When we constructed the first map of the zebrafish genome, we numbered Linkage Groups (LG) arbitrarily (1). In contrast, by cytogenetic convention, chromosomes are numbered by size. Thus, it is important to associate each of the 25 zebrafish chromosomes to specific cytogenetically identified chromosomes. Our initial association of LGs and physical chromosomes located the centromere on each of the 25 LGs by using meiotic half-tetrads (2). 

We have now associated genetically defined Linkage Groups to cytogenetically defined chromosomes (3). We assigned zebrafish genetic linkage groups to specific chromosomes using fluorescence in situ hybridization (FISH) with BAC probes containing genes we had previously mapped to each linkage group (LG) (Figure 1). Chromosomes were identified using a combination of relative size and arm ratios (Table 1, Table 2). We found that the largest genetic maps generally corresponded to the largest chromosomes, but genetic recombination tended to be elevated in the smaller chromosomes and near telomeres. Large insert clones containing genes near telomeres often hybridized to telomeres of multiple chromosome pairs, suggesting the presence of shared subtelomeric repetitive DNAs near telomeres