QTL mapping for glycogen content and shell pigmentation in the Pacific oyster Crassostrea gigas using microsatellites and SNPs

Glycogen content and shell pigmentation are two important economic traits of the Pacific oyster Crassostrea gigas. The first set of quantitative trait loci (QTLs) controlling the two traits was determined in an F1 full-sib family based on a sex-averaged linkage map. The linkage map was constructed using 120 SSRs, and 66 expressed sequence tag-derived single nucleotide polymorphisms (EST-SNPs). Two QTLs were found to be associated with glycogen content, explaining 0.27-79.05 % of the phenotypic variation. One QTL on LG9 were found to be related to shell pigmentation, the paternal and maternal alleles explaining 6.75 and 17.44 % of the phenotypic variation. The relationship of glycogen content with left shell depth and QTL linkage group analysis suggests that left shell depth and volume might be used to assist in indirect selection for glycogen content. The constructed linkage map and determined QTLs can provide a tool for further genetic analysis of the traits and be potential for marker-assisted selection in C. gigas breeding.