AQUAPEDIA / MEDAKAPEDIA / ORIGINAL ENGLISH RESEARCH

The Medaka Classification Field Guide

An independently written English guide to the visible traits, Japanese terminology, naming, and breeding questions used in the 2025 JMA classification system.

13 topical studies · 63 Japanese classification terms · 54 independently written breeder questions.

Original Aquapedia educational commentary. This is not a translation, substitute edition, or publication approved by the Japan Medaka Association. The publisher's original text, graphics, photos, charts, and page layouts are not reproduced.

JMA 2025, pp. 5–14, 68–73 · JMA primary source

1. What a classification can—and cannot—tell you

Ornamental medaka have accumulated an extraordinary range of visible features. Sellers often name a newly bred line to honor the breeder, describe its look, or distinguish a commercial selection. A name on a sales listing may therefore communicate a family history, a memorable brand, a phenotype, or some mixture of all three. Classification becomes useful when those different meanings are made explicit.

The central practical distinction is between a trait and a line. A trait is something observers can describe in the fish: a pattern on the scales, an eye condition, a particular form of reflective light, or a fin and body shape. A line describes ancestry or deliberate selection over generations. Two unrelated lines can independently produce similar-looking fish; offspring from the same line can vary dramatically in appearance. Neither relationship should be inferred solely from a nickname.

The Japan Medaka Association has developed standardized vocabulary so that a fish may be described through combinations of visible characteristics rather than by house name alone. The association has revised its guidance as new forms appear. Its nomenclature is voluntary and is not a genetic test, legal registration, or proof that a seller's pedigree is genuine.

Aquapedia records these as separate fields: observed phenotype; breeder or commercial name; claimed parental history with provenance; the evidence supporting a specific gene association; and confidence or unresolved questions. A label that is useful in the marketplace is not automatically a scientific genotype.

JMA 2025, pp. 11–15 and trait chapters · JMA primary source

2. A repeatable identification workflow

Begin with a healthy mature fish in more than one viewing position. From above, evaluate the overall silhouette, dorsal reflections, scattered scale sparkle, color patches, and the caudal fin. From the side, inspect the cheek and gill cover, the eye, the belly and peritoneum, the dorsal and anal fin shapes, and pigment present in fin rays or membranes. Photograph each view using neutral lighting.

Use consistent settings whenever you compare siblings. The perceived darkness of a fish can change with the container color, illumination, camera white balance, and its acclimation history. A black fish photographed in a dark tub should not be treated as equivalent evidence to the same fish after a controlled observation in a pale tub. Record the setup; do not subject the animal to abrupt temperature or water-quality changes simply to improve photographs.

Identify broad categories separately instead of forcing a famous strain name onto a fish: body color, scale transparency, eyes, reflective-pigment effects, pattern, fin structure, and overall body form. Then record any additional descriptors. If the trait is subtle or appears in only one individual, note it as provisional and seek repeat observations or a knowledgeable second reviewer.

Do not confuse phenotype with genetic certainty. Family photographs and repeated generations can support heritability, but a visually obvious effect does not by itself establish a named allele, its mode of inheritance, or genetic identity between independent breeder lines.

JMA 2025, pp. 19–28 · JMA primary source

3. Body color: what the background really shows

Color terms in the Japanese classification system are practical visual descriptions, not a single-color digital standard. Viewing light, maturity, sex, nutrition, and the combination of pigment cells influence what the eye sees. A sample judged yellow under one light source may look warmer under another, so keep lighting and background consistent and document the exact conditions of comparison.

The core 2025 vocabulary includes brown, yellow, white, blue, black, golden, amber, vermilion red, orange, and pink. The informal marketing term attached to a fish may name a color more poetically than the formal trait term does. It helps to preserve the original Japanese term where its conventional English translation could be confused with a specific commercial strain.

Separate a base body color from black mottling, reflective light, and colored fins. A fish that appears white with black patches is not automatically an independently inherited two-color genotype; it may be a body-color designation plus an observed mottled pattern. Likewise, intense coloration in fins may warrant a fin-related qualifier without changing the body-color term.

Some blue-class fish are described as green-tinted. The 2025 guidance treats certain green expressions within blue-related descriptions even though their pigment biology is more complicated than a literal reading of 'blue without yellow' might suggest. Aquapedia marks such placements as classification conventions rather than settled genetic proofs.

JMA 2025, pp. 29–31, 68–70; 2025 trait revisions · JMA primary source

4. Transparent, semi-transparent, and mirror-scale effects

Transparency is best evaluated at defined anatomical landmarks. The cheek and gill cover are especially useful: a classic transparent-scale appearance can expose red coloration from underlying tissue because reflective cells are reduced there. Not all lightly colored or translucent-bodied fish belong to that category, and an individual may look different on its two sides.

Semi-transparent scale—frequently encountered under the historical hobby term 'Aurora'—describes a more subtle appearance associated with altered reflective coverage. 'Aurora ancestry' and 'Aurora-looking fish' are not interchangeable statements. The first refers to a lineage claim; the second is a visual description that can be assessed directly.

Strongly see-through appearances, panda eyes, and albino conditions can overlap in ways that change what is visible through the head and abdomen. Classify eye pigment independently from scale transparency rather than assuming that one automatically proves the other.

Kagami (カガミ) is recorded in the 2025 material as a mirror-scale-related common descriptor. It should be treated as a scale characteristic, not as a standalone body color or proof of a single lineage. Record whether mirror-like plate reflections are uniform, how many scales are involved, and whether their expression persists as the fish matures; confirm the original Japanese wording before assigning an official composite name.

JMA 2025, pp. 32–38 · JMA primary source

5. Eye changes: an identification guide

Several eye traits that share a dramatic appearance have different diagnostics. For example, an albino-like red eye, a ruby-colored eye with some residual pigment, and a dark panda-style eye cannot be safely grouped under one genetic label. Compare the eye from above, the side, and a slight diagonal angle, without shining a harsh light directly into the animal's eyes.

Shape also matters. A protruding eye is not the same thing as a large eye: one describes the eye's position or projection, the other its size relative to the head. An eye angled toward the front creates yet another appearance. Reduced-eye traits can occur asymmetrically. Make records for left and right eyes separately when needed.

The more unusual eye forms, including bubble-like structures or highly reflective iris appearances, should be documented with clear photos and followed by an animal-welfare assessment. Never breed or grade a fish solely for an extreme eye condition without considering visibility, feeding success, and normal swimming.

JMA 2025, pp. 39–46 · JMA primary source

6. Understanding lamé, external light, and internal light

The word 'shimmer' hides several different structures. Lamé describes conspicuous sparkling points associated with individual scales. External body light is a broader reflective effect appearing on or along the surface of the back and sometimes other positions; it is central to the historic Miyuki phenotype. Internal body light, whole-body internal effects, and peritoneal reflections are not equivalent just because all can look bluish or metallic.

Under a diffuse overhead light, move the camera rather than the fish to test how a reflection behaves. Lamé remains associated with separate scales; external light often forms an elongated field or localized dorsal patch; internal-looking highlights appear beneath the skin in a different optical position. Multiple effects can coexist in one individual, so record each independently.

The Japanese vocabulary distinguishes colors, locations, and shapes of external illumination. A silver-white streak along the back, a pale head-only reflection, and an outline that follows individual scales should not all be labeled with one trade name. Scale-outlined light (Rinkō) and scattered Lamé may produce superficially similar photographs but differ on close inspection.

A Hikari body form can show dorsal silver reflection. That does not automatically mean the fish has the external-light trait: Hikari is fundamentally a body/fin configuration, while external light can appear in several body forms. Check the caudal and dorsal fins to separate those descriptions.

The genetics behind many ornamental reflective phenomena are not established at the level of a single causal variant in every commercial strain. Distinguish JMA's usable visual vocabulary from genomic research claims.

JMA 2025, pp. 47–48 · JMA primary source

7. Patterned fish: patches versus scale edging

Two dark-pattern categories are easily confused in small images. Buchi is irregular, patch-like black marking that can occupy distinct parts of the body. Black Rim emphasizes scales, giving the appearance of dark edging or organized pigment across multiple adjacent scales. One close-up image of a flank is rarely enough for a defensible assessment.

Dark markings may change in strength depending on the rearing background. Some selected lines retain deep black coloration even against a pale surface. The response to background belongs in observation notes, not in an invented claim about a universal gene. When recording red-and-white or three-color fish, write down the actual colors and black-pattern expression visible in each individual.

A breeder nickname may describe a visually balanced pattern even though pattern placement varies from offspring to offspring. Quality grading can be a separate judgment from trait identification: 'this fish has distinct black patches' is observational; 'this is the best balanced tricolor' is a preference that needs a disclosed judging standard.

JMA 2025, pp. 49–57 · JMA primary source

8. The many different ways fins change

Fin terminology is unusually prone to name collisions. A divided dorsal fin, a diamond-shaped caudal fin, a broad fin, and dramatically elongated fin tissue may all appear on fish marketed with fanciful names. Accurate identification starts by asking which fin is affected, which portion changed, and whether the modification is symmetric.

Samurai concerns splitting of the dorsal-fin structure. Hishio, a diamond-tail form, relates to the tail shape in fish that do not otherwise express the full Hikari body configuration. Maruko denotes absence of the dorsal fin. Meller and Swallow describe other distinctive patterns of altered fin development; these are not catch-all synonyms for ordinary long-finned fish.

Several different long-fin categories appear in modern Japanese terminology. A fish should not be labeled 'real longfin' just because it appears larger or older than an average fish. Measure and photograph comparable fish of similar body length and stage of maturity.

In show records, include the dorsal, caudal, anal, and pelvic fin appearances and whether asymmetry is intentional, stable, or plausibly due to damage. A torn fin or poor regrowth is not a breeding trait. Pay special attention to mobility and feeding when selecting fish with extreme fin length.

JMA 2025, pp. 58–60 · JMA primary source

9. Standard, Hikari, Daruma, and combined body forms

Hikari body form is recognized chiefly by the caudal and dorsal/anal fin configuration, including a conspicuous diamond-like tail. Strong dorsal brightness can accompany it, but lack of obvious dorsal shine does not necessarily rule it out. It is important not to diagnose the form on light alone.

Daruma fish are shortened-bodied. Breeders also use semi-Daruma for intermediate forms. Different degrees of shortening can exist among related offspring, so an unusually deep body on its own should not be used as a final classification. Short-bodied individuals may require extra attention to water quality, stable temperatures, feeding, and swimming ability.

Hikari-Daruma combines the visible shortened-body and Hikari fin/body characteristics. When recording such fish, separate the two components rather than assuming their combined expression has a uniquely verified genotype. Check for spinal curvature or other health issues before assigning breeding quality.

JMA 2025, pp. 61–67; September 2025 supplementary table · JMA primary source

10. Supplementary terms and the 2025 additions

JMA's supplementary vocabulary captures special appearances that may not be a top-level body color, pattern, or body-form category. Examples include unusually striking fin coloration (Hirebi), blue peritoneal appearance, changes in internal black pigmentation, certain illumination locations, background-response behavior, and newer common descriptors. These should be recorded as supplements to the main observed phenotype, not automatically promoted into wholly separate varieties.

The September 2025 list includes terms such as Kagami, Hige, Apex/Top Eye, Mosaic Panda, See-through, Side Light, and Powder among the common supplementary descriptors. Their casual English renderings are only orientation aids; the Japanese official terminology and its specific diagnostic criteria remain authoritative. Some terms describe localized structures or combinations that would be misleading if simplified to a general color.

A practical record should pair the Japanese term with a photograph of the feature, the viewing angle, and a status such as 'visible,' 'possible,' or 'not established.' Where the diagnostic detail in the original material is unclear, use the Japanese name and mark the English gloss provisional rather than creating a definitive new definition.

JMA 2025, pp. 68–73 and 74–84 · JMA primary source

11. Traits, inheritance, and why dominance cannot be guessed

A heritable visible characteristic is not automatically a simple dominant allele. Incomplete dominance, multiple contributing loci, modifier genes, developmental variation, age, sex, and environmental influences can produce overlapping appearance. A single attractive F1 fish does not establish how the feature will behave through later generations.

Use a pedigree with dated crosses, photographed parents, offspring counts, and known rearing conditions. For each generation, count phenotype classes and compare them with the predictions of several inheritance models. Where a marker or causal gene has actually been identified in primary research, cite the specific study; otherwise label 'dominant,' 'recessive,' and 'polygenic' as hypotheses rather than facts.

Background adaptation, nutrition, lighting, and maturation can strengthen or weaken visible colors. These can change an individual's appearance without creating a new heritable form. Evaluate stability across siblings, settings, and generations before claiming a distinct strain.

A fish can possess genetic variants that do not visibly express a named feature, and appearance cannot reliably reveal every hidden allele. JMA's visual classification is designed for practical communication; it is not a system for sequencing or assigning complete genotypes.

JMA 2025, pp. 70–84 · JMA primary source

12. From an attractive fish to a documented breeding line

Start with the selection goal stated in observable terms: for example, consistent side-scale reflection, a particular combination of body color and distinctive fin shape, or a reliable lack of background fading. Keep the original breeder name if it is known, but record the physical traits separately and do not add unverified parentage to a public genealogy diagram.

Photograph the founders, record mating dates, hatch and survival counts, and tag each generation. When offspring vary, report the full distribution rather than showing only the best specimen. A useful project log tracks the proportion expressing the target trait, sex ratios where measurable, deformities, fertility, and whether the color expression changes after maturation.

A new trait discovery differs from a new arrangement of already recognized traits. Both may be meaningful breeding achievements. In either case, documenting multigenerational transmission is stronger evidence than a one-time cross. If a show or association recognition is claimed, link to the dated judging or recognition record rather than repeating promotional copy as an established fact.

Preserve animal welfare in the selection criteria. Severe spinal changes, impaired eyesight, or extreme fins may reduce swimming, feeding, and survival. The breeding log should record those effects transparently instead of treating every visually unusual outcome as a desirable new variety.

Cross-cutting Aquapedia editorial synthesis · JMA primary source

13. Reading breeder listings and entering data into Aquapedia

An online listing can truthfully describe what the fish looks like yet overstate its documented ancestry. Ask for original images of the actual stock, parent and sibling photographs where available, the breeder's stated strain name in Japanese and romanization, and whether a line is a locally bred descendant or a recent import. Record provenance rather than inferring it from an attractive photograph.

Use separate fields for 'trade name,' 'JMA-observed traits,' 'breeder-reported ancestry,' 'published evidence,' and 'DNA-confirmed genotype.' If only the color/fin combination is visible, that still makes a useful descriptive record. It does not license an invented genealogy linking unrelated breeders.

In Aquapedia, label uncertainty visibly: VERIFIED when an authoritative source establishes a fact, BREEDER-REPORTED when a named breeder asserts it, COMMUNITY USAGE for common trade terminology, and UNKNOWN when parentage or the causal genetic mechanism is not documented. Link the source next to the claim and date the observation.

FIELD IDENTIFICATION

2025 Japanese trait vocabulary: an English observation atlas

Use these original observational notes to recognize 2025 classification vocabulary. These descriptions are not verbatim translations of JMA entries. English glosses are aids to reading, not a replacement for the association's official Japanese criteria.

Body-color vocabulary

Broad visual categories; shade, reflective overlays, and fin pigment should be documented separately. Source: JMA 2025 pp. 19–28.

Japanese termEnglish reading aidField observation / distinction
茶 / ChaBrownBaseline earthy coloration; document whether it is genuinely brown rather than dark blue under warmer lighting.
黄 / KiYellowYellow-bodied fish range widely in depth and can be visually affected by background and feed.
白 / ShiroWhiteRecord brightness, cream undertones and fin color when distinguishing white from very pale pink.
青 / AoBlueA muted blue or slate appearance; greenish and purple-looking expressions need precise notes, not invented separate genotype labels.
ブラックBlackCheck melanin intensity and whether the fish fades against a light container over time.
黄金 / ŌgonGoldenWarm metallic-looking body color; compare pigmentation separately from overlying reflective traits.
琥珀 / KohakuAmberBrown-orange or amber coloration; fin and light effects can alter perception.
朱赤 / ShuakaVermilion redThe established reddish-orange family associated with names such as Yang Guifei; evaluate color in consistent light.
オレンジOrangeIntermediate warm coloration; don't classify only by an oversaturated sales photograph.
ピンクPinkPale rosy appearance; fins can help distinguish it from cream-white or lightly pigmented white fish.

Scale appearance

Eye color and transparency are separate dimensions. Source: JMA 2025 pp. 29–31, 68–70.

Japanese termEnglish reading aidField observation / distinction
透明鱗 / TōmeirinTransparent scaleLook closely at the cheek/gill-cover region and record expression on each side.
半透明鱗 / HantōmeirinSemi-transparent scale (Aurora appearance)A subtler translucence; distinguish appearance from claimed Aurora-line ancestry.
カガミ / KagamiMirror-scale common descriptorA scale effect rather than a body color; keep original term until exact diagnostic criteria are reviewed.

Eyes

Compare pupils, eye position, reflection and both sides of the head. Source: JMA 2025 pp. 32–38.

Japanese termEnglish reading aidField observation / distinction
アルビノAlbinoRed-translucent eye appearance from strongly reduced melanin; do not assume the same allele across lines.
パンダPandaVery dark-looking eyes associated with reduced reflective coverage; side and top views may differ.
ルビーアイRuby eyeWine-red or dark ruby pupil; distinguish from classic albino and angle-changing red eyes.
スモールアイSmall eyeReduced-looking dark eye area; evaluate left and right eyes, and watch welfare.
出目 / DeméProtruding eyeDistinguish positional projection from overall enlargement.
目前 / MemaeForward-oriented eyeEye direction is displaced toward the fish's front; photograph from the front.
ビッグアイBig eyeDisproportionately large eye; enlargement does not imply protrusion.
水泡眼 / SuihōganBubble eyeUnusual bubble-like tissue near an eye; identify carefully and prioritize welfare.
アースアイEarth eyeA recognized eye-effect label; verify the precise Japanese feature criteria before formal naming.
プラチナアイPlatinum eyeA reflective eye-effect category; use side-angle close-ups and retain the Japanese label.

Reflective cells and light

Not all metallic effects are the same trait. Source: JMA 2025 pp. 39–46.

Japanese termEnglish reading aidField observation / distinction
ラメ / LaméLaméSeparate reflective points on individual scales; note coverage and color distribution.
体外光 / TaigaikōExternal body lightSurface dorsal or localized field of light; record color, thickness and location.
体内光 / TainaikōInternal body lightA deeper optical effect from internal-looking pigmentation or reflection.
全身体内光Whole-body internal lightA more widespread internally located light appearance; do not conflate with a bright back.
腹膜光 / FukumakukōPeritoneal lightLight associated with the abdominal lining; photograph lateral and underside views when possible.
ヒレラインFin lineA fin-related reflective line; describe which fin and where the line appears.
頭光 / TōkōHead light (external-light qualifier)Reflection localized toward the head rather than assuming continuous dorsal light.
横光 / YokohikariSide light (external-light qualifier)Reflection along the flank rather than the customary top-of-back position.
鱗光 / RinkōScale-outlined external lightLight tracing outlines of scales; a different diagnostic from scattered Lamé.
スポットラメSpotted external-light appearanceLocalized patches of light; the historical term is a light-shape qualifier, not necessarily ordinary Lamé.

Pattern

Pattern presence and aesthetic balance are different assessments. Source: JMA 2025 pp. 47–48.

Japanese termEnglish reading aidField observation / distinction
斑 / BuchiMottledIrregular black patches; describe number, location, size and stability.
ブラックリムBlack RimDark pigment emphasizing individual scale boundaries; compare close-ups before naming.

Fin modification

Which fin changes is usually more important than a marketing adjective. Source: JMA 2025 pp. 49–57.

Japanese termEnglish reading aidField observation / distinction
サムライSamuraiA split dorsal-fin configuration, often obvious in side view.
菱尾 / HishioDiamond tailA diamond-like tail in an otherwise non-Hikari body form.
マルコMarukoDorsal-fin absence; distinguish from injury or an early developmental stage.
メラーMellerAn unusual multiple-fin/fin-structure form; not a generic synonym for longfin.
スワローSwallowSelected extended sections or rays; record which fin rays form the projection.
ヒレ長Long fins (Hire-naga)Visible elongation; compare with age- and size-matched fish.
ロングフィンLongfinA Japanese technical category distinct from other named fin-elongation forms.
ワイドフィンWidefinGreater fin breadth; document profile and proportional measurements.
リアルロングフィンReal LongfinA specifically named fin morphology, not a marketing superlative.
モルフォMorphoA recognized specialized fin form; compare intact mature fins and avoid attributing all frills to this term.
フサヒレFusa-hireA tufted or bushy-finned expression; retain Japanese terminology for formal identification.
ナローフィンNarrowfinA narrow fin-related category; document fin width against comparable examples.

Body form

Check form separately from luminescence. Source: JMA 2025 pp. 58–60.

Japanese termEnglish reading aidField observation / distinction
ヒカリ / HikariHikariCharacteristic dorsal/anal fin relationship and diamond-like caudal fin; dorsal shine alone is insufficient.
ダルマ / DarumaDarumaShortened-bodied fish, sometimes called balloon/short-body; welfare and swimming need attention.
ヒカリダルマHikari-DarumaShortened body combined with Hikari fin/body signs.
半ダルマSemi-Daruma qualifierIntermediate body shortening.

Common supplementary vocabulary

Consult the official JMA source for the latest permitted combination and qualifier order. Source: JMA 2025 pp. 61–67 and 2025 updates.

Japanese termEnglish reading aidField observation / distinction
ヒレ美 / HirebiFin beautyUnusually vivid or extensive fin pigmentation beyond ordinary line characteristics.
腹膜青 / Fukumaku-aoBlue peritoneumBlue appearance around the abdominal/peritoneal region; distinct from internal light.
体内黒Internal blackDark internally appearing body effect; photograph from the side.
ヒレ光Fin lightLight/reflective appearance associated with fin structures.
一周光Circumferential lightA light effect expressed around more of the body perimeter; confirm exact category in JMA.
背地反応なしNo background responseDark pigmentation remains conspicuous on a pale background after acclimation.
ヒゲ / HigeWhisker-related common descriptorRetain the Japanese term and use clearly documented examples; not a color.
頂点眼Top-positioned eye descriptorAn eye-orientation supplement; preserve the Japanese term to avoid confusing it with other eye categories.
モザイクパンダMosaic PandaA particular mosaic eye/iridophore appearance; do not infer unique causative genotype.
シースルーSee-throughPronounced translucence; compare with panda and albino-associated appearance.
側面光Side-surface lightA lateral reflection supplement; avoid confusing with external light's separate qualifier without checking source.
パウダーPowderA newly listed appearance descriptor; keep label provisional until diagnostic photograph and original criteria are checked.

RESEARCH EVIDENCE / PIGMENT CELLS

From pigment cell to gene: a source-verified evidence map

The guide above classifies appearances. This research panel examines the different biological mechanisms that can contribute to those appearances. It is an original Aquapedia diagram, not an illustration or chart copied from the JMA manual.

Pigment-cell contributions to the visible medaka phenotype

MelanophoresBlack / brownBrown and black pigment

Melanin-bearing pigment cells influence dark skin coloration and dark markings; their spatial distribution and adaptation to background can change the visible pattern.

Scientific evidence ↗
XanthophoresYellow / orangeYellow to orange color

These cells contain yellow/orange pigment materials, including pteridines and carotenoids. Their development involves genes also connected to leucophore pathways.

Scientific evidence ↗
IridophoresSilvery reflectionReflective plates and structural shine

Guanine-bearing reflective structures contribute silvery iridescence and can conceal darker internal tissue; mutations may make fish appear more translucent.

Scientific evidence ↗
LeucophoresWhite reflectionWhite-reflective appearance

A medaka pigment-cell lineage with distinctive light-scattering properties; development involves some of the same regulatory systems that control xanthophores.

Scientific evidence ↗

Observed color, transparency, pattern and reflective effects

Important distinction: a documented gene in a research strain does not establish the genotype of a commercial medaka variety with a similar appearance. A named ornamental line needs its own molecular or traceable breeding evidence.

Six experimentally investigated medaka genes and what is actually known

Gene / studied locusDirect research findingInheritance evidenceWhat cannot be inferred about named breeder strains
tyr (tyrosinase)oculocutaneous albino iA transposable-element insertion in a tyrosinase gene was linked to the classical laboratory albino mutation; melanin production is impaired.

Evidence: Causal mutation identified for the reported laboratory allele

Recessive for the reported i albino laboratory mutant; do not generalize to every hobbyist 'albino' line.Albino-like red eyes can be described by appearance, but the exact causal mutation of an untested ornamental line is unknown.

Koga et al. (1995), doi:10.1007/BF00287101 ↗

pnp4aguanineless (gu)Gene-targeting and complementation tests identified pnp4a as causal for the guanineless reduction in visibly reflective iridophores.

Evidence: Causal gene confirmed in laboratory gu mutants

The study confirmed a phenotype in homozygous mutant and knockout fish; that result is not a dominance test for marketed glitter traits.A fish with reduced shine or see-through characteristics cannot be called 'pnp4a mutant' from photos alone.

Kimura et al. (2017), doi:10.1534/g3.117.040675 ↗

slc2a15bleucophore-free (lf)Molecular work identified this solute-carrier gene at the lf locus, with effects on coloration of leucophores and xanthophores.

Evidence: Causal locus/gene evidence in laboratory stocks

The laboratory lf locus lies on sex chromosomes in some described genetic stocks; simple autosomal dominant/recessive claims are inappropriate.The color of a commercial white line does not establish its slc2a15b genotype.

Kimura et al. (2014), PMID:24803434 ↗

pax7aleucophore-free-2 (lf-2)Mapping, mutation characterization and rescue experiments associated pax7a disruption with developmental defects in xanthophore and leucophore precursor lineages.

Evidence: Gene-level functional evidence in the lf-2 research strain

Study concerns an identified loss-of-function laboratory allele; no blanket inheritance assignment to hobby strains.Lack of white cells in a named breeder strain is not proof of the exact lf-2 mutation.

Kimura et al. (2014), PMID:24803434 ↗

slc2a11bwhite leucophore (wl)Gene disruption and rescue work found a slc2a11b locus affecting the leucophore color program.

Evidence: Gene-level functional evidence for a defined medaka mutant

Mutant results are allele- and laboratory-line-specific; do not label an unrelated fish 'dominant wl' without a controlled cross.An ornamental 'white' label alone cannot identify the white-leucophore locus.

Kimura et al. (2014), PMID:24803434 ↗

sox5many leucophores-3 (ml-3)Functional experiments showed that Sox5 regulates the choice between xanthophore and leucophore developmental pathways in medaka.

Evidence: Functional pigment-lineage regulator demonstrated in laboratory research

Study investigates a particular mutant and pigment-cell differentiation; inheritance of commercial two-tone/white varieties is not established by this result.This finding explains a biological pathway but does not authenticate any breeder's pedigree or named color strain.

Nagao et al. (2014), doi:10.1371/journal.pgen.1004246 ↗

Practical genetics interpretation

1. Does 'recessive' for one laboratory medaka mutant prove every visually similar breeder strain is recessive?

No. The inheritance assignment belongs to the actual tested allele and genetic background. Other lines can carry distinct variants with visually overlapping effects.

2. Why can a transparent-scale phenotype appear without a known pnp4a genotype?

Transparency is an optical outcome of several tissues and pigment-cell populations. A specific laboratory mutation is evidence of one mechanism, not a universal genetic diagnosis.

3. How should Aquapedia show a gene on a commercial strain profile?

Show gene-level support only when a molecular test, peer-reviewed genotype-to-phenotype study tied to that line, or sufficiently documented breeding evidence warrants it. Otherwise mark it as a candidate mechanism or unknown.

4. How do I record a dominant/recessive hypothesis?

Separate the observed ratios of offspring from the proposed model. Record parent identities, mating scheme, counts, sex, generation, environment, and whether an actual variant was genotyped.

Research sources with experiment-specific scope

Science-backed pigmentation appendix to Aquapedia's independently authored Medaka field guide. Studies document laboratory medaka mutants; they do not establish the genotype of named commercial medaka strains.

PRIMARY GENOMICS RESEARCH / 2026

What the newest ornamental-medaka DNA study actually shows

This section reviews a 2026 study of ornamental Japanese medaka. It provides an original evidence guide, not a copy of research figures or a certification of commercial breeder ancestry. The study links genetic variants to selected phenotypes, but the strength of those links differs from trait to trait.

86ornamental strains
181ornamental fish sequenced
34traits described
29traits analyzed by GWAS

Whole-genome sequences were studied for 181 individuals representing 86 ornamental strains; an additional 20 individuals came from five laboratory strains. The association analyses covered 29 phenotypes. This sampling is valuable but not a genotype certificate for all breeder lines that share a trade name.

Evidence levels are not interchangeable

Experimentally supported

A manipulation or previously characterized allele produces the relevant effect in the studied genetic background. Scope is limited to those experiments; it does not certify every fish sold under a strain name.

Candidate association

A GWAS region or suggestive variant points toward a gene, but its causal role has not been established for the observed ornamental phenotype.

Unresolved / conflicting

The association does not identify a definitive explanation; a superficially similar laboratory mutant or previous report should not be assumed to share a mechanism.

Eight gene–phenotype findings, with limitations

adcy5 — Orochi-like dark coloration

Experimentally supported

Research observation: Among sampled Orochi animals, 16 of 18 carried a homozygous deletion affecting the intron 7/exon 8 boundary. Sequencing showed exon 8 skipping. Experimentally generating an exon-8-deletion allele in Kiyosu medaka increased dark body pigmentation.

Limits and confidence: Strong functional support for a black-pigment mechanism in the studied fish; 2 of 18 sampled Orochi did not have the reported homozygous deletion, so do not call it universal for all Orochi breeders or descendants.

Inheritance: The research reports a homozygous allele in many sampled fish and an experimental phenotype; a complete breeder-level dominant/recessive segregation rule is not established here.

2026 paper, Fig. 6e–h / Results, body color · Read the original peer-reviewed study ↗

zic1 / zic4 — Hikari-style fin/body-axis organization

Experimentally supported

Research observation: The 2026 study confirmed a previously reported transposon insertion in the regulatory region near zic1/zic4 in all 35 sampled fish scored for the Hikari phenotype.

Limits and confidence: This is corroboration of a previously characterized enhancer mechanism in sampled fish, not a claim that all reflective Miyuki or dorsal-shiny fish share the Hikari body-form genotype.

Inheritance: Previous causal enhancer work and the 2026 carrier pattern are relevant; exact alleles and inheritance of a particular commercial fish require direct records.

2026 paper, Fig. 4g / Results, body shape · Read the original peer-reviewed study ↗

kcnq5a — Hire-naga / Swallow fin morphology

Candidate association

Research observation: Both traits had major GWAS signals on chromosome 15. The researchers identified a large intronic deletion near kcnq5a in sampled hire-naga fish but no phenotype-specific coding loss-of-function variant.

Limits and confidence: The potassium-channel gene is a strong candidate, not a demonstrated causal allele for both fin forms. The suggestion that forms involve distinct alleles at one gene remains a hypothesis.

Inheritance: Do not assign dominant, recessive or codominant status from the GWAS association alone.

2026 paper, Fig. 3d–e / fin GWAS · Read the original peer-reviewed study ↗

bmp5 — Demé (protruding eyes)

Candidate association

Research observation: GWAS in 15 Demé fish found a region on chromosome 15 containing bmp5. A nearby upstream SNV occurred in 12/15 Demé fish and 1/166 controls; the investigators did not find a shared coding change.

Limits and confidence: An associated marker can help identify a genomic interval without showing bmp5 itself is causal. Demé is an eye-position/head-shape feature, not automatically the same as Big Eye.

Inheritance: No universal Demé inheritance rule supported by this association.

2026 paper, Fig. 4c / eye morphology · Read the original peer-reviewed study ↗

kitlga — Aurora / reduced iridophore coverage

Candidate association

Research observation: An associated chromosome-6 region contained kitlga; a frameshift allele was homozygous in 10/23 Aurora samples versus 7/158 non-Aurora samples.

Limits and confidence: The variant enriches in sampled Aurora phenotypes but is not fully predictive. Aurora lineage and semi-transparent appearance must stay separate in Aquapedia.

Inheritance: No confirmed universal Aurora gene or dominance status; many Aurora fish lacked this homozygous allele.

2026 paper, Fig. 6a / color GWAS · Read the original peer-reviewed study ↗

slc24a5 (regional candidate) — Panda eye/reflective-cell reduction

Unresolved / conflicting

Research observation: Sixteen Panda samples showed a chromosome-3 association region containing 113 genes, including slc24a5. The study found no significant chromosome-5 pnp4a association or clear pnp4a coding variants in these Panda samples.

Limits and confidence: Do not equate ornamental Panda with the laboratory guanineless pnp4a mutant. The authors explicitly note slc24a5 may not explain the phenotype; the causal gene remains unresolved.

Inheritance: No resolved causal allele or inheritance mode for these Panda samples.

2026 paper, Results, panda comparison · Read the original peer-reviewed study ↗

uvrag — Sanshoku / Kurobuchi mottling

Candidate association

Research observation: A GWAS interval for patterned fish contained uvrag; a missense variant was noted in at least one sampled Sanshoku fish.

Limits and confidence: A candidate region and isolated variant do not demonstrate that uvrag causes three-color patterning across independent breeders.

Inheritance: Segregation and functional tests are required before making dominance claims.

2026 paper, Results, pigmentation pattern GWAS · Read the original peer-reviewed study ↗

slc45a2 — Black Rim pigmentation patterns

Candidate association

Research observation: Chromosome-12 GWAS intervals for Black Rim and another pigmentation phenotype included slc45a2, a gene with established roles in pigment biology.

Limits and confidence: Its pigmentation function does not prove which variant, if any, drives all black scale edging; distinct traits should not be collapsed into one genotype.

Inheritance: Not established for commercial Black Rim lines by this association.

2026 paper, Fig. 6c / GWAS color categories · Read the original peer-reviewed study ↗

Where the study did not find a clear association peak

Not finding a prominent peak in this study does not prove the trait has no genetic basis. It can reflect sample composition, genetic complexity, or inadequate power to distinguish a signal.

  • Yōkihi / vermilion-orange body color
  • Gold body color
  • Tōmeirin / transparent-scale appearance

How to use the results for a breeder pedigree

  1. Use the exact tested phenotype and species when reading a gene study: the laboratory guanineless mutation is not necessarily the commercial Panda eye trait.
  2. For a new commercial strain, log known breeder line, sex, body condition, lighting, and photographic anatomy separately from variant claims.
  3. An association may be driven by nearby linkage or shared ancestry. Confirm a proposed causal gene with a functional experiment and evaluate segregation across more than one background.
  4. An observed deletion in a research sample does not prove that every descendant or similarly branded fish has the same allele.
  5. Do not draw a solid lineage arrow between strains simply because their GWAS candidate genes overlap. Pedigree arrows require documented crosses.

Source: Kon, Tang, Kon-Nanjo et al. (2026). Genomic consequences of domestication and the diversification of body coloration and morphology in ornamental medaka strains. Molecular Biology and Evolution. DOI: 10.1093/molbev/msag021.

AQUAPEDIA BREEDER QUESTIONS

54 practical questions, answered independently

These are newly written Aquapedia research questions organized around practical identification and breeding problems. They are not translations of JMA's numbered FAQ. See the original Japanese manual for the association's own answers.

01. Why does the same fish appear under several shop names?

Breeders and retailers may use different house names even for matching trait combinations. Record the shop name as a trade label and describe the actual visible features separately.

02. Can a breeder's strain name replace the trait description?

Use both when available. The nickname identifies a market line or breeder selection, whereas the trait list helps readers compare photographs across sellers.

03. Does a JMA trait name mean JMA verified the parents?

No. A visual category is not a genetic pedigree certificate. Founder and parentage claims require independent records.

04. What is the first photograph to take when identifying a fish?

Start with top and side views in even light, then obtain close-ups of eyes, cheeks, scales and fins. The second view often resolves ambiguous sparkle or gill-cover interpretations.

05. Why can a black fish turn lighter in a white tub?

Pigment cells can respond to their surroundings. Record the background and duration of acclimation before concluding that the fish expresses background-independent black coloration.

06. Does stronger redness prove a different red variety?

Not by itself. Diet, age, hormones, lighting and selection influence intensity. Compare animals under consistent conditions and record the base color and all additional traits.

07. Can two fish look identical but have different genes?

Yes. Different ancestry or multiple genetic mechanisms may produce similar phenotypes. A photograph cannot fully reveal genotype.

08. Can one family yield several visibly different categories?

Yes. Segregation, modifiers and environmental effects can produce heterogeneous offspring. Count and document each phenotype in a generation.

09. How is body color different from Lamé?

Body color describes the broader pigmentation; Lamé concerns conspicuous sparkle on individual scales. Record both if both are visible.

10. How is Lamé different from the Miyuki-style sheen?

Lamé appears as separated reflective points associated with scales; external body light is typically a reflective field along the back or another specified region.

11. Is an internally blue belly the same as internal body light?

Not necessarily. The blue peritoneum descriptor and internal body light refer to different anatomical or optical observations in the Japanese vocabulary.

12. Does a shiny back automatically mean Hikari body form?

No. Inspect the tail and dorsal/anal-fin configuration. Reflective traits and body-form traits can overlap but are not synonyms.

13. What distinguishes a transparent-scale fish from a pale fish?

Look for a characteristic reduction in reflective coverage, especially around the gill cover; being light-colored alone is not evidence of transparent scales.

14. If only one cheek shows red, how should it be recorded?

Document left and right cheek appearance separately. A partial transparent-scale expression may be worth noting without assuming a distinct gene.

15. Is 'Aurora' always a physical feature?

No. It may mean a visible semi-transparent-scale expression or reported ancestry from an Aurora line. Those claims need different evidence.

16. Is Kagami a pink or blue variety?

Kagami denotes a mirror-scale-related characteristic, not a color category. Record the color separately.

17. How can I tell Panda eyes from albino eyes?

Compare melanin-related eye coloration and reflective coverage from several angles. They are not interchangeable categories.

18. Why do some red eyes look dark burgundy?

Partial pigment or other pigment/reflective differences can influence their appearance. Ruby Eye and albino are useful visual terms, but genetic identity needs evidence.

19. Are protruding eyes and enlarged eyes the same?

No. Eye position and eye size should be measured and photographed independently. Changes that compromise vision raise welfare concerns.

20. Can an eye feature be present on just one side?

Asymmetric appearance can occur. Document both sides and avoid assuming bilateral expression from a single photograph.

21. How can I separate mottling from Black Rim?

Mottling produces irregular discrete patches. Black Rim is more closely tied to scale outlines or organized darkening around scales.

22. Are red and white patches automatically inherited together?

Not necessarily. Different pattern and pigment components may segregate. Track stable transmission over several generations.

23. Does a divided dorsal fin count as Longfin?

Not simply on that basis. Samurai describes a split structure while longfin terms describe forms of extension. An animal may show more than one feature.

24. Could a fish with a diamond tail be misidentified as Hikari?

Yes. Hishio and Hikari can look similar in tail photographs. Check the full fin configuration and body features.

25. Does losing a dorsal fin always mean Maruko?

No. Injury or developmental issues must be excluded, and a reliable hereditary trait requires multigenerational evidence.

26. Does a very short fish automatically qualify as Daruma?

Compare total shape with age-matched fish and exclude disease or severe curvature. Semi-Daruma and other intermediate forms also occur.

27. Why can the same cross produce standard and short-bodied fry?

Inherited factors and their combinations can segregate, and morphology may vary. Collect offspring counts before proposing a genetic model.

28. How should unusually bright fins be described?

Photograph individual fins and record pigmentation as a supplementary feature when it is genuinely distinctive, rather than changing the base body color.

29. Can a light-reflection trait be multicolored?

Yes, reflections may vary by region or scale. Record the positions and colors carefully rather than inventing another underlying category.

30. How should I record a new or unfamiliar characteristic?

Use a provisional description, photograph multiple specimens and record whether it appears across generations. Avoid assigning an official name without source documentation.

31. What proves that a new breeding line is stable?

Repeated generations expressing the target combination, paired with dated parent and offspring records, provide stronger evidence than a single selected individual.

32. Is an F1 cross enough to claim a new variety?

An F1 fish can be a promising starting point, but it does not on its own demonstrate stable inheritance of the claimed look.

33. Does dominance mean every offspring shows a trait?

No. Dominance describes a genotype-phenotype relationship under a particular genetic model, not a blanket prediction without parent genotypes and penetrance details.

34. Can a trait be hereditary without simple dominant/recessive inheritance?

Yes. Multiple genes, modifiers, variable expression and other inheritance mechanisms can produce a heritable visual effect.

35. How do I test a genetic explanation responsibly?

Record parental phenotypes, mating pairs, offspring numbers and environments over repeated controlled generations, then compare predictions across plausible genetic models.

36. Does diet permanently change the strain's genotype?

No. Diet can change expression or health without rewriting inherited DNA. Distinguish environmental enhancement from lineage stability.

37. Can dark backgrounds make black fish appear better?

Yes, background adaptation can affect melanophore expression. That is why standardized photo conditions matter for fair comparisons.

38. Can very bright light ruin identification photos?

Yes. Glare, reflection and camera white balance may hide traits or exaggerate colors. Use diffuse lighting and no harsh eye illumination.

39. Should I rely on a single marketplace photograph?

No. Request top and side views of the actual stock, along with parent provenance when it is claimed.

40. What if a breeder says a fish descends from a celebrated strain?

Preserve that as breeder-reported lineage unless documented crosses and provenance verify the connection.

41. What if the same gene name appears in two separate sales listings?

Ask for the primary scientific reference or testing evidence. Community nicknames and breeder terminology do not establish identical variants.

42. How do I report an uncertain phenotype?

Write 'possible' or 'unconfirmed' with photos and observation conditions. Uncertainty is more useful than an invented definitive identification.

43. Can the original JMA classification vocabulary change?

Yes. The association revises its manual as new forms and terminology become accepted. Link the publication edition and date to your record.

44. Is the JMA manual a law that all breeders must obey?

No. It is an association classification resource intended to improve communication and judging, not a national breeding law.

45. How do I compare fish fairly in a competition?

Use a disclosed rubric that separates trait identity from quality of expression, health and body condition. Keep photos and scores attributable to a specific event.

46. Can a show-winning fish prove a stable genetic line?

An award evaluates an entry under that event's rules, not every descendant's genotype. Maintain the recognition date and breeding evidence separately.

47. Should Aquapedia display a pedigree tree without documented parents?

It should show an explicit 'parentage not documented' state rather than inventing ancestors. Supported arrows must link to credible breeder or breeding records.

48. Can two lines sharing an appearance be combined in one Aquapedia record?

Connect them through a shared trait term while retaining separate breeder and ancestry identities. Do not conflate trade names.

49. How do I treat an unverified English translation of a Japanese trait?

Show the original Japanese term, identify the English gloss as provisional and link the official source so experts can check the meaning.

50. Does an unusual fish feature always deserve selective breeding?

No. Consider feeding, normal swimming, sight, fertility and health before selecting dramatic structural abnormalities.

51. What is the minimum information for a breeder research entry?

Record the actual Japanese and trade names, breeder or region if sourced, observed phenotypes, breeding evidence, credible citations, dates, and uncertainties.

52. Should body color and fin color be stored separately?

Yes. The same fish can carry a base body color and a distinctive fin-related supplementary characteristic.

53. What if photographs disagree with the written strain description?

Preserve both the claim and actual observation with dates. Recheck age, viewing angle, lighting and whether the image depicts the same individual.

54. How do I verify a newly reported JMA trait?

Confirm it against the latest official Japanese trait table and association publications; save a dated source record before adding it as formally recognized.

Sources, editions and scope

This is an independently authored Aquapedia guide built from observable facts, current nomenclature, editorial comparisons and breeder-facing instruction. It does not copy or republish JMA's text, figures, photos, charts, layout or original FAQ. JMA has been contacted in Japanese for optional permission to distribute a separate complete English translation; that permission has not been granted.

Page citations are references to the 2025 original printed manual, not reprints of its contents. Original breeder claims and gene links need additional evidence before being labeled confirmed in Aquapedia.

Read the shorter JMA classification research companion · Browse all English articles