Nile Tilapia: A Model for Studying Teleost Color Patterns

Comparative Transcriptome Analysis Reveals Differential Cutaneous Gene Expression in the Color Variation of Two Ornamental Discus, Red Melon and Red Cover

Red Melon (RM) and Red Cover (RC) discus (Symphysodon spp.) are ornamental fish varieties that were selectively bred from the wild parental lineages of the brown discus S. aquafaciatus over many generations, resulting in distinct cutaneous patterns from juveniles to adults. To better understand the underlying mechanisms, skin samples were collected from juveniles aged 60 days and adults aged 1 year from RM and RC for investigations. Microscopic observation detected xanthophores and erythrophores in all samples, except RC juveniles with no erythrophores. Melanophores were presented only in RC. The comparative analysis revealed that genes involved in pteridine synthesis (gch1 and zgc:153031), one-carbon metabolism (aldh1l2 and zgc153031), and lipid metabolism (apoda and klf1) were differentially expressed in RM juveniles, which may be associated with the development of erythrophores and xanthophores. The temporal inhibition of melanophore differentiation and development was observed in RM juveniles, coupled with elevated expression of notum2 and sost, two antagonist genes in Wnt-signaling, suggesting their roles in melanophore development. Distinct pigment pattern between RM and RC since the juvenile stage may be driven by the differential expression of multiple axial developmental genes, including GATA, ankyrin, and mitotic spindle orientation proteins. This is the first report to describe the differential growth of cutaneous pigments and the molecular processes involved in red discus. The results provided valuable insights into pigment pattern differences in an interesting ornamental fish model.

Tilapia, a good model for studying reproductive endocrinology

The Nile tilapia (Oreochromis niloticus), with a system of XX/XY sex determination, is a worldwide farmed fish with a shorter sexual maturation time than that of most cultured fish. Tilapia show a spawning cycle of approximately 14 days and can be artificially propagated in the laboratory all year round to obtain genetically all female (XX) and all male (XY) fry. Its genome sequence has been opened, and a perfect gene editing platform has been established. With a moderate body size, it is convenient for taking enough blood to measure hormone level. In recent years, using tilapia as animal model, we have confirmed that estrogen is crucial for female development because 1) mutation of star2, cyp17a1 or cyp19a1a (encoding aromatase, the key enzyme for estrogen synthesis) results in sex reversal (SR) due to estrogen deficiency in XX tilapia, while mutation of star1, cyp11a1, cyp17a2, cyp19a1b or cyp11c1 affects fertility due to abnormal androgen, cortisol and DHP levels in XY tilapia; 2) when the estrogen receptors (esr2a/esr2b) are mutated, the sex is reversed from female to male, while when the androgen receptors are mutated, the sex cannot be reversed; 3) the differentiated ovary can be transdifferentiated into functional testis by inhibition of estrogen synthesis, and the differentiated testis can be transdifferentiated into ovary by simultaneous addition of exogenous estrogen and androgen synthase inhibitor; 4) loss of male pathway genes amhy, dmrt1, gsdf causes SR with upregulation of cyp19a1a in XY tilapia. Disruption of estrogen synthesis rescues the male to female SR of amhy and gsdf but not dmrt1 mutants; 5) mutation of female pathway genes foxl2 and sf-1 causes SR with downregulation of cyp19a1a in XX tilapia; 6) the germ cell SR of foxl3 mutants fails to be rescued by estrogen treatment, indicating that estrogen determines female germ cell fate through foxl3. This review also summarized the effects of deficiency of other steroid hormones, such as androgen, DHP and cortisol, on fish reproduction. Overall, these studies demonstrate that tilapia is an excellent animal model for studying reproductive endocrinology of fish.

Genome editing in East African cichlids and tilapias: state-of-the-art and future directions

African cichlid fishes of the Cichlidae family are a group of teleosts important for aquaculture and research. A thriving research community is particularly interested in the cichlid radiations of the East African Great Lakes. One key goal is to pinpoint genetic variation underlying phenotypic diversification, but the lack of genetic tools has precluded thorough dissection of the genetic basis of relevant traits in cichlids. Genome editing technologies are well established in teleost models like zebrafish and medaka. However, this is not the case for emerging model organisms, such as East African cichlids, where these technologies remain inaccessible to most laboratories, due in part to limited exchange of knowledge and expertise. The Cichlid Science 2022 meeting (Cambridge, UK) hosted for the first time a Genome Editing Workshop, where the community discussed recent advances in genome editing, with an emphasis on CRISPR/Cas9 technologies. Based on the workshop findings and discussions, in this review we define the state-of-the-art of cichlid genome editing, share resources and protocols, and propose new possible avenues to further expand the cichlid genome editing toolkit.

Butylparaben Exposure Induced Darker Skin Pigmentation in Nile Tilapia (Oreochromis niloticus)

Butylparaben (BuP), as an emerging contaminant with endocrine-disrupting effects, may exert effects on skin pigmentation in fish by interfering with the neuroendocrine system. Therefore, models of BuP exposure in Nile tilapia (Oreochromis niloticus) were established by adding different doses of BuP (0, 5, 50, 500, and 5000 ng/L) for 56 days. The obtained results showed that BuP exposure induced darker skin pigmentation, manifested as increased melanin content of skin, while genes related to melanin synthesis, including α-MSH and Asip2, significantly changed. In addition, BuP exposure reduced dopamine and γ-aminobutyric acid content in the brain, which is related to the synthesis of α-MSH. Furthermore, the release of neurotransmitters from the brain is affected by light. Thus, the relative gene expression levels in the phototransduction pathway were evaluated to explore the molecular mechanism of BuP-induced darker skin pigmentation, and the obtained results showed that Arr3a and Arr3b expression was significantly upregulated, whereas Opsin expression was significantly downregulated in a BuP dose-dependent manner, indicating that BuP inhibited phototransduction from the retina to the brain. Importantly, correlation analysis results showed that all melanin indexes were significantly positively correlated with Arr3b expression and negatively correlated with Opsin expression. This study indicated that BuP induced darker skin pigmentation in Nile tilapia via the neuroendocrine circuit, which reveals the underlying molecular mechanism for the effects of contaminants in aquatic environments on skin pigmentation in fish.

MiR-382 Functions on the Regulation of Melanogenesis via Targeting dct in Rainbow Trout (Oncorhynchus mykiss)

MicroRNAs (miRNAs) are a class of endogenous small noncoding RNAs that are involved in a diverse collection of biological processes as important post-transcriptional regulators. However, little is known about the molecular regulatory mechanism of miRNAs in fish skin pigmentation. In this study, we first confirmed that dopachrome tautomerase (dct), a key gene of melanogenesis, is a target of miR-382 in rainbow trout (Oncorhynchus mykiss) using luciferase reporter assay. The analysis of different developmental stages and tissue expression patterns between wild-type and yellow mutant rainbow trout suggested that miR-382 is a potential regulator during the process of skin pigmentation. In vitro, miR-382 mimics in rainbow trout primary liver cells significantly downregulated dct expression and resulted in decreased expression of key melanogenic genes including tyrosine-related protein 1 (tyrp1) and premelanosome protein (pmel), whereas the expression level of dct was markedly increased after transfected with miR-382 inhibitor. In vivo, overexpression of miR-382 by injection of miR-382 agomir significantly depressed the expression of dct in dorsal skin, tail fin, and liver and then reduced the expression levels of tyrp1 and pmel. Furthermore, transfection of miR-382 mimics inhibited cell proliferation and induced apoptosis. Taken together, our results identified a functional role of miR-382 in rainbow trout skin pigmentation through targeting dct, which facilitate understanding the regulatory mechanism of rainbow trout skin color at the post-transcriptional level and provide a theoretical basis for molecular breeding with skin color as the target trait.

Molecular and functional analysis of the microphthalmia-associated transcription factor (mitf) gene duplicates in red tilapia

In vertebrates, the microphthalmia-associated transcription factor (mitf) is at the hub of the melanin synthesis regulation network. However, little information is known about its molecular characterization, expression, location, or function in skin color differentiation and variation of red tilapia. The full-length cDNA sequences (1977 bp and 1999 bp) of mitfa and mitfb, encoding polypeptides of 491 and 514 amino acids, were effectively identified from red tilapia in this study. The Mitfa and Mitfb sequences of red tilapia clustered first with O. aureus, then with other teleost fish, according to phylogenetic analysis. Mitfa and mitfb mRNA were highly expressed in the brain, dorsal skin and eye tissues using quantitative real-time PCR. The mRNA expressions of mitfa and mitfb were the highest in the cleavage stage during the early development of red tilapia. Among three different colors of red tilapia, the expression levels of mitfa and mitfb were highest in the PB (pink with scattered black spots) dorsal skin. After overwintering, the mitfa and mitfb mRNA expressions were high in the dorsal skin of PB (color changed from pink to black). Mitfa and mitfb were mostly found in the epidermal layer of the dorsal skin, according to in situ hybridization (ISH) analysis. After injecting mitf-dsRNA duplicates along the tail vein of red tilapia, the activity of tyrosinase and the level of melanin in the dorsal skin both decreased significantly. The mRNA expressions of mitfa and its downstream genes (tyrb, tyrp1a and dct) decreased, whereas the mRNA expression of mitfb increased after mitfa-dsRNA injection. The mRNA expressions of mitfb, tyrb, tyrp1a and dct decreased, whereas the mRNA expression of mitfa increased after injecting mitfb-dsRNA. These findings suggest that mitf gene duplicates may play an important role in red tilapia skin color differentiation and variation via the melanogenesis pathway.

The Insertion in the 3' UTR of Pmel17 Is the Causal Variant for Golden Skin Color in Tilapia

Understanding of the relationships between genotypes and phenotypes is a central problem in biology. Although teleosts have colorful phenotypes, not much is known about their underlying mechanisms. Our previous study showed that golden skin color in Mozambique tilapia was mapped in the major locus containing the Pmel gene, and an insertion in 3' UTR of Pmel17 was fully correlated with the golden color. However, the molecular mechanism of how Pmel17 determines the golden skin color is unknown. In this study, knockout of Pmel17 with CRISPR/Cas9 in blackish tilapias resulted in golden coloration, and rescue of Pmel17 in golden tilapias recovered the wild-type blackish color, indicating that Pmel17 is the gene determining the golden and blackish color. Functional analysis in vitro showed that the insertion in the 3' UTR of Pmel17 reduced the transcripts of Pmel17. Our data supplies more evidence to support that Pmel17 is the gene for blackish and golden colors, and highlights that the insertion in the 3' UTR of Pmel17 is the causative mutation for the golden coloration.

CRISPR knockouts of pmela and pmelb engineered a golden tilapia by regulating relative pigment cell abundance

Premelanosome protein (pmel) is a key gene for melanogenesis. Mutations in this gene are responsible for white plumage in chicken, but its role in pigmentation of fish remains to be demonstrated. In this study we found that most fishes have two pmel genes arising from the teleost-specific whole genome duplication. Both pmela and pmelb were expressed at high levels in the eyes and skin of Nile tilapia. We mutated both genes in tilapia using CRISPR/Cas9. Homozygous mutation of pmela resulted in yellowish body color with weak vertical bars and a hypo-pigmented retinal pigment epithelium (RPE) due to significantly reduced number and size of melanophores. In contrast, we observed an increased number and size of xanthophores in mutants compared to wild-type fish. Homozygous mutation of pmelb resulted in a similar, but milder phenotype than pmela-/- mutants. Double mutation of pmela and pmelb resulted in loss of additional melanophores compared to the pmela-/- mutants, and also an increase in the number and size of xanthophores, producing a golden body color. The RPE pigmentation of pmela-/-;pmelb-/- was similar to pmela-/- mutants, with much less pigmentation than pmelb-/- mutants and wild-type fish. Taken together, our results indicate that, while both pmel genes are important for the formation of body color in tilapia, pmela plays a more important role than pmelb. To our knowledge, this is the first report on mutation of pmelb or both pmela;pmelb in fish. Studies on these mutants suggest new strategies for breeding golden tilapia, and also provide a new model for studies of pmel function in vertebrates.

Oca2 targeting using CRISPR/Cas9 in the Malawi cichlid Astatotilapia calliptera

Identifying genetic loci underlying trait variation provides insights into the mechanisms of diversification, but demonstrating causality and characterizing the role of genetic loci requires testing candidate gene function, often in non-model species. Here we establish CRISPR/Cas9 editing in Astatotilapia calliptera, a generalist cichlid of the remarkably diverse Lake Malawi radiation. By targeting the gene oca2 required for melanin synthesis in other vertebrate species, we show efficient editing and germline transmission. Gene edits include indels in the coding region, probably a result of non-homologous end joining, and a large deletion in the 3' untranslated region due to homology-directed repair. We find that oca2 knock-out A. calliptera lack melanin, which may be useful for developmental imaging in embryos and studying colour pattern formation in adults. As A. calliptera resembles the presumed generalist ancestor of the Lake Malawi cichlids radiation, establishing genome editing in this species will facilitate investigating speciation, adaptation and trait diversification in this textbook radiation.

Analysis of yellow mutant rainbow trout transcriptomes at different developmental stages reveals dynamic regulation of skin pigmentation genes

Yellow mutant rainbow trout (YR), an economically important aquaculture species, is popular among consumers due to its excellent meat quality and attractive appearance. Skin color is a key economic trait for YR, but little is known about the molecular mechanism of skin color development. In this study, YR skin transcriptomes were analyzed to explore temporal expression patterns of pigmentation-related genes in three different stages of skin color development. In total, 16,590, 16,682, and 5619 genes were differentially expressed between fish at 1 day post-hatching (YR1d) and YR45d, YR1d and YR90d, and YR45d and YR90d. Numerous differentially expressed genes (DEGs) associated with pigmentation were identified, and almost all of them involved in pteridine and carotenoid synthesis were significantly upregulated in YR45d and YR90d compared to YR1d, including GCH1, PTS, QDPR, CSFIR1, SLC2A11, SCARB1, DGAT2, PNPLA2, APOD, and BCO2. Interestingly, many DEGs enriched in melanin synthesis pathways were also significantly upregulated, including melanogenesis (MITF, MC1R, SLC45A2, OCA2, and GPR143), tyrosine metabolism (TYR, TYRP1, and DCT), and MAPK signaling (KITA) pathways. Using short time-series expression miner, we identified eight differential gene expression pattern profiles, and DEGs in profile 7 were associated with skin pigmentation. Protein–protein interaction network analysis showed that two modules were related to xanthophores and melanophores. In addition, 1,812,329 simple sequence repeats and 2,011,334 single-nucleotide polymorphisms were discovered. The results enhance our understanding of the molecular mechanism underlying skin pigmentation in YR, and could accelerate the molecular breeding of fish species with valuable skin color traits and will likely be highly informative for developing new therapeutic approaches to treat pigmentation disorders and melanoma.