To clarify whether heme oxygenase-1 (HO-1) plays an immunomodulatory and anti-apoptotic role in hypoxia stress of small yellow croaker. In this study, histological observation, biochemical detection, gene expression detection, gene interference and other methods were used to explore the effects of hypoxia stress on non-specific immunity and apoptosis of small yellow croaker and the changes of SYCF cell immunity, inflammation and apoptosis after interference with ho-1 at the individual and cell levels. The results showed that hypoxia stress resulted in a significant decrease in the height, width and muscle thickness of the intestinal villi of small yellow croaker, and the number of goblet cells decreased. Splenic red blood cell swelling, increased intercellular space. The activities of immune-related enzymes (SOD, ACP, AKP, LZM) and the relative expression of pro-inflammatory cytokines (IL-1β, IL-6, IL-8, IL-17c, TNF-α) mRNA in spleen, intestine, serum and SYCF cells were significantly changed under hypoxia stress, indicating that hypoxia stress induced inflammatory response and activated the immune system in small yellow croaker. The L. polyactis ho-1 orthologue (Lpho-1) was cloned and showed elevated mRNA and protein expression in intestinal and spleen tissues and cells under hypoxia. siRNA knock-down of Lpho-1 in SYCF cells followed by hypoxia reduced non-specific immune enzyme activities, up-regulated pro-inflammatory cytokine expression, decreased cell viability and increased caspase-3/8/9 activities. These data indicate that LpHO-1 protects L. polyactis against hypoxia by modulating immune enzyme activities, suppressing cytokine release and inhibiting apoptosis.

The large yellow croaker (Larimichthys crocea) is a key mariculture species in China, however, its industry is threatened by visceral white nodules disease (VWND) caused by the bacterium Pseudomonas plecoglossicida. A significant challenge in breeding is the potential genetic trade-off between growth and disease resistance. To investigate their genetic relationship, we constructed a high-density SNP-based genetic linkage map for L. crocea using a F1 full-sib family (n = 150). The map comprised 24 linkage groups with 32,429 bin markers and an average interval of 0.051 cM. Based on this map, we conducted QTL mapping for one yield trait (body weight), eight morphological traits, and three VWND-resistance traits (survival time, AT; spleen and liver pathogen loads). Phenotypic analysis revealed strong integration among growth traits and a moderate positive correlation between growth traits and AT. QTL mapping identified 53 QTLs for growth (PVE = 0.14-5.83%) and 20 for resistance (PVE = 0.78-8.93%). Notably, only two genomic intervals exhibited co-localization between a morphological trait (AL or BL) and AT, each explaining a modest phenotypic variance (0.66-5.99%). The largest-effect QTLs for growth and resistance were mapped to distinct linkage groups, and candidate genes within the co-localized intervals (Unc5d, SCN5A, HUS1) are involved in fundamental cellular processes rather than core growth or immune pathways. These results suggest that yield, morphological, and VWND-resistance traits in L. crocea are largely under independent genetic control within the studied family, indicating that simultaneous improvement of growth and disease resistance is feasible. This study provides a molecular basis for breeding strategies aimed at overcoming the trait trade-off bottleneck in this economically vital species.

Aquaculture is critical to global food security, yet bacterial epidemics threaten its sustainability. The defense mechanisms of fish remain poorly understood, hindering effective disease management. This study investigates the temporal immune response of the economically important marine teleost Larimichthys polyactis to Pseudomonas plecoglossicida, a pathogen that causes lethal white-nodule disease of internal organs. Integrated analyses of histopathology, biochemistry, and TUNEL assays revealed that infection triggered hepatic granulomatous nodulation and oxidative stress, culminating in apoptosis at 72-96 h post-infection (hpi). Transcriptomic and proteomic profiling showed the distinct time-dependent and stage-specific enrichment patterns of DEGs and DEPs. The early stages (6-48 hpi) involved endocrine regulation, immune signal transduction, and energy metabolism, whereas the later stages (72-96 hpi) were characterized by programmed cell death and immune defense. Integrated multi-omics analysis and expression validation indicated that upregulation of the apoptotic pathway may be associated with the host response to P. plecoglossicida infection. These findings deepen our insights into the dynamic response mechanisms of marine teleosts against P. plecoglossicida infection and provide a theoretical framework for host-pathogen interactions.

Ocean acidification has become a significant global ecological issue, particularly in coastal regions with intensive aquaculture. Fish farming is a crucial component of global food security, yet research on the impact of acidification on the aquaculture performance of economically important teleosts remains limited. In this study, we reared the fast-growing large yellow croaker (Larimichthys crocea) for 30 days under three different pH conditions: severe acidification (LA, pH 7.4), moderate acidification (MA, pH 7.8), and control (HA, pH 8.1). We comprehensively evaluated growth performance, survival rate, tissue structure, antioxidant enzyme activity, and innate immunity. The results showed that the LA group exhibited suppressed growth (significantly lower than the MA group, p < 0.05), elevated cortisol and T4 levels (p < 0.05), and trends of reduced antioxidant enzyme and innate immune enzyme activities, along with organ-specific pathological changes (vacuolation, structural loosening) in gills, liver, kidneys, and intestines, though most indices showed no significant difference from the HA group. Notably, the MA group showed optimal growth performance, stable physiological and immune responses. In conclusion, while acidification did not markedly affect the survival rate of L. crocea, severe acidification (pH 7.4) induces stress responses and tissue damage. These findings suggest that L. crocea exhibits a certain degree of tolerance to the acidification conditions tested, as several physiological parameters were not significantly affected. However, when considering the overall set of observations, including histological alterations across multiple tissues and changes in plasma and tissue parameters, long-term exposure to severe acidification (pH 7.4) appears to induce tissue damage and stress-related physiological disturbances, indicating potential health risks. This study provides empirical evidence regarding the potential risk posed by projected ocean acidification on L. crocea aquaculture and supports the development of climate change adaptation strategies for coastal mariculture.

Bisphenol A (BPA) is a widely distributed endocrine-disrupting chemical (EDCs) in aquatic ecosystems. Larimichthys polyactis is an economically important fish species in China's nearshore waters, characterized by unique sexual differentiation patterns. However, research on the effects of BPA exposure on this species remains limited. This study used 30 days post-hatching (dph) L. polyactis to assess the impact of BPA exposure at three concentrations: 1 μg·L-1, 50 μg·L-1, and 500 μg·L-1, with a control group (WT), over a 60-day immersion period. Survival rate, growth, gonadosomatic index (GSI), and histological changes were examined to evaluate BPA's effects on growth, gonad differentiation, and development. Recovery was also assessed for 60 days post-exposure. Results showed that L. polyactis exhibited a high tolerance threshold to BPA, with short-term exposure significantly affecting the GSI, gonad structure, and reproductive cell density. Long-term exposure caused gonadal abnormalities and growth retardation. BPA's effects were clearly dose-dependent, time-dependent, and exhibited gender-specific differences. Despite partial recovery in growth and gonadal structure post-exposure, changes followed a non-monotonic dose-response, indicating that BPA disrupts multiple physiological processes in L. polyactis. Furthermore, long-term low-dose exposure posed a greater threat than acute high-dose exposure. These findings provide a theoretical basis for formulating effective water pollution control strategies and preserving marine biodiversity and fisheries.

To investigate the potential functions of mitochondrial membrane proteins prohibitin (PHB) and stomatin-like protein 2 (SLP2) during spermatogenesis in Larimichthys polyactis, we analyze the molecular characteristics and expression profiles of Lp-PHB and Lp-SLP2, the co-localization characteristics of Lp-PHB, Lp-SLP2 and mitochondria during spermatogenesis, as well as the co-localization characteristics of Lp-PHB, ubiquitin, and mitochondria. The results showed that Lp-PHB consists of an N-terminal hydrophobic, a conserved SPFH domain and a C-terminal helical domain, while Lp-SLP2 only contains a conserved SPFH domain. Lp-PHB and Lp-SLP2 genes and their encoded proteins were highly expressed in the testis, Lp-PHB and Lp-SLP2 protein were localized in the mitochondria of spermatogenic cells. During spermatogenesis, the signals of Lp-PHB and Lp-SLP2, Lp-PHB and mitochondria, as well as Lp-SLP2 and mitochondria were co-localized: in spermatogonia and spermatocytes, the co-localization signals were randomly distributed in the perinuclear cytoplasm; during the differentiation of spermatids into sperm, the co-localization signals gradually migrated to the tail region on one side of the nucleus; and in mature sperm, the co-localization signals accumulated in the middle piece. Additionally, the signals of Lp-PHB and ubiquitin, as well as ubiquitin and mitochondria, were also consistently co-localized during spermatogenesis, with co-localization characteristics highly similar to those of Lp-PHB and mitochondria. These results suggest that Lp-PHB and Lp-SLP2 may cooperate through interaction to maintain mitochondrial functional homeostasis during spermatogenesis in L. polyactis, and Lp-PHB may be involved in the degradation of damaged or excess mitochondria by mediating mitochondrial ubiquitination, thereby facilitating the normal progression of spermatogenesis.

Visceral white-nodules disease (VWND), caused by Pseudomonas plecoglossicida, poses a severe threat to the large yellow croaker (Larimichthys crocea) aquaculture industry. Although breeding resistant strains is a promising strategy, the molecular basis of disease resistance in this host remains poorly understood. Here, 1500 fish were artificially infected, and extreme phenotypes (30 resistant, RL; 30 susceptible, SL) were selected based on survival time and liver pathogen load. Liver histopathology revealed that RL fish maintained intact architecture with only mild vacuolation, whereas SL fish exhibited widespread necrosis, inflammation, and hemosiderin deposition. Consistently, RL fish showed lower MDA levels and higher GSH-Px activity and TAC. Transcriptomic analysis identified 172 differentially expressed genes (DEGs): RL fish were characterized by upregulation of anti-inflammatory and tissue-protective genes (Epo, CAV3) and downregulation of pro-coagulant factors (PAI1, K1kb1). Proteomic analysis identified 111 differentially expressed proteins, with significantly enriched pathways including the peroxisome, pentose phosphate, and phagosome pathways. Integrated cross-omics analysis revealed eight co-enriched KEGG pathways; among them, arginine/proline metabolism, phagosome, oxidative phosphorylation, and focal adhesion were consistently upregulated in the RL group. These findings suggest that effective resistance to VWND in L. crocea may involve a coordinated, multi-layered defense program encompassing redox balance, regulated immune responses, metabolic reprogramming, and cellular homeostasis. Cross-omics-supported candidate factors (e.g., P4ha1, COX6B, RAB5A, CAV3) represent promising targets for functional validation via DNA-level experiments in independent sample sets, and the prominent enrichment of arginine-proline metabolism indicates a potential target for dietary intervention that merits further investigation.

The small yellow croaker (Larimichthys polyactis) is an important mariculture fish species, which necessitates systematic genetic analysis of growth-related traits to accelerate precision breeding. To address this, 1051 individuals from 26 full-sib families were evaluated as part of this study to determine the genetic parameters of nine growth-related traits at 10 months of age: total length, body length, head length, body height, caudal peduncle length, caudal peduncle height, trunk length, tail length and body weight. Family-level inbreeding coefficients ranged from 0.125 to 0.438, indicating moderate to high genetic relatedness within families. Genetic parameters were estimated with a single-trait animal model in which the corresponding trait measured at 6-month of age fitted as a linear covariate and days of age was included as a fixed effect. Heritability estimates for individual traits were moderate (0.29-0.42). Positive genetic and phenotypic correlations between trait pairs were consistently, ranging from 0.55 to 0.99, and 0.49 to 0.98, respectively. Repeatability estimates for the traits tested ranged from 0.60 to 0.87. Under a 30% selection ratio, the predicted genetic gain and relative genetic gain for body weight in the next generation were 3.54 and 7.95%, respectively. These results provide a robust framework for the development of selective breeding programs in small yellow croaker, enabling targeted enhancement of growth performance in aquaculture operations.

Heat stress severely hinders citrus yield and fruit quality. This study employed integrated physiological and transcriptomic analyses to investigate the effects of the exogenous application of abscisic acid (ABA) and brassinosteroid (BR) on heat stress responses in citrus. The results showed that the exogenous application of ABA and BR increased the contents of soluble sugar, proline, and ABA, and enhanced the activities of peroxidase and catalase under heat stress. Transcriptome trend analysis identified profiles 1, 6, and 7 as significantly enriched across exogenous ABA, BR, and control conditions. Profile 6 exhibited rapid upregulation followed by stabilization and showed a significantly higher gene count under both ABA and BR treatments than under the control. KEGG enrichment analysis revealed that genes in profile 6 were primarily enriched in amino sugar, nucleotide sugar, galactose, amino acids, 2-oxocarboxylic acid, glycerophospholipid, glucosinolate metabolism, MAPK signaling pathway, plant hormone signal transduction, protein processing in the endoplasmic reticulum, plant–pathogen interaction, and endocytosis. Furthermore, four genes encoding heat shock proteins (HSP), including HSP21A, HSP21B, HSP70-17, and HSP70A, were induced under heat stress and showed significant upregulation in response to exogenous ABA and BR treatments. In conclusion, these findings indicated that exogenous ABA and BR regulated ABA and osmoprotectant accumulation and antioxidant defense activation in response to heat stress.

Small yellow croaker, Larimichthys polyactis, is a marine fish species of significant commercial importance in China and Korea, yet it suffers from various challenges including genetic degradation and disease problem. Strains with good performance traits such as fast growth and strong disease resistance are needed in aquaculture. In the present study, a 100 K SNP array with exceptional genotyping quality was developed based on genomic resequencing, achieving a remarkable detection rate of 98.75

High temperatures present considerable challenges to global fish growth and production, yet the genetic basis of heat tolerance remains underexplored. This study combines quantitative trait locus (QTL) mapping and genome-wide association studies (GWAS) to examine the genetics of heat tolerance in Larimichthys polyactis. As a result, a genetic linkage map was constructed with 3237 bin markers spanning 24 linkage groups and totaling 1900.84 centimorgans, using genotyping-by-sequencing of a full-sib family comprising 120 progeny and their two parents. Based on this genetic linkage map, QTL mapping identified four QTLs associated with heat tolerance, which encompassed 18 single nucleotide polymorphisms and harbored 648 genes within the QTL intervals. The GWAS further disclosed 76 candidate genes related to heat tolerance, 56 of which overlapped with the QTL results. Enrichment analysis indicated that these genes are involved in immune response, development, lipid metabolism, and endocrine regulation. qPCR validation of 14 prioritized genes, which were simultaneously enriched in Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways, confirmed significant upregulation of smpd5, polr3d, rab11fip2, and gfpt1, along with downregulation of gpat4 and grk5 after 6 h of heat stress. These findings demonstrate their responsiveness to elevated high temperatures. This meta-analysis of QTL mapping and GWAS has successfully identified functional genes related to heat tolerance, enhancing understanding of the genetic architecture underlying this critical trait in L. polyactis. It also provides a molecular breeding tool to improve genetic traits associated with heat tolerance in cultured L. polyactis.

Artificial gynogenesis provides one of efficient strategies for fish germplasm improvement. But in aquaculture practice, it is still difficult to expand the offspring population and breeding scale owing to the unisexuality of gynogenetic strains. This study indicates that the gynogenesis blunt snout bream (GBSB), an all-female population, can be sex reversal to the pseudo-male at high temperatures of 34 +/- 1 degrees C. By hormone test experiments on GBSB, it is validated that higher temperature causes a decreasing estrogen level and an increasing androgen level. Observation results also show that the two-year old pseudo male GBSB reaches sexual maturity and produces functional haploid sperms. Genotypic sex identification further confirms that the absence of male genetic marker for blunt snout bream in the pseudo-male GBSB. It is concluded that high-temperature cultivation is an effective strategy of inducing the sex reversal of GBSB, and the results can lay a foundation for large scale breeding of gynogenesis strains in fish.

Hypoxia negatively affect metabolism, growth and development of fish. To explore the effects of hypoxic stress on energy metabolism in Larimichthys polyactis, we performed untargeted metabolomic analysis, biochemical assays, and real-time fluorescence quantitative PCR (RT-qPCR) to explore the dynamic changes in hepatic glucose and lipid metabolism under sustained 96 h hypoxic stress. The findings showed that after 6 h of hypoxia, starch and sucrose metabolism was significantly enriched, with potentially enhanced glycolysis and gluconeogenesis. After 96 h of hypoxia, steroid biosynthesis and unsaturated fatty acid biosynthesis were significantly enriched, with the potential for a significant increase in lipid decomposition. Additionally, in the first 24 h of hypoxia, the serum glucose, pyruvate, and lactate contents increased, whereas the activities of the aerobic respiratory enzymes pyruvate dehydrogenase (PDH) and succinate dehydrogenase (SDH) in the liver decreased. The activities of the anaerobic glycolytic enzymes, hexokinase (HK), phosphofructokinase (PFK), pyruvate kinase (PK), lactate dehydrogenase (LDH), as well as the glucose metabolism-related genes, glut1, hk2, pfkp, ldha, and mct4 mRNA levels in the liver increased. After 24 h of hypoxia, liver aerobic respiratory enzyme activity increased, whereas anaerobic glycolytic enzyme activity and gene expression levels decreased. At the same time, serum triglyceride (TG) levels decreased while free fatty acid (FFA) levels increased. Lipase (LPS) activity and lipid degradation-related genes hsl and mgl mRNA levels in the liver also increased. Conversely, acetyl-CoA carboxylase (ACC) activity and fatty acid synthesis-related genes acc1 and fasn mRNA levels decreased. Fatty acid oxidation enzyme-related gene cpt-1 mRNA level also decreased. These results indicate that during the early phase of hypoxia (in the first 24 h), aerobic respiration was inhibited, anaerobic glycolysis became the primary energy source. As the duration of hypoxia increased (after 24 h), anaerobic glycolysis decreased, lipid metabolism became an important energy pathway. Our study revealed the effects of different durations of hypoxic stress on glucose and lipid metabolism in the liver of L. polyactis, helping to elucidate metabolic adaptation mechanisms in fish under hypoxic conditions and providing theoretical guidance for screening and breeding new varieties of hypoxia-tolerant fish.

Anthropogenic acidification is a long-term challenge to marine ecosystems. Though coastal acidification is intensifying, the large yellow croaker (Larimichthys crocea) exhibits good adaptability to pH fluctuations, the underlying mechanisms of which remain poorly understood. This study investigated the morphology, antioxidant enzyme activity, and gene expression of L. crocea under varying acidification conditions (pH 8.1 (H group), 7.8 (M group), and 7.4 (L group)). Water pH fluctuations were also monitored to explore the physiological responses and potential adaptive molecular mechanisms of L. crocea under various acidified environments. The results indicated that the water pH decreased in the H group, significantly increased in the L group (p < 0.05), and remained stable in the M group during the experiment. The lowest MDA content and the highest antioxidant enzyme activities (CAT, SOD, GSH-Px) were observed in L. crocea at pH 7.8, suggesting pH 7.8 was optimal for L. crocea. Transcriptomic analysis revealed distinct gene expression patterns between the gills and kidneys under acidification stress. Differentially expressed genes (DEGs) in the gills were primarily observed between the M and L groups (62.3%), whereas in the kidneys, the majority of DEGs were observed between the M and H groups (43.2%). These findings suggested that the gills play a critical role in adapting to low pH in L. crocea, while the kidneys were more responsive to high pH. Enrichment analysis identified critical pathways, including vasopressin-regulated water reabsorption, mineral reabsorption, and aldosterone-regulated sodium reabsorption, which are associated with water and ion metabolism. These pathways play a pivotal role in the acid–base homeostasis and metabolism of L. crocea. These results provide insights into the adaptive mechanisms of L. crocea to acidified environments, with implications for aquaculture management and future ocean acidification adaptation.

Small yellow croaker (Larimichthys polyactis) represents an important commercial fish species in China. A high-quality genome is essential for evaluating the fine-scale genetic structure, which has significant implications for the conservation of wild stocks, fishery management, and the utilization of germplasm in L. polyactis. This study presents a chromosome-level genome of L. polyactis generated by employing the PacBio high-fidelity (HiFi) and high-throughput chromosome conformation capture (Hi-C) technologies. The complete genome spans 677.35 Mb with a scaffold N50 size of 28.51 Mb. A substantial portion of the genome, totaling 663.13 Mb (97.90%), was anchored to 24 chromosomes. Based on Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis, L. polyactis exhibits high genomic completeness (98.00%). A total of 28,640 annotated genes were identified, with 25,801 being functionally annotated. The comparisons of 24 chromosomes between L. polyactis and L. crocea proved high conservation of synteny between this pair of relatives. These findings provide valuable resources for the conservation, functional genomics, molecular breeding and evolutionary studies of L. polyactis.

This study aimed to determine the thermosensitive period and effect of temperature on sex differentiation in L. polyactis. The results showed that the male-biased sex ratio was 50.9, 57.8, and 97.9 % in the 18, 24, and 31 degrees C groups at 90 days post-fertilization (dpf), respectively. Additionally, eggs, larvae, or juvenile fish were transferred from untreated water to 18 and 31 degrees C every 6 - 9 days from 0 to 55 dpf to clarify the thermosensitive period. The results demonstrated that the critical thermosensitive period was 19 - 25 dpf and the male-biased ratio reached 77.8 %. Exposure to 31 degrees C resulted in 74.1 and 69.6 % male-biased ratios during the 25 - 31 and 31 - 37 dpf periods, respectively, after the critical thermosensitive period. Histological observations indicated that long-term exposure of juvenile fish to 31 degrees C induced oocytes and/or ovary degeneration, followed by sex reversal to the testis. This study demonstrates that the sex differentiation of L. polyactis is significantly affected by high temperatures during the thermosensitive period and provides basic information on the sex differentiation of L. polyactis. It also provides a theoretical foundation for the sex-controlled breeding of L. polyactis.

In this study, we compared the genetic diversity and structure of small yellow croaker (Larimichthys polyactis, LP), large yellow croaker (Larimichthys crocea, LC), and their reciprocal hybrids (LP ♀ × LC ♂ (LCP) and LC ♀ × LP ♂ (LPC)) using 14 microsatellite loci. Our results revealed that genetic diversity was highest in LCP, followed by LP and LPC, with LC exhibiting the lowest level. Additionally, among the two hybrid progenies, the number of loci in LCP deviating from Hardy–Weinberg equilibrium was lower. This suggests that LCP is a more appropriate choice as breeding material and has the potential to enhance germplasm resources. Based on the analysis of 14 microsatellite loci, we observed that both hybrid species clustered with their respective maternal parents. Specifically, LPC exhibited a closer genetic relationship to its maternal parent than LCP did. Furthermore, the majority of genes in LPC were inherited from its maternal parent (LP). In the LCP population, approximately 63% of individuals possessed gene profiles similar to those observed in LPC, while the remaining individuals displayed a mix from both parents. This study provides a strategic direction for the efficient utilization and management of novel germplasm resources in hybrid yellow croaker. Hybrid yellow croaker serves as an intermediate breeding material, playing a significant role in the genetic improvement of Larimichthys crocea and Larimichthys polyactis.

Pseudomonas plecoglossicida has emerged as a serious threat to aquaculture, causing visceral white-nodules disease (VWND) in a range of commercially valuable fish, including the small yellow croaker (Larimichthys polyactis). In this study, a pathogenic strain of P. plecoglossicida, designated XSLPP-1, was isolated from diseased L. polyactis. Controlled challenge experiments revealed an exceptionally low 96 h median lethal concentration of 1 × 103 CFU/mL. A high accuracy quantitative PCR assay targeting the gyrB gene was developed (standard curve: y = 119538.14e-0.58x - 3.45, R2 = 0.99), enabling precise quantification of bacterial burden in infected tissues throughout the course of infection. Additionally, three antimicrobial peptides (AMPs), namely Lp_piscidin, Lp_hepcidin, and Lp_NK-lysin, were identified in L. polyactis, each exhibiting high sequence conservation with homologs in Sciaenidae species. Tissue-specific expression profiling showed significant upregulation of these AMPs in immune-related organs such as the liver, spleen, head kidney, and intestine following infection. Notably, Lp_hepcidin expression in the liver exhibited a significant negative correlation with bacterial loads, suggesting its potential as both a biomarker for disease resistance and a target for future therapeutic strategies. This study provides new insights into the pathogenic mechanisms of P. plecoglossicida and the host innate immune strategies. The integrated approach combining pathogen characterization, diagnostic development, and host immune response analysis offers promising strategies for the effective management of VWND in aquaculture systems.

Interspecific hybrid combinations of Larimichthys crocea × Larimichthys polyactis exhibit heterosis in terms of growth traits; however, the molecular regulatory mechanism underlying this phenomenon remains unclear. DNA methylation plays a pivotal role in regulating gene expression and is involved in growth and development processes. In this study, we comprehensively investigated intricate regulatory processes by integrating transcriptome and methylome datasets from brain, liver, and muscle tissues. We analyzed a total of 72 sequence datasets, including transcriptome and genome-wide DNA methylome data, from 36 tissue samples using LC, LP, LPC and LCP. We elucidated the distinct expression patterns of these four populations and examined their interactions with DNA methylation. Our findings revealed diverse DNA methylation profiles and demonstrated a greater number of hypo-DMRs in hybrid yellow croakers than in their parental lines. The majority (86 92

Thyroid dysfunction may affect the intestinal microbiota through short-chain fatty acids (SCFAs) in marine fish. This study investigated the effects of triiodothyronine (T3, 20 ng/g) and thyroxine (T4, 20 ng/g), and propylthiouracil (PTU, 5000 ng/g) on growth performance, intestinal SCFA profiles, and microbiota composition in little yellow croakers Larimichthys polyactis. The results showed that dietary thyroid-active agent supplementation significantly decreased weight gain, and specific growth ratio. Moreover, dietary T3, T4, and PTU induced the states of hyperthyroidism, hyperthyroidism, and hypothyroidism, respectively, leading to differential alterations in intestinal SCFA profiles. Specifically, only dietary T4 supplementation significantly increased the diversity of intestinal microbiota. Our findings suggest that the genera Vibrio and Sediminibacterium play key roles in multiple metabolic pathways within the host intestine. Correlation analyses further indicated that intestinal acetic acid and isobutyric acid were characteristic metabolites involved in the alteration of the genus Vibrio abundance. These results provide a foundation for further investigation into the effects of thyroid-disrupting activities on growth, intestinal SCFA profiles, and microbiota composition in marine fish.