CH 7: Linkage and Recombination

Define linked genes

Genes that are located close together on the same chromosome, tend to be inherited together during meiosis, resulting in less genetic variation.

-Do not randomly assort, on the same chromosome

Can genes be on the same chromosome and be incompletely linked?

Yes! Genes sometimes travel together into a gamete, but they can also be separated through a crossing over event (do not sort independently)

If the F2 is in a 9:3:3:1 ratio, what does this tell you about their assortment?

Indicates the two genes controlling traits are sorting independently and are not linked

What is the equation for recombination freq.?

# of recombinants / total number of offspring x 100

In a single crossover between two genes, in which chromatids crossover in linked genes, which parts are involved?

Only the middle two chromatids

With a single crossover between two genes, what percentage of the genes will be recombinant? What is the maximum recombination frequency?

50% recombinant and 50% nonrecombinant (but always more nonrecombinant)

-Max recombination frequency is 50%

-**Note: if crossing over occurs 100% of the time, then 50% will be recombinants

How can you tell if genes are linked?

Carry out a test cross (cross homozygous recessive with a dominant)

-**If the genes are NOT linked, expect a 1: 1: 1: 1 and know they sort independently

-**If the genes ARE linked, expect the progeny to produce more of the parental phenotypes

How does the configuration of alleles (cis or trans) change the progeny phenotypic ratios?

-In cis configuration (both dominant or both recessive alleles on the same chromatid), more offspring will display the parental phenotypes

-In trans configuration (one dominant and one recessive allele on each chromatid), there will be a higher proportion of recombinant phenotypes.

Compare cis configuration (coupling) to trans configuration (repulsion)

Cis configuration (coupling) results in parental phenotypes being more common, while trans configuration (repulsion) increases the frequency of recombinant phenotypes.

-CIS: A B/ a b

-TRANS: A b/ a B

Define two-point testcross

-Determines the recombination frequency and distance between two linked genes

EX: Crosses a dihybrid (AaBb) with a homozygous recessive individual (aabb).

Define three-point testcross

-Testcross involving three linked genes to determine the recombination frequency and map distance between them.

-Determines their linear order, map distances, and account for double crossover events.

-More efficient and accurate because only 1 cross is needed rather than multiple crosses

-Also account for DCO events

EX: Crosses a trihybrid (AaBbCc) with a homozygous recessive individual (aabbcc).

Understand how to create a genetic map from a three-point testcross

1. Determine gene order

2. Rewrite genes in correct order

3. Locate crossovers

4. Calculate recombination frequencies

5. Construct gene map

6. Calculate coefficient of coincidence

7. Calculate interference

What is the equation to calculate coefficient of coincidence? How do you calculate expected DCO (and P of DCO)?

CC= observed DCO/ expected DCO

To find expected DCO, find Probability of DCO (mu between genes 1 and 2 X mu between genes 2 and 3)

Expected DCO= (P of DCO) x (total progeny #)

How do you calculate interference?

Interference = 1- CC

What does recombination mean? What are 2 causes?

-Meiosis generates gametes with different allelic combinations

than the original gametes the organism inherited.

-May be caused by loci on different chromosomes assorting independently or a physical crossing over between two loci on the same chromosome in prophase I

In a testcross for two genes, what type of gametes will be produced with complete linkage?

Only parental gametes will be produced; recombinant gametes will not form.

-recombination frequency is zero

In a testcross for two genes, what type of gametes will be produced with independent assortment?

-Will result in 50% of the gametes being recombinant and 50% being nonrecombinant, as would be observed for genes on two different chromosomes.

-May also be observed for genes on the same chromosome if they are far enough apart that one more more crossovers can occur between them in meiosis

In a testcross for two genes, what type of gametes will be produced with incomplete linkage?

Greater than 50% of the gametes produced are nonrecombinant and less than 50% of the gametes are recombinant; the recombination frequency is greater than 0 and less than 50%

What effect does crossing over have on linkage?

It is the physical exchange of alleles for loci located on homologous chromosomes and leads to new combinations of alleles and traits

-Breaks down the association of alleles and traits created by linkage

Why is the frequency of recombinant gametes always half the frequency of crossing over?

Because each crossover event results in two recombinant gametes, while only one crossover occurs per pair of chromosomes.

-Only half of the gametes from each crossing-over event are recombinant gametes

How does the arrangement of linked genes (whether they are in coupling configuration or in repulsion) affect the results of a genetic cross?

For genes in coupling, most of the progeny (nonrecombinants) will be either wt for both genes, or mutant for both genes, with few recombinants having wt for one gene and mutant for the other

-Repulsion: most of the progeny (nonrecombinants) will be mutant for one gene and wt for the other, with few recombinants having wt for both or mutant for both

How would you test to see if two genes are linked?

1. Testcross (cross heterozygous for both genes x homozygous for recessive)

• If the recombinant progeny is 50%, then there is no linkage and the genes are assorting independently

• If proportion of recombinants is less than 50% then the genes are linked

• **If unclear, then do a chi-square test and significant deviation results in linkage

Why do calculated recombination frequencies between pairs of loci that are located far apart underestimate the true genetic distances between loci?

The farther apart two loci are, the more likely they are to experience double crossovers between them. Unless there are marker genes between the loci, such double crossovers will be undetected because double crossovers give the same phenotypes as nonrecombinants. The calculated recombination frequency will underestimate the true crossover frequency because the double-crossover progeny are not counted as recombinants

What does interference tell you about the effect of one crossover on another?

-Positive interference means that the actual number of double crossovers observed is less than the number of double crossovers expected from single crossover frequencies

-Negative interference means that one crossover reduces the likelihood of another crossover occurring nearby, indicating an interaction between crossover events.

Explain how to determine, using numbers of progeny from a three-point cross, which of three linked loci is the middle locus.

The DCO should be alike in two genes and differ in one (when comparing to the nonrecombinants). The one that differs is the middle gene