DOI: 10.5061/dryad.rk744
title: Data from: Association mapping reveals candidate loci for resistance and anemic response to an emerging temperature-driven parasitic disease in a wild salmonid fish

description: Even though parasitic infections are often costly or deadly for the host,
 we know very little which genes influence parasite susceptibility and
 disease severity. Proliferative kidney disease (PKD) is an emerging and,
 at elevated water temperatures, potentially deadly disease of salmonid
 fishes that is caused by the myxozoan parasite Tetracapsuloides
 bryosalmonae. By screening &gt; 7.6 K SNPs in 255 wild brown trout
 (Salmo trutta) and combining association mapping and random forest
 approaches, we identified several candidate genes for both the parasite
 resistance (inverse of relative parasite load; RPL) and the severe anemic
 response to the parasite. The strongest RPL-associated SNP mapped to a
 noncoding region of the congeneric Atlantic salmon (S. salar) chromosome
 10, whereas the second strongest RPL-associated SNP mapped to an intronic
 region of PRICKLE2 gene, which is a part of the planar cell polarity
 signaling pathway involved in kidney development. The top SNP associated
 with anemia mapped to the intron of the putative PRKAG2 gene. The human
 ortholog of this gene has been associated with hematocrit and other
 blood-related traits, making it a prime candidate influencing
 parasite-triggered anemia in brown trout. Our findings demonstrate the
 power of association mapping to pinpoint genomic regions and potential
 causative genes underlying climate change-driven parasitic disease
 resistance and severity. Furthermore, this work illustrates the first
 steps towards dissecting genotype-phenotype links in a wild fish
 population using closely related genome information.
description: 62166_Reference_dRAD_lociFasta file containing 62166 Salmo trutta dRAD loci (or contigs) sequences which were used as a reference for the alignment of all the samples using bowtie2.Genotype fileA total of 12143 brown trout (Salmo trutta) SNPs are provided in Illumina format with first four columns represent Name ("dRAD locus id"-"position of SNP in dRAD locus"), chromosome (in Salmo salar), position in chromosome and strand (orientation of mapped dRAD locus on the S. salar chromosome). Other columns represent samples and each row represent a SNP. The file is required by the R script SNPFiltering_LD_AssociationAnalysis.R which will filter it to 7661 SNPs.255_genos.txtColony_InputThe zip file contains following two files which act as input for COLONY(version 2.0.6.1) for parentage and sibship inference run. Details about input file preparation and parameters for COLONY run are given in the README file.R Scripts For Random Forest AnalysisR code files for the Random Forest analysis performed in this study.RScriptsForRandomForestAnalysis.zipSNPFiltering_LD_AssociationAnalysisR code for SNP filtering, LD calculation and association analysis. The code requires 255_genos.txt (genotypes) and 255_phenotypes_genabel.txt(phenotypes) files to filter out 7661 SNPs and perform association and other analyses.Random Forest Analysis Required FilesThis zip file contains files required by Random Forest analysis or for only plotting the results using PLOTRF_FINAL.R.RandomForestAnalysisRequiredOutputFiles.zipPhenotype fileThis file contains phenotypes of 255 Salmo trutta sampled juveniles.255_phenotypes_genabel.txt