Sel’skokhozyaistvennaya Biologiya [Agricultural Biology], 2015, V. 50, № 6, pp. 746-755.

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

doi: 10.15389/agrobiology.2015.6.746eng

Acknowledgements:
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

VALIDATION OF THE SNP PANEL FOR PARENTAGE ASSIGNMENT
IN LOCAL RUSSIAN SHEEP BREEDS

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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