Cold
Spring Harbor QTL workshop
Genetics of Adaptation Lecture Borevitz
Power point Intro.
R Deorge
QTL Intro slides J Malamy
R qtl Example of mapping in Ler/Shah (.ppt)
For
QTL mapping lab
Raw image folder of seedling on plates
we were only missing RIL26 ---
set 85mm as width of outer diameter of plate see below
Use
ImageJ
to measure
seedlings (help
with macros see below)
Then, we pasted in the
measurements for each line into this file
and recorded measurer’s name as a covariate
to account for the fact that we
each measure slightly differently
also runt seedlings we just put
a couple small values in for 1.2,1.3 etc.. (our seed
wasn’t the greatest)
The next step is to use R to
estimate Best Linear Unbiased Predictors (means), using this R script
You
will need to have R installed, get if for your platform from http://cran.us.r-project.org
Find
a local mirror, download R base functions setup eg WinR2.3.1.
Follow
the commands in the script, by pasting a line or two into
R,
make sure
you have the working directory set to where seedling.csv is saved
The result is hypocotyl.blup.csv (see
histogram below)
These line BLUPs (means) are then used to map QTL
To do so we need the cross
file which has the Phenotypes (your seedling length) and genotypes are included
in the cross file made up for each cross, in our case
R code (txt) for qtl mapping
adjustri.R
a support file needed
.zip file of everything to
download together.
Other
examples of QTL mapping
http://naturalvariation.org/werner
http://naturalvariation.org/wernerNd
How
to use ImageJ
To
set scale to 85 mm outer diameter see pic below
Set
up some macros for labeling
To create a label shortcut
1. Go to Plugins
> Shortcuts > Create shortcut...
2. Scroll down in the
Command pull down menu until you find 'Label'
3. Enter 'L' in the shortcut
box
Click Ok,
To label, use Shift+L
Thanks
Results
Histogram of RIL mean distribution
Genetic
Map
R/QTL
interval Map
R/QTL
2D scan epistasis above diag
and Joint below,
no real evidence for interaction
bQTL genetic map
bQTL interval map
Linear
Bayes 10 gene model scan
Additive
effects of each QTL, Ler allele decreases length on
chr3,5
Increases length slightly in chr1
