An amplicon panel for high-throughput and low-cost genotyping of Yesso scallop Mizuhopecten yessoensis

The Yesso scallop Mizuhopecten yessoensis was imported from Japan to western Canada in the late 1980s to establish an economically viable scallop aquaculture industry. Since this time, the industry in Canada has operated with existing genetic diversity within the broodstock, which is considerably limited relative to wild populations. The sector has not been able to realise its full potential in part due to idiopathic hatchery failures and farm stock collapses due to disease outbreaks associated with the intracellular bacterial pathogen Francisella halioticida. To support Yesso scallop production and breeding, here we generate a low-density, genotyping-by-sequencing amplicon panel using high-heterozygosity markers that are evenly spaced across the M. yessoensis genome. The panel can exploit the high genetic polymorphism of the M. yessoensis genome, with de novo SNP calling identifying over 2,500 high quality SNPs from 579 sequenced amplicons. We demonstrate the versatility of this new genotyping tool for breeding applications by conducting parentage assignment of outplanted scallops, evaluating the potential for marker-assisted and genomic selection for F. halioticida resistance, and investigating but finding no evidence for hybridization between M. yessoensis and the weathervane scallop Patinopecten caurinus within the M. yessoensis breeding population at Vancouver Island University. The high versatility of this low-cost genotyping panel will accelerate breeding efforts for M. yessoensis for production traits in Canada and elsewhere.