We identified a significant QTL for fatty acid composition and fat melting temperature on the p-arm of SSC2. To explore candidate gene(s) for the QTL, we surveyed functional gene information associated with fat metabolism and modification in 30-Mb region around the QTL. There is a gene family of fatty acid desaturase (FADS) consisting of 3 isoform genes aligned in tandem, which may increase the degree of unsaturation of fatty acids. However, no complete gene sequences have been identified, nor function of each isoform has been investigated in pigs. Therefore we aimed to determine the genomic sequence including all porcine FADS isoforms and to clarify the gene expression pattern in liver, skeletal muscle and subcutaneous fat tissues. The full-length sequence of porcine FADS gene family stretched 143kbp. Order and direction of the FADS genes that we determined were identical with those in human, mouse and cattle, suggesting that formation of the gene family might have been evolutionally conserved in mammalian species. Interestingly, unlike other animal species, porcine FADS1 gene expressed alternatively spliced shorter transcript (FADS1S). Gene expression of porcine FADS1 and FADS2 was predominant in liver as observed in the other animals, whereas FADS1S and FADS3 were highly expressed in subcutaneous fat and skeletal muscle tissues, but scarce in liver. Functional analysis of the FADS isoforms on fatty acid composition in a porcine preadipocytes cell line is being carried out.