Association mapping reveals candidate loci for resistance and anaemic response to an emerging temperature‐driven parasitic disease in a wild salmonid fish

Abstract

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 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 anaemic 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 signalling pathway involved in kidney development. The top SNP associated with anaemia mapped to the intron of the putative PRKAG2 gene. The human ortholog of this gene has been associated with haematocrit and other blood-related traits, making it a prime candidate influencing parasite-triggered anaemia 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.

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness — Implications for brown trout conservation

“…3,800 SNPs than when using microsatellites (Linlokken, Haugen, Mathew, Johansen, & Lien, ). In contrast, 14 microsatellites and 1,728 SNPs agreed on 98% of full‐sibs identified from 255 individuals in brown trout from River Altja (Ahmad, Debes, Palomar, & Vasemägi, ; Debes et al, ). The different results on family identification with the two marker types can therefore be partly explained by sample size; in this study, <30 individuals from each population were genotyped using both markers, and Linlokken et al () used 47–48 individuals per population from three populations.…”

Know your enemy – transcriptome of myxozoanTetracapsuloides bryosalmonaereveals potential drug targets against proliferative kidney disease in salmonids

“…In order to assemble a host-free parasite transcriptome, the filtered reads were first mapped to the Atlantic salmon genome (GCF_000233375.1) and the unmapped reads were subsequently mapped to the northern pike ( Esox lucius , Esociformes) genome (GCF_000721915.2) using Hisat2 (v. 2.0.1; score-min = L,0,−0.4) (Kim et al ., 2015). We used chromosome level assembly of Atlantic salmon genome (Lien et al ., 2016), as it is evolutionarily close to brown trout (Ahmad et al ., 2018; Lemopoulos et al ., 2018), and at the time of analysis, genome assembly of S. trutta was not available. Esociformes represents the closest order to Salmoniformes (Rondeau et al ., 2014).…”

New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data

“…Candidates of selection unique to lakes belonging to metapopulation 2 are identified, namely five windows in coding regions uniquely shared between lakes Blanktjärnen, Grubbvattnet and Nils‐Jonsa (Table S12). These windows are overlapped by seven genes, of which three are described in fish: tsn associated with sperm quality in rainbow trout ( Oncorhynchus mykiss ; Nynca et al., 2014), loc115151923 which is near a SNP involved in immune response in brown trout (Ahmad et al., 2018) and meat tenderness in rainbow trout (Ali et al., 2019), and loc115195360 which is implied in immune response in stickleback ( Gasterosteus aculeatus ; Fuess et al., 2021).…”