Cat genetics

by Michael Broad · May 25, 2012

Contents – cat genetics

Introduction
Terms
Gene symbols
Use of these terms verbatim
Video on genetics generally
Genetic diseases in purebred cats
Cat Genetics – the cat breeds

I discuss the Singapura cat below

Introduction

This page contains a glossary of terms that are referenced by other pages on this site that deal with cat genetics. It is an expanding page. Expansion takes place organically (as and when required). It also contains some interesting information about the genetics of the cat breeds and their places of origin.

Genetics generally is complicated. Some of the following definitions or part definitions are reproduced therefore from Wikipedia® under their license, which allows verbatim reproduction (see Wikipedia® licensing). Wikipedia® in my view provides the most comprehensive information on the internet and the quality is consistently higher than most other sources. No source is perfect.

Why am I using Wikipedia®? Simple, to ensure accuracy. I cannot accurately present the information without studying genetics to a profound level. I have decided that that is not my role in creating this website. However, I have a good grasp of cat genetics. There is, though, a time to delegate to people who have more experience. Accuracy remains a important underlying philosophy of this website. One last point, I have added to the Wikipedia® definitions if I think that I can make it clearer or more layperson friendly. This is an ongoing process.

Cat genetics – Update 10th October 2008: I have added some alternative definitions. These are taken (not verbatim for copyright reasons) from Robinson’s Genetics for Cat Breeders & Veterinarians (4th Ed.) (“Robinson’s”)

Domestic cat genetic symbols – cat genetics

Caps = dominant
Lower case = recessive

Cat genetics source: The Cat, Its Behavior, Nuitrition & Health by Lind P Case

Wild Type		Mutant
Gene symbol	What is does	Gene symbol	What it does
A	Agouti ticked banded hair	a	non-agouti solid hair (self)
B	Black pigmented hair	b	Chocolate brown (Havana Brown)
		b¹	Cinammon
C	Full color & pigmentation	c^b	Dark sepia brown (Burmese)
D	Dense colour & full pigmentation	d	Dilute or faded colour (e.g. black turns to blue) Grey cats
Hr	Normal coat & full coat density	hr	Almost a hairless coat (Sphynx)
L	Normal coat & short hair	l	Longhair (see Persian)
Mc	Mackerel tabby	mc	Blotched tabby
R	Normal hair and coat	r	Cornish Rex coat
Re	Normal hair and coat	re	Devon Rex coat
Ro	Normal hair and coat	ro	Oregon Rex coat
se	Normal hair and coat	Se	Selkirk Rex coat
rd	Normal hair and coat	Rd	Dutch Rex coat
T	Abyssinian coat	t	No Abyssinian markings
dm	Dilute modifier & full pigmentation	Dm	Dilute modifier & faded colours
fd	Normal ears	Fd	Folded ears (Scottish Fold)
i	non-inhibitor	I	Inhibited or suppressed pigment (see smoke cats)
m	Normal tail	M	Shortened Manx type tail
o	Non-orange	O	Orange pigment that is linked to the cat’s sex (see orange Persian)
pd	Normal toes	Pd	Polydactylism (more than usual number of toes)
s	Normal colour	S	Piebald or white spotting gene
w	Normal colour	W	Dominant white gene
wh	Normal coat	Wh	Wirehair coat

Here’s some cat genetics terms. Of course cat genetics is the same at a fundamental level to any other organism’s genetics:

Terminology – cat genetics

Genetics
Genetics is a discipline of biology and is the science of heredity and variation in living organisms. Mendel observed that organisms inherit traits in a discrete manner – these basic units of inheritance are now called genes. Inherited traits (nature) combine with experience (nurture) to create the individual.

Genes – Cat genetics
Genes correspond to regions within DNA, a molecule composed of a chain of four different types of nucleotides—the sequence of these nucleotides is the genetic information organisms inherit. DNA naturally occurs in a double stranded form, with nucleotides on each strand complementary to each other. Each strand can act as a template for creating a new partner strand—this is the physical method for making copies of genes that can be inherited. The sequence of nucleotides in a gene is translated by cells to produce a chain of amino acids, creating proteins—the order of amino acids in a protein corresponds to the order of nucleotides in the gene. This is known as the genetic code. The amino acids in a protein determine how it folds into a three-dimensional shape; this structure is, in turn, responsible for the protein’s function. Proteins carry out almost all the functions needed for cells to live. A change to the DNA in a gene can change a protein’s amino acids, changing its shape and function: this can have a dramatic effect in the cell and on the organism as a whole.

Genes are arranged linearly along long chains of DNA sequence, called chromosomes.(this section is a Wikipedia® verbatim copy but some segments have been omitted to make it shorter)

A gene is basic unit of heredity. They are carried by chromosomes like beads on a string (src: Robinson’s – not vebatim)

Allele – Cat genetics
An allele (pronounced /ˈæliːl/ (UK), /əˈliːl/ (US)) (from the Greek αλληλος allelos, meaning each other) is one member of a pair or series of different forms of a gene. Usually alleles are coding sequences, but sometimes the term is used to refer to a non-coding sequence. An individual’s genotype for that gene is the set of alleles it happens to possess. In a diploid organism, one that has two copies of each chromosome, two alleles make up the individual’s genotype. (this section is a Wikipedia® verbatim copy of a part of a larger article)

Mutant forms of the same gene of which there may be more than one at the same position on the chromosome (locus). Strictly incorrectly, allele is sometimes used to mean gene. (src: Robinson’s – not verbatim)

Chromosomes – Cat genetics
Chromosomes are organized structures of DNA and proteins that are found in cells. A chromosome is a singular piece of DNA, which contains many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions. The word chromosome comes from the Greek χρῶμα (chroma, color) and σῶμα (soma, body) due to their property of being stained very strongly by some dyes. (this section is a Wikipedia® verbatim copy of a part of a larger article)

Genotype – Cat genetics
The genotype is the genetic constitution of a cell, an organism, or an individual (i.e. the specific allele makeup of the individual) usually with reference to a specific character under consideration. For instance, the human albino gene has two allelic forms, dominant A and recessive a, and there are three possible genotypes- AA (homozygous dominant), Aa (heterozygous), and aa (homozygous recessive). (this section is a Wikipedia® verbatim copy but some segments have been omitted to make it shorter)

In the cat, the Albino gene has five allelic forms, full color C, Burmese c^b, Siamese c^s, blue-eyed albino c^a and albino c.

Phenotype – Cat genetics
A phenotype is any observable characteristic of an organism, such as its morphology, development, biochemical or physiological properties, or behavior. Phenotypes result from the expression of an organism’s genes as well as the influence of environmental factors and possible interactions between the two. The genotype of an organism are the inherited instructions it carries within its genetic code. Not all organisms with the same genotype look or act the same way, because appearance and behavior are modified by environmental and developmental conditions.(this section is a Wikipedia® verbatim copy of a part of a larger article)

Homozygous– Cat genetics
An organism is referred to as being homozygous (basically meaning of the same alleles) at a specific locus when it carries two identical copies of the gene affecting a given trait on the two corresponding homologous chromosomes (e.g., the genotype is PP or pp when P and p refer to different possible alleles of the same gene). Such a cell or such an organism is called a homozygote. A homozygous dominant genotype occurs when a particular locus has two copies of the dominant allele (e.g. PP). A homozygous recessive genotype occurs when a particular locus has two copies of the recessive allele (e.g. pp). Pure-bred or true breeding organisms are homozygous. (this section is a Wikipedia® verbatim copy of a part of a larger article)

Heterozygous– Cat genetics
An organism is a heterozygote or is heterozygous at a locus or gene when it has different alleles occupying the gene’s position in each of the homologous chromosomes. In other words, it describes an individual that has 2 different alleles for a trait. In diploid organisms, the two different alleles were inherited from the organism’s two parents. For example a heterozygous individual would have the allele combination Pp. (this section is a Wikipedia® verbatim copy of a part of a larger article)

Locus
In the fields of genetics and evolutionary computation, a locus (plural loci) is a fixed position on a chromosome such as the position of a biomarker that may be occupied by one or more genes. A variant of the DNA sequence at a given locus is called an allele. The ordered list of loci known for a particular genome is called a genetic map. Gene mapping is the process of determining the locus for a particular biological trait. Diploid and polyploid cells whose chromosomes have the same allele at some locus are called homozygous, while those that have different alleles at a locus, heterozygous. (this section is a Wikipedia® verbatim copy of a part of a larger article)

The exact position on the chromosome where the gene in question is located. Normally in different cats and animals a particular gene occupies the same position on the chromosome.

Recessive gene – Cat genetics
The term “recessive allele” refers to an allele that causes a phenotype (visible or detectable characteristic) that is only seen in homozygous genotypes (organisms that have two copies of the same allele) and never in heterozygous genotypes. Every diploid organism, including humans, has two copies of every gene on autosomal chromosomes, one from the mother and one from the father. The dominant allele of a gene will always be expressed while the recessive allele of a gene will be expressed only if the organism has two recessive forms.Thus, if both parents are carriers of a recessive trait, there is a 25% chance with each child to show the recessive trait. The term “recessive allele” is part of the laws of Mendelian inheritance formulated by Gregor Mendel. Examples of recessive traits in Mendel’s famous pea plant experiments include the color and shape of seed pods and plant height. (this section is a Wikipedia® verbatim copy of a part of a larger article)

Another description might be an allele that is overriden by another allele at the same locus.

Dilution – cat genetics
The Dense pigment gene, D/d, codes for melanophilin, a protein involved in the transportation and deposition of pigment into a growing hair. When a cat has two of the recessive d alleles (Maltese dilution), black fur becomes “blue” (appearing gray), chocolate fur becomes “lilac” (appearing light brown), cinnamon fur becomes fawn, and orange fur becomes cream. (this section above is a Wikipedia® verbatim copy of a part of a larger article).

To add to this D represents dense and d dilution.

Autosomal
An autosome is a non-sex chromosome. It is an ordinarily paired type of chromosome that is the same in both sexes of a species. For example, in humans, there are 22 pairs of autosomes. The X and Y chromosomes are not autosomal. Non-autosomal chromosomes are usually referred to as sex chromosomes, allosomes or heterosomes. (this section above is a Wikipedia® verbatim copy of a part of a larger article)A gene that is found on the autosomes and not on the sex chromosomes.

Sex Chromosomes
Special chromosomes of which there are two that determine the gender (sex) of the cat. When the heterozygous (XY) the cat or animal is male and when homozygous for the X gene the cat is female. (src: Robinson’s – not verbatim)

Dominance
In genetics, dominance describes the effects of the different versions of a particular gene on the phenotype of an organism. Many animals (including humans) and plants have two copies of each gene in their genome, one inherited from each parent. The different variants of a specific gene (such as that coding for earlobes) are known as alleles. If an organism inherits two alleles that are at odds with one another, and the phenotype of the organism is determined completely by one of the alleles, then that allele is said to be dominant. The other allele, which has no tangible effect on the organism’s phenotype, is said to be recessive. (this section above is a Wikipedia® verbatim copy of a part of a larger article)

Monogenic – Cat genetics
A trait caused by a single gene.A character determined by a single major gene. (src: Robinson’s – not verbatim)

Incomplete penetrance – Cat genetics
Penetrance is a term used in genetics describing the proportion of individuals carrying a particular variation of a gene (an allele or genotype) that also express a particular trait (the phenotype). For example, known mutations in the gene responsible for Huntington disease have 95% penetrance, whereby 5% of those with the dominant allele for Huntington disease don’t develop the disease and 95% do. In other word, penetrance is the percentage of individuals with a specific genotype that possess an associated phenotype. For example, if 50% of the individuals carrying the “blue” allele are blue, the “blue” allele has 50% penetrance. Penetrance only considers whether individuals express the trait or not — for variation in the degree of expression of a given trait, see expressivity. If an allele is highly penetrant, the trait it produces will always or almost always be apparent in an individual carrying the allele. Penetrance is said to be reduced or incomplete when some individuals fail to express the trait, even though they carry the allele. An allele with low penetrance will only sometimes produce the symptom or trait with which it has been associated at a detectable level. In the case of low penetrance it is difficult to distinguish environmental from genetic factors. (this section above is a Wikipedia® verbatim copy of a part of a larger article)

This happens when a genes presence fails to be manifest as a character, health or appearance trait example.

Polygenes
A polygene, multiple factor, multiple gene inheritance, or quantitative gene is a group of nonallelic genes that together influence a phenotypic trait. The loci or identities of the nonallelic genes are frequently unknown to biologists, even though they are known to exist. The genes that contribute to type 2 diabetes are thought to be mostly polygenes. Polygenic inheritance occurs when one characteristic is controlled by two or more genes (usually by many different genes) at different loci on different chromosomes. These genes are described as polygenes. Examples of human polygenic inheritance are height, skin colour and weight. (this section above is a Wikipedia® verbatim copy of a part of a larger article)

Browning gene
The browning gene B/b/bl codes for tyrosinase related protein-1, an enzyme involved in the metabolic pathway for eumelanin pigment production. Its dominant form, B, will produce black color. Recessive variants are b, producing brown (or chocolate), and bl producing light brown or cinnamon. (this section is a Wikipedia® verbatim copy of a part of a larger article)

Inhibitor gene – Cat genetics
This is a dominant gene. It’s symbol is I. The gene suppresses the feeding of pigment into the growing hair. This typically results in white hairs with colored tips. The gene seems to suppress the production of the pigment phaeomelanin more than the pigment eumelanin. It expresses its presence widely from white fur to a white band at the base of the hair next to the skin. Sometimes there is no effect but the cats carry the gene and they breed as smokes (cats with a smoke effect coat). Typical examples of the presence of this gene are the silver tabbies and the chinchilla silver.

Pseudogene – Cat genetics
Pseudogenes are defunct relatives of known genes that have lost their protein-coding ability or are otherwise no longer expressed in the cell. Although they may have some gene-like features (such as Promoters, CpG islands, and splice sites), they are nonetheless considered nonfunctional, due to their lack of protein-coding ability resulting from various genetic disablements (stop codons, frameshifts, or a lack of transcription) or their inability to encode RNA (such as with rRNA pseudogenes). Thus the term, coined in 1977 by Jacq, et al.,is composed of the prefix pseudo, which means false, and the root gene, which is the central unit of molecular genetics. (this section is a Wikipedia® verbatim copy of a part of a larger article)

White Spotting Gene – Cat genetics
The white spotting or piebald spotting gene, S/s, has variable expression, so that an SS cat often has more extensive white patching than an Ss cat. It is this gene that creates the familiar white blaze across the face, a white bib, tuxedo pattern, or dappled paws. A hypothetical Sb allele (“gloving gene”) may cause the mittens in Birman and Snowshoe breeds. Some researchers believe that there are separate white spotting genes for distinct forms of white pattern, such as the white locket that some cats have on their neck or bellies. (this section is a Wikipedia® verbatim copy of a part of a larger article).

White spotted cats are very common. You see them a lot as feral cats in countries such as Greece and Japan. The white spotting gene expresses it presence in a wide range of ways. At one end of the spectrum the white hair (the result of the gene’s presence) can be seen in very small or small areas only such as on the chest or belly (this is low grade spotting e.g. Tuxedo cat). At the other end of the spectrum the cat be all white or practically all white except for small splashes of color (this is high grade spotting e.g. Turkish Van cat). In between, when the white hairs account for 40-60% of the total it is called medium grade spotting. Tortie/torbie and white cats have about 20% white hair: see cat coats Tortie Torbie and White.During the develop of the cat as an embryo the white spotting gene causes an alteration in the behavior and creation of certain embryonic cells that will produce the pigmentation for the cat’s hairs. These cells are melanocyte cells.

The white spotting gene dictates that there are less melanocyte cells than normal and that their journey from their source, the neural crest, is curtailed. This results in some parts of the body being deficient in these cells, which in turn results in a lack of color in the hairs in those areas.

Where the migration/journey from the neural crest is particularly slow/curtailed the cat will show high grade spotting. Where there is a marginal alteration to the movement of the melanocyte cells there will be lw grade spotting.

Agouti gene – cat genetics
The agouti gene, A/a which codes for agouti signaling protein. The dominant, wild-type A causes the agouti shift phenomenon which causes hairs to be black pigmented at the tips and orange pigmented at the roots (revealing the underlying tabby pattern), while the recessive non-agouti or “hypermelanistic” allele, a, prevents this shift in the pigmentation pathway. In its homozygous form, aa, this results in black pigment production throughout the growth cycle of the hair. Thus, the non-agouti genotype (aa) masks or hides the tabby pattern, although sometimes a suggestion of the underlying pattern can be seen (called “ghost striping”), especially in kittens. (this section is a Wikipedia® verbatim copy of a part of a larger article).

Agouti: this is the natural coloring for cats (and other mammals). Wildcats have agouti coats. These coats are classic (blotched), mackerel, spottend and ticked tabby coats. The hairs are banded with yellow.

Genetic Mutation
A mutation is a randomly derived change to the nucleotide sequence of the genetic material of an organism.Mutations can be caused by copying errors in the genetic material during cell division, or by exposure to mutagens (ultraviolet or ionizing radiation, mutagenic chemicals, or viruses), or can be induced by the organism itself, by cellular processes such as hypermutation. In multicellular organisms with dedicated reproductive cells, mutations can be subdivided into germ line mutations, which can be passed on to descendants through the reproductive cells, and somatic mutations, which involve cells outside the dedicated reproductive group and which are not usually transmitted to descendants. If the organism can reproduce asexually through mechanisms such as cuttings or budding the distinction can become blurred.

Mutation is generally accepted by biologists as the mechanism by which natural selection acts, generating advantageous new traits that survive and multiply in offspring as well as disadvantageous traits, in less fit offspring, that tend to die out.

Cat genetics to Home Page
From cat genetics to mixed breed cats

Cat Genetics – the Cat Breeds – cat genetics

This section deals with the growth of the various cat breeds and examines this from a genetic and geographic point of view. It is based on The Ascent of Cat Breeds: Genetic Evaluations of Breeds and Worldwide Random Bred Populations by Monika J. Lipinski et al.

Introduction – cat genetics

The eastern Mediterranean is the probable site where domestication of the wildcat first took place. A Scientific American study says the Fertile Crescent (see map opposite¹) is where cat domestication first took place. This is east of the Mediterranean Sea. It happened about 9 – 10,000 years ago. Although the “initiation” of this process, it is said, would have been thousands of years earlier. Studies in respect of the evolutionary relatedness (phylogenetic) of the domestic cat indicates that it is the result of a “single domestication event in the Near East”. Based on genetic analysis, this translates to cat domestication taking place in one place and their exportation to other parts of the world via the trade routes.

The initiation of the process of domestication would have been the change in lifestyle of people from hunters to farmers. The grain produced attracted rodents, which attracted the wild cats who then became beneficial to the farmers. A relationship started that ended in pure domestication and companionship beyond a functional role for the cat.

It has been suggested that feral cats not only controlled pests but zoonotic diseases (by, I presume, killing the pests that might spread zoonotic diseases; this benefit being greater than the detriment of the cat passing on disease). The creation of cat breeds as part of the cat fancy lagged behind the creation of dog breeds because of this underlying usefulness.

The modern domestic cat is not fully domesticated. It can revert to the wild and become feral usually (but not always – there is a story of an abandoned domestic cat who starved). The domestic cat is still very similar to the wild cat particularly the small wild cats such as the African jungle cat that is easy to domesticate.

CFA Breeds

Certain cats were then ultimately selected as potential cat breeds and developed. Selection was based on appearance not functionality. Although there is a cat breed that was selected for functionality, the American Keuda (new window).

Of the 41 CFA cat breeds 16 are so called natural breeds (called “foundation breeds” by the CFA) from certain geographic areas (e.g. the Turkish Van or Norwegian Forest cat to name two) meaning that they developed naturally outside and before the cat fancy. The foundation breeds are genetically distinguishable from the other breeds with a high level of certainty.

No American indigenous cat breeds

The Americas have no indigenous (originating in and characteristic of a particular region or country) cat breeds.

The greatest genetic diversity is found in cats from the Mediterranean region. Cats in Asia had lower genetic diversity.

Singapura same as Burmese

The following pairs of cat breeds could not be distinguished one from the other as distinct cat breeds but they could be distinguished from other breeds:

The Turkish Van and Turkish Angora are distinct from one another (comment: was this distinction artificially introduced?). I say that they were probably the same breed originally.

Some cats breeds can be subdivided

These cats have “multiple lineages”. In other words the breeds were subdivided:

Cat breeds have less genetic diversity that random breed cats (moggies, non-purebred cats called Household Pets by the CFA).

The genetic diversity of cat breeds

Cat breeds with the lowest heterozygosity (having two different alleles of the same gene) values were (genetic diversity is the variability of the genes in a species. It can be estimated by the mean levels of heterozygosity in a population, the mean number of alleles per locus, or the percentage of polymorphic loci.):

Cat breeds with the highest heterozygosity values were:

Siberians

High heterozygosity values are associated with better health for the individual and a better chance of survival for a species (cat breeds are not separate species please note). In descending order of heterozygosity values (the highest at the top) this is the status of the following cat breeds:

Siberian – “derived from a broad foundation stock”
Norwegian Forest
Japanese Bobtail
Sphynx – high genetic diversity
Maine Coon
Chartreux
American Shorthair
Turkish Angora
Korat
British Shorthair
Exotic Shorthair
Persian
Turkish Van
Egyptian Mau
Siamese (modern)
Russian Blue
Abyssinian
Birman
Sokoke
Havana Brown
Burmese – this cat breed is the most intensely inbred with the Singapura.
Singapura – breeders of the Burmes and Singapura should be concerned about their breeding practices.

Genetic diversity was not greatly increased by the movement of a population of cat types sharing common identity to other areas from the Mediterranean.

USA cat breeds are from Europe

Cat breeds in the United States are similar genetically to those in Western Europe indicating that the cat breeds in the USA are all from Europe and there has not been time since importation by the European settlers in the early 1600s for the genotypes to develop.

Random bred cats are less genetically diverse than humans while purebred cats were less genetically variable than the random bred populations. There is a 10% decreas in heterozygosity at each level.

Most cat breeds were developed in the past 150 years (from 2009) – mainly in the USA and Europe.

First USA registered cat breeds

Amongst the first cat breeds registered by cat associations were these breeds:

Persian
Russian Blue
Siamese (traditional surely)
Angora (is this the Turkish Angora?)

Cats from Asia and Europe were used (the research indicated) to create the Abyssinian and Japanese Bobtails.

Siamese derived breeds are one gene away from Siamese

The most dolichocephalic (long headed) breed is the Siamese cat. This means the modern Siamese cat please note. The Siamese has been used in breeding programs to develop:

Colorpoints (Javanese)
Orientals
Havana Browns
longhaired breed variants of the above (e.g. Balinese)

The Siamese derived breeds are listed as separate cat breeds as we know but they only vary from the Siamese by a single gene variant (e.g. hair length or color patterns). They are “likely be inseparable as distinct breeds”. The Havan Brown is considered a separate breed in the USA but a color variant of the Siamese in the UK.

Burmese used to breed Singapura

“Folklore” says that:

Burmese and Singapura cats come from Burma (Myanmar)
Burmese cats from the USA were exported to Singapore and breed with native cats there and the offspring exported to the USA as the Singapura.

Persian has lost it genes of origin

Although the Persians have originated in Persian (Iran) or the Near East, its genetic makeup today bears little or no trace of that history due to selective breeding for an extreme phenotype (appearance). Its genetic make up is nearer that of the cats of Western Europe.

The same oddity has happened in respect of the Japanese Bobtail. I remark on this on this page. The Japanese Bobtail does not seem to originate from Japan. The modern Japanese Bobtail would appear to have been influenced more by European cats than by cats in the Asian gene pool.

The Egyptian Mau is being developed in a manner that means it is losing its ancient roots in Egypt. Although breed histories are mostly accurate.

Cat genetics licensing

Where indicated in the text the terms are verbatim transcripes of parts of Wikipedia® articles as allowed under the Wikipedia® licensing agreement. If people want to use the definitions they should ensure that they comply with the Wikipedia® licensing agreement. I thank Wikipedia® for allowing me to use their information to create this article on cat genetics. I aslo thank the researchers mentioned to help me update this page on cat genetics.

Wikipedia®
Cat genetics – Click on this link to see the Wikipedia® License src: Wikipedia® published under GNU Free Documentation License, Version 1.2 or any later version, November 2002 Copyright (C) 2000,2001,2002 Free Software Foundation, Inc. 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA – – no other conditions to the license are added.

1. Wikmedia Commons file – Created by NormanEinstein, December 21, 2005 — see license

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