The innate immunity of marine bivalves is challenged upon exposure to heat stress, especially with increases in the frequency and intensity of heat waves. TLR4 serves a classical pattern recognition receptor in recognizing pathogenic microorganisms and activating immune responses. In this study, three genes, HMTLR4, HMMyD88 and HMTRAF6, were characterized as homologs of genes in the TLR4-MyD88 signaling pathway in the selected scallop strain “Hongmo No. 1”. According to RT-PCR, acute heat stress (32 °C) inhibited genes in the TLR4-MyD88 signaling pathway, and LPS stimulation-induced activation of TLR4-MyD88 signal transduction was also negatively affected at 32 °C. ELISA showed LPS-induced tumor necrosis factor alpha (TNF-α) or lysozyme (LZM) activity, but this was independent of temperature. RNA interference (RNAi) confirmed that HMTLR4 silencing suppressed the expression of its downstream gene, whether at 24 °C or at 32 °C. The level of TNF-α and the activity of LZM also decreased after injection with dsRNA, indicating a negative effect on the innate immunity of scallops. Additionally, acute heat stress affected the suppression of downstream gene expression when compared with that at 24 °C, which led us to the hypothesis that heat stress directly influences the downstream targets of HMTLR4. These results enrich the knowledge of scallop immunity under heat stress and can be beneficial for the genetic improvement of new scallop strains with higher thermotolerance.

Aquaculture has witnessed excellent growth in recent decades, with significant potential for protein nutrition security and jobs. Genomics has significantly enhanced aquaculture technologies across various species and culture processes, improving production efficiency and profitability. With the continuous advances in next-generation sequencing technologies and bioinformatics, substantial genomic resources have been obtained for dozens of aquaculture species. These include the development of high-quality whole-genome sequences, transcriptome databases, and molecular markers, mainly single nucleotide polymorphisms (SNPs), followed by the discovery of high-density linkages and physical maps. This review presents an overview of recent advancements in aquaculture genomics, including genome sequencing and assembly, molecular breeding, genetic characterization of traits, health and biodiversity assessments, and conservation biology of fish and shellfish. The review further examines the challenges impeding the effective implementation of genomics in aquaculture research, as the full potential remains underexploited within this sector. Finally, we highlight the available opportunities, including discussing the future priorities for technologies, auspicious science, and governmental policies for realizing the fullest benefit of genomic advancement in improving the aquaculture industry. The suggestions proposed in this review will facilitate using genomic-informed data to manage valuable aquaculture resources.

Hypoxia frequently triggers mass mortality events in pearl oysters during the summer months. Hypoxic preconditioning (HP), repeated exposure to sublethal low-oxygen conditions, has been proposed as a potential strategy to enhance stress resistance. Here, we investigated how HP affects hypoxia tolerance in the pearl oyster Pinctada fucata martensii, with emphasis on host apoptotic and immune regulation and the gut microbiota. Pearl oysters assigned to HP (experimental group, EG) and to a non-preconditioned control group (CG) were subjected to sustained hypoxic challenge (1.5 ± 0.1 mg/L DO for 15 days). HP significantly increased the expression of apoptosis- and immunity-related genes (MyD88, IκK, NF-κB) while suppressing JNK expression in gills after extended hypoxia (MyD88: EG 2.26 ± 0.65 vs. CG 0.96 ± 0.29, p < 0.05, ~2.3-fold increase; NF-κB: EG 1.50 ± 0.20 vs. CG 0.81 ± 0.31, p < 0.05, ~1.8-fold increase; IκK: EG 1.55 ± 0.38 vs. CG 0.65 ± 0.12, p < 0.05, ~4.0-fold increase; JNK: EG 0.49 ± 0.25 vs. CG 1.44 ± 0.51, p < 0.05, ~0.34-fold), consistent with a pre-activated yet controlled stress response. In parallel, HP markedly reshaped the intestinal microbial community under hypoxia, increasing alpha diversity (Ace, Chao, and Sobs indices) and enriching potentially beneficial bacterial phyla such as Planctomycetota, Nitrospirota, and Fusobacteriota, groups often linked to nutrient cycling and short-chain fatty acid production. Collectively, these results suggest that HP-enhanced hypoxia tolerance in P. f. martensii is associated with coordinated modulation of host apoptotic and immune signaling and concomitant shifts in gut microbiome diversity. These findings highlight the role of the host–microbiota axis in environmental acclimation and suggest that HP may be a practical tool for improving bivalve performance under hypoxic stress in aquaculture.

The estuarine Crassostrea hongkongensis is the major cultured oyster species in the South China, and mass mortality induced by hyper-salinity has heavily damaged the oyster farming, especially during dry season. To benefit the genetic improvement of hyper-salinity tolerance, three genes related to the intracellular concentration of glycine (Gly) that functions as important osmolyte were identified and investigated in C. hongkongensis. Serine hydroxymethyltransferase 1 in C. hongkongensis (CHSHMT1) was found to be upregulated in gill since 48 h transferred from 18‰ to 30‰ filtered seawater (FSW). While glycine dehydrogenase (CHGLDC) and ALA synthase gene (CHALAS) were significantly upregulated in oyster from 8 to 48 h exposed to 6‰ FSW when compared with that in 18‰ and 30‰ FSW. And the expression of the three genes agreed with that Gly content decreased under hypo-osmotic stress and increased under hyper-osmotic stress. RNA in situ hybridization (ISH) revealed that CHSHMT1 and CHGLDC were mainly expressed in the ciliated columnar cell of gill filament and epithelial cell of water tube wall, where oyster gill directly contacts with seawater when the animal is filtering. But positive signal of CHALAS mRNA showed no significant difference in intensity between various gill cells. Based on these findings, CHSHMT1, CHGLDC and CHALAS were supposed to contribute to the variation of Gly content under osmotic stress. Subsequent RNA interference (RNAi) confirmed the function of CHSHMT1 in the transformation from serine (Ser) to Gly under hyper-osmotic stress. Moreover, CHGLDC and CHALAS were found to be significantly upregulated when CHSHMT1 was silenced under hyper-osmotic stress. This was hypothesized that the expression of CHGLDC and CHALAS might be suppressed by CHSHMT1, but more evidence should be provided. This work enriched the understanding of oyster osmolyte system that prevent cell shrinking or swelling under osmotic stress and provided potential genes for the breeding of Hong Kong oyster strain with hyper-salinity tolerance.