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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.

The problem of marine noise pollution has a long history. Strong noise (>120 dB re 1 µPa) will affects the growth, development, physiological responses, and behaviors of fish, and also can induce the stress response, posing a mortal threat. Although many studies have reported that underwater noise may affect the survival of fish by disturbing their nervous system and endocrine system, the underlying causes of death due to noise stimulation remain unknown. Therefore, in this study, we used the underwater noise stress models to conduct underwater strong noise (50–125 dB re 1 µPa, 10–22,000 Hz) stress experiments on small yellow croaker for 10 min (short-term noise stress) and 6 days (long-term noise stress). A total of 150 fishes (body weight: 40–60 g; body length: 12–14 cm) were used in this study. Omics (metabolomics and transcriptomics) studies and quantitative analyses of important genes (HPA (hypothalamic–pituitary–adrenal)-axis functional genes) were performed to reveal genetic and metabolic changes in the important tissues associated with the HPA axis (brain, heart, and adrenal gland). Finally, we found that the strong noise pollution can significantly interfere with the expression of HPA-axis functional genes (including corticotropin releasing hormone (CRH), corticotropin releasing hormone receptor 2 (CRHR2), and arginine vasotocin (AVT)), and long-term stimulation can further induce metabolic disorders of the functional tissues (brain, heart, and adrenal gland), posing a lethal threat. Meanwhile, we also found that there were two kinds of death processes, direct death and chronic death, and both were closely related to the duration of stimulation and the regulation of the HPA axis.

Underwater noise pollution has become a potential threat to aquatic animals in the natural environment. The main causes of such pollution are frequent human activities creating underwater environmental noise, including commercial shipping, offshore energy platforms, scientific exploration activities, etc. However, in aquaculture environments, underwater noise pollution has also become an unavoidable problem due to background noise created by aquaculture equipment. Some research has shown that certain fish show adaptability to noise over a period of time. This could be due to fish’s special auditory organ, i.e., their “inner ear”; meanwhile, otoliths and sensory hair cells are the important components of the inner ear and are also essential for the function of the auditory system. Recently, research in respect of underwater noise pollution has mainly focused on adult fish, and there is a lack of the research on the effects of underwater noise pollution on the development process of the auditory system in the embryonic development period. Thus, in this study, we collected embryo–larval samples of the small yellow croaker (Larimichthys polyactis) in four important stages of otic vesicle development through artificial breeding. Then, we used metabonomics and transcriptomics analyses to reveal the development process of the auditory system in the embryonic development period under background noise (indoor and underwater environment sound). Finally, we identified 4026 differentially expressed genes (DEGs) and 672 differential metabolites (DMs), including 37 DEGs associated with the auditory system, and many differences mainly existed in the neurula stage (20 h of post-fertilization/20 HPF). We also inferred the regulatory mode and process of some important DEGs (Dnmt1, CPS1, and endothelin-1) in the early development of the auditory system. In conclusion, we suggest that the auditory system development of L. polyactis begins at least in the neurula stage or earlier; the other three stages (tail bud stage, caudal fin fold stage, and heart pulsation stage, 28–35 HPF) mark the rapid development period. We speculate that the effect of underwater noise pollution on the embryo–larval stage probably begins even earlier.

In this study, a panel of 14 microsatellite markers was screened to determine the parentage of 144 progenies in 12 Chinese hooksnout carp (Opsariichthys bidens) full-sib families. The combined exclusion probabilities for 14 loci were 97.6% and 99.9%, respectively, when there was no available parent information or only one parent information was provided. Simulation analysis demonstrated that the power of five loci to exclude false parents exceeded 99.0%, while that of eight loci reached 99.9% based on allele frequency data obtained from full-sib families (168 individuals). Moreover, the cumulative assignment success rate reached 100% with known parental and filial information when utilizing 13 or more loci, even in cases where no parent information was available. The results showed that this set of microsatellite markers proved to be a reliable and efficient tool for parentage determination of O. bidens.

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.

Larimichthys polyactis is a commercially important marine fish species in Eastern Asia, yet very few genetic resources exist. In particular, genetic linkage maps are critical tools for genetic breeding. In this study, we generated a high resolution linkage map from a family of 110 individuals and their parents by resequencing the individuals. 3,802 effective SNPs were mapped to 24 linkage groups (LGs). The map spanned 2,567.39 cm, with an average marker interval of 0.66 cm. We used the map to conduct QTL analysis for growth traits, and found 31 markers were significantly associated with growth-related traits. Specifically, three SNPs were identified for total length, nineteen SNPs for body length, and nine SNPs for body weight. The identified SNPs could explain 15.2–22.6% of the phenotypic variation. SNPs associated with growth traits were distributed on LG6 and LG11, and candidate genes included, kif26b , bat1 , gna1 , gbgt1 , and amfr , which may regulate growth. The linkage map and mapped QTLs would be useful for improving the quality of L. polyactis via marker-assisted selection.

Disease outbreaks in aquaculture have recently intensified. In particular, visceral white-nodules disease, caused by Pseudomonas plecoglossicida, has severely hindered the small yellow croaker (Larimichthys polyactis) aquaculture industry. However, research on this disease is limited. To address this gap, the present study employed a 100K SNP chip to genotype individuals from an F1 full-sib family, identify single nucleotide polymorphisms (SNPs), and construct a genetic linkage map for this species. A high-density genetic linkage map spanning a total length of 1395.72 cM with an average interval of 0.08 cM distributed across 24 linkage groups was obtained. Employing post-infection survival time as an indicator of disease resistance, 13 disease resistance-related quantitative trait loci (QTLs) were detected, and these regions included 169 genes. Functional enrichment analyses pinpointed 11 candidate disease resistance-related genes. RT-qPCR analysis revealed that the genes of chmp1a and arg1 are significantly differentially expressed in response to P. plecoglossicida infection in spleen and liver tissues, indicating their pivotal functions in disease resistance. In summary, in addition to successfully constructing a high-density genetic linkage map, this study reports the first QTL mapping for visceral white-nodules disease resistance. These results provide insight into the intricate molecular mechanisms underlying disease resistance in the small yellow croaker.

Background 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. Results 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% and concordance rate of 98.49%. A total of 946 individuals were genotyped for body weight, body length, and disease resistance (quantified by the survival time of fish injected with pathogen Pseudomonas plecoglossicida ) using the SNP array. Genomic selection (GS) was conducted using the restricted maximum likelihood (REML) and genomic best linear unbiased prediction (GBLUP) methods. The heritability estimates for body weight, body length, and survival time were 0.47 ± 0.05, 0.43 ± 0.05, and 0.33 ± 0.05, respectively. Notably, Ten-fold cross-validation using genomic BLUP gave a genomic prediction accuracy of 0.70 ± 0.04 for body length, and 0.43 ± 0.09 for body weight, exceeding that for disease resistance trait (0.40 ± 0.13). Evaluation results further indicated that implementing a 30% selection ratio translated into a relative genetic gain (ΔG′) of 17.62% for body weight and 4.28% for disease resistance per generation. Conclusions This study demonstrates the effectiveness and efficiency of the SNP arrays for applications in GS and breeding. The array and accompanying GS pipeline provide a practical for accelerating genetic improvement in small yellow croaker and can serve as a template for other aquaculture species.

Background The red claw crayfish ( Cherax quadricarinatus ) is a commercially and ecologically significant species that displays a unique intersex model with an ovotestis gonad and was identified to have functional testes and a vestigial ovary, which was inhibited by insulin-like androgenic gland hormone ( IAG ), but the underlying molecular mechanisms are still unclear. Results In this study, the structure and transcriptomic profiles of ovotestis and female and male gonad was analysis and compared, 406 differentially expressed genes were identified, among which membrane-anchored AG-specific factor ( MAG ) exhibited significantly greater expression in ovotestis gonads than in male or female gonads. The localization of MAG in type I or II cells of androgenic gland revealed its potential function of IAG hormone synthesis. Furthermore, the analyses of gene regulation relationship revealed that IAG positively regulates MAG expression, while MAG negatively regulates vitellogenin gene ( VTG ) expression. Conclusions Our research suggesting MAG participates in the IAG regulated ovarian suppression in the intersex red claw crayfish, which provides important information on the regulatory mechanism of the ovarian dysplasia in the ovotestis of intersex red claw crayfish. These results will enhance the knowledge of IAG -related pathways in the female reproductive axis, as well as the mechanisms of sexual differentiation in crustaceans.

Background 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. Results 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%) of these DMRs were observed within the CG context. Moreover, we found that most DMRs were located within promoter regions as well as exons and introns. A total of 1288 DMEGs were identified through correlation analysis between DNA methylation and transcriptional activity. Functional enrichment analysis revealed that most of the DMEGs were significantly enriched in pathways related to the protein export pathway, proteasome, terpenoid backbone biosynthesis, ubiquitin-mediated proteolysis, autophagy-other pathway. Furthermore, we screened candidate growth-related genes, such as stat2 , capn2 , akt1 , mTOR , and mef2aa . Among these, the expression levels of capn2 , mTOR , and akt1 exhibited a positive correlation with DNA methylation levels, whereas the expression levels of stat2 and mef2aa showed a negative correlation. These findings suggest that alterations in DNA methylation patterns may promote growth advantages in hybrid yellow croaker by modulating the expression of these genes. Conclusions Epigenetic changes exert distinct influences on genes related to growth heterosis. The presented data establish a foundation for comprehending the epigenetic and transcriptomic alterations underlying the growth of hybrid yellow croaker, thereby providing preliminary insights into the molecular mechanisms of growth heterosis. These findings have significant implications for breeding programs aimed at enhancing yellow croaker production.