Lecture 11

Question 1

RFLPs (Restriction length polymorphisms) can be used to calculate genetic distance between two alleles. They are good because they are.
(6)

Answer 1

• co-dominant
• the genetic map can be directly related to DNA-sequence
• Can be found new ANY gene
• Many markers per cross (they can even be anonymous)
• Can crease a genetic map with high marker density spanning the two genome
• Useful for many species

Question 2

Menedelizing Quantitative Traits

Answer 2

• Different segments of the genome can be marked with molecular variants that can be analysed individually with respect to the phenotype of interest.

Question 3

Monkey Flowers:

Answer 3

• A type of flower with two species (of interest), with a region of sympatry, but no hybrids. One (lewisii) is designed for bees, the other (cardinalis) for hummingbirds.

Question 4

Mimulus lewisii

Answer 4

• Designed for bees
• Pink
• Yellow nectar guides
• Vide corolla
• Small volume of concentrated nectar
• Short anther and stigmas

Question 5

Mimulus cardinalis:

Answer 5

• Designed for humming birds
• Red
• No nectar guides
• Tubular corolla
• High volume of nectar
• Long anther and stigmas

Question 6

Are the hybrids viable and fertile when artificially bred?!

Answer 6

Yes!

Question 7

Step 1 in QTL mapping

Answer 7

• Start with two lines that differ for the trait of interest
• Best if the genetic variation between the lines is maximised
• Best if the genegtic variation within lines is minimized

Question 8

Step 2 in QTL mapping

Answer 8

• Cross the two lines
• Allow recombination
• The more progeny, the more recombination, the greater the mapping resolution, can use F2 (3 progeny types, 2 homozygotes and 1 heterozygotes) or backcross (2 progeny types, 2 homozygotes)

Question 9

Step 3 in QTL mapping:

Answer 9

• Choose molecular markers (RFLPs, AFLPs, SNPs)
• Marker density must e informative to the cross
• Consider cost, labour, marker density and co-dominance

Question 10

Step 4 in QTL mapping:

Answer 10

• Score the F2 or backcross progeny and parents for molecular markers and create a linkage map

Question 11

Step 5 in QTL mapping:

Answer 11

• Score the F2 or backcross progeny and parents for trait of interest

Question 12

Step 6 in QTL mapping:

Answer 12

• For each marker (or interval) perform a statistical test for association with phenotype

Question 13

Input (dataset) for a QTL experiment:

3

Answer 13

• Trait values of individuals related by a known cross (eg. backcross of F2)
• Marker states for each individual
• Markers arranged in a map

Question 14

T-tests:

Answer 14

• Compares the mean between two populations, high and low, given their variance
• Generally the L marker will have a lower trait value than the H marker

Question 15

When the P value approaches 1:

Answer 15

• The means are about the same
• There is no significant difference
• There is no gene of interest there contributing to the effect

Question 16

P < 0.05:

Answer 16

There is a significant difference

Question 17

When there is a QTL above the threshold line:

Answer 17

• There is a significant association between the marker and the trait of interest, and they are correlated with our trait of interest
• They are our QTLs

Question 18

Flaws with QTL mapping:

Answer 18

• The markers are unlikely to be the causal variants, but they will be linked to the causal variants

Question 19

Thoday’s method for mapping QTLs within a chromosome:

4

Answer 19

• Use mapping stock with two closely linked phenotypic markers (a and b) on a chromosome containing the QTLs.
• Cross this to a stock that is WT at the two phenotypic markers (A and B) and differs from marker stock in the trait of interest (eg. has a higher number of bristles).
• The QTLS can be outside the phenotypic markers to between them
• We want to know which it is

Question 20

If the QTL is outside the markers:

2

Answer 20

• Progeny with the parental marker types will exhibit intermediate trait means with high variance (ignoring double cross overs)
• Recombinant type will be either high or low with little variance

Question 21

We can quantify where the QTL is in the interval:

Answer 21

• How many individuals are in the Ab low class? (5)
• How many individuals are in the aB high class? (3)
• There are 8 individuals that result from a recombination in region 1.
• Do the same for region two.. 12 from recombination in region two.
• The distance between our gene of interest and marker A is closer than that of our gene and marker B.

Question 22

We can quantify the effect size is as well..

Answer 22

• From a graph comparing trait score and marker class calculate the mean of each class and average it.