Molecular characterization and genetic structure of the Nero Siciliano pig breed

Abstract

Nero Siciliano is an autochthonous pig breed that is reared mainly in semi-extensive systems in northeastern Sicily. Despite its economic importance and well-appreciated meat products, this breed is currently endangered. Consequently, an analysis of intra-breed variability is a fundamental step in preserving this genetic resource and its breeding system. In this work, we used 25 microsatellite markers to examine the genetic composition of 147 unrelated Nero Siciliano pigs. The total number of alleles detected (249, 9.96 per locus) and the expected heterozygosity (0.708) indicated that this breed had a high level of genetic variability. Bayesian cluster analysis showed that the most likely number of groups into which the sample could be partitioned was nine. Based on the proportion of each individuals genome derived from ancestry, pigs with at least 70% of their genome belonging to one cluster were assigned to that cluster. The cluster size ranged from 7 to 17 (n = 108). Genetic variability in this sub-population was slightly lower than in the whole sample, genetic differentiation among clusters was moderate (FST 0.125) and the FIS value was 0.011. NeighborNet and correspondence analysis revealed two clusters as the most divergent. Molecular coancestry analysis confirmed the good within-breed variability and highlighted the clusters that retained the highest genetic diversity.

A multi-farm assessment of Greek black pig genetic diversity using microsatellite molecular markers

“…In our study, microsatellite markers showed a considerably high degree of genetic polymorphism within and between populations on the basis of their allele numbers per locus (N A ) and their genetic heterozygosity (H E ). The mean number of alleles per locus (N A = 12.27) was the highest among several European and Asian breeds including 11 European pigs breeds (N A = 10.6) (Laval et al, 2000), the Taihu pig breed (N A = 8) (Fan et al, 2002), the Iberian pig breed (N A = 7.2) (Fabuel et al, 2004), the Cinta Senese pig breed (N A = 9) (Scali et al, 2012), the Nero Siciliano pig breed (N A = 9.96) (Guastella et al, 2010), six Chinese indigenous pig breeds (N A = 10.35) (Wang et al, 2011), and the Croatian Turopolje pig breed (N A = 7.7) (Druml et al, 2012). However, the mean number of alleles per locus was significantly higher in several Chinese indigenous pig populations (NA = 24.8) (Li et al, 2004).…”

“…This severe loss of biodiversity has markedly affected animal production systems, especially in marginal areas (Guastella et al, 2010). To better comprehend the existing situation, it should be noted that according to FAO (2007), a comparison at the species level revealed that horses (23%), followed by rabbits (20%), pigs (18%), and cattle (16%), are the mammalian species that have the highest proportions of at-risk breeds.…”

“…Attempts to reverse this negative trend have led to research on the preservation and exploitation of local animal breeds, with efforts to identify and reintroduce potentially important genetic traits that have been overlooked by globalized production systems (Guastella et al, 2010). The need perceived internationally to conserve biodiversity, in parallel with increased public sensitivity to environmental problems caused by intensive pig farms, has encouraged the policy of the recovery and preservation of native species (Scali et al, 2012) particularly when these species are connected to high-quality traditional meat products.…”

Genetic admixture analysis in Prestice Black-Pied pigs

“…Because of comparison with our results, we cite the paper of Guastella et al (2010), who described parameters of diversity obtained by using microsatellites of the Italian Nero Siciliano pig breed. In his work, Ollivier (2009) summarized genetic diversity within and between European pigs.…”

“…Based on divergence in dendrograms in Ollivier (2007) and Megens et al (2008), we can compare heterozygosity in four microsatellite markers in Nero Siciliano. Guastella et al (2010) analysed four microsatellite markers that were identical to our (S0355, SW936, SW72 and SW24). Parameters of diversity in the given markers for Nero Siciliano vs. PC are as follows: locus S0355 -Na 8/5, Ho 0.43/0.39, F IS 0.12/0.38; locus SW936 -Na 11/7, Ho 0.68/0.75, F IS 0.09/−0.03; locus SW72 -Na 9/6, Ho 0.73/0.81, F IS 0.03/ − 0.08; and locus SW24 -Na 11/9, Ho 0.78/0.75, F IS 0.05/0.02.…”