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.
Highlights
In recent decades, many livestock breeds have experience a severe loss of biodiversity that has markedly affected animal production systems, especially in marginal areas
Nero Siciliano pigs showed considerable genetic variability and diversity, expressed in terms of the number of alleles per locus (NA) and expected heterozygosity (He): the values for these parameters were higher than for several European breeds (NA = 4.5 on average, He = 0.43-0.68), including Iberian breeds (NA = 3.44-5.86, He = 0.46-0.64) (Martinez et al, 2000), seven native and commercial breeds reared in Portugal (NA = 3.77-6.27, He = 0.49-0.69) (Vicente et al, 2008), and a population of Nero Siciliano pigs (NA = 6.70, He = 0.67) studied by SanCristobal et al (2006)
The number of effective alleles (4.53) was higher than in European breeds (2.74 on average) and Nero Siciliano pigs (4.03) studied by SanCristobal et al (2006) and higher than or comparable to those reported for several Chinese breeds (1.69-5.62) (Li et al, 2004; Fang et al, 2005), except for Lingao (4.76; Fang et al, 2005) and Nang Yang Black, Sheng Xian Spotted and Hai Nan (5.12, 5.21 and 5.62, respectively) (Li et al, 2004)
Summary
Many livestock breeds have experience a severe loss of biodiversity that has markedly affected animal production systems, especially in marginal areas. Attempts to reverse this negative trend have led to research in 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. Black pigs are rustic animals that thrive on roughage and a limited food supply, in addition to being resistant to diseases in harsh conditions This breed still retains its distinctiveness thanks to the geographical and orographical characteristics of the island and breeding area, but runs a high risk of losing its original traits because of the lack of a suitable plan to safeguard and exploit its production
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