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Hybridization between introduced and indigenous species can lead to loss of unique genetic resources and precipitate extinction. In Tanzania, the Nile tilapia (Oreochromis niloticus) and blue-spotted tilapia (Oreochromis leucostictus) have been widely introduced to non-native habitats for aquaculture and development of capture fisheries. Here, we aimed to quantify interspecific hybridization between these introduced species and the indigenous species Oreochromis esculentus, Oreochromis jipe and Oreochromis korogwe. In the Pangani basin, several hybrids were observed (O. niloticus × O. jipe, O. leucostictus × O. jipe, O. niloticus × O. korogwe), although hybrids were relatively uncommon within samples relative to purebreds. Hybrids between the native O. jipe × O. korogwe were also observed. In the Lake Victoria basin, no evidence of hybrids was found. Analysis of body shape using geometric morphometrics suggested that although purebreds could be discriminated from one another, hybrids could not be readily identified on body and head shape alone. These results provide the first evidence of hybridization between the introduced species and the Critically Endangered O. jipe in Tanzania. Given uncertainty regarding benefits of introduced species over large-bodied indigenous species in aquaculture and capture fisheries, we suggest that future introductions of hybridization-prone species should be carefully evaluated.

Sex in Oreochromis niloticus (Nile tilapia) is principally determined by an XX/XY locus but other genetic and environmental factors also influence sex ratio. Restriction Associated DNA (RAD) sequencing was used in two families derived from crossing XY males with females from an isogenic clonal line, in order to identify Single Nucleotide Polymorphisms (SNPs) and map the sex-determining region(s). We constructed a linkage map with 3,802 SNPs, which corresponded to 3,280 informative markers, and identified a major sex-determining region on linkage group 1, explaining nearly 96% of the phenotypic variance. This sex-determining region was mapped in a 2 cM interval, corresponding to approximately 1.2 Mb in the O. niloticus draft genome. In order to validate this, a diverse family (4 families; 96 individuals in total) and population (40 broodstock individuals) test panel were genotyped for five of the SNPs showing the highest association with phenotypic sex. From the expanded data set, SNPs Oni23063 and Oni28137 showed the highest association, which persisted both in the case of family and population data. Across the entire dataset all females were found to be homozygous for these two SNPs. Males were heterozygous, with the exception of five individuals in the population and two in the family dataset. These fish possessed the homozygous genotype expected of females. Progeny sex ratios (over 95% females) from two of the males with the \"female\" genotype indicated that they were neomales (XX males). Sex reversal induced by elevated temperature during sexual differentiation also resulted in phenotypic males with the \"female\" genotype. This study narrows down the region containing the main sex-determining locus, and provides genetic markers tightly linked to this locus, with an association that persisted across the population. These markers will be of use in refining the production of genetically male O. niloticus for aquaculture.

In gonochoristic vertebrates, sex determination mechanisms can be classified as genotypic (GSD) or temperature-dependent (TSD). Some cases of TSD in fish have been questioned, but the prevalent view is that TSD is very common in this group of animals, with three different response patterns to temperature. We analyzed field and laboratory data for the 59 fish species where TSD has been explicitly or implicitly claimed so far. For each species, we compiled data on the presence or absence of sex chromosomes and determined if the sex ratio response was obtained within temperatures that the species experiences in the wild. If so, we studied whether this response was statistically significant. We found evidence that many cases of observed sex ratio shifts in response to temperature reveal thermal alterations of an otherwise predominately GSD mechanism rather than the presence of TSD. We also show that in those fish species that actually have TSD, sex ratio response to increasing temperatures invariably results in highly male-biased sex ratios, and that even small changes of just 1-2 degrees C can significantly alter the sex ratio from 1:1 (males:females) up to 3:1 in both freshwater and marine species. We demonstrate that TSD in fish is far less widespread than currently believed, suggesting that TSD is clearly the exception in fish sex determination. Further, species with TSD exhibit only one general sex ratio response pattern to temperature. However, the viability of some fish populations with TSD can be compromised through alterations in their sex ratios as a response to temperature fluctuations of the magnitude predicted by climate change.

Background Osmotic stress is a widespread phenomenon in aquatic animal. The ability to cope with salinity stress and alkaline stress is quite important for the survival of aquatic species under natural conditions. Tilapia is an important commercial euryhaline fish species. What’s more tilapia is a good experimental material for osmotic stress regulation research, but the molecular regulation mechanism underlying different osmotic pressure of tilapia is still unexplored. Results To elucidate the osmoregulation strategy behind its hyper salinity, alkalinity and salinity-alkalinity stress of tilapia, the transcriptomes of gills in hybrid tilapia ( Oreochromis mossambicus ♀  ×  O. urolepis hornorum ♂ ) under salinity stress (S: 25‰), alkalinity stress(A: 4‰) and salinity-alkalinity stress (SA: S: 15‰, A: 4‰) were sequenced using deep-sequencing platform Illumina/HiSeq-2000 and differential expression genes (DEGs) were identified. A total of 1958, 1472 and 1315 upregulated and 1824, 1940 and 1735 downregulated genes ( P -value < 0.05) were identified in the salt stress, alkali stress and saline-alkali stress groups, respectively, compared with those in the control group. Furthermore, Kyoto Encyclopedia of Genes and Genomes pathway analyses were conducted in the significant different expression genes. In all significant DEGs, some of the typical genes involved in osmoregulation, including carbonic anhydrase (CA), calcium/calmodulin-dependent protein kinase (CaM kinase) II (CAMK2), aquaporin-1(AQP1), sodium bicarbonate cotransporter (SLC4A4/NBC1), chloride channel 2(CLCN2), sodium/potassium/chloride transporter (SLC12A2 / NKCC1) and other osmoregulation genes were also identified. RNA-seq results were validated with quantitative real-time PCR (qPCR), the 17 random selected genes showed a consistent direction in both RNA-Seq and qPCR analysis, demonstrated that the results of RNA-seq were reliable. Conclusions The present results would be helpful to elucidate the osmoregulation mechanism of aquatic animals adapting to saline-alkali challenge. This study provides a global overview of gene expression patterns and pathways that related to osmoregulation in hybrid tilapia, and could contribute to a better understanding of the molecular regulation mechanism in different osmotic stresses.

Oreochromis species are of economic importance in fisheries and aquaculture but threatened by human‐mediated activities. Effective conservation and their sustainable management require genetic monitoring tools that can assess genetic variation across species. Various neutral markers have been used to monitor biodiversity in organisms, but they are limited in cross‐amplification among various taxa. Non‐neutral markers such as Exon‐Primed Intron Crossing (EPIC) not only cross amplify various taxa but also target gene regions that are likely to be involved in adaptive responses to selective pressure. This study therefore developed 50 EPIC markers from Oreochromis niloticus reference genome targeting immune related genes to assess their potential to cross‐amplify Oreochromis species. Genetic diversity, population structure, and differentiation was measured among Oreochromis niloticus, O. jipe, O. esculentus and O. leucostictius species and their respective populations from eleven African water bodies and two aquaculture farms. 45 EPIC markers successfully amplified target regions across the four Oreochromis species. O. niloticus exhibited the highest diversity (He = 0.50), followed by O. jipe (He = 0.29), O. leucostictus (He =0.28) and O. esculentus with the lowest (He = 0.25). The highest differentiation values were observed among populations of different species while the lowest was among farmed O. niloticus. This was supported by AMOVA results that showed highest genetic differentiation among species. Population structure analyses were concordant with species boundaries while showing detailed intraspecific clustering patterns among the O. niloticus populations that reflected geographical origin. The observed genetic diversity, gene flow, and population differentiation confirms the applicability of EPIC markers as molecular tools for monitoring biodiversity and guiding the conservation of Oreochromis species under increasing anthropogenic and environmental pressures. This study developed 50 exon‐primed intron‐crossing (EPIC) markers in Oreochromis niloticus to assess their cross‐amplification potential in four Oreochromis species. Forty‐five markers successfully amplified across species, revealing significant genetic differentiation among species and populations. These findings demonstrate the utility of EPIC markers for monitoring genetic diversity and informing conservation of Oreochromis species under anthropogenic and environmental pressures.

Background Streptococcosis and Motile Aeromonad Septicemia (MAS) are important diseases of tilapia, Oreochromis spp. and causes huge economic losses in aquaculture globally. The feed-based vaccination may be an alternative to minimize major infectious diseases in tilapia. Thus, this study aims to evaluate the haemato-immunological responses and effectiveness of a newly developed feed-based killed bivalent vaccine against Streptococcus iniae and Aeromonas hydrophila in hybrid red tilapia. A total of 495 hybrid red tilapia of 61.23 ± 4.95 g were distributed into 5 groups (each with triplicate). The fish were immunized orally through bivalent (combined S. iniae and A. hydrophila ) spray vaccine (BS group), bivalent formulate vaccine (BF group), monovalent S. iniae vaccine (MS group), monovalent A. hydrophila vaccine (MA group) and unvaccinated as a control group. The vaccine was orally administered on days 0, 14 and 42 applied feed-based bacterin at 5% body weight. The blood and spleen samples were collected from all groups on 7, 21 and 49 days post-vaccination, and also 96 h post-infection to assess their haemato-immune responses. Results Compared with the unvaccinated group, leukocyte, lymphocytes, monocytes, granulocytes counts in vaccinated groups were significantly ( P  < 0.05) increased on 21, 49 days post-vaccination and also 96 h post-infection, while erythrocytes, haemoglobin and haematocrit in vaccinated groups were significantly ( P  < 0.05) enhanced only 96 h post-infection. Additionally, the lysozyme and phagocytic activity and, serum antibody (IgM) were significantly higher ( P  < 0.05) against S. iniae and A. hydrophila in vaccinated groups compared to the unvaccinated group in the pre- and post-infection. Results from the challenge through co-infection with S. iniae and A. hydrophila showed the relative percent survival (RPS) in BF group was 76.67 ± 4.71%, which had the capacity to induce significant protection ( P  < 0.05) compared to others groups. Conclusions This study demonstrates the bivalent formulate (BF) group could elicit significant non-specific and specific immunological responses with higher protection in hybrid red tilapia. In addition, this newly developed feed-based bivalent vaccination can be a promising technique for effective and large scale fish immunization in the aquaculture industry.

Tilapia is the second most farmed fish species after carp in the world. However, the production has come under threat due to emerging diseases such as tilapia lake virus (TiLV) that causes massive mortalities with high economic losses. It is largely unknown whether different tilapia strains are equally susceptible to TiLV infection. In the present study we compared the susceptibility of gray (Oreochromis niloticus x O. aureus) and red tilapia (Oreochromis spp.) to experimental TiLV infection. Virus was injected intraperitoneally at a concentration of 104 TCID50/mL. Our findings show that gray tilapia had a lower mortality, 86.44%, but statistically not significantly different (p = 0.068) from red tilapia (100%). The duration of the mortality period from onset to cessation was similar for the two species, starting at 2–3 days post challenge (dpc) with a median at 10–11 dpi and ending on 20–22 dpi. In addition, there was no difference between species in mean viral loads in brain, liver and headkidney from fish collected soon after death. As for host response, expression levels of IL-1β and TNFα were equally high in brain and headkidney samples while levels in liver samples were low for both red and gray tilapia, which coincides with lower viral loads in liver compared to brain and headkidney for both species. We find that red and gray tilapia were equally susceptible to TiLV infection with similar post challenge mortality levels, equal virus concentration in target organs and similar proinflammatory cytokine responses in target and lymphoid organs at time of death. Nonetheless, we advocate that the search for less susceptible tilapia strains should continue with the view to reduce losses from TiLV infection in aquaculture.

A high-carbohydrate diet could achieve a protein-sparing effect, but it may cause negative impacts on the growth condition of fish due to their poor utilisation ability of carbohydrate. How to reduce the adverse effects caused by a high-carbohydrate diet is important for the development of aquaculture. In the present study, we aimed to identify whether inulin could attenuate the metabolic syndrome caused by a high-carbohydrate diet in fish. Nile tilapia (Oreochromis niloticus) (1·19 (sd 0·01) g) were supplied with 35 % carbohydrate (CON), 45 % carbohydrate (HC) and 45 % carbohydrate + 5 g/kg inulin (HCI) diets for 10 weeks. The results showed that addition of inulin improved the survival rate when fish were challenged with Aeromonas hydrophila, indicating that inulin had an immunostimulatory effect. Compared with the HC group, the HCI group had lower lipid accumulation in liver and the gene expression analyses indicated that addition of inulin down-regulated genes related to lipogenesis and up-regulated genes relevant to β-oxidation significantly (P < 0·05). Higher liver glycogen and glucose tolerance were found in the HCI group compared with the HC group (P < 0·05). These results indicated that inulin could alleviate the metabolic syndrome induced by a high-carbohydrate diet. Furthermore, addition of inulin to a high-carbohydrate diet changed the intestinal bacterial composition and significantly increased the concentration of acetic acid and propionic acid in fish gut which have the potential to increase pathogen resistance and regulate metabolic characteristics in fish. Collectively, our results demonstrated a possible causal role for the gut microbiome in metabolic improvements induced by inulin in fish.

Fillet yield (FY) and harvest weight (HW) are economically important traits in Nile tilapia production. Genetic improvement of these traits, especially for FY, are lacking, due to the absence of efficient methods to measure the traits without sacrificing fish and the use of information from relatives to selection. However, genomic information could be used by genomic selection to improve traits that are difficult to measure directly in selection candidates, as in the case of FY. The objectives of this study were: (i) to perform genome-wide association studies (GWAS) to dissect the genetic architecture of FY and HW, (ii) to evaluate the accuracy of genotype imputation and (iii) to assess the accuracy of genomic selection using true and imputed low-density (LD) single nucleotide polymorphism (SNP) panels to determine a cost-effective strategy for practical implementation of genomic information in tilapia breeding programs. The data set consisted of 5,866 phenotyped animals and 1,238 genotyped animals (108 parents and 1,130 offspring) using a 50K SNP panel. The GWAS were performed using all genotyped and phenotyped animals. The genotyped imputation was performed from LD panels (LD0.5K, LD1K and LD3K) to high-density panel (HD), using information from parents and 20% of offspring in the reference set and the remaining 80% in the validation set. In addition, we tested the accuracy of genomic selection using true and imputed genotypes comparing the accuracy obtained from pedigree-based best linear unbiased prediction (PBLUP) and genomic predictions. The results from GWAS supports evidence of the polygenic nature of FY and HW. The accuracy of imputation ranged from 0.90 to 0.98 for LD0.5K and LD3K, respectively. The accuracy of genomic prediction outperformed the estimated breeding value from PBLUP. The use of imputation for genomic selection resulted in an increased relative accuracy independent of the trait and LD panel analyzed. The present results suggest that genotype imputation could be a cost-effective strategy for genomic selection in Nile tilapia breeding programs.

Recent studies have highlighted both the positive and negative impacts of species invasions. Most of these studies have been conducted on either immobile invasive plants or sessile fauna found at the base of food webs. Fewer studies have examined the impacts of vagile invasive consumers on native competitors. This is an issue of some importance given the controlling influence that consumers have on lower order plants and animals. Here, we present results of laboratory experiments designed to assess the impacts of unintended aquaculture releases of the Nile tilapia (Oreochromis niloticus), in estuaries of the Gulf of Mexico, on the functionally similar redspotted sunfish (Lepomis miniatus). Laboratory choice tests showed that tilapia prefer the same structured habitat that native sunfish prefer. In subsequent interspecific competition experiments, agonistic tilapia displaced sunfish from their preferred structured habitats. When a piscivore (largemouth bass) was present in the tank with both species, the survival of sunfish decreased. Based on these findings, if left unchecked, we predict that the proliferation of tilapia (and perhaps other aggressive aquaculture fishes) will have important detrimental effects on the structure of native food webs in shallow, structured coastal habitats. While it is likely that the impacts of higher trophic level invasive competitors will vary among species, these results show that consequences of unintended releases of invasive higher order consumers can be important.