Abstract
The purpose of this work was to establish DNA marker frequencies for genetic disorders, colour, horned/polled trait, and major genes of importance for productive and reproductive traits in Blanco Orejinegro (BON) cattle. The Blanco Orejinegro breed is a Colombian creole breed characterized by a white hair coat on black skin with black ears, black hair on the middle part of the legs, and absence of horns. We genotyped 420 animals of Colombia, 70 with the GGP-Bovine 150 K chip and 350 with the GGP-Bovine 50 K chip. The markers were associated with 50 genetic diseases, 52 major gene variants related to productive traits, and 12 variants related to coat coloration, presence of horns, and adaptation, selected from the information contained in the chips. Genotype frequencies were estimated using the R statistical program. Genetic disorder annotations were derived using the Online Mendelian Inheritance in Animals tool (OMIA) and the average inbreeding coefficient (F) (n = 7799) using the MTDFNRM program. Carriers were found for 16 of the genetic disorders evaluated but with low frequencies (0.24 to 2.46%); no homozygous animals were found for the disorders. Carriers were associated with disorders such as bovine leukocyte adhesion deficiency (BLAD), deficiency of uridine monophosphate synthase (DUMPS), syndactyly, and epidermolysis bullosa (EB). The F was 4.41%. Concerning the genes associated with colour (TYR, MC1R, and PMEL), alleles related to black pigmentation, the absence of horns (polledness), and slick coat (an adaptive trait) were highly frequent (> 81.90%). Markers associated with milk production and quality, yellow fat, and fertility showed variable frequencies, indicating selection potential. Allele frequency of genetic disorders in BON cattle was low, suggesting few genetic disorder problems, with syndactyly being the most frequent condition. The markers associated with colour and polledness were almost fixed, with a frequency at or near 100%. Production and reproduction markers showed variability for selection.
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The data sets generated and/or analyzed during the current study are available through the corresponding author upon reasonable request.
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Abbreviations
- BLAD:
-
Bovine leukocyte adhesion deficiency
- DUMPS:
-
Deficiency of uridine monophosphate synthase
- CMD2:
-
Congenital muscular dystonia type 2
- Pompes:
-
Glycogen storage disease II
- WS:
-
Weaver syndrome
- EB:
-
Epidermolysis bullosa
- HH1:
-
Holstein haplotype
- TYR :
-
Tyrosinase
- TYRP1 :
-
Tyrosinase-related protein 1
- MC1R (MSHR):
-
Melanocortin 1 Receptor
- PMEL :
-
Premelanosome protein (silver dilutor)
- Polled:
-
Absence of horns
References
Aldersey, J.E., Sonstegard, T.S., Williams, J.L. and Bottema, C.D.K., 2020. Understanding the effects of the bovine POLLED variants. Animal Genetics, 51, 166–176. https://doi.org/10.1111/age.12915
Berryere, T.G., Schmutz, S.M., Schimpf, R.J., Cowan, C.M. and Potter, J., 2003. TYRP1 is associated with dun coat colour in Dexter cattle or how now brown cow?. Animal Genetics, 34, 169–175. https://doi.org/10.1046/j.1365-2052.2003.00985.x
Caivio‐Nasner, S., López‐Herrera, A., González‐Herrera, L. G. and Rincón, J. C., 2021. Diversity analysis, runs of homozygosity and genomic inbreeding reveal recent selection in Blanco Orejinegro cattle. Journal of Animal Breeding and Genetics, 138, 613– 627. https://doi.org/10.1111/jbg.12549
Casas, E. and Kehrli, M.E., 2016. A review of selected genes with known effects on performance and health of cattle. Frontiers in Veterinary Science, 3, 1–11. https://doi.org/10.3389/fvets.2016.00113
Charlier, C., Coppieters, W., Rollin, F., Desmecht, D., Agerholm, J.S., Cambisano, N., Carta, E., Dardano, S., Dive, M., Fasquelle, C., Frennet, J.C., Hanset, R., Hubin, X., Jorgensen, C., Karim, L., Kent, M., Harvey, K., Pearce, B.R., Simon, P., Tama, N., Nie, H., Vandeputte, S., Lien, S., Longeri, M., Fredholm, M., Harvey, R.J. and Georges, M., 2008. Highly effective SNP-based association mapping and management of recessive defects in livestock. Nature Genetics, 40, 449–454. https://doi.org/10.1038/ng.96
Ciepłoch, A., Rutkowska, K., Oprządek, J. and Poławska, E., 2017. Genetic disorders in beef cattle: a review. Genes and Genomics, 39, 461–471. https://doi.org/10.1007/s13258-017-0525-8
Cole, J.B., Null, D.J. and VanRaden, P.M., 2016. Phenotypic and genetic effects of recessive haplotypes on yield, longevity, and fertility. Journal of Dairy Science, 99, 7274–7288. https://doi.org/10.3168/jds.2015-10777
Dikmen, S., Khan, F.A., Huson, H.J., Sonstegard, T.S., Moss, J.I., Dahl, G.E. and Hansen, P.J., 2014. The SLICK hair locus derived from Senepol cattle confers thermotolerance to intensively managed lactating Holstein cows. Journal of Dairy Science, 97, 5508–5520. https://doi.org/10.3168/jds.2014-8087
Drögemüller, C., Leeb, T., Harlizius, B., Tammen, I., Distl, O., Höltershinken, M., Gentile, A., Duchesne, A. and Eggen, A., 2007. Congenital syndactyly in cattle: Four novel mutations in the low density lipoprotein receptor-related protein 4 gene (LRP4). BMC Genetics, 8, 1–12. https://doi.org/10.1186/1471-2156-8-5
Duchesne, A., Gautier, M., Chadi, S., Grohs, C., Floriot, S., Gallard, Y., Caste, G., Ducos, A. and Eggen, A., 2006. Identification of a doublet missense substitution in the bovine LRP4 gene as a candidate causal mutation for syndactyly in Holstein cattle. Genomics, 88, 610–621. https://doi.org/10.1016/j.ygeno.2006.05.007
Gentile, A. and Testoni, S., 2006. Inherited disorders of cattle: a selected review. Slov vet res, 43, 17–29
Gill, J.L., James, V.M., Carta, E., Harris, D., Topf, M., Scholes, S.F.E., Hateley, G. and Harvey, R.J., 2012. Identification of congenital muscular dystonia 2 associated with an inherited GlyT2 defect in Belgian Blue cattle from the United Kingdom. Animal Genetics, 43, 267–270. https://doi.org/10.1111/j.1365-2052.2011.02255.x
Huson, H.J., Kim, E.S., Godfrey, R.W., Olson, T.A., McClure, M.C., Chase, C.C., Rizzi, R., O’Brien, A.M.P., Van Tassell, C.P., Garcia, J.F. and Sonstegard, T.S., 2014. Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle. Frontiers in Genetics, 5, 1–12. https://doi.org/10.3389/fgene.2014.00101
Johnson, E.B., Steffen, D.J., Lynch, K.W. and Herz, J., 2006. Defective splicing of Megf7/Lrp4, a regulator of distal limb development, in autosomal recessive mulefoot disease. Genomics, 88, 600–609. https://doi.org/10.1016/j.ygeno.2006.08.005
Kehrli, M.E., Schmalstieg, F.C., Anderson, D.C., Van der Maaten, M.J., Hughes, B.J., Ackermann, M.R., Wilhelmsen, C.L., Brown, G.B., Stevens, M.G. and Whetstone, C.A., 1990. Molecular definition of the bovine granulocytopathy syndrome: identification of deficiency of the Mac-1 (CD11b/CD18) glycoprotein. American journal of veterinary research, 51, 1826–1836.
Kinghorn, B. and Kinghorn, S., 2003. Pedigree viewer [Internet]. Armidale, Australia: University of New England. Available from: https://bkinghor.une.edu.au/pedigree.htm
Klungland, H., Vage, D.I., Gomez-Raya, L., Adalsteinsson, S. and Lien, S., 1995. The role of melanocyte-stimulating hormone (MSH) receptor in bovine coat color determination. Mammalian Genome, 6, 636–639. https://doi.org/10.1007/BF00352371
Kumar, A., Rout, P.K. and Roy, R., 2006. Polymorphism of β-lacto globulin gene in Indian goats and its effect on milk yield. Journal of Applied Genetics, 47, 49–53. https://doi.org/10.1007/BF03194598
Lawlor, T.J., VanRaden, P.M., Null, D., Levisee, J. and Dorshorst, B., 2014. Using haplotypes to unravel the inheritance of Holstein coat color In:, Proceedings, 10th World Congress of Genetics Applied to Livestock Production.
Martínez, A., Gama, L.T., Cañón, J., Ginja, C., Delgado, J. V, Dunner, S., Landi, V., Martín-Burriel, I., Penedo, M.C.T. and Rodellar, C., 2012a. Genetic footprints of Iberian cattle in America 500 years after the arrival of Columbus. PLoS One, 7, e49066. https://doi.org/10.1371/journal.pone.0049066
Martínez, R., Vásquez, R., Gallego, J., Gómez, Y., Moreno, F., Fernández, J., Tobon, J., Neira, J., Córdoba, S., Maldonado, J., Trujillo, L., Pedraza, A., Rocha, J., García, D., Onofre, G., Pérez, J., Cañón, J., Lucero, C., Lopera, J. and Quiceno, J., 2012b. Eficiencia productiva de la raza BON en el trópico Colombiano. Bogotá (Colombia), Electronic Material.
Meydan, H., Yildiz, M.A. and Agerholm, J.S., 2010. Screening for bovine leukocyte adhesion deficiency, deficiency of uridine monophosphate synthase, complex vertebral malformation, bovine citrullinaemia, and factor XI deficiency in Holstein cows reared in Turkey. Acta Veterinaria Scandinavica, 52, 1–8. https://doi.org/10.1186/1751-0147-52-56
Murgiano, L., Wiedemar, N., Jagannathan, V., Isling, L.K., Drögemüller, C. and Agerholm, J.S., 2015. Epidermolysa bullosa in Danish Hereford calves is caused by a deletion in LAMC2 gene. BMC Veterinary Research, 11. https://doi.org/10.1186/s12917-015-0334-8
Olson, T.A., Lucena, C., Chase, C.C. and Hammond, A.C., 2003. Evidence of a major gene influencing hair length and heat tolerance in Bos taurus cattle. Journal of Animal Science, 81, 80–90. https://doi.org/10.2527/2003.81180x
Online Mendelian Inheritance in Animals (OMIA). Sydney School of Veterinary Science, University of Sydney. MIA Number: Date last edited 2019: . World Wide Web URL: https://omia.org/
Ortega, M.S., Denicol, A.C., Cole, J.B., Null, D.J. and Hansen, P.J., 2016. Use of single nucleotide polymorphisms in candidate genes associated with daughter pregnancy rate for prediction of genetic merit for reproduction in Holstein cows. Animal Genetics, 47, 288–297. https://doi.org/10.1111/age.12420
Ortega, M.S., Denicol, A.C., Cole, J.B., Null, D.J., Taylor, J.F., Schnabel, R.D. and Hansen, P.J., 2017. Association of single nucleotide polymorphisms in candidate genes previously related to genetic variation in fertility with phenotypic measurements of reproductive function in Holstein cows. Journal of Dairy Science, 100, 3725–3734. https://doi.org/10.3168/jds.2016-12260
Pearse, M.J., Linklater, P.M., Hall, R.J. and Mackinlay, A.G., 1986. Effect of casein micelle composition and casein dephosphorylation on coagulation and syneresis. Journal of Dairy research, 53, 381–390.
Poli, M.A., Dewey, R., Semorile, L., Lozano, M.E., Albarino, G.G., Romanowski, V. and Grau, O., 1996. PCR screening for carriers of bovine leukocyte adhesion deficiency (BLAD) and uridine monophosphate synthase (DUMPS) in argentine holstein cattle. Journal of Veterinary Medicine Series A: Physiology Pathology Clinical Medicine, 43, 163–168. https://doi.org/10.1111/j.1439-0442.1996.tb00441.x
Porto-Neto, L.R., Bickhart, D.M., Landaeta-Hernandez, A.J., Utsunomiya, Y.T., Pagan, M., Jimenez, E., Hansen, P.J., Dikmen, S., Schroeder, S.G., Kim, E.S., Sun, J., Crespo, E., Amati, N., Cole, J.B., Null, D.J., Garcia, J.F., Reverter, A., Barendse, W. and Sonstegard, T.S., 2018. Convergent evolution of slick coat in cattle through truncation mutations in the prolactin receptor. Frontiers in Genetics, 9, 1–8. https://doi.org/10.3389/fgene.2018.00057
Prinzenberg, E., Krause, I. and Erhardt, G., 1999. SSCP analysis at the bovine CSN3 locus discriminates six alleles corresponding to known protein variants (A, B, C, E, F, G) and three new DNA polymorphisms (H, I, A1). Animal Biotechnology, 10, 49–62.
R Core Team, 2019. R: A Language and Environment for Statistical Computing (Vienna, Austria). https://www.r-project.org/fecha de visita diciembre 2019
Ribeiro, L.A., Baron, E.E., Martinez, M.L. and Coutinho, L.L., 2000. PCR screening and allele frequency estimation of bovine leukocyte adhesion deficiency in Holstein and Gir cattle in Brazil. Genetics and Molecular Biology, 23, 831–834. https://doi.org/10.1590/S1415-47572000000400021
Rosero, J.A., Álvarez, L.A., Muñoz, J.E., Durán, C. V and G Rodas, Á., 2012. Allelic frequency of the Kappa-Casein gene in Colombian and creole cattle breeds. Revista Colombiana de Ciencias Pecuarias, 25, 173–182.
Schmutz, S.M., Berryere, T.G., Ciobanu, D.C., Mileham, A.J., Schmidtz, B.H. and Fredholm, M., 2004. A form of albinism in cattle is caused by a tyrosinase frameshift mutation. Mammalian Genome, 15, 62–67. https://doi.org/10.1007/s00335-002-2249-5
Selvaggi, M., Laudadio, V., Dario, C. and Tufarelli, V., 2014. Investigating the genetic polymorphism of sheep milk proteins: A useful tool for dairy production. Journal of the Science of Food and Agriculture, 94, 3090–3099. https://doi.org/10.1002/jsfa.6750
Sun, D.X., Fan, X.H., Xie, Y., Chu, Q., Sun, Y., Zhang, Y., Zhang, S.L., Gong, W.J., Chen, S.H., Li, Y.H., Shi, W.H. and Zhang, Y., 2011. Short communication: Distribution of recessive genetic defect carriers in Chinese Holstein. Journal of Dairy Science, 94, 5695–5698. https://doi.org/10.3168/jds.2011-4345
Tian, R., Pitchford, W.S., Morris, C.A., Cullen, N.G. and Bottema, C.D.K., 2010. Genetic variation in the β, β-carotene-9′, 10′-dioxygenase gene and association with fat colour in bovine adipose tissue and milk. Animal Genetics, 41, 253–259. https://doi.org/10.1111/j.1365-2052.2009.01990.x
Utsunomiya, Y.T., Milanesi, M., Utsunomiya, A.T.H., Torrecilha, R.B.P., Kim, E.S., Costa, M.S., Aguiar, T.S., Schroeder, S., Do Carmo, A.S., Carvalheiro, R., Neves, H.H.R., Padula, R.C.M., Sussai, T.S., Zavarez, L.B., Cipriano, R.S., Caminhas, M.M.T., Hambrecht, G., Colli, L., Eufemi, E., Ajmone-Marsan, P., Cesana, D., Sannazaro, M., Buora, M., Morgante, M., Liu, G., Bickhart, D., Van Tassell, C.P., Sölkner, J., Sonstegard, T.S. and Garcia, J.F., 2017. A PLAG1 mutation contributed to stature recovery in modern cattle. Scientific Reports, 7, 1–15. https://doi.org/10.1038/s41598-017-17127-1
Van Vleck, L.D., and Boldman, K.G., 1993. Sequential transformation for multiple traits for estimation of (co)variance components with a derivative-free algorithm for restricted maximum likelihood. Journal of animal science, 71, 836-844. https://doi.org/10.2527/1993.714836x
VanRaden, P.M., Olson, K.M., Null, D.J. and Hutchison, J.L., 2011. Harmful recessive effects on fertility detected by absence of homozygous haplotypes. Journal of Dairy Science, 94, 6153–6161. https://doi.org/10.3168/jds.2011-4624
Yang, A., Larsen, T. and Tume, R., 1992. Carotenoid and retinol concentrations in serum, adipose tissue and liver and carotenoid transport in sheep, goats and cattle Australian. Journal of Agricultural Research, 43, 1809. https://doi.org/10.1071/ar9921809
Yang, F., Li, L., Liu, H., Cai, Y. and Wang, G., 2012. Polymorphism in the exon 4 of b-lactoglobulin variant B precursor gene and its association with milk traits and protein structure in Chinese Holstein. Molecular Biology Reports, 39, 3957–3964. https://doi.org/10.1007/s11033-011-1175-6
Zepeda-Batista, J.L., Parra-Bracamonte, G.M., Núñez-Domínguez, R., Ramírez-Valverde, R. and Ruíz-Flores, A., 2018. Screening genetic diseases prevalence in Braunvieh cattle. Tropical Animal Health and Production, 51, 25–31. https://doi.org/10.1007/s11250-018-1655-y
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We thank the managers of participating herds for supplying the information required to develop this study.
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The authors are thankful to MINCIENCIAS for financing this study (contract FP44842-015–2018), to Universidad Nacional de Colombia, Medellín campus, and Universidad Tecnológica de Pereira as co-financing and executing entities of the project, “Knowing our creole resources: genomic analysis and search for genome regions associated with productive, reproductive, and health traits in Blanco Orejinegro cattle” (code 110177658049).
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Material preparation, data collection, and analysis were performed by all authors. The first draft of the manuscript was written by Sindy Liliana Caivio-Nasner and Juan Carlos Rincón, and the other authors made their contributions to later versions of the paper.
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Caivio-Nasner, S., López-Herrera, A., González-Herrera, L.G. et al. Frequency of genotypic markers for genetic disorders, colour, polledness, and major genes in Blanco Orejinegro cattle. Trop Anim Health Prod 53, 546 (2021). https://doi.org/10.1007/s11250-021-02990-y
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DOI: https://doi.org/10.1007/s11250-021-02990-y