Topic 3 - Linkage & Mapping

Question 1

What is the MAIN difference between Independent Assortment and Linkage

Answer 1

Independent Assortment predicts that 50% of the gamete will be parental and the other 50% (4 total gametes) will be recombiant gametes.
Linkage predicts that the parental gametes are far more frequent than the recombinant gametes.

*Remember for Independent Assortment the genes are completely unlinked

Question 2

Why do we underestimate the recombination frequency?

*2 main reasons

Answer 2

1. Dominance masks genotype. Can have a recombinant genotype but same phenotype as parental.
2. Double Crossover events. Two cross over events bring back genotype to look like parental one but is genetically recombinant because of these crossover events.

Question 3

What is genetic linkage?

Answer 3

Genetic linkage occurs when genes are located on the same chromosome and tend to be inherited together.

Question 4

What does syntenic mean?

Answer 4

Genes that are located on the same chromosome are syntenic.

Question 5

Why do linked genes often violate Mendel’s Law of Independent Assortment?

Answer 5

Because chromosomes assort independently, not individual genes; genes on the same chromosome may stay together unless crossing over occurs.

Question 6

What is recombination?

Answer 6

The formation of new allele combinations due to crossing over.

Question 7

How does gene distance affect recombination frequency?

Answer 7

The farther apart two genes are, the more likely crossing over will occur between them which means a greater recombination frequency.

Question 8

Can multiple crossovers occur between two genes?

Answer 8

Yes, but multiple crossovers can sometimes mask recombination, making distant genes appear closer.

Question 9

What is a sex-linked gene?

Answer 9

A gene located on a sex chromosome (usually the X chromosome).

Question 10

Why are X-linked traits more common in males?

Answer 10

Males have only one X chromosome, so recessive alleles are always expressed.

Question 11

What is autosomal linkage?

Answer 11

Linkage between genes located on non-sex chromosomes.

Question 12

What did Thomas Hunt Morgan discover?

Answer 12

Genes are located on chromosomes

Genes have a specific linear order

Some genes are sex-linked

Linked genes do not assort independently

Question 13

3 Important things that result from Linkage Analysis

Answer 13

1. Finding location of specific gene helps in first step to studying genetic disease
2. With the location, we can isolate gene sequence to clone better
3. We can better predict the consequence of mutations

Question 14

How do we know if genes are linked?

Answer 14

Gametes containing the parental combinations of alleles will be produced significantly more often than predicted by chance.

Question 15

What phenotypic ratio is expected for unlinked genes in a test cross?

Answer 15

1 : 1 : 1 : 1

Question 16

What does deviation from a 1:1:1:1 ratio suggest?

Answer 16

Genes are linked

Question 17

Where does the 9:3:3:1 ratio come from?

Answer 17

It comes from the dihybrid cross when two genes are unlinked thus assorting independently (Mendel’s Law of Independent Assortment) during meiosis

Question 18

What is the purpose of a chi-square (χ²) test?

Answer 18

To determine whether observed deviations from expected ratios are due to chance.

Question 19

What is the null hypothesis (H₀)?

Answer 19

Any difference between observed and expected results is due to chance alone.

Question 20

What is the experimental hypothesis?

Answer 20

Something other than chance (e.g., linkage) explains the deviation.

Question 21

How do you calculate degrees of freedom (df)?

Answer 21

df = number of phenotypic categories − 1

Question 22

What does a low p-value mean?

Answer 22

The deviation is unlikely due to chance → reject the null hypothesis.

Question 23

What is a common significance threshold (α)?

Answer 23

α = 0.05 (5% chance of rejecting a true null hypothesis)

Question 24

What is recombination frequency (r)?

Answer 24

The proportion of recombinant offspring among total offspring.

Question 25

What does r = 0.5 indicate?

Answer 25

Genes are unlinked or assort independently.

Question 26

What does r < 0.5 indicate?

Answer 26

Genes are linked.

Question 27

What is a centiMorgan (cM)?

Answer 27

A unit of genetic distance equal to 1% recombination frequency.

Question 28

Who developed genetic mapping using recombination frequencies?

Answer 28

Alfred Sturtevant, a student of Morgan.

Question 29

How are linkage maps constructed?

Answer 29

By arranging genes based on recombination frequencies, with smaller values meaning closer genes.

Question 30

What is complete linkage?

Answer 30

No crossing over occurs; only parental gametes are produced.

Question 31

What is incomplete linkage?

Answer 31

Both parental and recombinant gametes are produced (most common case).

Question 32

What is a polymorphism?

Answer 32

A DNA variation that exists in multiple forms in a population.

Question 33

What is an SNP?

Answer 33

A single nucleotide polymorphism—a one-base change in DNA.

Question 34

What is a haplotype?

Answer 34

A group of alleles inherited together from a single parent.