This study examined age-associated variation in lipid composition and nutritional quality in the invasive clam Anadara kagoshimensis from the Sea of Azov. Fatty acid and sterol compositions were determined by gas chromatography in clams assigned by sclerochronology to five age classes (2-6 years). Several lipid-quality indices, including PUFA/SFA, IA, IT, hH, and HPI, exhibited their most favorable mean values in the 4-year group. The highest condition index (13.7) and the lowest n-3/n-6 ratio (1.1) were observed in the small and unbalanced group of 6-year-old clams. An exploratory linear discriminant analysis (LDA) workflow was used to examine whether primary lipid variables and mathematically derived composite features could enhance age-group separation. LDA based on primary variables yielded 78% leave-one-out classification within the present dataset. Data-driven composite-feature construction increased the within-dataset classification to 100% and graphical group separation to 85%, the values with yet restricted predictive accuracy due to the limited dataset. The results provide baseline information on age-associated lipid variation in A. kagoshimensis and illustrate a proof-of-concept workflow that can be tested in future studies using larger, balanced samples and special validation approaches.
The broad mite, Polyphagotarsonemus latus (Banks), is a highly polyphagous tarsonemid pest that causes severe damage to a wide range of agricultural and horticultural crops. The excessive and indiscriminate use of Fenazaquin, a mitochondrial electron transport inhibitor, resulted in the rapid development of resistance in P. latus. To elucidate the molecular mechanisms underlying acaricide resistance, a transcriptomic investigation was conducted on Fenazaquin-resistant (FEN-SEL) and susceptible (NBAIR-GR-TAR-01a) populations. The analysis identified putative genes involved in detoxification, including cytochrome P450 monooxygenases (CYPs), glutathione S-transferases (GSTs), choline and carboxyl esterases (CCEs), and ATP-binding cassette (ABC) transporters. Phylogenetic analysis revealed lineage-specific expansions of clan 3 CYPs, delta and acari-specific mu classes of GSTs, and ABCC, ABCG, and ABCH subfamilies of ABC transporters. Ten resistance-associated unigenes were validated using quantitative real-time PCR to assess gene expression patterns. The results showed significant upregulation of CYP4CL3, CYP4CF4, two delta-class GSTs, two CCEs belonging to clade J″, and two ABC transporters from subfamily C. However, CYP4725A2 and CYP4726A1 showed downregulation. These findings highlight the potential association of multiple metabolism-related gene families with Fenazaquin resistance and their possible contribution to the resistant phenotype. Overall, this study provides molecular insights into Fenazaquin resistance in P. latus, supporting the need for targeted resistance management strategies. Further research is warranted to evaluate the potential of these genes as molecular targets for sustainable broad mite management.
Long intergenic non-coding RNAs (lincRNAs) regulate gene expression across vertebrate physiological systems, yet their functional roles in teleost fish remain incompletely synthesized. This review systematically integrates current evidence through PRISMA-guided searches across PubMed, Web of Science, and Scopus, identifying ten lincRNA-focused functional studies with genetic, mechanistic, or developmental validation, complemented by twenty two supplementary contextual references. Findings span development, immunity, environmental adaptation, reproduction, regeneration, and toxicology, with each association graded as experimentally validated, bioinformatically predicted, correlational, or speculative. This synthesis offers three core contributions. First, it shows that cis-acting regulation on neighboring genes, mediated through Wnt, NF-κB, and AHR signaling, is the dominant validated lincRNA mechanism across teleost physiological domains. Second, it demonstrates that direct experimental validation, primarily via CRISPR-Cas9 and chromatin-capture assays, remains concentrated in zebrafish, whereas aquaculture-species associations remain largely correlational. Third, it identifies two findings that challenge current lincRNA classification: unexpected regulatory directionality at the slincR-sox9b locus, and micropeptide-encoding potential within annotated lincRNAs. Together, these contributions establish an evidence-graded foundation for future mechanistic studies and translational aquaculture applications.
The paddy-field carp, domesticated in paddy ecosystems and cocultured with rice in Qingtian for over a millennium, exhibits physiology, behavior and morphology shift from its local wild progenitor. To investigate genetic and morphological adaptations of pectoral girdle, a key locomotor structure for extremely shallow water, we integrated skeletal anatomy, SMRT full-length transcriptome sequencing, and Illumina RNA-seq across developmental stages. Anatomical comparisons revealed significant morphological shifts in pectoral girdle (including clavicle and scapula) relative to wild populations. SMRT sequencing identified 2215 novel genes, 25,226 annotated transcripts, 6290 long non-coding RNAs (lncRNAs), 42,594 alternative splicing (AS) events, and 10 transposon families. Notably, genes involved in skeletal development exhibited significant AS (P < 0.05). Using 12 cDNA libraries from one- and four-month-old fish, we identified differently expression genes (DEGs). Weighted gene co-expression network analysis of these DEGs revealed that genes related to pectoral girdle development were predominantly associated with the turquoise module, and KEGG enrichment analysis highlighted the Wnt signaling pathway. Further evidence suggests that lncRNAs are candidate modulators of Wnt inhibitors (sost and dkk1b), thereby repressing Wnt signaling and influencing pectoral girdle development. Protein-protein interaction networks identified key hub genes, and active transposons appear to contribute to developmental regulation. These findings suggest that transcriptional regulation is closely associated with the adaptive changes in paddy-field carp, providing a potential molecular basis for its morphological shift and offering insights into adaptive evolution in domesticated species.
The early developmental stages of fish exhibit the highest mortality and greatest environmental sensitivity throughout their life cycle. This period encompasses a series of crucial biological events, including morphogenesis, organ differentiation, and nutritional mode transition from fertilized eggs to newly hatched larvae. Although largemouth bass (Micropterus nigricans) is a commercially important fish species in China, the molecular regulatory mechanisms governing its endogenous nutritional stage remain largely unexplored. To elucidate the molecular basis of this critical period, we performed transcriptomic profiling across six consecutive developmental stages (Multicellular, Blastula, Gastrula, Neurula, Organogenesis, and 5 day post hatching larvae). Our results reveal stage-specific transcriptional programs: the multicellular-to-blastula transition is characterized by stage-specific enrichment of by cell cycle and DNA replication pathways, with MCM complex (mcm2-5) upregulation accelerating proliferation; the blastula-to-gastrula transition features activation of bmp4, fgfr2, and lft1 for germ layer induction; the neurula stage exhibits transcriptional bursts and enrichment of neural tube-related pathways; organogenesis involves simultaneous activation of focal adhesion (col1a1b, col4a5, tnc) and Wnt signaling (wnt1, wnt4, wnt3a) pathway; and 5 dph larvae show visual function maturation, with light transduction genes (gnat1, gnat2, gucy2f, pde6b) identified as hub genes. Mfuzz analysis further reveals sustained upregulation of Cluster 14 (igf2r、napin、vamp7、il1b、aco2) indicating functional maturation, while Cluster 29 (mcm10, espl1, cep152, cep44, cep295) confirms declining cell division activity. Collectively, this study provides a transcriptomic resource for understanding largemouth bass embryonic development and offers molecular insights for improving hatchery practices.
ATP-binding cassette (ABC) transporters constitute one of the largest transmembrane protein families and play essential roles in development and xenobiotic detoxification. The invasive freshwater snail Pomacea canaliculata exhibits rapid development, strong environmental adaptability, and high tolerance to various chemicals. However, the gene features and functional differentiation of its ABC transporters mediating these biological traits are largely unclear. This study conducted a genome-wide identification and characterization of ABC transporters in P. canaliculata, and integrated transcriptomic data to analyze their expression profiles. A total of 79 ABC transporters were identified and classified into eight subfamilies (ABCA-ABCH) based on phylogenetic tree, with a notable expansion in the ABCC subfamily. Collinearity analysis revealed that tandem duplication events were the primary driver of this subfamily-specific expansion. Transcriptome analysis revealed that PcABC genes exhibited distinct spatiotemporal and toxin-responsive expression patterns. PcABCF1 was highly expressed on day 1 post-oviposition, whereas PcABCA3, PcABCG5, and PcABCG8 were significantly upregulated during organ formation and on day 1 post-hatching. Exposure to the ethanol extract of Alternanthera philoxeroides leaves, PcABCB1.2, PcABCC5.1, PcABCG1.5, and PcABCG2 exhibited significant transcriptional responses. This study systematically characterizes the ABC transporter gene family in P. canaliculata and extends knowledge on the functional divergence of its members in embryonic development and toxic stress.
Chemosensation plays a pivotal role in foraging, mate recognition, and environmental adaptation for the invasive apple snail Pomacea canaliculata. However, the molecular foundations and ontogenetic dynamics of its olfactory system remain insufficiently characterized. In this study, we identified putative olfactory genes from whole-genome data and profiled their expression in nine different tissues, and also in cephalic tentacle tissues at four developmental stages. A total of 178 candidate olfactory-related genes were identified, including 90 olfactory receptors (ORs), 32 ionotropic receptors/ionotropic glutamate receptors (IRs/iGluRs), 16 lipocalins, 20 Niemann-Pick type C2 proteins (NPC2s), 4 sensory neuron membrane proteins (SNMPs), and 16 degenerin/epithelial sodium channels (DEG/ENaCs). Tissue expression analysis revealed strong chemosensory organ specificity, with the highest number of highly expressed genes detected in the left cephalic tentacle, followed by the osphradium. Notably, pronounced left-right cephalic tentacle asymmetry was observed, with generally lower expression levels in the right cephalic tentacle, suggesting potential functional specialization of bilateral sensory organs. During developmental progression, over half of the ORs and IRs/iGluRs peaked at the fully mature stage, whereas a secondary expression peak was observed in juvenile individuals. An integrated examination of genes demonstrating high expression at the fully mature stage and in the left cephalic tentacle identified ten candidate genes, including five ORs, four IR/iGluRs, and one DEG-ENaC gene. This study systematically profiles putative olfactory genes across tissues and developmental stages in P. canaliculata, providing foundational insights into its chemosensation processes and providing a molecular resource for future studies of chemosensory function in this invasive species.
Body size is an important property of fish, and the body weight is one of the major elements influencing fish metabolism and potentially the response to environmental stress such as high temperature. To investigate the size-dependent adaptation to summer heat stress, we performed an integrative analysis of serum biochemical parameters, transcriptomes, and metabolomes in triploid rainbow trout (Oncorhynchus mykiss) reared under naturally elevated summer temperatures (20 ± 1 °C). Individuals were categorized by body weight into small- (SRT, 1.02 ± 0.19 kg), middle- (MRT, 2.19 ± 0.27 kg), and large-sized (LRT, 3.38 ± 0.38 kg) groups. Our findings suggest that body weight was associated with distinct physiological and molecular profiles under a common thermal challenge. At the biochemical level, SRT fish exhibited a significantly higher superoxide dismutase (SOD) activity and lower protein carbonyl levels than LRT fish (P < 0.05), indicating that smaller individuals maintain superior antioxidant capacity and experience less oxidative damage, and they were associated with cellular maintenance over rapid growth under thermal stress. Transcriptomic analysis identified vdac3, plin1, lpl, and adipoqa as key genes differentially expressed across weight groups. Notably, plin1 and lpl both involved in lipid storage and mobilization, they were significantly upregulated in LRT fish, pointing to enhanced fat deposition capacity in larger individuals. Whereas vdac3 showed a decreasing expression trend with increasing body weight, hinting at reduced mitochondrial stress resilience in larger fish. Metabolomic profiling further revealed that the weight-dependent metabolic shifts were reflected in distinct pathway enrichment patterns, each carrying specific biological implications. Specifically, the enrichment of amino acid biosynthesis pathways (LRT vs. MRT) indicates enhanced protein turnover and anabolic activity in larger fish, supporting their continued somatic growth. The serotonergic synapse pathway (LRT vs. SRT) suggests that neuroendocrine regulation differs with body size, potentially reflecting altered stress-coping mechanisms in large versus small individuals. Meanwhile, fatty acid metabolism and degradation (MRT vs. SRT) point to differential energy utilization strategies, with medium-sized fish exhibiting distinct patterns of lipid catabolism compared to their smaller counterparts (P < 0.05). Integrative correlation analysis reinforced these interpretations, revealing significant associations between key lipid-metabolism genes (plin1, lpl) and metabolites such as arachidonic acid and 3-methyl-2-oxobutanoic acid-strong evidence that fat metabolism is a central, weight-dependent process under thermal stress. In summary, our multi-omics study, conducted under a common natural thermal challenge, suggests that smaller triploid rainbow trout were associated with greater antioxidant and immune defenses, whereas larger individuals were characterized by enhanced lipid metabolic and fat deposition capacities, revealing a weight-dependent divergence in adaptation strategy to elevated temperature.
Background Global climate warming has led to increasingly frequent and prolonged extreme summer heat events, posing severe environmental challenges to aquaculture systems. Extreme summer heat can disrupt the performance of pond-cultured ectotherms. The Chinese mitten crab (Eriocheir sinensis) is an economically important freshwater crustacean, but coordinated molecular differences following contrasting natural summers remain incompletely characterized. Results We performed a comprehensive multi-omics analysis integrating meteorological monitoring, mRNA/lncRNA transcriptomics, small-RNA profiling of miRNAs, DNA methylomics, and LC-MS metabolomics in E. sinensis populations collected from Yancheng, China, between 2020 and 2024. Across the ten farms, survival was significantly lower in 2024, whereas yield and the proportion of large individuals showed nonsignificant downward trends. Gene-set analyses showed negative enrichment of cellular heat-response, protein-folding, oxidative-phosphorylation, and mitochondrial ATP-production terms in the 2024 cohort at the time of sampling. The integrated transcript annotation contained 72,240 lncRNAs and 63,833 mRNAs, and CpG was the predominant methylation context. Differential methylation analysis identified 73 regions and 185 cytosines, with hypomethylated events predominating within the significant subset. Metabolomic profiles differed between annual cohorts and mapped to carbohydrate, lipid, and amino-acid pathways. Cross-omics integration prioritized eight candidate genes—ADCY9, UNC79, UBN1, IFT52, ACO2, LOC126986070, LOC127001126, and LOC126997895—and qPCR reproduced the reported directions of expression for selected RNAs. Conclusion This study provides the first integrative multi-omics framework for understanding chronic heat adaptation in E. sinensis. By linking transcriptomic, epigenomic, and metabolic remodeling, we elucidate the molecular mechanisms underlying energy imbalance, epigenetic reprogramming, and immune dysregulation during prolonged thermal stress. These findings offer valuable insights and genomic resources for breeding heat-tolerant crab strains and improving aquaculture resilience under ongoing climate change.
Interferon regulatory factors (IRFs) are DNA-binding transcription factors involved in immune regulation, yet the composition and physiological relevance of IRF repertoires in bivalve molluscs remain incompletely understood. In this study, comparative genomic, phylogenetic, structural and transcriptomic analyses were integrated to examine IRF evolution and immune-associated expression in bivalves. IRF genes were identified from representative bivalve proteomes and analyzed together with IRFs from model animals and previously characterized molluscan sequences. The dataset comprised 29 bivalve species from 12 families. Within this sampled dataset, IRF copy number ranged from two to four per species, with most species retaining three members, indicating a restricted IRF repertoire. Phylogenetic analysis of 113 IRF proteins from 34 species resolved four major subfamilies. Bivalve IRFs were mainly assigned to IRF1/2-like and IRF4/8/9-related lineages, whereas in the present dataset, clear bivalve representatives of vertebrate IRF3/7 and IRF5/6 clades were not detected. Motif and gene-structure analyses indicated conservation of the N-terminal IRF DNA-binding region, while the middle and C-terminal regions were more variable, particularly in IRF4/8-like members. In the noble scallop Mimachlamys nobilis, IRF genes and selected IRF-related genes, including MyD88, TRAF6-like, TBK1/IKKε-like and IKKα/β-like candidates, showed gene-specific expression patterns across tissues, with several genes reaching their highest mean expression in the gill, and showed distinct temporal expression profiles over 72 h of Vibrio parahaemolyticus exposure. Re-analysis of oyster and mussel transcriptomes further showed that IRF genes were expressed together with adaptor and kinase genes under bacterial exposure or in gill-associated immune contexts. These findings suggest that bivalves maintain a restricted but immune-relevant IRF repertoire, and that the potential functional diversification of molluscan IRFs is likely shaped by structural divergence, tissue-biased deployment and differential association with upstream innate immune signaling components rather than by extensive gene-family expansion.
Growth-related traits are major determinants of production performance in the giant freshwater prawn, Macrobrachium rosenbergii, but their genetic architecture remains incompletely resolved. An F1 full-sib family of 133 individuals and two parents was analyzed, with the two parents genotyped using high-depth whole-genome sequencing (WGS) and the progeny genotyped using IIB restriction-site associated DNA (2b-RAD) sequencing. A total of 858,375,066 paired-end reads were generated, and 9427 single nucleotide polymorphism markers were assigned to 59 linkage groups in the sex-averaged map. The map spanned 8591.22 cM, with a mean marker interval of 0.91 cM. Quantitative trait locus (QTL) mapping identified 22 QTLs for body weight (BW), body length (BL), carapace length (CL), carapace width (CW), carapace height (CH) and telson length (TeL) across nine linkage groups, and individual QTLs explained 9.96-28.13% of phenotypic variation. Functional annotation and enrichment analysis of genes within QTL-associated regions indicated that BW variation was mainly associated with nutrient sensing, extracellular matrix-receptor interaction, focal adhesion, actin-cytoskeleton regulation and calcium-dependent signaling, whereas BL was associated with insulin signaling, lipid metabolism, cyclic-nucleotide signaling, mitochondrial energy production and microtubule organization. To further evaluate key candidates, representative body weight- and body length-related genes were examined by real-time PCR in low-, medium- and high-growth groups. Growth-group real-time PCR analysis was performed for 32 representative body weight- and body length-related candidate genes, and the results prioritized a focused subset of expression-supported candidates, including InR, VAV, Itgβ-PS, Itgα-PS2, Col1A1, PLCD4, CaM4, PDE4C and PAK2 for body weight, and IRS2, HSL, MCD, LIP3, NDUFB7, TUBA1A, LamA, PMCA4, AC1, GC32E and Gαo for body length. These results provide a high-density linkage map, trait-associated QTLs and expression-supported candidate genes for future validation and molecular breeding of M. rosenbergii.
Reproductive migration draws heavily on somatic lipid reserves, but tissues involved in reproduction may differ in the extent to which they reflect recent physiological history. We profiled targeted lipids in muscle, liver, and ovary and untargeted muscle metabolites in 12 mature female Coilia nasus (ovarian stages IV-V) collected concurrently at Chongming (estuarine-end; n = 6) and Taizhou (freshwater mainstem; n = 6), with anadromy confirmed by otolith Sr/Ca profiles. Muscle alone showed significant global lipidomic differentiation (PERMANOVA R2 = 0.331, P = 0.039), although multivariate dispersion also differed between sites. Of 41 phosphatidylcholine species, 40 had higher abundance in Chongming and 19 met the exploratory candidate threshold; phosphatidylcholines were strongly enriched among candidate lipids (subclass enrichment FDR = 1.1 × 10-14). Of 47 targeted acylcarnitines, 43 had higher abundance in Taizhou, a pattern mirrored by 20 of 23 untargeted acylcarnitine features. N6,N6,N6-trimethyl-l-lysine was higher in Chongming (FDR = 0.010; Spearman ρ = -0.818, P = 0.0011), but this across-individual association was largely attributable to the between-site contrast and does not establish precursor-product flux. Liver showed concordant acylcarnitine enrichment, whereas ovary lacked detectable global differentiation and showed only limited differences in LPC, eicosanoid, and PE-O species. Body size and GSI did not differ, and ovarian-stage composition was balanced. Muscle therefore showed the strongest differentiation between corridor positions. These data provide a hypothesis-generating baseline, but covariation among salinity, migration distance, and population structure precludes causal attribution.
This study aimed to investigate the effect of seasonal changes (from May to November) with a dietary supplement of dihydroquercetin (DHQ), a bioflavonoid of plant origin, on the composition of the gastrointestinal tract (GIT) microbiota of rainbow trout (Oncorhynchus mykiss). At the beginning of the study, fish had an average weight of 546 ± 25.8 g and later at the end of the study the weight had changed significantly in the control group (2071.6 ± 84.7 g) and in the experimental group (1909.9 ± 101.1 g) that received a diet supplemented with DHQ for 6-month. Amplicon sequencing targeted to the V3-V4 region of 16S rRNA gene fragments was used for the taxonomic identification of the bacterial composition. Firmicutes (54.6 ± 3.3%), Proteobacteria (32.6 ± 3.4%), Fusobacteriota (6.0 ± 1.6%), and Bacteroidota (5.0 ± 0.9%) were the major phyla in the fish GIT of both control and experimental groups. According to the ADONIS test (weighted and unweighted UniFrac distances), significant effects of season and section of digestive tract have been shown, indicating that both of these factors are more relevant than DHQ supplementation. The functional composition associated with Mycoplasma in the gut remains less variable across sampling dates, suggesting that this dominant group acts as a stable core, resistant to environmental fluctuations in the water body. Dietary DHQ selectively affected total composition of the gastrointestinal microbiota in rainbow trout. This should be taken into account in the long-term assessment of the predictive role of bacterial communities and the effective search for new feed additives in order to obtain high-quality aquaculture products.
Salinity is a key environmental factor affecting the survival, growth, and reproduction of fish, and the euryhaline red tilapia (Oreochromis spp.) is an ideal model for investigating salinity adaptation mechanisms in fish. In this study, red tilapia (body weight 139.43 ± 41.74 g) were directly transferred from freshwater (control group, C) to water with a salinity of 15 ± 0.1‰ (experimental group, E) for 96 h of acute stress. Gill histological structure, physiological and biochemical parameters, and transcriptomic and metabolomic profiles were analyzed. The results showed that, compared with the 0 h group (control group), SOD activity was significantly elevated at all time points, GSH-Px activity was significantly elevated at 12-24 h, CAT activity was significantly elevated at 36-96 h, and MDA content was significantly increased at 12-48 h (P < 0.05). In gill tissue, slc15a4 expression first increased significantly, falling below the control level at 96 h, whereas cndp2 expression increased continuously and peaked at 96 h. Transcriptomic analysis identified a total of 1088 differentially expressed genes (339 up-regulated and 749 down-regulated), which were significantly enriched in focal adhesion, ECM-receptor interaction, the PI3K-Akt signaling pathway, glutathione metabolism, and the AMPK signaling pathway. Metabolomic analysis identified 250 differentially accumulated metabolites (135 up-regulated and 115 down-regulated), which were significantly enriched in β-alanine metabolism, ABC transporters and multiple metabolic pathways. Integrated multi-omics analysis further revealed that the differentially expressed genes and metabolites were jointly enriched in 12 pathways, including β-alanine metabolism, ABC transporters, neuroactive ligand-receptor interaction, and glycerophospholipid metabolism. In conclusion, β-alanine and arachidonic acid may be interconnected during salinity adaptation in red tilapia.
Chloride channels and transporters are important for cellular volume regulation and salinity adaptation in euryhaline crustaceans, yet the intestinal transcriptional relationship between plasma-membrane and intracellular chloride pathways remains unclear in Litopenaeus vannamei. In this study, RNA interference of anoctamin 1 (ANO1) was combined with intestinal transcriptome sequencing under the production-relevant low-salinity condition of salinity 3. ANO1 silencing produced a focused transcriptional response, with 16 differentially expressed genes (DEGs) identified (11 upregulated and 5 downregulated). Functional enrichment indicated that these genes were associated with transporter activity, cytoskeletal organization, extracellular matrix-receptor interaction, membrane lipid metabolism, and vesicular processes. Notably, a transcript encoding chloride channel protein 3 (CLC-3) was significantly upregulated following ANO1 knockdown, suggesting a potential transcriptional relationship between ANO1 and CLC-3 in chloride homeostasis. Based on this finding, CLC-3 was selected for full-length cDNA cloning, sequence characterization, salinity-gradient expression analysis, and RNAi-based functional assessment. The cloned CLC-3 cDNA was 2883 bp in length and encoded an 850 amino acid protein containing a conserved voltage-gated chloride channel (Voltage-CLC) domain and two cystathionine β-synthase domains. Phylogenetic analysis placed LvCLC-3 within the intracellular CLC-c clade, and tissue distribution analysis showed the highest CLC-3 expression in the intestine. Intestinal CLC-3 expression responded nonlinearly to salinity variation, peaking at salinity 20. Under salinity 3, CLC-3 knockdown reduced ANO1, Na+/K+-ATPase alpha subunit, and Na+-K+-2Cl- cotransporter transcript levels, whereas glutamate-gated chloride channel expression increased. Mild hepatopancreatic structural alterations were also observed after CLC-3 knockdown. These findings suggest that CLC-3 is a salinity-responsive intracellular chloride-transporter candidate associated with intestinal ion-transport-related transcriptional responses after ANO1 suppression in L. vannamei, although the underlying physiological mechanism requires further validation.
The Japanese flounder (Paralichthys olivaceus) is an important mariculture species. However, the genetic mechanisms underlying its growth traits remain poorly understood. To explore the genetic basis of growth variation, whole-genome resequencing was performed in a cultured cohort of 60 individuals, followed by exploratory genome-wide association analysis and candidate-gene prioritization. The results revealed heritability estimates of 0.40 for body weight and 0.24 for body length, with substantial overlap in associated loci between the two traits. Exploratory association and variant-annotation analyses prioritized ppiabl, which carries a nonconservative missense variant, as a candidate gene for further investigation. Tissue expression analysis showed that ppiabl was highly expressed in muscle tissue. This gene encodes a protein belonging to the conserved peptidyl-prolyl cis-trans isomerase family. In Japanese flounder primary muscle cells, ppiabl knockdown was associated with altered expression of growth-related genes and an increased G1-phase fraction, whereas overexpression produced changes in the opposite direction. In line with this, fast-growing individuals were found to have significantly larger muscle fiber areas than slow-growing ones. These findings suggest that ppiabl may be involved in muscle-related cellular processes associated with growth variation in Japanese flounder, although its contribution to whole-animal growth requires further validation. Overall, this exploratory study prioritizes ppiabl as a candidate gene potentially associated with growth-related cellular processes in Japanese flounder, although validation in larger independent populations and in vivo models is required.
