Multi-omics analysis of Pacific oyster “Haida No. 1” strain and wild population reveals growth-related genes and transcription regulatory network

Selective breeding has significantly enhanced the growth properties of Pacific oysters (Crassostrea gigas), but the molecular mechanisms behind these improvements remain largely unclear. In this study, we performed a comparative analysis of the adductor muscle transcriptome and proteome of the 10th-generation Pacific oyster strain “Haida No.1” and wild populations. Combining multi-omics analysis with published whole-genome resequencing and LC-MS metabolomics data of the “Haida No.1” strain and wild populations, we identified growth-related genes and transcription regulatory networks in C. gigas. Transcriptome analysis revealed 4110 differentially expressed genes (DEGs), significantly enriched in 49 pathways. Proteome analysis showed 105 differentially expressed proteins (DEPs) between “Haida No.1” and wild populations, which were enriched in 30 relevant pathways, including metabolic pathways, oxidative phosphorylation, ribosomes, phagosomes, and amino acid biosynthesis. Multi-omics analysis grouped these DEGs, DEPs, and selected genes (from Fst and XP_CLR analyses of previous whole-genome resequencing results) into 13 categories. The shared pathways were classified into five main classes: signal transduction, metabolism & biosynthesis, disease, cellular processes, and cellular components. Multi-generation selection has influenced the cellular behaviors and physiological processes of “Haida No.1”, which might explain its faster growth compared to wild populations. These findings provide novel insights into oyster growth regulation and offer candidate genes for oyster breeding programs.