Identification of quantitative trait loci in swine using a candidate gene approach
Ten genes--fatty acid binding protein ('FABP ') '3, 4, 5, 6' and histone deacetylase ('HDAC ') '1, 2, 3, 5, 6' and '8' were investigated for polymorphisms and associations with growth, carcass composition and meat quality in swine. A three-generation resource population ((H * D) * LW) with 429 progeny was developed from a cross of Hampshire (H), Duroc (D) and Large White pigs (LW). A total of 105 traits such as bodyweight, loin eye area, backfat thickness and intramuscular fat were measured. Thirteen polymorphic loci were identified in seven of the ten candidate genes examined in the resource population. Eight of these polymorphisms were selected for further genotyping and analysis; 'FABP3-HaeIII, FABP3-MspI, FABP4-BsmI, FABP5-AvaII, FABP5-Tsp509I, HDACI-HinfI, HDAC3-Tsp5091' and ' HDAC5-AciI'. Fifty-nine significant associations were revealed between the eight polymorphic loci and the tested traits. Thirteen were significant with modified Bonferroni correction. The 'FABP5-AvaII' locus had significant associations with two measures of backfat thickness (P < 0.0004 and 0.016), loin fat (P < 0.008), loin eye area at slaughter (P < 0.002) and weight of boneless back (P < 0.005), loin dry matter and untrimmed belly (P < 0.006). Allele 2 of the 'FABP5-AvaII' locus was associated with lower fat deposition, higher loin lean and higher dry matter, and allele 1 tended to be dominant over allele 2 in the effects. There were significant associations of the 'FABP5-Tsp509I' locus with body weight between 80 and 92 kg and loin fat P2 (fat depth measured at the point of the loin width measurement). Significant associations were found between the 'FABP3-HaeIII' locus and intramuscular fat content, and weights of primal shoulder and primal belly; between the ' FABP3-MspI' locus and body weight between 44 and 80 kg, and weight of tenderloin lean (P < 0.0003); and between the 'FABP4-BsmI' locus and body weight between 87 and 96 kg. There were significant associations of the 'HDAC1-HinfI' locus with body weight between 72 and 80 kg and backfat thickness at 73-kg body weight; and of the 'HDAC5-AciI ' locus with loin fat P1 (fat depth measured at the point of the loin depth measurement) and ham pH.