Abstract
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.
Highlights
In recent years the swine industry has improved production efficiency related traits, such as growth rate, reduced back fat thickness, and feed efficiency, through selective breeding of superior pigs based on available phenotypic information
Ten animals from five different commercial pig breeds representing Duroc, Large White, Landrace, Berkshire and Korean Native pigs were sequenced for the 15 primer sets
We report re-identification of single nucleotide polymorphism (SNP) on pig chromosome 2, SNP allelic frequencies between commercial breeds, and meat quality association of SNP alleles
Summary
In recent years the swine industry has improved production efficiency related traits, such as growth rate, reduced back fat thickness, and feed efficiency, through selective breeding of superior pigs based on available phenotypic information. The consumer’s demand for improved pork quality has increased, but the improvement of pork quality traits has been difficult with breeding schemes using phenotypic information because genetic improvement of meat quality traits requires extensive and expensive measurements of traits at slaughter. Many of the meat quality QTL were mapped to the intermediate region of SSC2 (SW2445-S0565). This identified chromosomal region spans about 100 cM, which contains four different human chromosomal fragments, HAS11, HSA19, HSA1 and HSA5 (Meyers et al, 2005).
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