Genetic diversity in different Italian pig breeds evaluated using Illumina PorcineSNP60 BeadChip data

High throughput genotyping tools make it possible to extract interesting genetic information from farm animal populations that could be applied to evaluate genetic relationships and the degree of inbreeding, to analyse selective sweeps, and to identify useful markers for breed allocation and authentication of monobreed products. Pork products derived from local pig breeds are usually considered of high value and sold at a higher price, compared to undifferentiated products, creating the needs for combating possible frauds derived by the financial incentives to substitute them with low value products. In this work, we tested the possibility to use the Illumina PorcineSNP60 BeadChip array to identify single nucleotide polymorphisms (SNPs) that could be useful to authenticate pork products derived from pig breeds. On the whole, 500 pigs from 3 Italian breeds were genotyped (360 Italian Large White, 92 Apulo-Calabrese and 48 Nero Siciliano). Then, 61,177 SNPs were filtered for subsequent analyses. Among these SNPs a subset of 96 polymorphisms was subsequently selected considering their informativity in the pair comparisons, that means SNPs with the larger allele frequency differences between the pairs of populations were chosen. Principal Component Analysis using this subset of SNPs showed a sharp separation between Italian Large White pigs and those of the two local pig populations that were not completely separated to each other. The same SNPs were also analysed using STRUCTURE software with 10,000 Burnin length period, 1000 repetitions and K=3, obtaining an Fst value of 0.37 indicating that intra-population variation is slightly higher than inter-population variation. This works provided useful information on the use of Illumina PorcineSNP60 BeadChip data to identify markers able to distinguish pork products from local and cosmopolitan pig breeds