Constructing a microsatellite-based linkage map and identifying QTL for pearl quality traits in triangle pearl mussel (Hyriopsis cumingii)

Hyriopsis cumingii is the most economically important aquaculture species for freshwater pearl production in China. A linkage map is an essential framework for mapping QTL. In this study, a genetic linkage map of the freshwater pearl mussel was constructed using microsatellites in an F1 outbred family. Five hundred and six microsatellite markers were mapped to 19 linkage groups (LGs). The number of LGs detected corresponded to the haploid chromosome number of the freshwater pearl mussel. The linkage map covered a genetic distance of 1922.3 cM with an average marker interval of 3.99 cM. The sex-specific maps were 1745.9 cM and 2078.8 cM in male and female, and the recombination rate for females was 1.14 times higher than that for males. Quantitative trait locus (QTL) mapping identified 23 putatively significant QTL, including two for shell width, two for body weight, three for shell weight, three for margin mantle weight, three for inner mantle weight, and 10 for shell nacre color on LG1, LG2, LG4, LG6, LG8, LG9, LG14, LG17, and LG18. The phenotypic variation explained by the QTL ranged from 14.6% to 38.2%. Four QTL on LG17 that were associated with shell nacre color explained 26.0% to 28.9% of the trait variation. These four QTL were significant at the genome-wide level (P < 0.01). The linkage map and the QTL associated with pearl quality traits will provide useful information for marker-assisted selection of the freshwater pearl mussel.