Microarray of SNPs for diverse applications in commercial pig breeding

Modern pig production needs new tools for fast, reliable, more effective breeding. In the present paper we present a chip containing 45 SNP (Single Nucleotide Polymorphisms) which enables the determining of 1 genetic disease (PSS-Porcine Stress Syndrome), 4 QTLs genes: PRKAG3, CAST, MC4R and ESR, which together with the remaining SNPs create a panel useful in marker-assisted selection and veterinary control. The SNPs were genotyped using the PCR-APEX (Arrayed Primer Extension) technique. Special attention is paid to evaluation of the 45 SNP chip as an alternative approach to parentage and identity control. Based on allele frequency estimations, for a sample of 88 individuals of commercial pig lines, the probabilities that a randomly chosen candidate parent would be excluded from paternity or maternity were estimated to be 99.9% when genotypes of both parents and a progeny were known, and 98% when the genotypes of only one parent and a piglet were available. The marker set presented here also reached a probability of identity in the order of 10(-16), which allows for unequivocal discrimination of animals or their products among billions of individuals. Further improvements for upcoming chip versions were also considered.