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The objective of this study was to characterize caprine GPR54 gene, a key mediator of molecular mechanism of reproduction (puberty and prolificacy) in mammals. A panel of 9 Indian goat breeds differing in sexual precocity and prolificacy (Black-Bengal, Malabari, Beetal, Barbari, Osmanabadi, Sangamneri, Jakhrana, Ganjam and Sirohi) were utilized for polymorphism scanning of GPR54 gene by direct DNA sequencing. Exon 1, 2 and 3 along with adjacent intronic regions of the GPR54 gene were amplified with 5 primer pairs and 2 novel SNPs, 1 each in exon 1 (C1122T) and intron 1 (T1830C) were recorded. All the variations and SNPs were synonymous. The results showed that these mutations existed in both, sexually precocious and late-maturing goat breeds as well as low and high prolificacy goat breeds. The results extend the limited information on genetic variation of the caprine GPR54 gene, which might contribute towards molecular breeding to enhance productivity of goat.