Caratterizzazione genetica del suino Nero Siciliano mediante tecniche di Next Generation Sequencing: Whole Genome sequencing, SNPs discovery ed identificazione di polimorfismi associati allo spessore del lardo dorsale

Abstract Background Local pig breeds represent an important genetic reserve to utilize mainly for the obtaining of typical products and for recover the primitive germplasm and biodiversity manteniment. Nero Siciliano pig is an autochthonous breed of Sicily (Italy). In contrast to modern livestock production systems, this breed is reared under semi-extensive conditions that ensure animal’s welfare and sustainability of its productions. In order to explore its genetic variability, here we present for the first time the whole genome sequencing and SNPs discovery of a male domestic Nero Siciliano pig versus the last pig reference genome Sus scrofa 11.1. Additionally, we further evaluate the genetic variation occurring in 21 selected fitness-related genes. Results A total of 346, 8 million paired reads were generated by sequencing the whole-genome of a single, male, Nero Siciliano pig. After quality control, 99.03% of the reads were mapped to the existing Sus scrofa reference genome, and over 11 million variants were detected. Genome-wide variation analysis revealed that Nero Siciliano pig contains, on average, 1 variant every 222 bases resulting in ~36% missense, ~0.4% nonsense and over 63% silent mutations. Structural variant analysis showed 1,261,412 indels, 196,971 replacements, 2,383 tandem duplications and 1,029 inversions. In a subset of genes involved in biological processes related to environmental adaptation and reproductive traits 6,747 variants were identified, resulting in a rate of 1 variant every ~276 bases. Among these variants, 1,132 were novel to the dbSNP151 database. Conclusions Explore the genetic variability of this breed can help to discover its genetic uniqueness (genes pool and alleles combination) that can explain genetic bases of its behavioural, physiological or morphological traits.