Large-Scale Development of Gene-Associated Single-Nucleotide PolymorphismMarkers for Molluscan Population Genomic, Comparative Genomic, and Genome-Wide Association Studies

Mollusca is the second most diverse group of animals in the world. Despite their perceived importance, omics-level studies have seldom been applied to this group of animals largely due to a paucity of genomic resources. Here, we report the first large-scale gene-associated marker development and evaluation for a bivalve mollusc, Chlamys farreri. More than 21,000 putative single-nucleotide polymorphisms (SNPs) were identified from the C. farreri transcriptome. Primers and probes were designed and synthesized for 4500 SNPs, and 1492 polymorphic markers were successfully developed using a high-resolution melting genotyping platform. These markers are particularly suitable for population genomic analysis due to high polymorphism within and across populations, a low frequency of null alleles, and conformation to neutral expectations. Unexpectedly, high cross-species transferability was observed, suggesting that the transferable SNPs may largely represent ancestral genetic variations that have been preserved differentially among sub-families of Pectinidae. Gene annotations were available for 73 % of themarkers, and 65 % could be anchored to the recently released Pacific oyster genome. Large-scale association analysis revealed key candidate genes responsible forscallopgrowthregulation,andprovidedmarkers for furthergenetic improvementofC. farreri in breeding programmes. Key words: mollusca; single-nucleotide polymorphism (SNP); transcriptome; high resolution melting (HRM); genome-wide association (GWAS) 1