Lecture 7 Flashcards
Explain some characteristics of non marker based methods of QTL detection.
In general have little/no power compared to marker based methods.
There is no interest in locating the gene on the chromosome and no marker - QTL (major gene) disequilibrium is needed and used
Explain some general characteristics of marker based methods of QTL detection,
In general they are much more powerful than non marker based methods.
There is interest in locating the gene on the chromosome and marker - QTL (major gene) disequilibrium is needed and used.
What are 4 examples of non marker based methods?
- test for departure from normality
- heterogeneity of sibship variance
- Major gene indices
- Mixture models: Complex segregation analysis
What are two characteristics of testing for departure from normality and heterogeneity of sibship variance?
- Little power
- Simple Calculation
What are two characteristics of Major gene indices and Mixture models: Complex segregation analysis?
- Low power (slightly more power than little power)
- Very computationally demanding
Give an example situation of a low power marker based method.
Only using information from 1 marker, 1 QTL, 1 trait and a simple pedigree structure.
Give an example situation of a high power marker based method.
-Using information from several markers, QTLs and traits and a complex pedigree structure.
What s the allele substitution effect?
The difference between progeny receiving the Q vs. q allele from the sire.
Can you conclude that there is no QTL?
NO, you can’t tell or conclude that there is no QTL. Can only say that there is no evidence of QTL given our marker
How do you find the size of a QTL?
You cannot make an inference on the size of the QTL :(
What is the problem with separating the contributions of a and r to D?
Since there are three parameters to estimate (µ, a and r) but only 2 marker group means, it is not possible to separate the contributions of a and r to D. ≥2 genetic markers and/or a deeper pedigree would be needed to untangle them.
How is the significance of D tested?
simple t-test
Explain the possible outcomes of a significance test for D and their implications.
Not significant = no evidence for QTL
Significant = Evidence of a QTL but we cant determine the size without further work.
Can marker QTL association be determined in dams? Under what conditions?
Yes they can be determined, as long as the dams are randomly distributed over the two marker groups of progeny
When backcrossing two inbred lines, if we make both backcrosses what do we get?
We can get independent estimates of a and d from estimates of a+d and a-d
When double backcrossing (backcrossing two inbred lines) how many parameter estimates and marker group means are there? What are they?
There are 4 parameters to estimate µ, a, d, and r
There are 4 marker group means; one mean from each backcross for the marker groups!
What two analyses can you do to estimate group means in a single sire family or backcross design?
One way ANOVA for QTL-marker association
Regression analysis of marker-QTL association
