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The aim of this research was to screen for polymorphism and to perform an association study of IFI6 with meat and carcass quality traits. A SNP (g.370A>G) was detected which was associated (P < 0.05) with meat colour, pH 24 h post mortem (p.m.) in ham, conductivity 45 min p.m. in loin and conductivity 24 h p.m. in ham, drip loss and carcass length in Duroc × Pietrain and with meat colour, muscle area and ham percentage in the Pietrain population. Highest expression of IFI6 mRNA was detected in skeletal muscle (longissimus dorsi) by qRT-PCR comparing different tissues. Both qRT-PCR and western blot revealed that the IFI6 gene and protein expressions were significantly (P < 0.05) higher in skeletal muscle with low drip loss compared to that of high drip loss. IFI6 protein was localized in the myocytes membrane. Results suggested that IFI6 might play roles in meat and carcass quality and is a potential positional, physiological and functional candidate gene for improving meat quality traits in pigs.

A Duroc-Pietrain resource population was built to detect quantitative trait loci (QTL) that affect growth, carcass composition, and pork quality. The data were analyzed by applying three least-squares Mendelian models: a line-cross (LC) model, a half-sib (HS) model, and a combined LC and HS model (CB), which enabled the detection of QTL that had fixed, equal, and different allele frequencies for alternate breed alleles, respectively. Permutation tests were performed to determine 5% chromosome-wide and 5% genome-wide threshold values. A total of 40 (137) QTL were detected at the 5% genome-wide (chromosome-wide) level for the 35 traits analyzed. Of the 137 QTL detected, 62 were classified as the LC type (LC-QTL), 47 as the HS type (HS-QTL), and 28 as the CB type (CB-QTL). The results indicate that implementation of a series of model-based framework is not only beneficial to detect QTL, but also provides us with a new and more robust interpretation from which further methodology could be developed.

Background Leg weakness issues are a great concern for the pig breeding industry, especially with regard to animal welfare. Traits associated with leg weakness are partly influenced by the genetic background of the animals but the genetic basis of these traits is not yet fully understood. The aim of this study was to identify quantitative trait loci (QTL) affecting leg weakness in pigs. Methods Three hundred and ten F2 pigs from a Duroc × Pietrain resource population were genotyped using 82 genetic markers. Front and rear legs and feet scores were based on the standard scoring system. Osteochondrosis lesions were examined histologically at the head and the condylus medialis of the left femur and humerus. Bone mineral density, bone mineral content and bone mineral area were measured in the whole ulna and radius bones using dual energy X-ray absorptiometry. A line-cross model was applied to determine QTL regions associated with leg weakness using the QTL Express software. Results Eleven QTL affecting leg weakness were identified on eight autosomes. All QTL reached the 5% chromosome-wide significance level. Three QTL were associated with osteochondrosis on the humerus end, two with the fore feet score and two with the rear leg score. QTL on SSC2 and SSC3 influencing bone mineral content and bone mineral density, respectively, reached the 5% genome-wide significance level. Conclusions Our results confirm previous studies and provide information on new QTL associated with leg weakness in pigs. These results contribute towards a better understanding of the genetic background of leg weakness in pigs.

The aim of the present study was to detect quantitative trait loci (QTL) for innate and adaptive immunity in pigs. For this purpose, a Duroc x Pietrain F(2) resource population (DUPI) with 319 offspring was used to map QTL for the immune traits blood antibodies and interferon-gamma using 122 microsatellites covering all autosomes. Antibodies response to Mycoplasma hyopneumoniae and tetanus toxoid vaccine and the interferon-gamma (IFNG) serum concentration were measured at three different time points and were used as phenotypes. The differences of antibodies and interferon concentration between different time points were also used for the linkage mapping. Line-cross and imprinting QTL analysis, including two-QTL, were performed using QTL Express. A total of 30 QTL (12, 6, and 12 for mycoplasma, tetanus antibody, and IFNG, respectively) were identified at the 5% chromosome-wide-level significant, of which 28 were detected by line-cross and 2 by imprinting model. In addition, two QTL were identified on chromosome 5 using the two-QTL approach where both loci were in repulsion phase. Most QTL were detected on pig chromosomes 2, 5, 11, and 18. Antibodies were increased over time and immune traits were found to be affected by sex, litter size, parity, and month of birth. The results demonstrated that antibody and IFNG concentration are influenced by multiple chromosomal areas. The flanking markers of the QTL identified for IFNG on SSC5 did incorporate the position of the porcine IFNG gene. The detected QTL will allow further research in these QTL regions for candidate genes and their utilization in selection to improve the immune response and disease resistance in pig.

A number of observations support the concept of important physiological interactions between the endocrine and immune systems. It could be confirmed that hormones secreted by the neuroendocrine system play an important role in communication and regulation of the cells of the immune system. Among protein hormones, this has been most clearly documented for prolactin (PRL), growth hormone (GH), and insulin-like growth factor 1 (IGF-1). A number of traits of the immune response in a Duroc x Berlin Miniature pig family (DUMI) were examined. The haemolytic complement activity in the classical complement pathway (CH50) and the alternative pathway (AH50)was examined at eight different time points in pigs that were vaccinated with different vaccines. Single nucleotide polymorphism (SNP) genotyping was employed to genotype the DUMI F2 animal for growth hormone (Gh), growth hormone releasing hormone (Ghrh), pituitary-specific transcription factor 1 (Pit1), and prolactin receptor (Prlr) loci, and also a microsatellite within insulin-like growth factor 1 (Igf1). Using a family-based association test (FBAT) program, a highly significant association of Gh, Pit1, and Prlr to AH50 (p < or = 0.01) and a significant association of Pit1 to CH50 (p < or = 0.05) were found. Using the SAS system for mixed model, a highly significant association of Gh, and Igf1 to AH50 and CH50 (p < or = 0.01) was detected, while Prlr and Ghrh had a highly significant association (p < or = 0.01) with CH50 only.

Understanding the genetic control of innate immunity in pigs would offer the opportunity to utilize natural variation and improve selective breeding programmes. As part of our porcine genome scan to identify quantitative trait loci (QTL) we examined immune response traits in a Duroc x Berlin miniature pig resource family (DUMI). Complement activity via classical (CH50) and alternative (AH50) pathways, antibody response to Mycoplasma hyopneumoniae (Mh), tetanus toxoid (TET) and PRRS virus (PRRSV), the complement component (C3c), and Haptoglobin serum concentration (HP) were used as phenotypes for linkage mapping. A total of 220 backcross animals were used for the QTL analysis. Blood was collected six times from each animal prior to and after vaccinations against Mycoplasma hyopneumoniae, tetanus toxoid and PRRS, respectively. Seventy-four microsatellites from 18 autosomes were used for QTL mapping. The analyses were performed treating the measurements of phenotypes at different time points as single traits. Forty-two significant and 24 highly significant QTL were detected, using the program QTL Express, for all immune traits using the single traits. Most QTL were detected on SSC3, SSC16, and SSC18. No significant F-value corresponded to data for SSC12and SSC13.

The mothering ability of a sow largely depends on the shape and function of the mammary gland. The aim of this study was to identify QTL for the heritable inverted teat defect, a condition characterized by disturbed development of functional teats. A QTL analysis was conducted in a porcine experimental population based on Duroc and Berlin Miniature pigs (DUMI). The significant QTL were confirmed by linkage analysis in commercial pigs according to the affected sib pair design and refined by family-based association test (FBAT). Nonparametric linkage (NPL) analysis revealed five significant and seven suggestive QTL for the inverted teat defect in the porcine experimental population. In commercial dam lines five significant NPL values were detected. QTL regions in overlapping marker intervals or close proximity in both populations were found on SSC3, SSC4, SSC6, and SSC11. SSC6 revealed QTL in both populations at different positions, indicating the segregation of at least two QTL. The results confirm the previously proposed polygenic inheritance of the inverted teat defect and, for the first time, point to genomic regions harboring relevant genes. The investigation revealed variation of the importance of QTL in the various populations due to either differences in allele frequencies and statistical power or differences in the genetic background that modulates the impact of the liability loci on the expression of the disease. The QTL study enabled us to name a number of plausible positional candidate genes. The correspondence of QTL regions for the inverted teat defect and previously mapped QTL for teat number are in line with the etiologic relationship of these traits.

We performed a genome-wide QTL scan for production traits in a line cross between Duroc and Pietrain breeds of pigs, which included 585 F(2) progeny produced from 31 full-sib families genotyped with 106 informative microsatellites. A linkage map covering all 18 autosomes and spanning 1987 Kosambi cM was constructed. Thirty-five phenotypic traits including body weight, growth, carcass composition and meat quality traits were analysed using least square regression interval mapping. Twenty-four QTL exceeded the genome-wide significance threshold, while 47 QTL reached the suggestive threshold. These QTL were located at 28 genomic regions on 16 autosomal chromosomes and QTL in 11 regions were significant at the genome-wide level. A QTL affecting pH value in loin was detected on SSC1 between marker-interval S0312-S0113 with strong statistical support (P < 3.0 x 10(-14)); this QTL was also associated with meat colour and conductivity. QTL for carcass composition and average daily gain was also found on SSC1, suggesting multiple QTL. Seventeen genomic segments had only a single QTL that reached at least suggestive significance. Forty QTL exhibited additive inheritance whereas 31 QTL showed (over-) dominance effects. Two QTL for trait backfat thickness were detected on SSC2; a significant paternal effect was found for a QTL in the IGF2 region while another QTL in the middle of SSC2 showed Mendelian expression.

Background Serum lipids are associated with many serious cardiovascular diseases and obesity problems. Many quantitative trait loci (QTL) have been reported in the pig mostly for performance traits but very few for the serum lipid traits. In contrast, remarkable numbers of QTL are mapped for serum lipids in humans and mice. Therefore, the objective of this research was to investigate the chromosomal regions influencing the serum level of the total cholesterol (CT), triglyceride (TG), high density protein cholesterol (HDL) and low density protein cholesterol (LDL) in pigs. For this purpose, a total of 330 animals from a Duroc × Pietrain F2 resource population were phenotyped for serum lipids using ELISA and were genotyped by using 122 microsatellite markers covering all porcine autosomes for QTL study in QTL Express. Blood sampling was performed at approximately 175 days before slaughter of the pig. Results Most of the traits were correlated with each other and were influenced by average daily gain, slaughter date and age. A total of 18 QTL including three QTL with imprinting effect were identified on 11 different porcine autosomes. Most of the QTL reached to 5% chromosome-wide (CW) level significance including a QTL at 5% experiment-wide (GW) and a QTL at 1% GW level significance. Of these QTL four were identified for both the CT and LDL and two QTL were identified for both the TG and LDL. Moreover, three chromosomal regions were detected for the HDL/LDL ratio in this study. One QTL for HDL on SSC2 and two QTL for TG on SSC11 and 17 were detected with imprinting effect. The highly significant QTL (1% GW) was detected for LDL at 82 cM on SSC1, whereas significant QTL (5% GW) was identified for HDL/LDL on SSC1 at 87 cM. Chromosomal regions with pleiotropic effects were detected for correlated traits on SSC1, 7 and 12. Most of the QTL identified for serum lipid traits correspond with the previously reported QTL for similar traits in other mammals. Two novel QTL on SSC16 for HDL and HDL/LDL ratio and an imprinted QTL on SSS17 for TG were detected in the pig for the first time. Conclusion The newly identified QTL are potentially involved in lipid metabolism. The results of this work shed new light on the genetic background of serum lipid concentrations and these findings will be helpful to identify candidate genes in these QTL regions related to lipid metabolism and serum lipid concentrations in pigs.