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Background  Both growth and nutritional traits are important economic traits of  Crassostrea gigas  ( C. gigas ) in industry. But few work has been done to study the genetic architecture of nutritional traits of the oyster. In this study, we constructed a high-density genetic map of  C. gigas  to help assemble the genome sequence onto chromosomes, meanwhile explore the genetic basis for nutritional traits via quantitative trait loci (QTL) mapping.    Results  The constructed genetic map contained 5024 evenly distributed markers, with an average marker interval of 0.68 cM, thus representing the densest genetic map produced for the oyster. According to the high collinearity between the consensus map and the oyster genome, 1574 scaffold (about 70%) of the genome sequence of  C. gigas  were successfully anchored to 10 linkage groups (LGs) of the consensus map. Using this high-qualified genetic map, we then conducted QTL analysis for growth and nutritional traits, the latter of which includes glycogen, amino acid (AA), and fatty acid (FA). Overall, 41 QTLs were detected for 17 traits. In addition, six candidate genes identified in the QTL interval showed significant correlation with the traits on transcriptional levels. These genes include growth-related genes  AMY  and  BMP1 , AA metabolism related genes  PLSCR  and  GR , and FA metabolism regulation genes  DYRK  and  ADAMTS .    Conclusion  Using the constructed high-qualified linkage map, this study not only assembled nearly 70% of the oyster genome sequence onto chromosomes, but also identified valuable markers and candidate genes for growth and nutritional traits, especially for AA and FA that undergone few studies before. These findings will facilitate genome assembly and molecular breeding of important economic traits in  C. gigas .    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4996-z) contains supplementary material, which is available to authorized users.

Construction of a high-density genetic map and fine QTL mapping for growth and nutritional traits of Crassostrea gigas