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The work aimed genetically to characterize the Murrah, Mediterranean and mixed-breed populations based on polymorphisms in the melatonin 1A receptor gene promoter (MTRN1A) and associate the genotypes with milk production. The haplotype A (position -1511 T and -1482 presents ACAA) and haplotype B (position -1511 C and -1482 does not present ACAA) were found in all groups. The haplotype frequencies were in Murrah breed (A=0.66 and B=0.34), Mediterranean breed (A=0.73 and B=0.27), and mixed-breed (A=0.65 and B=0.35). The Murrah breed had the genotypes AA (0.44), AB (0.44) and BB (0.12), and the Mediterranean and mixed-breed buffaloes had the genotypes AA (0.52) and (0.46), AB (0.42) and (0.39), and BB (0.06) and (0.15), respectively. For the Murrah, Mediterranean, and mixed-breed buffaloes, respectively, the expected heterozygosity values were 0.45, 0.40, and 0.45, the inbreeding coefficients were 0.04, -0.03, and 0.18, and the Hardy-Weinberg probabilities were 0.92, 0.24, and 0.59, respectively. The genotypes evaluated did not have an effect on milk production; however, the single nucleotide polymorphisms (SNP) and the insertion/deletion polymorphism (INDEL) can be used in studies on genetic variability.
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