SNiPORK – A Microarray of SNPs in Candidate Genes Potentially Associated with Pork Yield and Quality – Development and Validation in Commercial Breeds

Abstract

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.

Genome Wide Association Studies for Milk Production Traits in Chinese Holstein Population

“…With the advent of genome-wide panels of single nucleotide polymorphisms (SNPs), SNPs have been widely used for the detection and localization of QTL for complex traits in many species [7], and have proved powerful and useful in identification of casual mutations associated with economically important traits in livestock [8], [9], [10], [11], [12], [13], [14], [15] as well as human diseases [16], [17], [18], [19]. Most recently, along with maturing of genome sequencing and high throughput SNP genotyping technologies, genome-wide association studies (GWAS) are becoming practical for exploring genes associated with complex traits.…”

Expression level of the cytochrome P450c21 (CYP21) protein correlating to drip loss in pigs

“…The mean of drip loss in this study was 2.76% which indicated this was normal meat. A previously study revealed that the polymorphism A2991C of CYP21 gene discovered by Kami nski et al (2008) with bioinformatics approach is localized in the putative intron splicing site, suggesting possible influence on mRNA stability and CYP21 biosynthesis efficiency. A previously study revealed that the polymorphism A2991C of CYP21 gene discovered by Kami nski et al (2008) with bioinformatics approach is localized in the putative intron splicing site, suggesting possible influence on mRNA stability and CYP21 biosynthesis efficiency.…”

Associations of fifty single nucleotide polymorphisms within candidate genes with meatness in pigs

“…It should be stressed that all experimental animals were free from recessive mutation in RYR1 gene (Ryanodine Receptor) known to affect the meatness and meat quality. All fatteners were genotyped in 50 loci (Table 1) by the method described earlier (Kamiński et al, 2008). Whereas allelic frequencies in the loci studied for both breeds are listed in Table 2.…”