Use of SNPs from Illumina BovineSNP50K BeadChip v3 for imputation of microsatellite alleles for parentage verification and QTL reporting
The present study aimed to test the possibility of avoiding expensive retesting of the whole parental generation for single nucleotide polymorphisms (SNPs), to provide additional analysis of microsatellites in offspring in the transitional period and to analyse the likelihood of imputation of the International Society for Animal Genetics-recommended microsatellite markers from selected SNPs. The imputation and pedigree verification of 9 520 animals (representing 84 dairy bulls, 285 dairy cows, 3 202 beef bulls and 5 949 beef cows) were analysed by the method using 9 410 SNP haplotypes (incorporating an average of 73 SNPs per haplotype). The imputation method was confirmed to allow the parentage verification of up to 87% of the analysed animals without the need for retesting. The most problematic locus was TGLA53, with only 78% successful imputation. Seven loci (BM2113, ETH225, TGLA227, BM1824, SPS115, TGLA122 and TGLA126) had more than 90% imputing accuracy and success of imputation. The success of imputation also depends on the breed and the call rate of the test results. The highest imputation accuracy was found for the Holstein breed; the other six breeds had over 90% successful imputation rates, four breeds had imputation rates between 85.0 and 89.9%, and ten breeds (rarely bred in the Czech Republic) had imputation rates below 85.0%. A call rate of SNP tests lower than 90% indicates problems with haplotype construction and thus deterioration in the success of imputation. The analysis of a possibility of using all possible information from Illumina BovineSNP50K BeadChip v3 showed 109 SNPs encoding 51 quantitative trait loci markers. Haplotypes were designed for interpretation of the most important markers for diseases, exterior and performance. The most important markers for Holstein breeders were chosen as kappa- (variants A, B and E) and beta-casein (variants A1, A2), Holstein haplotypes affecting fertility (HH1, HH3, and HH4) and loci causing genetic defects, bovine leukocyte adhesion deficiency and deficiency of uridine monophosphate synthetase. The results estimated from bovine bead chips corresponded to the expected distribution of the incidence of these traits in the population and were verified by PCR-RFLP tests.
Allen AR, Talyor M, McKeown B, Curry AI, Lavery JF, Mitchell A, Hartshorne D, Fries R, Skuce RA. Compilation of a panel of informative single nucleotide polymorphisms for bovine identification in the Northern Irish cattle population. BMC Genet. 2010 Jan 25;11(1): [8 p.]. https://doi.org/10.1186/1471-2156-11-5
Barroso A, Dunner S, Canon J. Detection of bovine kappa-casein variants A, B, C, and E by means of polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). J Anim Sci. 1998 Jun;76(6):1535-8. https://doi.org/10.2527/1998.7661535x
Baruch E, Weller JI. Estimation of the number of SNP genetic markers required for parentage verification. Anim Genet. 2008 Oct;39(5):474-9. https://doi.org/10.1111/j.1365-2052.2008.01754.x
Bezdicek J. Allele and genotype frequencies of milk protein kappa-casein (CSN3) in artificial insemination bulls of Czech Fleckvieh and Holstein breed. Acta Univ Agric et Silvic Mendelianae Brun. 2007;5:17-22. https://doi.org/10.11118/actaun200755050017
Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 2007 Nov;81(5):1084-97. https://doi.org/10.1086/521987
Davis GP, Denise SK. The impact of genetic markers on selection. J Anim Sci. 1998 Sep 1;76(9):2331-9. https://doi.org/10.2527/1998.7692331x
Fernandez ME, Goszczynski DE, Liron JP, Villegas-Castagnasso EE, Carino MH, Ripoli MV, Rogberg-Munoz A, Posik DM, Garcia P, Giovambattista G. Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd. Genet Mol Biol. 2013 Sep;36(2):185-91. https://doi.org/10.1590/S1415-47572013000200008
Gomez-Raya L, Priest K, Rauw WM, Okomo-Adhiambo M, Thain D, Bruce B, Rink A, Torell R, Grellman L, Narayanan R, Beattie CW. The value of DNA paternity identification in beef cattle: Examples from Nevada’s free-range ranches. J Anim Sci. 2008 Jan;86(1):17-24. https://doi.org/10.2527/jas.2007-0068
ISAG – International Society for Animal Genetics. Cattle molecular markers and parentage testing workshop [Internet]. Edinburgh, Scotland; 2010 July 28 [cited 2020]. Available from: http://www.isag.us/Docs/CattleMMPTest_CT.pdf.
Jaiswal KP. PCR based genotyping of cross breed cattle for A1,A2 beta casein types [master’s thesis]. [Karnal, India]: National Dairy Research Institute; 2012. 67 p.
Kaminski S, Cieslinska A, Kostyra E. Polymorphism of bovine beta-casein and its potential effect on human health. J Appl Genet. 2007 Sep 1;48(3):189-98. https://doi.org/10.1007/BF03195213
Manga I, Dvorak J. TaqMan allelic discrimination assay for A1 and A2 alleles of the bovine CSN2 gene. Czech J Anim Sci. 2010 Aug 19;55(8):307-12. https://doi.org/10.17221/89/2009-CJAS
McClure M, Sonstegard T, Wiggans G, Van Tassell CP. Imputation of microsatellite alleles from dense SNP genotypes for parental verification. Front Genet. 2012 Aug 14;3: [9 p.]. https://doi.org/10.3389/fgene.2012.00140
McClure M, Sonstegard T, Wiggans G, Van Eenennaam A, Weber K, Penedo MC, Berry D, Flynn J, Garcia JF, Carmo A, Regitano L, Albuquerque M, Silva M, Machado M, Coffey M, Moore K, Boscher MY, Genestout L, Mazza R, Taylor J, Schnabel R, Simpson B, Marques E, McEwan J, Cromie A, Coutinho L, Kuehn L, Keele J, Piper E, Cook J, Williams R, Van Tassell C. Imputation of microsatellite alleles from dense SNP genotypes for parentage verification Gross multiple Bos taurus and Bos Indicus breed. Front Genet. 2013 Sep 18;4: [11 p.]. https://doi.org/10.3389/fgene.2013.00176
McLachlan CNS, inventor; A2 Corporation Limited, assignee. Breeding and milking cows for milk free of β-casein A1, United States patent US 7,094,949 B2. 2006 Aug 22.
Rincon G, Weber KL, Eenennaam AL, Golden BL, Medrano JF. Hot topic: Performance of bovine high-density genotyping platforms in Holsteins and Jerseys. J Dairy Sci. 2011 Dec;94(12):6116-21. https://doi.org/10.3168/jds.2011-4764
Schroffelova D, Nemcova L, Hromadkova J, Kucera J, Lipovsky D, Steiger V, Pribanova M. Optimalizace odberu alternativnich biologickych vzorku pro navaznou kvalitni izolaci genomicke DNA [Optimalization of alternative biologic samples collection for consequent DNA isolation] [certificated methodology]. Prague: CMSCH a.s.; 2018. 19 p. Czech.
Sharma A, Park JE, Park B, Park MN, Roh SH, Jung WY, Lee SH, Chai HH, Chang GW, Cho YM, Lim D. Accuracy of imputation of microsatellite markers from BovineSNP50 and BovineHD BeadChip in Hanwoo population of Korea. Genomics Inform. 2018 Mar;16(1):10-3. https://doi.org/10.5808/GI.2018.16.1.10