A Multistage Testing Strategy for Detection of Quantitative Trait Loci Affecting Disease Resistance in Atlantic Salmon

Abstract

A multistage testing strategy to detect QTL for resistance to infectious salmon anemia (ISA) in Atlantic salmon is proposed. First, genotyping of amplified fragment length polymorphisms (AFLP) and a transmission disequilibrium test (TDT) were carried out using dead offspring from a disease resistance challenge test. Second, AFLP genotyping among survivors followed by a Mendelian segregation test was performed. Third, within-family survival analyses using all offspring were developed and applied to significant TDT markers with Mendelian inheritance. Maximum-likelihood methodology was developed for TDT with dominant markers to exploit linkage disequilibrium within families. The strategy was tested with two fullsib families of Atlantic salmon sired by the same male and consisting of 79 offspring in total. All dead offspring from the two families were typed for 64 primer combinations, resulting in 340 scored markers. There were 26 significant results out of 401 TDTs using dead offspring. In the second stage, only 17 marker families showed Mendelian segregation and were tested in survival analysis. A permutation test was performed for all survival analyses to compute experimentwise P-values. Two markers, aaccac356 and agccta150, were significant at P Ͻ 0.05 when accounting for multiple testing in the survival analyses. The proposed strategy might be more powerful than current mapping strategies because it reduces the number of tests to be performed in the last testing stage.

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).…”

Construction of AFLP-based genetic linkage maps for the Chinese shrimp Fenneropaeneus chinensis

“…The genetic linkage maps are powerful tools for genetic improvement in aquaculture. The linkage map would facilitate marker-assisted selective breeding [12,13] , QTL mapping [14,15] , genetic basis of heterosis [16,17] , genome evolution [18] and the patterns of entire genomic divergence [19 22] .…”

Molecular and cellular studies in evolutionary physiology of natural vertebrate populations: influences of individual variation and genetic components on sampling and measurements

“…Gao et al, 2006;Kucerova et al, 2006) and researchers working with Drosophila (Mackay, 2001). Since QTL mapping has been used in production biology in particular, the methodology has mostly concentrated on traits that are important in animal husbandry, such as growth, temperature tolerance and immune responses (Moen et al, 2004;Perry et al, 2005;Reid et al, 2005). So far the methods have only seldom been applied to natural populations, because their effective implementation requires either controlled crosses or data from long pedigrees (e.g.…”