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Freshwaters are a very valuable resource in arid areas, such as Mediterranean countries. Freshwater systems are vulnerable ecological habitats, significantly disturbed globally and especially in arid areas. The Sea of Galilee is the largest surface freshwater body in the Middle East. It is an isolated habitat supporting unique fish populations, including endemic species and populations on the edge of their distribution range. Using the Sea of Galilee for water supply, fishing and recreation has been placing pressure on these fish populations. Therefore, efficient monitoring and effective actions can make a difference in the conservation of these unique fish populations. To set a baseline and develop molecular tools to do so, in this study, DNA barcoding was used to establish a database of molecular species identification based on sequences of Cytochrome C Oxidase subunit I gene. DNA barcodes for 22 species were obtained and deposited in Barcode of Life Database. Among these, 12 barcodes for 10 species were new to the database and different from those already there. Barcode sequences were queried against the database and similar barcodes from the same and closely related species were obtained. Disagreements between morphological and molecular species identification were identified for five species, which were further studied by phylogenetic and genetic distances analyses. These analyses suggested the Sea of Galilee contained hybrid fish of some species and other species for which the species definition should be reconsidered. Notably, the cyprinid fish defined as Garra rufa, should be considered as Garra jordanica. Taken together, along with data supporting reconsideration of species definition, this study sets the basis for further using molecular tools for monitoring fish populations, understanding their ecology, and effectively managing their conservation in this unique and important habitat and in the region. [ABSTRACT FROM AUTHOR]

Background: Infectious disease outbreaks form major setbacks to aquaculture production and to further development of this important sector. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus widely hampering production of common carp (Cyprinus carpio), one of the most farmed fish species worldwide. Genetically disease resistant strains are highly sought after as a sustainable solution to this problem. To study the genetic basis and cellular pathways underlying disease resistance, RNA-Seq was used to characterize transcriptional responses of susceptible and resistant fish at day 4 after CyHV-3 infection. Results: In susceptible fish, over four times more differentially expressed genes were up-regulated between day 0 and 4 compared to resistant fish. Susceptible and resistant fish responded distinctively to infection as only 55 (9%) of the up-regulated genes were shared by these two fish types. Susceptible fish elicited a typical anti-viral response, involving interferon and interferon responsive genes, earlier than resistant fish did. Furthermore, chemokine profiles indicated that the two fish types elicited different cellular immunity responses. A comparative phylogenetic approach assisted in chemokine copies annotation pointing to different orthologous copies common to bony-fishes and even carp-specific paralogs that were differentially regulated and contributed to the different response of these two fish types. Susceptible fish up-regulated more ccl19 chemokines, which attract T-cells and macrophages, the anti-viral role of which is established, whereas resistant fish up-regulated more cxcl8/il8 chemokines, which attract neutrophils, the antiviral role of which is unfamiliar. Conclusions: Taken together, by pointing out transcriptional differences between susceptible and resistant fish in response to CyHV-3 infection, this study unraveled possible genes and pathways that take part in disease resistance mechanisms in fish and thus, enhances our understanding of fish immunogenetics and supports the development of sustainable and safe aquaculture. [ABSTRACT FROM AUTHOR]

The Sea of Galilee has great significance as a natural habitat and a freshwater source for Israel. Anthropogenic impacts have been placing significant pressure on the species inhabiting this lake, among which is Sarotherodon galilaeus, an omnivorous fish with a relatively large population and significance for commercial fishing. An alarming decline in annual catch towards 2008 suggested that this unique population might be at risk. With that in mind, we characterized the current genetic variation of this species in Israel with reference to fish from Ghana, based on D-loop and microsatellite markers. Genetic variation and differentiation were found mostly among fish from Ghanaian localities and between fish from Israel and Ghana, whereas fish from all Israeli localities had uniform and limited variation, a signature compatible with historical founder effect followed by local adaptations. Such historical processes could leave a population vulnerable as reflected in the sudden and recent population decline. Comparing genetic variation between archived 30 year-old scales and modern lake fish revealed further reduction in genetic variation coincident with the recent population decline. Thus, a recently occurring genetic bottleneck had placed this unique and isolated population at an even higher risk. We carefully discuss the events leading to the current risk status for S. galilaeus in Israel and highlight the need for vigilant monitoring and active management to support a more sustainable future for this and other fish communities in this important habitat. [ABSTRACT FROM AUTHOR]

Sustainability and further development of aquaculture production are constantly challenged by outbreaks of fish diseases, which are difficult to prevent or control. Developing fish strains that are genetically resistant to a disease is a cost-effective and a sustainable solution to address this challenge. To do so, heritable genetic variation in disease resistance should be identified and combined together with other desirable production traits. Aquaculture of common carp has suffered substantial losses from the infectious disease caused by the cyprinid herpes virus type 3 (CyHV-3) virus and the global spread of outbreaks indicates that many cultured strains are susceptible. In this research, CyHV-3 resistance from the feral strain "Amur Sassan" was successfully introgressed into two susceptible cultured strains up to the first backcross (BC1) generation. Variation in resistance of families from F1 and BC1 generations was significantly greater compared to that among families of any of the susceptible parental lines, a good starting point for a family selection program. Considerable additive genetic variation was found for CyHV-3 resistance. This phenotype was transferable between generations with contributions to resistance from both the resistant feral and the susceptible cultured strains. Reduced scale coverage (mirror phenotype) is desirable and common in cultured strains, but so far, cultured mirror carp strains were found to be susceptible. Here, using BC1 families ranging from susceptible to resistant, no differences in resistance levels between fully scaled and mirror full-sib groups were found, indicating that CyHV-3 resistance was successfully combined with the desirable mirror phenotype. In addition, the CyHV-3 viral load in tissues throughout the infection of susceptible and resistant fish was followed. Although resistant fish get infected, viral loads in tissues of these fish are significantly lesser than in those of susceptible fish, allowing them to survive the disease. Taken together, in this study we have laid the foundation for breeding CyHV-3-resistant strains and started to address the mechanisms underlying the phenotypic differences in resistance to this disease. [ABSTRACT FROM AUTHOR]

In accordance with their tropical origin, the optimal water temperature for most tilapia species is between 25 and 28 °C. The lethal temperature varies as a function of environmental effects, individual fish histories and genetic effects; however, the genetic basis of cold tolerance in tilapia has not been investigated in detail. Blue tilapia ( Oreochromis aureus) is considered as one of the most cold-tolerant tilapia species, and, in this study, we have used a fish from a three-generation selective breeding program for enhanced cold tolerance. Four crosses within and between resistant and sensitive fish were used in this study. Forty families were challenged for cold tolerance, and a strong maternal effect was observed in two consecutive experiments. Expression patterns of the mitochondrial ATP6 gene were strongly correlated with cold tolerance; however, an analysis that applied an individual animal model restricted maximum likelihood on a three-generation pedigree, implies that an epigenetic effect rather than mitochondrial inheritance is the main source of the observed maternal effect. This study demonstrates that maternal effects can play a significant role in the inheritance of cold tolerance and that maternally-transferred genetic components should be targeted when adaptation to low temperature is studied in tilapia. [ABSTRACT FROM AUTHOR]

Background: The probable influence of genes and the environment on sex determination in Nile tilapia suggests that it should be regarded as a complex trait. Detection of sex determination genes in tilapia has both scientific and commercial importance. The main objective was to detect genes and microRNAs that were differentially expressed by gender in early embryonic development. Results: Artificial fertilization of Oreochromis niloticus XX females with either sex-reversed ΔXX males or genetically-modified YY ‘supermales’ resulted in all-female and all-male embryos, respectively. RNA of pools of all-female and all-male embryos at 2, 5 and 9 dpf were used as template for a custom Agilent eArray hybridization and next generation sequencing. Fifty-nine genes differentially expressed between genders were identified by a false discovery rate of p < 0.05. The most overexpressed genes were amh and tspan8 in males, and cr/20β-hsd, gpa33, rtn4ipl and zp3 in females (p < 1 × 10−9). Validation of gene expression using qPCR in embryos and gonads indicated copy number variation in tspan8, gpa33, cr/20β-hsd and amh. Sequencing of amh identified a male-specific duplication of this gene, denoted amhy, differing from the sequence of amh by a 233 bp deletion on exonVII, hence lacking the capability to encode the protein motif that binds to the transforming growth factor beta receptor (TGF-β domain). amh and amhy segregated in the mapping family in full concordance with SD-linked marker on LG23 signifying the QTL for SD. We discovered 831 microRNAs in tilapia embryos of which nine had sexually dimorphic expression patterns by a false discovery rate of p < 0.05. An up-regulated microRNA in males, pma-mir-4585, was characterized with all six predicted target genes including cr/20β-hsd, down-regulated in males. Conclusions: This study reports the first discovery of sexually differentially expressed genes and microRNAs at a very early stage of tilapia embryonic development, i.e. from 2 dpf. Genes with sexually differential expression patterns are enriched for copy number variation. A novel male-specific duplication of amh, denoted amhy, lacking the TGF-β domain was identified and mapped to the QTL region on LG23 for SD, thus indicating its potential role in SD. [ABSTRACT FROM AUTHOR]

Genetic parameters and selection responses were obtained for harvest body weight of blue tilapia ( Oreochromis aureus) from data collected over three generations in a selected population. A total of 18 194 records representing 186 sires and 201 dams were used in the analysis. Within generation heritability estimates for harvest body weight ranged from 0.18 to 0.58. When data from more than one generation were included in the analysis, heritability estimates became more stable (0.33-0.40) and it was 0.33 when all data were included in the analysis. The common full-sib effect accounted for 10% of the phenotypic variance in the full data set. Heritability for survival from stocking to harvest was estimated at 0.01 and 0.09 in actual units (fitting an animal model) and in the logit (sire model) scale respectively. The genetic correlation between harvest body weight and survival was 0.22 and not significantly different from zero. The total selection response for harvest body weight over the three generations of selection measured as the difference between least-squares means of selected and control lines was 17.7%. The corresponding figure when response was measured as the difference between mean breeding values of selected and control lines was 19.6%. The average inbreeding coefficient was 0.003 after three generations of selection. These results indicate that there are good prospects for the genetic improvement of harvest body weight in blue tilapia. [ABSTRACT FROM AUTHOR]

The physiological response of Mozambique and Nile tilapia transferred from fresh to brackish (15 ppt) water was compared during a one-week time course. Response in the pituitary was measured by the gene expression pattern of prolactin (PRL I), growth hormone (GH), and calcium-sensing receptor (CaSR), while the response in the gills was measured by the gene expression pattern of the prolactin receptor (PRL-R), Na/K/2Cl cotransporter (NKCC) and Na/Cl cotransporter (NCC), and by activity and expression of Na/K-ATPase (NKA). The time-course curves of plasma osmolality levels indicate a rapid elevation 24 h after transfer, which later decreased and maintained at stable level. PRL I expression decreased in both species, but with stronger response in the Nile tilapia, while no differences were found in the slightly elevated levels of GH mRNA. The branchial response demonstrated a faster up-regulation of NKA and NKCC in the Mozambique tilapia, but similar levels after a week, while Nile tilapia had stronger and constant down-regulation of NCC. The time-course response of the measured osmoregulatory parameters indicate that 24 h after transfer is a critical time point for brackish-water adaptation. The differences in responses to saltwater challenge between Mozambique and Nile tilapia shown in this study may be associated with the differences in saltwater tolerance between these two tilapiine species. [ABSTRACT FROM AUTHOR]

The large-scale bacterial artificial chromosome-end sequencing project of Nile tilapia ( Oreochromis niloticus) has generated extensive sequence data that allowed the examination of the repeat content in this fish genome and building of a repeat library specific for this species. This library was established based on Tilapiini repeat sequences from GenBank, sequences orthologous to the repeat library of zebrafish in Repbase, and novel repeats detected by genome analysis using MIRA assembler. We estimate that repeats constitute about 14% of the tilapia genome and also give estimates for the occurrence of the different repeats based on the Basic Local Alignment Search Tool searches within the database of known tilapia sequences. The frequent occurrence of novel repeats in the tilapia genome indicates the importance of using the species-specific repeat masker prior to sequence analyses. A web tool based on the RepeatMasker software was designed to assist tilapia genomics. [ABSTRACT FROM AUTHOR]

The worldwide use of Nile tilapia ( Oreochromis niloticus Linnaeus, 1758) in aquaculture represents a somewhat unique scenario. The natural distributions and global genetic resources of tilapias are in Africa, yet the main centers of utilization for aquaculture are primarily in Asia. Within a few decades, Nile tilapia graduated from being an ‘orphan commodity’ (i.e. of interest to only resource-poor fish farmers) to a globally traded commodity. Most aquaculture production of Nile tilapia in Asia and elsewhere has relied on a narrow genetic base. The natural genetic resources have not yet been fully documented and tapped for use in aquaculture, and many natural populations are under severe threat of irreversible change or loss. Although genetic improvement is now well underway, an important question is how the wealth of Nile tilapia wild genetic resources shall be used for the benefit of a wide range of users, at present outside Africa. This review focuses on documenting the status of Nile tilapia genetic resources (including the potential threats), providing a case for their conservation and for the judicious utilization of genetic diversity for the benefit of all stakeholders; and on analysis of the lessons learnt from a major Nile tilapia genetic improvement initiative, the genetic improvement of farmed tilapia (GIFT) project. Information about other genetic improvement efforts by means of hybridization, sex reversal and YY male technology is also presented. [ABSTRACT FROM AUTHOR]

This study was aimed at detecting differences among tilapia species in immunological and biochemical parameters that are indicators for fish health. In addition, six blood parameters that are indicators of stress were measured, glucose concentration, ceruloplasmin activity, lysozyme activity, respiratory burst activity, haematocrit and leucocrit, and their levels were compared among groups. A calibration experiment was conducted with commercial stock of tilapia to optimize a protocol for measuring stress response in tilapia. An air exposure stress was induced to six groups of fish and blood samples were taken at six different times: 15 min, 1, 2.5, 4.5, 6 and 24 h, after inducing stress. The highest responses to stress were observed after 2.5–4.5 h. A second experiment was conducted with four tilapia species:Oreochromis aureus(Steindachner),O. mossambicus(Peters), a red strain and the wild type ofO. niloticusL. Levels of serum biochemical components and parameters of the innate immunity response to stress were compared in ten fish from each species. Significant differences were observed.Oreochromis aureusdiffered from the other three species (notably fromO. mossambicus) in most of the measured immune response traits (glucose concentration, lysozyme activity, haematocrit and levels of total protein and IgM after stress) and serum biochemical components (protein, albumin, triglyceride, cholesterol, calcium, magnesium, phosphorus, bilirubin andβ-hydroxybotiric acid). The identified differences suggest that hybrid families fromO. aureusandO. mossambicusmay be used to construct a segregating population for genetic analysis of the innate immune response to stress. Thus, these two species were bred for segregating F2 population, suitable for quantitative trait loci studies for the innate immune response to stress. [ABSTRACT FROM AUTHOR]

A genome scan, searching for quantitative trait loci (QTL) for the traits cold tolerance and body weight in tilapia, was performed on a cross between a ( Oreochromis niloticus× Sarotherodon galilaeus) male and a ( O. mossambicus× O. aureus) female. Fifty-four microsatellites and 23 amplified fragment length polymorphism (AFLP) primer combinations were genotyped and tested for marker–trait associations. Sex-specific linkage maps were constructed from this data. Twenty-three point-wise significant marker–trait associations were found in the genome scan, and putative QTL were subsequently tested in another ( On× Sg) × ( Om× Oa) family. None of the putative QTL from the first experiment were significant in the second experiment. However, one microsatellite, UNH130, found to be associated to weight in the first experiment, was found to be strongly associated to cold tolerance in the second experiment. Since QTL for cold tolerance and body weight were recently found on the linkage group containing UNH130 (linkage group 23) in another study, this linkage group was investigated more closely using interval mapping. The results provide indications, but not conclusive evidence, of a QTL for cold tolerance on linkage group 23. [ABSTRACT FROM AUTHOR]

This study presents two experiments addressing growth and size variation in fingerling silver perch ( Bidyanus bidyanus. In the first experiment, fish close to mean population size were raised either in the presence or absence of five larger fish for 60 days. Mean specific growth rate ( SGR) and increases in the coefficient of variation and skewness were lower in the presence of larger fish, indicating a negative effect of large fish on the growth of smaller ones. In the second experiment, fingerlings were graded into groups smaller and larger than the median size of the population and raised in size-sorted groups of 60 large or small fish and mixed groups of 30 fish of each size category, for 60 days. There was no difference in mean SGR among groups, nor between the mixed group ad the weighted mean of the small and large groups. Biomass gain was higher in the mixed groups than in the weighted small-and-large groups, probably due to a slightly lower survival in the groups comprised of large fish. The fact that the effect of large fingerlings on the growth of smaller ones was evident in the first, but not the second, experiment may be attributed to higher size disparity between large and small fingerlings in the first experiment. [ABSTRACT FROM AUTHOR]

Optimal conditions were determined for induction of meiotic diploid gynogenesis in white bass Morone chrysops. In two series of experiments, ultraviolet light (UV) irradiation doses to inactivate sperm genome and optimal temperature shock to restore diploidy were established. Eggs of white bass were inseminated with sperm from striped bass M. saxatilis diluted (1:30) in saline and irradiated with UV at doses ranging from 50 to 1,200 J/m2. A typical “Hertwig effect” was observed with increasing UV dose. Larvae obtained at doses of 400 J/m2 and greater were abnormally developed (haploid syndrome) and had a haploid chromosome number (n = 24). Heat shocks to cause retention of the second polar body were applied. Heat shocks of 2-min duration at 36°C, 38°C, or 40°C were applied at 2 or 3 min after insemination to white bass eggs inseminated with irradiated (800 J/m2) striped bass sperm. The best results were obtained after application of 36°C heat shock at 3 min after insemination, which induced a significant increase in yield of diploid gynogens (24–39%, from initial numbers of gynogenetic embryos) and provided relatively high postshock embryo survival. The gynogenetic origin of diploids obtained was confirmed by the lack of melanophores in putative gynogens (contrary to pigmented control hybrid larvae). [ABSTRACT FROM PUBLISHER]

Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations. [ABSTRACT FROM AUTHOR]