UDC 636.32/.38:575.113:577.2.08:51-76

doi: 10.15389/agrobiology.2015.6.746eng

The equipment of Bioresources and Bioengineering Center of L.K. Ernst All-Russian Research Institute of Animal Husbandry was used.
Supported by the Russian Science Foundation, project № 14-36-00039


T.E. Deniskova1, A.V. Dotsev1, E.A. Gladyr’1, A.A. Sermyagin1,
V.A. Bagirov1, U.V. Hompodoeva1, 2, A.N. Il’in1, 2, G. Brem1, 3,
N.A. Zinovieva1

1L.K. Ernst All-Russian Research Institute of Animal Husbandry, Federal Agency of Scientific Organizations,
pos. Dubrovitsy, Podolsk Region, Moscow Province, 142132 Russia,
e-mail tandeniss@rambler.ru;
2Yakutsk Research Institute of Agriculture, Federal Agency of Scientific Organizations, 23/1, ul. Bestuzheva-Marlynskogo, Yakutsk, Sakha Republic, 677001 Russia;
3Institut für Tierzucht und Genetik, VMU (University of Veterinary Medicine), Veterinärplatz, A-1210, Vienna, Austria,
e-mail gottfried.brem@agrobiogen.de

Received September 20, 2015

Creating panels for parentage assignment based on the most informative SNPs (minor allele frequency, MAF≥ 0.3) is an important problem of the modern sheep breeding. International Society of Animal Genetics (ISAG) recommends the parentage panel consisting of 88 autosomal SNPs, developed by the International Sheep Genomics Consortium. However, selection of SNPs, which were included into the panel, was performed on the base of DNA profiles of North American, Australian and New Zealand sheep. There were no Russian breeds in these researches, and the possibility of applying ISAG panel to parentage testing of these sheep must be studied. We have performed the whole genome SNP study in four local Russian sheep breeds — Romanov (ROM, n = 22), Baikal’s fine-fleeced (ZBL, n = 7), Buryat sheep Buubey (BUB, n = 15), and Tuvan short fat tailed (TUV, n = 16) using Ovine SNP50k BeadChip. Data were processed for the total number of markers (54241 SNPs) and for 88 autosomal SNPs, recommended by ISAG. We estimated percentage of markers with MAF ≥ 0.3, mean MAF value, probability of identity (PI) and probabilities exclusion (P1, P2, P3) to evaluate the power of parentage panel for each of single breed and for entire sample. The universality of the panel was evaluated by comparing the degree of genetic differentiation of breeds based on the study of the entire number of SNPs and panel ISAG. For this purpose, we took in account such criteria as pairwise values of Fst (AMOVA) and results of principal component analysis (PCA-plot). We did summary statistics in Plink 1.09 and GenAlEx 6.5. After the quality control of the entire sample, we selected 47385 SNPs with mean MAF of 0.292±0.131 for the further analysis. The mean MAF for 88 parentage SNPs was 0.380±0.091. Analysis of the SNPs’ distribution depending on theirs MAF showed that most of the SNPs (81.8 %) were informative (MAF≥ 0.3). Proportion of informative SNPs differed between breeds and was 56.8 % in ROM, 63.4 % in ZBL, 71.6 % in BUB and 72.7 % in TUV. Twenty-one SNPs (23.9 %) were highly informative in all four breeds, while 37 SNPs (42.0 %), 17 SNPs (19.3 %) and 10 SNPs (11.4 %) were informative, respectively, in three, two or only one breed. Marker DU196132_525.1 was monomorphic in TUV (MAF = 0). Three SNPs with MAF < 0.3 (DU232924_365.1, DU501115_497.1 and DU372582_268.1) were not informative for all four breeds. Lower pairwise values of Fst based on 88 SNPs with the same character of genetic relations compared with those using whole genome SNP profiles shown high flexibility of ISAG panel. PCA confirmed the low breed’s dependence of SNP panel by creating purely consolidated overlapping areas corresponding to different breeds. The probability of identity for 88 SNPs ranged from 4.32×10-33 in TUV to 7.48×10-33 in BUB. Probability of exclusion was P1 ≥ 99.99 % for all four breeds. The value of P2 was the highest in TUV (P2 ≥ 99.99 %) with P2 ≥ 99.98 % for others. The value of P3 was 99.9 % for all breeds. Instead of some breed-dependent character of DNA profiles of 88 autosomal SNPs, our results confirmed the possibility of applying of ISAG panel for parentage testing in four local Russian sheep breeds.

Keywords: SNP genotyping, local sheep`s breeds, MAF, ISAG panel, parentage assignment in sheep.


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  1. Dodds K.G., Tate M.L., Sise J.A. Genetic evaluation using parentage information from genetic markers. J. Anim. Sci., 2005, 83: 2271-2279.
  2. Zinovieva N.A., Kharzinova V.R., Sizareva E.I., Gladyr' E.A., Kostyunina O.V., Lugovoi S.I., Tapikha V.A., Gamko L.N., Ovseenko E.V., Shavyrina K.M., Ernst L.K. Sel'skokhozyaistvennaya biologiya [Agricultural Biology], 2012, 6: 35-42 CrossRef, CrossRef
  3. Tautz D., Renz M. Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucl. Acids Res., 1984, 12: 4127-4138 CrossRef
  4. Dakin E.E., Avise J.C. Microsatellite null alleles in parentage analysis. Heredity, 2004, 93: 504-509 CrossRef
  5. Zinovieva N.A., Kharzinova V.R., Logvinova T.I., Gladyr' E.A., Sizareva E.I., Chinarov Yu.I. Sel'skokhozyaistvennaya biologiya [Agricultural Biology], 2011, 6: 47-53.
  6. Novgorodova I.P., Volkova V.V., Gladyr' E.A., Selionova M.I., Rastovarov E.I., Fisinin V.I., Zinovieva N.A. Dostizheniya nauki i tekhniki APK, 2011, 10: 66-67.
  7. Kiseleva T.Yu., Podoba B.E., Zabludovskii E.E., Terletskii V.P., Vorob'ev N.I., Kantanen Yu. Sel'skokhozyaistvennaya biologiya [Agricultural Biology], 2010, 6: 20-25.
  8. Khlestkina E.K. Vavilovskii zhurnal genetiki i selektsii, 2013, 17(4/2): 1044-1054.
  9. Werner F.A., Durstewitz G., Habermann F.A., Thaller G., Kramer W., Kollers S., Buitkamp J., Georges M., Brem G., Mosner J., Fries R. Detection and characterization of SNPs useful for identity control and parentage testing in major European dairy breeds. Anim. Genet., 2004, 35: 44-49 CrossRef
  10. 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. A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PLoS ONE, 2009, 4: e4668 CrossRef
  11. Hayes B.J. Technical note: Efficient parentage assignment and pedigree reconstruction with dense single nucleotide polymorphism data. J. Dairy Sci., 2011, 94: 2114-2117 CrossRef
  12. Clarke S.M., Henry H.M., Dodds K.G., Jowett T.W.D., Manley T.R., Anderson R.M., McEwan J.C. A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep. PLoS ONE, 2014, 9(4): e93392 CrossRef
  13. Heaton M.P., Leymaster K.A., Kalbfleisch T.S., Kijas J.W., Clarke S.M., McEwan J., Maddox J.F., Basnayake V., Petrik D.T., Simpson B., Smith T.P.L., Chitko-McKown C.G., the International Sheep Genomics Consortium. SNPs for parentage testing and traceability in globally diverse breeds of sheep. PLoS ONE, 2014, 9(4): e94851 CrossRef
  14. Gill P. An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes. Int. J. Legal Med., 2001, 114: 204-210 CrossRef
  15. Li L., Li C.-T., Li R.-Y., Liu Y., Lin Y. SNP genotyping by multiplex amplification and microarrays assay for forensic application. Forensic Sci. Int., 2006, 162: 74-79 CrossRef
  16. Rohrer G.A., Freking B.A., Nonneman D. Single nucleotide polymorphisms for pig identification and parentage exclusion. Anim. Genet., 2007, 38(3): 253-258 CrossRef
  17. Heaton M.P., Harhay G.P., Bennett G.L., Stone R.T., Grosse W.M., Casas E., Keele J.W., Smith T.P.L., Chitko-McKown C.G.,  Laegreid W.W. Selection and use of SNP markers for animal identification and paternity analysis in U.S. beef cattle. Mammalian Genome, 2002, 13: 272-281 CrossRef
  18. Fisher P.J., Malthus B., Walker M.C., Corbett G., Spelman R.J. The number of single nucleotide polymorphisms and on-farm data required for whole-herd parentage testing in dairy cattle herds. J. Dairy Sci., 2009, 92: 369-374 CrossRef
  19. Dodds K.G. The number of markers required for parentage assignment. Proc. Association for the Advancement of Animal Breeding and Genetic. Melbourne, Victoria, Australia, 2003, 15: 39-42.
  20. Jones A.G., Small C.M., Paczolt K.A., Ratterman N.L. A practical guide to methods of parentage analysis. Molecular Ecology Resources, 2010, 10: 6-30 CrossRef
  21. Jones A.G., Ardren W.R. Methods of parentage analysis in natural populations. Mol. Ecol., 2003, 12: 2511-2523 CrossRef
  22. Chakraborty R., Stivers D.N. Paternity exclusion by DNA markers: effects of paternal mutations. J. Forensic Sci., 1996, 41: 671-677 CrossRef.
  23. Kijas J.W., Lenstra J.A., Hayes B., Boitard S., Porto Neto L.R., San Cristobal M., Servin B., McCulloch R., Whan V., Gietzen K., Paiva S., Barendse W., Ciani E., Raadsma H., McEwan J., Dalrymple B. Genome wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS ONE, 2012, 10: e1001258 CrossRef
  24. Consortium ISG (2013) ISGC SNP Loci for Parentage Assignment (http://www.sheephap-map.org/news/parentage_page.php, http://sheephapmap.org/news/89_CorePanel.pdf).
  25. Bell A., Henshall J., Gill S., Gore K., Kijas J. Success rates of commercial SNP based parentage assignment in sheep. Proc. 20th Biennial Conference of the Association for the Advancement of Animal Breeding and Genetics 2013 /N.L. Villalobos (ed.). Napier, New Zealand, 2013: 278-282.
  26. ISAG (2012) (http://www.isag.us/Docs/AppGenSheepGoat2012.pdf).
  27. Kijas J.W., McEwan J., Clarke S., Henry H., Maddox J., McCulloch R., Driver F., Ilic K., Heaton M. Development of a SNP Panel for Parentage Assignment in Sheep. International Sheep Genomics Consortium, 2012 (http://sheep-hapmap.org/news/PAG_2012_ParentagePoster.pdf).
  28. Weir B.S., Cockerham C.C. Estimating F-statistics for the analysis of population structure. Evolution, 1984, 38: 1358-1370.
  29. 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. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet., 2007, 81: 559-575 CrossRef
  30. R Development Core Team. R: A language and environment for statistical computing. 2009. R Foundation for statistical computing. Vienna, Austria, 2005 (ISBN 3-900051-07-0) (http://www.Rproject.org).
  31. Waits L.P., Luikart G., Taberlet P. Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol. Ecol., 2001, 10: 249-256 CrossRef
  32. Jamieson A. The effectiveness of using co-dominant polymorphic allelic series for (1) checking pedigrees and (2) distinguishing full-sib pair members (in Festschrift in Honour of Dr Clyde J. Stormont). Anim. Genet., 1994, 25(Suppl. 1): 37-44.
  33. Jamieson A., Taylor S.C.S. Comparisons of three probability formulae for parentage exclusion. Anim. Genet., 1997, 28: 397-400 CrossRef
  34. Peakall R., Smouse P.E. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research — an update. Bioinformatics, 2012, 28: 2537-2539 CrossRef
  35. Baruch E., Weller J.I. Estimation of the number of SNP genetic markers required for parentage verification. Anim. Genet., 2008, 39: 474-479 CrossRef