Abstract
Bacterial cold water disease (BCWD) is one of the frequent causes of elevated mortality in salmonid aquaculture. Previously, we identified and validated microsatellites on chromosome Omy19 associated with QTL (quantitative trait loci) for BCWD resistance and spleen size in rainbow trout. Recently, SNPs (single nucleotide polymorphism) have become the markers of choice for genetic analyses in rainbow trout as they are highly abundant, cost-effective and are amenable for high throughput genotyping. The objective of this study was to identify SNP markers associated with BCWD resistance and spleen size using both genome-wide association studies (GWAS) and linkage-based QTL mapping approaches. A total of 298 offspring from the two half-sib families used in our previous study to validate the significant BCWD QTL on chromosome Omy19 were genotyped with RAD-seq (restriction-site-associated DNA sequencing), and 7,849 informative SNPs were identified. Based on GWAS, 18 SNPs associated with BCWD resistance and 20 SNPs associated with spleen size were identified. Linkage-based QTL mapping revealed three significant QTL for BCWD resistance. In addition to the previously validated dam-derived QTL on chromosome Omy19, two significant BCWD QTL derived from the sires were identified on chromosomes Omy8 and Omy25, respectively. A sire-derived significant QTL for spleen size on chromosome Omy2 was detected. The SNP markers reported in this study will facilitate fine mapping to identify positional candidate genes for BCWD resistance in rainbow trout.
Highlights
Bacterial cold water disease (BCWD) is one of the frequent causes of elevated mortality in salmonid aquaculture (Nematollahi et al, 2003; Starliper, 2011; Loch and Faisal, 2015)
Based on genome-wide association studies (GWAS), 18 SNPs associated with BCWD resistance and 20 SNPs associated with spleen index were identified
In this study we conducted a wholegenome scan in two half-sib rainbow trout mapping families with the aim to identify SNPs associated with BCWD resistance and spleen size using both GWAS and linkage-based QTL mapping approaches
Summary
Bacterial cold water disease (BCWD) is one of the frequent causes of elevated mortality in salmonid aquaculture (Nematollahi et al, 2003; Starliper, 2011; Loch and Faisal, 2015). The etiological agent of BCWD is a Gram-negative bacterium, Flavobacterium psychrophilum, which causes rainbow trout fry syndrome in small fish. There is no licensed commercial vaccine for BCWD. SNP for BCWD resistance for emergence of antibiotic-resistant pathogens. Host resistance can be improved through selective breeding (Leeds et al, 2010), and a fall-spawning line with improved BCWD resistance evaluated in both laboratory and on-farm tests has been developed (Wiens et al, 2013a). There is interest in improving BCWD resistance of other populations of different origin and spawn times. Conventional family based selection for BCWD resistance relies on indirect phenotype evaluation of siblings, which does not take advantage of the genetic variation within families. The development of molecular markers associated with BCWD resistance would facilitate marker-assisted selection for BCWD resistance and enable direct selection of breeding candidates
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