Search Results (19)

Temperature fluctuations caused by climate change and global warming pose a threat to fish. The burbot (lota lota) population is particularly sensitive to increased water temperature, but the systematic impacts of high-temperature exposure on their liver and intestinal health remain unclear. In January of 2025, we collected wild adult burbot individuals from the Ussuri River (water temperature: about 2 °C), China. The burbot were exposed to 2 °C, 7 °C, 12 °C, 17 °C, and 22 °C environments for 96 h; then, the liver and intestinal contents were subsequently collected for histopathology observation, immunohistochemistry, biochemical index assessment, and transcriptome/16S rDNA sequencing analysis. There was obvious liver damage including hepatocyte necrosis, fat vacuoles, and cellular peripheral nuclei. Superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px) activities were elevated and subsequently decreased. Additionally, the malondialdehyde (MDA) level significantly increased with increasing temperature. These results indicate that 7 °C (heat stress temperature), 12 °C (tipping point for normal physiological metabolism status), 17 °C (tipping point for individual deaths), and 22 °C (thermal limit) are critical temperatures in terms of the physiological response of burbot during their breeding period. In the hepatic transcriptome profiling, 6538 differentially expressed genes (DEGs) were identified, while KEGG enrichment analysis showed that high-temperature stress could affect normal liver function by regulating energy metabolism, immune, and apoptosis-related pathways. Microbiomics also revealed that acute heat stress could change the intestinal microbe community structure. Additionally, correlation analysis suggested potential regulatory relationships between intestinal microbe taxa and immune/apoptosis-related DEGs in the liver. This study revealed the potential impact of environmental water temperature changes in cold habitats in winter on the physiological adaptability of burbot during the breeding period and provides new insights for the ecological protection of burbot in the context of global climate change and habitat warming. Full article

Background/Objectives: The giant red shrimp, Aristaeomorpha foliacea, is a valuable marine fishing resource. The conservation of species, especially exploited ones, depends on a good knowledge of their biology, as well as the development of appropriate management plans based on the identification of genetically differentiated units or genetic stocks. Microsatellites are widely used molecular markers to detect genetic stocks in penaeoid shrimps and prawns. This study aimed to develop and characterize new microsatellites for A. foliacea. Methods: Next-generation sequencing based on 454 pyrosequencing revealed 58 candidate microsatellite loci for A. foliacea. These were tested on a panel of 8 individuals representative of its worldwide geographical distribution, and 19 polymorphic loci were identified and subsequently validated and characterized in 30 individuals from a single population in the Mediterranean Sea. Results: As a result, 10 polymorphic loci were identified, which did not present linkage disequilibrium and showed a range of alleles per locus and an observed and expected heterozygosity of 2–10, 0.0667–0.5567, and 0.0661–0.8511, respectively. Nine out of these loci were under Hardy–Weinberg equilibrium and showed a combined exclusion probability of 0.9202 and 0.9968 in parentage and identity analysis, respectively. Conclusions: This set of loci will provide a strong set of tools to (i) perform parentage studies and (ii) examine connectivity patterns (horizontal and vertical), including examining the population structure of this species at a variety of geographical scales and, particularly, between exploited populations in shallow waters and deeper unexploited populations. Full article

Genetic polymorphisms may influence mercury (Hg) toxicity. The aims of this study were to evaluate individual factors, such as the presence of the GSTP1 rs1695 polymorphism, associated with internal Hg dose and child neurodevelopment in indigenous people from the Brazilian Amazon chronically exposed to Hg. Eighty-two indigenous children were clinically evaluated, hair Hg was measured, and the GSTP1 rs1695 polymorphism was genotyped. The mean age was 4.8 years, the median Hg was 5.5 µg/g, and 93.8% of children exceeded the safe limit (2.0 µg/g). Fish consumption was associated with Hg levels (p = 0.03). The GSTP1 rs1695 A>G polymorphism was in the Hardy–Weinberg equilibrium and the highest prevalence of the GSTP1 AA genotype (80%) was found in Sawré Aboy, which had the highest Hg levels (10 µg/g) among the studied villages. The Hg levels tended to increase over the years in males and in carriers of the GSTP1 AA genotype (0.69 µg/g and 0.86 µg/g, respectively). Nine children failed the neurodevelopmental test, all of whom had Hg > 2.0 µg/g, and 88.9% carried the GSTP1 AA or AG genotypes, previously associated with the highest internal Hg doses and neurocognitive disorders. The genetic counseling of this population is important to identify the individuals at greater risk for neurodevelopmental disorders resulting from chronic Hg exposure. Full article

Multiple myeloma (MM) is a multifactorial genetic disorder caused by interactive effects of environmental and genetic factors. The proper locus of the TP53 gene (17p13.1) and its protein is essential in genomic stability. The most common variant of the TP53 gene—p.P72R (rs1042522)—shows functional variation. The aim of our study was a complex analysis of the TP53 p.P72R variant and TP53 gene expression in relation to chromosomal changes of the TP53 gene locus, as well as MM risk and outcome. Genomic DNA from 129 newly diagnosed MM patients was analyzed by methods of automated DNA sequencing (for TP53 variant analysis) and cIg-FISH (for chromosomal aberrations analysis). RNA was used in real-time PCR to determine the TP53 expression. In MM patients, the TP53 variant was not in Hardy–Weinberg equilibrium. The RR genotype was associated with lower MM risk (OR = 0.44, p = 0.004). A higher number of plasma cells was found in patients with RR genotype in comparison to those with PP + PR genotypes (36.74% vs. 28.30%, p = 0.02). A higher expression of the TP53 gene was observed in PP + PR genotypes vs. RR homozygote (p < 0.001), in smokers vs. non-smokers (p = 0.02). A positive Pearson’s correlation was found between the TP53 expression level and the number of plasma cells (r = 0.26, p = 0.04). The presence of chromosome 17 aberrations with or without TP53 locus did not affect the MM risk and outcome. Similar results were observed in the case of TP53 gene expression and the p.P72R variant. Full article

To clarify the population genetic structure, intrapopulation diversity, and interpopulation differentiation of yellowtail kingfish (Seriola aureovittata), we sampled 143 individuals from five collections of yellowtail kingfish: farmed (n = 30) and wild (n = 33) collections in China, a wild collection in Japan (n = 20), and farmed (n = 31) and wild (n = 29) collections in Australia. Using 2b-RAD simplified genome sequencing, we obtained an average of 287,594 unique tags per population, with an average sequencing depth of 27.13×. Our final genotype dataset included 48,710 SNPs (Single Nucleotide Polymorphisms). The five collections were all in Hardy–Weinberg equilibrium, and the interpopulation differentiation varied among the sample collections. The genetic differentiation coefficients (Fst) between the Chinese and Japanese yellowtail kingfish collections were low and the gene flow (Nm) values were high. These results suggest continuous gene flow occurs frequently between the collections, indicating that they belong to the same population. In contrast, genetic differentiation was high between the Australian collections and the Chinese and Japanese populations, suggesting different evolutionary origins and belonging to different populations. The farmed and wild Australian collections fell into distinct clades in a neighbor-joining phylogeny tree, suggesting farmed fish have begun to differentiate from the wild collection. A similar level of genetic diversity between the wild collections in China and Japan suggests that they originated from the same spawning ground. This, therefore, reminds us that in future aquaculture processes attention is needed regarding implementing targeted breeding strategies. In addition, our data will contribute to Chinese yellowtail kingfish genetic breeding and the sustainable use of Chinese yellowtail kingfish germplasms. Full article

Microphysogobio rapidus, an endemic cyprinid fish species found exclusively in Korea, has been identified in only two tributaries of the Nakdong River. The species predominantly occupies the near-gravel bottom waters within shallow sections of the middle and lower reaches of the river, characterized by swift currents. M. rapidus is currently recognized as a critically endangered species due to its distinct habitat preference, as well as the negative impacts of stream dam development and water environment pollution. In this study, we used 10 microsatellite markers to examine the genetic diversity of M. rapidus in the upper Nam (UN), lower Nam (LN), and Deokcheon Rivers (DC) in Korea, with a specific focus on assessment of the impact of dam development. Fish sampled from the UN and LN showed a greater average number of alleles and allelic richness (A = 18.3–18.4, A_R = 13.8) compared to those from DC (A = 11.8, A_R = 11.5). The observed heterozygosity among the fish examined ranged from H_O = 0.748 (LN) to 0.766 (DC). All three fish groups exhibited a significant departure from Hardy–Weinberg equilibrium (HWE) (p < 0.05). Despite having the largest effective population size (N_e = 175 and 157, respectively), the fish sampled from UN and LN showed the highest inbreeding coefficients (F_IS = 0.056–0.053, respectively), which were highly significant (p < 0.01). In contrast, the fish sampled from DC exhibited the smallest effective population size (N_e = 61) and showed an inbreeding coefficient close to zero (p > 0.05). BOTTLENECK analysis and estimated M-ratio values (0.341–0.372) revealed indications of past population size reduction in all fish groups examined. No significant genetic differentiation (F_ST < 0.05) was detected using the DAPC, STRUCTURE, and AMOVA among the fish studied. However, pairwise comparisons of F_ST between fish sampled from the Nam and Deokcheon Rivers revealed significant values (p < 0.001) ranging from 0.013 to 0.014. In addition, the closest genetic distance (0.026) was observed between UN and LN, while the greatest distance (0.087) was found between UN and DC. Analysis of gene flow rates among the fish examined indicated asymmetrical gene exchange within the Nam River, which was 31.51% in the downstream direction (from UN to LN), with a minimal gene flow rate (0.41%) in the upstream (from LN to UN) direction. The opposite trend was recorded between DC and LN, with a higher gene flow rate (29.74%) in the upstream direction compared to the downstream direction (0.12%). Our study highlighted the importance of implementing long-term conservation efforts focused on maintaining river integrity by removing water barriers such as weirs that impede fish migration and implementing active protection measures, such as aquaculture breeding and reasonable stocking practices, to preserve M. rapidus in the study area. Full article

The European flounder (Platichthys flesus), which is closely related to the recently discovered Baltic flounder (Platichthys solemdali), is currently the third most commercially fished species in the Baltic Sea. According to the available data from the Polish Fisheries Monitoring Center and fishermen’s observations, the body condition indices of the species in the Baltic Sea have declined in recent years. The aim of the present study was to obtain information on the current patterns of genetic variability and the population structure of the European flounder and to verify whether the Baltic flounder is present in the southern Baltic Sea. Moreover, we aimed to verify whether the observed decline in the body condition indices of the species in the Baltic Sea might be associated with adaptive alterations in its gene pool due to increased fishing pressure. For this purpose, 190 fish were collected from four locations along the central coastline of Poland, i.e., Mechelinki, Władysławowo, the Vistula Lagoon in 2018, and the Słupsk Bank in 2020. The fish were morphologically analyzed and then genetically screened by the application of nineteen microsatellite DNA and two diagnostic SNP markers. The examined European flounder specimens displayed a high level of genetic diversity (PIC = 0.832–0.903, I = 2.579–2.768). A lack of significant genetic differentiation (Fst = 0.004, p > 0.05) was observed in all the examined fish, indicating that the European flounder in the sampled area constitutes a single genetic cluster. A significant deficiency in heterozygotes (Fis = 0.093, p < 0.05) and overall deviations from Hardy–Weinberg expectations (H-WE) were only detected in fish sampled from the Słupsk Bank. The estimated effective population size (Ne) among the sampled fish groups varied from 712 (Słupsk Bank) to 10,115 (Władysławowo and Mechelinki). However, the recorded values of the Garza–Williamson indicator (M = 0.574–0.600) and the lack of significant (p > 0.05) differences in Heq > He under the SMM model did not support the species’ population size changes in the past. The applied SNP markers did not detect the presence of the Baltic flounder among the fish sampled from the studied area. The analysis of an association between biological traits and patterns of genetic diversity did not detect any signs of directional selection or density-dependent adaptive changes in the gene pool of the examined fish that might be caused by increased fishing pressure. Full article

In coastal and abiding zones, ground water continuously faces a very slight but alarmingly increasing trend in salinity due to several reasons such as the excess loss or use of it, with the constant dissolution of salts from the Earth’s surface and heat-trapping pollution from human activities, rising sea levels and finally, high flooding. Many recent studies have indicated that even a slight elevation in ground water salinity may affect freshwater inhabitants, highlighting the importance of research on the effects of low salinity stress on coastal zone freshwater inhabitants. Along with abiotic factors such as salinity, dissolved oxygen, pH, and alkalinity, anthropogenic factors also cause a lot of stress on the inhabitants in coastal zones. Climatic factors also play an important role in influencing the life of coastal water inhabitants. For example, statistics such as those obtained by correlation and discriminant function analysis indicate that sublethal salinity acts as a strong modulator in the physiology of inhabiting fish in fresh as well as coastal water. Parameters such as increase in body weight, feed intake and irregularities in morphometry increase under higher salinities, which are confirmed by a decline in the growth of fishes. Similarly, blood physiology aspects, such as a significant loss in hemoglobin content, the RBC count and eosinophils, are coupled with amelioration in neutrophil count at the higher salinities of 6 and 9 ppt in few freshwater organisms. Normal histoarchitecture is also lost in most fish under high salinity conditions and higher anthropogenic loads. The generation of tissue damage in terms of oxidative stress is prominent under high fluctuations in abiotic factors including higher salinity or under high anthropogenic loads. Hence, a loss in compromised normal physiology due to the toxic effects of low- or high-salinity saline water or in fresh inhabitants including hardy fishes under changing climatic conditions are evident. This raises concerns about maintaining water quality in coastal and allied zones globally in the coming decades. Full article

Since the 1960s, Grassy Narrows First Nation (Ontario, Canada) has been exposed to methyl mercury (Hg) through fish consumption, resulting from industrial pollution of their territorial waters. This cross-sectional study describes the visual characteristics of adults with documented Hg exposure between 1970 and 1997. Oculo-visual examinations of 80 community members included visual acuity, automated visual fields, optical coherence tomography [OCT], color vision and contrast sensitivity. Median age was 57 years (IQR 51–63) and 55% of participants were women. Median visual acuity was 0.1 logMAR (Snellen 6/6.4; IQR 0–0.2). A total of 26% of participants presented a Visual Field Index inferior to 62%, and qualitative losses assessment showed concentric constriction (18%), end-stage concentric loss (18%), and complex defects (24%). On OCT, retinal nerve fiber layer scans showed 74% of participants within normal/green range. For color testing with the Hardy, Rand, and Rittler test, 40% presented at least one type of color defect, and with the Lanthony D-15 test, median color confusion index was 1.59 (IQR 1.33–1.96). Contrast sensitivity showed moderate loss for 83% of participants. These findings demonstrate important loss of visual field, color vision, and contrast sensitivity in older adults in a context of long-term exposure to Hg in Grassy Narrows First Nation. Full article

Cheilinus undulatus is a valuable seawater economic fish with tender meat, fresh taste, and high nutritional value; however, its population is rapidly declining because of massive fishing and habitat destruction. Assessing changes in genetic diversity and inbreeding levels is a very valuable monitoring tool, and multiplex PCR has the advantages of being time-efficient and economical. Here, we selected 12 pairs of polymorphic microsatellite loci, developed two multiplex PCR amplification systems based on these microsatellites, and used them to examine 30 C. undulatus specimens. The number of alleles (Na) for the 12 microsatellite markers ranged from 2 to 8. The effective allele number (Ne) ranged from 1.724 to 4.592. The expected heterozygosity (He) and observed heterozygosity (Ho) ranged from 0.420 to 0.782 and 0.100 to 0.900, respectively. The polymorphic information content (PIC) ranged from 0.422 to 0.746, with a mean value of 0.557. 5 loci deviated from Hardy-Weinberg equilibrium (HWE, p < 0.05 after Bonferroni correction). The multiplex PCR amplification system established in this study provides a basis for germplasm identification, genetic diversity analysis, and assessment of the effects of accretion and release of C. undulatus. Full article

Black porgy is an important marine aquaculture fish species whose production is at the fifth position in all kinds of marine-cultured fishes in China. In this study, Illumina high-throughput sequencing technology was used to sequence the total RNA of black porgy. Sixty-one candidate SNPs (Single Nucleotide Polymorphism) were screened out and genotyped through GATK4 (Genome Analysis ToolKit) software and MALDI-TOF MS (Matrix-Assisted Laser Desorption/ Ionization Time of Flight Mass Spectrometry). The experimental results showed that a total of sixty SNPs were successfully genotyped, with a success rate of 98.36%. The results of principal component analysis and correlation analysis of growth traits showed that body weight was the first principal component, with a cumulative contribution rate of 74%. There were significant correlations (p < 0.05) or extremely significant correlations (p < 0.01) between different growth traits. The results of genetic parameter analysis and association analysis showed that scaffold12-12716321, scaffold13-4787950, scaffold2-13687576 and scaffold290-11890 were four SNPs that met the requirement of polymorphic information content and conformed to the Hardy–Weinberg equilibrium. There were significant differences between their genotype and the phenotype of growth traits. The four SNP molecular markers developed in this research will lay a foundation for further exploration of molecular markers related to the growth traits of black porgy and will provide a scientific reference for the further study of its growth mechanisms. At the same time, these molecular markers can be applied to the production practices of black porgy, so as to realize selective breeding at the molecular level and speed up the breeding process. Full article

Major carps, native freshwater fish in South Asian nations, are economically valuable fish species with high market demand. Coastal rural people can cultivate them in their own seasonal, largely underutilized, small homestead ponds with low input and understanding. However, the major problems with fish production in this region are the lack of quality carp seed and appropriate culture techniques. Therefore, this research was carried out on growth performance, survival rate, yield, feed conversion ratio (FCR), and profit of carp polyculture systems stocking with hatchery-produced and wild sourced fish seed in homestead ponds located in a coastal area along the Bay of Bengal. Three different treatments (T1–T3), each treatment with three replications, were designed for culturing carps, Gibelion catla, Labeo rohita, Labeo calbasu, and Cirrhinus mrigala using two local hatcheries seeds (T1 and T2), and wild seeds from the Halda River (T3). For all treatments, the stocked fish were maintained in the same size, weight, density, and ratio. Water quality parameters were measured at intervals of seven days, and the mean values were found to be within an acceptable range for fish farming and, in most cases, did not differ significantly from each other. The specific growth rate (SGR) was found higher in T3 for G. catla (1.16 ± 0.012%/day), L. rohita (1.19 ± 0.035%/day), and C. mrigala (1.06 ± 0.03%/day) and significantly differed (p < 0.05) among the treatments. Additionally, there were significant differences between the treatments in terms of ultimate weight, weight gain, survival rate, fish production, and return on investment (ROI) (p < 0.05). The lower FCR in T3 (2.65 ± 0.10) than in T1 (3.32 ± 0.31) and T2 (3.21 ± 0.33) indicated that stocking wild seed had higher profitability potentials. High genetic variety in the population of naturally occurring, free-living fish, resistance to disease, a high rate of survival, and the hardiness of wild seed are all factors that might contribute to the better performance of wild seed stock. However, the total yield and total return from the T3 treatment also emphasized that carp farming using wild seed is not viable because of the variable amount, high seed cost, low transportation facilities, and very small natural seed-stock supplies from the river. Inbreeding and reduced genetic variety in the hatchery stock could result in the production of poor-quality seed, which had an impact on the production performance in culture treatments stocked with hatchery seed. Full article

Oreochromis fishes exhibit variability of sex-determination (SD) genes whose characterization contributes to understanding of the sex differentiation network, and to effective tilapia farming, which requires all-male culture. However, O. niloticus (On) amh is the only master-key regulator (MKR) of SD that has been mapped (XY/XX SD-system on LG23). In O. aureus (Oa), LG3 controls a WZ/ZZ SD-system that has recently been delimited to 9.2 Mbp, with an embedded interval rich with female-specific variation, harboring two paics genes and banf2. Developing genetic markers within this interval and using a hybrid Oa stock that demonstrates no recombination repression in LG3, we mapped the critical SD region to 235 Kbp on the orthologous On physical map (p < 1.5 × 10⁻²⁶). DNA-seq assembly and peak-proportion analysis of variation based on Sanger chromatograms allowed the characterization of copy-number variation (CNV) of banf2. Oa males had three exons capable of encoding 90-amino-acid polypeptides, yet in Oa females, we found an extra copy with an 89-amino-acid polypeptide and three non-conservative amino acid substitutions, designated as banf2w. CNV analysis suggested the existence of two to five copies of banf2 in diploidic Cichlidae. Disrupting the Hardy–Weinberg equilibrium (p < 4.2 × 10⁻³), banf2w was concordant with female determination in Oa and in three cichlids with LG3 WZ/ZZ SD-systems (O. tanganicae, O. hornorum and Pelmatolapia mariae). Furthermore, exclusive RNA-seq expression in Oa females strengthened the candidacy of banf2w as the long-sought LG3 SD MKR. As banf genes mediate nuclear assembly, chromatin organization, gene expression and gonad development, banf2w may play a fundamental role inducing female nucleus formation that is essential for WZ/ZZ SD. Full article

Dibothriocephalus dendriticus is one of the causative agents of the fish-borne zoonosis diphyllobothriosis. Polymorphic microsatellite markers were originally developed for future genetic studies using microsatellite library screening and next-generation sequencing (NGS). Out of 128 microsatellite candidates selected after NGS analysis, 126 yielded PCR products of the expected size. A declared repetitive motif was confirmed in 92 loci by Sanger sequencing. The level of polymorphism was tested by fragment analysis. Statistical tests for observed and expected heterozygosities and deviations from Hardy–Weinberg equilibrium revealed 14 polymorphic microsatellite loci suitable for studies on the finer genetic structure of global populations of D. dendriticus. Full article

The endorheic Lake Eyre Basin drains 1.2 million square kilometres of arid central Australia, yet provides habitat for only 30 species of freshwater fish due to the scarcity of water and extreme climate. The majority are hardy riverine species that are adapted to the unpredictable flow regimes, and capable of massive population booms following heavy rainfall and the restoration of connectivity between isolated waterholes. The remainder are endemic specialists from isolated springs with very restricted ranges, and many are listed under relevant state and national endangered species legislation and also by the International Union for Conservation of Nature (IUCN). For these spring communities, which are sustained by water from the Great Artesian Basin, survival is contingent on suitable habitat persisting alongside extractive mining, agriculture and the imposition of alien species. For the riverine species, which frequently undertake long migrations into ephemeral systems, preservation of the natural flow regime is paramount, as this reinstates riverine connectivity. In this study, fish were sampled from the Bulloo River in the east to the Mulligan River in the west, along a temporal timeframe and using a standard set of sampling gears. Fish presence was influenced by factors such as natural catchment divides, sampling time, ephemerality and the occurrence of connection flows and flooding. Despite the comparatively low diversity of species, the aquatic systems of this isolated region remain in good ecological condition, and as such they offer excellent opportunities to investigate the ecology of arid water systems. However, the presence of both endangered species (in the springs) and invasive and translocated species more widely indicates that active protection and management of this unique area is essential to maintain biodiversity and ecosystem integrity. Full article