RICERCA E VALIDAZIONE DI SNP IN GENI CANDIDATI PER LA QUALITÀ DELLA CARNE E APPLICAZIONE DELL'ANALISI GENOMICA ALLA SPECIE SUINA

Abstract

An important aim of pig selection in Italy is to obtain animals having a high aptitude for the PDO dry-cured ham production, such as Parma or S. Daniele ham. Over the past years, advances in the porcine genetic map have led to valuable gene and trait information being discovered. Since that time, sequences for the pig genome have been generated from various tissues, the sequencing of candidate genes, and more recently large scale genomic sequencing projects. These efforts are also being directed to SNPs identification for future large scale association studies. In the next years, the efficiency and accuracy of the traditional pig selection schemes could be improved by the implementation of molecular data into breeding programs. In this work, seven swine candidate genes for meat quality were investigated in order to identify informative SNPs. Molecular analyses were performed on twenty-two animals representing the extreme tails of the Gaussian distribution for three selected phenotypes (muscle compactness, fat thickness and the principal component 1) of 231 Large White x Landrace individuals. Among the nine identified SNPs, only two SNPs in the CRADD gene, two SNPs in the PTPRD gene and one SNP in the PIK3R2 gene showed a MAF (Minor Allele Frequency) more than 5% in the animals tested and therefore were considered for the subsequent association analysis. Association analysis between these five SNPs and the three phenotypes considered in this study was carried out using the GML procedure. The SNP CRADD g343 [A/G] showed a good association with the compactness of the muscles (P = 0,0498), the SNP PTPRD g30194 [G/T] showed a good association with the compactness of the muscles (P = 0,0195) and fat thickness dorsal (P = 0,0265), the SNP PIK3R2 g.3008 [C/T] showed a very good association with the compactness of muscle mass (P = 00,0014) and thickness of backfat (P = 0,0087). Therefore, the PIK3R2SNP g.3008 [C / T] was genotyped on all 231 animals of the population. The analysis showed a significant effect of this SNP on the following variables: marbling (P < 0.0001), fat cover (P < 0.05), fat thickness (P < 0.05), Prin1 (P < 0.05), Prin3 (P < 0.01); Prin4 (P < 0.01). In particular, the CC genotype was positively associated with marbling and fat cover. Moreover, the SNP in PIK3R2 gene was tested on 600 samples of three different Italian breeds (Large White, Duroc, Landrace) obtained from the National Association of Pig Breeders of Italy. Within each breed, the 100 individuals with the highest and the 100 individuals with the lowest values for EBVs (Estimated Breeding Values) for average daily weight gain were analyzed, resulting this SNP polymorphic in each breed. The association analyses between this SNP and these extreme EBVs showed a good association with backfat thikness, average daily gain, feed conversion rate and thigh weight in Landrace individuals. The two SNPs identified in CRADD gene and the two SNPs identified in the PTPRD gene were tested in another group of 560 Italian Large White animals with extreme EBVs…