Development of a medium density combined-species

48 SNP arrays are enabling tools for high-resolution studies of the genetic basis of 49 complex traits in farmed and wild animals. Oysters are of critical importance in many 50 regions from both an ecological and economic perspective, and oyster aquaculture 51 forms a key component of global food security. The aim of our study was to design a 52 combined-species medium density SNP array for Pacific oyster (C. gigas) and 53 European flat oyster (O. edulis), and to test the performance of this array on farmed 54 and wild populations from multiple locations, with a focus on European populations. 55 SNP discovery was carried out by whole genome sequencing of pooled genomic DNA 56 samples from eight C. gigas populations, and RAD Sequencing of 11 geographically 57 diverse O. edulis populations. Nearly 12 million candidate SNPs were discovered and 58 filtered based on several criteria including preference for SNPs segregating in multiple 59 populations and SNPs with monomorphic flanking regions. An Affymetrix Axiom® 60 Custom Array was created and tested on a diverse set of samples (n = 219) showing 61 ~ 27 K high quality SNPs for C. gigas and ~ 11 K high quality SNPs for O. edulis 62 segregating in these populations. A high proportion of SNPs were segregating in each 63 of the populations, and the array was used to detect population structure and levels of 64 linkage disequilibrium. Further testing of the array on three C. gigas nuclear families 65 (n = 165) revealed that the array can be used to clearly distinguish between families 66 both based on identity-by-state clustering parental assignment software. This medium67 density, combined-species array will be publicly available through Affymetrix, and will 68 be applied for genome-wide association and evolutionary genetic studies, and for 69 genomic selection in oyster breeding programs. 70