An integrated genetic map based on EST-SNPs and QTL analysis of shell color traits in Pacific oyster Crassostrea gigas

Shell color polymorphism is common in nature for the marine mollusks. The Pacific oyster Crassostrea gigas, is widely cultured and one of the most economically important bivalve species with various shell color variants. Here, a total of 1061 single nucleotide polymorphism markers, developed from expressed sequence tags (EST-SNPs), were used to construct two genetic linkage maps based on reciprocal-cross between black shell and white shell oysters (MF-A and MF-B) respectively. The two separate linkage maps were combined into an integrated map spanning 947.31 cM in total length. The integrated map was composed of 351 EST-SNP markers distributing on 10 linkage groups, with an average interval of 2.78 cM between adjacent markers. For the MF-A, 11 quantitative trait loci (QTLs) for shell color traits and five QTLs for growth traits were detected, explaining 8.1%-13.8% (mean = 11.76%) and 10.4%-11.0% (mean = 10.66%) phenotypic variance respectively. For the MF-B, nine QTLs for shell color traits and eight QTLs for growth traits were detected, explaining 8.8%-21.7% (mean = 12.84%) and 8.4%-9.4% (mean = 8.88%) phenotypic variance respectively. QTLs clustering was found on the linkage group 2 of the MF-A and the linkage group 8 of the MF-B, and the QTLs showed that pleiotropism could affect at most three traits. Three shared-QTLs associated with shell color traits were identified on the integrated map, and one of them (qA-a* 4) was significantly homologous to C. gigas calmodulin-like protein. The QTLs identified in the present study could be useful in finding candidate genes for the shell color and growth-related traits in future, and potentially applied to marker-assisted selection breeding programs for C. gigas.