Abstract
Simmental is the one of the most popular dual-purpose cattle breed in Russia, which in number is inferior only to the Black-and-White and Holstein breeds. Annually, 106.4 thousand Simmental cows in 298 herds from 33 regions are recorded. The aim of our study was to examine genetic differences and admixture level between Simmental bulls of different origin using genome-wide scanning. The Illumina Bovine 50K chip was used for genotyping. PLINK 1.07, Admixture 1.3, SnEP 1.1, SplitsTree 4.14.5 software and R package “diveRsity” were used to perform the statistical analyses. After quality control, 34149 SNPs were selected. 80 Simmental bulls were distributed among three groups according to their origin: Russian Simmental (SIM_RUS, n=32), imported European Fleckvieh (FLVH,n=38) and Simmental improved by Holsteins (SIM_HOL,n=10). Holstein purebred individuals were taken as an outgroup (HOL,n=29). MDS and Neighbor-Net analyses revealed the clear clustering of all the studied groups. SIM_RUS and FLVH formed common cluster (F(st)=0.025) and were distant from HOL (F(st)=0.097 and 0.101, respectively). SIM_HOL was located between the parent breeds – SIM_RUS, FLVH and HOL (F(st)=0.049, 0.054 and 0.044, respectively). The admixture analysis at K=3, which was assumed as the most probable number of clusters showed that HOL and SIM_HOL shared 55.3% of common ancestry, while SIM_RUS and FLVH - 25.5%. Inbreeding coefficient was the lowest for SIM_RUS (F(is)=-0.004, CI=-0.006…-0.002) and the highest in admixed population SIM_HOL (F(is)=-0.067, CI=-0.070…-0.063). For FLVH this value was -0.021 (CI=-0.023…-0.019). The effective population size in SIM_RUS and FLVH was changed similarly over past 50 generations and currently achieves the values of 204 and 225, respectively. In SIM_HOL this parameter was much lower – 58. Our results demonstrated the clear population structure in Russian Simmental cattle. It will be useful in the genomic selection program for improvement and enlargement of the national reference population. Supported by RFBR №17-29-08030.