Development and validation of a 40 K liquid SNP array in autotetraploid Pacific oyster (Crassostrea gigas)

Autotetraploid Crassostrea gigas is a significant economic species that plays a crucial role in the production of triploid C. gigas . Molecular markers are essential for oyster selective breeding, but the lack of an efficient high-throughput genotyping platform for autotetraploid C. gigas has limited genetic improvement. In this study, we develop the world’s first 40 K liquid SNP array for autotetraploid C. gigas , designated “LuDongLiXin-4N-I”, using genotyping by target sequencing (GBTS) platform. The SNP array contains 41,270 high-quality SNPs and demonstrates a high individual calling rate (97.55%) and sequencing depth (241.20 X). Based on the SNP array, three populations are clearly distinguished, with four methods yielding consistent clustering results. For shell height (0.470), shell length (0.605), shell width (0.520), and total weight (0.581), six genomic prediction models (Bayes A, Bayes B, Bayes C, Bayes Lasso, GBLUP, and RKHS) achieve similarly high prediction accuracies. Furthermore, 52 SNPs and candidate genes associated with growth traits are identified based on genome-wide association analysis (GWAS). In conclusion, the world’s first SNP array “LuDongLiXin-4N-I” provides an efficient, cost-effective, and robust genotyping platform for autotetraploid C. gigas . The application of “LuDongLiXin-4N-I” provides a new technical pathway for constructing high-quality autotetraploid C. gigas populations and breeding improved varieties, and lays an important foundation for the efficient and sustainable development of autotetraploid C. gigas aquaculture industry.