Fish Pigmentation Research Articles

Color change and pigmentation in a color polymorphic cichlid fish

In many haplochromine cichlids, body coloration is an important communication cue during social interactions. In some cichlids, individuals can change color, but we have little information about the underlying physiological mechanisms. We examined the regulation of coloration in the color polymorphic cichlid fish Astatotilapia burtoni where males are either blue or yellow. Previous studies implicated the melanocortin system, a neuroendocrine center that regulates pigmentation and the stress response, in regulating the color polymorphism in this species. We found that both blue and yellow males express a high density of yellow xanthophores. Dispersal of xanthophore pigments in both yellow and blue morphs occurred within minutes in a dose-dependent manner. Similarly, exogenous α-melanocyte stimulating hormone (α-MSH, a melanocortin hormone) increased yellowness of the body in a dose-independent fashion. We observed many color changes in males housed in social communities with the proportion of yellow males increasing over the 2-week experimental period. However, color phenotype or color change was not influenced by experimental alteration of the stability of the social hierarchy. The effects of α-MSH suggest that the melanocortin system contributes to the polymorphism in coloration in A. burtoni but the role of social interactions and social stress in regulating color remains unclear.

Differential predation alters pigmentation in threespine stickleback (Gasterosteus aculeatus).

Animal pigmentation plays a key role in many biological interactions, including courtship and predator avoidance. Sympatric benthic and limnetic ecotypes of threespine stickleback (Gasterosteus aculeatus) exhibit divergent pigment patterns. To test whether differential predation by cutthroat trout contributes to the differences in pigmentation seen between the ecotypes, we used a within-generation selection experiment on F2 benthic-limnetic hybrids. After 10months of differential selection, we compared the pigmentation of fish under trout predation to control fish not exposed to trout predation. We found that stickleback exhibited more lateral barring in ponds with trout predation. Ponds with trout were also less turbid, and a greater degree of barring was negatively correlated with the magnitude of turbidity across pond replicates. A more benthic diet, a proxy for habitat use, was also correlated with greater lateral barring and green dorsal pigmentation. These patterns suggest that differential exposure to cutthroat trout predation may explain the divergence in body pigmentation between benthic and limnetic ecotypes.

CRISPR mutagenesis confirms the role of oca2 in melanin pigmentation in Astyanax mexicanus

Understanding the genetic basis of trait evolution is critical to identifying the mechanisms that generated the immense amount of diversity observable in the living world. However, genetically manipulating organisms from natural populations with evolutionary adaptations remains a significant challenge. Astyanax mexicanus exists in two interfertile forms, a surface-dwelling form and multiple independently evolved cave-dwelling forms. Cavefish have evolved a number of morphological and behavioral traits and multiple quantitative trait loci (QTL) analyses have been performed to identify loci underlying these traits. These studies provide a unique opportunity to identify and test candidate genes for these cave-specific traits. We have leveraged the CRISPR/Cas9 genome editing techniques to characterize the effects of mutations in oculocutaneous albinism II (oca2), a candidate gene hypothesized to be responsible for the evolution of albinism in A. mexicanus cave populations. We generated oca2 mutant surface A. mexicanus. Surface fish with oca2 mutations are albino due to a disruption in the first step of the melanin synthesis pathway, the same step that is disrupted in albino cavefish. Hybrid offspring from crosses between oca2 mutant surface and cavefish are albino, definitively demonstrating the role of this gene in the evolution of albinism in this species. This research elucidates the role oca2 plays in pigmentation in fish, and establishes that this gene is solely responsible for the evolution of albinism in multiple cavefish populations. Finally, it demonstrates the utility of using genome editing to investigate the genetic basis of trait evolution.

Skin Spotting Variation Associated with Biometric and Reproductive Parameters in Naturalized Populations of Rainbow Trout, Oncorhynchus mykiss, from Southern Chile

Background:Skin pigmentation in fish is involved in various biological processes. In salmonids, the interactions of skin spottiness with biometric and reproductive parameters are mostly unknown, especially in naturalized populations influenced by different ecological factors.Objective:To associate skin spottiness variation with biometric and reproductive parameters in broodstocks of naturalized rainbow trout populations from southern Chile.Method:The number of dark spots below the lateral line was assessed in male and female broodstocks of rainbow trout from two reproductive seasons, years 2007 and 2012, and then this dataset was associated with biometric and reproductive parameters of the same individuals, using multivariate data analysis in the form of stepwise forward multiple regression.Results:Male body weight from year 2007 had a significant negative influence on the number of dark spots below the lateral line (P< 0.01), while the reproductive variables egg diameter and spawning time of females from years 2007 and 2012, respectively, had a significant positive influence on this parameter (P< 0.01).Conclusion:Our results indicate that there are male biometric parameters with a significant negative influence on skin spottiness. Our data also reveal that some reproductive parameters have a positive influence on skin spottiness. The identification of these reproductive parameters related to spottiness variation would reflect the reproductive quality of female broodstocks living in natural environments.

The integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in Japanese flounder (Paralichthys olivaceus) albinism.

Albinism, a phenomenon characterized by pigmentation deficiency on the ocular side of Japanese flounder (Paralichthys olivaceus), has caused significant damage. Limited mRNA and microRNA (miRNA) information is available on fish pigmentation deficiency. In this study, a high-throughput sequencing strategy was employed to identify the mRNA and miRNAs involved in P. olivaceus albinism. Based on P. olivaceus genome, RNA-seq identified 21,787 know genes and 711 new genes by transcripts assembly. Of those, 235 genes exhibited significantly different expression pattern (fold change ≥2 or ≤0.5 and q-value≤0.05), including 194 down-regulated genes and 41 up-regulated genes in albino versus normally pigmented individuals. These genes were enriched to 81 GO terms and 9 KEGG pathways (p≤0.05). Among those, the pigmentation related pathways-Melanogenesis and tyrosine metabolism were contained. High-throughput miRNA sequencing identified a total of 475 miRNAs, including 64 novel miRNAs. Furthermore, 33 differentially expressed miRNAs containing 13 up-regulated and 20 down-regulated miRNAs were identified in albino versus normally pigmented individuals (fold change ≥1.5 or ≤0.67 and p≤0.05). The next target prediction discovered a variety of putative target genes, of which, 134 genes including Tyrosinase (TYR), Tyrosinase-related protein 1 (TYRP1), Microphthalmia-associated transcription factor (MITF) were overlapped with differentially expressed genes derived from RNA-seq. These target genes were significantly enriched to 254 GO terms and 103 KEGG pathways (p<0.001). Of those, tyrosine metabolism, lysosomes, phototransduction pathways, etc., attracted considerable attention due to their involvement in regulating skin pigmentation. Expression patterns of differentially expressed mRNA and miRNAs were validated in 10 mRNA and 10 miRNAs by qRT-PCR. With high-throughput mRNA and miRNA sequencing and analysis, a series of interested mRNA and miRNAs involved in fish pigmentation are identified. And the miRNA-mRNA regulatory network also provides a solid starting point for further elucidation of fish pigmentation deficiency.

The melanocortin system regulates body pigmentation and social behaviour in a colour polymorphic cichlid fish.

The melanocortin system is a neuroendocrine system that regulates a range of physiological and behavioural processes. We examined the extent to which the melanocortin system simultaneously regulates colour and behaviour in the cichlid fish Astatotilapia burtoni We found that yellow males are more aggressive than blue males, in line with previous studies. We then found that exogenous α-melanocyte-stimulating hormone (α-MSH) increases yellowness of the body and dispersal of xanthophore pigments in both morphs. However, α-MSH had a morph-specific effect on aggression, with only blue males showing an increase in the rate of aggression. Exogenous agouti signalling peptide (ASIP), a melanocortin antagonist, did not affect coloration but reduced the rate of aggression in both colour morphs. Blue males had higher cortisol levels than yellow males. Neural gene expression of melanocortin receptors (mcr) and ligands was not differentially regulated between colour morphs. In the skin, however, mc1r and pro-opiomelanocortin (pomc) β were upregulated in blue males, while asip 1 was upregulated in yellow males. The effects of α-MSH on behaviour and body coloration, combined with morph-specific regulation of the stress response and the melanocortin system, suggest that the melanocortin system contributes to the polymorphism in behaviour and coloration in A. burtoni.

Phaeodactylum tricornutum in finishing diets for gilthead seabream: effects on skin pigmentation, sensory properties and nutritional value

Microalgal biomasses are known to play a major role in fish pigmentation, which is particularly important in farmed fish, since colour and external appearance are the first cue for customers when choosing seafood. A study was undertaken to assess the potential of microalgae biomass from the diatom Phaeodactylum tricornutum as a functional ingredient for gilthead seabream (Sparus aurata) feeds. Three experimental diets were designed: a control diet (CTRL), this same diet supplemented with 2.5% of P. tricornutum wild strain (diet MA20); and a third diet with 2.5% of P. tricornutum biomass (diet MA37) cultivated under different temperature and light regimes that resulted in higher levels of fucoxanthin. Microalgae diets led to a reduction (P < 0.05 in MA37) of whole-body fat and lower lipid retention (P < 0.05 in MA20 and MA37). Microalgae did not impact odour, flavour, whiteness, and fatness perception in cooked fillets. Overall, colour analysis showed that P. tricornutum biomass led to significant differences compared to control in specific areas: the MA37 diet induced a significantly (P < 0.05) lighter and more vivid yellow colouration of seabream operculum (ΔE* ≈ 5) perceptible to the human eye; ventral skin lightness was also affected by the dietary treatments (P = 0.040), being higher for microalgae-fed groups, though this difference was not perceptually strong (ΔE* ≈ 1.7). Phaeodactylum tricornutum biomass can be used as a functional ingredient, improving external pigmentation and thus contributing to meet consumer expectations in relation to farmed gilthead seabream.

Dietary astaxanthin improved the body pigmentation and antioxidant function, but not the growth of discus fish (Symphysodonspp.)

To assess the effects of dietary astaxanthin on the growth and body colour of red discus fish (Symphysodon spp.), synthetic astaxanthin was added into the basal diet (beef heart hamburger) with the levels of 0 (control diet), 50, 100, 200, 300 and 400 mg kg−1 respectively. The six experimental diets were fed to discus fish with an initial body weight of 10.3 ± 0.8 g for 8 weeks. The results showed that the supplementation of 50–200 mg kg−1 astaxanthin had no significant effects on growth performance of discus fish, but the high supplementation of astaxanthin (300 or 400 mg kg−1) significantly reduced the weight gain and increased the feed coefficient ratio (P < 0.05). After 4 or 8 weeks of feeding, the L* (lightness) values in astaxanthin-supplemented groups were significantly lower, while a* (redness), b* (yellowness) and skin astaxanthin contents were significantly higher than the control group (P < 0.05). When the astaxanthin supplementation reached 200 mg kg−1, skin redness and astaxanthin contents remained relatively stable. When b* was relatively stable, the supplemental astaxanthin was 300 (4 weeks) and 50 mg kg−1 (8 weeks) respectively. With the supplemental astaxanthin increasing, the astaxanthin retention rate significantly decreased and hepatic total antioxidant capacity was strengthened. The dietary astaxanthin also significantly increased the reduced glutathione level (P < 0.05) when the astaxanthin inclusion was higher than 50 mg kg−1. The above results showed that dietary astaxanthin could effectively improve the skin pigmentation of red discus fish in 4 weeks and the supplementation level was suggested to be 200 mg kg−1.

The Involvement of Mig1 from Xanthophyllomyces dendrorhous in Catabolic Repression: An Active Mechanism Contributing to the Regulation of Carotenoid Production.

The red yeast X. dendrorhous is one of the few natural sources of astaxanthin, a carotenoid used in aquaculture for salmonid fish pigmentation and in the cosmetic and pharmaceutical industries for its antioxidant properties. Genetic control of carotenogenesis is well characterized in this yeast; however, little is known about the regulation of the carotenogenesis process. Several lines of evidence have suggested that carotenogenesis is regulated by catabolic repression, and the aim of this work was to identify and functionally characterize the X. dendrorhous MIG1 gene encoding the catabolic repressor Mig1, which mediates transcriptional glucose-dependent repression in other yeasts and fungi. The identified gene encodes a protein of 863 amino acids that demonstrates the characteristic conserved features of Mig1 proteins, and binds in vitro to DNA fragments containing Mig1 boxes. Gene functionality was demonstrated by heterologous complementation in a S. cerevisiae mig1- strain; several aspects of catabolic repression were restored by the X. dendrorhous MIG1 gene. Additionally, a X. dendrorhous mig1- mutant was constructed and demonstrated a higher carotenoid content than the wild-type strain. Most important, the mig1- mutation alleviated the glucose-mediated repression of carotenogenesis in X. dendrorhous: the addition of glucose to mig1- and wild-type cultures promoted the growth of both strains, but carotenoid synthesis was observed only in the mutant strain. Transcriptomic and RT-qPCR analyses revealed that several genes were differentially expressed between X. dendrorhous mig1- and the wild-type strain when cultured with glucose as the sole carbon source. The results obtained in this study demonstrate that catabolic repression in X. dendrorhous is an active process in which the identified MIG1 gene product plays a central role in the regulation of several biological processes, including carotenogenesis.

Image analysis-based classification of pigmentation patterns in fish: A case study of pseudo-albinism in Senegalese sole

We present new objective tools for extraction and classification of skin colour and textural features in fish using a Gray Level Co-Occurrence matrix (GLCM) method followed by data dimension reduction procedures. To achieve this, we examined the skin pigmentation patterns in Senegalese sole, Solea senegalensis early juveniles showing several degrees of pigmentation patterns ranging from pseudo-albinosis to normal pigmentation. Four textural descriptors were chosen to extract the textural features of sole skin from the GLCM image (contrast, energy, homogeneity and correlation). Effective classification and discrimination procedures of sole skin textural descriptors were analyzed and compared by means of Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA). Results indicated that LDA was more suitable for this task and by using it we could easily differentiate between albino and pseudo-albino soles. Therefore, we propose an open source classification system based on image analysis that can be used in studies on fish pigmentation patterns and defects. The description of the work contained herein also suggests how this classification system, together with an appropriately designed mechanical sorting system, might be used in separating abnormal fish during aquaculture production. Statement of relevanceThis contribution presents new tools for extraction and classification of skin colour and textural features in fish using a Gray Level Co-Occurrence matrix (GLCM) method followed by data dimension reduction procedures. These procedures are of special interest in flatfish hatcheries where pigmentary disorders are common; the use of the image analysis procedures may allow the proper identification of malpigmented fish and the assessment of their quality in terms of pigmentation patterns.

당근추출물의 참돔(Pagrus major) 치어 표피색 및 혈청 라이소자임 활성에 대한 효과

The effect of dietary carrot extract on skin pigmentation and non-specific immunity of red seabream was evaluated in a six-week feeding trial compared to that of astaxanthin. Fish were fed different experimental diets supplemented with three levels of carrot extract (30, 100, and 300 mg <TEX>${\beta}$</TEX>-carotene/kg diet or CE30, CE100, and CE300), 100 mg astaxanthin/kg diet (AXT100), or a diet without supplement as control for 6 weeks. Our results revealed that the specific growth rate and feed conversion rate were not significantly (p>0.05) affected by carrot extract or astaxanthin supplementation for 6 weeks. After 3 weeks of feeding, the dietary carrot extract significantly (p<0.05) influenced the redness (<TEX>$a^*$</TEX>) and hue (<TEX>$H^*{_{ab}}$</TEX>) of fish skin. CE300 showed the highest <TEX>$a^*$</TEX> and the lowest <TEX>$H^*{_{ab}}$</TEX>, suggesting that carrot extract increased the redness of skin color. However, after 6 weeks of feeding, dietary carrot extract significantly (p<0.05) increased the values of yellowness <TEX>$b^*$</TEX> at all three levels. In contrast, AXT100 significantly (p<0.05) increased the values of <TEX>$a^*$</TEX> but decreased the value of <TEX>$H^*{_{ab}}$</TEX>. Only CE300 significantly (p<0.05) increased the serum lysozyme activity. These findings suggest that dietary carrot extract can be utilized as a natural feed additive to improve skin pigmentation and health condition of fish.

Heart pigmentation in the gray bichir, Polypterus senegalus (Actinopterygii: Polypteriformes).

The occurrence of pigment cells in the heart is well documented in amphibians, birds and mammals. By contrast, information on heart pigmentation in fish is extremely sparse. The aim is to report the presence of pigment cells over the entire surface of the heart in the gray bichir, Polypterus senegalus. The sample consisted of 12 hearts, which, after gross anatomical examination, were studied using histochemical and immunohistochemical techniques for light microscopy, and transmission electron microscopy. The pigment cells were located in the subepicardium, showing a regular distribution pattern across the whole heart, except for the anterior end of the outflow tract, where the pigmentation was much more intense. The cells contained dark, ovoid-shaped organelles which was consistent with a melanosome cell identity. As in other vertebrates, the physiological role of the pigment cells in the heart of the gray bichir is unknown. The absence of such cells in hearts of other polypteriforms suggests that cells containing melanin are not essential for normal fish heart function. Basing on literature data concerning tetrapods, it can be inferred that the pigment cells of the heart of the gray bichir derive from the neural crest. If this were true, our findings would provide the first evidence for the presence of neural crest-derived cells in the subepicardium of adult hearts of early actinopterygians.

Origin of fish pigment cell for pattern

Making Stripes Zebrafish stripes arise from the interactions of pigment cells: black melanophores, iridescent iridophores, and yellow-orange xanthophores. Melanophores and iridophores develop from nerve-associated stem cells, but the origin of xanthophores is unclear. Two studies now reveal that adult xanthophores originate from xanthophores in embryonic and larval fish, when they proliferate to cover the skin before the arrival of black and silver cells in a striped arrangement. Mahalwar et al. show that xanthophores change their final shape and color depending on their location. In black cells, xanthophores appear faint and stellate, but in silver cells, they are bright and compact. Precise superposition creates the blue and golden colors. McMenamin et al. observe the loss of pigment in embryonic xanthophores and the later reappearance in the adult. They show that redifferentiation depends on the thyroid hormone that also limits melanophore population expansion. Science , this issue p. [1362][1] and p. [1358][2] ![Figure][3] PHOTO: LARISSA B. PATTERSON AND DAVID M. PARICHY [1]: /lookup/volpage/345/1362?iss=6202 [2]: /lookup/doi/10.1126/science.1256251 [3]: pending:yes

Local reorganization of xanthophores fine-tunes and colors the striped pattern of zebrafish.

The pattern of alternating blue and golden stripes displayed by adult zebrafish is composed of three kinds of pigment cells: black melanophores, yellow xanthophores, and silvery-blue iridophores. We analyzed the dynamics of xanthophores during stripe morphogenesis in vivo with long-term time-lapse imaging. Larval xanthophores start to proliferate at the onset of metamorphosis and give rise to adult xanthophores covering the flank before the arrival of stem-cell-derived iridophores and melanophores. Xanthophores compact to densely cover the iridophores forming the interstripe, and they acquire a loose stellate shape over the melanophores in the stripes. Thus, xanthophores, attracted by iridophores and repelling melanophores, sharpen and color the pattern. Variations on these cell behaviors may contribute to the generation of color pattern diversity in fish.

Effects of dietary antioxidant of tomato extract and lycopene on Carassius auratus and Xiphophorus maculatus

ABSTRACTObjective. Evaluate the effect on tegument pigmentation, survival, growth and antioxidant capacity in diets supplemented with tomato extract and lycopene as additives in experimental feed for Carassius auratus and Xiphophorus maculatus. Materials and methods. The additives were added in different concentrations to a basic diet. We performed beginning and an ending biometrics for 100% of the population in each bioassay. The growth and survival of organisms were evaluated. The antioxidant capacity was analyzed by ABTS assay, both in the tomato extract sample as well as in foods used in different bioassays. The concentration of lycopene was determined in food and liver and muscle samples of fish fed with it. Acquired pigmentation of fish was assessed through photographs analyzed with Adobe Photoshop®. The results were evaluated by analysis of variance, and when differences were found (p&lt;0.05) the means were compared by the Tukey test. Results. No significant effect (p&gt;0.05) on pigmentation and growth of the organisms under the established experimental conditions was obtained. Significant differences in antioxidant capacity (p&lt;0.05) were obtained in foods with added lycopene. Conclusions. The inclusion of lycopene or tomato extract in food for the organisms used is not recommended to improve pigmentation, but further studies are needed to demonstrate antioxidant effect.

Effect of Plant Meal as a Carotenoid Source on the Development of Pigmentation in Dwarf Gourami, Colisa lalia (Hamilton, 1822)

Dwarf gourami, (Colisa lalia) is an ornamental fish of great economic importance which fetches a good price in market because of its colour and behaviour. The pigmentation of fish is one of the important qualities which attract the consumer. Carotenoids are responsible for pigmentation in skin of the ornamental fish. In the present experiment marigold (Calenduleae officinalis) petal powder was used as a carotenoid source for enhancing pigment in C. lalia. Experiment was conducted for 40 days in three groups. Carotenoid content in the tissue of the three groups was analysed at the end of the experiment. The present study showed that brightness and colour of C. lalia can be enhanced by adding the marigold petal powder in the diet of the fish by increasing carotenoid content in the tissue of the fish. 10 g per 100 g of marigold petal powder in diet was found to be more effective as compared to lower doses as given to other groups in order to enhance the carotenoid content in dwarf gourami. Total maximum carotenoid content (0.121 μg per wet weight of tissue) was recorded in the group fed with 10.0 g marigold petal powder which was significantly different (P < 0.05) from the other groups.

The sensitivity of Turing self-organization to biological feedback delays: 2D models of fish pigmentation

Turing morphogen models have been extensively explored in the context of large-scale self-organization in multicellular biological systems. However, reconciling the detailed biology of morphogen dynamics, while accounting for time delays associated with gene expression, reveals aberrant behaviours that are not consistent with early developmental self-organization, especially the requirement for exquisite temporal control. Attempts to reconcile the interpretation of Turing's ideas with an increasing understanding of the mechanisms driving zebrafish pigmentation suggests that one should reconsider Turing's model in terms of pigment cells rather than morphogens (Nakamasu et al., 2009, PNAS, 106: , 8429-8434; Yamaguchi et al., 2007, PNAS, 104: , 4790-4793). Here the dynamics of pigment cells is subject to response delays implicit in the cell cycle and apoptosis. Hence we explore simulations of fish skin patterning, focussing on the dynamical influence of gene expression delays in morphogen-based Turing models and response delays for cell-based Turing models. We find that reconciling the mechanisms driving the behaviour of Turing systems with observations of fish skin patterning remains a fundamental challenge.

Self-organized optical device driven by motor proteins

Protein molecules produce diverse functions according to their combination and arrangement as is evident in a living cell. Therefore, they have a great potential for application in future devices. However, it is currently very difficult to construct systems in which a large number of different protein molecules work cooperatively. As an approach to this challenge, we arranged protein molecules in artificial microstructures and assembled an optical device inspired by a molecular system of a fish melanophore. We prepared arrays of cell-like microchambers, each of which contained a scaffold of microtubule seeds at the center. By polymerizing tubulin from the fixed microtubule seeds, we obtained radially arranged microtubules in the chambers. We subsequently prepared pigment granules associated with dynein motors and attached them to the radial microtubule arrays, which made a melanophore-like system. When ATP was added to the system, the color patterns of the chamber successfully changed, due to active transportation of pigments. Furthermore, as an application of the system, image formation on the array of the optical units was performed. This study demonstrates that a properly designed microstructure facilitates arrangement and self-organization of molecules and enables assembly of functional molecular systems.

MicroRNA regulation of skin pigmentation in fish

Summary MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play crucial roles in numerous biological processes. However, the role of miRNAs in skin color determination in fish has not been completely determined. Here, we identified that 13 miRNAs are differentially expressed between red and white skin. The analysis of miRNA spatial and temporal expression patterns suggests that miR-429 is a potential regulator of skin pigmentation. miR-429 silencing results in an obvious change in skin pigmentation. Bioinformatics analysis and a luciferase reporter assay show that miR-429 directly regulates expression of Foxd3 by targeting its 3′-untranslated (3′-UTR) region. miR-429 silencing leads to a substantial increase in the expression of Foxd3 in vivo, thereby repressing the transcription of MITF and its downstream genes, such as TYR, TYRP1 or TYRP2. These findings would provide a novel insight into the determination of skin color in fish.

Mapping of pigmentation QTL on an anchored genome assembly of the cichlid fish, Metriaclima zebra

BackgroundPigmentation patterns are one of the most recognizable phenotypes across the animal kingdom. They play an important role in camouflage, communication, mate recognition and mate choice. Most progress on understanding the genetics of pigmentation has been achieved via mutational analysis, with relatively little work done to understand variation in natural populations. Pigment patterns vary dramatically among species of cichlid fish from Lake Malawi, and are thought to be important in speciation. In this study, we crossed two species, Metriaclima zebra and M. mbenjii, that differ in several aspects of their body and fin color. We genotyped 798 SNPs in 160 F2 male individuals to construct a linkage map that was used to identify quantitative trait loci (QTL) associated with the pigmentation traits of interest. We also used the linkage map to anchor portions of the M. zebra genome assembly.ResultsWe constructed a linkage map consisting of 834 markers in 22 linkage groups that spanned over 1,933 cM. QTL analysis detected one QTL each for dorsal fin xanthophores, caudal fin xanthophores, and pelvic fin melanophores. Dorsal fin and caudal fin xanthophores share a QTL on LG12, while pelvic fin melanophores have a QTL on LG11. We used the mapped markers to anchor 66.5% of the M. zebra genome assembly. Within each QTL interval we identified several candidate genes that might play a role in pigment cell development.ConclusionThis is one of a few studies to identify QTL for natural variation in fish pigmentation. The QTL intervals we identified did not contain any pigmentation genes previously identified by mutagenesis studies in other species. We expect that further work on these intervals will identify new genes involved in pigment cell development in natural populations.