Population Structure and Phylogeny of the Russian Cattle Breeds Determined By Whole Genome Genotyping

This study focused on revealing the genetic structure and history of the Russian native cattle breeds. Samples were collected from 18 breeds (Bestuzhevskaya, Black-Pied, Buryatian cattle, Kazakh Whitehead, Kalmykian, Kostromskaya, Kholmogorsakaya, Tagilskaya, Ukrainian Whitehead, Yakutian cattle, Yaroslavskaya, Red-Stepped, Alatauskaya, Red Gorbatovskaya, Istobenskaya, Yurinskaya, Red-Pied, Ukrainian Grey). The number of samples varied from two to 39 animals with the average of 20 per breed. Genotyping was performed either on the 150K GGP Bovine array (Neogen) or the Illumina 50K Bovine array. We performed the phylogenetic analysis of the breeds for the genotypes shared between the arrays, identified the most genetically distinct breeds within our set as well estimated the effective population sizes (Ne) for the breeds. The admixture analysis allowed for the identification of the optimal number of populations (K) and the groups of related breeds. Comparison of our data with those obtained for 134 world breeds performed by Decker et al. (2014), suggested close relations between majority of breeds from Russia and the breeds of the European origin. However, the Yakutian, Kalmykian and Buryatian cattle formed a cluster close to Asian breeds. Known historical relations between the Alatauskaya and Kostromskaya breeds as well as between the Kazakh Whitehead and Hereford breeds were confirmed. This work is a first step toward revealing the population structure, history, and signatures of selection within the native Russian cattle made to facilitate application of genomic technologies to improve breeding procedures and to increase the effectiveness of genomic selection for livestock in Russia.