A first generation microsatellite-based linkage map of the Chinese mitten crab Eriocheir sinensis and its application in quantitative trait loci (QTL) detection

Genetic linkage maps provide excellent tools for detecting quantitative trait loci (QTL) and understanding genome organization and evolution. By taking advantage of a large number of microsatellite markers isolated from the genome of the Chinese mitten crab Eriocheir sinensis in our previous study, here we constructed a first generation genetic linkage map for this species using 1300 microsatellite markers that genotyped a F1 full-sib family from an intercross between northern and southern populations in China. A total of 674 markers (52%) were informative and grouped on the two parental maps. The number of linkage groups is quite close to the actual number of the crab haploid chromosomes (n=73). The female linkage map contained 466 markers which mapped to 71 linkage groups, spanning a total genetic distance of 2430.9cM with an average marker space of 6.2cmd The male map contained 457 markers which mapped to 70 linkage groups, spanning 2658.4cM with an average marker space of 6.9cmd The crab genome length was estimated to be 3390.0cM, covering 71.7% of genome for the female map, and 3678.8cM covering 72.3% of genome for the male map. Furthermore, the linkage maps were used for preliminary detection of QTL. Nine growth-related QTL for body length, width and weight were mapped to seven linkage groups. Additionally, two QTL were identified to be associated with sexual precocity. The linkage maps and the identified QTL will be valuable for marker-assisted selection breeding programs of the mitten crab. A first generation genetic linkage map of the Chinese mitten crab was created using 1300 microsatellite markers. Nine growth-related QTL and two sexual precocity-related QTL were identified, which will be valuable for further studies of the genetic mechanisms of development and sexual precocity, and marker-assisted selection breeding programs for this species. •A first SSR-based linkage map of the mitten crab (Eriocheir sinensis) was constructed.•466 markers were assigned to 71 linkage groups with an average marker space of 6.2cM in the female map.•457 markers were mapped to 70 linkage groups with an average marker space of 6.9cM in the male map.•Nine growth-related QTL and two sexual precocity-related QTL were identified.