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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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Genome scan for caffeine resistance QTL.Scans for population pA and pB are shown in blue and red curves, respectively, and the horizontal dotted lines represent population-specific genomewide 5% permutation thresholds (pA, LOD = 8.1; pB, LOD = 7.4). Genetic distances along the chromosomes are indicated along the x-axis. The centromeres are at positions 54 and 47 on chromosomes 2 and 3, respectively. The positions of the ten QTL we describe in the text are indicated on the plot for ease of reference. Intervals implicated by these QTL are highlighted as vertical bars, with pA-specific QTL in light blue, pB-specific QTL in pink, and QTL identified in both panels in yellow.
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pgen.1005663.g001: Genome scan for caffeine resistance QTL.Scans for population pA and pB are shown in blue and red curves, respectively, and the horizontal dotted lines represent population-specific genomewide 5% permutation thresholds (pA, LOD = 8.1; pB, LOD = 7.4). Genetic distances along the chromosomes are indicated along the x-axis. The centromeres are at positions 54 and 47 on chromosomes 2 and 3, respectively. The positions of the ten QTL we describe in the text are indicated on the plot for ease of reference. Intervals implicated by these QTL are highlighted as vertical bars, with pA-specific QTL in light blue, pB-specific QTL in pink, and QTL identified in both panels in yellow.

Mentions: Using the same approach we have used previously [15, 31], we mapped QTL for caffeine resistance separately in both pA and pB DSPR mapping populations, identifying ten QTL contributing to resistance (Fig 1 and Tables 1 and S1). Three QTL are common to both populations (i.e., the 2-LOD support intervals overlap), one is unique to pA, and six are unique to pB. Given that the seven unique QTL generally explain smaller fractions of the heritability than the three common QTL (Table 1), it is possible we simply had insufficient power to detect them in the other panel of RILs. However, we cannot discount the possibility that alleles underlying these panel-specific QTL are private to a given panel. Under the assumption the QTL mapped are independent, and act additively, the total variance explained by all mapped QTL is simply the sum of the individual estimated heritability values. On this basis, in the pA population the four mapped QTL explain 31.9% of the broad-sense heritability for the trait, while in pB the nine mapped QTL explain 50.2% of the heritability.


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)

Genome scan for caffeine resistance QTL.Scans for population pA and pB are shown in blue and red curves, respectively, and the horizontal dotted lines represent population-specific genomewide 5% permutation thresholds (pA, LOD = 8.1; pB, LOD = 7.4). Genetic distances along the chromosomes are indicated along the x-axis. The centromeres are at positions 54 and 47 on chromosomes 2 and 3, respectively. The positions of the ten QTL we describe in the text are indicated on the plot for ease of reference. Intervals implicated by these QTL are highlighted as vertical bars, with pA-specific QTL in light blue, pB-specific QTL in pink, and QTL identified in both panels in yellow.
© Copyright Policy
Related In: Results  -  Collection

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

pgen.1005663.g001: Genome scan for caffeine resistance QTL.Scans for population pA and pB are shown in blue and red curves, respectively, and the horizontal dotted lines represent population-specific genomewide 5% permutation thresholds (pA, LOD = 8.1; pB, LOD = 7.4). Genetic distances along the chromosomes are indicated along the x-axis. The centromeres are at positions 54 and 47 on chromosomes 2 and 3, respectively. The positions of the ten QTL we describe in the text are indicated on the plot for ease of reference. Intervals implicated by these QTL are highlighted as vertical bars, with pA-specific QTL in light blue, pB-specific QTL in pink, and QTL identified in both panels in yellow.
Mentions: Using the same approach we have used previously [15, 31], we mapped QTL for caffeine resistance separately in both pA and pB DSPR mapping populations, identifying ten QTL contributing to resistance (Fig 1 and Tables 1 and S1). Three QTL are common to both populations (i.e., the 2-LOD support intervals overlap), one is unique to pA, and six are unique to pB. Given that the seven unique QTL generally explain smaller fractions of the heritability than the three common QTL (Table 1), it is possible we simply had insufficient power to detect them in the other panel of RILs. However, we cannot discount the possibility that alleles underlying these panel-specific QTL are private to a given panel. Under the assumption the QTL mapped are independent, and act additively, the total variance explained by all mapped QTL is simply the sum of the individual estimated heritability values. On this basis, in the pA population the four mapped QTL explain 31.9% of the broad-sense heritability for the trait, while in pB the nine mapped QTL explain 50.2% of the heritability.

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