Exam 2: quantitative Loci

Question 1

5 steps of finding QTL

Answer 1

1. Identify two true breeding lines that differ in the trait of interest.
2. Produce F1 and F2
3. Find marker loci that differ between the parents.
4. Use marker loci to find regions of the chromosome that segregate with the trait.
5. Find functional loci that are linked to the markers that influence the trait of interest.

Question 2

Types of ways to get “true breeding” types

Answer 2

1. Selected lineages
2. Different populations
3. Different species

Just have to make sure that they can hybridize!

Question 3

Sources of variation in the F2 generation

Answer 3

Independent assortment at unlinked QTL.

Recombination of linked loci.

Question 4

Linkage disequilibrium

Answer 4

Non-random association of alleles at different loci. Both alleles are inherited with each other more than would be expected if they were inherited independently.

Question 5

Marker Loci

Answer 5

• detected cheaply and easily.
• at which alleles differ between those that are phenotypically different.
• used to find linked functional loci that influence the trait of interest.
• have known DNA sequence at a known location.
• there should be many of them widely distributed over the chromosome.

Question 6

Micro satellite Loci

Answer 6

• type of marker loci
• regions of tandem repeats which are flanked on either side with a unique sequence that is used to identify the micro satellite.
• vulnerable to mistakes due to repetition.
• alleles differ in number of tandem repeats.
• are not thought to affect the phenotype.
• if they influence the phenotype then it is seen as evidence that they are linked near a QTL.
• these allelic differences are fondness between species that can still interbreed.

Question 7

Informative loci

Answer 7

• these are loci at which two parents do not share the same allele.
• this is so that one can determine by the allele which parents the nearby DNA is from.
• not necessarily useful unless the locus is close to a QTL.

Question 8

QTL

Answer 8

Loci that influence quantitative traits. Loci that have subtle effects.

Question 9

D4DR

Answer 9

• nuerotransmitter receptor
• 48 base pair tandem repeat
• repeats between 2-8 times. Different repeats have different properties.
• influences thought and behavior.
• individuals with one long allele(6-8repeats) versus individuals with short alleles(2-5repeats) had scored three points higher in the novelty seeking test.
• explained 3-4% of variance.

Question 10

3020insC allele(Crohn’s disease)

Answer 10

• mutation caused shorter less functional protein in many crohns patients.
• patients parents carried the allele.
• if the allele played no role then it should have been transmitted to patients in 50% of cases but the allele was transferred 70% of the time which implies the role of the allele in the disease.

Question 11

Candidate locus approach

Answer 11

Find the locus based on it having similar functions in other organisms.

Used this approach in EDA locus and lateral plates, Pitx-1 and pelvic girdle and D4DR.

Question 12

Monkey flowers

Answer 12

The difference between the m.cardinalis and m.lewisii was not simply due to Mendelian traits.

They found that the alleles at most alleles displayed dominance instead of incomplete dominance.

For 9/12 traits, at least one locus had a large (greater than 25%) effect in the variance.

Some even explained as much as 90% of the variance.

Question 13

EDA gene

Answer 13

• EDA is ectodysplasian A protein which is an important developmental gene.
• causes developmental defects in zebra fish, mice, dogs and humans.
• saw Pitx-l as a candidate locus.
• stickleback fish with developmental defects did not have PitX-l.

Question 14

Reverse genetics

Answer 14

Modify the genetic sequences to examine the phenotypic response.

Question 15

Forward genetics

Answer 15

Asks about the genetic cause of phenotypic variation.

Looks at differences between species, populations, and lineages.