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Meat quality is important both to consumers and to the meat processing industry. Commonly used measures of porcine meat quality are the pH and color of the meat. The purpose of this study was to identify SNP associated with these meat quality traits in Finnish Yorkshire using the Illumina PorcineSNP60 BeadChip. The association of each SNP with the quality traits was tested with a weighted linear model. The relatedness of samples was accounted for by a random polygenic genetic effect with the accompanying full relationship matrix. The original EBV from single-trait evaluations were deregressed before analysis. The statistical significance of SNP was established using the Bonferroni correction to adjust for multiple testing. Three genomic regions were significant for the meat quality traits. The PRKAG3 region on chromosome 15 was significant for pH measured from loin and ham and for a* (redness) measured from loin. The smallest P-value in the region was obtained for pH measured from loin (ASGA0070634, P-value = 3.8 × 10(-13)). The allele substitution effect (-0.047) of the unfavorable allele A corresponds to 1 SD of the polygenic effect. The second significant region, on chromosome 2 at around 31 megabases (Mb), was associated with pH and L* (lightness) measured from loin. The most significant SNP (ASGA0009814, P-value = 3.89 × 10(-10)) had an allele substitution effect of 0.86, corresponding to 0.7 SD of the polygenic effect of L*. The third region, located on chromosome 6 at around 83 Mb, was significant for a* measured from ham. The P-value of the best SNP (ALGA0035896) was 8.71 × 10(-7) and the allele substitution effect -0.38, corresponding to 0.5 SD of the polygenic effect of a*. The significant association of PRKAG3 with pH was not due to the known AA substitutions. The candidate gene on chromosome 2 associated with color L* is RCN1, which has a high affinity Ca(2+)-binding motif, the EF hand. The significant region on chromosome 6 for color a* contains several genes, so more data are needed to identify the causative gene. Our results indicate that instead of the known AA substitutions of PRKAG3, some yet-unknown AA substitutions are causative for the pH variation in Finnish Yorkshire. Also, a new major QLT for L* was found on chromosome 2. The significant SNP identified in this study can be used in marker-assisted selection.

The extent of linkage disequilibrium (LD) and effective population size in Finnish Landrace and Finnish Yorkshire pig populations were studied using a whole genome SNP panel (Illumina PorcineSNP60 BeadChip) and pedigree data. Genotypic data included 86 Finnish Landrace and 32 Finnish Yorkshire boars. Pedigree data included 608,138 Finnish Landrace 554,237 and Finnish Yorkshire pigs, and on average 15 ancestral generations were known for the reference animals, born in 2005 to 2009. The breeding animals of the 2 populations have been kept separate in the breeding programs. Based on the pedigree data, the current effective population size for Finnish Landrace is 91 and for Finnish Yorkshire 61. Linkage disequilibrium measures (D' and r(2)) were estimated for over 1.5 million pairs of SNP. Average r(2) for SNP 30 kb apart was 0.47 and 0.49 and for SNP 5 Mb apart 0.09 and 0.12 for Finnish Landrace and Finnish Yorkshire, respectively. Average LD (r(2)) between adjacent SNP in the Illumina PorcineSNP60 BeadChip was 0.43 (57% of the adjacent SNP pairs had r(2) > 0.2) for Finnish Landrace and 0.46 (60% of the adjacent SNP pairs had r(2) > 0.2) for Finnish Yorkshire, and average r(2) > 0.2 extended to 1.0 and 1.5 Mb for Finnish Landrace and Finnish Yorkshire, respectively. Effective population size estimates based on the decay of r(2) with distance were similar to those based on the pedigree data: 80 and 55 for Finnish Landrace and Finnish Yorkshire, respectively. Thus, the results indicate that the effective population size of Finnish Yorkshire is smaller than of Finnish Landrace and has a clear effect on the extent of LD. The current effective population size of both breeds is above the recommended minimum of 50 but may get smaller than that in the near future, if no action is taken to balance the inbreeding rate and selection response. Because a moderate level of LD extends over a long distance, selection based on whole genome SNP markers (genomic selection) is expected to be efficient for both breeds.

Reproduction traits play an important role in economically viable piglet production and are closely related to the quality and length of the produc- tive life of the sow. A increased removal rate of young sows is undesirable not only because of the associ- ated financial penalties incurred, but also because of ethical concerns. Candidate genes and gene pathways have been identified for fertility in model species, and recent studies have provided evidence that polymor- phisms within these genes are associated with repro- duction traits in American Yorkshire/Large White and Landrace populations. In this study we evaluated the impact of single polymorphisms (n = 7) in 7 candi- date genes on reproductive efficiency in Finnish York- shire (n = 280) and Landrace (n = 271) populations: IGFBP1, IGFBP2, IGFBP3, IGFBP5, CPTIA (carni- tine O-palmitoyltransferase I), COX2 (PG-endoperox- ide synthase 2, also known as cyclooxgenase-2), and SLC22A5 (organic cation/carnitine transporter 2 (sol- ute carrier family member I), OCTN2). In the Finnish Yorkshire population, only 4 of the analyzed markers were polymorphic. Significant effects on farrowing time were detected from the Yorkshire data, with polymor- phisms within the genes CPT1A (a (allele substitution effect of allele A) = 2.97 d for age at first farrowing)), IGFBP3 (a = 0.54 d for farrowing interval of parities >1), and IGFBP5 (a = 3.22, 1.27, and 0.85 d for age at first farrowing and farrowing interval in the first and later parities, respectively). For the Landrace popula- tion, 6 markers were polymorphic, and significant ef- fects were detected for traits affecting litter size. The polymorphism within the COX2 gene had an additive effect of 0.3 piglets for litter size in parities >1, and the IGFBP1 gene had an additive effect of 0.21, 0.26, and 0.11 piglets for litter size in the first parity, pari- ties >1, and stillborn in parities >1, respectively. The additive effect of the SNP within the IGFBP2 gene was 0.16, 0.09, and 0.09 piglets for litter size in parities >1 and stillborn in the first and later parities, respec- tively. Finally, the IGFBP5 gene had an additive effect of 0.18, 0.07, and 0.07 piglets for litter size in the first parity, stillborn in parities >1, and mortality between farrowing and weaning in the first parity, respectively. These results support the suitability of the candidate gene approach for identification of markers to improve the reproductive performance of sows and to provide potential markers for marker-assisted selection.

Association between pre-eclampsia (PEE1) and the dimethylarginine dimethylaminohydrolase (DDAH) 1 and 2 genes, which play a role in the regulation of nitric oxide synthesis and release, was studied. In a case –control study design single nucleotide polymorphisms (SNPs) were determined at eight sites in the DDAH1 gene and at one site (Pro231Pro) in the DDAH2 gene from 132 women with pre-eclampsia and 112 healthy controls. Three SNPs in the DDAH1 gene were associated with preeclampsia, showing complete linkage disequilibrium with each other, but none of the associations in the allele or genotype data reached statistical significance in either of the genes after the correction for multiple testing. Haplotype frequencies were estimated using a population based on a maximum likelihood method (EM algorithm). Four common DDAH1 haplotypes were present and a significant association of haplotypes H2 and H3 with pre-eclampsia (P 5 0.03) was found. The risk of pre-eclampsia was greatest in individuals (odds ratio: 3.93; 95% confidence interval: 1.54 –9.99) who had two copies of the high-risk haplotypes (H2 or H3). The observed haplotypic association provides the first evidence of the importance of DDAH1 polymorphisms in pre-eclampsia susceptibility.

Background: Human serum paraoxonase eliminates carcinogenic lipid-soluble radicals. Because expression of the main human paraoxonase gene PON1 varies widely in humans, certain PON1 polymorphisms might be associated with increased risks of cancer. We sought new functional mutations in PON1 and determined whether known or new PON1 mutations were associated with the risk for prostate cancer in a prospective, random, population-based sample of Finnish men and in a case–control study. Methods: Serum paraoxonase activity was measured in 835 healthy men in the Kuopio Ischaemic Heart Disease Risk Factor Study. PON1 mutations were identified by hierarchical phenotype-targeted sequencing in DNAs from the 100 men with the lowest paraoxonase activity in this cohort, and 1595 men in the cohort were genotyped for PON1 mutations by restriction fragment length polymorphism. Multivariable analysis was used to investigate the association of known and new PON1 mutations with incident prostate cancer in 1569 cancer-free men in the cohort followed for 9–14 years. In a case–control study of Finnish men, the association of prostate cancer with the PON1 mutation identified in the cohort study was investigated in 69 case patients with familial prostate cancer and 69 unmatched healthy control subjects. Results: We identified a new single-nucleotide PON1 polymorphism associated with decreased serum paraoxonase activity that caused an isoleucine→valine change at codon 102 in exon 4 (I102V). Of the 1569 men cancer-free at baseline, 56 (3.6%) were carriers of the I102V mutation. After adjusting for age and cholesterol-lowering medications, the relative risk for developing prostate cancer during follow-up was 6.3 (95% confidence interval [CI] = 2.1 to 19.2) among 102V allele carriers compared with noncarriers. Other PON1 alleles were not statistically significantly associated with prostate cancer. In the case–control study, patients with familial prostate cancer were more likely to be carriers of the PON1 I102V mutation than control subjects (odds ratio = 4.3, 95% CI = 0.9 to 21.5). Conclusion: The PON1 102V allele appears to be associated with an increased risk for prostate cancer. [J Natl Cancer Inst 2003;95:812–8]