Whole genome SNPs discovery in Nero Siciliano pig

Authors: Enrico D’Alessandro, Domenico Giosa, Irene Sapienza, Letterio Giuffrè, Riccardo Aiese Cigliano, Orazio Romeo, Alessandro Zumbo

Institutions:

Department of Veterinary Sciences, Division of Animal Production, University of Messina, Messina, Italy.
Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy.
Sequentia Biotech SL, Barcelona, Spain.
Scientific Institute for Research, Hospitalization and Health Care (IRCCS) – Centro Neurolesi “Bonino-Pulejo”, Messina, Italy.

Publication: Scielo

Date: November 2019

Full paper: https://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572019005021102&tlng=en

Abstract:

Autochthonous pig breeds represent an important genetic reserve to be utilized mainly for the production of typical products. To explore its genetic variability, here we present for the first time whole genome sequencing data and SNPs discovered in a male domestic Nero Siciliano pig compared to the last pig reference genome Sus scrofa11.1.A total of 346.8 million paired reads were generated by sequencing. After quality control, 99.03% of the reads were mapped to the reference genome, and over 11 million variants were detected.Additionally, we evaluated sequence diversity in 21 fitness-related loci selected based on their biological function and/or their proximity to relevant QTLs. We focused on genes that have been related to environmental adaptation and reproductive traits in previous studies regarding local breeds. A total of 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. This study represents a first step in the genetic characterization of Nero Siciliano pig and also provides a platform for future comparative studies between this and other swine breeds.