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Mapping of a chromosome 12 region associated with airway hyperresponsiveness in a recombinant congenic mouse strain and selection of potential candidate genes by expression and sequence variation analyses.

Kanagaratham C, Marino R, Camateros P, Ren J, Houle D, Sladek R, Vidal SM, Radzioch D - PLoS ONE (2014)

Bottom Line: Candidate genes within the QTL were selected based on expression differences in mRNA from whole lungs, and the presence of coding non-synonymous mutations that were predicted to have a functional effect by amino acid substitution prediction tools.One QTL for AHR was identified on Chromosome 12 with its 95% confidence interval ranging from 54.6 to 82.6 Mbp and a maximum LOD score of 5.11 (p = 3.68 × 10(-3)).Within the QTL, genes with deleterious coding variants, such as Foxa1, and genes with expression differences, such as Mettl21d and Snapc1, were selected as possible candidates for the AHR phenotype.

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, McGill University, Montreal, Quebec, Canada.

ABSTRACT
In a previous study we determined that BcA86 mice, a strain belonging to a panel of AcB/BcA recombinant congenic strains, have an airway responsiveness phenotype resembling mice from the airway hyperresponsive A/J strain. The majority of the BcA86 genome is however from the hyporesponsive C57BL/6J strain. The aim of this study was to identify candidate regions and genes associated with airway hyperresponsiveness (AHR) by quantitative trait locus (QTL) analysis using the BcA86 strain. Airway responsiveness of 205 F2 mice generated from backcrossing BcA86 strain to C57BL/6J strain was measured and used for QTL analysis to identify genomic regions in linkage with AHR. Consomic mice for the QTL containing chromosomes were phenotyped to study the contribution of each chromosome to lung responsiveness. Candidate genes within the QTL were selected based on expression differences in mRNA from whole lungs, and the presence of coding non-synonymous mutations that were predicted to have a functional effect by amino acid substitution prediction tools. One QTL for AHR was identified on Chromosome 12 with its 95% confidence interval ranging from 54.6 to 82.6 Mbp and a maximum LOD score of 5.11 (p = 3.68 × 10(-3)). We confirmed that the genotype of mouse Chromosome 12 is an important determinant of lung responsiveness using a Chromosome 12 substitution strain. Mice with an A/J Chromosome 12 on a C57BL/6J background have an AHR phenotype similar to hyperresponsive strains A/J and BcA86. Within the QTL, genes with deleterious coding variants, such as Foxa1, and genes with expression differences, such as Mettl21d and Snapc1, were selected as possible candidates for the AHR phenotype. Overall, through QTL analysis of a recombinant congenic strain, microarray analysis and coding variant analysis we identified Chromosome 12 and three potential candidate genes to be in linkage with airway responsiveness.

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Association of Chromosome 12 markers with airway responsiveness in BcA86 mice.(A) Distribution of LOD scores of markers on Chromosome 12 used to genotype BcA86F2 mice. Dashed line at LOD  = 2.97 represents the 95% LOD threshold for significance generated from 10,000 permutations of randomized associations of the BcA86F2 genotype and phenotype data. Bayes 95% credible interval (CI) was used to determine the QTL confidence interval delimited by markers (grey dots) D12Mit285 at 54.6 Mbp (LOD score  = 4.68) and D12Mit158 at 82.6Mbp (LOD score  = 4.47). The most significant marker in the region is D12Mit52 (★) at 77.0Mbp with a LOD score of 5.11 and p = 3.68×10−3. (B) Distribution of log2(Penh) among the three possible genotypes at D12Mit52 (AA = homozygous for A/J, BB = homozygous for C57BL/6J and AB = heterozygous). Groups with A/J genotype at D12Mit52 (AA and AB) have significantly greater mean log2(Penh) value than homozygous C57BL/6J group (BB) (AA: 1.264 ± 0.151, AB: 0.879 ± 0.114, and BB: 0.102 ± 0.157). Data are presented as mean ± SEM and *** represents p<0.001 from one-way ANOVA and Bonferroni correction.
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pone-0104234-g003: Association of Chromosome 12 markers with airway responsiveness in BcA86 mice.(A) Distribution of LOD scores of markers on Chromosome 12 used to genotype BcA86F2 mice. Dashed line at LOD  = 2.97 represents the 95% LOD threshold for significance generated from 10,000 permutations of randomized associations of the BcA86F2 genotype and phenotype data. Bayes 95% credible interval (CI) was used to determine the QTL confidence interval delimited by markers (grey dots) D12Mit285 at 54.6 Mbp (LOD score  = 4.68) and D12Mit158 at 82.6Mbp (LOD score  = 4.47). The most significant marker in the region is D12Mit52 (★) at 77.0Mbp with a LOD score of 5.11 and p = 3.68×10−3. (B) Distribution of log2(Penh) among the three possible genotypes at D12Mit52 (AA = homozygous for A/J, BB = homozygous for C57BL/6J and AB = heterozygous). Groups with A/J genotype at D12Mit52 (AA and AB) have significantly greater mean log2(Penh) value than homozygous C57BL/6J group (BB) (AA: 1.264 ± 0.151, AB: 0.879 ± 0.114, and BB: 0.102 ± 0.157). Data are presented as mean ± SEM and *** represents p<0.001 from one-way ANOVA and Bonferroni correction.

Mentions: BcA86F2 mice were genotyped at 88 markers located within the previously identified nine recombinant regions of the BcA86 strain [10], [15]. To identify which genomic regions of BcA86 are associated with the AHR phenotype we did a QTL mapping analysis using the phenotype and genotype data of BcA86F2 mice. Of the 88 markers, nine consecutive markers on Chromosome 12 were significantly associated with the AHR phenotype, and surpassed the 95% threshold generated from 10,000 permutations (LOD threshold  = 2.97) (Table 1 and Table S1). One 28Mbp QTL was identified on Chromosome 12 whose 95% confidence interval was delimited on the left and right by markers D12Mit285 and D12Mit158, at 54.6Mbp and 82.6Mbp, respectively (Figure 3A). This QTL explains 12.5% of the phenotypic variance observed in the BcA86F2 mice. All eight markers within this region surpassed the 95% and 99% LOD threshold generated from 10,000 permutations (LOD threshold  = 2.97 and 3.65, respectively) (Table 1). The most significant marker among these eight markers is D12Mit52 at 77.0 Mbp, with a LOD score of 5.11 (p = 3.68×10−3). The distribution of phenotypes among the possible genotypes at D12Mit52 showed that the replacement of a C57BL/6J allele with an A/J allele causes an increase in log2(Penh). Mean log2(Penh) of animals with homozygous A/J genotype (AA) or heterozygous genotype (AB) was significantly higher than animals with homozygous C57BL/6J genotypes (BB) (Figure 3B). Two-QTL analysis did not identify any additional loci apart from the significant one on Chromosome 12.


Mapping of a chromosome 12 region associated with airway hyperresponsiveness in a recombinant congenic mouse strain and selection of potential candidate genes by expression and sequence variation analyses.

Kanagaratham C, Marino R, Camateros P, Ren J, Houle D, Sladek R, Vidal SM, Radzioch D - PLoS ONE (2014)

Association of Chromosome 12 markers with airway responsiveness in BcA86 mice.(A) Distribution of LOD scores of markers on Chromosome 12 used to genotype BcA86F2 mice. Dashed line at LOD  = 2.97 represents the 95% LOD threshold for significance generated from 10,000 permutations of randomized associations of the BcA86F2 genotype and phenotype data. Bayes 95% credible interval (CI) was used to determine the QTL confidence interval delimited by markers (grey dots) D12Mit285 at 54.6 Mbp (LOD score  = 4.68) and D12Mit158 at 82.6Mbp (LOD score  = 4.47). The most significant marker in the region is D12Mit52 (★) at 77.0Mbp with a LOD score of 5.11 and p = 3.68×10−3. (B) Distribution of log2(Penh) among the three possible genotypes at D12Mit52 (AA = homozygous for A/J, BB = homozygous for C57BL/6J and AB = heterozygous). Groups with A/J genotype at D12Mit52 (AA and AB) have significantly greater mean log2(Penh) value than homozygous C57BL/6J group (BB) (AA: 1.264 ± 0.151, AB: 0.879 ± 0.114, and BB: 0.102 ± 0.157). Data are presented as mean ± SEM and *** represents p<0.001 from one-way ANOVA and Bonferroni correction.
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Related In: Results  -  Collection

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pone-0104234-g003: Association of Chromosome 12 markers with airway responsiveness in BcA86 mice.(A) Distribution of LOD scores of markers on Chromosome 12 used to genotype BcA86F2 mice. Dashed line at LOD  = 2.97 represents the 95% LOD threshold for significance generated from 10,000 permutations of randomized associations of the BcA86F2 genotype and phenotype data. Bayes 95% credible interval (CI) was used to determine the QTL confidence interval delimited by markers (grey dots) D12Mit285 at 54.6 Mbp (LOD score  = 4.68) and D12Mit158 at 82.6Mbp (LOD score  = 4.47). The most significant marker in the region is D12Mit52 (★) at 77.0Mbp with a LOD score of 5.11 and p = 3.68×10−3. (B) Distribution of log2(Penh) among the three possible genotypes at D12Mit52 (AA = homozygous for A/J, BB = homozygous for C57BL/6J and AB = heterozygous). Groups with A/J genotype at D12Mit52 (AA and AB) have significantly greater mean log2(Penh) value than homozygous C57BL/6J group (BB) (AA: 1.264 ± 0.151, AB: 0.879 ± 0.114, and BB: 0.102 ± 0.157). Data are presented as mean ± SEM and *** represents p<0.001 from one-way ANOVA and Bonferroni correction.
Mentions: BcA86F2 mice were genotyped at 88 markers located within the previously identified nine recombinant regions of the BcA86 strain [10], [15]. To identify which genomic regions of BcA86 are associated with the AHR phenotype we did a QTL mapping analysis using the phenotype and genotype data of BcA86F2 mice. Of the 88 markers, nine consecutive markers on Chromosome 12 were significantly associated with the AHR phenotype, and surpassed the 95% threshold generated from 10,000 permutations (LOD threshold  = 2.97) (Table 1 and Table S1). One 28Mbp QTL was identified on Chromosome 12 whose 95% confidence interval was delimited on the left and right by markers D12Mit285 and D12Mit158, at 54.6Mbp and 82.6Mbp, respectively (Figure 3A). This QTL explains 12.5% of the phenotypic variance observed in the BcA86F2 mice. All eight markers within this region surpassed the 95% and 99% LOD threshold generated from 10,000 permutations (LOD threshold  = 2.97 and 3.65, respectively) (Table 1). The most significant marker among these eight markers is D12Mit52 at 77.0 Mbp, with a LOD score of 5.11 (p = 3.68×10−3). The distribution of phenotypes among the possible genotypes at D12Mit52 showed that the replacement of a C57BL/6J allele with an A/J allele causes an increase in log2(Penh). Mean log2(Penh) of animals with homozygous A/J genotype (AA) or heterozygous genotype (AB) was significantly higher than animals with homozygous C57BL/6J genotypes (BB) (Figure 3B). Two-QTL analysis did not identify any additional loci apart from the significant one on Chromosome 12.

Bottom Line: Candidate genes within the QTL were selected based on expression differences in mRNA from whole lungs, and the presence of coding non-synonymous mutations that were predicted to have a functional effect by amino acid substitution prediction tools.One QTL for AHR was identified on Chromosome 12 with its 95% confidence interval ranging from 54.6 to 82.6 Mbp and a maximum LOD score of 5.11 (p = 3.68 × 10(-3)).Within the QTL, genes with deleterious coding variants, such as Foxa1, and genes with expression differences, such as Mettl21d and Snapc1, were selected as possible candidates for the AHR phenotype.

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, McGill University, Montreal, Quebec, Canada.

ABSTRACT
In a previous study we determined that BcA86 mice, a strain belonging to a panel of AcB/BcA recombinant congenic strains, have an airway responsiveness phenotype resembling mice from the airway hyperresponsive A/J strain. The majority of the BcA86 genome is however from the hyporesponsive C57BL/6J strain. The aim of this study was to identify candidate regions and genes associated with airway hyperresponsiveness (AHR) by quantitative trait locus (QTL) analysis using the BcA86 strain. Airway responsiveness of 205 F2 mice generated from backcrossing BcA86 strain to C57BL/6J strain was measured and used for QTL analysis to identify genomic regions in linkage with AHR. Consomic mice for the QTL containing chromosomes were phenotyped to study the contribution of each chromosome to lung responsiveness. Candidate genes within the QTL were selected based on expression differences in mRNA from whole lungs, and the presence of coding non-synonymous mutations that were predicted to have a functional effect by amino acid substitution prediction tools. One QTL for AHR was identified on Chromosome 12 with its 95% confidence interval ranging from 54.6 to 82.6 Mbp and a maximum LOD score of 5.11 (p = 3.68 × 10(-3)). We confirmed that the genotype of mouse Chromosome 12 is an important determinant of lung responsiveness using a Chromosome 12 substitution strain. Mice with an A/J Chromosome 12 on a C57BL/6J background have an AHR phenotype similar to hyperresponsive strains A/J and BcA86. Within the QTL, genes with deleterious coding variants, such as Foxa1, and genes with expression differences, such as Mettl21d and Snapc1, were selected as possible candidates for the AHR phenotype. Overall, through QTL analysis of a recombinant congenic strain, microarray analysis and coding variant analysis we identified Chromosome 12 and three potential candidate genes to be in linkage with airway responsiveness.

Show MeSH
Related in: MedlinePlus