Ici mapping Manual

For the RIL population mapping QTL

Donghee Hoh
2017.03
 You need before do map QTLs
Genotypic data
Phenotypic data

If these are high quality, you would get QTLs!

Before using genotype data, you should clean the data ( bad markers, monomorphic etc)
This will be in appendix
Process
1. SNP markers
2. ICIM input file
3. BIN
4. MAP
-> make BIP file for the mapping

5. Phenotype data
6. Map QTLs
(7.find the candidate gene) not open source right now
 1. SNP markers
The list of parental lines
and progenies

List of markers

The marker coding of this

genotype is AB format
(possible to R/qtl
packaged). For the Ici
mapping, AB format to
change numeric coding -
next page
Users manual page 6
Using replace function in
excel, easily replace the
AA to 2,
BB to 0,
AB to 1,
missing data to -1
2. ICIM input file

For the RIL mapping,

please change
Number of markers and
population size

Three tabs are required

First tab should contains
general information
showing above
For the genotype data tab (2nd tab),
Copy paste of SNP data you generated 1st step
except parental lines
Make sure there is no additional lines above first
markers
For the anchor data tab (3rd tab),
You need consensus map and individual linkage
map
- Need more steps please see the next page
2)
Use vlookup fuction in excel like this

3) When you got linkage data,

Copy & paste in your input file
as a value only

4) Delete cMap. Left tabs should be only

Three tabs without equations

1)
Copy & paste cMap next tab
3. BIN

Binning of Redundant Markers (BIN)

By redundant markers, we mean markers which are completely correlated in a
population, and therefore they cannot provide additional information. This is
more common when we have a limited-size population, but do genotyping for
thousands of molecular markers. An algorithm for identifying bins of redundant
has been developed. Based on the algorithm, a tool called BIN has been
implemented in QTL IciMapping. This tool can help identify and remove
redundant markers in a dataset, and can also remove markers with high missing
rates.

Users manual page 54

1) Make new project
Click BIN function
If you cant find the file, try to changed the file extension here
Opening the file,
Takes a while (1 min?)
SNP data is up loaded in program
1) Keep the default menu
2) Click the binning
If the markers have same 0: leave it ( is not redundant)
BinID, those markers are 1: deleted
belong to same bin (means
cosegregating)

Once the binning is done, you can see the state message
 2) Click map function
1) Click open button
Find the map files
When you open the MAP file, you can see this
Click anywhere in this box,
Then you can see the parameters in bottom
Before you go further, there is very important steps for linkage map
You have to check the linkage map and consensus map check whether the markers are
inversed or not.

To check this, OLIVER program is useful.

Before you upload the files to OLIVER, you have to have little modification

Linkage map : \\Vboxsvr\vb\genetic map practice\genetic

map practice 2\marker data preprocess_trial
for
manual\MAP\ICIM_input\Results\ICIM_input.
met
Open met file from your result of MAP folder
Copy and paste linkage map
Manipulate the data
1) data-> text to columns
2) Change the second column and third column
3) Add column lable like this
4) Save as tab deliminated format

Do same as consensus map

If you have trouble with that,

Just let Donghee know!
When you upload the two files, and make bands (view-> overlay bands) you can see like this
In this case 4,8,9,10 LG was flipped. You should reverse the marker order.
Right click and reverse
Do outputting again and save
Check the Lkmap and Cmap again
Do same as before, now you can get not-inversed order markers.
Now, you can make bip for further steps!
Now, you created bip file for the mapping
Next you have to prepare is phenotype data for the mapping.
The list of parental lines
and progenies

You have to make sure this phenotype data and genotype data should be same order. If
there is missing phenotype data, you need add "NA", "na", "*", ".", or "-100.0" to represent
missing phenotypic values
To check the this, you need vlookup fuction
Vlookup function

To use vlookup function, you need raw data here

1) Copy previous sheet
2) paste in transpose
3) #N/A-> -100 using
replace menu
1) Open BIP file 2) Copy & paste except progenies name like this

3) Save it!
Now, you are ready to map QTL!
Open the bip file contaning snp data and phenotyping data
When you click here, you could get parameters setting in bottom
SMA: single marker analysis
IM-ADD: Interval Mapping of segregation distortion loci

Single Marker Analysis (SMA), Interval

Mapping for QTL with additive (and
dominance) effects (IM-ADD), ICIM for QTL
with additive (and dominance) effects (or one
dimensional scanning) (ICIM-ADD),