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

• Main Authors: Ahmad, Freed, Debes, Paul, Palomar, Gemma, Vasemägi, Anti
• Format: Dataset
• Language: English
• Published: Dryad 2018
• Subjects: Bioinfomatics; association study; wild population; Host resistance; Parasite-induced Anemia; Phyloinfomatics; Atlantic salmon; Salmo salar
• Online Access: https://dx.doi.org/10.5061/dryad.rk744; https://datadryad.org/stash/dataset/doi: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 ... : 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 ...