Genetic diversity analysis in dairy cows of Nariño, southwestern Colombia
DOI:
https://doi.org/10.5433/1679-0359.2022v43n6p2563Palabras clave:
Bos taurus, Dairy yield, Polymorphism, SNP.Resumen
In Colombia, different dairy breeds were introduced from Europe and the United States, which underwent different crossing and selection processes that generated specific qualities or differences and which likely have their own genomic structure. To characterize genetic diversity, population structure, and admixture, we used genotypes from 23,182 autosomal single nucleotide polymorphisms (SNPs) of 130 animals representing four dairy cattle breed groups from Nariño. In addition, we merged genotypes from 43,043 autosomal SNPs, from 137 animals from the Decker database (Decker et al., 2014) (DRYAD doi:10.5061/dryad.th092). After the quality control process of pruning the merged dataset, we were left with 7,475 autosomal SNPs shared by both databases of Nariño (127 samples) and Decker (135 samples). Genetic diversity levels were moderate in all breeds (average observed heterozygosity = 0.40). Based on the fixation index values, we conclude that Brahman individuals were more differentiated than the taurine breeds (-0.374 to 0.076 for Brown Swiss). Pairs between taurine breeds showed low genetic differentiation (0.011-0.479). Principal component analysis revealed that in both the Nariño and Decker databases, the taurine formed the most compact cluster compared with other breeds known not to share the same ancestry, and Jersey, Brown Swiss, and Normand individuals exhibited high similarity with Holstein individuals. Hierarchical cluster analysis with Admixture revealed that Brahman, Jersey, Normand, and Holstein from the Decker databases most of which were clustered together with the dairy breeds of the Nariño highland tropics are not able to create different groups, thus having greater similarity with each other. This can be explained by the crosses made by farmers to increase milk production volume, always based on the Holstein breed with semen of bulls from America and Canada. Detrimental impacts due to intensive selection might cause some specific traits from the region to be fixed in the offspring, which can influence their adaptive capacity to the highland tropics.
Métricas
Citas
Ajmone-Marsan, P., Garcia, J. F., & Lenstra, J. A. (2010). On the origin of cattle: how aurochs became cattle and colonized the world. Evolutionary Anthropology: Issues, News, and Reviews, 19(4), 148-157. doi: 10.1002/evan.20267 DOI: https://doi.org/10.1002/evan.20267
Alexander, D. H., Novembre, J., & Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19(9), 1655-1664. doi:10.1101/gr.094052.109 DOI: https://doi.org/10.1101/gr.094052.109
Bejarano, D., Pedraza, A., Rocha, F., & Martinez, R. (2012). Variabilidad genética en subpoblaciones comerciales de la raza criolla colombiana Romosinuano. Genética, Reproducción y Mejoramiento Animal, 13(1), 97-107. doi: 10.21930/rcta.vol13_num1_art:24 DOI: https://doi.org/10.21930/rcta.vol13_num1_art:246
Black IV, W. C., Baer, C. F., Antolin, M. F., & DuTeau, N. M. (2001). Population genomics: genome-wide sampling of insect populations. Annual Review of Entomology, 46(1), 441-469. doi: 10.1146/annurev.ento.46.1.441 DOI: https://doi.org/10.1146/annurev.ento.46.1.441
Calus, M. P. L., & Vandenplas, J. (2018). SNPrune: an efficient algorithm to prune large SNP array and sequence datasets based on high linkage disequilibrium. Genetics Selection Evolution, 50(34), 1-11. doi: 10.1186/s12711-018-0404-z DOI: https://doi.org/10.1186/s12711-018-0404-z
Carulla, J. E. (2016). Sistemas de producción lechera en Colombia : retos y oportunidades dairy production systems of Colombia: challenges and opportunities. Archivos Latinoamericanos de Producción Animal, 24(2), 9-13. https://ojs.alpa.uy/index.php/ojs_files/article/view/2526
Chagunda, M. G. G., Mujibi, F. D. N., Dusingizimana, T., Kamana, O., Cheruiyot, E., & Mwai, O. A. (2018). Use of high density Single Nucleotide Polymorphism (SNP) arrays to assess genetic diversity and population structure of dairy cattle in smallholder dairy systems: the case of girinka programme in rwanda. Frontiers in Genetics, 9(438), 1-8. doi: 10.3389/fgene.2018.00438 DOI: https://doi.org/10.3389/fgene.2018.00438
Decker, J. E., McKay, S. D., Rolf, M. M., Kim, J. W., Molina Alcalá, A., Sonstegard, T. S., Hanotte, O., Götherström, A., Seabury, C. M., Praharani, L., Babar, M. E., Correia de Almeida Regitano, L., Yildiz, M. A., Heaton, M. P., Liu, W. S., Lei, C. Z., Reecy, J. M., Saif-Ur-Rehman, M., Schnabel, R. D., & Taylor, J. F. (2014). Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genetics, 10(3), doi: 10.1371/journal.pgen.1004254 DOI: https://doi.org/10.1371/journal.pgen.1004254
Doormaal, B. J. Van, Miglior, F., Kistemaker, G., & Brand, P. (2005). Genetic diversification of the holstein breed in Canada and internationally.
Edea, Z., Bhuiyan, M. S. A., Dessie, T., Rothschild, M. F., Dadi, H., & Kim, K. S. (2015). Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds. Animal: An International Journal of Animal Bioscience, 9(2), 218-226. doi: 10.1017/S1751731114002560 DOI: https://doi.org/10.1017/S1751731114002560
Excoffier, L., Laval, G., & Schneider, S. (2005). Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionry Bioinformatics, 1(1), 47-50. doi: 10.1111/j.1755-0998.2010.02847.x DOI: https://doi.org/10.1177/117693430500100003
Federacion Colombiana de Ganaderos (2017). Balance y perspectivas del sector Ganadero Colombiano 2016 -2017. FEDEGAN. https://doi.org/www.fedegan.org.co
Gautier, M., Faraut, T., Moazami-Goudarzi, K., Navratil, V., Foglio, M., Grohs, C., Boland, A., Garnier, J. G., Boichard, D., Lathrop, G. M., Gut, I. G., & Eggen, A. (2007). Genetic and haplotypic structure in 14 European and African cattle breeds. Genetics, 177(2), 1059-1070. doi: 10.1534/genetics.107.075804 DOI: https://doi.org/10.1534/genetics.107.075804
Isaza, J. V., Lopez, A., & Echeverri, J. (2017). Análisis poblacional del ganado Holstein de Antioquia a partir de un polimorfismo del gen POU1F1. Archivos de Zootecnia, 66(254), 287-299. doi: 10.21071/az.v66i254.2324
Lenstra, J. A., Groeneveld, L. F., Eding, H., Kantanen, J., Williams, J. L., Taberlet, P., Nicolazzi, E. L., Sölkner, J., Simianer, H., Ciani, E., Garcia, J. F., Bruford, M. W., Ajmone-Marsan, P., & Weigend, S. (2012). Molecular tools and analytical approaches for the characterization of farm animal genetic diversity. Animal Genetics, 43(5), 483-502. doi: 10.1111/j.1365-2052.2011.02309.x DOI: https://doi.org/10.1111/j.1365-2052.2011.02309.x
Madrid, S., Lopez, A., & Echeverri, J. (2015). INHA A192G polymorphism and its association with dairy traits in Antioquia Holstein cattle. Archivos de Zootecnia, 64(246), 147-154. https://www.redalyc.org/articulo.oa?id=49545650008 DOI: https://doi.org/10.21071/az.v64i246.389
Mastrangelo, S., Saura, M., Tolone, M., Salces-Ortiz, J., Di Gerlando, R., Bertolini, F., Fontanesi, L., Sardina, M. T., Serrano, M., & Portolano, B. (2014). The genome-wide structure of two economically important indigenous Sicilian cattle breeds. Journal of Animal Science, 92(11), 4833-4842. doi: 10.2527/jas.2014-7898 DOI: https://doi.org/10.2527/jas.2014-7898
Mejía, L. G., Hernández, R. A., Rosero, C. Y., & Solarte-Portilla, C. E. (2015). Análisis de la diversidad genética de ganado bovino lechero del trópico alto de Nariño mediante marcadores moleculares heterólogos de tipo microsatélite. Revista de La Facultad de Medicina Veterinaria y de Zootecnia, 62(3), 18-33. doi: 10.15446/rfmvz.v62n3.54938 DOI: https://doi.org/10.15446/rfmvz.v62n3.54938
Melka, M. G., & Schenkel, F. S. (2012). Analysis of genetic diversity in Brown Swiss, Jersey and Holstein populations using genome-wide single nucleotide polymorphism markers. BMC Research Notes, 5(161), 1-8. doi: 10.1186/1756-0500-5-161 DOI: https://doi.org/10.1186/1756-0500-5-161
Nicolazzi, E. L., Picciolini, M., Strozzi, F., Schnabel, R. D., Lawley, C., Pirani, A., Brew, F., & Stella, A. (2014). SNPchiMp: a database to disentangle the SNPchip jungle in bovine livestock. BMC Genomics, 15(123), 1-6. doi: 10.1186/1471-2164-15-123 DOI: https://doi.org/10.1186/1471-2164-15-123
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., & Sham, P. C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics, 81(3), 559-575. doi: 10.1086/519795 DOI: https://doi.org/10.1086/519795
Rincon, J. C., Lopez, A. H., & Echeverri, J. Z. (2011). Variabilidad en dos SNP´s localizados en dos secuencias codificantes. Actas Iberoamericanas de Conservación Animal, 1(1), 154-156. https://www.uco.es/conbiand/aica/templatemo_110_lin_photo/articulos/2011/Rincon2011_1_154_156.pdf
Rincon, J. C., Lopez, A. H., & Echeverri, J. Z. (2013). Estructura y diversidad genética en vacas holstein de antioquia usando un polimorfismo del gen bGH. Revista MVZ Cordoba, 18(1), 3346-3354. doi: 10.21897/rmvz.197 DOI: https://doi.org/10.21897/rmvz.197
Rincon, J. C., Lopez, A., & Echeverri, J. (2018). Identifying signatures of recent selection in Holstein cattle in the tropic. Revista Colombiana de Ciencias Pecuarias, 31(1), 45-58. doi: 10.17533/udea.rccp.v31n1a06 DOI: https://doi.org/10.17533/udea.rccp.v31n1a06
Rodríguez, N. C., López, A. H., & Echeverri, J. Z. (2013). Estructura genética poblacional del gen lactoferrina bovino en vacas holstein del departamento de antioquia. Revista MVZ Cordoba, 18(1), 3355-3361. doi: 10.21897/rmvz.198 DOI: https://doi.org/10.21897/rmvz.198
Rodríguez-Ramilo, S. T., Fernández, J., Toro, M. A., Hernández, D., & Villanueva, B. (2015). Genome-wide estimates of coancestry, inbreeding and effective population size in the spanish holstein population. PLoS ONE, 10(4), e0124157. doi: 10.1371/journal.pone.0124157 DOI: https://doi.org/10.1371/journal.pone.0124157
Šidlová, V., Moravčíková, N., Trakovická, A., Ferenčaković, M., Curik, I., & Kasarda, R. (2015). Production type of Slovak Pinzgau cattle in respect of related breeds. Acta Fytotechnica et Zootechnica, 2015(2), 25-29. doi: 10.15414/afz.2015.18.02.25 DOI: https://doi.org/10.15414/afz.2015.18.02.25-29
Signer-Hasler, H., Burren, A., Neuditschko, M., Frischknecht, M., Garrick, D., Stricker, C., Gredler, B., Bapst, B., & Flury, C. (2017). Population structure and genomic inbreeding in nine Swiss dairy cattle populations. Genetics Selection Evolution, 49(83), 1-13. doi: 10.1186/s12711-017-0358-6 DOI: https://doi.org/10.1186/s12711-017-0358-6
Solarte-Portilla, C. E., & Zambrano-Burbano, G. L. (2012). Characterization and genetic evaluation of Holstein cattle in Nariño, Colombia. Revista Colombiana de Ciencias Pecuarias, 25(4), 539-547. doi: http://www.redalyc.org/articulo.oa?id=295024922002
Solarte-Portilla, C. E., Rosero-Galindo, C. Y., Burgos-Paz, W. O., & Caviedes-Castro, I. F. (2009). Caracterización y Evaluación Genética de la Población Bovina Lechera del Trópico Alto de Nariño para la Conformación de Núcleos de Selección. doi: 10.13140/2.1.3396.1762
Sponenberg, D. P., & Bixby, D. E. (2007). Managing breeds for a secure future: strategies for breeders and breed associations.
Suhada, H., Anwar, S., Maulana, H., & Yurnalis, D. (2016). Diversity of growth hormone gene and its relation with average daily gain in Simmental cattle in West Sumatera Province, Indonesia. African Journal of Biotechnology, 15(45), 2565-2571. doi: 10.5897/AJB2016.15553 DOI: https://doi.org/10.5897/AJB2016.15553
Verardo, L. L., Silva, F. F. e, Machado, M. A., Carmo Panetto, J. C. do, Lima Reis Faza, D. R. de, Otto, P. I., Almeida Regitano, L. C. de, Silva, L. O. C. da, Egito, A. A. do, Socorro Maués Albuquerque, M. do, Zanella, R., & Silva, M. V. G. B. da. (2021). Genome-wide analyses reveal the genetic architecture and candidate genes of indicine, taurine, synthetic crossbreds, and locally adapted cattle in Brazil. Frontiers in Genetics, 12, e702822.1-15. doi: 10.3389/fgene.2021.702822 DOI: https://doi.org/10.3389/fgene.2021.702822
Weir, B. S., & Cockerham, C. (1990). Genetic data analysis II: methods for discrete population genetic data. Sinuer Assoc.
Wright, S. (1965). The Interpretation of population structure by f-statistics with special regard to systems of mating. Evolution, 19(3), 395-420. doi: 10.2307/2406450 DOI: https://doi.org/10.1111/j.1558-5646.1965.tb01731.x
Zambrano, M. F. B., Flórez, J. C. R., Ríos, A. C. H., Portilla, C. E. S., & Jesús Bedoya Berrio, G. de. (2020). Evaluation of runs of homozygosity and genomic inbreeding in Holstein cattle from Colombia. Semina: Ciencias Agrarias, 41(6), 3397-3418. doi: 10.5433/1679-0359.2020v41n6Supl2p3397 DOI: https://doi.org/10.5433/1679-0359.2020v41n6Supl2p3397
Zenger, K. R., Khatkar, M. S., Cavanagh, J. A. L., Hawken, R. J., & Raadsma, H. W. (2007). Genome-wide genetic diversity of Holstein Friesian cattle reveals new insights into Australian and global population variability, including impact of selection. Animal Genetics, 38(1), 7-14. doi: 10.1111/j.1365-2052.2006.01543.x DOI: https://doi.org/10.1111/j.1365-2052.2006.01543.x
Descargas
Publicado
Cómo citar
Número
Sección
Licencia
Derechos de autor 2022 Semina: Ciências Agrárias
Esta obra está bajo una licencia internacional Creative Commons Atribución-NoComercial 4.0.
Os Direitos Autorais para artigos publicados são de direito da revista. Em virtude da aparecerem nesta revista de acesso público, os artigos são de uso gratuito, com atribuições próprias, em aplicações educacionais e não-comerciais.
A revista se reserva o direito de efetuar, nos originais, alterações de ordem normativa, ortográfica e gramatical, com vistas a manter o padrão culto da língua e a credibilidade do veículo. Respeitará, no entanto, o estilo de escrever dos autores.
Alterações, correções ou sugestões de ordem conceitual serão encaminhadas aos autores, quando necessário. Nesses casos, os artigos, depois de adequados, deverão ser submetidos a nova apreciação.
As opiniões emitidas pelos autores dos artigos são de sua exclusiva responsabilidade.
