Hyperspectral imaging (HSI) has been applied to assess the texture profile analysis (TPA) of processed meat. However, whether the texture profiles of live fish muscle could be assessed using HSI has not been determined. In this study, we evaluated the texture profile of four muscle regions of live common carp by scanning the corresponding skin regions using HSI. We collected skin hyperspectral information from four regions of 387 scaled and live common carp. Eight texture indicators of the muscle corresponding to each skin region were measured. With the skin HSI of live common carp, six machine learning (ML) models were used to predict the muscle texture indicators. Backpropagation artificial neural network (BP-ANN), partial least-square regression (PLSR), and least-square support vector machine (LS-SVM) were identified as the optimal models for predicting the texture parameters of the dorsal (coefficients of determination for prediction (r_p) ranged from 0.9191 to 0.9847, and the root-mean-square error for prediction ranged from 0.1070 to 0.3165), pectoral (r_p ranged from 0.9033 to 0.9574, and RMSEP ranged from 0.2285 to 0.3930), abdominal (r_p ranged from 0.9070 to 0.9776, and RMSEP ranged from 0.1649 to 0.3601), and gluteal (r_p ranged from 0.8726 to 0.9768, and RMSEP ranged from 0.1804 to 0.3938) regions. The optimal ML models and skin HSI data were employed to generate visual prediction maps of TPA values in common carp muscles. These results demonstrated that skin HSI and the optimal models can be used to rapidly and accurately determine the texture qualities of different muscle regions in common carp.

Female common carp grow faster than male individuals, implying that rearing females could be more profitable in aquaculture. Non-coding RNAs (ncRNAs) serve as versatile regulators with multiple functions in diverse biological processes. However, the roles of ncRNAs in the sex differentiation of common carp are less studied. In this study, we investigated the expression profiles of ncRNAs, including miRNAs, lncRNAs, and circRNAs, in the gonads to comprehend the roles of ncRNAs in sex differentiation in common carp. A substantial number of differentially expressed (DE) ncRNAs in ovaries and testes were identified. Some miRNAs, notably miR-205, miR-214, and miR-460-5p, might modulate hormone synthesis and thus maintain sex. A novel miRNA, novel_158, was predicted to suppress the expression of foxl3. DE lncRNAs were associated with oocyte meiosis, GnRH signaling pathways, and steroid biosynthesis, while DE circRNA target genes were enriched in the WNT signaling pathway and MAPK signaling pathway. We also analyzed ncRNA-mRNA interactions to shed light on the crosstalk between competing endogenous RNAs (ceRNAs), which is the critical mechanism by which lncRNAs and circRNAs function. Some lncRNAs and circRNAs may be able to competitively bind novel_313, a new miRNA, and thus regulate hsd17β3. Our research will provide a valuable resource for understanding the genetic basis of gonadal differentiation and development in common carp.

The polyunsaturated fatty acids (PUFAs), particularly eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are critical determinants of the nutritional quality of fish. To rapidly and non-destructively determine the muscular PUFAs in living fish, an accuracy technique is urgently needed. In this study, we combined skin hyperspectral imaging (HSI) and machine learning (ML) methods to assess the muscular PUFAs contents of common carp. Hyperspectral images of the live fish skin were acquired in the 400–1000 nm spectral range. The spectral data were preprocessed using Savitzky–Golay (SG), multivariate scattering correction (MSC), and standard normal variable (SNV) methods, respectively. The competitive adaptive reweighted sampling (CARS) method was applied to extract the optimal wavelengths. With the skin spectra of fish, five ML methods, including the extreme learning machine (ELM), random forest (RF), radial basis function (RBF), back propagation (BP), and least squares support vector machine (LS-SVM) methods, were used to predict the PUFAs and EPA + DHA contents. With the spectral data processed with the SG, the RBF model achieved outstanding performance in predicting the EPA + DHA and PUFAs contents, yielding coefficients of determination (R²_P) of 0.9914 and 0.9914, root mean square error (RMSE) of 0.3352 and 0.3346, and mean absolute error (MAE) of 0.2659 and 0.2660, respectively. Finally, the visualization distribution maps under the optimal model would facilitate the direct determination of the fillet PUFAs and EPA + DHA contents. The combination of skin HSI and the optimal ML method would be promising to rapidly select living fish having high muscular PUFAs contents.

Epigenetic modifications are critical in precisely regulating gene expression. The common carp (Cyprinus carpio) is an economically important fish species, and females exhibit faster growth rates than males. However, the studies related to epigenetic modifications in the common carp gonads are limited. In this study, we conducted the Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) and Bisulfite sequencing (BS-seq) to explore the roles of epigenetic modifications in the common carp gonads. We identified 84,207 more accessible regions and 77,922 less accessible regions in ovaries compared to testes, and some sex-biased genes showed differential chromatin accessibility in their promoter regions, such as sox9a and zp3. Motif enrichment analysis showed that transcription factors (TFs) associated with embryonic development and cell proliferation were heavily enriched in ovaries, and the TFs Foxl2 and SF1 were only identified in ovaries. We also analyzed the possible regulations between chromatin accessibility and gene expression. By BS-seq, we identified 2087 promoter differentially methylated genes (promoter-DMGs) and 5264 gene body differentially methylated genes (genebody-DMGs) in CG contexts. These genebody-DMGs were significantly enriched in the Wnt signaling pathway, TGF-beta signaling pathway, and GnRH signaling pathway, indicating that methylation in gene body regions could play an essential role in sex maintenance, just like methylation in promoter regions. Combined with transcriptomes, we revealed that the expression of dmrtb1-like, spag6, and fels was negatively correlated with their methylation levels in promoter regions. Our study on the epigenetic modifications of gonads contributes to elucidating the molecular mechanism of sex differentiation and sex maintenance in the common carp.

The common carp (Cyprinus carpio) is a crucial freshwater species cultivated worldwide for food consumption. Female carp have better growth performance than males, which fascinates scholars to uncover the mechanism of gonadal differentiation and produce mono-sex populations. However, the mechanism of ovarian development at single-cell resolution is limited. Here, we conducted single-nucleus RNA sequencing in adolescent common carp ovaries. Our study obtained transcriptional profiles of 13,155 nuclei and revealed 13 distinct cell clusters in the ovaries, including three subtypes of germ cells and four subtypes of granulosa cells. We subsequently performed pseudotime trajectory analysis to delineate potential mechanisms underlying the development of germ cells and granulosa cells. We identified 1250 dynamic expression genes in germ cells and 1815 in granulosa cells (q-value < 0.01), including zp3, eif4a2 and aspm in germ cells and fshr and esr1 in granulosa cells. The functional annotation showed that dynamic expression genes in germ cells were involved in sperm–egg recognition and some terms related to meiosis, such as sister chromatid segregation and homologous recombination. Genes expressed dynamically in granulosa cells were related to the TGF-β signaling pathway, response to gonadotropin, and development of primary female sexual characteristics. In addition, the dynamic genes expressed in granulosa cells might relate to the complex communication between different cell types. In summary, our study provided a transcriptome profile of common carp ovaries at single-nucleus resolution, and we further revealed the potential cell type-specific mechanisms underlying oogenesis and the differentiation of granulosa cells, which will facilitate breeding all-female common carp populations.

Fatty acids (FAs), especially the polyunsaturated fatty acids (PUFAs), play pivotal roles in growth and development. Fish possess a remarkable ability to synthesize PUFAs, rendering them a crucial and significant source of these essential FAs for human consumption. Despite extensive research on the metabolic processes of FAs, the primary processes underlying FA content variation and corresponding regulatory mechanisms remain largely unexplored. We quantified the muscular FA profiles of 304 common carp samples. High variation in muscle FA content among samples was observed, with the coefficients of variation ranging from 0.36 to 0.92. With genome-wide association studies (GWAS), we identified 1410 SNPs significantly associated with the FA content. The genetic variation at genes participating in oxidation, ubiquitination, and transcriptional factors was associated with the content of multiple FAs, while few variants were observed in the FA-synthesis genes. For the total PUFA (TPUFA) content, transcriptome analysis of groups with the highest and lowest TPUFA content identified 715 differentially expressed genes (DEGs), including genes involved in oxidation and ubiquitination. Using multiple genomic selection programs with the associated SNPs for FA content, we obtained high and positive correlations ranging from 0.65 to 0.92 between the real FA contents and estimated breeding values. These findings manifested the major-effect processes governing the differences in muscular FA content and their regulatory mechanisms. The optimal genomic selection programs provide novel and feasible perspectives to enhance FA content in common carp.