Data from: Association mapping reveals candidate loci for resistance and anemic response to an emerging temperature-driven parasitic disease in a wild salmonid fish
Ahmad, Freed, University of Turku
Debes, Paul, University of Helsinki, University of Turku
Palomar, Gemma, University of Oviedo
Vasemägi, Anti, Estonian University of Life Sciences, University of Turku
Published Feb 01, 2018 on Dryad.
Cite this dataset
Ahmad, Freed; Debes, Paul; Palomar, Gemma; Vasemägi, Anti (2018). Data from: Association mapping reveals candidate loci for resistance and anemic response to an emerging temperature-driven parasitic disease in a wild salmonid fish [Dataset]. Dryad. https://doi.org/10.5061/dryad.rk744
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 > 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.
Fasta 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.
A 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.
The zip file contains following two files which act as input for COLONY(version 184.108.40.206) 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 Analysis
R code files for the Random Forest analysis performed in this study.
R 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 Files
This zip file contains files required by Random Forest analysis or for only plotting the results using PLOTRF_FINAL.R.
This file contains phenotypes of 255 Salmo trutta sampled juveniles.