Pigs have been one of the most important sources of meat for humans, and their productivity has been substantially improved by recent strong selection. Here, we present whole-genome resequencing analyses of 55 pigs of five breeds representing Korean native pigs, wild boar and three European origin breeds. 1,673.1 Gb of sequence reads were mapped to the Swine reference assembly, covering ∼99.2% of the reference genome, at an average of ∼11.7-fold coverage. We detected 20,123,573 single-nucleotide polymorphisms (SNPs), of which 25.5% were novel. We extracted 35,458 of non-synonymous SNPs in 9,904 genes, which may contribute to traits of interest. The whole SNP sets were further used to access the population structures of the breeds, using multiple methodologies, including phylogenetic, similarity matrix, and population structure analysis. They showed clear population clusters with respect to each breed. Furthermore, we scanned the whole genomes to identify signatures of selection throughout the genome. The result revealed several promising loci that might underlie economically important traits in pigs, such as the CLDN1 and TWIST1 genes. These discoveries provide useful genomic information for further study of the discrete genetic mechanisms associated with economically important traits in pigs.

In livestock social interactions, social genetic effects (SGE) represent associations between phenotype of one individual and genotype of another. Such associations occur when the trait of interest is affected by transmissible phenotypes of social partners. The aim of this study was to estimate SGE and direct genetic effects (DGE, genetic effects of an individual on its own phenotype) on average daily gain (ADG) in Landrace pigs, and to conduct single-step genome-wide association study using SGE and DGE as dependent variables to identify quantitative trait loci (QTLs) and their positional candidate genes. A total of 1,041 Landrace pigs were genotyped using the Porcine SNP 60K BeadChip. Estimates of the two effects were obtained using an extended animal model. The SGE contributed 16% of the total heritable variation of ADG. The total heritability estimated by the extended animal model including both SGE and DGE was 0.52. The single-step genome-wide association study identified a total of 23 QTL windows for the SGE on ADG distributed across three chromosomes (i.e., SSC1, SSC2, and SSC6). Positional candidate genes within these QTL regions included PRDM13, MAP3K7, CNR1, HTR1E, IL4, IL5, IL13, KIF3A, EFHD2, SLC38A7, mTOR, CNOT1, PLCB2, GABRR1, and GABRR2, which have biological roles in neuropsychiatric processes. The results of biological pathway and gene network analyses also support the association of the neuropsychiatric processes with SGE on ADG in pigs. Additionally, a total of 11 QTL windows for DGE on ADG in SSC2, 3, 6, 9, 10, 12, 14, 16, and 17 were detected with positional candidate genes such as ARL15. We found a putative pleotropic QTL for both SGE and DGE on ADG on SSC6. Our results in this study provide important insights that can help facilitate a better understanding of the molecular basis of SGE for socially affected traits.

ABSTRACT. Meat pH is an important factor influencing meat quality traits in swine. This study evaluated a large number of genetic variants that covered all of the swine chromosomal regions. Approximately 68,000 single nucleotide polymorphisms (SNPs), found on Illumina Porcine SNP chips, were tested for associations with meat pH values. A genome-wide association study (GWAS) found that 19 SNPs on Sus scrofa chromosome 4 were significantly associated with pH. Two major candidate genomic regions were defined: a 1.08-Mb region (at nucleotide 30118313 to 31207050) contained 10 significant SNPs, based on an effect value of 5.0; and a 2.7-Mb genomic region (at nucleotide 73293076 to 76023681) contained 9 significant SNPs. Three putative genes -PKHD1L1, VCPIP1, and LOC102166532 -were identified by GWAS near significant SNPs. These genes may account for variations in pH levels. Three pseudogenes and two non-coding RNAs were also detected by GWAS analysis. Estimations of expected and observed P values for pH revealed significant departures from the null hypothesis. A total of 9 haplotype blocks (HB) were constructed: HBs 1, 3, and 5 showed significant effects on pH 24 and pH 45 , whereas an association was not confirmed between pH 24 and HBs 4, 6, 15669 Identification of genomic region for the ultimate pH ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (4): 15668-15682 (2015) and 8. Findings from this study indicate that the three genes identified may influence pH of pig meat.