The Pacific oyster (Crassostrea gigas) is one of themost 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 AFLPmarkersweremapped 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 codominant
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