Polymorphic SNPs were identified using BovineSNP50 BeadChip in three groups of cervids: farmed Red deer (n = 3), and free range Red deer (n = 5) and Fallow deer (n = 2). From the total of 54 609 SNPs, 53.85% could be genotyped. Out of 28 502 successfully genotyped autosomal SNPs only 5.3% were polymorphic. The average minor allele frequency within cervids was 0.23 (number of polymorphic SNPs ranged from 467 to 686). Results of the molecular variance analysis showed that 67.38% of variation occurred within individuals and the rest was explained by a species difference (FST = 0.32). The value of FIT (0.33) indicated a higher proportion of homozygote genotypes in the analyzed dataset. Pairwise FST values showed very clearly the genetic differentiation between Red and Fallow deer which ranged from 0.06 (farmed and free range deer) to 0.74 (farmed Red and Fallow deer). A similar result was found for Nei’s genetic distances that ranged from 0.01 (among Fallow deer) to 0.79 (among farmed Red and Fallow deer). The genetic differentiation of the analyzed cervid species was evaluated also by the principal component analysis with the involvement of 6 other species from the family Cervidae, which showed a division of the Cervidae cluster into 7 subpopulations. The panels of SNPs primarily produced for a model species are becoming the marker of choice for the application in other species, but the best methods of their discovery, validation, and genotyping in non-model species need further investigations.
Albrechtsen A., Nielsen F. C., Nielsen R. (): Ascertainment Biases in SNP Chips Affect Measures of Population Divergence. Molecular Biology and Evolution, 27, 2534-2547 https://doi.org/10.1093/molbev/msq148
Bixley M.J., Ward J.F., Brauning R., Archer J.A., Fisher P.J. (2009): Building a deer SNP chip. Proceedings of the Association for the Advancement of Animal Breeding and Genetics, 18, 300–303.
Cooper T.A., Wiggans G.R., VanRaden P.M. (2013): Short communication: Relationship of call rate and accuracy of single nucleotide polymorphism genotypes in dairy cattle1. Journal of Dairy Science, 96, 3336-3339 https://doi.org/10.3168/jds.2012-6208
Decker J. E., Pires J. C., Conant G. C., McKay S. D., Heaton M. P., Chen K., Cooper A., Vilkki J., Seabury C. M., Caetano A. R., Johnson G. S., Brenneman R. A., Hanotte O., Eggert L. S., Wiener P., Kim J.-J., Kim K. S., Sonstegard T. S., Van Tassell C. P., Neibergs H. L., McEwan J. C., Brauning R., Coutinho L. L., Babar M. E., Wilson G. A., McClure M. C., Rolf M. M., Kim J., Schnabel R. D., Taylor J. F. (): Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proceedings of the National Academy of Sciences, 106, 18644-18649 https://doi.org/10.1073/pnas.0904691106
Hassanin Alexandre, Douzery Emmanuel J. P. (2003): Molecular and Morphological Phylogenies of Ruminantia and the Alternative Position of the Moschidae. Systematic Biology, 52, 206-228 https://doi.org/10.1080/10635150390192726
HAUSER LORENZ, BAIRD MELISSA, HILBORN RAY, SEEB LISA W., SEEB JAMES E. (2011): An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon ( Oncorhynchus nerka
) population. Molecular Ecology Resources, 11, 150-161 https://doi.org/10.1111/j.1755-0998.2010.02961.x
Haynes G.D., Latch E.K. (2012): Identification of novel single nucleotide polymorphisms (SNPs) in deer (Odocoileus spp.) using the BovineSNP50 BeadChip. PLoS One, 7, e36536.
HELYAR S. J., HEMMER-HANSEN J., BEKKEVOLD D., TAYLOR M. I., OGDEN R., LIMBORG M. T., CARIANI A., MAES G. E., DIOPERE E., CARVALHO G. R., NIELSEN E. E. (2011): Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Molecular Ecology Resources, 11, 123-136 https://doi.org/10.1111/j.1755-0998.2010.02943.x
Lepoittevin C., Frigerio J.M., Garnier-Gere P., Salin F., Cervera M.T., Vornam B., Harvengt L., Plomin C. (2010): In vitro vs in silico detected SNPs for the development of a genotyping array: What can we learn from a non-model species? PLoS One, 5, e11034.
Lewontin R.C. (1964): The interaction of selection and linkage. I. General considerations; heterotic models. Genetics, 49, 49–67.
MANEL STÉPHANIE, JOOST STÉPHANE, EPPERSON BRYAN K., HOLDEREGGER ROLF, STORFER ANDREW, ROSENBERG MICHAEL S., SCRIBNER KIM T., BONIN AURÉLIE, FORTIN MARIE-JOSÉE (2010): Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Molecular Ecology, 19, 3760-3772 https://doi.org/10.1111/j.1365-294X.2010.04717.x
Michelizzi Vanessa N. (): A Global View of 54,001 Single Nucleotide Polymorphisms (SNPs) on the Illumina BovineSNP50 BeadChip and Their Transferability to Water Buffalo. International Journal of Biological Sciences, , 18-27 https://doi.org/10.7150/ijbs.7.18
MILLER J.M., POISSANT J., KIJAS J.W., COLTMAN D.W. (2011): A genome-wide set of SNPs detects population substructure and long range linkage disequilibrium in wild sheep. Molecular Ecology Resources, 11, 314-322 https://doi.org/10.1111/j.1755-0998.2010.02918.x
Miller J. M., Kijas J. W., Heaton M. P., McEwan J. C., Coltman D. W. (2012): Consistent divergence times and allele sharing measured from cross-species application of SNP chips developed for three domestic species. Molecular Ecology Resources, 12, 1145-1150 https://doi.org/10.1111/1755-0998.12017
Morin Phillip A., Luikart Gordon, Wayne Robert K., the SNP workshop group (2004): SNPs in ecology, evolution and conservation. Trends in Ecology & Evolution, 19, 208-216 https://doi.org/10.1016/j.tree.2004.01.009
Nei M. (1982): Evolution of human races at the gene level. In: Bonne-Tamir B. (ed.): Human Genetics, Part A: The Unfolding Genome. Alan R. Liss, New York, USA, 167–181.
SEEB J. E., CARVALHO G., HAUSER L., NAISH K., ROBERTS S., SEEB L. W. (2011): Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Molecular Ecology Resources, 11, 1-8 https://doi.org/10.1111/j.1755-0998.2010.02979.x
VASEMÄGI A., PRIMMER C. R. (2005): Challenges for identifying functionally important genetic variation: the promise of combining complementary research strategies. Molecular Ecology, 14, 3623-3642 https://doi.org/10.1111/j.1365-294X.2005.02690.x
Williams Larissa M, Ma Xin, Boyko Adam R, Bustamante Carlos D, Oleksiak Marjorie F (2010): SNP identification, verification, and utility for population genetics in a non-model genus. BMC Genetics, 11, 32- https://doi.org/10.1186/1471-2156-11-32
Wu Jun Jing, Song Li Jun, Wu Fang Jie, Liang Xian Wei, Yang Bing Zhuang, Wathes D. Claire, Pollott Geoff E., Cheng Zhangrui, Shi De Shun, Liu Qing You, Yang Li Guo, Zhang Shu Jun (2013): Investigation of transferability of BovineSNP50 BeadChip from cattle to water buffalo for genome wide association study. Molecular Biology Reports, 40, 743-750 https://doi.org/10.1007/s11033-012-1932-1
Zheng X. (2013): A Tutorial for the R Package SNPRelate. University of Washington, Washington, USA.