QTL mapping for orange shell color and sex in the Pacific oyster (Crassostrea gigas)

Molluscan shellfish have a diverse form of shell coloration and sex determination, understanding the genetic mechanism under these two traits is crucial to their germplasm exploitation and conservation. In our breeding program, a novel orange-shell variant of C. gigas was obtained, and an F2 family was constructed by crossing an orange-shell male with a black-shell female. This F2 family provided an ideal material for QTL mapping of orange shell color and sex traits of C. gigas simultaneously. Here, a high-density genetic linkage map containing 1799 SNP markers was constructed using this F2 family by genotyping-by-sequencing. These markers were distributed on 10 linkage groups and the total map size was 828.31 cM, with an average marker interval of 0.58 cM. Based on this map, six chromosome-level significant QTLs associated with orange shell color were detected, with the phenotypic variance explained ranging from 9.10% to 12.30%. Within the QTL regions, four candidate genes, 3-ketoacyl-CoA thiolase A, fibroblast growth factor receptor 4, poly [ADP-ribose] polymerase tankyrase-1 and tripartite motif-containing protein 45-like, related to the organic matrix of mollusk shells or collagen were identified. Additionally, only one genome-wide significant sex-related QTL was detected, which explained 19.30% of phenotypic variance. Two sex-related genes, proteasome subunit beta type-3 and G-protein coupled estrogen receptor 1 were identified within the QTL region. The QTLs and candidate genes identified in this study provide valuable resources for further investigations on the molecular mechanisms of shell color and sex in C. gigas.

Automated summary

Genetic mechanism underlying shell coloration and sex determination in molluscan shellfish, particularly in the case of a novel orange-shell variant of C. gigas, was investigated in this study. A high-density genetic linkage map revealed significant QTLs associated with orange shell color and identified candidate genes related to shell organics. Additionally, a genome-wide significant sex-related QTL and sex-related genes were detected, providing valuable resources for further molecular mechanism investigations.