The genomic architecture of the Russian population of Saanen goats in comparison with worldwide Saanen gene pool from five countries

The Saanen goat breed is valued for its high milk productivity and good adaptive qualities, which contributed to its worldwide distribution outside Switzerland. In Russia, the Saanen is a popular breed that had been officially recommended for breeding and had a pedigree status. Breeding in local environments as well as regional specifics of the used breeding strategies can lead to a significant change in the allele pool of breeds, and therefore, it is relevant to conduct genomic studies of national populations of world breeds to establish their current genetic status. Here, for the first time we presented the results of whole-genome analysis of the Russian population of goats of the Saanen breed in comparative aspect with the original (Switzerland) and the world gene pool of the Saanen breed, represented by four countries. The aim of our work was to assess genetic diversity and to study population structure of the Saanen goats of Russian selection in comparison with representatives of this breed from five different countries (Switzerland, Italy, France, Argentina and Tanzania) whose whole-genome SNP-profiles were obtained from the database of the AdaptMap project. The studies were conducted on 21 goats of the Saanen breed (RUS), bred in one of the Russian breeding farms, in 2019-2020. DNA was extracted from the selected ear fragments using DNA Extran-2 kits (Syntol CJSC, Russia). Genotyping was performed using a GoatSNP50 BeadChip DNA chip (Illumina, Inc., USA) containing 53347 SNPs and providing coverage of the average interval between SNPs in 40 kb. To assess the genetic diversity and to perform comparative analysis of the Russian goat population with the representatives goats of this breed from five different countries, we used SNP-profiles of the Saanen goats bred in Switzerland (SWI, n = 38), Italy (ITA, n = 22), France (FRA, n = 55), Argentina (ARG, n = 11) and Tanzania (TNZ, n = 8), which were downloaded from the publicly available digital data repository Dryad and generated in within the AdaptMap project. The Swiss population of the Saanen breed was assumed as a sample of the original gene pool. Bioinformatic processing and visualization of whole-genome genotyping data was performed in the PLINK 1.90, Admixture 1.3, SplitsTree 4.14.5 software, in R packages “diveRsity” and “pophelper”. The observed heterozygosity varied from 0.381 in SWI to 0.423 in FRA and was high in RUS (Ho = 0.418). In SWI, ITA, FRA populations the values of the inbreeding coefficient were close to zero level; RUS, ARG, and TNZ showed heterozygote deficiencies, which were 1.5%, 8.9, and 6.0%, respectively. Allelic richness was maximal in ARG, RUS, and FRA (Ar ³ 1.979) and minimal in SWI (Ar = 1.934). The Principal component analysis and the phylogenetic tree showed a clear differentiation between the national and original populations of the Saanen breed. Analysis of population structure demonstrated the presence of the genetic component of the SWI cluster in goats from the RUS group. RUS had the smallest genetic distances with FRA (FST = 0.02; RST = 0.189) and ITA (FST = 0.023; RST = 0.215); and RUS was highly differentiated from TNZ (FST = 0.054; RST = 0.311) and SWI (FST = 0.06; RST = 0.276). Thus, different selection strategies resulted in genetic differences between the national goat populations of the Saanen breed. However, genomic components of the original gene pool are still present in the Russian goat population of the Saanen breed.