10.5061/DRYAD.R5V40
Marriage, Tara N.
University of Kansas
King, Elizabeth G.
University of California, Irvine
Long, Anthony D.
University of California, Irvine
Macdonald, Stuart J.
University of Kansas
Data from: Fine-mapping nicotine resistance loci in Drosophila using a
multiparent advanced generation inter-cross population
Dryad
dataset
2015
DSPR
Nicotine
QTL mapping
2015-04-29T00:00:00Z
2015-04-29T00:00:00Z
en
https://doi.org/10.1534/genetics.114.162107
3985656937 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Animals in nature are frequently challenged by toxic compounds, from those
that occur naturally in plants as a defense against herbivory, to
pesticides used to protect crops. On exposure to such xenobiotic
substances, animals mount a transcriptional response, generating
detoxification enzymes and transporters that metabolize and remove the
toxin. Genetic variation in this response can lead to variation in the
susceptibility of different genotypes to the toxic effects of a given
xenobiotic. Here we use Drosophila melanogaster to dissect the genetic
basis of larval resistance to nicotine, a common plant defense chemical
and widely used addictive drug in humans. We identified quantitative trait
loci (QTL) for the trait using the DSPR (Drosophila Synthetic Population
Resource), a panel of multiparental advanced intercross lines. Mapped QTL
collectively explain 68.4% of the broad-sense heritability for nicotine
resistance. The two largest-effect loci—contributing 50.3 and 8.5% to the
genetic variation—map to short regions encompassing members of classic
detoxification gene families. The largest QTL resides over a cluster of
ten UDP-glucuronosyltransferase (UGT) genes, while the next largest QTL
harbors a pair of cytochrome P450 genes. Using RNA-seq we measured gene
expression in a pair of DSPR founders predicted to harbor different
alleles at both QTL and showed that Ugt86Dd, Cyp28d1, and Cyp28d2 had
significantly higher expression in the founder carrying the allele
conferring greater resistance. These genes are very strong candidates to
harbor causative, regulatory polymorphisms that explain a large fraction
of the genetic variation in larval nicotine resistance in the DSPR.
R script for QTL analysis (B population)This R script allows a user to
read in genotype data for the DSPR (Drosophila Synthetic Population
Resource, FlyRILs.org) and nicotine resistance phenotype data, and
recapitulate the QTL mapping results presented in Marriage et al. for the
"B" population of DSPR RILs.Nicotine_pB_AnalysisCode.RR script
for QTL analysis (A population)This R script allows a user to read in
genotype data for the DSPR (Drosophila Synthetic Population Resource,
FlyRILs.org) and nicotine resistance phenotype data, and recapitulate the
QTL mapping results presented in Marriage et al. for the "A"
population of DSPR RILs.Nicotine_pA_AnalysisCode.RNicotine Resistance
Phenotypes (A population)This file contains nicotine resistance measures
for a large number of A lines from the Drosophila Synthetic Population
Resource (DSPR, www.FlyRILs.org). Line identifiers are presented in the
"patRIL" column, and phenotypes are presented in the
"NicotineViability" column. Together with genotype data and
analytical R code this file allows users to generate the QTL mapping
results presented in Marriage et al. for the A population of DSPR
RILs.NicotinePheno_A.txtNicotine Resistance Phenotypes (B population)This
file contains nicotine resistance measures for a large number of B lines
from the Drosophila Synthetic Population Resource (DSPR, www.FlyRILs.org).
Line identifiers are presented in the "patRIL" column, and
phenotypes are presented in the "NicotineViability" column.
Together with genotype data and analytical R code this file allows users
to generate the QTL mapping results presented in Marriage et al. for the B
population of DSPR RILs.NicotinePheno_B.txtDSPR Genotypes (A
population)This file contains genotypes for the population A RILs
(Recombination Inbred Lines) of the DSPR (Drosophila Synthetic Population
Resource). The genotypes were originally published in King et al. (Genome
Research 2012, 22:1558-66) and are also available at www.FlyRILs.org (Data
Release 2 - HMM Results for pA RILs at regularly spaced 10 kb intervals).
The genotypes are derived from a Hidden Markov Model (HMM) at regularly
spaced 10KB positions along the Drosophila melanogaster genome. There are
no column headers in the file. Columns are: chromosome, genome position,
line identifier, 36 columns of founder genotype probabilities, and 8
columns of additive probabilities. The precise names for each of the
columns are listed in the analysis R code file for population A. Together
with this code, and the nicotine resistance phenotype scores, a user can
recapitulate the QTL mapping from Marriage et al.HMMregA_R2.tgzDSPR
Genotypes (B population)This file contains genotypes for the population B
RILs (Recombination Inbred Lines) of the DSPR (Drosophila Synthetic
Population Resource). The genotypes were originally published in King et
al. (Genome Research 2012, 22:1558-66) and are also available at
www.FlyRILs.org (Data Release 2 - HMM Results for pB RILs at regularly
spaced 10 kb intervals). The genotypes are derived from a Hidden Markov
Model (HMM) at regularly spaced 10KB positions along the Drosophila
melanogaster genome. There are no column headers in the file. Columns are:
chromosome, genome position, line identifier, 36 columns of founder
genotype probabilities, and 8 columns of additive probabilities. The
precise names for each of the columns are listed in the analysis R code
file for population B. Together with this code, and the nicotine
resistance phenotype scores, a user can recapitulate the QTL mapping from
Marriage et al.HMMregB_R2.tgz