Kelp grouper (Epinephelus bruneus) is an important aquaculture species in Japan, Korea and China. Mariculture
production of the species has increased due to its high demand and market price. However, some problems affect
kelp grouper aquaculture such as the low growth rate, high mortality due to diseases and low ability to survive
the larval stage. To analyze economically important traits, genetic linkage maps are an effective tool. We constructed
sex-specific linkage maps of kelp grouper using 222 microsatellite markers. The male map consisted
of 23 linkage groups with 161 markers and the female map consisted of 25 linkage groups with 173 markers.
The total lengths of the male and female maps were 650.5 cM and 944.4 cM, respectively, and the average intervals
were 5.0 cM and 6.7 cM, respectively. The average ratio of recombination between males and females was
1:1.5. Moreover, syntenic sequence comparisons provided basic information of several potential candidate
genes affecting organism physiological and biochemical reactions. Based on the linkage map, further quantitative
trait loci (QTL) or candidate gene(s) detection can be anticipated to contribute to assist breeding programs of kelp
grouper. In addition, by providing basic genome information of kelp grouper, the map provides a first step towards
comparative QTL as well as comparative genome analyses with other groupers in the future.