Whole genome SNPs discovery and analysis of genetic diversity in Nero siciliano pig

Nero Siciliano is a local pig breed reared under extensive or semi-extensive management mainly in the Nebrodi mountains of Sicily (Italy). This breed has been rediscovered by farmers who have established a consortium with the aim to protect, exploit and characterize the products obtained from it. In order to discover tipical Nero Siciliano signatures, here we present a whole genome SNPs discovery investigation against the Sus Scrofa reference nuclear genome (SScrofa 11.1). Genomic DNA was extracted from leucocytes of fresh whole blood sample from a male of Nero Siciliano pig with Wizard® Genomic DNA Purification Kit (Promega Corporation), then was quantified with Qubit 2.0 Fluorometer (Thermo Fisher). DNA quality was evaluated by Nanophotometer P-330 (Implen GmbH) and 1μg di gDNA was used for TruSeq DNA PCR-Free Library preparation (insert size 350 bp) following the protocol provided by Illumina. Illumina HiSeq X Ten sequencing produced 346.832.803 paired-end raw reads and after cleaning, performed with Trimmomatic (v.0.36), 346.573.870 (99,92%) good quality reads (phred score ≥ 30) were mapped using bwa aligner against the reference genome (Genbank GCA_000003025.6). SNPs discovery was performed using SUPER-CAP and the potential effects of detected mutations were evaluated by SnpEff software (v4_3m_core). Analysis resulting in 9.837.410 SNPs, 1.635.077 indels and 786.682 deletions. More than 5 million of those SNPs were alternative homozygous. Furthermore, over 40% of intronic variants, ~38% of non coding transcript variants and ~9% of intergenic variants were identified. The estimated variant rate was of 1 variant every 204 bases, showing a very high degree of variability among studied breeds.