Identification and mapping of a SCAR marker linked to a locus involved in shell pigmentation of the Pacific oyster (Crassostrea gigas)

•A major gene influencing shell pigmentation in C. gigas was observed.•Seven AFLP fragments tightly associated with shell pigmentation were identified.•One co-dominant SCAR marker was successfully developed.•The SCAR marker was located onto a reference genetic map.

The Pacific oyster (Crassostrea gigas) is one of the most important farmed oysters worldwide. To improve breeding progress, research was done to identify molecular markers linked to shell pigmentation, which has been viewed as a key factor for product value. An F1-segregating population exhibiting a bimodal distribution of shell pigmentation intensity was obtained by crossing two wild oysters with opposite shell pigmentation. Genomic DNA from nine individuals with lightest shell pigmentation and nine individuals with darkest shell pigmentation were equally pooled for amplified fragment length polymorphism (AFLP) screening. In bulked segregant analysis, six out of 225 selective primer pair combinations produced seven polymorphic fragments tightly associated with shell pigmentation across the segregating population. The seven AFLP markers were mapped onto a single linkage group, and 80% of phenotypic variance could be explained by this locus. In conversion of the seven fragments into sequence-characterized amplified region (SCAR) markers, only one was successfully converted into a co-dominant SCAR marker, named SP-170. The SCAR marker was integrated into a previously constructed linkage map. The SCAR marker obtained in this study will be useful for marker-assisted selection of the Pacific oyster.