UCP2 and PPARG gene polymorphisms and their association with milk yield and composition traits in goats

•Polymorphisms in the UCP2 and PPARG genes were identified.•Polymorphisms in the goat UCP2 gene are associated with milk production and quality.•Polymorphism in the goat PPARG gene is associated with milk production and quality.•Polymorphisms were identified by an unconventional electrophoresis migration pattern. With the present study, we aimed to identify polymorphisms in the genes encoding mitochondrial uncoupling protein 2 (UCP2) and peroxisome proliferator-activated receptor gamma (PPARG), and to evaluate their associations with breeding values for milk production and composition traits in goats. Breeding values were estimated from milk yield and composition data of Saanen and Alpine animals using a single-trait model. The number of animals used for the estimation of breeding values ranged from 1,094 to 1,292, depending on the trait studied. After identification of the polymorphisms, the animals were genotyped for association analysis. Among animals with estimated breeding values, we randomly genotyped 185 for the UCP2.29614171G/A polymorphism located in the promoter region of the UCP2 gene, 176 for the UCP2.29615319G/A polymorphism located in exon 2 of the UCP2 gene, and 194 for the PPARG-A/B polymorphism located in the promoter region of the PPARG gene. For the UCP2 gene, the UCP2.29614171G/A polymorphism showed association (P