ABSTRACT:The melatonin receptors are G protein-coupled receptors (GPCR) that bind melatonin. Three types of melatonin receptors have been cloned. The MTNR1A (or Mel1A or MT1) and MTNR1B (or Mel1B or MT2) receptor subtypes are present in humans and other mammals, while an additional melatonin receptor subtype MTNR1C (or Mel1C or MT3) has been identified in amphibians and birds. Previous research has shown that the three common melatonin receptors regulate physiological processes, including seasonal reproduction and ovarian physiology. However, whether or not any polymorphisms of the different melatonin receptor subtypes are associated with reproductive traits in chickens is not known. In this study, we performed candidate gene analysis to identify single-nucleotide polymorphisms (SNPs) in the MTNR1A, MTNR1B, and MTNR1C genes in the Erlang Mountain Chicken population. SNP discovery was achieved by sequencing pooled DNA samples. Direct PCR-sequencing, PCR-SSCP/PCR-sequencing, and PCR-RFLP method were used to genotype the MTNR1A, MTNR1B, and MTNR1C genes, respectively. The GLM Procedure was used to estimate the statistical significance of association between genotypes at each locus and reproductive traits of chickens. In a sample of 460 chickens, four novel polymorphisms (JQ249890:g.384T>C, JQ249891:g.387T>C, JQ249894:g.63C>T, and JQ249896:g.294G>A) were detected in the melatonin receptor genes MTNR1A, MTNR1B, and MTNR1C, respectively. A statistically significant association (P < 0.01) was found between two SNPs (MTNR1A SNP, MTNR1C SNP) and reproductive traits: egg number at 300 days of age (EN) and age at first egg (AFE).