME, Cole JB, et al. Genomic imputation and evaluation using high-density Holstein genotypes. J Dairy Sci. 2013; 96(1):668–678. https://doi.org/10.3168/jds.2012-5702 Sargolzaei M, Chesnais JP, Schenkel FS. A new approach for efficient genotype imputation using information from relatives. BMC Genomics. 2014; 15: 478. https://doi.org/10.1186/1471-2164-15-478 Weigel KA, Van Tassell CP, O’Connell JR, VanRaden PM, Wiggans GR. Prediction of unobserved single nucleotide polymorphism genotypes of Jersey cattle using reference panels and population-based imputation algorithms. J Dairy Sci. 2010; 93(5):2229-2238. https://doi.org/10.3168/jds.2009-2849 Zhang Z, Druet T. Marker imputation with low-density marker panels in Dutch Holstein cattle. J Dairy Sci. 2010; 93(11):5487-5494. https://doi.org/10.3168/jds.2010-3501 Wiggans GR, Cole JB, Hubbard SM, Sonstegard TS. Genomic Selection in Dairy Cattle: The USDA Experience. Ann Rev Anim Biosci. 2017; 5(1):309–327. https://doi.org/10.1146/annurev-animal-021815-111422 Rincón JC, Zambrano JC, Echeverri JJ. Estimation of genetic and phenotypic parameters for production traits in Holstein and Jersey from Colombia. Rev MVZ Córdoba. 2015; 20(Supl):4962-4973. https://doi.org/10.21897/rmvz.11 Echeverri J, Zambrano JC, López-Herrera A. Genomic evaluation of Holstein Cattle in Antioquia (Colombia): a case study. Rev Colomb Cienc Pecu. 2014; 27(4):306-314. http://www.scielo.org.co/scielo.php?script=sci_arttext&pid=S0120-06902014000400009 Zambrano JC, Rincón JC, López A, Echeverri JJ. Estimation and comparison of conventional and genomic breeding values in Holstein cattle of Antioquia, Colombia. Rev MVZ Córdoba. 2015; 20(3):4739-4753. https://doi.org/10.21897/rmvz.44 Martínez R, Gómez Y, Rocha JFM. Genome-wide association study on growth traits in Colombian creole breeds and crossbreeds with Zebu cattle. Genet Mol Res. 2014; 13(3):6420-6432. https://doi.org/10.4238/2014.august.25.5 Martínez R, Mar JF, Bejarano D, Burgos W. Genomic predictions and accuracy of weight traits in a breeding program for Colombian Zebu Brahman [On line]. Proceedings of the World Congress on Genetics Applied to Livestock Production. 2018. http://www.wcgalp.org/system/files/proceedings/2018/genomic-predictions-and-accuracy-weight-traits-breeding-program-colombian-zebu-brahman.pdf Ali AK, Shook GE. An Optimun transformation for somatic cell concentration in milk. J Dairy Sci. 1980; 63(3):487-490. https://doi.org/10.3168/jds.s0022-0302(80)82959-6 Kizilkaya k, Fernando RL, Garrick DJ. Genomic Prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes. J Anim Sci. 2010; 88(2):544-551. https://doi.org/10.2527/jas.2009-2064 Verbyla KL, Bowman PJ, Hayes BJ, Raadsma H, Goddard ME. Sensitivity of genomic selection to using different prior distributions. BMC Proc 2010; 4(1):S5. https://doi.org/10.1186/1753-6561-4-s1-s5 Meuwissen T, Hayes B, Goddard M. Accelerating Improvement of livestock with Genomic Selection. Annu Rev Anim Biosci. 2013; 1(1):221-237. https://doi.org/10.1146/annurev-animal-031412-103705 Chen L, Li C, Zargolzaei M, Schenkel F. Impact of genotypes imputation on the performance of GBLUP and bayesian methods for genomic prediction. PLoS ONE. 2014; 9(7):e101544. https://doi.org/10.1371/journal.pone.0101544 Vázquez AI, Rosa GJ, Weigel KA, de los Campos G, Gianola D, Allison DB. Predictive ability of subsets of single nucleotide polymorphisms with and without parent average in US Holsteins. J Dairy Sci. 2010; 93(12):5942–5949. https://doi.org/10.3168/jds.2010-3335 Habier D, Rohan LF, Kizilkaya K, Garrick DJ. Extension of the bayesian alphabet for genomic Selection. BMC Bioinformatics. 2011; 12(1):186. https://doi.org/10.1186/1471-2105-12-186 Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME. Invited review: Genomic selection in dairy cattle: Progress and challenges. J Dairy Sci 2009; 92(2):433–443. https://doi.org/10.3168/jds.2008-1646 https://doi.org/pdf/10.4081/ijas.2013.e91 Nicolazzi EL, Negrini R, Chamberlain AJ, Goddard ME, Marsan PA, Hayes BJ. Effect of Prior Distributions on Accuracy of Genomic Breeding Values for Two Dairy Traits. Ital J Anim Sci 2013; 12(e91):555-561. https://www.tandfonline.com/doi/pdf/10.4081/ijas.2013.e91 Colombani C, Legarra A, Fritz S, Guillaume F, Croiseau P, Ducrocq V, et al. Application of Bayesian least absolute shrinkage and selection operator (LASSO) and BayesCπ methods for genomic selection in French Holstein and Montbéliarde breeds. J Dairy Sci. 2013; 96(1):575–591. https://doi.org/10.3168/jds.2011-5225
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dc.relation.citationedition.spa.fl_str_mv	Núm. 2 , Año 2019 : Revista MVZ Córdoba Volumen 24(2) Mayo-Agosto 2019
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dc.rights.spa.fl_str_mv	Juan C. Zambrano, José Julián Echeverri Zuluaga, Albeiro López Herrera - 2019
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spelling	Zambrano, Juan C.282461b5-6439-436d-8095-c83ded848763-1Echeverri Zuluaga, José Julián0d9b8137-a1ad-4eac-b887-f65a1b7abe3d-1López Herrera, Albeiroe3682b25-a921-4014-ac48-1b7f3dea44dd-12019-04-11 00:00:002022-07-01T21:01:15Z2019-04-11 00:00:002022-07-01T21:01:15Z2019-04-110122-0268https://repositorio.unicordoba.edu.co/handle/ucordoba/601810.21897/rmvz.1704https://doi.org/10.21897/rmvz.17041909-0544application/pdfapplication/pdfapplication/xmlapplication/xmlapplication/zipapplication/zipspaUniversidad de CórdobaJuan C. Zambrano, José Julián Echeverri Zuluaga, Albeiro López Herrera - 2019https://creativecommons.org/licenses/by-nc-sa/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2https://revistamvz.unicordoba.edu.co/article/view/1704Genotypinggenomic selectionsingle nucleotide polymorphismGenotipificaciónpolimorfismo de nucleótido simpleselección genómicaEvaluación genómica en ganado Holstein Colombiano, usando genotipos imputados a densidad mediaGenomic Evaluation of Colombian Holstein Cattle Using Imputed Genotypes at Medium DensityArtículo de revistaJournal articleinfo:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501http://purl.org/coar/resource_type/c_6501http://purl.org/coar/resource_type/c_2df8fbb1info:eu-repo/semantics/publishedVersionTexthttp://purl.org/redcol/resource_type/ARTREFhttp://purl.org/coar/version/c_970fb48d4fbd8a85Goddard ME, Hayes BJ. Genomic Selection. J Anim Breed Genet. 2007; 124(6):323-330. https://doi.org/10.1111/j.1439-0388.2007.00702.xWang L, Zhu G, Johnson W, Kher M. Three new approaches to genomic selection. Plant Breeding. 2018;137(5):673–681. https://doi.org/10.1111/pbr.12640Meuwissen TH, Hayes BJ, Goddard ME: Prediction of total genetic value using genome-wide dense marker maps. Genetics. 2001; 157(4):1819–1829. https://www.ncbi.nlm.nih.gov/pubmed/11290733Boichard D, Chung H, Dassonneville R, David X, Eggen A, Fritz S. et al. Design of a bovine low-density SNP array optimized for imputation. PLoS ONE. 2012; 7(3):e34130. https://doi.org/10.1371/journal.pone.0034130Weng Z, Zhang Z, Ding X, Fu W, Ma P, Wang C, Zhang Q. Application of imputation methods to genomic selection in Chinese Holstein cattle. J Anim Sci Biotechnol. 2012, 3(1):6. https://doi.org/10.1186/2049-1891-3-6Khatkar MS, Moser G, Hayes BJ, Raadsma HW. Strategies and utility of imputed SNP genotypes for genomic analysis in dairy cattle. BMC Genomics. 2012; 13(1):538. https://doi.org/10.1186/1471-2164-13-538Schefers J, Weigel KA. Genomic selection in dairy cattle: Integration of DNA testing into breeding programs. Anim Front. 2012; 12(1):4-9. https://doi.org/10.2527/af.2011-0032Huang YJ, Hickey JM, Cleveland MA, Maltecca C. Assessment of alternative genotyping strategies to maximize imputation accuracy at minimal cost. Genet Sel Evol. 2012; 44(1):25. https://doi.org/10.1186/1297-9686-44-25Scheet P, Stephens M. A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet. 2006; 78(4):629-644. https://doi.org/10.1086/502802Browning BL, Browning SR. A unified approach to genotype imputation and haplotype phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet. 2009; 84(2):210-223. https://doi.org/10.1016/j.ajhg.2009.01.005Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 2009; 5(6):e1000529. https://doi.org/10.1371/journal.pgen.1000529VanRaden PM, Null DJ, Sargolzaei M, Wiggans GR, Tooker ME, Cole JB, et al. Genomic imputation and evaluation using high-density Holstein genotypes. J Dairy Sci. 2013; 96(1):668–678. https://doi.org/10.3168/jds.2012-5702Sargolzaei M, Chesnais JP, Schenkel FS. A new approach for efficient genotype imputation using information from relatives. BMC Genomics. 2014; 15: 478. https://doi.org/10.1186/1471-2164-15-478Weigel KA, Van Tassell CP, O’Connell JR, VanRaden PM, Wiggans GR. Prediction of unobserved single nucleotide polymorphism genotypes of Jersey cattle using reference panels and population-based imputation algorithms. J Dairy Sci. 2010; 93(5):2229-2238. https://doi.org/10.3168/jds.2009-2849Zhang Z, Druet T. Marker imputation with low-density marker panels in Dutch Holstein cattle. J Dairy Sci. 2010; 93(11):5487-5494. https://doi.org/10.3168/jds.2010-3501Wiggans GR, Cole JB, Hubbard SM, Sonstegard TS. Genomic Selection in Dairy Cattle: The USDA Experience. Ann Rev Anim Biosci. 2017; 5(1):309–327. https://doi.org/10.1146/annurev-animal-021815-111422Rincón JC, Zambrano JC, Echeverri JJ. Estimation of genetic and phenotypic parameters for production traits in Holstein and Jersey from Colombia. Rev MVZ Córdoba. 2015; 20(Supl):4962-4973. https://doi.org/10.21897/rmvz.11Echeverri J, Zambrano JC, López-Herrera A. Genomic evaluation of Holstein Cattle in Antioquia (Colombia): a case study. Rev Colomb Cienc Pecu. 2014; 27(4):306-314. http://www.scielo.org.co/scielo.php?script=sci_arttext&pid=S0120-06902014000400009Zambrano JC, Rincón JC, López A, Echeverri JJ. Estimation and comparison of conventional and genomic breeding values in Holstein cattle of Antioquia, Colombia. Rev MVZ Córdoba. 2015; 20(3):4739-4753. https://doi.org/10.21897/rmvz.44Martínez R, Gómez Y, Rocha JFM. Genome-wide association study on growth traits in Colombian creole breeds and crossbreeds with Zebu cattle. Genet Mol Res. 2014; 13(3):6420-6432. https://doi.org/10.4238/2014.august.25.5Martínez R, Mar JF, Bejarano D, Burgos W. Genomic predictions and accuracy of weight traits in a breeding program for Colombian Zebu Brahman [On line]. Proceedings of the World Congress on Genetics Applied to Livestock Production. 2018. http://www.wcgalp.org/system/files/proceedings/2018/genomic-predictions-and-accuracy-weight-traits-breeding-program-colombian-zebu-brahman.pdfAli AK, Shook GE. An Optimun transformation for somatic cell concentration in milk. J Dairy Sci. 1980; 63(3):487-490. https://doi.org/10.3168/jds.s0022-0302(80)82959-6Kizilkaya k, Fernando RL, Garrick DJ. Genomic Prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes. J Anim Sci. 2010; 88(2):544-551. https://doi.org/10.2527/jas.2009-2064Verbyla KL, Bowman PJ, Hayes BJ, Raadsma H, Goddard ME. Sensitivity of genomic selection to using different prior distributions. BMC Proc 2010; 4(1):S5. https://doi.org/10.1186/1753-6561-4-s1-s5Meuwissen T, Hayes B, Goddard M. Accelerating Improvement of livestock with Genomic Selection. Annu Rev Anim Biosci. 2013; 1(1):221-237. https://doi.org/10.1146/annurev-animal-031412-103705Chen L, Li C, Zargolzaei M, Schenkel F. Impact of genotypes imputation on the performance of GBLUP and bayesian methods for genomic prediction. PLoS ONE. 2014; 9(7):e101544. https://doi.org/10.1371/journal.pone.0101544Vázquez AI, Rosa GJ, Weigel KA, de los Campos G, Gianola D, Allison DB. Predictive ability of subsets of single nucleotide polymorphisms with and without parent average in US Holsteins. J Dairy Sci. 2010; 93(12):5942–5949. https://doi.org/10.3168/jds.2010-3335Habier D, Rohan LF, Kizilkaya K, Garrick DJ. Extension of the bayesian alphabet for genomic Selection. BMC Bioinformatics. 2011; 12(1):186. https://doi.org/10.1186/1471-2105-12-186Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME. Invited review: Genomic selection in dairy cattle: Progress and challenges. J Dairy Sci 2009; 92(2):433–443. https://doi.org/10.3168/jds.2008-1646 https://doi.org/pdf/10.4081/ijas.2013.e91Nicolazzi EL, Negrini R, Chamberlain AJ, Goddard ME, Marsan PA, Hayes BJ. Effect of Prior Distributions on Accuracy of Genomic Breeding Values for Two Dairy Traits. Ital J Anim Sci 2013; 12(e91):555-561. https://www.tandfonline.com/doi/pdf/10.4081/ijas.2013.e91Colombani C, Legarra A, Fritz S, Guillaume F, Croiseau P, Ducrocq V, et al. Application of Bayesian least absolute shrinkage and selection operator (LASSO) and BayesCπ methods for genomic selection in French Holstein and Montbéliarde breeds. J Dairy Sci. 2013; 96(1):575–591. https://doi.org/10.3168/jds.2011-5225https://revistamvz.unicordoba.edu.co/article/download/1704/2006https://revistamvz.unicordoba.edu.co/article/download/1704/2007https://revistamvz.unicordoba.edu.co/article/download/1704/2299https://revistamvz.unicordoba.edu.co/article/download/1704/2300https://revistamvz.unicordoba.edu.co/article/download/1704/2301https://revistamvz.unicordoba.edu.co/article/download/1704/2302Núm. 2 , Año 2019 : Revista MVZ Córdoba Volumen 24(2) Mayo-Agosto 201972552724824Revista MVZ CórdobaPublicationOREORE.xmltext/xml3225http://172.16.14.198/bitstreams/39c7dcf3-c59f-457c-a210-d6c5d7ce0059/download29fe82d048eea51870116cbf1c567989MD51ucordoba/6018oai:172.16.14.198:ucordoba/60182023-10-06 00:45:16.862https://creativecommons.org/licenses/by-nc-sa/4.0/Juan C. Zambrano, José Julián Echeverri Zuluaga, Albeiro López Herrera - 2019metadata.onlyhttp://172.16.14.198Repositorio Universidad de Córdobabdigital@metabiblioteca.com

Evaluación genómica en ganado Holstein Colombiano, usando genotipos imputados a densidad media

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