Yanming Sui

Muscle-associated lipids influence fish flesh composition, nutritional value, and sensory quality, but inconsistent definitions obscure comparisons among studies. This review distinguishes adipose tissue between anatomically distinct muscles, adipocytes within muscle connective tissue, lipid droplets within myofibers, and chemically measured muscle lipid content. In salmonids, myoseptal adipose tissue occupies the partitions between adjacent myomeres, whereas perimysial adipocytes lie within myomeres. We examine how these compartments develop, how their lipid storage is regulated, and how genetic and nutritional approaches can improve flesh quality. Salmonid precursor cultures support adipogenic differentiation involving PPARγ and C/EBPs, while evidence for depot-specific progenitor lineages remains limited. Genetic studies identify heritable variation and associated genomic regions for muscle lipid traits, but association, expression, and functional evidence frequently address different phenotypes or tissues. Translating these findings requires standardized sampling, spatially resolved measurements, and functional testing of candidate mechanisms. Research priorities include distinguishing adipocyte recruitment from lipid loading, separating cell-composition changes from intracellular regulation, and connecting causal variants with depot-specific phenotypes. Breeding objectives should integrate lipid distribution and fatty acid composition with processing quality, growth, feed efficiency, and environmental robustness. Imaging and multi-omics can support this integration when calibrated against defined biological traits and validated across populations and production environments.

Rainbow trout (Oncorhynchus mykiss) is a globally cultured cold-water salmonid, yet triploid larvae often develop spinal ventral lordosis and conjoined twin malformations with unclear molecular mechanisms. Here, RNA-seq of 15 dph normal (N), spinal-deformed (SD) and conjoined (CT) triploid larvae yielded 54.13 Gb of valid data, identifying 4292, 3601 and 2699 DEGs for SD vs. N, CT vs. SD and CT vs. N groups, respectively. Five shared disrupted cascades (cell adhesion, neuroactive ligand-receptor interaction, phagosome, cytokine-receptor interaction, and PI3K-Akt signaling) were identified, while potential calcium/MAPK and steroid-biosynthesis-related pathways were predominantly perturbed in SD and CT larvae, respectively. Filtered PPI sub-networks displayed distinct predicted topological phenotype-associated candidate transcripts, with coagulation and complement transcripts forming core hubs in SD larvae and steroid-related transcripts showing weak connectivity in CT groups. Three discriminative transcripts with inverse expression patterns were screened. This study reveals conserved and phenotype-specific transcriptional phenotype-associated candidate transcripts of the two malformations and provides candidate phenotype-associated transcripts for subsequent functional verification of larval malformations. It should be noted that all transcriptomic data originate from whole-larval homogenates; expression signatures of conjoined-twin larvae may be confounded by altered tissue-type proportions rather than malformation-exclusive regulatory mechanisms.

Rainbow trout (Oncorhynchus mykiss) is a globally important cold-water aquaculture species, yet the molecular events underlying the transition from embryo to free-living larva remain poorly resolved. In this study, eukaryotic reference-based transcriptome sequencing was used to compare genome-wide gene expression profiles between eggs (eyed-egg stage) and newly hatched larvae of O. mykiss. A total of 618 differentially expressed genes (DEGs) were identified, of which 297 were upregulated and 321 downregulated. Gene Ontology (GO) enrichment analysis showed that DEGs were significantly enriched in immune system process, response to stimulus, and biological regulation. Within the immune system process category, 4 DEGs were upregulated and 11 were downregulated in larvae, indicating a more complex remodelling of immune-related gene expression than simple activation. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified only Glycolysis/Gluconeogenesis (map00010) as significantly enriched (padj < 0.05). Nitrogen metabolism (map00910) and tryptophan metabolism (map00380) showed enrichment trends but were not statistically significant after multiple-testing correction. Because these pathways contained only a small number of DEGs and displayed mixed regulation, no overall pathway-level up- or down-regulation was inferred. These results suggest a possible metabolic remodelling during the transition from yolk-dependent anabolism to catabolic utilization in larvae. Transcript assembly further identified 134,770 potential novel isoforms and 2902 intergenic transcripts classified as putative novel transcripts, enriching the genome annotation of O. mykiss. Trend clustering indicated coordinated regulation of immune and stress-response genes together with downregulation of amino acid and energy metabolism genes, revealing programmed temporal regulation during this developmental transition. These findings provide foundational data for understanding early development in rainbow trout and candidate molecular targets for health-oriented aquaculture management.

Frozen mysid shrimp is the primary feed for farmed medicinal seahorses, yet no standardized storage duration exists, and whether storage-related feed changes affect the lipid-based medicinal quality of seahorses remains unknown. This study used targeted lipidomics to compare 98 lipid species across six lipid classes in three farmed seahorse species—Hippocampus erectus, H. abdominalis, and H. trimaculatus—fed mysid shrimp frozen for either 2 or 10 months. Prolonged storage did not cause a uniform decline in lipid quality; instead, each species exhibited a distinct response pattern. H. erectus showed compensatory increases in fatty acids, whereas phospholipids predominantly decreased; H. abdominalis exhibited broad attenuation across multiple lipid classes; and H. trimaculatus displayed an intermediate, class-dependent pattern. Notably, oxidized sterol derivatives declined consistently across all three species despite divergent fatty acid and phospholipid responses, suggesting that oxidized sterol derivatives may serve as candidate cross-species indicators of storage-related feed changes, although validation is required. Acylcarnitine profiles remained stable in H. erectus but decreased in the other two species, suggesting possible differences in lipid utilization among species. These preliminary results suggest that frozen-storage guidelines may need to be evaluated on a species-specific basis in future studies, with sterol monitoring as a candidate indicator for further evaluation.

The hard clam Meretrix meretrix is a commercially important bivalve species in China, yet its aquaculture industry is increasingly threatened by germplasm degradation and recurrent mass summer mortality events associated with elevated temperatures and Vibrio infections. To characterize candidate germplasm resources with potential value for heat-tolerance breeding and to elucidate the genetic basis of adaptive differentiation, we integrated genotyping-by-sequencing (GBS) and gill transcriptome sequencing across five wild populations spanning the entire latitudinal range of China: Dandong (LD), Weihai (SW), and Rudong (JR) in the north, and Beihai (GB) and Qinzhou (GQ) in the south. Phylogenetic and population structure analyses resolved the five populations into two distinct genetic lineages corresponding to northern and southern clusters, with the Beihai population exhibiting the highest genetic diversity and the Weihai population showing signs of inbreeding that were elevated relative to the other populations. Comparative transcriptomic analysis revealed that differentially expressed genes between northern and southern populations were significantly enriched in immune-related pathways (including NOD-like receptor and IL-17 signaling pathways) and lipid metabolic pathways (including cholesterol and steroid biosynthesis). Notably, populations with similar genomic backgrounds still displayed pronounced transcriptional divergence, indicating that transcriptional divergence can arise even in the absence of strong genomic differentiation; because this conclusion is based on observational data, it cannot fully separate long-term genetic adaptation from environmentally induced transcriptional plasticity. These findings provide fundamental data for germplasm conservation and for future selective breeding programs targeting stress resistance in M. meretrix.

This study investigated the individual and interactive effects of body size, water temperature, and ambient salinity on survival and weight gain of Oncorhynchus mykiss during salinity acclimation using a three-factor, three-level orthogonal design to identify optimal acclimation regimes. Nine experimental treatments were established across three body sizes (100, 250, and 500 g), three temperatures (10, 15, and 20 ℃), and three salinities (10, 20, and 30 ppt). Standard feeding protocols and daily tank maintenance were implemented across the entire 60-day experimental period. Survival rate and weight gain rate were calculated after cultivation, and all data were subjected to three -way ANOVA and range analysis. Salinity significantly affected fish survival, whereas body size and temperature did not. None of the three factors significantly affected weight gain. Range analysis revealed that salinity was the primary driver of variation in survival (R = 51.13), followed by temperature (R = 30.43) and body size (R = 1.50). By contrast, body size was the predominant factor governing weight gain (R = 30.40), with a much higher contribution than salinity (R = 3.10) and temperature (R = 2.40). Large-sized trout (500 g) reared at 10 ℃ and 10 ppt achieved the highest survival, and small-sized individuals (100 g) cultured at 10 ℃ and 20 ppt obtained maximum weight increment. A comprehensive evaluation of survival and growth performance demonstrated that the optimal domestication combination for survival was 500 g-15℃-10 ppt, which is particularly applicable to large O. mykiss is undergoing seawater transition. The optimal growth conditions are 100 g, 10 ℃, 20 ppt. This may be more suitable for juvenile growth-oriented cultivation. Our findings provide practical technical references for the domestication of O. mykiss in brackish and seawater and support the industrial advancement of its mariculture.

Salinity, temperature and body weight dominate seawater acclimation in rainbow trout (Oncorhynchus mykiss), yet few studies simultaneously explore their main effects and potential correlative interactive patterns in hepatic responses. A 60-day L₉ (3³) orthogonal trial was performed on triploid rainbow trout with three gradients of body weight, temperature and salinity. Hepatic transcriptomics revealed that salinity drove global transcriptional remodeling and high salinity induced far fewer DEGs than medium salinity. WGCNA screened a salinity-positive blue module (r = 0.408, p = 0.0346), while alternative splicing confirmed extensive salinity-dependent post-transcriptional regulation. Semi-quantitative histology showed that 20 °C was associated with more pronounced salinity-caused hepatocellular vacuolation and karyopyknosis in the orthogonal test. Survival statistics indicated that salinity was the only factor with significant main effects (p < 0.05), and the 500 g-10 °C-10 ppt group obtained the highest survival. This multi-omics and histological dataset reveals a suggestive regulatory hierarchy-like pattern: salinity acts as the primary driver, temperature serves as a synergistic amplifier, and body weight plays a minor modulatory role. These findings provide a theoretical basis for developing size-specific salinity acclimation protocols in commercial triploid rainbow trout farming.

Understanding niche differentiation and interspecific coexistence patterns of macrobenthos provides critical references for ecological assessment of bivalve aquaculture. Seasonal field surveys (Autumn 2023–Summer 2024) across 12 sampling sites were conducted in an intensive Meretrix meretrix tidal flat farm in Rudong, Jiangsu. Synchronous water depth, sediment grain size and total organic carbon (TOC), and salinity were measured at each station to characterize habitat gradients; no unfarmed reference tidal flats were included, so all community patterns only reflect within-farm variation. The study area has sustained 10-year continuous bottom culture with baseline juvenile stocking density of 250 ind./m² and twice-yearly manual harvesting. A total of 58 macrobenthic taxa were identified, and 13 dominant species were screened with a dominance index threshold Y > 0.02. All abundance data were fourth-root-transformed before Bray–Curtis community analysis to reduce bias of hyper-abundant taxa. Standardized Shannon niche breadth (0–1 normalized, r = 48 site–season composite units) and permutation-tested (999 replicates) Pianka niche overlap/similarity coefficients were calculated to quantify resource utilization similarity. Niche breadth ranged from 0.018 to 0.971, with farmed M. meretrix showing the maximum value, indicating broader seasonal resource adaptation. High niche overlap (>0.50) was detected between M. meretrix and four wild dominant species (Nephtys californiensis, Moerella iridescens, Lingula anatina, Umbonium thomasi). Notably, niche metrics derived solely from spatial abundance data cannot directly confirm interspecific competition or trophic segregation; the stable coexistence observed in our assemblage is tentatively hypothesized to be driven by vertical sediment partitioning and divergent feeding guilds based on published functional studies, without direct in situ trophic or stratified sediment evidence from this work. Hierarchical UPGMA clustering (0.35 Bray–Curtis distance threshold) and corrected NMDS ordination (48 site–season units, dominant-species fitted vectors) illustrated distinct functional groups. Based on the observed niche convergence among filter-feeding bivalves under local farming conditions, the range of 230–280 ind./m² is presented as an observational reference. Controlled manipulative experiments with gradient stocking densities are needed to test whether this range can balance aquaculture yield and benthic biodiversity.

Thermal elevation and residual chlorine pollution are two anthropogenic stressors that co-occur in estuarine waters affected by coastal power plant effluents. A 30-day exposure experiment was established with six treatment combinations comprising three temperatures (27 °C, 28 °C, and 30 °C) and two residual chlorine concentrations (0 mg/L and 0.02 mg/L) on Meretrix meretrix. Sampling was conducted on days 0, 10, 20 and 30 of the trial. The results indicated that elevated temperature (30 °C) significantly suppressed shell height and total body weight, while residual chlorine (0.02 mg/L) exerted time-dependent effects on shell length and width, with a significant interactive effect on shell length only at day 30. Crude lipid content declined with increasing temperature and residual chlorine exposure, whereas moisture and ash contents showed significant two-way interactions at all sampling time points. Intestinal amylase activity was continuously regulated by both stressors, with interactive responses on days 10 and 20, and was significantly suppressed under combined high temperature and residual chlorine stress. Collectively, we infer that combined exposure to elevated temperature and residual chlorine impairs shell growth, muscle biochemical composition and intestinal amylase activity of M. meretrix. Long-term experiments are required to further clarify the joint toxic effects of thermal stress and residual chlorine on the clam species.

Using a three-factor orthogonal design, we investigated the transcriptomic and histological responses of triploid rainbow trout (Oncorhynchus mykiss) gills across three salinities (10, 20, and 30 ppt) over 60 days, with temperature and body size as background conditions. Results showed that 20 ppt was associated with extensive transcriptional reprogramming, with 3333 differentially expressed transcripts (DETs), whereas 30 ppt induced only 120 DETs; WGCNA further identified salinity-correlated modules involved in ion transport and ribosome biogenesis. Histological alterations remained within physiological ranges with no salinity-dependent severity gradient, as confirmed by semi-quantitative scoring. These findings demonstrate that triploid rainbow trout gills employ distinct molecular strategies at medium versus high salinity. Within the 10–30 ppt range examined, 20 ppt was the salinity at which transcriptional reprogramming was most active, suggesting that this intermediate salinity warrants further investigation as a potential acclimation stage.