Genetic structure of autochthonous and commercial pig breeds using a high-density SNP chip

Abstract

One of the main objectives in TREASURE project is the genetic characterisation of European autochthonous pig breeds through genetic and genomic tools. The aim of the current pilot study was to evaluate the usefulness of the GeneSeek Genomic Profiler porcine SNP chip to describe genetic diversity of five Mediterranean autochthonous and three commercial pig breeds. 44 animals from Iberian (12), Krskopolje (4), Casertana (5), Cinta Senese (5), Apulo Calabrese (5), Duroc (5), Large White (4) and Landrace (4) breeds were genotyped. All DNA samples were successfully genotyped (call rates ≥0.98). A total of 59,193 SNPs were used in the genetic analyses after QC filtering. Observed (Ho) and expected (He) heterozygosities, FIS statistic and genetic distances (DS and FST) were computed. The overall FST value was 0.15. Ho and Hs values per breed ranged from 0.25 to 0.36 (Ho) and from 0.26 to 0.40 (Hs). Calabrese and Duroc were the breeds with the highest (0.16) and lowest (-0.01) FIS values, respectively. DS and FST genetic distances were very similar. Duroc and Large-White were the closest breeds, since DS and FST were 0.09 and 0.19, respectively and Landrace and Duroc the furthest ones, being DS and FST values equal to 0.22 and 0.34. Distribution of minor allele frequencies (MAF) showed that Iberian is the breed with the highest number of monomorphic SNPs (25.3%) and Landrace and Krskopolje have more alleles at intermediate frequencies. These results provide insights on the genetic diversity and relationships among the investigated breeds. This study will be enlarged to characterize the structure of European autochthonous pig populations using the same SNP chip. Funded by European Union's H2020 RIA program (grant agreement no. 634476).