RICERCA E VALIDAZIONE DI SNP IN GENI CANDIDATI PER LA QUALIT� DELLA CARNE E APPLICAZIONE DELL'ANALISI GENOMICA ALLA SPECIE SUINA
Creators: name: RASCHETTI, MARTA
Publisher: name: Universit� degli Studi di Milano
Year: 2010

description: 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 &lt; 0.0001), fat cover (P &lt; 0.05), fat thickness (P &lt; 0.05), Prin1 (P &lt; 0.05), Prin3 (P &lt; 0.01); Prin4 (P &lt; 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 for fat thickness. Three of the four SNPs resulted polymorphic also in this population. Then, association analysis between these three SNPs and EBVs for fat thickness were performed, showing the association of the SNP g29962[A/G ] of PTPRD gene with thigh weight. Another aim of this PhD thesis is the genetic characterization of a swine genetic type, the ?Nero di Garlasco?, expressing both ancient and recent biodiversity. Although in the last years admirable efforts have been made to recover pig biodiversity, extremely endangered, today only few Italian local breeds can withstand the competition with commercial foreign breeds (i.e. the Large White, Landrace and Duroc) and with the commercial crosses today more and more widespread in the market. To date, at the national Herd Book only few breeds are registered as the Cinta senese, Mora Romagnola, Nero Siciliano, Casertana, Apulo-Calabrese and the Sarda. A very limited number with respect to the tens of breeds and lines cited in the textbooks of agronomy of the second postwar period. The majority of the extinct pig breeds were adapted to free range breeding, and were characterized by dark coat color (to defend themselves form the sun), slow growth and extensive fat deposits. In recent years, an ancient genetic type barely still existing (Razza di Garlasco) is reconstructing in the province of Pavia (Lomellina). In this case, pig phenotypes consisted of dark coat color and, surprisingly, high growth rates, similar to the commercial breeds. These two characteristics made these animals well adapted for the non-industrial production, where animals can be bred in free range, because the dark color protects them from the sun. To achieve this goal, a genetic characterization of the model population should be conducted. The tight bottleneck, through which this small population has passed, allows the fixation of genetic markers that enable precise traceability of the fresh and transformed products. This can give an added value to the breeding of theses animals that responds to the request for security and sustainability of the animal production system. Thanks to innovative technologies, a population of 96 animals, belonging to the Nero di Garlasco breed, was analyzed using the PorcineSNP60 BeadChip, in order to screen about 60,000 SNPs. The obtained data allowed a first description of the genetic structure of this population, but further studies are required to characterize this swine genetic type.