Whole-genome association analysis of pork meat pH revealed three significant regions and several potential genes in Finnish Yorkshire pigs.

BACKGROUND: One of the most commonly used quality measurements of pork is pH measured 24 h after slaughter. The most probable mode of inheritance for this trait is oligogenic with several known major genes, such as PRKAG3. In this study, we used whole-genome SNP genotypes of over 700 AI boars; after a quality check, 42,385 SNPs remained for association analysis. All the boars were purebred Finnish Yorkshire. To account for relatedness of the animals, a pedigree-based relationship matrix was used in a mixed linear model to test the effect of SNPs on pH measured from loin. A bioinformatics analysis was performed to identify the most promising genes in the significant regions related to meat quality. RESULTS: Genome-wide association study (GWAS) revealed three significant chromosomal regions: one on chromosome 3 (39.9 Mb-40.1 Mb) and two on chromosome 15 (58.5 Mb-60.5 Mb and 132 Mb-135 Mb including PRKAG3). A conditional analysis with a significant SNP in the PRKAG3 region, MARC0083357, as a covariate in the model retained the significant SNPs on chromosome 3. Even though linkage disequilibrium was relatively high over a long distance between MARC0083357 and other significant SNPs on chromosome 15, some SNPs retained their significance in the conditional analysis, even in the vicinity of PRKAG3. The significant regions harbored several genes, including two genes involved in cyclic AMP (cAMP) signaling: ADCY9 and CREBBP. Based on functional and transcription factor-gene networks, the most promising candidate genes for meat pH are ADCY9, CREBBP, TRAP1, NRG1, PRKAG3, VIL1, TNS1, and IGFBP5, and the key transcription factors related to these genes are HNF4A, PPARG, and Nkx2-5. CONCLUSIONS: Based on SNP association, pathway, and transcription factor analysis, we were able to identify several genes with potential to control muscle cell homeostasis and meat quality. The associated SNPs can be used in selection for better pork. We also showed that post-GWAS analysis reveals important information about the genes' potential role on meat quality. The gained information can be used in later functional studies.

Strategic use of anti-GnRH vaccine allowing selection of breeding boars without adverse effects on reproductive or production performances.

Boar stations raise only entire male pigs for selection as reproductive boars, but the majority of them will fail the selection process, ending at slaughter with a high risk of boar tainted meat. The aim of this study was to investigate whether a single dose of Improvac given to 16-week old boars had a negative effect on their subsequent sperm numbers and motility in 16 artificial insemination boars. We also aimed to generate more knowledge on incidence of boar taint at slaughter among Finnish pigs, compare production performances as average daily gain, feed conversion ratio, and carcass and meat quality (lean meat percentage, back fat, pH, color, androstenone, and skatole) of immunocastrated boars (n = 248) with those of entire boars (n = 268). Moreover, we aimed also to explore whether a fat biopsy taken at 16 weeks of age could already reveal the presence of boar taint compounds and be predictive of boar taint development at slaughter age. We found that 32% of entire boars (Figen Landrace, Figen Large White, and their crossbreed) slaughtered at an age of 25 weeks presented levels of androstenone and/or skatole above the threshold for boar taint in their meat. These boars (control) had higher androstenone and skatole levels in the back fat samples at slaughter (0.77 ± 0.55 and 0.09 ± 0.06 µg/g, respectively, mean ± standard deviation) than those in the immuno group (0.20 ± 0.25 and 0.06 ± 0.03 µg/g, respectively, P < 0.001). A single dose of anti-GnRH vaccine, given at 16 weeks of age, did not affect future sperm numbers and motility of boars selected for artificial insemination. We found no difference in the levels of testosterone, anti-GnRH antibodies titers, testicle morphology, and sperm numbers and motility between the boars vaccinated once, at 16 weeks of age, with anti-GnRH vaccine and the control boars (no vaccination). There were no differences in average daily gain, feed conversion ratio, lean meat percentage, and back fat between the immunocastrated boars and entire boars. Meat from immunocastrated boars had a higher pH and better color than meat from entire boars (P < 0.001), suggesting slightly improved meat quality.

Large-scale association study for structural soundness and leg locomotion traits in the pig.

BACKGROUND: Identification and culling of replacement gilts with poor skeletal conformation and feet and leg (FL) unsoundness is an approach used to reduce sow culling and mortality rates in breeding stock. Few candidate genes related to soundness traits have been identified in the pig. METHODS: In this study, 2066 commercial females were scored for 17 traits describing body conformation and FL structure, and were used for association analyses. Genotyping of 121 SNPs derived from 95 genes was implemented using Sequenom's MassARRAY system. RESULTS: Based on the association results from single trait and principal components using mixed linear model analyses and false discovery rate testing, it was observed that APOE, BMP8, CALCR, COL1A2, COL9A1, DKFZ, FBN1 and VDBP were very highly significantly (P < 0.001) associated with body conformation traits. The genes ALOX5, BMP8, CALCR, OPG, OXTR and WNT16 were very highly significantly (P < 0.001) associated with FL structures, and APOE, CALCR, COL1A2, GNRHR, IHH, MTHFR and WNT16 were highly significantly (P < 0.01) associated with overall leg action. Strong linkage disequilibrium between CALCR and COL1A2 on SSC9 was detected, and haplotype -ACGACC- was highly significantly (P < 0.01) associated with overall leg action and several important FL soundness traits. CONCLUSION: The present findings provide a comprehensive list of candidate genes for further use in fine mapping and biological functional analyses.