Open Access Open Badges Research article

A second generation genetic linkage map of Japanese flounder (Paralichthys olivaceus)

Cecilia Castaño-Sánchez1, Kanako Fuji1, Akiyuki Ozaki12, Osamu Hasegawa3, Takashi Sakamoto1, Kagayaki Morishima4, Ichiro Nakayama4, Atsushi Fujiwara2, Tetsuji Masaoka2, Hiroyuki Okamoto2, Kengo Hayashida5, Michihira Tagami5, Jun Kawai5, Yoshihide Hayashizaki5 and Nobuaki Okamoto1*

Author Affiliations

1 Faculty of Marine Science, Tokyo University of Marine Science and Technology, Minato, Tokyo, Japan

2 National Research Institute of Aquaculture, Fisheries Research Agency, Watarai, Mie, Japan

3 Kanagawa Prefectural Fisheries Technology Center, Miura, Kanagawa, Japan

4 National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan

5 RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan

For all author emails, please log on.

BMC Genomics 2010, 11:554  doi:10.1186/1471-2164-11-554

Published: 11 October 2010



Japanese flounder (Paralichthys olivaceus) is one of the most economically important marine species in Northeast Asia. Information on genetic markers associated with quantitative trait loci (QTL) can be used in breeding programs to identify and select individuals carrying desired traits. Commercial production of Japanese flounder could be increased by developing disease-resistant fish and improving commercially important traits. Previous maps have been constructed with AFLP markers and a limited number of microsatellite markers. In this study, improved genetic linkage maps are presented. In contrast with previous studies, these maps were built mainly with a large number of codominant markers so they can potentially be used to analyze different families and populations.


Sex-specific genetic linkage maps were constructed for the Japanese flounder including a total of 1,375 markers [1,268 microsatellites, 105 single nucleotide polymorphisms (SNPs) and two genes]; 1,167 markers are linked to the male map and 1,067 markers are linked to the female map. The lengths of the male and female maps are 1,147.7 cM and 833.8 cM, respectively. Based on estimations of map lengths, the female and male maps covered 79 and 82% of the genome, respectively. Recombination ratio in the new maps revealed F:M of 1:0.7. All linkage groups in the maps presented large differences in the location of sex-specific recombination hot-spots.


The improved genetic linkage maps are very useful for QTL analyses and marker-assisted selection (MAS) breeding programs for economically important traits in Japanese flounder. In addition, SNP flanking sequences were blasted against Tetraodon nigroviridis (puffer fish) and Danio rerio (zebrafish), and synteny analysis has been carried out. The ability to detect synteny among species or genera based on homology analysis of SNP flanking sequences may provide opportunities to complement initial QTL experiments with candidate gene approaches from homologous chromosomal locations identified in related model organisms.