An AFLP-based approach for the identification of sex-linked markers in rainbow trout (Oncorhynchus mykiss)

A DNA AFLP-fingerprinting approach has been used in this study for the identification of sex-linked markers in rainbow trout. Using a sex-typed pool strategy we analyzed a total of 486 different primer combinations of which 19 gave sex-associated amplification across the pooled DNA samples. Segregation analysis showed that 18 out of 19 AFLPs (95%) were informative for individual sexing and genetic mapping. Fifteen AFLPs that showed sex-associated amplification in the pooled segregant analysis were converted into single locus markers (SCARs). One out of 15, the SCAR Omy-163, was Y chromosome-linked and mapped near the sex locus in all of four genetically diverse male clonal lines of rainbow trout examined. Three microsatellites, Ots517NWFSC, OmyFGT19TUF and Omm1026, which were previously mapped on the sex linkage group in rainbow trout, were also analyzed. The SCAR Omy-163, Ots517NWFC and OmyFGT19TUF showed low levels of intraspecific allelic polymorphism. Y chromosome-linked AFLP markers were relatively strain-specific suggesting an intraspecific genetic polymorphism of the rainbow trout Y-chromosome. Estimation of the level of polymorphism for AFLPs using one of our strains revealed that approximately 34,506 putative loci were tested in our study of which about 4374 were polymorphic. Considering 11 Y-linked polymorphic loci in this strain, we estimated that 0.25% of polymorphic loci (11/4374) were confined to a single sex. Assuming that the length of the rainbow trout genome is estimated to be 2627.5 cM (2.4×106 kb), the male-determining region detected using our screen may span 6.6 cM (6100 kb). The AFLP technique provides an efficient marker system for revealing polymorphic loci and for linkage map construction. An AFLP approach in combination with a sex-type pool strategy resulted in a quick analysis for identifying sex-linked loci in rainbow trout. Similar approaches may be useful for molecular mapping of markers linked to genes of interest in other species.