SNiPORK - a microarray of SNPs in candidate genes potentially associated with pork yield and quality - development and validation in commercial breeds

SNiPORK is an oligonucleotide microarray based on the arrayed primer extension (APEX) technique, allowing genotyping of single nucleotide polymorphisms (SNPs) in genes of interest for pork yield and quality traits. APEX consists of a sequencing reaction primed by an oligonucleotide anchored with its 5' end to a glass slide and terminating one nucleotide before the polymorphic site. Extension with one fluorescently labeled dideoxynucleotide complementary to the template reveals the polymorphism. Ninety SNPs were selected from those associated directly or potentially with pork traits. Of the 90 SNPs, 5 did not produce a positive signal. For 85 SNPs, 100% repeatiblity was proved by double genotyping of 13 randomly chosen boars. In addition, the accuracy of genotyping was verified in 2 sib-families by a Mendelian inheritance of 49-50 homozygous genotypes from sire to sons. Three genotype discrepancies were found (97% accuracy rate). All inaccurities were confirmed by an alternative method (sequencing and PCR-RFLP assays). Moreover, the exclusion power of the chip was evalueted by an SNP inheritance analysis of unrelated boars within each sib-family. In the validation step, 88 boars (13 Pietrain, 31 Landrace, 16 Large White, 8 Duroc, 7 Hampshire x Pietrain crosses, and 13 other hybrid lines) were screened to validate SNPs. Among the 85 selected SNPs, 12 were found to be monoallelic, the rest showing at least two genotypes for the entire population under study. The primary application of the SNiPORK chip is the simultaneous genotyping of dozens of SNPs to study gene interaction and consequently better understand the genetic background of pork yield and quality. The chip may prospectively be used for evolutionary studies, evaluation of genetic distances between wild and domestic pig breeds, traceability tests, as well as the starting point for developing a platform for identification and paternity analysis.