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The UCP-1 gene is linked with obesity-related characteristics, non-shivering thermogenesis, and the quality and amount of milk and meat produced. The goal of this research was to discover genetic variations in the UCP-1 gene in three indigenous goat breeds from Sindh, Pakistan, with the hope of improving their breeding prospects. According to the results of this study, there were eight single-nucleotide variants found in the UCP-1 gene across all three goat breeds. Three mutations in the Sindh Desi goat breed were discovered using PCR-Gel Electrophoresis and DNA sequencing methods, while three mutations in the Barbari goat breed were identified, and two mutations in the Tapri breed were uncovered using DNA sequencing techniques. Depending on their genetic coding, these mutations may be classified as one of three kinds of point mutations. For example, in the Sindh Desi goat breed, two missense mutations and one silent mutation have been identified; in the Barbari goat breed, there has been one missense mutation and two silent mutations identified; and in the Tapri goat breed, there has been one missense mutation and one silent mutation identified. Our results may be used as a reference and guidance for choosing high-quality milk and meat for industrial purposes and when crossbreeding and genetic improvement activities are carried out on the animals.