Portuguese oyster (Magallana angulata) is one of the most important shellfish species worldwide. Although significant improvements in growth have been achieved through artificial selection breeding, the genetic basis underlying these traits remains unclear. Thus, this study aimed to (i) estimate variation and heritability for growth-related traits and (ii) identify SNPs and candidate genes associated with growth traits in Portuguese oyster. Five growth-related traits, including shell height (SH), shell length (SL), shell width (SW), whole weight (WW), and soft tissue weight (STW), were measured and analyzed in 114 one-year-old individuals from a cultivated population in Fujian Province, China. Through whole-genome sequencing and genotyping, we obtained 8,183,713 high-quality SNPs. Based on the genomic relationship matrix, heritability for the five traits was estimated, ranging from 0.071 to 0.695. Through genome-wide association analysis (GWAS), a total of nine SNPs were identified as significantly or suggestively associated with one of the growth-related traits, each explaining phenotypic variation ranging from 14.13% to 18.56%. Differentially expressed genes (DEGs) between individuals with extreme phenotypes were identified using comparative transcriptome analysis, ranging from 868 to 2274 for each trait. By combining GWAS and comparative transcriptome analysis, a total of seven candidate genes were identified, with biological functions related to growth inhibition, stress response, cell cycle regulation, and immune defense. The associations between the candidate genes and the growth-related traits were validated by using single-marker association analysis in other populations. Based on SNPs in these candidate genes, 16 haplotypes associated with growth-related traits were obtained. This study contributes to a deeper understanding of the genetic mechanisms of growth traits, and provides a theoretical basis and genetic markers for the breeding of fast-growing strains of the Portuguese oyster.

Sex determination is a fundamental biological process governing animal reproduction. Although substantial progress has been made in elucidating its genetic basis, the genetic architecture underlying complex sex determination systems remains poorly understood. In this study, we identify sex-associated insertion–deletion (indel) variants, screen candidate genes, and compare sex-associated variation across populations with different genetic backgrounds in the Fujian oyster (Magallana angulata). Based on whole-genome resequencing data of a culture strain (designated FL), a total of 299,774 high-quality indels were identified. By integrating genome-wide association analysis (GWAS), fixation index (F_ST) analysis, and sex-biased genotype frequency comparisons, 77 overlapping sex-associated indels were identified, predominantly clustered within a 1.8 Mb (8.3–10.1 Mb) region on chromosome 9. Principal component analysis (PCA) based on the sex-associated markers and their subsets consistently separated male and female individuals in the FL strain. For two representative sex-associated indels, PCR-based genotyping methods were developed and validated. Functional annotation identified putative candidate genes for sex determination, including PKD1L1, 5-HTRL, SCP, and CCKRa. Comparative analysis of variants within PKD1L1 across wild, farmed, and selectively bred populations revealed a progressive enrichment of male-linked alleles in domesticated and selectively bred groups, particularly in male individuals. This study provides direct evidence that sex in the Fujian oyster is genetically determined and reveals that domestication and artificial selection may drive the emergence of major sex-determining loci, offering important insights into the genetic basis of sex determination in the Fujian oyster, and establishing a theoretical and practical foundation for molecular marker-assisted breeding of monosex lines for this species.

Crassostrea hongkongensis is an economically important mariculture species in southern China, and hybrid breeding has been applied to improve its growth traits. However, the molecular mechanisms underlying growth heterosis remain poorly understood. In this study, inter-population hybrid (HG) and intra-population (IG) groups of C. hongkongensis were compared using integrated transcriptomic and metabolomic analyses to investigate the regulatory basis of growth heterosis. Shell length and shell height were significantly greater in HG than in IG (p < 0.01). Transcriptomic analysis identified 474 false discovery rate (FDR)-supported significant differentially expressed genes (DEGs) (233 upregulated and 241 downregulated), which were treated as the primary statistically robust findings; a broader set of 3161 candidate DEGs, including genes associated with growth regulation and shell biomineralization, was retained for exploratory functional and multi-omics analyses. Metabolomic analysis detected 345 differential metabolites (DMs), which were mainly enriched in energy metabolism, nucleotide metabolism, and arachidonic acid metabolism. Exploratory pathway-level multi-omics integration revealed significant concordance between the transcriptomic and metabolomic profiles (M² = 0.1962, p = 0.001) and highlighted the tricarboxylic acid cycle, oxidative phosphorylation, branched-chain amino acid degradation, nucleotide metabolism, and arachidonic acid metabolism. These findings suggest that growth heterosis in C. hongkongensis is associated with altered energy metabolism, biosynthetic processes, shell formation-related pathways, and potential changes in the growth–defense balance, providing molecular insights for genetic improvement and selective breeding.