Comparative Genomics and Positional Cloning

Genetic linkage maps of molecular markers have facilitated the identification of quantitative trait loci (QTL) for economically important traits in a variety of cultured fish species (Tao and Boulding 2003, Cnaani et al. 2004, Reid et al. 2005). In rainbow trout, several QTLs have been identified for disease resistance (Palti et al. 1999, Ozaki et al. 2001), environmental stress tolerance (Danzmann et al. 1999, Perry et al. 2001), and spawning dates (Sakamoto et al. 1999, O'Malley et al. 2003). In tilapia, QTLs for sex determination and stress response have been identified in several different species (Lee et al. 2003, Lee et al. 2004, Cnaani et al. 2004). The next obvious goal is to identify the causative genes underlying these QTLs. By identifying these genes, and studying their function, we will gain insight into the physiological mechanisms underlying traits such as growth rate, salinity tolerance, and disease resistance. Identification of the genes also lays the groundwork for marker-assisted selective breeding to improve commercial stocks. Positional cloning to identify the genes underlying QTL is still a very challenging task, and requires a convergence of three genetic resources. The first of these is a large population segregating for the QTL. Fortunately, most aquaculture species are fecund, and rearing large F2 or backcross families is not difficult. The second resource is a collection of closely spaced molecular markers to allow fine-scale genetic mapping of the QTL. These are typically microsatellite markers, but increasingly single-nucleotide polymorphisms (SNP) are being used. The third essential resource is an ordered collection of physical clones, or even better, the DNA sequence, spanning the region containing the QTL. Because research funds are finite, it is not likely that complete genome sequences for the great diversity of fish species used in aquaculture will be available soon. Only a few biomedical model species (e.g., Fugu, Tetraodon, Oryzias, Danio) have been sequenced to date. Even if genome sequencing is initiated for important aquaculture species, it will likely progress only as far as a relatively incomplete draft assembly. For the foreseeable future, genome resources for these species will be limited to moderate density genetic linkage maps of microsatel-lite markers, and physical maps based on restriction fingerprints of large-insert bacterial artificial chromosome (BAC) clones (Table 19.1). Nevertheless, even with this minimal set of resources, it should be possible to positionally clone genes for important traits. Positional cloning is the process of mapping QTL to ever-smaller …