DNA PANEL DESIGN FOR GENOMIC STUDIES IN RUSSIAN CATTLE BREEDS

A panel of 96 DNA samples that reflects the breadth of genetic diversity in popular Russian cattle breeds has been designed. The panel of cattle DNA contains 11 dairy breeds and 6 beef and beef-dairy breeds. The numbers of animals in each breed group vary from 4 to 8. The main criterion for selection of individual animals within each breed is to maximize the total number of unshared haploid genomes according to pedigree data. The resulting panel is equivalent to USDA MARC Beef Cattle Diversity Panel version 2.1 in the power of SNP identification (number of unshared haploid genomes = 186,1, minimum allele frequency required for its detection with 95 % probability – 1,6 %). Analysis of three SNPs shows an insignificant difference between the allele frequencies in Galloway, Hereford, Grey Ukrainian, and Black Pied herds and those in the panel. Thus, the diversity panel may be useful for identification of genetic markers associated with economically important traits in cattle, evaluation of purebred and crossbred animals, and, probably, for tentative estimation of allele frequencies in commercial populations.

1. Агросервер. Мясные породы КРС. 2014. http://www.agroserver.ru/articles/178.htm.

2. Алтухов Ю.П., Салменкова Е.А., Курбатова О.Л. и др. Динамика популяционных генофондов при антропогенных воздействиях. М.: Наука, 2004. 620 с.

3. Сивкин Н.В., Стрекозов Н.И., Чинаров В.И. Молочные породы крупного рогатого скота: племенные ресурсы // Молочн. пром-сть. 2011. № 6. С. 62–64.

4. Столповский Ю.А., Ахани Азари М., Кол Н.В. и др. Дифференциация генофонда пород крупного рогатого скота по ISSR-PCR-маркерам // Изв. ТСХА. 2009. № 3. С. 89–97.

5. Юдин Н.С., Нефедова М.В., Кобзев В.Ф. и др. Полиморфизм второго интрона гена SDF1 у галловейской, герефордской и черно-пестрой пород крупного рогатого скота // Генетика. 2011. Т. 47. № 2. С. 279–283.

6. Bovine HapMap Consortium, Gibbs R.A., Taylor J.F. et al. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds // Science. 2009. V. 324. No. 5926. P. 528–532.

7. Database of Single Nucleotide Polymorphisms (dbSNP). Bethesda (MD): National Center for Biotechnology Information, National Library of Medicine. 2014. available at http://www.ncbi.nlm.nih.gov/SNP/

8. Gibson G. Rare and common variants: twenty arguments // Nat. Rev. Genet. 2012. V. 13. No. 2. P. 135–145.

9. Hayes B.J., Bowman P.J., Chamberlain A.J., Goddard M.E. Invited review: Genomic selection in dairy cattle: progress and challenges // J. Dairy Sci. 2009. V. 92. No. 2. P. 433–443.

10. Heaton M.P., Chitko-McKnown C.G., Grosse W.M. et al. Interleukin-8 haplotype structure from nucleotide sequence variation in commercial populations of U.S. beef cattle // Mamm. Genome. 2001. V. 12. No. 3. P. 219–226.

11. Heaton M.P., Harhay G.P., Bennett G.L. et al. Selection and use of SNP markers for animal identifi cation and paternity analysis in U.S. beef cattle // Mamm. Genome. 2002. V. 13. No. 5. P. 272–281.

12. Heaton M.P., Leymaster K.A., Freking B.A. et al. Prion gene sequence variation within diverse groups of U.S. sheep, beef cattle, and deer // Mamm. Genome. 2003. V. 14. No. 11. P. 765–777.

13. Heaton M.P., Keen J.E., Clawson M.L. et al. Use of bovine single nucleotide polymorphism markers to verify sample tracking in beef processing // J. Am. Vet. Med. Assoc. 2005. V. 226. No. 8. P. 1311–1314.

14. Konnai S., Usui T., Ikeda M. et al. Tumor necrosis factor-alpha genetic polymorphism may contribute to progression of bovine leukemia virus-infection // Microbes Infect. 2006. V. 8. No. 8. P. 2163–2171.

15. Matukumalli L.K., Lawley C.T., Schnabel R.D. et al. Development and characterization of a high density SNP genotyping assay for cattle // PLoS One. 2009. V. 4. No. 4. P. e5350.