The Better Breeding Blog
The International Alpaca Reference Library

Articles by Alpaca World Magazine:

Genetics 101

Kylie Munyard PhD

This article is designed to explain some basic concept in genetics. Genetics is the science of genes. As alpaca breeders you are, effectively, practising Geneticists. You might not have white coats and expensive equipment, but nevertheless each and every time you join two alpacas you are performing an experiment. Why do some matings produce productive, well conformed cria, and others not? Setting aside environmental factors, genetics is the culprit. If you don?t understand genetics, you will have a much harder time producing the type of alpacas you want. Are you one of the thousands of people who get completely lost when a scientist starts talking about alleles, and epistasis and polygenic traits? Well, you don?t need to be. Genetics is complicated, if it wasn?t we wouldn?t need experts. However, each and every breeder is capable of learning enough genetics to prevent them from making uneducated breeding decisions.

Most of you already know that each individual is the product of the combination of equal amounts of genetic material from each of its parents. Thus, for each trait that an animal has (be that physical, mental or physiological) half of the blueprint comes from Mum and half from Dad. Most of you have also heard of chromosomes as well. The blueprint (DNA) from each parent comes in neat packages called chromosomes. Did you know that alpacas, and other Camelids, have 36 pairs of chromosomes? Humans have 23. All of the pairs, except one, have two identical chromosomes. The one exception is the pair that determines sex. As in humans, male alpacas have one X chromosome and one Y chromosome, while females have two X chromosomes. This arrangement of pairs, coupled with the process of meiosis during which sex cells, gametes, are formed, ensures that each cria not only gets half of its DNA from Mum and half from Dad, but it ensures that each chromosome pair is made up of one from Mum and one from Dad.

Before you can begin to fully understand genetics you need to know the definitions of the many specific words that are used. At first they may seem to be jargon, gobbledegook, or worse?complete drivel! But when you communicate with someone it is very important that both parties know exactly what is meant, and so precise technical language is crucial. For instance, if you describe your fiercely protective flock guardian alpaca as a ?wonderful alpaca?, what does that mean to someone who doesn?t know your alpaca? To someone wanting a calm pet, that ?wonderful alpaca? could be a disaster waiting to happen.

So, what is a gene? A gene is the basic unit of inheritance. It is a segment of DNA that contains the blueprint for a single step in a biological process. That single step might be to regulate the action of another gene, or it might be to produce a specific protein. Because each gene is present in two copies, because we get one copy from Mum and one from Dad, there is a possibility that the two copies are not identical. Indeed, it is very common for there to be more than one version of a gene present in each chromosome pair. These different versions of genes are called alleles. You can think of it as a product and a brand. The gene is a product, and the different alleles are brands. So, there might be a gene for chocolate cake, and the alleles are homemade, packet or bought. They are all chocolate cakes, but there are differences between them.

The location of the gene within the chromosome is called its locus. Many genes are the same in different species, but they aren?t necessarily located in the same place on the same chromosome. Thus, you can say that chromosome 4 has the gene for chocolate cake and that there are three versions, and you would be describing the chromosomal locus of a gene with three alleles. If, at a given locus a gene has the same allele present on both copies, then that locus is said to be homozygous. If there are two different alleles present at that locus then it is heterozygous. Some genes have many more than two alleles. It is possible for a population to have as many alleles at a particular locus as it wants. However, each individual can only have a maximum of two alleles. If there are three, or more, alleles for a gene at a locus of an individual, then it doesn?t matter which two are present, it is still considered heterozygous.

Now that you know that any given locus can be homozygous or heterozygous the next thing to understand is what that means in the finished product, that is, in the animal. This neatly introduces the concept of genotype versus phenotype. The phenotype is the physical manifestation of the genotype. Obviously not every allele or gene will make its mark physically because some are regulatory genes, some are instructions to other genes and some are discernible or not depending on what other alleles on other genes are present. When there are two or more alleles for a gene, and one of these alleles only needs to be present on one chromosome for that trait to be visible in the animal, that allele is said to be dominant over the other allele(s). The allele that can be ?masked? by the dominant allele is called a recessive allele. The Agouti gene is a good example of this. This gene is well characterised in mammals, and our recent research strongly suggests that it acts the same way in alpacas. The Agouti locus has over 30 different alleles in mice, we don?t know how many alleles exist in alpacas, but we suspect at least four. In this example only the most dominant and the most recessive alleles will be considered. Two fawn alpacas can produce either fawn or black cria. Two black alpacas can produce only black cria. A word of explanation here?this example assumes that ONLY the agouti gene is in operation, these outcomes can change if other genes, namely MC1R are in action as well. The fawn allele is dominant, and the black allele is recessive. A fawn alpaca (phenotype = fawn) can have one of two genotypes. It can have two fawn alleles, or it can have one black and one fawn allele. In the latter case the fawn alpaca is said to be ?carrying black? or a black ?carrier?, because the black allele is being carried, unseen. Unless we have proof of the genotype, you can?t tell by looking at a fawn alpaca whether it has one or two fawn alleles. Proof of the genotype would be that one of its parents was black, or that the alpaca had produced a black cria. In this example we have two alleles (black and fawn), three genotypes (black + black, black + fawn and fawn + fawn) and two phenotypes (black and fawn). This is a cumbersome way of writing things, and when you progress to more than one locus, it can get very complicated. So, we abbreviate locus names to make things simpler. In this instance, because the gene is Agouti the abbreviation is A. Because the fawn allele is dominant it is written Awt (this is a historical naming convention from sheep genetics). The black allele is recessive and so is written as a lowercase a (not ?b?). By keeping all the letter designations for different alleles the same within a locus, we can quickly identify which alleles belong to which locus. So, a fawn alpaca that carries black would be written Awta, while a genetically homozygous black alpaca would be written aa, and a fawn alpaca that is homozygous for fawn would be written AwtAwt.

Unfortunately, though, not all interactions between alleles are that simple. We can also have incompletely dominant, co-dominant and sex-linked alleles. And that doesn?t even begin to touch on the so-called ?modifying genes? that can affect the way any of these alleles is expressed!
The roan gene is an example of a ?co- dominant? allele. Sometimes the roan gene is thought of as being dominant, because it takes only one roan allele to produce a roan animal. However, we know that in the case of a truly dominant allele there are only two phenotypes. With the roan gene we can produce three phenotypes, solid (coloured), roan and white. The merle gene is written R, so solid (coloured) would be RR, roan is Rr and white is rr. So, putting those two bits of information together, you can read the following Rr Awta and say that the alpaca is a fawn roan and carries black.

These technical terms and their explanations are only the tip of a complex, but fascinating subject.