Evaluation of runs of homozygosity and genomic inbreeding in Holstein cattle from Colombia
DOI:
https://doi.org/10.5433/1679-0359.2020v41n6Supl2p3397Palavras-chave:
Dairy cattle, Genomic, Linkage disequilibrium, Population.Resumo
Traditional selection programs for dairy cattle, based on quantitative principles, have worked well and allowed strong selection processes in the world over many decades. The objectives of this work were to estimate linkage disequilibrium (LD) levels at varying SNPs densities, to evaluate the effective population size of Holstein cattle, to characterize runs of homozygosity (ROH) distribution through Holstein cattle from Nariño and, to estimate and compare inbreeding coefficient (F) based on genomic markers information, runs of homozygosity (FROH), genomic relationship matrix (FGRM), and excess of homozygous (FSNP). After quality control, the dataset used was composed of 606 Holstein animals and 22200 SNP markers. PLINK program was used to identify LD, Ne, ROH segment and FROH and FSNP, FGRM was calculated with BLUPF90 family of programs. The average of r2 in all chromosomes was 0.011, the highest r2 was found in BTA3 (0.0323), and the lowest in BTA12 (0.0039). 533 ROH segments were identified in 319 animals; findings obtained in this study suggest that on average 0,28% of Holstein genome is autozygous. Total length of ROH was composed mostly of small segments (ROH1-4Mb and ROH4-8Mb). These segments accounted for approximately 96%, while larger ROH (ROH>8Mb) were 3.37% of all ROH detected. Inbreeding averages FROH, FSNP and FGRM methodologies were 0.28%, 3.11% and 3.36% respectively. The Pearson’s correlation among these different F values was: 0.49 (FROH-FSNP), 0.25 (FROH-FGRM), 0.22 (FSNP-FGRM). The distribution of ROH shared regions identified on 19 autosome chromosomes, cover a relevant number of genes inside these ROH. Our result evidenced lowest LD extension levels compared with other Holstein populations; inbreeding results suggest that FGRM and FSNP may be useful estimators of individual autozygosity in Holstein from Colombia. Genes related with production and reproduction were found, but the most important are the two that may be related to adaptation to Colombian high tropics. This work is a pioneer and be the starting point for programs of genetic improvement and genomic population studies in the country and mainly in high tropic areas where the dairy breeds have an important production.Downloads
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Referências
Badke, Y. M., Bates, R. O., Ernst, C. W., Schwab, C., & Steibel, J. P. (2012). Estimation of linkage disequilibrium in four US pig breeds. BMC Genomics, 13, 24. doi: 10.1186/1471-2164-13-24
Bansal, N., Fox, P. F., & McSweeney, P. L. H. (2008). Factors that affect the aggregation of rennet-altered casein micelles at low temperatures. International Journal of Dairy Technology, 61(1), 56-61. doi: 10. 1111/j.1471-0307.2008.00366.x
Biegelmeyer, P., Gulias-Gomes, C. C., Caetano, A. R., Steibel, J. P., & Cardoso, F. F. (2016). Linkage disequilibrium, persistence of phase and effective population size estimates in Hereford and Braford cattle. BMC Genetics, 17, 32. doi: 10.1186/s12863-016-0339-8
Bjelland, D. W., Weigel, K. A., Vukasinovic, N., & Nkrumah, J. D. (2013). Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding. Journal of Dairy Science, 96(7), 4697-4706. doi: 10.3168/jds.2012-6435
Burgos, S. A., Kim, J. J. M., Dai, M., & Cant, J. P. (2013). Energy depletion of bovine mammary epithelial cells activates AMPK and suppresses protein synthesis through inhibition of mTORC1 signaling. Hormone and Metabolic Research, 45(3),183-189. doi: 10.1055/s-0032-1323742
Chen, S. Y., Costa, V., Azevedo, M., Baig, M., Malmakov, N., Luikart, G.,… Beja-Pereira, A. (2008). Short communication: new alleles of the bovine K-casein gene revealed by resequencing and haplotype inference analysis. Journal of Dairy Science, 91(9), 3682-3686. doi: 10.3168/jds.2008-1211
Chitu, V., & Stanley, E. R. (2006). Colony-stimulating factor-1 in immunity and inflammation. In Current Opinion in Immunology,18(1), 39-48. doi: 10.1016/j.coi.2005.11.006
Crosby, K., Yatko, C., DerSimonian, H., Pan, L., & Edge, A. S. B. (2004). A novel monoclonal antibody inhibits the immune response of human cells against porcine cells: identification of a porcine antigen homologous to CD58. Transplantation, 77(8), 1288-1294. doi: 10.1097/01.TP.0000120377.57543.D8
Curik, I., Ferenčaković, M., & Sölkner, J. (2014). Inbreeding and runs of homozygosity: a possible solution to an old problem. Livestock Science, 166(1), 26-34. doi: 10.1016/j.livsci.2014.05.034
Davis, A. J., Yan, Z., Martinez, B., & Mumby, M. C. (2008). Protein phosphatase 2A is targeted to cell division control protein 6 by a calcium-binding regulatory subunit. Journal of Biological Chemistry, 283(23), 16104-16114. doi: 10.1074/jbc.M710313200
De Roos, A. P. W., Hayes, B. J., Spelman, R. J., & Goddard, M. E. (2008). Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. Genetics, 179(3), 1503-1512. doi: 10. 1534/genetics.107.084301
Deb, R., Singh, U., Kumar, S., Kumar, A., Singh, R., Sengar, G.,... Sharma, A. (2014). Genotypic to expression profiling of bovine calcium channel, voltage-dependent, alpha-2/delta subunit 1 gene, and their association with bovine mastitis among Frieswal (HFX Sahiwal) crossbred cattle of Indian origin. Animal Biotechnology, 25(2), 128-138. doi: 10.1080/10495398.2013.836106
Decker, J. E., Vasco, D. A., McKay, S. D., McClure, M. C., Rolf, M. M., Kim, J. W.,… Taylor, J. F. (2012). A novel analytical method, Birth Date Selection Mapping, detects response of the Angus (Bos taurus) genome to selection on complex traits. BMC Genomics, 13, 606. doi: 10.1186/1471-2164-13-606
Dobashi, S., Katagiri, T., Hirota, E., Ashida, S., Daigo, Y., Shuin, T.,… Nakamura, Y. (2009). Involvement of TMEM22 overexpression in the growth of renal cell carcinoma cells. Oncology Reports, 21(2), 305-12. doi: 10.3892/or_00000222
Dobromylskyj, M., & Ellis, S. (2007). Complexity in cattle KIR genes: transcription and genome analysis. Immunogenetics, 59, 463-472. doi: 10.1007/s00251-007-0215-9
Dustin, M. L. (1997). Adhesive bond dynamics in contacts between t lymphocytes and glass supported planar bilayers reconstituted with the immunoglobulin-related adhesion molecule CD58. Journal of Biological Chemistry, 272(25), 15782-15788. doi: 10.1074/jbc.272.25.15782
Ekman, A., Ilves, M., & Iivanainen, A. (2012). B lymphopoiesis is characterized by pre-B cell marker gene expression in fetal cattle and declines in adults. Developmental and Comparative Immunology, 37(1), 39-49. doi: 10.1016/j.dci.2011.12.009
Ferenčaković, M., Sölkner, J., & Curik, I. (2013). Estimating autozygosity from high-throughput information: Effects of SNP density and genotyping errors. Genetics Selection Evolution, 45(1), 42. doi: 10.1186/1297-9686-45-42
Forutan, M., Ansari Mahyari, S., Baes, C., Melzer, N., Schenkel, F. S., & Sargolzaei, M. (2018). Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle. BMC Genomics, 19, 98. doi: 10.1186/s12864-018-4453-z
Gibson, J., Morton, N. E., & Collins, A. (2006). Extended tracts of homozygosity in outbred human populations. Human Molecular Genetics, 15(5), 789-795. doi: 10.1093/hmg/ddi493
Goddard, M. E., & Hayes, B. J. (2007). Genomic selection. Journal of Animal Breeding and Genetics, 124(6), 323-330. doi: 10.1111/j.1439-0388.2007.00702.x
Goddard, M. E., Hayes, B., McPartlan, H., & Chamberlain, A. J. (2006). Can the same genetic markers be used in multiple breeds? Proceedings of the World Congress on Genetics Applied to Livestock Production, Belo Horizonte, MG, Brazil, 8.
Hall, S. J. G. (2016). Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data. Animal, 10(11), 1778-1785. doi: 10.1017/S1751731116000914
Hayes, B. J., Bowman, P. J., Chamberlain, A. J., & Goddard, M. E. (2009). Invited review: genomic selection in dairy cattle: progress and challenges. Journal of Dairy Science, 92(2),433-443. doi: 10. 3168/jds.2008-1646
Hayes, B. J., Visscher, P. M., McPartlan, H. C., & Goddard, M. E. (2003). Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Research, 13(4), 635-643. doi: 10.1101/gr.387103
Heimer, G., Kerätär, J. M., Riley, L. G., Balasubramaniam, S., Eyal, E., Pietikäinen, L. P.,… Hayflick, S. J. (2016). MECR mutations cause childhood-onset dystonia and optic atrophy, a mitochondrial fatty acid synthesis disorder. American Journal of Human Genetics, 99(6), 1229-1244. doi: 10.1016/j.ajhg.2016. 09.021
Hill, W. G., & Robertson, A. (1968). Linkage disequilibrium in finite populations. TAG. Theoretical and Applied Genetics, 38, 226–231. doi: 10.1007/BF01245622
Huang, Y. L., Zhao, F., Luo, C. C., Zhang, X., Si, Y., Sun, Z.,... Gao, X. J. (2013). SOCS3-mediated blockade reveals major contribution of JAK2/STAT5 signaling pathway to lactation and proliferation of dairy cow mammary epithelial cells in vitro. Molecules, 18(10), 12987-13002. doi: 10.3390/molecules 181012987
Huang, Y. Z., Zhan, Z. Y., Li, X. Y., Wu, S. R., Sun, Y. J., Xue, J.,… Chen, H. (2014). SNP and haplotype analysis reveal IGF2 variants associated with growth traits in Chinese Qinchuan cattle. Molecular Biology Reports, 41(2),591-598. doi: 10.1007/s11033-013-2896-5
Jiang, Q., Wang, Z., Moore, S. S., & Yang, R. C. (2012). Genome-wide analysis of zygotic linkage disequilibrium and its components in crossbred cattle. BMC Genetics,13, 65. doi: 10.1186/1471-2156-13-65
Kang, M., Jeong, W., Bae, H., Lim, W., Bazer, F. W., & Song, G. (2018). Bifunctional role of ephrin A1-Eph system in stimulating cell proliferation and protecting cells from cell death through the attenuation of ER stress and inflammatory responses in bovine mammary epithelial cells. Journal of Cellular Physiology, 233(3), 2560-2571. doi: 10.1002/jcp.26131
Keller, M. C., Visscher, P. M., & Goddard, M. E. (2011). Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data. Genetics, 189(1), 237-249. doi: 10.1534/genetics.111.130922
Kim, E. S., Cole, J. B., Huson, H., Wiggans, G. R., Van Tassel, C. P., Crooker, B. A.,… Sonstegard, T. S. (2013). Effect of artificial selection on runs of homozygosity in U.S. Holstein cattle. PLoS ONE, 8(11), e80813. doi: 10.1371/journal.pone.0080813
Kisliouk, T., Friedman, A., Klipper, E., Zhou, Q.-Y., Schams, D., Alfaidy, N., & Meidan, R. (2007). Expression pattern of prokineticin 1 and its receptors in bovine ovaries during the estrous cycle: involvement in corpus luteum regression and follicular atresia. Biology of Reproduction, 76(5), 749-758. doi: 10.1095/biolreprod.106.05473
Kukučková, V. Š., Moravčíková, N., Trakovická, A., Kadlečík, O., & Kasarda, R. (2016). Genetic differentiation of Slovak Pinzgau, Simmental, Charolais and Holstein cattle based on the linkage disequilibrium, persistence of phase and effective population size. Acta Argiculturae Slovenica, 107(Suppl. 5), 37-40.
Li, B., Xi, P., Wang, Z., Han, X., Xu, Y., Zhang, Y., & Miao, J. (2018). PI3K/Akt/mTOR signaling pathway participates in Streptococcus uberis-induced inflammation in mammary epithelial cells in concert with the classical TLRs/NF-ĸB pathway. Veterinary Microbiology, 227, 103-111. doi: 10.1016/j.vetmic. 2018.10.031
Liu, Y. X., Xu, C. H., Gao, T. Y., & Sun, Y. (2012). Polymorphisms of the ATP1A1 gene associated with mastitis in dairy cattle. Genetics and Molecular Research : GMR, 11(1), 651-660. doi: 10.4238/2012. March.16.3
Liu, Y. X., Zhou, X., Li, D. Q., Cui, Q. W., & Wang, G. L. (2010). Association of ATP1A1 gene polymorphism with heat tolerance traits in dairy cattle. Genetics and Molecular Research, 9(2), 891-896. doi: 10.4238/vol9-2gmr769
Lv, Y., Wei, C., Zhang, L., Lu, G., Liu, K., & Du, L. (2011). Association between polymorphisms in the SLC27A1 gene and milk production traits in chinese Holstein cattle. Animal Biotechnology, 22(1), 1-6. doi: 10.1080/10495398.2011.527567
Lu, L. M., Li, Q. Z., Huang, J. G., & Gao, X. J. (2012). Proteomic and functional analyses reveal MAPK1 regulates milk protein synthesis. Molecules (Basel, Switzerland), 18(1), 263-275. doi: 10.3390/ molecules18010263
Magalhães Araújo da Silva, M. H., Mendes Malhado, C. H., Costa, J. L., Jr., Araujo Cobuci, J., Napolis Costa, C., & Souza Carneiro, P. L. (2016). Population genetic structure in the Holstein breed in Brazil. Tropical Animal Health and Production, 48(2), 331-336. doi: 10.1007/s11250-015-0956-7
Maiwashe, A., Nephawe, K. A., Westhuizen, R. R. Van Der, Mostert, B. E., & Theron, H. E. (2006). Rate of inbreeding and effective population size in four major South African dairy cattle breeds. South African Journal of Animal Science, 36(1), 50-57. doi: 10.4314/sajas.v36i1.3986
Makina, S. O., Taylor, J. F., Van Marle-Köster, E., Muchadeyi, F. C., Makgahlela, M. L., MacNeil, M. D., & Maiwashe, A. (2015). Extent of linkage disequilibrium and effective population size in four South African sanga cattle breeds. Frontiers in Genetics, (6), 337. doi: 10.3389/fgene.2015.00337
Mastrangelo, S., Saura, M., Tolone, M., Salces-Ortiz, J., Di Gerlando, R., Bertolini, F.,... 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
Mastrangelo, S., Tolone, M., Di Gerlando, R., Fontanesi, L., Sardina, M. T., & Portolano, B. (2016). Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds. Animal, 10(5), 746-754. doi: 10.1017/S1751731115002943
Matin, A., & Otani, H. (2002). Cytotoxic and antibacterial activities of chemically synthesized κ-casecidin and its partial peptide fragments. Journal of Dairy Research, (69), 329-334. doi: 10.1017/S002202990 2005435
McQuillan, R., Leutenegger, A. L., Abdel-Rahman, R., Franklin, C. S., Pericic, M., Barac-Lauc, L.,… Wilson, J. F. (2008). Runs of homozygosity in european populations. American Journal of Human Genetics, 83(3), 359-372. doi: 10.1016/j.ajhg.2008.08.007
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
Misztal, I., Tsuruta, S., Lourenco, D., Aguilar, I., Legarra, A., & Vitezica, Z. (2015). Manual for BLUPF90 family of programs. Athens, USA: University of Georgia. Retrieved from http://nce.ads.uga.edu/wiki/ lib/exe/fetch.php?media=blupf90_all2.pdf
Nafikov, R. A., Schoonmaker, J. P., Korn, K. T., Noack, K., Garrick, D. J., Koehler, K. J.,... Beitz, D. C. (2013). Association of polymorphisms in solute carrier family 27, isoform A6 (SLC27A6) and fatty acid-binding protein-3 and fatty acid-binding protein-4 (FABP3 and FABP4) with fatty acid composition of bovine milk. Journal of Dairy Science, 96(9), 6007-6021. doi: 10.3168/jds.2013-6703
Nielsen, R. (2005). Molecular signatures of natural selection. Annual Review of Genetics, (39), 197-218. doi: 10.1146/annurev.genet.39.073003.112420
O’Brien, A. M. P., Höller, D., Boison, S. A., Milanesi, M., Bomba, L., Utsunomiya, Y. T.,… Sölkner, J. (2015). Low levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations. Genetics Selection Evolution, 47(1), 31. doi: 10.1186/s12711-015-0109-5
Palmer, D. S., Christensen, A. U., Sørensen, J., Celik, L., Qvist, K. B., & Schiøtt, B. (2010). Bovine chymosin: a computational study of recognition and binding of bovine k-Casein. Biochemistry, 49(11), 2563-2573. doi: 10.1021/bi902193u
Parker, N., & Porter, A. C. G. (2004). Identification of a novel gene family that includes the interferon-inducible human genes 6-16 and ISG12. BMC Genomics, 5, 8. doi: 10.1186/1471-2164-5-8
Pemberton, T. J., Absher, D., Feldman, M. W., Myers, R. M., Rosenberg, N. A., & Li, J. Z. (2012). Genomic patterns of homozygosity in worldwide human populations. American Journal of Human Genetics, 91(2), 275-292. doi: 10.1016/j.ajhg.2012.06.014
Peripolli, E., Stafuzza, N. B., Munari, D. P., Lima, A. L. F., Irgang, R., Machado, M. A.,... Silva, M. V. G. B. da. (2018). Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle. BMC Genomics, 19(1), 34. doi: 10.1186/s12864-017-4365-3
Pertoldi, C., Elschot, K., Ruiz-Gonzalez, A., van de Zande, L., Zalewski, A., Muñoz, J.,… Bijlsma, R. (2014). Genetic variability of central-western European pine marten (Martes martes) populations. Acta Theriologica, 59(4), 503-510. doi: 10.1007/s13364-014-0196-7
Porto, L. R., Neto, Kijas, J. W., & Reverter, A. (2014). The extent of linkage disequilibrium in beef cattle breeds using high-density SNP genotypes. Genetics Selection Evolution, 46, 22. doi: 10.1186/1297-96 86-46-22
Pritchard, J. K., & Przeworski, M. (2001). Linkage disequilibrium in humans: models and data. The American Journal of Human Genetics, 69(1), 1-14. doi: 10.1086/321275
Pritchard, J. K., & Rosenberg, N. A. (1999). Use of unlinked genetic markers to detect population stratification in association studies. The American Journal of Human Genetics, 65(1), 220-228. doi: 10. 1086/302449
Pryce, J. E., Hayes, B. J., & Goddard, M. E. (2012). Novel strategies to minimize progeny inbreeding while maximizing genetic gain using genomic information. Journal of Dairy Science, 95(1), 377-388. doi: 10. 3168/jds.2011-4254
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D.,… 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
Purfield, D. C., Berry, D. P., McParland, S., & Bradley, D. G. (2012). Runs of homozygosity and population history in cattle. BMC Genetics, 13, 70. doi: 10.1186/1471-2156-13-70
Qanbari, S., Pimentel, E. C. G., Tetens, J., Thaller, G., Lichtner, P., Sharifi, A. R., & Simianer, H. (2010). The pattern of linkage disequilibrium in German Holstein cattle. Animal Genetics, 41, 377-389. doi: 10. 1111/j.1365-2052.2009.02011.x
Ramírez, J. R., & Ayala, M. A. (2014). Enzimas: ¿Qué son y cómo funcionan? Revista Digital Universitaria UNAM, 15(12), 1607-6079. Available from: http://www.revista.unam.mx/vol.15/num12/art91/#
Rao, T. V. L., Ramesha, K., Barani, A., Chauhan, S., & Basavaraju, M. (2013). Association of GSTP1 gene polymorphisms with performance traits in Deoni cattle. African Journal of Biotechnology, 12(24), 3768-3773. doi: 10.5897/AJB2013.12403
Rexroad, C. E., & Vallejo, R. L. (2009). Estimates of linkage disequilibrium and effective population size in rainbow trout. BMC Genetics, 10, 83. doi: 10.1186/1471-2156-10-83
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.v31n1 a06
Robledo, G., Dávila-Fajardo, C. L., Márquez, A., Ortego-Centeno, N., Callejas Rubio, J. L., De Ramón Garrido, E.,… Martín, J. (2012). Association between -174 interleukin-6 gene polymorphism and biological response to rituximab in several systemic autoimmune diseases. DNA and Cell Biology, 31(9), 1486-1491. doi: 10.1089/dna.2012.1684
Rodríguez-Ramilo, S. T., Elsen, J. M., & Legarra, A. (2019). Inbreeding and effective population size in French dairy sheep: comparison between genomic and pedigree estimates. Journal of Dairy Science, 102(5), 4227-4237. doi: 10.3168/jds.2018-15405
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
Sandra, S., Alexander, M., & Dalgleish, D. G. (2007). The rennet coagulation mechanism of skim milk as observed by transmission diffusing wave spectroscopy. Journal of Colloid and Interface Science, 308(2), 364-373. doi: 10.1016/j.jcis.2007.01.021
Sargolzaei, M., Schenkel, F. S., Jansen, G. B., & Schaeffer, L. R. (2008). Extent of linkage disequilibrium in holstein cattle in north America. Journal of Dairy Science, 91(5), 2106-2117. doi: 10.3168/jds.2007-05 53.
Scraggs, E., Zanella, R., Wojtowicz, A., Taylor, J. F., Gaskins, C. T., Reeves, J. J.,… Neibergs, H. L. (2014). Estimation of inbreeding and effective population size of full-blood wagyu cattle registered with the American Wagyu Cattle Association. Journal of Animal Breeding and Genetics, 131(1), 3-10. doi: 10. 1111/jbg.12066
Seabury, C. M., Cargill, E. J., & Womack, J. E. (2007). Sequence variability and protein domain architectures for bovine Toll-like receptors 1, 5, and 10. Genomics, 90(4), 502-515. doi: 10.1016/j. ygeno.2007.07.001
Sherr, C. J., Roussel, M. F., & Rettenmier, C. W. (1988). Colony stimulating factor 1 receptor (cfms). In Journal of Cellular Biochemistry, 38(3), 179-187. doi: 10.1002/jcb.240380305
Silió, L., Rodríguez, M. C., Fernández, A., Barragán, C., Benítez, R., Óvilo, C., & Fernández, A. I. (2013). Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP-derived metrics. Journal of Animal Breeding and Genetics, 130(5), 349-360. doi: 10.1111/jbg.12031
Slatkin, M. (2008). Linkage disequilibrium - understanding the evolutionary past and mapping the medical future. In Nature Reviews Genetics, 9, 477-485. doi: 10.1038/nrg2361
Smith, L. P., & Kuhner, M. K. (2009). The limits of fine-scale mapping. Genetic Epidemiology, 33(4), 344-356. doi: 10.1002/gepi.20387
Solarte-Portilla, C. E., & Zambrano-Burbano, G. L. (2012). Characterization and genetic evaluation of Holstein cattle in Nariño, Colombia. Revista Colombiana de Ciencias Pecuarias, 92, 539-547. Available from: http://www.scielo.org.co/scielo.php?script=sci_arttext&pid=S0120-069020120004000 02&lng=en&tlng=en
Sørensen, A. C., Sørensen, M. K., & Berg, P. (2005). Inbreeding in danish dairy cattle breeds. Journal of Dairy Science, 88(5),1865-1872. doi: 10.3168/jds.S0022-0302(05)72861-7
Sved, J. A. (1971). Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theoretical Population Biology, 2(2), 125-141. doi: 10.1016/0040-5809(71)90011-6
Tenesa, A., Navarro, P., Hayes, B. J., Duffy, D. L., Clarke, G. M., Goddard, M. E., & Visscher, P. M. (2007). Recent human effective population size estimated from linkage disequilibrium. Genome Research,17(4), 520-526. doi: 10.1101/gr.6023607
Thompson, J. R., Everett, R. W., & Hammerschmidt, N. L. (2000). Effects of inbreeding on production and survival in holsteins. Journal of Dairy Science, 83(8), 1856-1864. doi: 10.3168/jds.S0022-0302(00)75 057-0
Toro Ospina, A. M., Maiorano, A. M., Curi, R. A., Pereira, G. L., Zerlotti-Mercadante, M. E., Santos Gonçalves Cyrillo, J. N. dos,... Josineudson, J. A. I. I. (2019). Linkage disequilibrium and effective population size in Gir cattle selected for yearling weight. Reproduction in Domestic Animals, 54(12), 1524-1531. doi: 10.1111/rda.13559
VanRaden, P. M. (2008). Efficient methods to compute genomic predictions. Journal of Dairy Science, 91(11), 4414-4423. doi: 10.3168/jds.2007-0980
VanRaden, P. M., Sanders, A. H., Tooker, M. E., Miller, R. H., Norman, H. D., Kuhn, M. T., & Wiggans, G. R. (2004). Development of a national genetic evaluation for cow fertility. Journal of Dairy Science, 87(7), 2285-2292. doi: 10.3168/jds.S0022-0302(04)70049-1
VanRaden, P. M., Van Tassell, C. P., Wiggans, G. R., Sonstegard, T. S., Schnabel, R. D., Taylor, J. F., & Schenkel, F. S. (2009). Invited review: reliability of genomic predictions for North American Holstein bulls. Journal of Dairy Science, 92(1), 16-24. doi: 10.3168/jds.2008-1514
VanRaden, P. M., O’Connell, J. R., Wiggans, G. R., & Weigel, K. A. (2011). Genomic evaluations with many more genotypes. Genetics Selection Evolution, 43(1), 10. doi: 10.1186/1297-9686-43-10
Velez, J. C., & Donkin, S. S. (2005). Feed restriction induces pyruvate carboxylase but not phosphoenolpyruvate carboxykinase in dairy cows. Journal of Dairy Science, 88(8), 2938-2948. doi: 10. 3168/jds.S0022-0302(05)72974-X
Wahl, C., Muller, W., Leithauser, F., Adler, G., Oswald, F., Reimann, J.,...Wegenka, U. M. (2009). IL-20 receptor 2 signaling down-regulates antigen-specific T cell responses. The Journal of Immunology, 182(2) 802-810. doi: 10.4049/jimmunol.182.2.802
Weigel, K. A., & Lin, S. W. (2002). Controlling inbreeding by constraining the average relationship between parents of young bulls entering ai progeny test programs. Journal of Dairy Science, 85(9), 2376-2383. doi: 10.3168/jds.S0022-0302(02)74318-X
Weller, J. I., & Ezra, E. (2005). Analysis of inbreeding in the israeli holstein dairy cattle population. Proceedings of the 2005 Intrbull Meeting, Uppsala, Sweden, 33. Retrieved from https://journal.interbull. org/index.php/ib/article/viewFile/880/871
Werling, D., Piercy, J., & Coffey, T. J. (2006). Expression of TOLL-like receptors (TLR) by bovine antigen-presenting cells-Potential role in pathogen discrimination? Veterinary Immunology and Immunopathology, 112(1-2), 2-11. doi: 10.1016/j.vetimm.2006.03.007
White, H. M., Koser, S. L., & Donkin, S. S. (2012). Regulation of bovine pyruvate carboxylase mRNA and promoter expression by thermal stress. Journal of Animal Science, 90(9), 2979-2987. doi: 10.2527/jas. 2010-3408
Williams, S. (1996). Pearson’s correlation coefficient. In the New Zealand Medical Journal, 109(1015), 38. doi: 10.1136/bmj.e4483
Wright, S. (1922). Coefficients of inbreeding and relationship. The American Naturalist, 56(645), 330-338. doi: 10.1086/279872
Zambrano-Burbano, G. L., Eraso-Cabrera, Y. M., Solarte-Portilla, C. E., & Rosero-Galindo, C. Y. (2012). Relationship between kappa casein genes (CSN3) and industrial yield in holstein cows in Nariño-Colombia. In book: Milk Protein, 265-282. doi: 10.5772/47818
Zimin, A. V, Delcher, A. L., Florea, L., Kelley, D. R., Schatz, M. C., Puiu, D.,… Salzberg, S. L. (2009). A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology, 10(4), R42. doi: 10.1186/ gb-2009-10-4-r42
Bansal, N., Fox, P. F., & McSweeney, P. L. H. (2008). Factors that affect the aggregation of rennet-altered casein micelles at low temperatures. International Journal of Dairy Technology, 61(1), 56-61. doi: 10. 1111/j.1471-0307.2008.00366.x
Biegelmeyer, P., Gulias-Gomes, C. C., Caetano, A. R., Steibel, J. P., & Cardoso, F. F. (2016). Linkage disequilibrium, persistence of phase and effective population size estimates in Hereford and Braford cattle. BMC Genetics, 17, 32. doi: 10.1186/s12863-016-0339-8
Bjelland, D. W., Weigel, K. A., Vukasinovic, N., & Nkrumah, J. D. (2013). Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding. Journal of Dairy Science, 96(7), 4697-4706. doi: 10.3168/jds.2012-6435
Burgos, S. A., Kim, J. J. M., Dai, M., & Cant, J. P. (2013). Energy depletion of bovine mammary epithelial cells activates AMPK and suppresses protein synthesis through inhibition of mTORC1 signaling. Hormone and Metabolic Research, 45(3),183-189. doi: 10.1055/s-0032-1323742
Chen, S. Y., Costa, V., Azevedo, M., Baig, M., Malmakov, N., Luikart, G.,… Beja-Pereira, A. (2008). Short communication: new alleles of the bovine K-casein gene revealed by resequencing and haplotype inference analysis. Journal of Dairy Science, 91(9), 3682-3686. doi: 10.3168/jds.2008-1211
Chitu, V., & Stanley, E. R. (2006). Colony-stimulating factor-1 in immunity and inflammation. In Current Opinion in Immunology,18(1), 39-48. doi: 10.1016/j.coi.2005.11.006
Crosby, K., Yatko, C., DerSimonian, H., Pan, L., & Edge, A. S. B. (2004). A novel monoclonal antibody inhibits the immune response of human cells against porcine cells: identification of a porcine antigen homologous to CD58. Transplantation, 77(8), 1288-1294. doi: 10.1097/01.TP.0000120377.57543.D8
Curik, I., Ferenčaković, M., & Sölkner, J. (2014). Inbreeding and runs of homozygosity: a possible solution to an old problem. Livestock Science, 166(1), 26-34. doi: 10.1016/j.livsci.2014.05.034
Davis, A. J., Yan, Z., Martinez, B., & Mumby, M. C. (2008). Protein phosphatase 2A is targeted to cell division control protein 6 by a calcium-binding regulatory subunit. Journal of Biological Chemistry, 283(23), 16104-16114. doi: 10.1074/jbc.M710313200
De Roos, A. P. W., Hayes, B. J., Spelman, R. J., & Goddard, M. E. (2008). Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. Genetics, 179(3), 1503-1512. doi: 10. 1534/genetics.107.084301
Deb, R., Singh, U., Kumar, S., Kumar, A., Singh, R., Sengar, G.,... Sharma, A. (2014). Genotypic to expression profiling of bovine calcium channel, voltage-dependent, alpha-2/delta subunit 1 gene, and their association with bovine mastitis among Frieswal (HFX Sahiwal) crossbred cattle of Indian origin. Animal Biotechnology, 25(2), 128-138. doi: 10.1080/10495398.2013.836106
Decker, J. E., Vasco, D. A., McKay, S. D., McClure, M. C., Rolf, M. M., Kim, J. W.,… Taylor, J. F. (2012). A novel analytical method, Birth Date Selection Mapping, detects response of the Angus (Bos taurus) genome to selection on complex traits. BMC Genomics, 13, 606. doi: 10.1186/1471-2164-13-606
Dobashi, S., Katagiri, T., Hirota, E., Ashida, S., Daigo, Y., Shuin, T.,… Nakamura, Y. (2009). Involvement of TMEM22 overexpression in the growth of renal cell carcinoma cells. Oncology Reports, 21(2), 305-12. doi: 10.3892/or_00000222
Dobromylskyj, M., & Ellis, S. (2007). Complexity in cattle KIR genes: transcription and genome analysis. Immunogenetics, 59, 463-472. doi: 10.1007/s00251-007-0215-9
Dustin, M. L. (1997). Adhesive bond dynamics in contacts between t lymphocytes and glass supported planar bilayers reconstituted with the immunoglobulin-related adhesion molecule CD58. Journal of Biological Chemistry, 272(25), 15782-15788. doi: 10.1074/jbc.272.25.15782
Ekman, A., Ilves, M., & Iivanainen, A. (2012). B lymphopoiesis is characterized by pre-B cell marker gene expression in fetal cattle and declines in adults. Developmental and Comparative Immunology, 37(1), 39-49. doi: 10.1016/j.dci.2011.12.009
Ferenčaković, M., Sölkner, J., & Curik, I. (2013). Estimating autozygosity from high-throughput information: Effects of SNP density and genotyping errors. Genetics Selection Evolution, 45(1), 42. doi: 10.1186/1297-9686-45-42
Forutan, M., Ansari Mahyari, S., Baes, C., Melzer, N., Schenkel, F. S., & Sargolzaei, M. (2018). Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle. BMC Genomics, 19, 98. doi: 10.1186/s12864-018-4453-z
Gibson, J., Morton, N. E., & Collins, A. (2006). Extended tracts of homozygosity in outbred human populations. Human Molecular Genetics, 15(5), 789-795. doi: 10.1093/hmg/ddi493
Goddard, M. E., & Hayes, B. J. (2007). Genomic selection. Journal of Animal Breeding and Genetics, 124(6), 323-330. doi: 10.1111/j.1439-0388.2007.00702.x
Goddard, M. E., Hayes, B., McPartlan, H., & Chamberlain, A. J. (2006). Can the same genetic markers be used in multiple breeds? Proceedings of the World Congress on Genetics Applied to Livestock Production, Belo Horizonte, MG, Brazil, 8.
Hall, S. J. G. (2016). Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data. Animal, 10(11), 1778-1785. doi: 10.1017/S1751731116000914
Hayes, B. J., Bowman, P. J., Chamberlain, A. J., & Goddard, M. E. (2009). Invited review: genomic selection in dairy cattle: progress and challenges. Journal of Dairy Science, 92(2),433-443. doi: 10. 3168/jds.2008-1646
Hayes, B. J., Visscher, P. M., McPartlan, H. C., & Goddard, M. E. (2003). Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Research, 13(4), 635-643. doi: 10.1101/gr.387103
Heimer, G., Kerätär, J. M., Riley, L. G., Balasubramaniam, S., Eyal, E., Pietikäinen, L. P.,… Hayflick, S. J. (2016). MECR mutations cause childhood-onset dystonia and optic atrophy, a mitochondrial fatty acid synthesis disorder. American Journal of Human Genetics, 99(6), 1229-1244. doi: 10.1016/j.ajhg.2016. 09.021
Hill, W. G., & Robertson, A. (1968). Linkage disequilibrium in finite populations. TAG. Theoretical and Applied Genetics, 38, 226–231. doi: 10.1007/BF01245622
Huang, Y. L., Zhao, F., Luo, C. C., Zhang, X., Si, Y., Sun, Z.,... Gao, X. J. (2013). SOCS3-mediated blockade reveals major contribution of JAK2/STAT5 signaling pathway to lactation and proliferation of dairy cow mammary epithelial cells in vitro. Molecules, 18(10), 12987-13002. doi: 10.3390/molecules 181012987
Huang, Y. Z., Zhan, Z. Y., Li, X. Y., Wu, S. R., Sun, Y. J., Xue, J.,… Chen, H. (2014). SNP and haplotype analysis reveal IGF2 variants associated with growth traits in Chinese Qinchuan cattle. Molecular Biology Reports, 41(2),591-598. doi: 10.1007/s11033-013-2896-5
Jiang, Q., Wang, Z., Moore, S. S., & Yang, R. C. (2012). Genome-wide analysis of zygotic linkage disequilibrium and its components in crossbred cattle. BMC Genetics,13, 65. doi: 10.1186/1471-2156-13-65
Kang, M., Jeong, W., Bae, H., Lim, W., Bazer, F. W., & Song, G. (2018). Bifunctional role of ephrin A1-Eph system in stimulating cell proliferation and protecting cells from cell death through the attenuation of ER stress and inflammatory responses in bovine mammary epithelial cells. Journal of Cellular Physiology, 233(3), 2560-2571. doi: 10.1002/jcp.26131
Keller, M. C., Visscher, P. M., & Goddard, M. E. (2011). Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data. Genetics, 189(1), 237-249. doi: 10.1534/genetics.111.130922
Kim, E. S., Cole, J. B., Huson, H., Wiggans, G. R., Van Tassel, C. P., Crooker, B. A.,… Sonstegard, T. S. (2013). Effect of artificial selection on runs of homozygosity in U.S. Holstein cattle. PLoS ONE, 8(11), e80813. doi: 10.1371/journal.pone.0080813
Kisliouk, T., Friedman, A., Klipper, E., Zhou, Q.-Y., Schams, D., Alfaidy, N., & Meidan, R. (2007). Expression pattern of prokineticin 1 and its receptors in bovine ovaries during the estrous cycle: involvement in corpus luteum regression and follicular atresia. Biology of Reproduction, 76(5), 749-758. doi: 10.1095/biolreprod.106.05473
Kukučková, V. Š., Moravčíková, N., Trakovická, A., Kadlečík, O., & Kasarda, R. (2016). Genetic differentiation of Slovak Pinzgau, Simmental, Charolais and Holstein cattle based on the linkage disequilibrium, persistence of phase and effective population size. Acta Argiculturae Slovenica, 107(Suppl. 5), 37-40.
Li, B., Xi, P., Wang, Z., Han, X., Xu, Y., Zhang, Y., & Miao, J. (2018). PI3K/Akt/mTOR signaling pathway participates in Streptococcus uberis-induced inflammation in mammary epithelial cells in concert with the classical TLRs/NF-ĸB pathway. Veterinary Microbiology, 227, 103-111. doi: 10.1016/j.vetmic. 2018.10.031
Liu, Y. X., Xu, C. H., Gao, T. Y., & Sun, Y. (2012). Polymorphisms of the ATP1A1 gene associated with mastitis in dairy cattle. Genetics and Molecular Research : GMR, 11(1), 651-660. doi: 10.4238/2012. March.16.3
Liu, Y. X., Zhou, X., Li, D. Q., Cui, Q. W., & Wang, G. L. (2010). Association of ATP1A1 gene polymorphism with heat tolerance traits in dairy cattle. Genetics and Molecular Research, 9(2), 891-896. doi: 10.4238/vol9-2gmr769
Lv, Y., Wei, C., Zhang, L., Lu, G., Liu, K., & Du, L. (2011). Association between polymorphisms in the SLC27A1 gene and milk production traits in chinese Holstein cattle. Animal Biotechnology, 22(1), 1-6. doi: 10.1080/10495398.2011.527567
Lu, L. M., Li, Q. Z., Huang, J. G., & Gao, X. J. (2012). Proteomic and functional analyses reveal MAPK1 regulates milk protein synthesis. Molecules (Basel, Switzerland), 18(1), 263-275. doi: 10.3390/ molecules18010263
Magalhães Araújo da Silva, M. H., Mendes Malhado, C. H., Costa, J. L., Jr., Araujo Cobuci, J., Napolis Costa, C., & Souza Carneiro, P. L. (2016). Population genetic structure in the Holstein breed in Brazil. Tropical Animal Health and Production, 48(2), 331-336. doi: 10.1007/s11250-015-0956-7
Maiwashe, A., Nephawe, K. A., Westhuizen, R. R. Van Der, Mostert, B. E., & Theron, H. E. (2006). Rate of inbreeding and effective population size in four major South African dairy cattle breeds. South African Journal of Animal Science, 36(1), 50-57. doi: 10.4314/sajas.v36i1.3986
Makina, S. O., Taylor, J. F., Van Marle-Köster, E., Muchadeyi, F. C., Makgahlela, M. L., MacNeil, M. D., & Maiwashe, A. (2015). Extent of linkage disequilibrium and effective population size in four South African sanga cattle breeds. Frontiers in Genetics, (6), 337. doi: 10.3389/fgene.2015.00337
Mastrangelo, S., Saura, M., Tolone, M., Salces-Ortiz, J., Di Gerlando, R., Bertolini, F.,... 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
Mastrangelo, S., Tolone, M., Di Gerlando, R., Fontanesi, L., Sardina, M. T., & Portolano, B. (2016). Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds. Animal, 10(5), 746-754. doi: 10.1017/S1751731115002943
Matin, A., & Otani, H. (2002). Cytotoxic and antibacterial activities of chemically synthesized κ-casecidin and its partial peptide fragments. Journal of Dairy Research, (69), 329-334. doi: 10.1017/S002202990 2005435
McQuillan, R., Leutenegger, A. L., Abdel-Rahman, R., Franklin, C. S., Pericic, M., Barac-Lauc, L.,… Wilson, J. F. (2008). Runs of homozygosity in european populations. American Journal of Human Genetics, 83(3), 359-372. doi: 10.1016/j.ajhg.2008.08.007
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
Misztal, I., Tsuruta, S., Lourenco, D., Aguilar, I., Legarra, A., & Vitezica, Z. (2015). Manual for BLUPF90 family of programs. Athens, USA: University of Georgia. Retrieved from http://nce.ads.uga.edu/wiki/ lib/exe/fetch.php?media=blupf90_all2.pdf
Nafikov, R. A., Schoonmaker, J. P., Korn, K. T., Noack, K., Garrick, D. J., Koehler, K. J.,... Beitz, D. C. (2013). Association of polymorphisms in solute carrier family 27, isoform A6 (SLC27A6) and fatty acid-binding protein-3 and fatty acid-binding protein-4 (FABP3 and FABP4) with fatty acid composition of bovine milk. Journal of Dairy Science, 96(9), 6007-6021. doi: 10.3168/jds.2013-6703
Nielsen, R. (2005). Molecular signatures of natural selection. Annual Review of Genetics, (39), 197-218. doi: 10.1146/annurev.genet.39.073003.112420
O’Brien, A. M. P., Höller, D., Boison, S. A., Milanesi, M., Bomba, L., Utsunomiya, Y. T.,… Sölkner, J. (2015). Low levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations. Genetics Selection Evolution, 47(1), 31. doi: 10.1186/s12711-015-0109-5
Palmer, D. S., Christensen, A. U., Sørensen, J., Celik, L., Qvist, K. B., & Schiøtt, B. (2010). Bovine chymosin: a computational study of recognition and binding of bovine k-Casein. Biochemistry, 49(11), 2563-2573. doi: 10.1021/bi902193u
Parker, N., & Porter, A. C. G. (2004). Identification of a novel gene family that includes the interferon-inducible human genes 6-16 and ISG12. BMC Genomics, 5, 8. doi: 10.1186/1471-2164-5-8
Pemberton, T. J., Absher, D., Feldman, M. W., Myers, R. M., Rosenberg, N. A., & Li, J. Z. (2012). Genomic patterns of homozygosity in worldwide human populations. American Journal of Human Genetics, 91(2), 275-292. doi: 10.1016/j.ajhg.2012.06.014
Peripolli, E., Stafuzza, N. B., Munari, D. P., Lima, A. L. F., Irgang, R., Machado, M. A.,... Silva, M. V. G. B. da. (2018). Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle. BMC Genomics, 19(1), 34. doi: 10.1186/s12864-017-4365-3
Pertoldi, C., Elschot, K., Ruiz-Gonzalez, A., van de Zande, L., Zalewski, A., Muñoz, J.,… Bijlsma, R. (2014). Genetic variability of central-western European pine marten (Martes martes) populations. Acta Theriologica, 59(4), 503-510. doi: 10.1007/s13364-014-0196-7
Porto, L. R., Neto, Kijas, J. W., & Reverter, A. (2014). The extent of linkage disequilibrium in beef cattle breeds using high-density SNP genotypes. Genetics Selection Evolution, 46, 22. doi: 10.1186/1297-96 86-46-22
Pritchard, J. K., & Przeworski, M. (2001). Linkage disequilibrium in humans: models and data. The American Journal of Human Genetics, 69(1), 1-14. doi: 10.1086/321275
Pritchard, J. K., & Rosenberg, N. A. (1999). Use of unlinked genetic markers to detect population stratification in association studies. The American Journal of Human Genetics, 65(1), 220-228. doi: 10. 1086/302449
Pryce, J. E., Hayes, B. J., & Goddard, M. E. (2012). Novel strategies to minimize progeny inbreeding while maximizing genetic gain using genomic information. Journal of Dairy Science, 95(1), 377-388. doi: 10. 3168/jds.2011-4254
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D.,… 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
Purfield, D. C., Berry, D. P., McParland, S., & Bradley, D. G. (2012). Runs of homozygosity and population history in cattle. BMC Genetics, 13, 70. doi: 10.1186/1471-2156-13-70
Qanbari, S., Pimentel, E. C. G., Tetens, J., Thaller, G., Lichtner, P., Sharifi, A. R., & Simianer, H. (2010). The pattern of linkage disequilibrium in German Holstein cattle. Animal Genetics, 41, 377-389. doi: 10. 1111/j.1365-2052.2009.02011.x
Ramírez, J. R., & Ayala, M. A. (2014). Enzimas: ¿Qué son y cómo funcionan? Revista Digital Universitaria UNAM, 15(12), 1607-6079. Available from: http://www.revista.unam.mx/vol.15/num12/art91/#
Rao, T. V. L., Ramesha, K., Barani, A., Chauhan, S., & Basavaraju, M. (2013). Association of GSTP1 gene polymorphisms with performance traits in Deoni cattle. African Journal of Biotechnology, 12(24), 3768-3773. doi: 10.5897/AJB2013.12403
Rexroad, C. E., & Vallejo, R. L. (2009). Estimates of linkage disequilibrium and effective population size in rainbow trout. BMC Genetics, 10, 83. doi: 10.1186/1471-2156-10-83
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.v31n1 a06
Robledo, G., Dávila-Fajardo, C. L., Márquez, A., Ortego-Centeno, N., Callejas Rubio, J. L., De Ramón Garrido, E.,… Martín, J. (2012). Association between -174 interleukin-6 gene polymorphism and biological response to rituximab in several systemic autoimmune diseases. DNA and Cell Biology, 31(9), 1486-1491. doi: 10.1089/dna.2012.1684
Rodríguez-Ramilo, S. T., Elsen, J. M., & Legarra, A. (2019). Inbreeding and effective population size in French dairy sheep: comparison between genomic and pedigree estimates. Journal of Dairy Science, 102(5), 4227-4237. doi: 10.3168/jds.2018-15405
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
Sandra, S., Alexander, M., & Dalgleish, D. G. (2007). The rennet coagulation mechanism of skim milk as observed by transmission diffusing wave spectroscopy. Journal of Colloid and Interface Science, 308(2), 364-373. doi: 10.1016/j.jcis.2007.01.021
Sargolzaei, M., Schenkel, F. S., Jansen, G. B., & Schaeffer, L. R. (2008). Extent of linkage disequilibrium in holstein cattle in north America. Journal of Dairy Science, 91(5), 2106-2117. doi: 10.3168/jds.2007-05 53.
Scraggs, E., Zanella, R., Wojtowicz, A., Taylor, J. F., Gaskins, C. T., Reeves, J. J.,… Neibergs, H. L. (2014). Estimation of inbreeding and effective population size of full-blood wagyu cattle registered with the American Wagyu Cattle Association. Journal of Animal Breeding and Genetics, 131(1), 3-10. doi: 10. 1111/jbg.12066
Seabury, C. M., Cargill, E. J., & Womack, J. E. (2007). Sequence variability and protein domain architectures for bovine Toll-like receptors 1, 5, and 10. Genomics, 90(4), 502-515. doi: 10.1016/j. ygeno.2007.07.001
Sherr, C. J., Roussel, M. F., & Rettenmier, C. W. (1988). Colony stimulating factor 1 receptor (cfms). In Journal of Cellular Biochemistry, 38(3), 179-187. doi: 10.1002/jcb.240380305
Silió, L., Rodríguez, M. C., Fernández, A., Barragán, C., Benítez, R., Óvilo, C., & Fernández, A. I. (2013). Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP-derived metrics. Journal of Animal Breeding and Genetics, 130(5), 349-360. doi: 10.1111/jbg.12031
Slatkin, M. (2008). Linkage disequilibrium - understanding the evolutionary past and mapping the medical future. In Nature Reviews Genetics, 9, 477-485. doi: 10.1038/nrg2361
Smith, L. P., & Kuhner, M. K. (2009). The limits of fine-scale mapping. Genetic Epidemiology, 33(4), 344-356. doi: 10.1002/gepi.20387
Solarte-Portilla, C. E., & Zambrano-Burbano, G. L. (2012). Characterization and genetic evaluation of Holstein cattle in Nariño, Colombia. Revista Colombiana de Ciencias Pecuarias, 92, 539-547. Available from: http://www.scielo.org.co/scielo.php?script=sci_arttext&pid=S0120-069020120004000 02&lng=en&tlng=en
Sørensen, A. C., Sørensen, M. K., & Berg, P. (2005). Inbreeding in danish dairy cattle breeds. Journal of Dairy Science, 88(5),1865-1872. doi: 10.3168/jds.S0022-0302(05)72861-7
Sved, J. A. (1971). Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theoretical Population Biology, 2(2), 125-141. doi: 10.1016/0040-5809(71)90011-6
Tenesa, A., Navarro, P., Hayes, B. J., Duffy, D. L., Clarke, G. M., Goddard, M. E., & Visscher, P. M. (2007). Recent human effective population size estimated from linkage disequilibrium. Genome Research,17(4), 520-526. doi: 10.1101/gr.6023607
Thompson, J. R., Everett, R. W., & Hammerschmidt, N. L. (2000). Effects of inbreeding on production and survival in holsteins. Journal of Dairy Science, 83(8), 1856-1864. doi: 10.3168/jds.S0022-0302(00)75 057-0
Toro Ospina, A. M., Maiorano, A. M., Curi, R. A., Pereira, G. L., Zerlotti-Mercadante, M. E., Santos Gonçalves Cyrillo, J. N. dos,... Josineudson, J. A. I. I. (2019). Linkage disequilibrium and effective population size in Gir cattle selected for yearling weight. Reproduction in Domestic Animals, 54(12), 1524-1531. doi: 10.1111/rda.13559
VanRaden, P. M. (2008). Efficient methods to compute genomic predictions. Journal of Dairy Science, 91(11), 4414-4423. doi: 10.3168/jds.2007-0980
VanRaden, P. M., Sanders, A. H., Tooker, M. E., Miller, R. H., Norman, H. D., Kuhn, M. T., & Wiggans, G. R. (2004). Development of a national genetic evaluation for cow fertility. Journal of Dairy Science, 87(7), 2285-2292. doi: 10.3168/jds.S0022-0302(04)70049-1
VanRaden, P. M., Van Tassell, C. P., Wiggans, G. R., Sonstegard, T. S., Schnabel, R. D., Taylor, J. F., & Schenkel, F. S. (2009). Invited review: reliability of genomic predictions for North American Holstein bulls. Journal of Dairy Science, 92(1), 16-24. doi: 10.3168/jds.2008-1514
VanRaden, P. M., O’Connell, J. R., Wiggans, G. R., & Weigel, K. A. (2011). Genomic evaluations with many more genotypes. Genetics Selection Evolution, 43(1), 10. doi: 10.1186/1297-9686-43-10
Velez, J. C., & Donkin, S. S. (2005). Feed restriction induces pyruvate carboxylase but not phosphoenolpyruvate carboxykinase in dairy cows. Journal of Dairy Science, 88(8), 2938-2948. doi: 10. 3168/jds.S0022-0302(05)72974-X
Wahl, C., Muller, W., Leithauser, F., Adler, G., Oswald, F., Reimann, J.,...Wegenka, U. M. (2009). IL-20 receptor 2 signaling down-regulates antigen-specific T cell responses. The Journal of Immunology, 182(2) 802-810. doi: 10.4049/jimmunol.182.2.802
Weigel, K. A., & Lin, S. W. (2002). Controlling inbreeding by constraining the average relationship between parents of young bulls entering ai progeny test programs. Journal of Dairy Science, 85(9), 2376-2383. doi: 10.3168/jds.S0022-0302(02)74318-X
Weller, J. I., & Ezra, E. (2005). Analysis of inbreeding in the israeli holstein dairy cattle population. Proceedings of the 2005 Intrbull Meeting, Uppsala, Sweden, 33. Retrieved from https://journal.interbull. org/index.php/ib/article/viewFile/880/871
Werling, D., Piercy, J., & Coffey, T. J. (2006). Expression of TOLL-like receptors (TLR) by bovine antigen-presenting cells-Potential role in pathogen discrimination? Veterinary Immunology and Immunopathology, 112(1-2), 2-11. doi: 10.1016/j.vetimm.2006.03.007
White, H. M., Koser, S. L., & Donkin, S. S. (2012). Regulation of bovine pyruvate carboxylase mRNA and promoter expression by thermal stress. Journal of Animal Science, 90(9), 2979-2987. doi: 10.2527/jas. 2010-3408
Williams, S. (1996). Pearson’s correlation coefficient. In the New Zealand Medical Journal, 109(1015), 38. doi: 10.1136/bmj.e4483
Wright, S. (1922). Coefficients of inbreeding and relationship. The American Naturalist, 56(645), 330-338. doi: 10.1086/279872
Zambrano-Burbano, G. L., Eraso-Cabrera, Y. M., Solarte-Portilla, C. E., & Rosero-Galindo, C. Y. (2012). Relationship between kappa casein genes (CSN3) and industrial yield in holstein cows in Nariño-Colombia. In book: Milk Protein, 265-282. doi: 10.5772/47818
Zimin, A. V, Delcher, A. L., Florea, L., Kelley, D. R., Schatz, M. C., Puiu, D.,… Salzberg, S. L. (2009). A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology, 10(4), R42. doi: 10.1186/ gb-2009-10-4-r42
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2020-11-06
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Zambrano, M. F. B., Flórez, J. C. R., Rios, A. C. H., Portilla, C. E. S., & Berrio, G. de J. B. (2020). Evaluation of runs of homozygosity and genomic inbreeding in Holstein cattle from Colombia. Semina: Ciências Agrárias, 41(6Supl2), 3397–3418. https://doi.org/10.5433/1679-0359.2020v41n6Supl2p3397
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