High density mapping of BAC end sequences onto medaka linkage groups

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Physical mapping of medaka chromosomes was constructed based on the length polymorphism between two inbred strains, HNI and AA2. Fluorescent primers designed by BAC end sequences and nucleotide sequences having (CA) repeats were generated. 607 primer sets showing length polymorphism between the two strains were selected and were further used for typing to map onto the medaka linkage groups.More than 15% of the primers generated showed length polymorphism, confirming the high genomic polymorphism between the two strains.This information is the first systematic STS markers on medaka genomes and provides a powerful tool for anchoring BAC onto the linkage groups and for walk to the region of interest.Estimated physical length do not correspond to that estimated by anonymous markers such as RFLP and RAPD. Especially the length of linkage group 23 is estimated to be much longer than that estimated before. Regions of repression of recombination are different between female and male. It is inclined that recombination in male occurs more frequently at the distal regions of the linkages.