Abstract
Ploidy level exerts profound influences on the phenotypic and physiological traits of Crassostrea gigas. Compared to diploids, triploids exhibit desirable characteristics such as sterility, a faster growth rate, and improved meat quality. In contrast, tetraploids often suffer from slow growth, yet the mechanisms underlying these polyploid-associated traits remain unclear. This study aimed to elucidate these mechanisms by comparing differences in growth-related phenotypes and gene expression among diploid, triploid, and tetraploid oysters. We identified 1533 differentially expressed genes (DEGs) between diploids and triploids, 946 DEGs between triploids and tetraploids, and 1326 DEGs between diploids and tetraploids. Through trend analysis, we clustered genes with similar expression changes across ploidy levels and conducted functional enrichment analysis on these gene clusters. The results revealed that genes associated with the innate immune response were significantly up-regulated in tetraploids, whereas genes related to biomineralization and metabolism were markedly up-regulated in triploids. These findings suggest that tetraploid oysters may mount a stronger innate immune response compared to diploids and triploids, while triploids demonstrate superior growth performance. This study provides valuable resources for investigating the functional aspects of genes related to polyploid phenotype differences.