The most important traits of animal are affected by quantitative trait loci and environmental effects. Peroxisome proliferator’s active receptor gamma co activator 1 alpha (PPARGC1A) gene is a member of transcription co activators family, which plays a central role in cellular energy hemostasis regulating. In this study, blood samples were collected from hundred Brown Swiss cow and DNA was extracted from whole blood by modified salting out procedure. Two SNP positions, one located in the 3́-untranslated region (A/C) and the other one in iron 9 of PPARGC1A-T19C were genotyped by PCR-RFLP. Breeding values were individually predicted for milk production, fat and protein milk percent traits by DFREML model one. Association between polymorphisms and breeding values were investigated by SAS at 5% significant level. Genotype frequencies of AA, AC and CC genotypes at PPARGC1a-A968C were 0.593, 0.385 and 0.022, as well as, the allele frequencies of A and C were 0.786 and 0.214, respectively. Genotype frequencies of TT, TC and CC for PPARGC1a-T19C were 0.165, 0.428 and 0.407 and the allele frequencies of T and C were 0.379 and 0.621, respectively. Chi-square test of the both SNPs indicated Hardy-Weinberg expectations (P<0.05). In the both separated and common analyze of polymorphisms, there was no significant associations between genotypes of polymorphisms and breeding values of milk production, fat and protein percent traits, however, increasing the samples are recommended for more precise of statistical analysis and decreasing the mean square of error.
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