Up to now we have been considering situations where were we have had
one dominant allele and one recessive allele. In a diploid plant
there can only be a maximum of two different alleles at any one gene
location, but if we consider a population of plants there can be more
than two different alleles of any given gene within that population.
These multiply alleles can, and often do cause problems when we try to
analyze inheritance patterns.
In an earlier lesson I covered the basics of how genes perform their functions. Briefly, genes are made up of sequences of nucleotides which get read in pairs of three and are transcribed into a linear sequence of amino acids that then act as enzymes. Some of these amino acids can form strong bonds among themselves and give the sequence of amino acids a three dimensional structure. It's the three dimensional structure of the protein combined with reactive sites that allows the enzyme to take some precursor chemical and convert it to an end product.
A dominant allele of a gene appears dominant because it produces an enzyme that takes a precursor and converts it to an end product. A recessive allele appears as a recessive because the gene produces an enzyme that fails to convert a precursor to an end product.
We have been using an example (totally made up) where a colorless precursor is converted to a red pigment by the "R" or "red flower" gene. The r allele produced white flowers because it failed to convert the colorless precursor to the red pigment.
As a further simplification I made up an example where we have an enzyme made up of 100 amino acids where the amino acids at location 25 and 75 bond strongly with each other. This forces the linear chain to form a U shape. However, this still leaves the two ends flopping around. Lets assume that there are also amino acids at locations 4 and 97 that strongly bond with each other. This gives a nice tight U shape. Now, lets assume that the amino acids at locations 1 and 100 are the reactive sites that does something that converts the colorless precursor to a chemical that is a red pigment. This example is totally made up and somewhat over simplified, but it illustrates the complexity of multiply alleles.
For this example we've assumed that the two amino acids at the ends of the chain (locations 1 and 100) grabs hold of the precursor like a lock and key and changes the precursor into a new chemical which is a red pigment. Now, lets assume a mutation comes along and changes amino acid #1 into a different amino acid that doesn't have any idea of what it is suppose to do. Thus, this new protein can't convert the precursor into a red pigment, so we see this form of the "red" gene as a recessive mutation and we call it the r allele.
Now, lets go back to the original enzyme that converts the precursor to the red pigment. Now, lets take the amino acids at locations 4 and 97 that holds the two arms of the U shaped protein into a tight U shape and remove one of them, or change it to a different amino acid that doesn't bond with the other one. Now, the protein still has something of a U shape, but the two arms can flop around, so instead of a tight U shape we have a protein that has more of a bowl shape. Now, the two reactive amino acids at the ends are too far apart, so they can't grab onto the precursor and thus, the precursor is not converted to a red pigment. We would also see this mutation as a recessive allele and would likely call it the r allele.
But, now we have a bit of a dilemma. We have two alleles that behave as recessive genes because they can't convert the precursor to the red pigment, but they are NOT the same allele. One allele lacks the reactive site while the other allele lacks the tight lock and key to carry out the reaction. However, they both appear as recessive genes and both alleles are likely to be called the "r"allele!
Lets now consider another situation. During meiosis something happens and part of the gene gets duplicated and instead of the protein being 100 amino acids long it is now 102 amino acids long and the two amino acids were added between positions 99 and 100. The amino acids at positions 4 and 97 still bond tightly, but now one arm is two amino acids longer then the other arm. The two reactive sites are still there and the lock and key is still a snug fit, but the reactive sites don't line up perfectly. The two amino acids at the ends are now misaligned and it is difficult for them to carry out the reaction that converts the precursor to the red pigment. Put your hands together in a pray position and open and close your fingers. The tips of your fingers easily touch each other. Now, slide one of the hands up half a hand. You can still touch your fingers tips together, but it takes a lot more effort. Our enzyme may still function, but it is going to do so at a much slower rate and produce only a small amount of red pigment. A low concentration of red pigment will appear pink. We now have an allele of the red gene that produces pink flowers! Lets call this allele r+.
(Note, I am going to put a slash "/" between the alleles to make it easier to read. So, genotype Rr will be written R/r.)
Now, if we have a F1 hybrid R/r+ and self it, we have a situation where red is dominant over pink, and if we didn't know better we would say that pink is recessive. However, if we have a F1 hybrid r+/r , which will be pink, we will conclude that pink is dominant and white is recessive. In reality, red is dominant over pink which is dominant over white: red > pink > white.
Now, to throw in a bit more confusion. If we have a r+/r+ hybrid it will be a darker pink then a r+/r hybrid because it is producing more red pigment. We could then take a red flower of genotype R/r+ and cross it to a pink flower of genotype r+/r and we get genotypes R/r+, R/r, r+/r+ and r+/r. The first two are red, the next is dark pink and the last is pink. Thus, we crossed a red flower with a pink flower and get a 2:1:1 segregation for red:darkpink:pink. Also, when we self the red F2's we get half of them segregating for red vs pink while the other half segregate for red vs white.
Lets now go back to our original 100 amino acid protein that functions to produce red pigment from a colorless precursor - the R allele. The amino acids at positions 4 and 97 bond and the amino acids at positions 25 and 75 bond to give a tight U shape to our enzyme. Now, lets assume a mutation occurs and replaces the amino acid at position 25 with a different amino acid that does not bond with the amino acid at position 75. The two reactive amino acids at the ends of the enzyme will likely still function even though the enzyme may not have the same tight U shape. The bottom part of the U shape can now move about more freely, but the enzyme still functions reasonably well because the amino acids in positions 4 and 97 bond and provide the essential structure for the reactive ends to do their job. This gene still produces red flowers, but it isn't the same red allele as our original red allele.
Now lets throw in a bit of a monkey wrench. Lets say that the amino acids at positions 4 and 97 can also bond with the amino acid at position 75. Remember the amino acid at position 25 has been changed so that it is no long able to bond to the amino acid at position 75. We now have a situation where the amino acids at either positions 4 or 97 can now bond with the amino acid at position 75 or they can bond with each other like they are suppose to. If the amino acids at positions 4 and 97 bond, then the enzyme will function. If either of the amino acids at positions 4 or 97 bond with the amino acid at position 75 (which the original enzyme didn't do), then the enzyme will have a completely different shape with one side of the U folded back on itself to give something of a J shape. A plant that is homozygous for this altered red gene will produce enzyme molecules some of which will function and some will not function. Lets call this allele r^.
Lets now say that allele r^ has some other properties such that under a certain temperature (cool) the amino acids at positions 4 and 97 bond like they are suppose to and produce a red flower (or close to red), but at a certain warm temperature almost all the enzymes assume the J shape rather than the U shape. Thus, a plant of genotype r^/r^ under cool conditions will produce red flowers, under warm conditions produce almost white flowers, but at intermediate temperatures produce shades of pink!
We have been dealing with a single locus, but by introducing some very slight modifications to the gene we have produced plants with completely different behavior from the same gene. A single, simple gene produces different phenotypes depending on which allele is present. Imagine the confusion that can be created when these various alleles are combined in various combinations.
Finally, lets go back to our original R allele with the two reactive sites at the ends, the amino acids at positions 4 and 97 that bond and the amino acids at position 25 and 75 that bond to give a overall tight U shape. The enzyme is 100 amino acids long, but there are only 6 critical locations that provide the necessary three dimensional shape and the reactive site for this simplified example. If any of these 6 critical amino acids are changed it can have very significant effects on how the enzyme functions, if it functions at all. For this example it would make relatively little difference what amino acids were between positions 26 and 74 - the amino acids at the bottom of the U shape. Some amino acids could be removed to make a shorter U or some amino acids could be added to make a longer U and it would not effect how the enzyme functions. There could be hundreds of different "R" alleles that have a different linear sequence of amino acids that all would appear as dominant red alleles. I'll try to explain some of the significance of this in the next lesson, or maybe later.