PSX-3 Estimation of biodiversity of four Russian local pig breeds and wild boar based on SNP-analysis.

Abstract

Russia is the place of origination more than twenty local pig breeds since 19th century. Although originally developed from imported breeds, pigs in Russia were adapted to the local harsh climate and low feeding conditions, forming unique characteristics. The processes of drift and leaching of genes in local species cause interest in the problem of preserving their biodiversity. The development of genomic technologies allows us to accelerate the process of studying these issues. Here the porcine 60K BeadChip (Illumina Inc., USA) was used for analysis and describing of biodiversity and population structure of local pigs and wild boars from European part of Russia for comparison (BR – Breitov (n=18), LIV – Livni (n=16), MUR – Murom (n=12), URZ – Urzhum (n=9), RUEU – Russian wild boar (n=69)). For data processing Plink 1.9., Tassel and Archaeopteryx plugin, Treemix 1.1, SNEP and Vienny 2.1 were used. After QC (geno=0.1, maf=0.05) 35600 SNPs were remained. On MDS plot and NJ-tree, local pigs form a common cluster while RUEU are equally remote from most representatives of local pigs subgroup on PC1. We can observe that URZ locates separately from remained animals. However, all local pigs illustrated close parallel divergence across all generations (13–750). We detect strong migration of RUEU (0.45) to MUR and URZ to LIV (0.3). This may be due to free conditions of detention outside the closed premises several generations ago, which caused to crossing with a wild boar. In total, both populations had 80.9% of common SNPs, and only BR and MUR had unique SNPs (825 and 1193 respectively). The research was performed within the framework of the Federal Agency of Scientific Organizations No. АААА-А18-118021590138-1.