AVIAN GENETICS

The purpose of this section is to address the mechanisms of intragenic complementation and crossover. The recessive blue mutation found in various parrot species has been applied to this discussion as a working example but in no way does this discussion fully describe the various alleles of this gene locus or accurately portray their intragenic processes. The latter is still under investigation.

As we know, a gene is a strand of DNA. The DNA strand is composed of nucleotide base pairs. If two different mutations for a particular gene (DNA strand) occur at the same nucleotide site then they are considered to be homoalleles. If the mutations occur at different nucleotide sites then they are considered heteroalleles.

In the figure below, let's assume that we have a gene composed of 12 nucleotides: each nucleotide is represented by a box. If Allele A (or Gene A) experiences a nucleotide replacement (i.e., mutation) at the second nucleotide (designated M1) and Allele B experiences a nucleotide replacement at the second nucleotide site but a replacement different than that of Allele A (designated M2) then Allele A and Allele B are considered homoalleles. Simply put, if two different types of mutations (i.e., nucleotide replacements, additions or deletions) occur at the same nucleotide site on a gene's DNA strand then both genes are considered homoalleles.

Now, let's assume we are dealing with the same gene locus as shown above. If mutations occur at different nucloeotide sites then the alleles of this gene are considered to be heteroalleles. In the figure below, Allele B is a heteroallele of Allele C.

Allele C is also considered a heteroallele of Allele A.

All alleles, regardless of their nature, can be categorized as either: 1.) fully functional producing full color; 2.) leaky, only partially defective and capable of producing some color; or 3.) totally defective and producing no color. There are situations when two totally defective alleles, but defective in different regions of their DNA strand, are capable of producing some product of color as is seen with the Budgerigar heterozygous for Blue Mutant 1 and Blue Mutant 2. There are also situations where heteroalleles when in the heterozygous state are capable of producing more color than either allele in the homozygous state. Such a situation occurs when the Budgerigar Goldenface allele is complemented by the Blue Mutant 1 allele. When both alleles are present in a bird the bird is green, whereas if homozygous Goldenface only traces of yellow are produced beyond the head region of the bird and if homozygous Blue Mutant 1, no yellow is apparent. Intragenic Complementation (also referred to as allelic complementation, intracistronic complementation and just complementation) is the term used to describe heteroalleles complementing to produce more color than either allele could produce on their own. I prefer to use the term intragenic complementation since this term makes reference to a single gene locus. Complementation by itself is ambiguous since this term can also refer to genes at different loci that complement to produce a different phenotype.

Current information supports the concept that there are two blue mutations (Blue Mutant 1 and Blue Mutant 2) and two partial (parblue) mutations (Goldenface and Yellowface) within Budgerigars. The parblue mutations are an intermediate color between green and blue and thus could be considered leaky alleles.

The Blue Mutant 1 allele (b^m1) and the Blue Mutant 2 allele (b^m2) have been classified as heteroalleles. When a Budgerigar is homozygous for Blue Mutant 1 (b^m1,b^m1) or homozygous for Blue Mutant 2 (b^m2,b^m2) it shows no signs of yellow and thus is a true blue. However, when the Budgerigar contains both the Blue Mutant 1 and the Blue Mutant 2 alleles (b^m1,b^m2) it displays some yellow coloring suggesting intragenic complementation.

To understand how intragenic complementation occurs, a more detailed explanation of the genetic product must be presented. Genes are responsible for producing proteins (enzymes) that are involved in biochemical reactions. All the various colors on a bird are the result of biochemical reactions. Each gene is responsible for producing a single protein also referred to as a polypeptide chain. An enzyme involved in a biochemical reaction may just consist of a single polypeptide chain; it may consist of multiple copies of the same polypeptide chain bonded together in a particular configuration; or it may consist of different polypeptide chains produced by different gene loci bonded together in a particular configuration. Each enzyme whether a single polypeptide chain or multiple polypeptide chains will contain one or more functional domains. A functional domain is an independent portion of the enzyme actively involved with its respective biochemical process. Simply put, a biochemical process requires one or more functional domains from an enzyme to properly complete the final product processing.

There are two methods by which intragenic complementation can occur. I will apply the blue mutation to both cases. It should be understood that we currently do not know the type of enzyme produced by the blue locus and thus the method of intragenic complementation.

The first method of intragenic complementation deals with the gene being responsible for producing a protein (enzyme) that has two or more functional domains that act independently. The figure below shows a hypothetical enzyme with two functional domains.

If Blue Mutant 1 effects one functional domain and Blue Mutant 2 effects another different functional domain then it would be possible to see some yellow color in the heteroallelic offspring. A creamface bird will be produced when both defective enzymes are present at the biochemical process and complementing each other with functional domains. If this is the true case for the blue mutation, then we can explain partial yellow production being attributed to the fact that one normal enzyme is much more efficient than two defective enzymes trying to do the job.

I have applied the hypothetical enzyme to the example below to show how two defective enzymes could produce some yellow coloration.

Reactions will also occur that produce no final product.

The second method for intragenic complementation deals with the yellow coloring process being controlled by a protein (enzyme) composed of two or more identical polypeptide chains. The gene responsible for the yellow phenotype produces the polypeptide chain that when combined in two or more (number undetermined) allows the yellow coloration process to take place and thus produce a green bird. If the Blue Mutant 1 produces one defective form of the polypeptide (poly-A) and Blue Mutant 2 produces another different but still defective form of the polypeptide (poly-B) then it is possible that the two different types of defective polypeptides could assemble in a specific configuration to produce a partially functional enzyme that will produce a creamface bird. In this situation the bird will be producing at least three different types of enzymes: a non-functional poly-A/poly-A enzyme; a non-functional poly-B/poly-B enzyme; and a partially functional poly-A/poly-B enzyme. Functional domains also apply to this case.

The only major difference between the two cases presented is that in the first case two different proteins are complementing as individual units to bring about a biochemical process where as in the second case two different proteins are complementing as a single bonded unit to bring about a biochemical process.

Another interesting point to be made about heteroalleles is their potential for intragenic crossover. The previous chapter discussed crossover between chromosomes where genes relocated from one homologue to another. With intragenic crossover, crossover is occurring within the gene. Intragenic crossover occurs at an extremely low frequency. The Bird Tracker software does not consider intragenic crossover for the blue or any other mutation when performing a computation.

The figure below demonstrates intragenic crossover. If we take our heteroalleles from above, each having a mutated nucleotide at a different area, and apply intragenic crossover we end up with an allele having two mutated nucleotides and a normal allele.

Applying the example above to the two blue mutant alleles will produce the following possible gametes when breeding a heteroallelic blue Budgerigar (b^m1,b^m2):

When intragenic crossover is applied to the blue locus there is a potential for eight different types of alleles as shown below in the hypothetical illustration. For simplicity, I have displayed the Goldenface, Yellowface and Blue Mutant 2 as homoalleles. If in reality they are not homoalleles, then additional double mutated alleles will be produced. The double mutated alleles (b^{gf m1}, b^{yf m1}, and b^{m2 m1}) will most likely appear identical to the Blue Mutants 1 and 2.

The table below summarizes the phenotypes that could be expected if a bird possesses the specified combination of genes.

As mentioned, the goldenface, yellowface and blue mutant 2 genes were displayed above as homoalleles for the purpose of simplicity. Proving a homoallelic condition is much harder than proving a heteroallelic one. What we do know is that intragenic complementation does not occur when any of these genes are paired to each other (i.e., b^gf,b^y2; b^gf,b^m2; or b^y2,b^m2). The fact that intragenic complementation does not occur for these genes would strongly suggest that the protein produced by each have damage to the same functional domain. If intragenic crossover were to be observed between any of these alleles, then the homoallelic condition would be ruled out for these alleles. For example, if a Goldenface Blue Mutant 2 (b^gf,b^m2) was crossed to a Blue Mutant 2 (b^m2,b^m2), then we would expect all offspring to be Goldenface Blue Mutant 2 (b^gf,b^m2) and Blue Mutant 2 (b^m2,b^m2). If any Green birds appeared then it would most likely be the result of an intragenic crossover. Of course you can not rule out the very remote possibility of a reverse mutation that fixes one of the mutated genes.