Whole genome SNPs discovery in Nero Siciliano pig

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.

Sicilian Black Pig: An Overview

“…The height at the withers is approximately 62-67 cm (see Figure 1). SB pigs are known to be adapted to difficult conditions and are valued for their reproductive performance, disease resistance, and meat production [14][15][16][17]. In Table 1, the information relating to adult body morphology of the SB pig breed (ANAS, [13]) expressed as an average value is shown.…”

“…A total of 11 million variants were detected. Of these,~82% were SNPs, while~12% and~5% were short insertions and deletions, respectively [15]. Furthermore, more than 58% of detected SNPs (6,555,556 variants) were heterozygous, while the remaining 42% were found in an alternative homozygosity state.…”

“…In detail, a total of 6747 variants were identified. Among these, 1132 were new to the dbSNP151 database, consisting of 476 that were heterozygous and 656 in an alternative homozygosity form [15]. Several GWASs have been performed in pigs to identify the genomic regions implicated in phenotypic variability between breeds [68,69].…”

Estimation of population differentiation using pedigree and molecular data in Black Slavonian pig

“…Therefore, the minimization of those occurrences preserves the fluctuation of allelic frequencies within the population (Diniz-Filho et al, 2012). The adoption of appropriate conservation management is essential to preserve local populations since they are often considered to be part of the historical and cultural tradition (D'Alessandro et al, 2019). Population subdivision arises from the joint effects of multiple factors, the most influential being genetic drift, gene flow and selection (Lacy, 1987, Ma et al, 2015.…”

Genetic Diversity and Population Structures in Chinese Miniature Pigs Revealed by SINE Retrotransposon Insertion Polymorphisms, a New Type of Genetic Markers

“…Mingguang small ear pig samples were taken from the national Mingguang small ear pig conservation farm in Tengchong, Yunnan Province. Sicilian black pig is an autochthonous genetic type that lives in the woods of the Nebrodi and Madonie mountains on the northern coast of the Mediterranean island of Sicily (Italy) [ 24 ]. The Landrace pig samples, used as a positive outbreed control, were taken from the breeding farm in Xuzhou China.…”