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Identifying Loci Contributing to Natural Variation in Xenobiotic Resistance in Drosophila.

Najarro MA, Hackett JL, Smith BR, Highfill CA, King EG, Long AD, Macdonald SJ - PLoS Genet. (2015)

Bottom Line: Furthermore, copy number variation at Cyp12d1 is strongly associated with phenotype in the DSPR, with a trend in the same direction observed in the DGRP (Drosophila Genetic Reference Panel).No additional plausible causative polymorphisms were observed in a full genomewide association study in the DGRP, or in analyses restricted to QTL regions mapped in the DSPR.Just as in human populations, replicating modest-effect, naturally-segregating causative variants in an association study framework in flies will likely require very large sample sizes.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America.

ABSTRACT
Natural populations exhibit a great deal of interindividual genetic variation in the response to toxins, exemplified by the variable clinical efficacy of pharmaceutical drugs in humans, and the evolution of pesticide resistant insects. Such variation can result from several phenomena, including variable metabolic detoxification of the xenobiotic, and differential sensitivity of the molecular target of the toxin. Our goal is to genetically dissect variation in the response to xenobiotics, and characterize naturally-segregating polymorphisms that modulate toxicity. Here, we use the Drosophila Synthetic Population Resource (DSPR), a multiparent advanced intercross panel of recombinant inbred lines, to identify QTL (Quantitative Trait Loci) underlying xenobiotic resistance, and employ caffeine as a model toxic compound. Phenotyping over 1,700 genotypes led to the identification of ten QTL, each explaining 4.5-14.4% of the broad-sense heritability for caffeine resistance. Four QTL harbor members of the cytochrome P450 family of detoxification enzymes, which represent strong a priori candidate genes. The case is especially strong for Cyp12d1, with multiple lines of evidence indicating the gene causally impacts caffeine resistance. Cyp12d1 is implicated by QTL mapped in both panels of DSPR RILs, is significantly upregulated in the presence of caffeine, and RNAi knockdown robustly decreases caffeine tolerance. Furthermore, copy number variation at Cyp12d1 is strongly associated with phenotype in the DSPR, with a trend in the same direction observed in the DGRP (Drosophila Genetic Reference Panel). No additional plausible causative polymorphisms were observed in a full genomewide association study in the DGRP, or in analyses restricted to QTL regions mapped in the DSPR. Just as in human populations, replicating modest-effect, naturally-segregating causative variants in an association study framework in flies will likely require very large sample sizes.

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Related in: MedlinePlus

Founder haplotype means and 1-SDs for the three QTL mapped in both panels of DSPR RILs.Means are presented for both pA (light gray bars) and pB (dark gray bars), and the number of RILs for which we assign a founder genotype (probability > 0.95) is listed at the bottom of each bar. Only founder means associated with at least 5 observations are presented. Since line AB8 was used to found both synthetic populations, and the haplotype mean was independently estimated from pA and pB RILs, the line is presented twice in each plot.
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pgen.1005663.g002: Founder haplotype means and 1-SDs for the three QTL mapped in both panels of DSPR RILs.Means are presented for both pA (light gray bars) and pB (dark gray bars), and the number of RILs for which we assign a founder genotype (probability > 0.95) is listed at the bottom of each bar. Only founder means associated with at least 5 observations are presented. Since line AB8 was used to found both synthetic populations, and the haplotype mean was independently estimated from pA and pB RILs, the line is presented twice in each plot.

Mentions: For each QTL we estimated the phenotypic effects associated with each founder haplotype (Figs 2 and S3). In many cases it is difficult to clearly discriminate a pattern indicating that just two functional alleles, i.e., "high" and "low" resistance alleles, segregate at mapped loci. It is possible these QTL represent loci segregating for a series of alleles, as we have suggested previously for toxicity and expression QTL mapped in the DSPR [32, 36], and others have observed for QTL mapped in other populations derived from multiple founders [26, 37]. Nevertheless, given we are mapping QTL to intervals ~500-kb, and because multiple very-closely linked QTL would also be expected to yield non-biallelic patterns of founder effects, we cannot be confident that QTL are truly multi-allelic.


Identifying Loci Contributing to Natural Variation in Xenobiotic Resistance in Drosophila.

Najarro MA, Hackett JL, Smith BR, Highfill CA, King EG, Long AD, Macdonald SJ - PLoS Genet. (2015)

Founder haplotype means and 1-SDs for the three QTL mapped in both panels of DSPR RILs.Means are presented for both pA (light gray bars) and pB (dark gray bars), and the number of RILs for which we assign a founder genotype (probability > 0.95) is listed at the bottom of each bar. Only founder means associated with at least 5 observations are presented. Since line AB8 was used to found both synthetic populations, and the haplotype mean was independently estimated from pA and pB RILs, the line is presented twice in each plot.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664282&req=5

pgen.1005663.g002: Founder haplotype means and 1-SDs for the three QTL mapped in both panels of DSPR RILs.Means are presented for both pA (light gray bars) and pB (dark gray bars), and the number of RILs for which we assign a founder genotype (probability > 0.95) is listed at the bottom of each bar. Only founder means associated with at least 5 observations are presented. Since line AB8 was used to found both synthetic populations, and the haplotype mean was independently estimated from pA and pB RILs, the line is presented twice in each plot.
Mentions: For each QTL we estimated the phenotypic effects associated with each founder haplotype (Figs 2 and S3). In many cases it is difficult to clearly discriminate a pattern indicating that just two functional alleles, i.e., "high" and "low" resistance alleles, segregate at mapped loci. It is possible these QTL represent loci segregating for a series of alleles, as we have suggested previously for toxicity and expression QTL mapped in the DSPR [32, 36], and others have observed for QTL mapped in other populations derived from multiple founders [26, 37]. Nevertheless, given we are mapping QTL to intervals ~500-kb, and because multiple very-closely linked QTL would also be expected to yield non-biallelic patterns of founder effects, we cannot be confident that QTL are truly multi-allelic.

Bottom Line: Furthermore, copy number variation at Cyp12d1 is strongly associated with phenotype in the DSPR, with a trend in the same direction observed in the DGRP (Drosophila Genetic Reference Panel).No additional plausible causative polymorphisms were observed in a full genomewide association study in the DGRP, or in analyses restricted to QTL regions mapped in the DSPR.Just as in human populations, replicating modest-effect, naturally-segregating causative variants in an association study framework in flies will likely require very large sample sizes.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America.

ABSTRACT
Natural populations exhibit a great deal of interindividual genetic variation in the response to toxins, exemplified by the variable clinical efficacy of pharmaceutical drugs in humans, and the evolution of pesticide resistant insects. Such variation can result from several phenomena, including variable metabolic detoxification of the xenobiotic, and differential sensitivity of the molecular target of the toxin. Our goal is to genetically dissect variation in the response to xenobiotics, and characterize naturally-segregating polymorphisms that modulate toxicity. Here, we use the Drosophila Synthetic Population Resource (DSPR), a multiparent advanced intercross panel of recombinant inbred lines, to identify QTL (Quantitative Trait Loci) underlying xenobiotic resistance, and employ caffeine as a model toxic compound. Phenotyping over 1,700 genotypes led to the identification of ten QTL, each explaining 4.5-14.4% of the broad-sense heritability for caffeine resistance. Four QTL harbor members of the cytochrome P450 family of detoxification enzymes, which represent strong a priori candidate genes. The case is especially strong for Cyp12d1, with multiple lines of evidence indicating the gene causally impacts caffeine resistance. Cyp12d1 is implicated by QTL mapped in both panels of DSPR RILs, is significantly upregulated in the presence of caffeine, and RNAi knockdown robustly decreases caffeine tolerance. Furthermore, copy number variation at Cyp12d1 is strongly associated with phenotype in the DSPR, with a trend in the same direction observed in the DGRP (Drosophila Genetic Reference Panel). No additional plausible causative polymorphisms were observed in a full genomewide association study in the DGRP, or in analyses restricted to QTL regions mapped in the DSPR. Just as in human populations, replicating modest-effect, naturally-segregating causative variants in an association study framework in flies will likely require very large sample sizes.

Show MeSH
Related in: MedlinePlus