BIOL 2500 - Topic 6

Why is it important to know where genes are located on chromosomes

1.) It allows us to understand complex genotypes and their interactions (i.e. genetic interactions)

2.) It allows us to understand gene structure and function, and how mutations changes both the structure and function

3.) It helps us infer evolutionary relationships between related organisms, based on how many bp have changed

Chromosome map

Refers to the arrangement of genes on the chromosome

Loci

Term used for the location of genes

Two kinds of chromosome maps

1.) Recombination maps (i.e. relative maps)

2.) Physical maps

Recombination maps

1.) It maps the loci of genes that have been identified by mutant phenotypes that show single-gene inheritance patterns

2.) The distance between them are measured relative to one another, using recombination frequency or map units

What can we use to build recombination maps

Linkage analysis

Physical maps

Maps that show the specific gene locations on a chromosome, by measuring the distances between them using kbp (i.e. the number of nucleotides)

Independent assortment

It is when different genes on different chromosomes assort independently, since chromosomes assort independently

Homologous recombination

Refers to the crossing over that occurs during prophase I, which results in recombinant chromosomes (i.e. non-parental chromosomes)

Four possible gametes from independent assortment, with homologous recombination

It results in 4 possible gametes, two parental and two recombinant, but all of which have a 1:1:1:1 ratio

Parental/non-recombinant chromosomes

Refers to chromosomes that do not cross over and therefore retain the same alleles as the parent chromosome

Syntenic genes

Refers to genes that are located on the same chromosome

Consequences of syntenic genes

Genes that are very close to one another may not be able to independently assort, therefore resulting in genetic linkage

Genetic linkage

1.) It produces a distinctive pattern of gamete genotypes, since they recombine less during meiosis, such that the 1:1:1:1 ratio is not seen

2.) Instead, you see a higher frequency in parental chromosomes and a lower frequency for recombinant chromosomes (since not a lot of crossing over is occurring)

Syntenic genes that are far apart from one another

They do assort following Mendel’s law of independent assortment

Parental and recombinant are ________ to what the parents are

Relative

Parental and recombinant are relative to what the parents are

1.) This means that the parental is not always homozygous, sometimes it is heterozygous

2.) Parental just means it is the same as the parent, not that it is homozygous

2.) Recombinant means it is different from the parent, not that it is heterozygous

Frequency of gamete genotypes/progeny phenotypes when unlinked

1.) Independent assortment occurs, therefore the parental gametes will be produced the same amount as recombinant gametes

2.) Such that in a test cross, 4 genetically different gamete combnations are produced, with a 1:1:1:1 ratio

Frequency of gamete genotypes/progeny phenotypes when linked

Independent assortment does not occur, therefore the parental gametes will be produced more by chance (>50%) and the recombinant gametes will be produced less by chance (<50%)

Bateson and Punnett

They studied sweet peas, specifically the flower colour and pollen grain shape, which is what led them to the discovery of linkage

Bateson and Punnett looking at the two sweet pea traits separately

When studies separately, the two traits generated the usual 3:1 phenotypic ratio in F2

Bateson and Punnett looking at the two sweet pea traits together

1.) They crossed the homozygous dominant x homozygous recessive genotypes together, resulting in the homozygous phenotype in F1

2.) But in F2, the typical 9:3:3:1 ratio was not observed, as there were more parental phenotypes observed than recombinant phenotypes

Bateson and Punnett: coupling

The term they used when they noticed that certain traits were inherited together

Thomas Morgan

In 1911, he confirmed genetic linkage and constructed one of the first genetic maps

Thomas Morgan experiment (part 1)

1.) He looked at the autosomal genes for eye colour and wing length

2.) He crossed a double WT with a double mutant, resulting in an F1 with the dominant phenotypic traits

3.) He then did a testcross with the F1, to see what the phenotypic ratio would be

Testcross results from Morgan’s first F1 experiment

He saw more of the parental (homozygous genotypes) and less of the recombinants (heterozygous genotypes)

Why do we see more parental than recombinants?

Because males do not undergo recombination, only females do

Thomas Morgan experiment (part 2)

1.) He repeated the experiment, but with different gene combinations, such that he crossed a two true-breeding heterozygotes

2.) He then did a testcross with the result F1 progeny

Testcross results from Morgan’s second F1 experiment

1.) He got more of the parental (heterozygotes) and less of the recombinants (homozygous)

2.) Therefore, he concluded that these two genes were linked/inherited together

Final conclusion of Morgan’s experiment

Dihybrid testcrosses of linked genes will have…

1.) Equally frequent nonrecombinant classes, which occur more than 50%

2.) Equally frequent recombinant classes, which occur less than 50%

Two conformations of linked genes in a dihybrid testcross

1.) Cis formation

2.) Trans formation

Cis formation

Both the dominant alleles of the two genes are on the same homolog and the recessive alleles are on the other homolog (i.e. PRVG / prvg)

Trans formation

The dominant alleles of the two genes are on different homologs (i.e. PRvg / prVG)

/ meaning

Represents being on separate homologs

• meaning

Genes are on the same chromosome

Discovery of cytological evidence of recombination (i.e. crossing over)

It was first demonstrated simultaneously by Creighton, McClintock, and Stern

Creighton and McClintock experiment

1.) They observed recombination in corn, using chromosome 9 homologs, with two genes

2.) One homolog was normal and carried the two genes

3.) The other homolog was slightly altered, with a knob and translocated bit of chromosome 8 on the ends

Creighton and McClintock experiment results

1.) They observed an actual physical exchange of genetic information between the homologs, such that the translocated bit was transferred to the normal homolog

2.) Therefore, it has a different genotype than what the parents started with

Crossover occurs between __________ chromatids

Nonsister

What helped explain crossing over between non-sister chromatids?

Tetrad analysis

How many gametes do we get when crossing over occurs between two homologs??? *ASK J*

2 kinds of gametes

What tetrad analysis has shown us about crossing over

Multiple crossovers can occur along a homologous pair, such that two or more chromatids can exchange genetic material (i.e. any of the non sister chromatids can crossover)

Single crossovers

When two linked genes cross over (AB x ab)

Double crossovers

When three linked genes cross over at the same time (ABC x abc)

Importance of recombination frequency

It is the key to chromosomal mapping, as it tells us if genes are near or far from each other

Recombination frequency role in chromosomal mapping

1.) Genes that are farther apart on the same chromosome have a higher chance of a crossover event, allowing for the formation of recombinant gametes and a recombination frequency of more than 50%

2.) Genes that are closer together are inherited together, because they have a lower chance of a crossover event, resulting in a recombination frequency of less than 50%

Complete linkage

When the genes are side by side, resulting in a recombination frequency of zero

Incomplete linkage

Recombination that occurs between homologs that produces a mixture of parental and recombinant gametes, such that the genes may be close together, but they are not always inherited together like in complete linkage

Common incomplete linkage results

1.) It results in 4 genetically different gametes, 2 parental and 2 recombinants

2.) However, the typical 9:3:3:1 ratio is not observed, as the frequency of the parental gametes are different from the recombinant gametes

Frequency of the parental genes

The two have the same frequency, which is equal to >50%

Frequency of recombinant gametes

The two have the same frequency, which is equal to <50%

What does it mean when the frequency of parental gametes is 100%?

It means that no crossing over occurs at all

Linked genes do not assort _________

Independently

Linked genes are always…

They are always syntenic and located near one another on the chromosome

Syntenic genes that are far apart

They are not linked, as they assort independently due to crossing over of homologous alleles

Genetic linkage expected gamete frequencies

It leads to the production of different expected gamete frequencies, where we expect a greater number of parental gametes than recombinant gametes

Crossing over is less/more likely to…

It is less likely to occur between linked genes that are closer together and more likely to occur between those apart

Frequency of crossing over proportions

It is roughly proportionate to the distance between genes

Sturtevant

Morgan’s undergraduate student who produced the first linkage map and is credited for discovering that we can use recombination frequencies to map genes

Smaller recombination frequencies =

Genes are closer together

Larger recombination frequencies =

Genes are further apart

Linkage maps

It shows the relative position of traits, based on how often cross over occurs

Units used for linkage maps

1 map unit (m.u.) = 1% recombination frequency

Maps are ________

Additive

Arrangement of genes

They are arranged in a linear order

What is the problem with using recombination frequency to produce linkage maps

You get multiple maps on the possible order of the genes

What can we do if we know the recombination frequency between two genes

We can predict the phenotypes of parentals and recombinants

If Morgan’s data show 11% recombinance, what is the recombination frequency of the parentals

100 - 11 = 89%

Therefore, each parental phenotype would be 44.5%

Proportion of parental to recombinant chromosomes depends on…

The frequency of crossing-over

Recombination frequency (definition)

The probability that we get a crossing over event between syntenic genes

Recombination frequency formula

r = number of recombinant offspring / total number of offspring

Interpreting recombination frequency in 2 ways

1.) Crossing over occurs at a higher rate between genes that are further apart than closer together OR

2.) Linked genes with higher recombinant frequencies are more distant from each other, than other linked genes with lower recombinant frequencies

Linked genes in humans

1.) Hair and eye colour

2.) Hereditary elliptocytosis

Hereditary elliptocytosis

1.) An autosomal dominant trait that results in elliptical RBCs instead of biconcave RBCs

2.) It has variable penetrance and expressivity

3.) It confers some resistance to malaria

Gene for hereditary elliptocytosis is close to…

It is close to the gene that determines your Rh factor, being only 4 map units away

Two-point test crosses use

It helps calculates the recombination frequency between two linked genes, which we can then use to infer the distance between the genes

Two-point test cross disadvantage

It is not the most effective way to build a map

Three-point test cross

It is a test cross designed to identify genetic linkage between 3 genes and helps determine recombination frequencies between linked genes, which helps with determining gene order

Three-point test crosses can be used for…

It can be used with autosomal genes, as well as sex-linked genes, using trihybrid females and hemizygous males

Resulting genotypes in three-point test crosses

It results in 8 genetically different genotypes from each parent, 2 being parental and 6 being recombinant

Recombinant genotypes in a three-point test cross

4 single crossovers and 2 double crossovers

Single crossovers in three-point test crosses

2 are between genes a and b and then the other 2 are between b and c

Genotypic ratio of three-point test crosses

You get independent assortment? But the the genotypic frequencies are unequal (meaning it is incomplete linkage)

How can you identify the parentals?

They are the two that are the most observed

How can you identify double crossed recombinants

They are the two that are least observed

Null hypothesis for three-point test crosses

The genes are unlinked

Expected number of phenotypes in three-point test crosses

You expect a 1:1:1:1 ratio (meaning it is unlinked)

SCO vs. DCO

SCO —> Single cross over

DCO —> Double cross over

How do we know which gene is in the middle?

Compare the parentals with the DCO recombinants, such that all of the genes should be the same except for one, which is your middle gene

Regular recombination frequency formula

(Number of recombinants / Total observed number) x 100

Calculating the RF for the two genes at the ends

(ALL of the recombinants / Total observed number) x 100

Why are their less DCOs then SCOs

Because the probability of two crossovers happening right next to each other is small

Interference

It refers to the fact that the observed number of DCOs relative to the expected number is reduced, if two 2 SCO events happen independently

What does interference indicate?

It indicates that certain processes can limit the number of crossovers that can occur in short-length chromosomes

Interference value essentially compares…

It essentially compares the frequency of observed DCO events with the expected number of DCOs

Expected DCO (formula)

(RF₁) x (RF₂) x Total number of progeny

Coefficient of coincidence (COC)

Observed DCO / Expected DCO

Interference formula

1 - COC

Positive Interference number

1.) It represents the proportion of DCO that was expected but not produced in the experiment

2.) If I = 0.40, then the number of DCO’s was 40% lower than expected

Negative Interference number

This is when we get more DCOs produced than expected