PBG/MCB 622 QTL Cartographer exercise 11/16/2012
We have a population of 94 doubled haploid lines derived from the F1 of a cross between OWBDominant and OWB-Recessive. This is called the Oregon Wolfe Barley.
We have genotyped the population with 400 markers: morphological, SSRs, RFLPs, SNPs and DArTs.
For each locus, the alleles are already coded as “a” like the OWB-Dominant parent or “b” like the OWBRecessive parent. The map was built using Joinmap 4.
The 94 lines were planted in the field and after harvest we measured the weight of 100 grains.
With the genotypic information, the map and the phenotypic data for grain weight we will try to find
QTL responsible for grain weight
You will have to follow these steps:
1. Open QTL Cartographer and create a new file. You provide some information about your data in
the first window:
 Number of chromosomes:7
 Number of traits: 1
 Number of individuals: 94
 Population type: Ri0 (Doubled haploids)
 Save the file to the default folder: C/NCSU/WindQTLcart2.5. Remember this
location because we will continue working with the same project in the next
class
 Allele codes for the genotypic class AA=”a” and for the genotypic class aa=”b”.
Missing genotypic data is “-“.
2. Upload the .txt files with your data: “Chromosome labels” , “Marker labels”, “Marker positions”
and “Genotypes_phenotypes”.
3. The file created has a .mcd extension. Now we can start with the analysis.
4. Go to View->Data Summary and check the histogram for grain weight:
5. Go to Method-> Single marker analysis->view info:
6. Go to Method-> Interval Mapping. Perform analysis using a threshold of 11.5 (by manual input).
7. In the results window click on Settings and select: “Show marker names”, “Show chromosome
names” and “trace coordinates on graph”.
8. Also in the same results window click on Tools->Show QTL information->Automatic location of
QTL (Set the minimum distance between QTL to 30 cM). This will create a file in your working
folder called: “Your name-at.qtl”
9. Also in the same results window click on File->save as EQTL file. This will create a file in your
working folder called: “Your name- i-eqtl.txt”
10. Open both files: “Your name-at.qtl” and “Your name- i-eqtl.txt” and fill the following table
QTL
number
Chromosome
Position
(cM)
2-LOD confidence
interval
Closest marker to the
peak
LOD
Effect
R2
1
2
11. Go to Method-> Interval Mapping. Calculate the significance threshold with 100 permutations
12. Go to Method-> Composite Interval Mapping (CIM). Set the threshold that you got with the
permutations (by manual input). Click in “Control” and the in regression method select : Forward
and Backward.
13. Repeat steps 8 and 9
Fill the following table
QTL
number
1
2
Chromosome
Position
(cM)
2-LOD confidence
interval
Closest marker to the
peak
LOD
Effect
R2