Population structure and genetic characterization of two native Danish sheep breeds

References

• Alexander, D. H., Novembre, J. & Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Research 19 (9), 1655–1664.
   PubMed Web of Science ®Google Scholar
• Barker, J. S. F. (2001). Conservation and management of genetic diversity: A domestic animal perspective. v. 31.
   Google Scholar
• Beynon, S. E., Slavov, G. T., Farre, M., Sunduimijid, B., Waddams, K., Davies, B., Haresign, W., Kijas J., MacLeod, I. M., Newbold, C. J., Davies, L., Larkin, D. M. (2015). Population structure and history of the Welsh sheep breeds determined by whole genome genotyping. Bmc Genetics 16, 65.
   PubMed Web of Science ®Google Scholar
• Boakes, E. H., Wang, J. & Amos, W. (2007). An investigation of inbreeding depression and purging in captive pedigreed populations. Heredity (Edinb) 98 (3), 172–182. doi:10.1038/sj.hdy.6800923.
   PubMed Web of Science ®Google Scholar
• Boettcher, P. J. & Hoffmann, I. (2009). Conserve livestock genetic resources, too. Science 326 (5951), 365. doi:10.1126/science.326_365b.
   PubMed Web of Science ®Google Scholar
• Bruford, M. W., Ginja, C., Hoffmann, I., Joost, S., Orozco-terWengel, P., Alberto, F. J., Amaral, A. J., Barbato, M., Biscarini, F., Colli, L., Costa, M., Curik, I., Duruz, S., Ferenčaković, M., Fischer, D., Fitak, R., Groeneveld, L. F., Hall, S. J. G., Hanotte, O., Hassan, F.-L., Helsen, P., Iacolina, L., Kantanen, J., Leempoel, K., Lenstra, J. A., Ajmone-Marsan, P., Masembe, C., Megens, H.-J., Miele, M., Neuditschko, M., Nicolazzi, E. L., Pompanon, F., Roosen, J., Sevane, N., Smetko, A., Štambuk, A., Streeter, I., Stucki, S., Supakorn, C., Telo Da Gama, L., Tixier-Boichard, M., Wegmann, D., Zhan, X. (2015). Prospects and challenges for the conservation of farm animal genomic resources, 2015–2025. Frontiers in Genetics 6, 314. doi:10.3389/fgene.2015.00314.
   PubMed Web of Science ®Google Scholar
• Caballero, A., Bravo, I. & Wang, J. (2017a). Inbreeding load and purging: Implications for the short-term survival and the conservation management of small populations. Heredity (Edinb) 118 (2), 177–185. doi:10.1038/hdy.2016.80.
   PubMed Web of Science ®Google Scholar
• Caballero, A., Bravo, I. & Wang, J. (2017b). The risk of forcing inbreeding in conservation programmes: A reply to Theodorou and Couvet. Heredity (Edinb) 119 (1), 51–53. doi:10.1038/hdy.2017.17.
   PubMed Web of Science ®Google Scholar
• Ciani, E., Lasagna, E., D’Andrea, M., Alloggio, I., Marroni, F., Ceccobelli, S., Bermejo, J. V. D., Sarti, F. M., Kijas, J., Lenstra, J. A., Pilla, F. (2015). Merino and Merino-derived sheep breeds: A genome-wide intercontinental study. Genetics Selection Evolution 47, 64.
   PubMed Web of Science ®Google Scholar
• Deniskova, T. E., Dotsev, A. V., Selionova, M. I., Kunz, E., Medugorac, I., Reyer, H., Wimmers, K., Barbato, M., Traspov, A. A., Brem, G., Zinovieva, N. A. (2018). Population structure and genetic diversity of 25 Russian sheep breeds based on whole-genome genotyping. Genetics Selection Evolution 50 (1), 29. doi:10.1186/s12711-018-0399-5.
   PubMedGoogle Scholar
• Dyrmundsson, O. R. & Niznikowski, R. (2010). North European short-tailed breeds of sheep: A review. Animal 4 (8), 1275–1282.
   PubMed Web of Science ®Google Scholar
• FAO. (2007). The state of the world’s animal genetic resources for food and agriculture. In B. Rischkowsky & D. Pilling (eds.). (Rome: FAO Commission on Genetic Resources for Food and Agriculture Assessments), pp. 1–511.
   Google Scholar
• FAO. (2015). The second report on the state of the World’s animal genetic resources for Food and agriculture. In B. D. Scherf & D. Pilling (eds.) (Rome: FAO Commission on Genetic Resources for Food and Agriculture Assessments), pp. 1–562.
   Google Scholar
• FAO. (2011). Domestic Animal Diversity Information System (DAD-IS). The database. http://www.fao.org/dad-is/en /.
   Google Scholar
• Farid, A., Makarechian, M. & Strobeck, C. (1987). Inbreeding under a cyclical mating system. Theoretical and Applied Genetics 73 (4), 506–515. doi:10.1007/Bf00289187.
   PubMed Web of Science ®Google Scholar
• Groeneveld, L. F., Lenstra, J. A., Eding, H., Toro, M. A., Scherf, B., Pilling, D., Negrini, R., Finlay, E. K., Jianlin, H., Groeneveld, E., Weigend, S. (2010). Genetic diversity in farm animals–a review. Animal Genetics 41 (Suppl 1), 6–31. doi:10.1111/j.1365-2052.2010.02038.x.
   PubMed Web of Science ®Google Scholar
• Hoffmann, I. (2010). Climate change and the characterization, breeding and conservation of animal genetic resources. Animal Genetics 41 (Suppl 1), 32–46. doi:10.1111/j.1365-2052.2010.02043.x.
   PubMedGoogle Scholar
• Honda, T., Nomura, T. & Mukai, F. (2004). Reduction of inbreeding in commercial females by rotational mating with several sire lines. Genetics Selection Evolution 36 (5), 509–526. doi:10.1051/gse:2004014.
   PubMed Web of Science ®Google Scholar
• Kijas, J. W., Lenstra, J. A., Hayes, B., Boitard, S., Neto, L. R. P., San Cristobal, M., Servin, B., McCulloch, R., Whan, V., Gietzen, K., Paiva, S., Barendse, W., Ciani, E., Raadsma, H., McEwan, J., Dalrymple, B., Tyler-Smith, C. (2012). Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. Plos Biology 10 (2), e1001258.
   PubMed Web of Science ®Google Scholar
• Kijas, J. W., Townley, D., Dalrymple, B. P., Heaton, M. P., Maddox, J. F., McGrath, A., Wilson, P., Ingersoll, R. G., McCulloch, R., McWilliam, S., Tang, D., McEwan, J., Cockett, N., Oddy, V. H., Nicholas, F. W., Raadsma, H., International Sheep Genomics Consortium. (2009). A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. Plos One 4 (3), e4668.
   PubMed Web of Science ®Google Scholar
• Lawson Handley, L. J., Byrne, K., Santucci, F., Townsend, S., Taylor, M., Bruford, M. W. & Hewitt, G. M. (2007). Genetic structure of European sheep breeds. Heredity 99, 620–631.
   PubMed Web of Science ®Google Scholar
• Leberg, P. L. & Firmin, B. D. (2008). Role of inbreeding depression and purging in captive breeding and restoration programmes. Molecular Ecology 17 (1), 334–343. doi:10.1111/j.1365-294X.2007.03433.x.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Lewis, R. M. & Simm, G. (2000). Selection strategies in sire referencing schemes in sheep. Livestock Production Science 67 (1–2), 129–141. doi:10.1016/S0301-6226(00)00182-2.
   Google Scholar
• McQuillan, R., Leutenegger, A. L., Abdel-Rahman, R., Franklin, C. S., Pericic, M., Barac-Lauc, L., Smolej-Narancic, N., Janicijevic, B., Polasek, O., Tenesa, A., MacLeod, A. K., Farrington, S. M., Rudan, P., Hayward, C., Vitart, V., Rudan, I., Wild, S. H., Dunlop, M. G., Wright, A. F., Campbell, H., 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.
   PubMed Web of Science ®Google Scholar
• Meadows, J. R., Hanotte, O., Drogemuller, C., Calvo, J., Godfrey, R., Coltman, D., Maddox, J. F., Marzanov, N., Kantanen, J. & Kijas, J. W. (2006). Globally dispersed Y chromosomal haplotypes in wild and domestic sheep. Animal Genetics 37 (5), 444–453. doi:10.1111/j.1365-2052.2006.01496.x.
   PubMed Web of Science ®Google Scholar
• Meuwissen, T. H. (1997). Maximizing the response of selection with a predefined rate of inbreeding. Journal of Animal Science 75 (4), 934–940. doi:10.2527/1997.754934x.
   PubMed Web of Science ®Google Scholar
• Milanesi, Marco, Capomaccio, Stefano, Vajana, Elia, Bomba, Lorenzo, Garcia, José Fernando, Ajmone-Marsan, Paolo & Colli, Licia. (2017). BITE: An R package for biodiversity analyses. BioRxiv.
   Google Scholar
• Ministry of Environment and Food of Denmark. (2016). Denmark’s report for the state of the world’s biodiversity for food and agriculture. In The Danish Agrifish Agency (Copenhagen: The Danish AgriFish Agency), pp. 1–43.
   Google Scholar
• Mukiibi, R., Rochus, C. M., Andersson, G. & Johansson, A. M. (2015). The use of endogenous retroviruses as markers to describe the genetic relationships among local Swedish sheep breeds. Animal Genetics 46 (2), 220–223. doi:10.1111/age.12264.
   PubMed Web of Science ®Google Scholar
• Nicolazzi, Ezequiel Luis, Picciolini, Matteo, Strozzi, Francesco, Schnabel, Robert David, Lawley, Cindy, Pirani, Ali, Brew, Fiona & Stella, Alessandra. (2014). SNPchimp: A database to disentangle the SNPchip jungle in bovine livestock. BMC Genomics 15, 123.
   PubMed Web of Science ®Google Scholar
• Notter, D. R. (1999). The importance of genetic diversity in livestock populations of the future. Journal of Animal Science 77 (1), 61–69. doi:10.2527/1999.77161x.
   PubMed Web of Science ®Google Scholar
• Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., Genschoreck, T., Webster, T. & Reich, D. (2012). Ancient admixture in human history. Genetics 192 (3), 1065–1093.
   PubMed Web of Science ®Google Scholar
• Patterson, N., Price, A. L. & Reich, D. (2006). Population structure and eigenanalysis. PLoS Genetics 2 (12), e190.
   PubMed Web of Science ®Google Scholar
• Peter, C., Bruford, M., Perez, T., Dalamitra, S., Hewitt, G., Erhardt, G. & Consortium, Econogene. (2007). Genetic diversity and subdivision of 57 European and Middle-Eastern sheep breeds. Animal Genetics 38 (1), 37–44. doi:10.1111/j.1365-2052.2007.01561.x.
   PubMed Web of Science ®Google Scholar
• Pickrell, J. K. & Pritchard, J. K. (2012). Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genetics 8 (11), e1002967.
   PubMed Web of Science ®Google Scholar
• Porter, V. (2002). Mason’s World Dictionary of Livestock Breeds, Types and Varieties. 5th ed. (Wallingford, UK: CABI Pub).
   Google Scholar
• Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A. & Reich, D. (2006). Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics 38 (8), 904–909.
   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. 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.
   PubMed Web of Science ®Google Scholar
• Purfield, D. C., Berry, D. P., McParland, S. & Bradley, D. G. (2012). Runs of homozygosity and population history in cattle. Bmc Genetics 13, 70.
   PubMed Web of Science ®Google Scholar
• Purfield, D. C., McParland, S., Wall, E. & Berry, D. P. (2017). The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds. Plos One 12 (5), e0176780. doi:10.1371/journal.pone.0176780.
   PubMed Web of Science ®Google Scholar
• R Core Team. (2019). R: A Language and Environment for Statistical Computing (Vienna, Austria: R Foundation for Statistical Computing).
   Google Scholar
• Reich, D., Thangaraj, K., Patterson, N., Price, A. L. & Singh, L. (2009). Reconstructing Indian population history. Nature 461 (7263), 489–494.
   PubMed Web of Science ®Google Scholar
• Sørensen, L. H., & Nielsen, V. H. (2017). Danske Husdyrgenetiske Resourcer. In DCA Rapport (Tjele: DCA – Nationalt Center for Fødevarer og Jordbrug, Aarhus University), pp. 26–30.
   Google Scholar
• Taberlet, P., Coissac, E., Pansu, J. & Pompanon, F. (2011). Conservation genetics of cattle, sheep, and goats. Comptes Rendus Biologies 334 (3), 247–254. doi:10.1016/j.crvi.2010.12.007.
   PubMed Web of Science ®Google Scholar
• Tapio, M., Marzanov, N., Ozerov, M., Cinkulov, M., Gonzarenko, G., Kiselyova, T., Murawski, M., Viinalass, H. & Kantanen, J. (2006). Sheep mitochondrial DNA variation in European, Caucasian, and Central Asian areas. Molecular Biology and Evolution 23 (9), 1776–1783. doi:10.1093/molbev/msl043.
   PubMed Web of Science ®Google Scholar
• Tapio, M., Ozerov, M., Tapio, I., Toro, M. A., Marzanov, N., Cinkulov, M., Goncharenko, G., Kiselyova, T., Murawski, M. & Kantanen, J. (2010). Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia. Bmc Genetics 11, 76.
   PubMed Web of Science ®Google Scholar
• Tapio, M., Tapio, I., Grislis, Z., Holm, L. E., Jeppsson, S., Kantanen, J., Miceikiene, I., Olsaker, I., Viinalass, H. & Eythorsdottir, E. (2005). Native breeds demonstrate high contributions to the molecular variation in Northern European sheep. Molecular Ecology 14 (13), 3951–3963.
   PubMed Web of Science ®Google Scholar
• Theodorou, K. & Couvet, D. (2015). The efficiency of close inbreeding to reduce genetic adaptation to captivity. Heredity (Edinb) 114 (1), 38–47. doi:10.1038/hdy.2014.63.
   PubMed Web of Science ®Google Scholar
• Thompson, E. A. (2013). Identity by descent: variation in meiosis, across genomes, and in populations. Genetics 194 (2), 301–326. doi:10.1534/genetics.112.148825.
   PubMed Web of Science ®Google Scholar
• Verrier, Etienne, Audiot, Annick, Bertrand, Christine, Chapuis, Hervé, Charvolin, Eléonore, Danchin-Burge, Coralie, Danvy, Sophie et al. (2015). Assessing the risk status of livestock breeds: a multi-indicator method applied to 178 French local breeds belonging to ten species. Animal Genetic Resources 57, 105–118.
   Google Scholar
• Williams, Thomas, Kelley, Colin, Campbell, John, Cunningham, Robert, Denholm, David, Elber, Gershon, Fearick, Roger et al. (2013). Gnuplot 4.6: An interactive plotting program. http://gnuplot.sourceforge.net.
   Google Scholar
• Windig, J. J. & Kaal, L. (2008). An effective rotational mating scheme for inbreeding reduction in captive populations illustrated by the rare sheep breed Kempisch Heideschaap. Animal 2 (12), 1733–1741. doi:10.1017/S1751731108003029.
   PubMed Web of Science ®Google Scholar
• Windig, J. J., Verweij, M. J. W. & Oldenbroek, J. K. (2019). Reducing inbreeding rates with a breeding circle: Theory and practice in Veluws Heideschaap. Journal of Animal Breeding and Genetics 136 (1), 51–62. doi:10.1111/jbg.12371.
   PubMed Web of Science ®Google Scholar