THE USE OF GENETICS IN BREEDING CHAMPIONS
INTRODUCTION
This part should actually have followed on parts 1 to 3, seeing that it fits well with the processes of cell division and reproduction. I intentionally discussed Mendelian Laws first, because chromosomes and their behaviour also links very well with quantitative genetics, which is what we will discuss next.
When one looks at enlargements of chromosomes you begin to realize how little we really know about genetics, not to mention how almost impossible it is for us pigeon fanciers, who are not experts at genetics and do not have laboratories and sophisticated equipment at our disposal, to use the little we know to breed top quality racers.
Experts in genetics claim that chromosomes are highly ordered, organized packages designed for the storage of genetic material, its condensation during cell division and regulation of gene expression. Classical transmission electron microscopy shows no hint of this high degree of organization, at least not to me. There are even more precise ways of identifying genetic material and sequences, for example “Fluorescence In Situ Hybridization”, or FISH, also called “chromosome painting”. Chromosome painting may involve other types of labeling tools, such as autoradiography for radioactive probes. (http://cellbio.utmb.edu/cellbio/nucleus2.htm.) Fortunately for us we have the Internet where we can read about the sophisticated research being done by others and from which we can, perhaps, also benefit.
In this chapter we will limit our discussion to concepts and processes that we pigeon fanciers can use in breeding good quality pigeons, or of which we need to know a little more in order to understand why we should or should not do certain things when breeding racing pigeons.
GENE INTERACTION
There are various ways in which genes at different loci interact with each other. The ability of a gene at one locus to effect the expression of one or more alleles at another locus is termed epistasis. There are various forms of epistasis. They are as follows (http://www.cabinsoftware.biz/Genetics_Tutorial/Part13.htm.):
Genes that act together to produce differences in the degree between phenotypes are termed polygenes. This form of inheritance is different than the classical Mendelian type gene or major gene. A single pair of genes controls not all traits – numerous genes perhaps up to a 100 or more can control a trait.
ALLELIC INTERACTION
There are various ways that alleles at the same loci can act with each other to produce a particular phenotype. Allelic interactions at the same loci are categorised a follows:
Keep in mind that phenotypes controlled by genes at different loci can interact to create the appearance of a particular case mentioned above (e.g. duplicate dominant gene interactions).
In the very first article I mentioned that the concept of multiple alleles becomes very interesting and important when working with a population (such as our breeding lofts). The reason for this is that, while a given bird gets a sampling of 2 genes for every locus, the population may have 3, 5 or even 10 different alleles available for a given locus. The frequency of each of these alleles in the population is what determines our breeding progress. If the population is at equilibrium and random matings occur, the frequencies of the various alleles does not change. Our goal in breeding then is to 1) assure we have the desired alleles (of the larger gene pool of pigeons) present in our sample of that gene pool (our breeding loft) and 2) to increase the frequency of those desirable alleles while eliminating or reducing the frequency of those that are either less valuable or outright undesirable. The challenge of breeding better pigeons is further compounded by that fact that many, if not most, of the traits for which we are interested are coded by more than one locus.
The terms used to describe how often a gene displays itself are penetrance and expressivity. Penetrance is defined as the percentage of individuals with a particular gene combination (genotype) that exhibit the corresponding character to any degree. If the dominant gene in the heterozygous condition was not expressed all the time then the penetrance is some percentage less than 100%. Most dominant genes have a peneterance of 100%. Expressivity is the degree of effect produced by a particular penetrant genotype. The Pied trait is a good example of expressivity – ranging from several white patches in some pigeons to completely white in others.
LINKAGE
As you probably know by now, all genes are not inherited independently. Furthermore, genes are arranged on chromosomes, which are essentially long strands of DNA residing in the nucleus of the cell. This opens the possibility that two otherwise unrelated genes could reside on the same chromosome. This raises the question: Does independent inheritance hold for those genes?
To start with, we need to consider the rather complex process that forms gametes (egg and sperm cells, each with only one copy of each chromosome) from normal cells with two copies of each chromosome, one derived from each parent. What happens in practice is that the maternally-derived chromosome (chromosome coming from the hen) lines up with the corresponding paternally-derived chromosome (chromosome coming from the cock), and only one of the two goes to a specific gamete. This sounds quite simple, but in reality the process is somewhat more complicated, because, while the paternal and maternal chromosomes are lined up, they can and do exchange segments, so that by the time they actually separate, each of the two chromosomes will most likely contain material from both parents.
At this point we need to define a couple of terms which we did not use yet. Two genes are linked if they are close together on the same chromosome and thus tend to be inherited together. Linkage in common usage, however, may apply to a single gene having more than one effect. Thus, the same gene could easily influence more than one process – different traits may be associated. This is due to what is called pleiotropic (affecting the whole body) effects of the single gene.
In true linkage, there is always the possibility that linked genes can cross over. Imagine each chromosome as a piece of rope, with the genes marked by colour stripes. The matching of the maternal and paternal chromosomes is more or less controlled by the colour stripes, which tend to line up. But the chromosomes are flexible. They bend and twist around each other. They are also self-healing, and when both the maternal and paternal chromosomes break, they may heal onto the paired chromosome. This happens often enough that genes far apart on long chromosomes appear to be inherited independently, but if genes are close together, a break is much less likely to form between them than at some other part of the paired chromosomes.
Establishing linkage between actual traits is rare. The lack of examples does not, however, imply that linkage does not exist, but rather that the breeder is working with traits for which linkage is difficult to demonstrate. The traits that enable a pigeon to be a top class racer are probably complex traits inherited in a quantitative manner. Researchers believe that genes at many loci influence these traits, with the effects of single genes being miniscule. Linkage between loci cannot be demonstrated until the influence of single alleles can be distinguished.
Linkage groups, that is, collections of loci known to be on the same chromosome, must exist in these pigeons, but this can only be confirmed by establishing gene maps for pigeons.
Enormous numbers of genes are contained within the genetic material of each pigeon. These genes are arranged on the physical units of inheritance, the chromosomes. The conclusion to be drawn from these facts is that each chromosome must carry genes at many loci, influencing a multitude of traits. Because such loci are physically linked together, they cannot be expected to obey Mendel’s third law (the Law of Independent Assortment) because the physical ligature between them would tend to cause the alleles to be inherited together rather than allowing them to reassort freely during gamete formation. (van Vleck, et al: 67.)
Chromosomes break and rejoin during the cycle of miotic cell division. This breakage and reunion occur when chromosomes pairs are lined up and before the pairs separate. The rejoining often occurs between lengths of separate chromatids, such that alleles at different loci may be reassorted during meiosis. Hence, when the chromosome pairs separate, they may carry with them new combinations of alleles along their arms. Logically, the new combinations must be represented in the progeny. Thus, linked traits do not segregate independently but neither are they tied together so tightly that new combinations are never seen.
The fraction of new combinations, called recombinants, appearing in each generation should indicate how closely the loci are linked together. The greater the distance between the loci, the more chance there would be for a breakage and rejoining to occur and, therefore, the more recombinants that should be observed in progeny. Conceivably, loci that are very far apart on the same chromosome would have so many breakages between them that they would appear to be assorted independently. Alternatively, pairs of loci situated very closely together on the chromosome should have few intervening breakages, so new combinations would be hard to create and very few would be detected in the progeny.
Such breaks, called “crossing over” do occur, and occur often enough that they are used to map where genes are located on specific chromosomes. In general, neither linkage nor crossing over is of much importance to the average pigeon breeder, though one should certainly keep in mind the possibility that the spread of an undesirable gene through a strain is due to the undesirable gene being linked to a gene valued in the strain. Crossing over is also important in the use of marker genes for testing whether a pigeon carries a specific gene, most often a gene producing a health problem.
MUTATIONS
Mutations are sudden changes in the traits of a family of pigeons that cannot (logically) be attributed to gene combinations. Yellow eyes in pigeons are generally regarded as the original colour (also called a wild type trait), while white eyes are the mutations. The colour pied is also regarded as a mutation. Through the ages mutation had an influence on the racing ability, ability to orientate, etc of our pigeons. Chances that any one of us will ever find a mutation in our lofts are incredibly small, so don’t use it as an excuse when you sell someone a pigeon with yellow eyes whose parents both have white eyes. Yellow is a dominant eye colour and white recessive, but a pigeon with white eyes can only have homozygote allel gene pairs. (If both genes carry the same trait, such as white eye colour, we have homozygosity, and if the genes carry different traits, e.g. white eye colour originating from the cock and yellow eye colour originating from the hen, we have heterozygosity.)
DNA TESTING
DNA testing is used to identify pigeons carrying specific, undesirable genes. DNA testing can be a rather complicated process. However, it can be of much value in eliminating unwanted traits from our pigeons, so that we cannot ignore it. There are two distinct ways of using DNA testing to identify pigeons carrying specific, undesirable genes. The first (and preferable) is actually to sequence the undesirable gene and its normal allele. This allows determination of whether the pigeon is homozygous normal, a heterozygous carrier, or homozygous affected.
Since the genes themselves are being looked at, the results should be unambiguous. (The breeding decisions based on these results are still going to depend on the priorities of the breeders.)
In some tests, however, a marker gene is found that appears to be associated with the trait of interest, but is not actually the gene producing that trait. Such a marker is tightly linked to the gene actually causing that trait. As an example - Rontondo (1991: Part II: 4) claims that, if a pigeon’s end flights (10 th flights) are the only white ones, then this bird will be a good breeder but not much of a racer. I do not know if the claim is true, but this is a good example of how a marker gene may be associated with a visible trait. This does not work at all badly providing that the group on which the test was validated is closely related to the group to which the test was applied.
Especially in pigeons there is always the possibility that at some point in the breeding history a crossover occurred. Quite a large fraction of the population (strain – I am referring to a “strain” rather than a “breed”, because of the short space of time between different generations, compared to human beings and bigger animals, such as cattle and dogs) may have the original relationship between the marker gene and the problem gene, but if a crossover occurred in an individual who later had a considerable influence on the strain, the strain may also contain individuals in which the marker gene is associated with the opposite form of the problem/good gene. Since the relationship between individuals of the same strain may go back many generations, there is a chance of the crossover occurring in each generation, linked markers need to be used with caution and with constant checking that marker test results correlate with observation of, for example, racing performance.
But is marker tests of any value at all for us pigeon fanciers? I believe yes. A marker gene can assist in finding and sequencing the unwanted or wanted gene. If the marker gene can be identified externally, e.g. if it is linked to a particular colour, one should be able to identify carriers of the unwanted genes. For example, if a pigeon pair produces two different colours offspring, and, through observation, you find that one colour group of pigeons race well while the other colour group does not, one can conclude that the unwanted gene is present in the non-performing colour offspring only. But marker tests are accurate only so long as neither parent of the individual has a crossover chromosome. The linkage of a marker with the unwanted genes is generally based on studies of how the marker is linked to the genes in that particular family.
An efficient way for pigeon fanciers to determine if a pigeon is a carrier of recessive genetic defects is by observing the performance of our pigeons. There is clearly something wrong with a pigeon that regularly underperforms. We are fortunate that such carriers of unwanted genes are often sorted out by the racing system – they mostly don’t return from road training or races for many different reasons.
TEST BREEDING
Test breeding is a form of DNA testing that can be done by the pigeon fancier without necessarily having much scientific expertise in genetics and without needing a laboratory and sophisticated equipment. It is mostly done with one of two purposes in mind: to determine the genotype of a specific pigeon (to determine whether a pigeon carries a recessive gene), or to determine the fundamental genetics of a trait.
The first step will be to make a guess. Of course it should be an informed guess – you must have reasonable indicators that the gene is present, for example based on the colour or behaviour of the pigeon. Racing performance can also be regarded as behaviour, since it is often a good indicator of speed, perseverance, ability to orientate, etc. In order to elevate the guess to the level of a hypothesis, you need to work out what your guess predicts in terms of what the pigeon’s parents can produce and then breed to see if that is really what happens.
Pedigree information may help determine whether a pigeon is a known or likely carrier of a recessive allele. A pigeon showing the phenotype of the dominant allele (the dominant phenotype) is known to be a carrier if either parent had a homozygous recessive genotype. Progeny of a known carrier are likely to be carriers.
When phenotypical traits are at stake, one can improve upon the guesswork by examining the pedigree of each parent. If either parent of a yellow-eyed chick was the direct offspring of a white-eyed father or mother, we could positively determine its genotype to be Yw (Y for dominant yellow and w for recessive white). This is because a white eyed parent can only contribute a ‘w” gene to the offspring and a pigeon can only have yellow eyes if they have at least one “Y” gene. (http://www.shewmaker.com/digest94.html.)
If we don’t have accurate pedigrees, we can still narrow the possibilities down by mating pigeons with different partners with different or the same eye-colour and then note the eye-colour of the resulting offspring. This, however, can take many generations before we will have accurate information. The situation becomes even more complex if we try to determine the genetic makeup in terms of traits such as speed, endurance, attitude, will-power, etc.
Dr Jaap Nel. Email: jaap7@iafrica.com.