Part I - Breeding and Genetics: Introduction
Like most of you, I have been breeding alpacas for a relatively short period of time, yet a little over a year ago I had started to question some of the current wisdom on breeding choices available to me at the time. How exactly do I improve the average quality of my herd, which traits are important to me, have I established what my primary goals are and what criteria should I be using to differentiate between one herd sire over another. Reading many articles in the alpaca press led me to believe that the answers do exist and that I should be able to benefit from the wisdom and experiences of other alpaca breeders. In breeding terms the UK is at a disadvantage at the moment because of its short life. There is no depth of genealogy to draw upon and as we shall see, the ultimate viability of a superior male alpaca rests only in the ability to assess the genetic quality of many of his progeny.
Now is a good time to start understanding the many issues involved. In this way as we grow and have the opportunity to make assessments, we will improve our chances of making the right selection choices. It was clear to me that if I wanted to accelerate my improvement programme I needed to know much more about the science of inheritance. Over the last year I have been researching as much published literature as time will allow me and I am hopeful that I can prompt you all to improve your own understanding.
UK alpaca breeders have much to learn on this subject but we are fortunate to be able to draw upon the experiences of far more qualified people than I to assist us in our breeding decisions. For this short series of articles I have drawn heavily on the published works of Mike Safley, Dr. Philip Sponenberg and Chris Tuckwell as they seem to me to have encapsulated the basics in an easily assimilated format. I hope you agree.
Firstly, I am no expert. I have no formal training in the medical sciences but have however become fascinated with the challenges that alpaca breeding presents. Genetics is the science of how traits are passed on from one generation to the next. Contrary to what I had originally thought, it is not a predictive science. It must be viewed rather as a science of possibilities, predicting a range of expected types within offspring from certain pairs. It should be part of the toolbox that we use in our decision making process. All of us who have a clear vision of what we want to achieve need to understand its strengths and weaknesses to enable us to benefit the most. We can learn a lot from an understanding of the basic principles involved in genetics and breeding systems. As alpaca breeders we should not ignore the experiences of other stock industries.
The basis of modern day genetics goes back to the nineteenth century when the Austrian monk Gregor Mendel published works on his breeding experiments with sweet peas. Mendel's laws of inheritance or Mendelian Genetics and the later Galton's Inheritance Law have formed the building blocks for all later work. We will start with some definitions of the words and concepts and then cover some useful concepts for developing breeding philosophy, breeding systems and structures, methods of selection and measurement of results.
Chromosomes and Genes
The essence of Mendelism is that inheritance is by particles or units, existing in pairs. Each unit maintains its identity generation upon generation. They do not blend with others to form new units and for each of the many different unit pairs, a parent will donate one unit each to its offspring, thus donating half of its own inheritance.
Bodies of all higher organisms are composed of cells, each of which contains these heredity units called genes. These are located along strips of DNA called chromosomes that occur in pairs, an essential concept. Alpacas have thirty-seven pairs of chromosomes, each individual getting one member of the pair from the sire and one from the dam. The genes are the basic unit of heredity that maintains the individual identity between generations. The laws of chance and probability governing which gene from each pair is passed on is the essence of inheritance. Common parents can transmit different inheritances to different offspring.
Dominance and Recessive
Within the pairing of genes there are two types possible, dominant and recessive. A dominant gene is so named because when there is a mixed pair of genes, it is the one that expresses its character over the recessive, whose character is partly or completely concealed. Life however is not that simple in reality, dominance can be a matter of degree such that mixed genes may give rise to intermediate characteristics. Genetic birth defects are caused by recessive genes and since these do not often express themselves when paired with dominants such defects can remain hidden for many matings until chance dictates a double recessive pairing for that trait (many birth defects can be the result of multiple genes, but the principle remains the same).
Homozygous and Heterozygous
An individual alpaca is said to be homozygous for a trait if the two genes it carries for that trait are the same. The donation to an offspring will then always be the same. The pair of similar genes, are homozygous.
The opposite to this is heterozygous. The two donated genes for a particular trait are dissimilar and an offspring could end with either, the choice is random. A mixed pair of genes for a trait are heterozygous. The pairs of genes can react in different ways. One is that only one of the specific pair is expressed, and the other is hidden. In this case the one that is expressed is called dominant, and the one that is not expressed is called recessive. This is a key issue as dominant genes essentially cover up recessive genes. Codominance is where each member of the dissimilar pair is expressed and shows up in the phenotype. Blood type is an example of this where all is expressed, nothing remains hidden. In horses, colour is co-dominant. Two dark genes produce a chestnut. One dark and one light produces the palomino and two light will produce a cream with blue eyes.
Quantitative and Qualitative Traits
We also have to define both quantitative and qualitative traits. The former are those influenced by many genes and cannot be identified. They are easily influenced by the environment and exhibit continuous variation. Their description and analysis is undertaken on a population basis rather than an individual one.
Only a few genes that are identifiable influence qualitative traits. They are not easily influenced by the environment and produce measurable classes of phenotype described and analysed in terms of individuals.
By way of an example to explain the above concepts we should consider a simplistic hypothetical case where say the crimp of an alpaca is a qualitative trait and is controlled by only one gene pairing on the DNA thread. The range of crimp genes that would be available could be:
A = good crimp
Aa = mediocre crimp
a = poor crimp
Here we are using the capital letters to indicate a dominant gene and Aa indicating a gene expressing incomplete dominance.
One result could be when both parents are homozygous for the A gene, then it follows that the cria will also have good crimp as the donation of gene from each parent will always be A. The cria will have dominant AA genes for crimp.
A second result could be when both parents are heterozygous for the both good and bad crimp genes. We then have the following statistical probabilities for the expression of crimp as a percentage of all matings:
Aa x Aa = One AA or 25% with good crimp
Two Aa or 50% with mediocre crimp
One aa or 25% with poor crimp
In the real world of alpacas this simplistic approach is unlikely as crimp will be determined by a number of paired genes at different locations in the DNA. However the example of the polled gene in cattle for the absence of horns is a single dominant paired gene found at a single location.
The goal for an alpaca breeder should be to develop animals which are homozygous for a positive trait. In this example if one of the alpacas was homozygous (AA) for good crimp and the other heterozygous (Aa), all of the resulting cria would have either good or mediocre crimp since it would not be possible to produce a cria which was homozygous for poor crimp (aa). If it was the male who was (AA) and was bred to all females in the herd, over time fewer and fewer cria would be born with mediocre crimp since each would have a minimum of one good crimp A gene. If on the other hand the male was homozygous for poor crimp it wouldn't be long before the entire herd had poor crimp.
These are obviously simplified examples but in principle, if a male alpaca has positive dominant qualitative traits in his makeup he will be producing progeny with a high proportion of positive traits.
It is also worth considering at this point the implications of Galton's Law of inheritance. An alpaca is half its sire and half its dam, the parents in their turn are only half of their parents, and so on back through the family tree. The contribution from each parent is only half of its genetic makeup so the chance of getting a certain character from a parent is only half of a half, or from a grandparent a quarter of a quarter.
Galton's law considers the mathematical probability of a given ancestor's influence on a specific animal, based on averages. The implication here is that selection in succeeding generations does not easily offset the average mathematical expectations of inheritance. An exception to this might be if an outstanding stud appears close to the specific animal in question on the genealogy, or if the same stud appears many times throughout the tree. The cumulative effect then adds up to outweigh the mathematical average and can be used to good effect by the observant breeder. Herds of alpacas bred on a random or constant out-cross basis can only be expected to achieve the average quality of the entire herd.
Genotype and Phenotype
The final makeup of an animal is the result of its genetic makeup and the environment it lives in. Genotype refers to an alpacas genetic makeup whereas the phenotype is the result of the expressed portion of the genetic makeup and the environment to which it is exposed. Phenotype refers to the appearance of measurable characteristics of an individual alpaca. Examples would include such features as its head, conformation, fleece quality, measurable quantities such as weight, fleece clip weight, reproductive organs and anything that covers the physical appearance of the animal.
Alpacas that express positive phenotype traits will not necessarily breed true to these. Environment plays a large role in the expression. Conversely an alpaca that is genotypically heterozygous for a particular trait may express itself as homozygous because of the dominance of one of its genes. As alpaca breeders we need to establish breeding programmes that will allow us to distinguish animals that are genetically consistent for the trait we require, regardless of the environment. Phenotype does not always reveal the genotype.
The disappointing end result of all of this is that when assessing the merit of breeding animals the only certain way to judge its genotype is by the quality of many of its descendants. Plant breeding is considered genetically sound. It has over many years evolved a system where genotype selection has been used rather than on an individual phenotype basis. In this way breeders have managed to disregard the environment and other factors unrelated to the genotype when making selection decisions. Alpaca breeding needs to follow the same rules, yet the slow reproduction rate, the importance of individual animals to us and our desire to choose stud males at an early age all based on our ideal of beauty or phenotype expression can lead to inefficient selection decisions.
There are some solutions. With proper selection and use of effective breeding programmes based on a fuller understanding of the principles involved, the genetic merit and overall quality of the alpaca can over time become predictable. In the next article we will cover some of the more practical aspects of deciding on a breeding philosophy, the different breeding methods available, heritability and the all important subject of selection.
Chas Brooke - MileEnd Alpacas