Marine Biotechnology最新文献

Reproductive traits are of paramount importance as economic traits in shrimps, playing a vital role in enhancing commercial larval production within the aquaculture industry. Identifying genetic markers associated with reproductive traits is essential for implementing genomic and marker-assisted selection strategies to enhance reproductive performance. However, the existing knowledge of such genetic markers in Exopalaemon carinicauda remains relatively limited. In this study, we utilized next-generation sequencing coupled with bulked segregant analysis to identify molecular markers and candidate genes associated with reproductive traits in E. carinicauda using a F₂ population. A total of 31,048,793 SNPs and 3193 indels were identified between the two pools. Six candidate regions, spanning 72.24 Mb on chromosomes 6, 14, 15, 21, 23, and 35, were consistently identified through Euclidean distance and ΔSNP-index analyses, encompassing 609 genes. Kyoto Encyclopedia of Genes and Genomes analysis revealed significant associations with pathways such as ovarian steroidogenesis, oocyte meiosis, insulin signaling, GnRH signaling, and estrogen signaling. Among these, 22 genes showed strong links to ovarian development based on comparative transcriptomic analysis across 4 ovarian development stages. The integrated analysis of whole genome and transcriptome data showed that four genes (juvenile hormone esterase carboxylesterase, aurora kinase A, insulin-like peptide receptor, and Argonaute 3) might play important roles in regulating reproductive traits of E. carinicauda. Five SNP loci were validated employing a general linear model that are significantly associated with fecundity traits in the F₂ population. These findings not only offer valuable insights into the genetic underpinnings of reproductive traits but also provide a strong foundation for the development of genomic and marker-assisted selection strategies aimed at enhancing fecundity traits in E. carinicauda.

The aims of this study were to investigate marker-growth trait associations and construct a SNP-based linkage map for an Asian seabass (KU) population from Thailand. First, we performed GWAS using phenotypes (weight and length) and genotypes (25,647 SNPs) for 1100 390-day-old fish. We selected the top 70 SNPs with allele substitution effects, ranging from 6.84 to 81.91 g for weight and from 0.12 to 1.8 cm for length for further analyses. Cross-validation of 70 SNPs using GBLUP yielded breeding value prediction accuracies 0.65 to 0.70. Second, we utilized previously published genome-wide SNPs and mapping data from multiple populations and the KU data to predict the genetic linkage map for the KU population using the Marey map approach. The KU linkage map consisted of 24 chromosomes spanning 567 Mb, with average marker spacing of 0.07 cM. The number of markers ranged from 598 to 1334, with an average of 1099 markers per chromosome. The predicted local recombination rates varied from 4.76 to 43.40 cM/Mb with an average of 2.35 cM/Mb. Lastly, Kompetitive allele-specific PCR (KASP) markers were developed from 70 SNPs and validated in 200 fish. The KASP assays were successful for all 70 SNPs in 196 fish with SNP call rates of 98.2 to 100%. Fifty-eight SNPs were found to have segregated across the genome, except for chromosomes 23 and 24. The linkage map obtained in this study provides a framework for future QTL mapping of growth-related traits in the KU population.

The crustacean hyperglycemic hormone (CHH) family is a group of key neuroendocrine regulators of molting, metabolism, and reproduction in crustaceans. Litopenaeus vannamei, the most widely farmed shrimp, exhibits pronounced sexual growth dimorphism, yet the role of CHH family genes in this process remains poorly understood. Here, we identified an ion transport peptide-like (ITP-like) gene in L. vannamei, and demonstrated its male-biased expression and sexually dimorphic functions. The ITP-like gene was predominantly expressed in eyestalks, with significantly higher levels in males than females, suggesting its role in sex-specific physiological regulation. Functional experiments using RNA interference (RNAi) and recombinant protein injection revealed its divergent and sex-dependent roles: ITP-like knockdown enhanced male growth but reduced female growth, while recombinant ITP-like protein showed opposing effects. Transcriptomic analysis of eyestalks identified differentially expressed genes linked to digestive enzymes, cuticle formation, lipid metabolism, and phototransduction, revealing a complex regulatory network underpinning the sexually dimorphic effects of ITP-like. Our findings demonstrate that ITP-like influences shrimp growth by modulating metabolic pathways, molting processes and photoreceptive responses, providing new insights into crustacean endocrine regulation. This study advances understanding of the mechanisms underlying sex-biased growth in L. vannamei and highlights potential targets for aquaculture improvement.

Host defense peptides (HDPs) are vital to immunity due to their antimicrobial and immunomodulatory properties. While extensively studied in mammals, their immunomodulatory roles remain complex, and research on HDPs in fish is limited. This study aimed to predict physicochemical properties and mechanisms of action of seven HDPs in gilthead seabream (Sparus aurata): two piscidins (piscidin 1, piscidin 2) and five hepcidins (hepcidin H1, H2C, H2E, H2H, H2I). Predictions indicated heterogeneity among HDPs, all exhibiting antioxidant capacity and bioactive potential. In vitro analyses of these synthetic HDPs on head kidney leucocytes of gilthead seabream revealed minimal direct effects on leucocyte activities. RT-PCR gene expression analysis in leukocytes after 2 h of HDP incubation showed significant upregulation of bax-1 (hepcidin H2I), il-6 (piscidin 2), tnf-α (piscidin 1), tlr-7 (piscidin 1), and tlr-8 (piscidin 1), and downregulation of casp-3 (hepcidin H1), bcl-2 (hepcidin H2C), il-1β (hepcidin H1, H2C, H2E, H2H, H2I), tnf-α (piscidin 2, hepcidin H1, H2E, H2I), tlr-7 (piscidin 2, hepcidin H2E), and tlr-8 (piscidin 2, hepcidin H2H). The results indicate that HDPs demonstrate diverse immunomodulatory impacts on seabream white blood cells, playing a crucial role in regulating genes associated with programmed cell death, inflammatory responses, and Toll-like receptors. This complex function highlights the adaptability and significance of the studied HDPs in the immune system of gilthead seabream.

Microalgae are gaining attention as promising candidates for CO₂ fixation and biomaterial production due to their non-competition with food and feed resources, as well as their high growth rates and photosynthetic efficiency. To expand their application as hosts for biomaterial production, it is essential to develop efficient and versatile gene modification technologies for microalgal metabolic engineering. Achieving this requires the establishment of an effective and broadly applicable material delivery method across diverse microalgal species. In this study, we developed a novel nanoinjection technique for single microalgal cells, utilizing electroosmotic flow through a nano-sized pipette (nanopipette). This nanopipette enables precise, automated delivery of solutions into cells at the femtoliter scale. Optimum injection conditions, including cell morphology, injection voltage, and injection time, were identified using fluorescein isothiocyanate (FITC)-labeled dextran in two green microalgae species, Haematococcus sp. and Tetraselmis sp. The method achieved injection efficiencies of 44% for Haematococcus sp. and 45% for Tetraselmis sp. This technique demonstrates substantial potential for efficient genome editing and subsequent metabolic engineering in a wide range of microalgae species.

Microplastics (MPs; less than 5 mm in size) are becoming increasingly prevalent in both terrestrial and aquatic ecosystems. As these particles enter the food chain, they have the potential to pose significant risks to human health. However, their effects on vital fish tissues, such as skeletal muscle, are not yet fully understood. In this study, we examined Nile tilapia (Oreochromis niloticus) from two distinct sites on the Nile River in Egypt: the Nile branch (Damietta branch) and Riah El-Towfiqi. Using Fourier Transform Infrared Spectroscopy (FTIR) and histological study, we confirmed the presence of MPs in both gastrointestinal and muscle tissues. We focused on understanding how MPs might affect fish muscle by investigating the expression of genes involved in muscle atrophy and hypertrophy using Real Time-PCR and histological alterations in muscle tissues of tilapia collected from the two studied sites in the four seasons. Our results revealed histological alterations in muscle tissues collected from the two sites studied in the four seasons. The expression levels of atrophy-related genes, Atrogin-1 (Fbxo32), Capn-1, and the apoptosis marker Caspase3a (Casp3a), showed increased expression, especially during the summer at both sites. On the other hand, the hypertrophy-related gene Igf-1 exhibited a significant decrease while, muscle stem cell genes (Pax3, Pax7) and muscle differentiation gene markers (Myf5, Mrf6) displayed seasonal upregulation, with heightened activity during winter and summer, depending on the location. Additionally, immune-related genes (Ccr9, Irak4, Igl-1, Tlr1) demonstrated notable seasonal changes, with a peak during summer at the Nile branch. These findings demonstrate that MPs can disrupt muscle integrity and immune function in fish, with implications for ecosystem health and potential risks to human food security.

Heterosis refers to the phenomenon in which the progeny resulting from the cross of two parents with different genetic backgrounds exhibit superior traits compared to their parents, such as faster growth rate, higher yield, stronger stress resistance, and better adaptability. In this study, we used the hybrid progeny (150 days of age) of two wild populations of R. philippinarum in northern China (Dalian and Weihai) as samples to preliminarily explore the growth heterosis. In addition, transcriptome sequencing was performed on the hybrid group and the inbred group, showing that there were 2510 DEGs in the DW vs DD groups, 1755 DEGs in the WD vs DD groups, 781 DEGs in the DW vs WW groups, 115 DEGs in the WD vs WW groups, and 582 DEGs in the WD vs DW groups. The MEGF, BMP10, and NOTCH genes play an important role in early development after hybridization. In addition, qPCR results were consistent with RNA-seq data, indicating the reliability of RNA-seq data. Our results provide molecular insights into heterosis.

Single-cycle viruses generated by the deletion of gene(s) essential for viral replication in the genome can be a way to enhance the safety of attenuated virus-based vaccines because single-cycle viruses can infect cells only once and cannot produce infective viral particles. In the present study, not only to guarantee safety as a prophylactic vaccine but also to enhance the protective efficacy, a single-cycle viral hemorrhagic septicemia virus (VHSV) lacking the G gene and containing olive flounder (Paralichthys olivaceus) interferon-γ (IFNγ) ORF between N and P genes of the viral genome (rVHSV-A-IFNγ-ΔG) was rescued using reverse genetic technology, and its protective potential was evaluated through the immunization of olive flounder. In the challenge experiment, the cumulative mortality in the control group reached 80%, while groups of fish immunized with various doses of rVHSV-A-IFNγ-ΔG (ranging from 1 × 10³ to 1 × 10⁵ pfu/fish) showed no mortalities. In contrast, fish immunized with various doses of rVHSV-ΔG exhibited 0–20% mortality in a dose-dependent manner. Serum ELISA analysis revealed that groups receiving the highest doses of rVHSV-ΔG and rVHSV-A-IFNγ-ΔG showed significantly elevated titers compared to the control group. Although no statistically significant differences in ELISA titers were observed among groups immunized with lower doses of recombinant VHSVs, particularly at 1 × 10³ pfu/fish, and the control group, the markedly higher protection compared to the control group suggests that these single-cycle viruses possess a limited capacity to induce antibody responses, yet are capable of conferring protective immunity against VHSV independently of humoral mechanisms. Moreover, the complete protection achieved with low-dose immunization of rVHSV-A-IFNγ-ΔG indicates its strong potential as a highly effective prophylactic vaccine candidate.

In diploid organisms, deleterious recessive alleles represent a significant component of genetic mutations and often result in lethal effects when in a homozygous state. Large yellow croaker (Larimichthys crocea), a critical marine aquaculture species in China, has shown signs of inbreeding depression due to its limited natural distribution along the coasts of Fujian, Guangdong, and Zhejiang provinces, combined with intensive artificial propagation practices. Identifying loci with deleterious recessive homozygous genotypes is therefore crucial for sustainable industry development. In this study, 1844 large yellow croaker across three consecutive generations were analyzed, resulting in the preliminary identification of 131 loci with missing recessive homozygous genotypes. After excluding false positives through parentage analysis, large-scale validation was conducted using genotype data from 4663 individuals from the MinDong population and 830 individuals from the Daqu population. Ultimately, 22 loci with complete absence of homozygous recessive genotypes were identified across 7337 individuals. The average minor allele frequency (MAF) of these loci was 0.16. Except for LG17_2296176 and LG17_4414232, which exhibited moderate linkage disequilibrium, the remaining 20 loci were largely independent with no observed linkage disequilibrium. Annotation of the 22 loci identified 12 associated genes, including vegfa, sntg2, tcf7, kif2a, lage3, ano10, mpdu1, and others. These genes are involved in key biological processes such as signal transduction regulation, cytoskeletal organization, neural function, and glycan synthesis. To further verify the reliability of the loci with missing recessive homozygous genotypes, heterozygous parental fish carrying 6 randomly selected loci were paired to establish independent families. None of the offspring exhibited recessive homozygous genotypes at these loci, supporting the accuracy of the prior identification. By analyzing genotype data from large yellow croaker populations, this study identifies key loci with missing recessive homozygous genotypes. These findings may offer guidance for selective breeding strategies aimed at minimizing lethal mutations, thereby enhancing population fitness and supporting the sustainable development of the aquaculture industry.

The fillet yield phenotype is a trait that can be improved in aquaculture species through conventional selective breeding. This approach was applied to rainbow trout for three consecutive generations of selection to produce a high-yield line (HY) that exhibits 2.5 percentage points higher fillet yield compared to a low-yield line (LY). To characterize the genetic and physiological mechanisms contributing to the HY phenotype, transcriptomic analysis of liver and skeletal muscle was performed at three stages of development, 2 g, 60 g, and 300 g, which corresponded to 35, 208, and 277 days post-hatch. Functional analysis of differentially expressed genes (DEG) suggests that increased muscle yield in the HY line is partially driven by greater hyperplasia at 60 g; although, higher rates of protein accretion, primarily attributed to lower rates of protein degradation, promote muscle cell hypertrophy during all stages of development. Additionally, DEGs support reductions in glycolysis in the HY muscle, with increased activity of the more efficient citric acid cycle and oxidative phosphorylation reactions for energy production compared to the LY line. In the liver, DEGs indicate unique nutrient utilization mechanisms in the HY line that support reduced visceral adiposity compared to the LY line. These findings provide insight into the physiology and metabolism driving the high fillet yield phenotype; this information is useful for the development of genomic markers to enhance breeding strategies toward the improvement of performance traits.