Effect of melatonin on the circadian phenotype of Clock/+ mice. (A) Histogram of pineal melatonin content in N2 hybrid mice. Data are from 61 [(C3H/HeJ × C57BL/6J)F1 × C57BL/6J]N2 and 66 [(C3H/HeJ × BALB/cJ)F1 × BALB/cJ]N2 hybrid mice. A horizontal bar indicates those animals scored as melatonin positive. (B) Loci on the distal ends of chromosomes 11 and X are tightly linked to melatonin content. A total of 9 mice (4 from a C3H/HeJ × BALB/cJ cross and 5 from a C3H/HeJ × C57BL/6J cross) were genotyped with a custom SNP panel described previously (29). Two candidate suppressor loci were identified on these chromosomes: Aanat on 11 and Asmt on X. A two-way ANOVA was significant in the C57BL/6J × C3H/HeJ cross for Aanat genotype [F(1, 57) = 11.65, P = 0.001), Asmt genotype [F(1,57) = 9.37, P = 0.0033] and their interaction [F(1,57) = 5.07, P = 0.028]. In the BALB/cJ × C3H/HeJ cross, a two-way ANOVA was significant for Aanat genotype [F(1,61) = 7.16, P = 0.0095] and Asmt genotype [F(1,61) = 15.85, P = 0.00018]. Their interaction was not significant [F(1,61) = 1.88, P = 0.17]. Blue indicates BALB/cJ or C57BL/6J genome and pink indicates C3H/HeJ genome. (C) Effect of strain background on pineal melatonin content in Clock/+ [(C3H/HeJ × C57BL/6J)F1 × C57BL/6J]N2 mice. A total of 105 progeny were genotyped for the Aanat and Asmt loci. Mice carrying C3H alleles at both the Aanat and Asmt loci had significantly higher pineal melatonin content than animals with one or more B6 alleles. A two-way ANOVA was significant for Aanat genotype [F(1,101) = 21.7, P = 9.6 × 10−6], Asmt genotype [F(1,101) = 34.4, P = 6.0 × 10−8], and their interaction [F(1,101) = 12.4, P = 6.4 × 10−4]. For the Aanat locus, B stands for B6/B6 and H stands for B6/C3H genotypes. For the Asmt locus, B stands for either B6/B6 (female) or B6 (male). H stands for either B6/C3H (female) or C3H (male). (D) Effect of genotype of Aanat and Asmt on circadian free-running period in 157 [(C3H/HeJ × C57BL/6J)F1 × C57BL/6J]N2 mice. Mice carrying C3H alleles at Aanat and Asmt expressed shorter free-running periods than those carrying B6 alleles at either locus. A two-way ANOVA was significant for Aanat genotype [F(1,153) = 15.35, P = 1.3 × 10−4] and Asmt genotype [F(1,153) = 9.25, P = 2.7 × 10−3]. The interaction between Aanat and Asmt was not significant [F(1,153) = 0.31, P = 0.57]. Abbreviations of genotype are the same as in Fig. 3C.