Dr. Dulai's Bio 184 section Lab 1.3 notes

Updated: 9 February, 2006

Information on group presentations added

Bio 184 Practical 1

A. Linkage Mapping in Drosophila melanogaster

ii) Pedigree Primer

This appears to be an area of genetics that you either latch on to quite well from the onset or you don't. I will try to initially present my slant on the topic, with several alternative views later on this page. So read the section that you connect with best, then try to see if you can then follow all the other example given here. If you still have questions or concerns then please do come to me.

What is Pedigree Analysis?

A type of genetic analysis in which a trait is traced through several generations of a family to determine how the trait is inherited. The information is displayed in a pedigree chart using standard symbols.

What symbols are used in the pedigree charts?

There are standard way of representing these symbols. You will come across slight variations, especially with regard to the symbols for twins. Here are some important ones.

	Male		Gender Unknown
	Female		Miscarriage during pregnancy
	Affected Individual		Elective terminated in pregnancy
	Carrier Individual		Deceased

	Mating		Consangious Marriage
	Identical twins		Non-identical twins

	Offspring in birth order from left to right; I and II are generations; offspring would be numbered II-1 and II-2

Lets start with some basics. Assume that we are dealing with very simple situations - no penetrance issues, nor other complicating factors, and just one gene locus is involved. It is our task each time to eliminate all the possibilities with 100% certainty - then try to explain what is left. There may be more than one answer in these cases! I suggest that you use a system to make sure you test all the permutations. I make use of the following simple chart:

Possibilities	Test		Test		Test
Sex-linked		dominant		homozygous
				heterozygous
		recessive		homozygous mate
				heterozygous mate
Autosomal		dominant		homozygous
				heterozygous
		recessive		homozygous mate
				heterozygous mate
Other

Cross out when you have completely ruled out that mode of transmission.

Some simple rules:

1) An autosomal dominant trait does not miss generations.

2) A dominant x-linked trait goes from father to all daughters who are all affected.

3) A recessive x-linked trait goes from father (who is always affected) to all his daughter who will always be carriers, unless they are affected too due to their mother also giving them the defective gene.

4) A y-linked trait always is transmitted to ALL sons.

5) Pedigrees also apply to non-human families.

EXAMPLE 1

Here we see that one of the parents (father) is exhibiting the trait, as are half his children (irrespective of sex). Which possible conclusion can be drawn for this limited pedigree?

If we assume the trait in question is very rare, then it is very unlikely to be sex-linked because this would require the mother to be a carrier and the father to possess the allele as well (two rare independent events are much less likely than 1 rare event).

Possibilities	Test		Test		Test
Sex-linked	X	dominant	X	homozygous	X
				heterozygous	X
		recessive	X	homozygous mate	X
				heterozygous mate	X
Autosomal		dominant		homozygous
				heterozygous
		recessive		homozygous mate
				heterozygous mate
Other

Either the gene is autosomal or other (such as mitrochondrial).

AUTOSOMAL DOMINANT TRAIT:
If we assume that the gene is autosomal dominant, then the father can be either AA (homozygous), or Aa (heterozygous). Let's test both these possibilities.

i) Homozygous Father (AA): The mother must be homozygous (aa) and she would produce just one class of egg (a). These would be fertilized by only one class of sperm from the father (A).

If we make use of the Punnett Square,

Gametes	a	a
A	Aa	Aa
A	Aa	Aa

all the offspring will be afflicted with the condition. We are not seeing this!

Possibilities	Test		Test		Test
Sex-linked	X	dominant	X	homozygous	X
				heterozygous	X
		recessive	X	homozygous mate	X
				heterozygous mate	X
Autosomal		dominant		homozygous	X
				heterozygous
		recessive		homozygous mate
				heterozygous mate
Other

The mother cannot be heterozygous (Aa) beacuse she would then be afflicted under these assumptions.

ii) Heterozygous Father (Aa): Again the mother is homozygous (aa) she would produce one type class of egg (a). These would be fertilized by either form of sperm from the father (A) or (a).

If we make use of the Punnett Square,

Gametes	a	a
A	Aa	Aa
a	aa	aa

they should produce children of both phenotypes in equal numbers. We observe this to be true from the pedigree.

Possibilities	Test		Test		Test
Sex-linked	X	dominant	X	homozygous	X
				heterozygous	X
		recessive	X	homozygous mate	X
				heterozygous mate	X
Autosomal		dominant		homozygous	X
				heterozygous	O
		recessive		homozygous mate
				heterozygous mate
Other

But we must not stop here, because we have not as yet ruled out all the remaining possibilities.

Next, we attempt to see if the pattern matches the possibility that the gene is autosomal recessive.

AUTOSOMAL RECESSIVE: The father must be (aa) by definition, so all his sperm are (a).

i) The mother may be homozygous (AA), and all her eggs would be (A).

Gametes	A	A
a	Aa	Aa
a	Aa	Aa

we see that the resulting offspring will all be normal. This is not what we see. We would label the mother a homozygous mate for the purposes of the table below.

Possibilities	Test		Test		Test
Sex-linked	X	dominant	X	homozygous	X
				heterozygous	X
		recessive	X	homozygous mate	X
				heterozygous mate	X
Autosomal		dominant		homozygous	X
				heterozygous	O
		recessive		homozygous mate	X
				heterozygous mate
Other

ii) The mother may be heterozygous (Aa), and her eggs will be equally (A) and (a).

Gametes	A	a
a	Aa	aa
a	Aa	aa

it is again evident that there we would get equal numbers of normal and afflicted progeny. This is what we are seeing in the pedigree.

Possibilities	Test		Test		Test
Sex-linked	X	dominant	X	homozygous	X
				heterozygous	X
		recessive	X	homozygous mate	X
				heterozygous mate	X
Autosomal		dominant		homozygous	X
				heterozygous	O
		recessive		homozygous mate	X
				heterozygous mate	O
Other

CONCLUSION: The gene presented in the pedigree is Autosomal but is could be either dominant or recessive in its transmission.
This example illustrates a very important flaw in pedigree analysis: if the data is presented by a small pedigree one may not be able to deduce the actual nature of the genetic system.

EXAMPLE 2

In this example we see that two normal F1 parents (generation II) have four children, of which one is afflicted with a disease. How can we explain this?

Since neither parent is affected we would be right in assuming that the trait is recessive. It is NOT dominant.

The pattern of inheritance is consistent with both parents being heterozygous for the locus, so both are carriers (we could indicate this by adding the dots onto their symbols).
So we can deduce that the Punnett square would predict that the gametes of these two parents would allow for the generation of:

25% of the time Homozygous children
50% of the time Heterozygous carrier children
25% of the time Homozygous affected children,

and this is exactly what we are seeing.

Possibilities	Test		Test		Test
Sex-linked	O	dominant	X	homozygous	X
				heterozygous	X
		recessive	O	homozygous mate	X
				heterozygous mate	O
Autosomal	O	dominant	X	homozygous	X
				heterozygous	X
		recessive	O	homozygous mate	O
				heterozygous mate	O
Other

CONCLUSION: Autosomal recessive. It is not possible to tell which of the children are carriers, without looking at their children. Is it sex-linked as we see it in a male offspring? Well it could be carried in the heterzygous state by both the grandmother and mother.

Pedigree Analysis

Introduction

A pedigree is a diagram of family relationships that uses symbols to represent people and lines to represent genetic relationships. These diagrams make it easier to visualize relationships within families, particularly large extended families. Pedigrees are often used to determine the mode of inheritance (dominant, recessive, etc.) of genetic diseases. A sample pedigree is below.

In a pedigree, squares represent males and circles represent females. Horizontal lines connecting a male and female represent mating. Vertical lines extending downward from a couple represent their children. Subsequent generations are therefore written underneath the parental generations and the oldest individuals are found at the top of the pedigree.

If the purpose of a pedigree is to analyze the pattern of inheritance of a particular trait, it is customary to shade in the symbol of all individuals that possess this trait.

In the pedigree above, the grandparents had two children, a son and a daughter. The son had the trait in question. One of his four children also had the trait.

In the exercises below, assume that the trait in question is a genetic disease or abnormality. We will learn patterns of inheritance that have the following modes of inheritance:

autosomal dominant
autosomal recessive
X-linked recessive

Developing Conclusions About Different Modes of Inheritance

Autosomal Dominant

1. The pedigree below is for a genetic disease or abnormality. We do not yet know if it is dominant or recessive. We will determine if it is possible that the trait is autosomal dominant. If the trait were dominant, we would use the following designations:

A = the trait (a genetic disease or abnormality, dominant)
a = normal (recessive)

If the trait were recessive, we would use the following designations:

A = normal (dominant)
a = the trait (a genetic disease or abnormality, recessive)

a) Assume for the moment that the trait is dominant (we don't know yet). The pedigree shows that three of the individuals have the recessive (normal) phenotype and one individual has the dominant (abnormal) phenotype. Write the genotype of the affected (abnormal) individual next to her symbol in the pedigree below. If you only know one of the genes (letters), use a "?" for the unknown letter. Write the genotype of the three recessive individuals next to their symbols. As you write the genotypes, keep in mind that the pedigree may not be possible for a dominant trait.

b) Is it possible that the pedigree above is for an autosomal dominant trait?

c) Write the genotypes next to the symbol for each person in the pedigree below assuming that it is for a dominant trait.

d) Is it possible that this pedigree is for an autosomal dominant trait?

e) What can you conclude from these two examples about the parents of a child that has a dominant characteristic? Put your answer to this question in the summary table (item #1) in the answer sheet.

2. We will determine if the pedigree below can be for a trait that is autosomal dominant. Use "A" and "a" as you did for the pedigrees above.

a) Write the genotype of each individual next to the symbol.

b) Is it possible that this pedigree is for an autosomal dominant trait?

c) In conclusion, can two individuals that have an autosomal dominant trait have unaffected children? Put your answer to this question in the summary table (item #2) in the answer sheet.

Autosomal Recessive

3. We will determine if the pedigree below can be for a trait that is autosomal recessive. Use the following designations:

A = normal
a = the trait (a genetic disease or abnormality)

a) Assuming that the trait is recessive, write the genotype of each individual next to the symbol.

b) Is it possible that the pedigree above is for an autosomal recessive trait?

c) Assuming that the pedigree below is for a recessive trait, write the genotype next to the symbol for each person.

d) Is it possible that this pedigree is for an autosomal recessive trait?

e) If a trait is autosomal recessive, what can you conclude about the children if both parents are affected? Put your answer to this question in the summary table (item #3) in the answer sheet.

4. We will determine if the pedigree below can be for a trait that is autosomal recessive. Use "A" and "a" as you did for the previous example.

a) Write the genotype of each individual next to the symbol.

b) Is it possible that this pedigree is for an autosomal recessive trait?

c) If a trait is autosomal recessive, what can you conclude about the children of two parents that are not affected? Put your answer to this question in the summary table (item #4) in the answer sheet.

5. We will determine if the pedigree below can be for a trait that is autosomal recessive.

a) Write the genotype of each individual next to the symbol.

b) Is it possible that this pedigree is for an autosomal recessive trait?

c) In this pedigree, two generations have been skipped. What can you conclude about recessive traits skipping generations? Put your answer to this question in the summary table (item #5) in the answer sheet.

X-Linked Recessive

The conclusions that you made for autosomal recessive traits apply to X-linked traits. In this exercise, we will work on some additional conclusions because males have only one X chromosome and females have two.

6. We will determine if the pedigrees below can be for a trait that is X-linked recessive. Use the following designations:

XA = normal
Xa = the trait (a genetic disease or abnormality)
Y = Y chromosome (males only)

a) Write the genotype of each individual next to the symbol.

b) Is it possible that the pedigree above is for an X-linked recessive trait?

c) Write the genotype next to the symbol for each person in the pedigree below.

d) Is it possible that this pedigree is for an X-linked recessive trait?

e) Write the genotype next to the symbol for each person in the pedigree below.

f) Is it possible that this pedigree is for an X-linked recessive trait?

g) Write the genotype next to the symbol for each person in the pedigree below.

h) Is it possible that this pedigree is for an X-linked recessive trait?

i) What can you conclude about the children of mothers affected with an X-linked recessive characteristic? Put your answer to this question in the summary table (item #6) in the answer sheet.

7. We will determine if the pedigree below can be for a trait that is X-linked recessive. We will continue to use the designations "XA and Xa".

a) Write the genotype of each individual next to the symbol.

b) Is it possible that this pedigree is for an X-linked recessive trait?

c) Which parent did the son get the Xa gene from?

d) What can you conclude about father-to-son transmission of X-linked traits? Put your answer to this question in the summary table (item #7) in the answer sheet.

8. We will determine if the pedigree below can be for a trait that is X-linked recessive.

a) Write the genotype of each individual next to the symbol.

b) Is it possible that this pedigree is for an X-linked recessive trait?

c) What can you conclude about the children if both parents are affected with an X-linked recessive trait?

d) How does this conclusion compare with the one you made earlier if about both parents being affected by an autosomal recessive trait?

e) Do the conclusions that you made for autosomal recessive traits apply to X-linked recessive traits? Put your answer to this question in the summary table (item #8) in the answer sheet.

9a. If a genetic disease is X-linked recessive, what is the phenotype of a female that has only one disease allele (Xa)?

b. What is the phenotype of a male with one disease allele?

c. What can you conclude about the number of males that would have the disease compared to the number of females? Put your answer to this question in the summary table (item #9) below.

Adapted from

Presented below is another method by which a pedigree analysis may be performed (does this work better for you?)

Another way to present the results of crosses is a pedigree. Pedigrees are usually used when few individuals and many generations are involved - this is often the case with human genetic data.

Pedigree symbols

There is a standard set of pedigree symbols used to denote the phenotype of individuals in a family.

Solving Pedigree Problems

Because of the small number of progeny, pedigrees can often be ambiguous - more than one model may explain the observed pattern of inheritance. For this reason, we often assume that the genetic abnormality is rare in the population. This means that, in a given family, very few (usually one) of the first generation individuals carry the abnormality and very few (usually none) individuals who "marry" into the family carry the abnormality. This assumption may help to rule out certain models.

Here is a sample human pedigree and one way to analyze it. Use A or a to represent the abnormality if it is dominant or recessive, respectively.

Try the possible models one by one.

- if the abnormality were Y-linked:
Y - normal Y chromosome
Y* - Y chromosome carrying abnormality (it doesn't matter if it is dominant or recessive, since males are haploid for the Y chromosome)
It would appear only in males, as is observed. However, 1 or 3 would also have to have Y* and be abnormal in order to pass it on to his sons. This does not fit the data so it is not Y-linked.

- if the abnormality were due to a dominant mutation in a gene on an autosome (autosomal dominant):
A - dominant abnormal allele
a - recessive n