Genomic assessment of inbreeding in the Kholmogor, Yaroslavl and Holstein breeds of cattle
The inbreeding level in a population should be taken into account in the framework of breeding programs in order to avoid the transition of lethal and semi-lethal recessive alleles into a homozygous state and resulting in inbreeding depression. The assessment of inbreeding level based only on the information from pedigree is not always correct. Calculation of inbreeding indices based on genome-wide data allows evaluation of the heterozygosity degree both individually and population-wise. The work was aimed at conducting the genomic assessment of inbreeding in cattle populations of the Kholmogor, Yaroslavl and Holstein breeds using two methods - sMLH and F(ROH). We performed the genome-wide SNP analysis (SNP - single nucleotide polymorphism) of individuals of the above listed breeds. Data processing, calculations and visualization of the results were carried out in the programs PLINK 1.9, Admixture 1.3 and R packages pophelper, detectRUNS, inbreedR, ggplot2. After quality control, 36837 SNPs were selected for the analyses. Cluster analysis showed a clear differentiation of the Russian breeds both from each other and from Holstein. The highest average values of the inbreeding coefficient F(ROH) (0,126±0,005) and sMLH (1,018±0,006) were observed in Holstein animals. It can be caused by the ascertainment bias due to the design features of the chip. Therefore the assessment of the inbreeding degree in populations using the whole-genome SNP analysis is advisable when taking into account the chip design.