The Porcine SNP database has a huge number of SNPs, but these SNPs are mostly found by computer data-mining procedures and have not been well characterized. We re-sequenced 1,439 porcine public SNPs from four commercial pig breeds and one Korean domestic breed (Korean Native pig, KNP) by using two DNA pools from eight unrelated animals in each breed. These SNPs were from 419 protein-coding genes covering the 18 autosomes, and the re-sequencing in breeds confirmed 690 public SNPs (47.9%) and 226 novel mutations (173 SNPs and 53 insertions/deletions). Thus, totally, 916 variations were found from our study. Of the 916 variations, 148 SNPs (16.2%) were found across all the five breeds, and 199 SNPs (21.7%) were breed specific polymorphisms. According to the SNP locations in the gene sequences, these 916 variations were categorized into 802 non-coding SNPs (785 in intron, 17 in 3'-UTR) and 114 coding SNPs (86 synonymous SNPs, 28 non-synonymous SNPs). The nucleotide substitution analyses for these SNPs revealed that 70.2% were from transitions, 20.0% from transversions, and the remaining 5.79% were deletions or insertions. Subsequently, we genotyped 261 SNPs from 180 genes in an experimental KNP × Landrace F2 cross by the Sequenom MassARRAY system. A total of 33 traits including growth, carcass composition and meat quality were analyzed for the phenotypic association tests using the 132 SNPs in 108 genes with minor allele frequency (MAF)>0.2. The association results showed that five marker-trait combinations were significant at the 5% experiment-wise level (ADCK4 for rear leg, MYH3 for rear leg, Hunter B, Loin weight and Shearforce) and four at the 10% experiment-wise level (DHX38 for average daily gain at live weight, LGALS9 for crude lipid, NGEF for front leg and LIFR for pH at 24 h). In addition, 49 SNPs in 44 genes showing significant association with the traits were detected at the 1% comparison-wise level. A large number of genes that function as enzymes, transcription factors or signalling molecules were considered as genetic markers for pig growth (RNF103, TSPAN31, DHX38, ABCF1, ABCC10, SCD5, KIAA0999 and FKBP10), muscling (HSPA5, PTPRM, NUP88, ADCK4, PLOD1, DLX1 and GRM8), fatness (PTGIS, IDH3B, RYR2 and NOL4) and meat quality traits (DUSP4, LIFR, NGEF, EWSR1, ACTN2, PLXND1, DLX3, LGALS9, ENO3, EPRS, TRIM29, EHMT2, RBM42, SESN2 and RAB4B). The SNPs or genes reported here may be beneficial to future marker assisted selection breeding in pigs.
These results suggest that hOGG1 is associated with the susceptibility to CaP and its aggressive clinicopathological characteristics.
The pork from black-coated pigs is famous among-consumers for better eating quality. The loci affecting black coat color was identified in pig chromosome 6 in which several genetic effects on pork quality have been reported. The melanocortin 1 receptor (MC1R) gene is a major gene which plays a key role in regulation of eumelanin (black/brown) and phaeomelanin (red/yellow). In this study, the MC1R gene polymorphism was analyzed for pig breed determination and genetic association with pork quality traits. MC1R Ala243Thr variation was analyzed to determine a specific genotype for four commercial pig breeds (Landrace, Yorkshire, Berkshire and, Duroc) and a Korean native pigs (KNP). Then we developed original KNP-specific DNA markers to determine the pork from black-coated pigs using MC1R DNA sequences. The total length of the MC1R coding sequence ranged 1451bp in KNP. KNP had the 0201 allele pertaining to E D1 but some of the KNP had the E P allele, probably reflecting the geneticintrogression of E P allele into KNP. Furthermore, a relationship between Leu102Pro single nucleotide polymorphism (SNP) genotype and pork quality phenotype were analyzed in F2 reciprocal-crossbred population between KNP and Yorkshire. Association analysis indicated that the allele of the MC1R gene has no effect on pork quality. These results suggest that black coat-color is not directly associated with preferred pork quality, but the black-coat color pig breed may have other genetic components for superior pork quality.
Several studies have reported quantitative trait loci (QTL) for meat quality on porcine chromosome 2 (http://www.animalgenome.org/QTLdb/pig.html). For application of the molecular genetic information to the pig industry through marker-assisted selection, single nucleotide polymorphism (SNP) markers were analyzed by comparative re-sequencing of polymerase chain reaction (PCR) products of 13 candidate genes with DNA from commercial pig breeds such as Berkshire, Yorkshire, Landrace, Duroc and Korean Native pig. A total of 34 SNPs were identified in 15 PCR products producing an average of one SNP in every 253 bp. PCR restriction fragment length polymorphism (RFLP) assays were developed for 11 SNPs and used to investigate allele frequencies in five commercial pig breeds in Korea. Eight of the SNPs appear to be fixed in at least one of the five pig breeds, which indicates that different selection among pig breeds might be applied to these SNPs. Polymorphisms detected in the PTH, CSF2 and FOLR genes were chosen to genotype a Berkshire-Yorkshire pig breed reference family for linkage and association analyses. Using linkage analysis, PTH and CSF2 loci were mapped to pig chromosome 2, while FOLR was mapped to pig chromosome 9. Association analyses between SNPs in the PTH, CSF2 and FOLR suggested that the CSF2 MboII polymorphism was significantly associated with several pork quality traits in the Berkshire and Yorkshire crossed F2 pigs. Our current findings provide useful SNP marker information to fine map QTL regions on pig chromosome 2 and to clarify the relevance of SNP and quantitative traits in commercial pig populations.
A total of 5450 sequences obtained from the NCBI pig SNP database were consolidated into 465 unique sequences (189 singleton sequences and 276 contigs). These 465 sequences contained 1787 putative SNPs and had strong sequence homology to 433 human protein-coding genes based on blast analyses. These genes were assigned to the pig QTL maps (http://www.animalgenome.org/QTLdb/pig.html) via the human and pig comparative maps established by a pig radiation hybrid (RH) map. The SNP information characterized from this study provides a useful functional gene variation resource to facilitate QTL data mining in the pig genome.
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