Genetic differentiation between subpopulations of Swedish mountain (Fjäll and Fjällnära) cattle

References

• Aleandri, R., Buitazzoni, L.G. & Schneider, J.C. (1990). The effects of milk protein polymorphisms on milk components and cheese-producing ability. J. Dairy Sci. 73, 241–255. doi: 10.3168/jds.S0022-0302(90)78667-5
   Web of Science ®Google Scholar
• Alexander, D.H., Novembre, J. & Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664. doi:10.1101/gr.094052.109.
   PubMed Web of Science ®Google Scholar
• Behr, A.A., Liu, K.Z., Liu-Fang, G., Nakka, P. & Ramachandran, S. (2016). Pong: Fast analysis and visualization of latent clusters in population genetic data. Bioinformatics 32, 2817–2823. doi:10.1093/bioinformatics/btw327.
   PubMed Web of Science ®Google Scholar
• Dennis, J.A., Healy, P.J., Beaudet, A.L. & O'Brien W.E. (1989). Molecular definition of bovine argininosuccinate synthetase deficiency. Proc. Natl. Acad. Sci. USA 86, 7947–7951. doi: 10.1073/pnas.86.20.7947
   PubMed Web of Science ®Google Scholar
• Drögemüller, C., Leeb, T., Harzelius, B., Tammen, I., Distl, O., Höltershinken, M., Gentile, A., Duchesne, A. & Eggen, A. (2007). Congenital syndactyly in cattle: Four novel mutations in the low density lipoprotein receptor-related protein 4 gene (LRP4). BMC Genetics 8, 5. doi:10.1186/1471-2156-8-5.
   PubMed Web of Science ®Google Scholar
• Eriksson, K. (1943). Hereditary Forms of Sterility in Cattle. Biological and Genetical Investigations. (Lund: Håkan Ohlssons Boktryckeri), p. 155.
   Google Scholar
• Gustavsson, F., Buitenhuis, A.J., Johansson, M., Bertelsen, H.P., Glantz, M., Poulsen, N.A., Lindmark-Månsson, H., Stålhammar, H., Larsen, L. B., Bendixen, C., Paulsson, M. & Andrén, A. (2014). Effects of breed and casein genetic variants on protein profile in milk from Swedish Red, Danish Holstein, and Danish Jersey cows. J. Dairy Sci. 97, 3866–3877. doi: 10.3168/jds.2013-7312
   PubMed Web of Science ®Google Scholar
• Jombart, T. (2008). Adegenet: A R package for the multivariate analysis of genetic markers. Bioinformatics. 24, 1403–1405. doi: 10.1093/bioinformatics/btn129
   PubMed Web of Science ®Google Scholar
• Kantanen, J., Olsaker, I., Holm, L. E., Lien, S., Vilkki, J., Brusgaard, K., Eythorsdottir, E., Danell, B. & Adalsteinsson, S. (2000). Genetic diversity and population structure f 20 north European cattle breeds. J. Hered. 91 (6), 446–457. doi: 10.1093/jhered/91.6.446
   PubMed Web of Science ®Google Scholar
• Kantanen, J., Edwards, C.J., Bradley, D.G., Viinalass, H., Thessler, S., Ivanova, Z., Kiselyova, T., Cinkulov, M., Popov, R., Stojanovic, S., Ammosov, I. & Vilkki, J. (2009). Maternal and paternal genealogy of Eurasian taurine cattle (Bos Taurus). Heredity 103, 404–415. doi: 10.1038/hdy.2009.68
   PubMed Web of Science ®Google Scholar
• Lien, S., Kantanen, J., Olsaker, I., Holm, L.-E., Eythorsdottir, E., Sandberg, K., Dalsgard, B. & Adalsteinsson, S. (1999). Comparison of milk protein allele frequencies in Nordic cattle breeds. Anim. Genet. 30, 85–91. doi: 10.1046/j.1365-2052.1999.00434.x
   PubMed Web of Science ®Google Scholar
• Pembleton, L.W., Cogan, N.O.I. & Forster, J.W. (2013) StAMPP: An R package for calculation of genetic differentiation and structure of mixed-ploidy level populations. Mol. Ecol. Resour. 13, 946–952. doi:10.1111/1755-0998.12129.
   PubMed Web of Science ®Google Scholar
• Poulsen, N.A., Glantz, M., Rosengaard, A.K., Paulsson, M. & Larsen, L.B. (2017). Comparison of milk protein composition and rennet coagulation properties in native Swedish dairy cow breeds and high-yielding Swedish Red cows. J. Dairy Sci. 100, 8722–8734. doi: 10.3168/jds.2017-12920
   PubMed Web of Science ®Google Scholar
• Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A.R., Bender, D., Maller, J., Sklar, P., de Bakker, P.I., Daly, M.J. & Sham, P.C. (2007). PLINK: A tool set for whole-genome association and population-based linkage analyses. Am. J. Hu. Gene. 81, 559–575. doi: 10.1086/519795
   PubMed Web of Science ®Google Scholar
• R Core Team (2013). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing (Vienna, Austria). Available at: http://www.R-project.org/.
   Google Scholar
• Schaar, J., Hansson, B. & Pettersson, H.E. (1985). Effects of genetic variants of κ-casein and β-lactoglobulin on cheesemaking. J. Dairy Res. 52, 429–437. doi: 10.1017/S002202990002433X
   Web of Science ®Google Scholar
• Schliep K.P. (2011). Phangorn: Phylogenetic analysis in R. Bioinformatics 27, 592–593. doi:10.1093/bioinformatics/btq706.
   PubMed Web of Science ®Google Scholar
• Schwenger, B., Tammen, I. & Aurich, C. (1994). Detection of homozygous recessive genotype for deficiency of uridine monophosphate synthase by DNA typing among bovine embryos produced in vitro. J. Reprod. Fertil. 100, 511–514. doi: 10.1530/jrf.0.1000511
   PubMedGoogle Scholar
• Settergren, I. (1964). The Ovarian Morphology in Clinical Bovine Gonadal Hypoplasia with Some Aspects of its Endogrine Relations (Stockholm: Stockh Almqvist Wiksells), p. 108.
   Google Scholar
• Shuster, D.E., Kehrli, M.E. Jr., Ackermann, M.R. & Gilbert, R.O. (1992). Identification and prevalence of a genetic defect that causes leukocyte adhesion deficiency in Holstein cattle. Proc. Natl. Acad. Sci. U.S.A. 89, 9225–9229.
   Google Scholar
• Svensk Fjällrasavel. (2019). Available at September 2019 http://www.fjallko.se/mjolkkaseiner/ostkaseiner
   Google Scholar
• Tapio, I., Värv, S., Bennewitz, J., Maleviciute, J., Fimland, E., Grislis, Z., Meuwissen, T.H.E., Miceikiene, I., Olsaker, I., Viinalass, H., Vilkki, J. & Kantanen, J. (2006). Prioritization for conservation of northern European cattle breeds based on analysis of microsatellite data. Conserv. Biol. 20, 1768–1779. doi: 10.1111/j.1523-1739.2006.00488.x
   PubMed Web of Science ®Google Scholar
• Upadhyay, M., Eriksson, S., Mikko, S., Strandberg, E., Stålhammar, H., Groenen, M.A.M., Crooijmans, R.P.M.A., Andersson, G. & Johansson, A.M. (2019). Genomic relatedness and diversity of Swedish native cattle breeds. Genet. Sel. Evol. 51, 56. doi: 10.1186/s12711-019-0496-0
   PubMed Web of Science ®Google Scholar
• Växa Sverige. (2019). Cattle Statistics 2019. 39. Available at September 2019 https://www.vxa.se/globalassets/dokument/statistik/husdjursstatistik-2019.pdf
   Google Scholar
• Venhoranta, H., Pausch, H., Wysocki, M., Szczerbal, I., Hänninen, R., Taponen, J., Uimari, P., Flisikowski, K., Lohi, H., Fries, R., Switonski, M. & Andersson, M. (2013). Ectopic KIT copy number variation underlies impaired migration of primordial germ cells associated with gonadal hypoplasia in cattle (Bos Taurus). PLoS ONE 8(9), e75659. doi: 10.1371/journal.pone.0075659
   PubMed Web of Science ®Google Scholar
• Wang, X., Maltecca, C., Tal-Stein, R., Lipkin, E. & Khatib, H. (2008). Association of bovine fibroblast growth factor 2 (FGF2) gene with milk fat and productive life: an example of the ability of the candidate pathway strategy to identify quantitative trait genes. J. Dairy Sci. 91(6), 2475–2480. doi: 10.3168/jds.2007-0877
   PubMed Web of Science ®Google Scholar
• Wedholm, A., Larsen, L.B., Lindmark Månsson, H., Karlsson, A.H. & Andrén, A. (2006). Effect of protein composition on the cheese-making properties of milk from individual dairy cows. J. Dairy Sci. 89, 3296–3305. doi: 10.3168/jds.S0022-0302(06)72366-9
   PubMed Web of Science ®Google Scholar
• Zheng, X., Levine, D., Shen, J., Gogarten, S.M., Laurie, C. & Weir, B.S. (2012).A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 28, 3326–3328. doi: 10.1093/bioinformatics/bts606
   PubMed Web of Science ®Google Scholar
• Zheng, X., Gogarten, S.M., Lawrence, M., Stilp, A., Conomos, M.P., Weir, B.S., eLaurie, C. & Levine, D. (2017). Seqarray – a storage-efficient high-performance data format for WGS variant calls. Bioinformatics 33, 2251–2257. doi: 10.1093/bioinformatics/btx145
   PubMed Web of Science ®Google Scholar