In silico analysis of meat quality candidate genes among Nero Siciliano, and Italian heavy pigs genomes

In a modern context, where consumers are becoming better educated and oriented towards native animal breeds including meat with a high nutritional profile, the autochthonous pig breeds represent an important genetic reserve to be utilized mainly for the production of typical Italian products. Autochthonous pig breeds represent a valuable genetic reserve to be utilized for typical products linked to italian gastronomic traditions, or for recovering some organoleptic proprieties of pork which have been lost through of severe selective programmes. This can be a strong stimulus for the conservation of local breeds. The Food and Agriculture Organization (FAO) has expressed concern about the lack of interest in local breeds compared to high-output animals and conservation programs have been implemented by various countries worldwide. In this study we report an in silico comparison of 48 candidate genes involved in meat quality traits in pig. The genes were analyzed from different pig breeds (Nero Siciliano (NS), Large White (LW), Landrace (LAN) and Duroc (DU)) whose genomes were previously sequenced and published. In particular, we focused on genes related to muscle mass deposition and carcass fatness as these traits influence technological processes adopted for long matured pork meats products such as cured ham.More than twenty thousand variants were identified by comparing the gene set of each breed to the reference genome assembly. Of these ~22,000 were SNPs, ~3,000 short insertions and ~1400 short deletions. Transitions/transversions ratio was 2,650 while missense/silent ratio resulting in 0.526. Furthermore, over 40% of intronic variants and ~45% of non coding transcript variants were also identified.Among all variants detected in this study, more than 3,000 were shared among NS, LW and LAN while ~7,000 were unique for NS, ~2,000 for LW and ~6000 for LAN, showing a high degree of genetic variability among studied breeds.This study represents a fist preliminary study of genetic characterization of Nero Siciliano pig and also provides a platform for future comparative studies between this and other swine breeds.