Screening 52 single nucleotide polymorphisms for extreme value of glycolytic potential and drip loss in pigs.

Summary Low heritability of meat quality traits and the lack of their systematic registration in breeding programs have encouraged the search for single nucleotide polymorphisms (SNPs) located within genes coding the proteins involved in muscle and fat metabolism. In this report, a panel of 52 SNPs was used to find which alleles and genotypes are more/less frequent in groups of pigs differentiated by extreme value of glycolytic potential (GP) and drip loss (DL). The analysis was carried out in 52 fatteners (chosen from 246 pigs), of which 28 were Landrace and 27 Landrace x Yorkshire. Two designs were performed: I, fatteners were divided into two groups showing extreme value of GP (<125 versus >145), II, fatteners were divided into two groups showing extreme value of DL (<6.0 versus >6.0). Allele frequency differences between the phenotypic groups of extreme GL or DL were not influenced by the breed. The frequency of 52 SNPs alleles for each of group was calculated and a chi-squared test was used to estimate the significance of differences in allele frequencies between alternative groups in each experimental design. Three SNPs (DECR1, PPARGC1, MC4R) and another two (CYP21, SFRS1) showed significant differences between groups of extreme GP and DL, respectively. To exemplify and validate potential associations of candidate SNPs for GP and DL, 293 fatteners representing three commercial breeds/crosses (95 Landrace, 66 Landrace x Yorkshire and 132 Landrace x Yorkshire x Duroc were genotyped for DECR1 and CYP21 by PCR-RFLP assays. DECR1 showed significant associations with GP in Landrace and Landrace x Yorkshire x Duroc fatteners. CYP21 showed significant associations with DL in all breeds/crosses. Interestingly, the CYP21 polymorphism revealed adverse associations trend in Landrace x Yorkshire x Duroc pigs in comparison to Landrace and Landrace x Yorkshire fatteners.

Additive effects of 19 porcine SNPs on growth rate, meat content and selection index.

A total of 306 boars (108 Large White and 198 Landrace) were genotyped for 52 candidate SNPs to determine which of the polymorphisms influence growth rate, meat content and selection index. The effects of SNPs were estimated by a mixed linear model including a random additive polygenic animal effect, fixed effects of SNPs including additive, and pairwise additive-by-additive epistases, year*season of birth, breed and RYR1 genotype. In order to estimate all possible pairwise SNP combinations without overparameterising the model a stochastic approach was adopted. A total of 1 350 replications of the model were generated, each containing five randomly selected SNPs. The final estimates of the fixed effects of the model equaled an average out of the replications. The hypothesis of a nonzero effect of SNP was tested by the Wald test. Among 4 257 estimates calculated, many significant (P<0.01), but mostly minor effects (below 1 phenotypic standard deviation) were recorded. The selected SNPs will be further investigated to determine which may be used in MAS.

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.