PMC:1181811 / 13863-19047 JSONTXT

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Though we considered all three of these to be valid possibilities, we initially focused on the likelihood that deletion or mutation within the coding sequence of a single D2 Tas2r would correlate with the QHCl taste insensitivity phenotype.\nTwenty-four intact Tas2rs, along with three apparent Tas2r pseudogenes, have been identified in the distal chromosome 6 cluster of B6 mice [19] (Figure 4). We designed oligonucleotides to non-coding regions flanking the coding sequence of each intact Tas2r [see Additional file 2]. Using these oligos, we amplified each Tas2r coding sequence from D2 genomic DNA. PCR products were subcloned into cloning vectors and sequenced. Comparisons of the sequences of B6 and D2 orthologues revealed that only two of the twenty-four Tas2r alleles examined, Tas2r106 and Tas2r124, were identical across strains at the amino acid level (data not shown). A third, Tas2r120, could not be amplified from D2 genomic DNA (Figure 5) using either of two pairs of oligonucleotides (Additional file 2), suggesting that this Tas2r is deleted in D2 mice. Two D2 alleles, Tas2r103 and Tas2r117, contained numerous missense mutations and small deletions that create frame shifts and premature termination; these two genes may be pseudogenes in this strain. The remaining 19 Tas2rs contained between one and 16 missense mutations. All 24 Tas2rs examined have different alleles in B6 and D2 mice, and 307 single nucleotide polymorphisms are present within coding exons (data not shown). Although polymorphic residues between B6 and D2 Tas2rs are found in all regions of the receptors, 23% of the amino acid changes seen are within the first two extracellular loops of the T2Rs (data not shown).\nFigure 5 Allelic variation across strains for four Tas2rs. B6 and D2 alleles of four Tas2rs can be differentiated based on diagnostic restriction digests of amplified PCR products (Tas2r105, Tas2r116 and Tas2r131) or on the presence or absence of a PCR product (Tas2r120). In each of the 17 BXD strains tested, Tas2r genotype was always correlated with QHCl taster phenotype (blue = B6 taster phenotype, red = D2 taster phenotype). See additional file 1: Table 3 for restriction enzymes and oligonucleotides. The variability between orthologous receptors in these two inbred strains suggested that it might be possible to narrow the physical boundaries of the QHCl taste QTL by determining which Tas2r alleles are correlated with QHCl taste sensitivity. Therefore, we proceeded to screen genomic DNA from 29 available BXD RI lines, including the 17 that we had used in taste testing, for the Tas2r alleles they contained. In most cases, we were able to identify diagnostic restriction endonuclease digests that would allow us to quickly identify whether a particular Tas2r PCR product was amplified from a B6 or D2 allele. We did not analyze three genes (Tas2r104, Tas2r114 and Tas2r110) where no diagnostic restriction endonuclease could be identified. For Tas2r120, which is likely deleted in D2 mice, the absence of a PCR product was diagnostic of the D2 genotype for this gene.\nSurprisingly, we discovered that there have been no apparent recombination events within the distal chromosome 6 cluster during the generation of the BXD RI lines. For all RI lines tested, every Tas2r within an individual RI line originated from the same parental strain (Figures 5, 6). Furthermore, the genotype of each Tas2r gene always correlated with the QHCl taste phenotype (Figures 6, 7), suggesting that the entire Tas2r cluster is a single haplotype that varies with QHCl taster status.\nFigure 6 The Tas2r cluster is a single haplotype in BXD/Ty RI mice. The coding exon of each of 21 Tas2rs in the distal chromosome 6 cluster was amplified genomic DNA from 29 BXD/Ty RI strains. Each Tas2r within an individual BXD strain originated from the same parental strain (B6 allele = gray, D2 allele = white). The 17 BXD strains that were behaviorally tested in this study are indicated (*).\nFigure 7 Tas2r genotype correlates with QHCl taste phenotype. Mean lick ratios of B6, D2 and BXD strains reported in Figure 1 are grouped based on Tas2r haplotype (B6 haplotype = blue, D2 haplotype = red). B6 mice (blue line on left panel) are more sensitive to 1 mM and 3 mM QHCl than are D2 mice (red line on left panel) in brief access taste tests. Similarly, BXD strains with the B6 Tas2r haplotype (blue lines, right panel) are more sensitive to QHCl than are BXD strains with the D2 Tas2r haplotype (red lines, right panel). The BXD strains are listed in order from least to most sensitive to 1 mM 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