A first-generation linkage map of the Pacific lion-paw scallop (Nodipecten subnodosus): Initial evidence of QTL for size traits and markers linked to orange shell color

The first genetic linkage maps of the Pacific lion-paw scallop were created using microsatellite and AFLP genotyping of a full-sibling family spawned from a single, pairwise mating. As an important step in the development of genomic resources for this species, the maps were then used in an effort to identify putative quantitative trait loci (QTL) for the size traits of shell length, height, and width, as well as total mass, soft tissue mass, muscle mass, and orange shell color. The female map contains 147 markers on 27 linkage groups, covering 919.7 cM, while the male map contains 149 markers placed on 20 linkage groups spanning 963.7 cM. Combining all available markers resulted in a consensus map of 320 loci (56 microsatellites and 264 AFLPs) on 22 linkage groups with an average spacing of 3.8 cM and a total map distance of 1124.14 cM. Non-parametric, Kruskal–Wallis tests found significant linkage at α = 0.005 for two size traits: total biomass in the loci segregating in the female parent, and shell width in the male. Interval mapping showed chromosome-wide significance for many traits on two primary linkage groups in the female map and one in the male. Highly correlated, 91.7% of the variation among the six size phenotypes could be explained by the first principal component, which explained 9 and 7.8% of the variance in the female and male maps, respectively. With the exception of muscle mass mapped when maturation stage was considered as a covariate, no significant LOD scores for size traits were identified using the combined map. Finally, orange shell color was mapped to a 1 cM region of linkage group Nsub9. The development of these maps and identification of linkage groups linked to size traits provide a foundation for future quantitative studies, which could ultimately result in marker assisted selection to improve scallop growth in aquaculture.

► A genetic linkage map was created from 85 progeny of a single-pairwise mating.
► 264 AFLPs and 56 microsatellites are in the final map, which has 22 linkage groups.
► QTL mapping found preliminary evidence for linkage to size traits.
► Orange shell color was mapped to a 1 cM region of one linkage group.
► The results indicate that marker assisted selection may be feasible in this species.