QTL Mapping by Example
I. Raw data for QTL mapping
A F2 population with 184 individuals and 1536 SNP data: “QTL_example_raw_10112014.xlx”.
QTL_example_rawD
ata_10102014.xlsx
II. Tools for QTL analysis
We will use the example data to do QTL mapping using five tools: JoinMap, WinQTLCart, QGene,
QTLNetwork, and Mapchart. JoinMap is used to create the genetic maps for the population;
WinQTLCart, QGene, and QTLNetwork are used to conduct QTL analysis and identify SNP markers
associated with the traits; and Mapchart is used to create a nice looking images for the QTL maps.
The tools web sites are:
1.
2.
3.
4.
5.
JoinMap 4.1: http://www.kyazma.nl/index.php/mc.JoinMap/sc.Evaluate/
WinQTLCart: http://statgen.ncsu.edu/~shchwang/WQTLCart.htm
Qgene: http://www.qgene.org/qgene/download.php
QTLNetwork 2: http://ibi.zju.edu.cn/software/qtlnetwork/download.htm
Mapchart 2.2: https://www.wageningenur.nl/en/show/Mapchart.htm
Please download the software and the user manuals! And then Install them to you computers.
III. Data Format and quality check
We use ABH- genetic data for running JoinMap, WinQTLCart, and QGene; use 1, 2, 3, and . (123.) format
for QTLNetwork.
We first check data quality using a Visual Basic (VB) codes, and transfer SNP nucleotide data (AA, CC, GG,
TT, AC, AG, AT, CG, CT, GT, and -) to ABH- format, which, Usually, ‘A’ is for female allele, ‘B’ for male, and
‘H’ for heterogonous like F1; however, if male has same allele as female, we also use ‘A’ for male.
Below attached the Excel file (QTL-example_ABH_ratio_10112014.xlsb) how to do data quality check: (1)
check F2 individuals whether it is true/false and selfing, (2) transfer SNP nucleotide format to ABH format,
meanwhile check each SNP whether it fits 1:2:1 ratio in F2 population; and (3) select good SNPs for genetic
mapping. The VB codes are with the excel file and also see blow attached.
QTL_example_ABH_r
atio_10112014.xlsb
ABH_format_ratio.txt
IV. Create Genetic Maps for the F2 population
F2_above_progeny_true_false_selfing_tesying.txt
We use JoinMap to create genetic maps. Download user manual 4.0 and 4.1plus at
http://www.kyazma.nl/index.php/mc.JoinMap/sc.Manual/ or watch it from Youtube at
http://www.youtube.com/watch?v=dTtUrUo53ZI
Below attached the excel file (QTL_example_forJoinMap_10112014.xlsb) shows how to make .loc file to
run JoinMap, and also includes the output from JoinMap. The .loc file (PMR16_1.loc) for running JoinMap
and the VB code for formatting data for running JoinMap attached below.
We will add how to run JoinMap.
QTL_example_forJoi
nMap_10112014.xlsb
PMR16_1.loc
format_for_JoinMap.txt
V. Format files for running QGene, WinQTLCart, and QTLNetwork
We use WinQTLCart, QGene, and QTLNetwork to conduct QTL analysis and identify SNP markers
associated with the traits.
Below attached the excel file (QTL_example_formatQgene_QTLCart_Network_10112014.xlsb) shows
how to make .mcd, .qdf, .txt + .map files to run tools, which are also attached below:
PMR16_for_WinQtlCart10122014.mcd for WINQTLCart; PMR16_forQGene1012201.qdf for Qgene; and
PMR16_forQtlNetwork10122014.txt + PMR16_for_QTLNetwork_Map.map for QTLNetwork.
QTL_example_foram
PMR16_for_WinQtlCart10122014.mcd
tQgene_QTLCart_Network_10122014.xlsb
PMR16_forQtlNetwork10122014.txt
PMR16_forQGene10122014.qdf
PMR16_for_QTLNetwork_Map.map
VI. Run WinQTLCart, QGene, and QTLNetwork
1. Download the Windows QTL Cartographer 2.5 User Manual or view manual or view online help
how to use the WinQTLCart HERE!
2. Download QGene Manual at http://www.qgene.org/qgene/Download_QGene_all.php, view
QGene 4.3 user manual online!
3. Download QTLNetwork User Manual and the article or view them online!
4. Article examples: 1|
5. Online web sites are:

WinQtlCart user manual at
http://statgen.ncsu.edu/qtlcart/HTML/index.html?whentousewinqtlcart.htm or download it
from http://statgen.ncsu.edu/qtlcart/WQTLCart-3.htm

Qgene user manual at
http://www.qgene.org/qgene/current/docs/manual/Main_window.html or Download QGene
Manual at http://www.qgene.org/qgene/Download_QGene_all.php
QTLNetwork uaer manual at http://ibi.zju.edu.cn/software/qtlnetwork/QTLNetworkUserManual.pdf or
http://bioinformatics.oxfordjournals.org/content/24/5/721.full.pdf+html or
http://ibi.zju.edu.cn/BCL/softwareNetwork.html
Attached the Excel file: QTL_example_output_10112014.xlsx.
QTL_example_outp
ut_10112014.xlsx
VII.
Run MapChart to create better maps
Attached files for run MapChart below. We will add how to format files and how to run MapChart.
VIII.
PMR16__Mapchart_qtl4.mct
PMR16-qtl4_SMLE.txt
PMR16-qtl4_SMIM.txt
PMR16-qtl4_BIM.txt
Public lessons
1. http://www.extension.org/share/PBG/ConifercapModule9/index.html
2. Genetic Mapping and QTL Analysis at http://www.extension.org/pages/67854/genetic-mappingand-qtl-analysis#.VCuqv00o6M8
X. Ouput
1. Genetic Map
The 20 linkage groups created by JoinMap 4.1 and drawn using WinQTLCart 2.5.
2. Output from QGene
The F2 distributions of PMR1 and PMT1t are near normal, indicating the two traits are quantitative
traits.
3. Output from WinQTLCart
4.
Output from QTLNetwork
5.
Output from MapChart
Ch4
Ch4
0.8
M008021
M043247
M050013
M065663
M041383
M013297 M018693
M043129
M008241
M046788 M057253
M065783
M041027
M048777
M015167
M032467
0.7
128.3
130.7
132.9
135.9
151.7
160.8
163.6
163.8
165.8
166.1
167.7
169.4
169.7
172.0
0.6
M020735
0.5
M060257
PMR16-qtl4_BIM
97.1
107.3
0.4
M065469
M010119
M008079
M018911
M063079
M065789
M041457
M035255
M015165
M060901
M019105
M010813
M038327
M059885
M063365
M010977
M064941
M029531
0.3
18.0
29.9
31.6
33.3
33.6
38.0
52.4
55.5
58.4
66.1
66.4
67.2
67.5
67.7
68.0
68.3
71.1
79.1
0.2
M055465
M064613
M046624
0.1
0.0
1.7
3.1
0.0
18
16
14
12
M008021
M043247
M050013
M065663
M041383
M013297 M018693
M043129
M008241
M046788 M057253
M065783
M041027
M048777
M015167
M032467
8
128.3
130.7
132.9
135.9
151.7
160.8
163.6
163.8
165.8
166.1
167.7
169.4
169.7
172.0
10
M020735
PMR16-qtl4_SMIM
M060257
PMR16-qtl4_SMLE
97.1
107.3
6
M065469
M010119
M008079
M018911
M063079
M065789
M041457
M035255
M015165
M060901
M019105
M010813
M038327
M059885
M063365
M010977
M064941
M029531
4
18.0
29.9
31.6
33.3
33.6
38.0
52.4
55.5
58.4
66.1
66.4
67.2
67.5
67.7
68.0
68.3
71.1
79.1
2
M055465
M064613
M046624
0
0.0
1.7
3.1