Mapping of a quantitative trait locus for resistance against infectious salmon anaemia in Atlantic salmon (Salmo Salar): comparing survival analysis with analysis on affected/resistant data

Abstract

Background: Infectious Salmon Anaemia (ISA) is a viral disease affecting farmed Atlantic salmon (Salmo salar) worldwide. The identification of Quantitative Trait Loci (QTL) affecting resistance to the disease could improve our understanding of the genetics underlying the trait and provide a means for Marker-Assisted Selection. We previously performed a genome scan on commercial Atlantic salmon families challenge tested for ISA resistance, identifying several putative QTL. In the present study, we set out to validate the strongest of these QTL in a larger family material coming from the same challenge test, and to determine the position of the QTL by interval mapping. We also wanted to explore different ways of performing QTL analysis within a survival analysis framework (i.e. using time-to-event data), and to compare results using survival analysis with results from analysis on the dichotomous trait 'affected/resistant'.

A major effect quantitative trait locus for whirling disease resistance identified in rainbow trout (Oncorhynchus mykiss)

“…It is unlikely, however, that a single gene is causing resistance to both of these parasites given that salmonid strains resistant to C. shasta are susceptible to M. cerebralis (Hedrick et al, 2001). Another salmonid disease that has mapped to the O. mykiss Omy9 homolog in Atlantic salmon is infectious salmon anemia (Moen et al, 2007). Therefore, it is possible that this chromosome is enriched for salmonid disease resistance genes, although without a sequenced genome, this is highly speculative.…”

Major Quantitative Trait Loci Affect Resistance to Infectious Pancreatic Necrosis in Atlantic Salmon (Salmo salar)

“…mbb.sfu.ca/GRASPlinkage.html), which combines molecular marker and mapping data from the Genomic Research on Atlantic Salmon Project (GRASP) (http:// grasp.mbb.sfu.ca/), the Salmon Genome Project (SGP) (http:/ /www.salmongenome.no/cgi-bin/sgp.cgi), and the European Union collaborative SALMAP project (http:/ / www.salmongenome.no/cgi-bin/sgp.cgi). These maps have facilitated the detection of QTL in salmon affecting body weight and condition factor (Reid et al 2005), while molecular markers have also been linked to disease resistance against infectious salmon anemia (ISA) (Grimholt et al 2003;Moen et al 2004bMoen et al , 2007, furunculosis (Grimholt et al 2003), and the ectoparasite Gyrodactylus salaris (Gilbey et al 2006). Furthermore, in the closely related rainbow trout, two QTL have been identified with a highly significant effect on freshwater IPN resistance in a backcross family (Ozaki et al 2001).…”

Genomics and Genome Sequencing: Benefits for Finfish Aquaculture

“…Previous studies determined that there is a genetic component to ISA resistance in Atlantic salmon (Gjøen & Bentsen 1997, Ødegård et al, 2007 and a QTL for this trait was mapped . A more recent study confirmed this QTL and showed that it explains 6% of the phenotypic variation and 32-47% of the additive genetic variation (Moen et al, 2007). A comparative genomics analysis of the most likely QTL region suggested several candidate genes for ISA resistance (Li et al, 2011a).…”

“…It is no surprise therefore, that several QTL have been identified for body weight and condition factor in Atlantic salmon (Baranski et al, 2010;Boulding et al, 2008;Moghadam et al, 2007;Reid et al, 2005) (Moghadam et al, 2007;Kuttner et al, 2011). QTL for several other traits in salmonids have been mapped, including upper temperature tolerance (Jackson et al, 1998;Perry et al, 2001;Somorjai et al, 2003), spawning time (O'Malley et al, 2003), developmental rate (Nichols et al, 2008), and resistance to pathogens Gilbey et al, 2006;Houston et al , 2009Houston et al , 2010Jones et al, 2002;Moen et al 2007Moen et al , 2009a. Given that many of the microsatellite markers derived from one salmonid species amplify the DNA from other salmonid species, it has been relatively straightforward to carry out comparative analyses of the rainbow trout, Arctic charr and Atlantic salmon genomes .…”