Genetics is the science of studying and predicting patterns of inheritance.
Any discussion on colour inheritance requires a short list of essential definitions for a basic genetic vocabulary, to give an understanding of the genetic mechanisms involved.
The cell is the basic unit of life. Large complex animals such as alpacas and humans are made up of millions of cells. The cell contains a nucleus, which is composed of DNA or deoxyribonucleic acid. DNA is the biological code, which contains all the information required to create the animal. The code is set in the form of individual pieces of information, called genes. Genes are organised into long threads of DNA, called chromosomes, which are found in pairs within the nucleus. Genes also occur in pairs, and the members of each pair are called alleles. Each gene pair has a specific position on a given chromosome. Each species of animal has a particular number of chromosome pairs that sets them apart from other species. Humans have 23 pairs of chromosomes, and alpacas have 37 pairs.
Reproduction in higher mammals involves duplication and then halving of the chromosome pairs, so that each sperm or egg contains only half the original number of chromosomes. At fertilization, the original number of chromosomes is restored, with half of the genetic material coming from the mother, and half from the father. The new baby has the same number of chromosome pairs as its parents, but it is not a clone of either, as the recombination of any two halves is an entirely random event. Each mating event is therefore a completely separate event from the one before it, and the one that will come after it. This is the basis of variation within a species.
The genotype is the full complement of gene pairs for the alpaca. This is fixed from the moment of fertilization of an egg by a sperm, and cannot be altered (except by gene technology). The phenotype is the physical expression of those genes, which is what we can see or measure on the alpaca.
The expression of those genes can be altered by any number of environmental effects, such as time, temperature, day length, chemicals, different foods and so on. Alleles in the genotype are said to be dominant, when they are always expressed in the phenotype. Dominant alleles require only one copy of the gene in the genotype to be expressed. If two dominant alleles are present, one is usually inactive. Alleles that require two copies of the gene in the genotype, to be expressed in the phenotype, are called recessive. When the alleles in the genotype are the same as each other, they are called homozygous. When they are different, they are called heterozygous.
Usually when we talk about the “genotype” of an animal, we are really only referring to a few genes whose expression we are interested in, eg fleece type or colour.
There appear to be three main series of genes, which interact in various combinations to control pattern and colour in mammals. The first is called Extension, which controls the other two. The second is Agouti and the third is the black/brown locus. Dr Phillip Sponenberg of the USA considered that the Agouti locus was the most important locus for determining coat colour; and proposed a series of phenotypes to fit with observed patterns and colours in alpacas.
There is a complex interdependence between the first two series, in that Agouti alleles require the presence of Extension wild type allele for their full expression.
The various alleles at the Extension locus either extend or reduce the amount of eumelanin in the coat. These alleles give a uniform coat colour, with no shading or variation. They are both antagonistic and epistatic to Agouti series alleles. There are three main alleles. The Extension series is designated by the letter E with superscripts of D, dominant black; +, wild type; and ee, recessive red.
Agouti is the reverse of Extension, in that it runs from light to dark, but it requires the presence of the Extension wild type allele for expression of the Agouti alleles. The Agouti series is designated by the letter A. The top dominant for the Agouti series is the lightest allele for that species. It may be called “dominant white”.
The black/brown locus – determines whether the eumelanin present is black or its recessive brown. As these are two alleles of the one gene, the animal cannot have both black and brown together in the one coat. The Black/ brown locus is designated by the letter B, with superscripts of B (dominant black); and bb, recessive brown.
Agouti itself is a protective colouration more often seen in smaller animals, such as cats and rodents, where both red and black pigment may be found in the one hair. Guard hair is often uniformly dark. Agouti also produces the effect of the ventral part of the body being lighter than the dorsal part in many species.
In the larger grazing animals, this translates to symmetrical, fairly well defined patterns of red and black areas in the coat. Patterns with more red dominate over patterns with more black. Domestic horses and cattle with these patterns are called “bays”; they have generally redbrown bodies and black points, that is, any combination of the ears/face/mane/tail or lower legs. The shade of red, particularly in horses, can vary from light red yellow to very darkest mahogany, where the black points are sometimes hidden.
Dr Sponenberg considered that the red colour on nearly all fawn, red, tan and “brown” alpacas was phaeomelanic red, and that most alpacas described as “browns” would have black fibre on them, and would therefore be bays. The important point here is that the “brown” colour, on an animal that appears to be both black and brown, is phaeomelanic red, and not eumelanic brown.
An alpaca could be homozygous or heterozygous for each of the three gene pairs. It could be homozygous for all three genes, but it would be more likely to be heterozygous for at least one of them.
Alpaca fleece colours have been described from the colour of the fleece on the blanket. These colours were originally decided by the mills that used the fleece. Patterns of colour have been largely ignored, or at least not recognised, either by alpaca breed societies or by breeders themselves. The colour charts are meaningless from the point of view of genetics. This has led to the confusion with alpaca colour genetics.
Drawn from ‘The Alpaca Colour Key” by Elizabeth Paul November 2002.