Editing Cuniculture (section)

==Genetics==
{{More citations needed section|date=January 2021}}
The study of rabbit genetics is of interest to medical researchers, fanciers, and the fur and meat industries. Each of these groups has different needs for genetic information. In the biomedical research community and the [[pharmaceutical industry]], rabbits genetics are important for producing antibodies, [[Toxicity test|testing toxicity of consumer products]], and in [[model organism]] research. Among rabbit fanciers and in the fiber and fur industry, the genetics of coat color and hair properties are paramount. The [[meat industry]] relies on genetics for disease resistance, [[feed conversion ratio]], and reproduction potential.

The rabbit [[Whole genome sequencing|genome has been sequenced]] and is publicly available.<ref>{{cite web|title=Genome of Oryctolagus cuniculus (rabbit)|work=NCBI.NLM.NIH.gov|publisher=[[United States National Institutes of Health]]|location=Washington, D.C.|url=https://www.ncbi.nlm.nih.gov/genome?term=oryctolagus%20cuniculus|access-date=July 24, 2015}}</ref> The mitochondrial DNA has also been sequenced.<ref>{{cite journal|last1=Gissi|first1=C.|last2=Gullberg|first2=A.|last3=Arnason|first3=U.|title=The complete mitochondrial DNA sequence of the rabbit, Oryctolagus cuniculus|journal=Genomics|volume=50|date=1998|issue=2|pages=161–169|doi=10.1006/geno.1998.5282|pmid=9653643}}</ref> In 2011, parts of the rabbit genome were re-sequenced in greater depth in order to expose [[Single-nucleotide polymorphism|variation]] within the genome.<ref>{{cite journal|last=Carneiro|first=M.|title=The Genetic Structure of Domestic Rabbits|url= |journal=Molecular Biology and Evolution|volume=28|year=2011|issue=6|pages=1801–1816|doi=10.1093/molbev/msr003|pmc=3695642|pmid=21216839}}</ref>

===Gene linkage maps===
{{anchor|Linkage maps|reason=This is the old section title. (Changed to "Gene linkage maps" 18 February 2018.)}}
[[File:American Grand Champion Dutch Rabbit.jpg|thumb|right|{{Unbulleted list|Gene: du|Pattern: Dutch|Gene: B|Color: Black (on white)}}|215px]]
[[File:Oryctolagus cuniculus (AM LM819-4).jpg|thumb|right|Gene: A (Agouti)|215px]]
The early genetic research focused on linkage distance between various gross [[phenotypes]] using [[linkage analysis]]. Between 1924 and 1941, the relationship between c, y, b, du, En, l, r1, r2, A, dw, w, f, and br was established (phenotype is listed below).

:*c: albino
:*y: yellow fat
:*du: Dutch coloring
:*En: English coloring
:*l: angora
:*r1, r2: rex genes
:*A: Agouti
:*dw: dwarf gene
:*w: wide intermediate-color band 
:*f: furless
:*br: [[brachydactyly]]

The distance between these genes is as follows, numbered by [[chromosome]]. The format is gene1—distance—gene2.
<ref>{{cite journal|last1=Castle|first1=W. E.|last2=Sawin|first2=P. B.|title=Genetic linkage in the rabbit|journal=Proceedings of the National Academy of Sciences|volume=27|issue=11|year=1941|pages=519–523|doi=10.1073/pnas.27.11.519|pmid=16588495|pmc=1078373|bibcode=1941PNAS...27..519C|doi-access=free}}</ref>

:# c — 14.4 — y — 28.4 — b
:# du — 1.2 — En — 13.1 — l
:# r1 — 17.2 — r2
:# A — 14.7 — dw — 15.4 — w
:# f — 28.3 — br

===Color genes===
There are 11 color [[gene]] groups (or [[Locus (genetics)|loci]]) in rabbits. They are A, B, C, D, E, En, Du, P, Si, V, and W. Each locus has [[Dominance (genetics)|dominant]] and [[recessive]] genes. In addition to the loci there are also modifiers, which [[Modifications (genetics)|modify]] a certain gene. These include the [[rufous]] modifiers, color intensifiers, and plus/minus (blanket/spot) modifiers. A rabbit's coat has either two [[pigment]]s ([[pheomelanin]] for yellow, and [[eumelanin]] for dark brown) or no pigment (for an [[albino]] rabbit).<ref name="ARR1-RG">{{cite web|last1=Hinkle|first1=Amy|title=Rabbit [Color] Genes|url=http://www.amysrabbitranch.com/Color&Genetics/Allele%20List%202011.pdf|website=Amy's Rabbit Ranch|access-date=21 February 2018|archive-url=https://web.archive.org/web/20160303214855/http://www.amysrabbitranch.com/Color%26Genetics/Allele%20List%202011.pdf|archive-date=3 March 2016|url-status=dead}}</ref><ref name="ARR2-RCG">{{cite web|last1=Hinkle|first1=Amy|title=[Rabbit Color] Genotypes|url=http://www.amysrabbitranch.com/Color&Genetics/Genotype%20List%202011.pdf|website=Amy's Rabbit Ranch|access-date=21 February 2018|archive-url=https://web.archive.org/web/20111012193541/http://amysrabbitranch.com/Color%26Genetics/Genotype%20List%202011.pdf|archive-date=12 October 2011|url-status=dead}}</ref>

Within each group, the genes are listed in order of dominance, with the most dominant gene first. In parentheses after the description is at least one example of a color that displays this gene.
[[File:Kaninchen3.jpg|thumb|right|Gene: c(ch2) (medium chinchilla)|215px]]
[[File:Lapin Japonais.jpg|thumb|right|Gene: e(j) (Japanese [[Brindle|brindling]] (harlequin))|215px]]
[[File:Broken Mini Rex.JPG|thumb|right|{{Unbulleted list|Gene: Enen|Pattern: Broken|Gene: D|Color: Chocolate (on white)|Gene: r1, r2|Fur type: Rex}}|215px]]
[[File:Eithel, black Silver Fox doe.jpg|thumb|right|Gene: si (silvering of the hair shaft)|215px]]

:''Note: lower case are recessive and capital letters are dominant''
*"A" represents the agouti locus (multiple bands of color on the hair shaft). The genes are:
**A: agouti ("wild color" or chestnut agouti, opal, chinchilla, etc.)
**a(t): tan pattern (otter, tan, silver marten)
**a: self- or non-agouti (black, chocolate)
*"B" represents the brown locus. The genes are:
**B: black (chestnut agouti, black otter, black)
**b: brown (chocolate agouti, chocolate otter, chocolate)
*"C" represents the color locus. The genes are:
**C: full color (black)
**c(ch3): dark chinchilla, removes yellow pigmentation (chinchilla, silver marten)
**c(ch2): medium (light) chinchilla, slight reduction in eumelanin creating a more sepia tone in the fur rather than black.
**c(ch1): light (pale) chinchilla (sable, sable point, smoke pearl, seal)
**c(h): color sensitive expression of color. Warmer parts of the body do not express color. Known as Himalayan, the body is white with extremities ([[Point (coat color)|points]]) colored in black, blue, chocolate or lilac. Pink eyes.
**c: albino (ruby-eyed white or REW)
*"D" represents the dilution locus. This gene dilutes black to blue and chocolate to lilac.<ref>{{cite journal|pmid=24320228|doi=10.1111/age.12104|volume=45|issue=2|title=A frameshift mutation in the melanophilin gene causes the dilute coat color in rabbit (Oryctolagus cuniculus) breeds|year=2014|journal=Animal Genetics|pages=248–255|last1=Fontanesi|first1=L.|last2=Scotti|first2=E.|last3=Allain|first3=D.|last4=Dall'Olio|first4=S.}}</ref>
**D: dense color (chestnut agouti, black, chocolate)
**d: diluted color (opal, blue or lilac)
*"E" represents the extension locus. It works with the 'A' and 'C' loci and rufous modifiers. When it is recessive, it removes most black pigment. The genes are:
**E(d): dominant black
**E(s): steel (black removed from tips of fur, which then appear golden or silver)
**E: normal
**e(j): Japanese brindling (harlequin), black and yellow pigment broken into patches over the body. In a broken color pattern, this results in Tricolor.
**e: most black pigment removed (agouti becomes red or orange, self- becomes tortoise)
*"En" represents the plus/minus (blanket/spot) color locus. It is [[incompletely dominant]] and results in three possible color patterns:
**EnEn: "Charlie" or a lightly marked broken with color on ears, on nose, and sparsely on body
**Enen: "Broken" with roughly even distribution of color and white
**enen: Solid color with no white areas
*"Du" represents the Dutch color pattern (the front of the face, the front part of the body, and rear paws are white; the rest of the rabbit has colored fur). The genes are:
**Du: absence of Dutch pattern
**du(d): Dutch (dark)
**du(w): Dutch (white)
*"V" represents the vienna white locus. The genes are:
**V: normal color
**Vv: Vienna carrier; carries blue-eyed white gene. May appear as a solid color, with snips of white on nose and/or front paws, or Dutch marked.
**v: vienna white (blue-eyed white or BEW)
*"Si" represents the silver locus. The genes are:
**Si: normal color
**si: silver color (silver, silver fox)
*"W" represents the middle yellow-white band locus and works with the agouti gene. The genes are:
**W: normal width of yellow band
**w: doubles yellow bandwidth (otter becomes tan, intensified red factors in [[Thrianta]] and Belgian Hare)
*"P" represents the [[Oculocutaneous albinism#Types|OCA type II form of albinism]]. P is used because it is an integral [[OCA2|P protein mutation]]. The genes are:
**P: normal color
**p: albinism mutation. Removes eumelanin and causes pink eyes. (Will change, for example, a chestnut agouti into a shadow)