A genetic linkage map of the Japanese eel (Anguilla japonica) based on AFLP and microsatellite markers

The first genetic linkage map of the Japanese eel (Anguilla japonica) was constructed based upon Amplified Fragment Length Polymorphism (AFLP) and microsatellite (STR) markers with an F1 pseudo-testcross strategy. The segregation of 106 microsatellite loci, which included 74 newly developed, and 463 polymorphic loci identified from 56 AFLP primer combinations was studied in 46 F1 individuals derived from a single female and a male. A total of 319 markers (99 STRs + 220 AFLP) are placed on the female map and 314 markers (91 STRs + 223 AFLP) on the male map. The female map spans 1732.4 cM (Kosambi) in 22 linkage groups with an average spacing of 7.2 cM; the male map spans 964.9 cM in 22 linkage groups with an average spacing of 6.3 cM. The average ratio of male:female recombination rates was 1:2.11. The estimated coverage of the genome was 82.4% for the female map and 74.0% for the male map. This map is the first linkage map in the order Anguilliformes and provides a basis for mapping quantitative trait loci (QTL) and for breeding applications.