Chapter 5: Linkage, Recombination, and Gene Mapping

How large is the human haploid genome

3 × 10^6 base pairs, 20-25,000 genes

How many genes are located on the X-chromosome

800-900 genes

What is the word used to describe genes located on the same chromosome

Syntenic

Are syntenic genes Mendelian

No because they don’t separate

If genes are Mendelian, what do you expect from a F1 testcross and what are the frequencies of parental and recombinant offspring

F1 testcross: 1:1:1:1

50% Parental

50% Recombinants

What parental and recombinant frequencies do you get when crossing a white eyed female with WT body to a WT eyed male with yellow body

99% Parental

1% Recombinant

When are genes assumed to be linked to a certain chromosome

Genes are assumed linked when # of F2 parental progeny > # of F2 recombinant progeny

How can linkage be tested

Chi-squared

Linked alleles ____ assort independently

dont

In linkage crosses, parental phenotypes __ recombinant phenotypes

>

____ are used to determine relative distances between linked loci

Recombinant Frequencies

The closer linked alleles are the ___ likely crossing over will occur between them

less

Completely linked genes ____ produce recombinants

don’t

What does recombination frequency depend on

Proximity of linked alleles

farther apart = higher rf %

When genes are linked on sex chromosomes, what do you look at for the testcross. what about on autosomes

sex chromosomes - F2 male progeny

autosomes - all F2 progeny

What Drosophila traits are linked to the X chromosomes

white eye color

yellow body color

miniature body size

What is the maximum rf linked genes could have

50%, these linked genes may appear unlinked

Explain Trans (repulsion) allelic arrangement

alleles are located across from each other on a pair of homologous chromosomes

(WT and mutant allele on one chromosome with respective mutant and WT allele on other chromosome)

Explain Cis (coupling) allelic arrangement

alleles are located on the same chromosome

(both WT alleles on one chromosome with respective mutant alleles on other)

What are the 3 main things that Alfred Sturdevant proposed

1. Genes on chromosomes appear in a linear fashion

2. Proposed recombination frequency as a way to measure relative distances between genes

3. 1% recombination = 1 map unit - 1 centimorgan

NCOs and SCOs

No cross over

Single cross over

Recombinant gametes are ___ common than parental gametes

less

What are limitations to 2 Point Crosses (chromosome mapping)

Gene order is difficult to determine

2-map distances do not always agree

Why are 3 point crosses more useful than two point crosses

• can determine gene order

• know who is in the middle

• allows for more accurate maps (sum of shorter distances)

What kind of events are DCOs

two independent events (“and”)

Ho do you calculate DCO observed, expected

DCOobs freq = (from data) # + # / 6823

DCOexp freq = (rf 1 / 100)(rf 2 / 100)

What do NCOs predict

Non cross overs predict cis, trans allele arrangement

what do DCOs predict

Double cross overs predict gene order

How do you determine map distances

use RFs (recombination frequenceis)

Formula for Coefficient of Coincidence

DCO frequency obs / DCO frequency exp

Formula to calculate interference

1 - coefficient of coincidence

Complete interference

1, no DCOs

Interference = 0 means…

DCOs Exp = DCOs Obs