Polymorphisms in Promoter Regions of Lipid/Adipocyte-Related Genes in Pigs and Their Distribution Among Different Breeds

Polymorphisms on the genomic sequence may cause variation of phenotypes in livestock animals. Particularly, polymorphisms in the sequences recognized by transcription factors are candidates that may affect expression of the corresponding genes, resulting in alteration of the phenotypes. We surveyed polymorphisms within the genomic sequences upstream of the genes related to lipid biosynthesis and adipocyte differentiation. We selected pig genes corresponding to the human genes according to the Gene Ontology terms related to lipid biosynthesis and adipocyte differentiation, as well as loci on the pig genome corresponding to transcripts the expression of which was upregulated during adipocyte differentiation shown by a microarray analysis. Probes to concentrate approximately 10 Mb genomic DNA in total, covering 4 kb-upstream regions of the selected loci were then designed. Western (30) and Chinese (11) breed pigs and Asian wild boars (8) were subjected to genomic DNA concentration and sequencing by an ionPGM system. We detected more than 110,000 SNPs within the concentrated genomic regions among the sequenced animals. SNPs within the sequences estimated as binding sites of transcription factors related to lipid biosynthesis and adipocyte differentiation, implied by the JASPAR2014 database, were more than 11,000. Furthermore, the SNP set included 182 SNPs showing almost segregated distribution of alleles between Western and Chinese breed groups (MAF ≤ 0.05). Further investigation on the relationship of the SNPs with known QTLs and influence on expression of the genes will provide clues to clarify genes/polymorphisms responsible to fat-related traits.