Local breeds are a resource of great interest both from the genetic point of view, since they can be a repository of allelic combinations rare or absent in the selected breeds, and for the maintenance of marginal areas, since they can easily be associated to typical products helping farmers manage and protect the environment. Nero Siciliano, an autochthonous black pig reared in the natural park of the Nebrodi Mountains, is an example of such possibility. Used to produce high quality meat, including salami and cured ham, it has known an important increase in the number of farms and in sow reared in the last ten years thanks also to the creation of a Protected Designation of Origin label for Nero Siciliano meat and other related products. Genetic characterization is a fundamental prerequisite for managing genetic resources and can be exploited for setting up molecular authentication protocols. To characterize the breed a representative sample of 93 Nero Siciliano pigs was selected from 22 farms well distributed in the Nebrodi area and analyzed using the PorcineSNP60 Genotyping BeadChip v2 (Illumina, San Diego, CA, USA), containing 61,565 SNP. Descriptive parameters were calculated (heterozygosity, LD, etc.) and a comparison with data obtained from the Italian Large White, Landrace and Duroc breeds using the same genotyping platform was performed. Different SNP sets (200, 150, and 100 randomly selected SNP, a subset of 100 SNP monomorphic in the Nero Siciliano or in the other three breeds) were tested with Structure and GeneClass2 software in order to distinguish the Nero Siciliano from the cosmopolitan breeds. The results suggest that a 100 random SNP dataset is sufficient to discriminate among the four breeds. Structure software was also used on 80 samples for which microsatellite data were also available to evidence potential population structures among the Nero Siciliano breed. Similar results were obtained with both microsatellite and SNP markers.
Genomic analysis for the valorization of Nero Siciliano swine breed
S Chessa;R Moretti;B Castiglioni
2013
Abstract
Local breeds are a resource of great interest both from the genetic point of view, since they can be a repository of allelic combinations rare or absent in the selected breeds, and for the maintenance of marginal areas, since they can easily be associated to typical products helping farmers manage and protect the environment. Nero Siciliano, an autochthonous black pig reared in the natural park of the Nebrodi Mountains, is an example of such possibility. Used to produce high quality meat, including salami and cured ham, it has known an important increase in the number of farms and in sow reared in the last ten years thanks also to the creation of a Protected Designation of Origin label for Nero Siciliano meat and other related products. Genetic characterization is a fundamental prerequisite for managing genetic resources and can be exploited for setting up molecular authentication protocols. To characterize the breed a representative sample of 93 Nero Siciliano pigs was selected from 22 farms well distributed in the Nebrodi area and analyzed using the PorcineSNP60 Genotyping BeadChip v2 (Illumina, San Diego, CA, USA), containing 61,565 SNP. Descriptive parameters were calculated (heterozygosity, LD, etc.) and a comparison with data obtained from the Italian Large White, Landrace and Duroc breeds using the same genotyping platform was performed. Different SNP sets (200, 150, and 100 randomly selected SNP, a subset of 100 SNP monomorphic in the Nero Siciliano or in the other three breeds) were tested with Structure and GeneClass2 software in order to distinguish the Nero Siciliano from the cosmopolitan breeds. The results suggest that a 100 random SNP dataset is sufficient to discriminate among the four breeds. Structure software was also used on 80 samples for which microsatellite data were also available to evidence potential population structures among the Nero Siciliano breed. Similar results were obtained with both microsatellite and SNP markers.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
