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Mendel Was Wrong?!
Mendel Was Wrong?!
Sometimes, Mendel's laws just don't explain the whole story. That's when these inheritance patterns come into play. You will need to be able to recognize these inheritance patterns given information about the genotypes and/or phenotypes of a genetic cross. These traits will not follow the typical pedigree patterns and phenotypic/genotypic ratios as the Mendelian traits we have seen up till now.
A. Incomplete Dominance
A. Incomplete Dominance
Many of the non-Mendelian inheritance patterns result from alleles being neither dominant nor recessive. This first inheritance pattern, incomplete dominance, is one such example. In incomplete dominance, two alleles exist, but neither dominates completed over the other. As a result, the phenotype for an individual who has both alleles (aka a heterozygote) is somewhere in the middle of the two extremes you might expect given the alleles.
It is easiest to look at an example for this case: In this example, you can see 3 phenotypes... 3! We have only seen 2 up until now. That's your first clue.
Now let's investigate these phenotypes. You can see that there are red flowers, white flowers, and pink flower. Heterozygotes, when a trait is incompletely dominant, will have a "blended" appearance. Basically, it's like you took each allele's phenotype and mixed them together. This is best shown in an example involve color such as this. Red and white blend together to make pink. So, you can be red, white, or pink. Pink is what occurs when an individual has two different alleles - one white and one red. Let's take a look at a genetic cross for this trait to see if we can understand a bit more clearly...
In this cross, you can see two parent plants, one red (RR) and one white (WW). First, please note that neither of these alleles is lowercase... that is because neither of these alleles is recessive!
Assume there are only red and white alleles - there is no purple possibility, for instance. So, in order to have red petals, you must be homozygous for the red allele (RR). To be white, you must be homozygous for the white allele (WW). So, if you cross a red flower with a white flower, we just need to look at the possible gametes each can create and pass to offspring.
The red parent will always pass a red allele, R, because that's all it has to pass. The white parent will always pass a white allele, W, because that's all it has to pass. As a result, all offspring of this cross with be heterozygotes and have the 'blended' pink petal phenotype.
These pink flowers form our F1 generation. If we wanted to, we could investigate what a possible F2 generation cross would look like (see here).
You can see that it will resemble the genotypic ratios of Mendelian F2 generations (1:2:1).
However, the phentoypic ratio is 1 red: 2 pink: 1 white because there are three phenotype possibilities - one for each genotype. That is what sets this kind of a trait apart from the Mendelian genetic crosses we've seen up until now.
B. Codominance
B. Codominance
The good news is that you have already done the hardest part of understanding this next inheritance pattern, codominance. The crosses will look the same because, just like in incomplete dominance, there are 3 genotypes, each with their own phenotypes.
However, codominance is different because the alleles both get expressed equally. So, instead of the alleles blending together and getting a phenotype somewhere in the middle of the two extremes, the alleles will both be expressed independently. So, instead of red and white blending together, they will remain separate and you will see both red and white in the phenotype.
Codominance and incomplete dominance are easily confused. In order to keep them clear in my mind, I like to remember this image associate with codominance.
Dad has horizontal stripes (HH) and Mom has vertical stripes (VV). When they cross (have offspring), Dad will pass an H and Mom will pass a V.
As a result, the offspring will have a genotype of HV. As a result, because the trait is codominant, you will see both vertical and horizontal stripes.
Note: They did NOT blend together to form some kind of diagonal line. That only would've occurred if this were incomplete dominance.
C. Sex-Linked Traits
C. Sex-Linked Traits
What are Sex Chromosomes?
What are Sex Chromosomes?
Up until now, all traits we have investigated have been located on autosomes, or just regular chromosomes. However, humans (and many others) have sex chromosomes as well. These sex chromosomes are chromosomes as well (hence the name...), so that means that they have genes.
There are traits that are coded for on the sex chromosomes! The traits are called sex-linked traits. In humans, the sex chromosomes are the X and Y chromosomes. Females have two X chromosomes and males have an X and a Y chromosome, of course.
Please note: In using terms such as 'males' and 'females', I will be referring to biological sex, not gender. Gender is a social construct but sex is the biological term determined by your chromosomes. There are intersex individuals, however, and we will hopefully get time to explore some of that later in the year.
How to Identify a Sex-Linked Trait
How to Identify a Sex-Linked Trait
The easiest way to identify a possible sex-linked trait is, of course, to make observations. Specifically, you should observe how a trait seems to affect (or not affect) a particular sex. Can you think of a trait that is more common in males or females? We can also look at pedigrees to do this analysis, and we will practice with that shortly. It is important that you do the analysis or have a significant sample size before you are certain that the trait is sex-linked. It could always be sampling error if you look at just one small family.
Typically, the first thing people think of in this context is colorblindness. And, indeed, colorblindness IS a sex-linked trait. Please note: there are many different kinds of colorblindness, and I will only be referring to one kind here. We do not need to focus on the differences or any other kinds for this course.
Colorblindness is much more common in males than in females, but let's investigate why by examining the crosses of some sex-linked traits.
Notation of Sex-Linked Traits
Notation of Sex-Linked Traits
First, we have to discuss how to represent sex-linked traits. As mentioned previously, these traits are determined by genes found ON the sex chromosomes. As a result, we must represent the sex chromosomes anytime we include alleles. In order to do so, we simply will write the chromosome and follow it with the allele as an superscript (like an exponent).
Every example of a sex-linked trait we will discuss in this class will be found on the X chromosome. So, our notation for a dominant allele, R, found on the X chromosome would be XR and our notation for a recessive allele, r, found on the X chromosome would be Xr.
Genotypes and Phenotypes of an X-Linked Trait
Genotypes and Phenotypes of an X-Linked Trait
Because males and females have different numbers of X chromosomes, it is important that we take that into account when we think about genotypes and phenotypes of individuals for these traits.
For this example, I am showing the possible female genotypes and phenotypes separately from the males in order to help consolidate them in your head.
For this example, there are two alleles: XW and Xw. Note that these are the same letter, but one is capitalized. So we have a dominant/recessive situation. Also note that the Y chromosome does not have an allele for this gene. It has entirely different genes!
Let's take a look at just females to start:
Homozygous dominant:
Genotype - XWXW
Phenotype - Red Eyes
Heterozygous (aka a carrier):
Genotype - XWXw
Phenotype - Red Eyes
Homozygous recessive:
Genotype - XwXw
Phenotype - White Eyes
So now let's investigate the males:
Hemizygous dominant:
Genotype - XWY
Phenotype - Red Eyes
Hemizygous recessive :
Genotype - XwY
Phenotype - White Eyes
So, from just the females, we can tell that red is dominant to white. So for a female to have white eyes, how many white alleles must she have?
2, of course. If the female has a single dominant allele (such as the heterozygote), she will have red eyes because red is dominant. This looks pretty normal so far...
The first difference to note is that there are only two possible genotypes for the males! This is because there is only one copy of the X chromosome. You will also note this term hemizygous. This is referring to the fact that the males only have one copy of the allele. So there is no true homozygosity or heterozygosity for this trait in males! That's weird. You do not need to memorize this term hemizygous, but you do need to understand the strange nature of X-linked traits in males.
So, how many copies of the recessive alleles do males have to have in order to show the recessive phenotype? Only one... So it is 'easier' for a male to have the recessive trait than for a female. This is why we see things like colorblindness being more common in males than in females. Females might have a copy of the recessive allele, but as long as their other copy is 'normal', then they will not be colorblind!
Genetic Crosses with X-Linked Traits
Genetic Crosses with X-Linked Traits
Genetic crosses with X-linked traits follow the same rules as normal Mendelian traits... the only difference is the chromosome involved. So, the male parent should always have one X and one Y chromosome. Which of these two that the father passes to the offspring determines the sex of the offspring. So, if Dad passes an X chromosome, the child will be a female. If Dad passes a Y, it will be a male.
The Punnett square above shows a cross between a carrier mother (XHXh) and a normal father (XHY). The trait in question is hemophilia (or, literally, blood-loving). No, this trait is not another name for vampirism. These individuals cannot form any blood clots. So even a tiny cut will never truly heal on its own. Most people who have this trait die quite young, as you can imagine.
Mom has a 50% chance to pass a normal allele and a 50% chance to pass a disease allele. Dad has a 50% chance to pass a normal allele and have a daughter and a 50% chance to pass no allele and have a son. Take a look at the possible offspring between these parents. These parents could have an unaffected daughter who is not a carrier, and unaffected daughter who is a carrier, an unaffected son, or an affected son. That is a wide variety of options for such a scary disease!
You do not need to understand hemophilia perfectly, you simply need to be able to create and analyze a Punnett square much like this one.
Here is another representation of different crosses. The chromosomes with the diseased allele are represented in red in this particular case.
Again, you need not memorize any of these crosses! You just need to be able to apply normal Mendelian genetics principles to an X-linked trait, remembering the males will only have one allele for that trait, and interpreting the effects of such.
Sex-Linked Traits on a Pedigree
Sex-Linked Traits on a Pedigree
Now that we have seen Punnett squares for X-linked traits, you can apply those principles to pedigrees and start assigning genotypes to said pedigrees. Try doing that to this pedigree you have seen before briefly:
If that was difficult for you, don't feel bad. This pedigree is huge. But what I really wanted you to get out of this is recognizing that all mothers of hemophiliac sons must have been carriers. That is the only way for a son to have received the allele! Why? Well, the dad passes the Y chromosome, so if you have a son, the X chromosome had to come from mom. If that X chromosome had a diseased allele, it had to have come from mom! It's all a little bit of a logic puzzle and gets quite fun the more you practice it. We will practice quite a bit in class, of course.
D. Polygenic Traits
D. Polygenic Traits
Polygenic traits are exactly what you'd expect given the name. 'Poly' means many and 'genic' refers to genes. So these are traits that are determined or influenced by many different genes. There are so many examples of this in humans: eye color, skin color, height, etc. It is more common for a trait you think of to be polygenic than monogenic.
Even this image is grossly oversimplified for eye color. You do not need to be able to analyze an polygenic traits - you are just responsible for knowing what the term means.
E. Multiple Alleles
E. Multiple Alleles
Another stark difference between the typical traits and the ones we discuss in class is that genes will often have more than just two alleles. This is dubbed multiple alleles because there are more than just the two options. So instead of there being just an R and an r allele, you also have a W allele, for instance.
The most common example of this, and one that we will practice with in class, is that of blood types. There are 4 phenotypes for blood type - A, B, AB, and O. There are three alleles: IA, IB, and i. Notice that two of these are capitalized (because they are codominant) and one is lowercase (because it is recessive). This makes the genetic crosses even more difficult. You not only have dominant and recessive aspects to worry about, but also codominance! And this is all not including the positive and negative aspects of blood type. The would incorporate multiple genes (polygenic) too!
I do not expect you to be an expert in blood typing (especially not the aspects of antigens and transfusions). But you should be able to, provided the phenotype or genotype of individuals, perform and interpret a genetic cross of these alleles. We will practice this in class, but it really just comes down to understanding the basics of crosses and the phenotypes and genotypes for the blood groups shown here.
F. Linked Genes
F. Linked Genes
There's one more thing that we need to cover that Mendel wasn't aware of - linked genes. Remember Mendel's Law of Independent Assortment? It stated that each allele assorts independently of any other. So basically, if you are tracking two genes, such as body color (B - black or b - brown) and wing type (W - normal or w - vestigial), you would expect the body color allele to be passed on to gametes regardless of what wing type allele was passed on. If we had an individual who is heterozygous (BbWw) for these two alleles, what gametes would you expect that individual to produce? Well, if you're applying Mendel's laws correctly, you should see gametes with the following genotypes: BW, Bw, bW, and bw in equal proportions.
Well...unfortunately that's an oversimplification for some genes. Some genes are linked, meaning that they are close to one another on the same chromosome. As a result, they are very rarely, if ever, separated from one another during crossing over. As a result, black body alleles might be passed more often alongside normal wings (BW) than alongside vestigial wings (Bw).
When two genes are linked, they will rarely cross over separately. This means that, generally, the gametes produced by an individual will usually have the same combination of alleles (genotypes) as the original chromosome in the parent (see figure above). In this example, these two genes are linked. As a result, the combinations you see in the parental chromosomes (A with B and a with b) will be the most common combinations passed on to gametes. Only occasionally do you see a different combinations (called recombinant genotypes) like A with b and a with B.
In other words, our normal predictions and Punnett squares will not suffice for these genes. So how do we determine if two genes are linked???
Genetic Recombination with Test-Crosses
Genetic Recombination with Test-Crosses
Often a test-cross is performed when working in genetics. This is when you cross an individual with an individual of a known, recessive genotype. For instance, crossing a female fly with a male fly whose genotype must be aabb. This will allow us to analyze the offspring quickly and easily, counting how many have each phenotype. A similar experiment is diagrammed here. Please note that this example seemingly has more complicated alleles, but they simply are using the scientific standard for these alleles rather than simple a and b letters. The patterns you can see will be the same.
If the two genes are not linked, the female fly should be able to produce 4 unique haploid gametes in equal proportions. If, however, the genes are linked, you will see that the vast majority (if not all) of the offspring will resemble the two parents. Note the predicted ratios for each offspring genotype at the bottom of the image.
So, if all (or the vast majority) of the offspring resemble the parents in a test-cross such as this, you have evidence that these genes are linked. This image shows the possible zygotes produced in the above alleles are linked:
Linkage Map
Linkage Map
The further apart two genes are on the same chromosome, the more likely that they will be separated during crossing over. As a result, the closer together two genes are on a chromosome, the less likely they will separate. So how can we measure how far apart genes are?
The easiest way to do so is by taking a look at the offspring in a test-cross. The higher the recombination frequency (how often the chromosomes crossed over in such a way that they created new combinations of the alleles for those 2 genes), the further apart two genes are.
If this cross is performed, let's analyze the offspring produced. The vast majority of the offspring look just like the parents (gray-normal and black-vestigial). A minority of offspring have different genotypes (and therefore phenotypes) from the parents. These are the individuals that got recombinant genotypes, or different combinations of alleles, from the mother (dad was homozygous recessive for each because this is a test-cross).
So, let's take a look at the proportion of individuals who are recombinant. 391 of the 2,300 offspring are recombinants, which is 17%. In other words, 17% of the mom's gametes had chromosomes that were different from her own (in regards to these two genes).
If we take all of this data, we can form a linkage map, or a genetic map that is based on these percentages. A linkage map looks like this in its simplest form:
One map unit = 1% recombination frequency.
In other words, those offspring give us an idea of the relative distance between these genes - how close together they are. According to Mendel's laws, each allele should have an equal chance of being passed on with each other allele. So, a 50% recombination is what Mendel would have predicted. If the % recombination frequency is 50%, those two genes are not linked. Anything less than that, such as our 17% here, indicates that these alleles are passed together far more often than Mendel's laws would predict. These genes are linked. As a result, the gametes will have allele combinations (aka genotypes) just like their parents' chromosomes for those genes.
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