Background: Edwardsiella tarda causes acute symptoms with ascites in Japanese flounder ( Paralichthys olivaceus ) and is a major problem for China’s aquaculture sector. Genomic selection (GS) has been widely adopted in breeding industries because it shortens generation intervals and results in the selection of individuals that have great breeding potential with high accuracy. Based on an artificial challenge test and re-sequenced data of 1099 flounders, the aims of this study were to estimate the genetic parameters of resistance to E. tarda in Japanese flounder and to evaluate the accuracy of single-step GBLUP (ssGBLUP), weighted ssGBLUP (WssGBLUP), and BayesB for improving resistance to E. tarda by using three subsets of pre-selected single nucleotide polymorphisms (SNPs). In addition, SNPs that are associated with this trait were identified using a single-SNP genome-wide association study (GWAS) and WssGBLUP. Results: We estimated a heritability of 0.13 ± 0.02 for resistance to E. tarda in Japanese flounder. One million SNPs at fixed intervals were selected from 4,978,724 SNPs that passed quality controls. GWAS identified significant SNPs on chromosomes 14 and 24. WssGBLUP revealed that the putative quantitative trait loci on chromosomes 1 and 14 contained SNPs that explained more than 1% of the genetic variance. Three 50 k-SNP subsets were pre-selected based on different criteria. Compared with pedigree-based prediction (ABLUP), the three genomic methods evaluated resulted in at least 7.7% greater accuracy of predictions. The accuracy of these genomic prediction methods was almost unchanged when pre-selected trait-related SNPs were used for prediction. Conclusions: Resistance to E. tarda in Japanese flounder has a low heritability. GWAS and WssGBLUP revealed that the genetic architecture of this trait is polygenic. Genomic prediction of breeding values performed better than ABLUP. It is feasible to implement genomic selection to increase resistance to E. tarda in Japanese flounder with 50 k SNPs. Based on the criteria used here, pre-selection of SNPs was not beneficial and other criteria for pre-selection should be considered.

The high proportion of males in C. semilaevis hinders their industrial development. The genetic ZW individual can become a pseudomale by sex reversal. And the pseudomale can produce Z-sperm (with epigenetic information to cause sex reversal) while W-sperm is absent, which leads to an even higher male proportion in offspring. Recently, with the development of transcriptomic technologies, research on spermatogenesis in C. semilaevis has been focused on the ubiquitination pathway. In this study, we analyzed the function of the ubiquitin ligase rnf34 gene on the Z chromosome. A qPCR experiment showed that its expression level in the gonad was the highest among different tissues. In the ovary, the expression gradually increased with development from 40 days post-hatching (dph) to 1.5 years post-hatching (yph). In the testis, rnf34 showed increased expression from 40 dph to 6 months post-hatching (mpf) and stabilized up until 1.5 ypf. In situ hybridization showed that the mRNA of rnf34 was mainly distributed in the germ cells of the testis and the ovary. In vivo siRNA-mediated knockdown of the rnf34 gene in male fish affected the expression of a series of genes related to sex differentiation and spermatogenesis. These results provide genetic data on the molecular mechanisms of gonadal development and spermatogenesis in C. semilaevis.

As an RA-metabolizing enzyme, cyp26b1 has a substantial impact on RA-signaling pathways. The cyp26b1 gene from the Chinese tongue sole was cloned and identified in this investigation. The cyp26b1 ORF was 1536 bp in length and encoded a 512 amino acid protein. A quantitative real-time PCR (qPCR) indicated that the cyp26b1 expression is no significant sexual dimorphism in the gonads at the 80 days post-hatching (dph) stages. After 4 months post-hatching (mph), the expression of cyp26b1 showed sexual dimorphism and lower level of expression in the ovaries than in the testes. An in situ hybridization demonstrated that cyp26b1 mRNA was primarily located in the testis. Interestingly, the cyp26b1 mRNA probe was also detected in the ovaries. These results suggested that cyp26b1 participates in the sex-differentiation and gonadal development of the Chinese tongue sole.

As the largest green macroalgal bloom in the Yellow Sea of China, the overgrowth and degradation of Ulva prolifera (U. prolifera) have a harmful effect on marine organisms and the aquaculture industry. However, the regulation mechanism of U. prolifera stress on the antioxidant capacity and inflammatory response of marine fish is still not completely understood. A 15-day exposure experiment was conducted to evaluate the effects of U. prolifera stress on the antioxidant capacity and inflammatory response of the Japanese flounder (Paralichthys olivaceus) (283.11 ± 6.45 g). The results showed that U. prolifera stress significantly decreased their survival rate. Serum total antioxidant capacity (T-AOC) and non-specific immune-related enzyme activities were significantly impacted under U. prolifera conditions. Moreover, U. prolifera stress significantly decreased T-AOC, superoxide dismutase (SOD) activity, and catalase (CAT) activities in the liver, while malondialdehyde (MDA) contents were significantly increased. Similarly, antioxidant-related gene (cat, nrf2, and keap1) expressions were synchronously downregulated in the liver under U. prolifera stress. Furthermore, U. prolifera stress significantly upregulated pro-inflammatory gene (tnf-α, il-1β, ifn-γ, and p65) expressions and the phosphorylation levels of the p38 and JNK MAPK pathways in the head kidney. In addition, endoplasmic reticulum (ER) stress-related gene and protein expressions were also upregulated in the head kidney. Overall, these results revealed that U. prolifera stress suppressed the antioxidant capacity and induced an inflammatory response in the Japanese flounder. This study could advance the understanding of the adverse effects of U. prolifera stress on marine benthic fish and promote the sustainable development of aquaculture.

Massive macroalgae blooms, primarily caused by the overgrowth of Ulva prolifera (U. prolifera) in the Yellow Sea of China, pose a severe risk to both marine organisms and the aquaculture industry. This study’s aim was to evaluate the impact of U. prolifera degradation on the growth performance and antioxidant capacity of Japanese flounder (Paralichthys olivaceus) and select some potential Japanese flounder families (labeled 2101–2108, established by crossbreeding) tolerating U. prolifera degradation conditions. Thus, a 60-day U. prolifera exposure experiment was conducted. The results showed that the contents of Na, K, Mg, and Fe elements in the U. prolifera degradation water were significantly increased. The specific growth rate and survival rate of flounder were significantly decreased under the U. prolifera degradation condition, while the 2101 and 2103 flounder families showed a better growth performance compared with the positive control (PC) group. Moreover, the results showed that activities of total antioxidant capacity (T-AOC), transaminases, and alkaline phosphatase (AKP) in serum were significantly decreased, while the 2103 flounder family showed higher activities. Furthermore, U. prolifera degradation significantly increased superoxide dismutase (SOD) activity and glutathione (GSH) content while decreasing catalase (CAT) activity and malondialdehyde (MDA) content in the liver. Specifically, SOD and CAT activities of the 2103 flounder family were higher than the 2101 flounder family and PC group. In addition, the gill SOD and CAT activities of the 2103 flounder family were significantly higher than the PC group. Similarly, the antioxidant-related gene (sod and cat) expressions were synchronously upregulated or downregulated in the liver and gills in response to U. prolifera degradation. These results revealed that U. prolifera degradation decreased the growth performance and influenced the antioxidant capacity of Japanese flounder, while the 2103 flounder family had better advantages in the U. prolifera degradation condition. Therefore, the 2103 flounder family could be regarded as the potential flounder family tolerating U. prolifera degradation. The increased Fe content in the U. prolifera degradation water may be one of the main causes of the physiological alterations observed in Japanese flounder.

Ras-related associated with diabetes (RRAD) is a member of the Ras GTPase superfamily that plays a role in several cellular functions, such as cell proliferation and differentiation. In particular, the superfamily acts as an NF-κB signaling pathway inhibitor and calcium regulator to participate in the immune response pathway. A recent transcriptome study revealed that rrad was expressed in the spleen of disease-resistant Japanese flounder (Paralichthys olivaceus) individuals compared with disease-susceptible individuals, and the results were also verified by qPCR. Thus, the present study aimed to explore how rrad regulates antimicrobial immunity via the NF-κB pathway. First, the coding sequence of P. olivaceus rrad was identified. The sequence was 1092 bp in length, encoding 364 amino acids. Based on phylogenetic and structural relationship analyses, P. olivaceus rrad appeared to be more closely related to teleosts. Next, rrad expression differences between disease-resistant and disease-susceptible individuals in immune-related tissues were evaluated, and the results revealed that rrad was expressed preferentially in the spleen of disease-resistant individuals. In response to Edwardsiella piscicida infection, rrad expression in the spleen changed. In vitro, co-culture was carried out to assess the hypo-methylated levels of the rrad promoter in the disease-resistant spleen, which was consistent with the high mRNA expression. The siRNA-mediated knockdown of rrad performed with the gill cell line of P. olivaceus affected many rrad-network-related genes, i.e., dcp1b, amagt, rus1, rapgef1, ralbp1, plce1, rasal1, nckipsd, prkab2, cytbc-1, sh3, and others, as well as some inflammation-related genes, such as bal2 and Il-1β. In addition, flow cytometry analysis showed that rrad overexpression was more likely to induce cell apoptosis, with establishing a link between rrad‘s function and its potential roles in regulating the NF-κB pathway. Thus,. the current study provided some clarity in terms of understanding the immune response about rrad gene differences between disease-resistant and disease-susceptible P. olivaceus individuals. This study provides a molecular basis for fish rrad gene functional analysis and may serve as a reference for in-depth of bacterial disease resistance of teleost.