1. Fall 2016 - HORT6033 Molecular Plant Breeding
Instructor: Ainong Shi

2. Fall 2016 - HORT6033 Molecular Plant Breeding
Lecture Week 10 (10/24/2016)
QTL Mapping Data Format
Examples

3. QTL Mapping Data Format Procedure
SNP Data
Phenotypic Data
Allele Ratio
Quality Check
JMP
F2 true/false
WinQTLCart
Data Format
MapChart
QGene
QTL Analysis
QTLNetwork
SNP
LOD
R^2
R298331
8.753
0.378
R347577
6.972
0.315
R296495
6.766
0.307
QTL Map
SNP Marker

4. QTL Mapping Data Format Procedure
1. SNP data format
(1) Using IUPAC nucleotide code (
A, C, G, T, R, Y, S, W, K,W, N, and ‘-’ (left Table)
(2) Using two characters:
AA, AC, AG, AT,
CC, CG, CT
GG, GT TT
NN or ‘-’

5. QTL Mapping Data Format Procedure
1. SNP data format
How to transfer SNP from IUPAC nucleotide code to diploid type ?
SNP
two_allels
SNP_type
chrom
pos
L235347
L437586C
L567733
L587674B
L253665B
L594398B
L567696B M CT
C/T 1 T C M H M AG
A/G G A M U M M M GT
G/T M M M M M
* A, C, G, and T are homozygous allele, H = heterozygous; and U=missing

6. How to transfer SNP from IUPAC nucleotide code to diploid type ?
* A, C, G, and T are homozygous allele, H = heterozygous; and U=missing
Sub mono_SNP_trans_di_SNP()
' define some parameters
Dim cln_marker_data_start As Integer
Dim row_marker_data_start As Integer
'find the last column of the active sheet
clnLast = Cells(1, ActiveSheet.Columns.Count).End(xlToLeft).Column
'assign the last row for marker data
row_last = Cells(50000, 1).End(xlUp).Row
cln_marker_data_start = 6
row_marker_data_start = 2
For i = row_marker_data_start To row_last
For k = 1 To cln_marker_data_start - 1
Cells(row_last + 2, k) = Cells(1, k)
Cells(i + row_last + 1, k) = Cells(i, k)
Next k
For j = cln_marker_data_start To clnLast
Cells(row_last + 2, j) = Cells(1, j)
If Cells(i, j) = "A" Then
Cells(i + row_last + 1, j) = "AA"
ElseIf Cells(i, j) = "C" Then
Cells(i + row_last + 1, j) = "CC"
ElseIf Cells(i, j) = "G" Then
Cells(i + row_last + 1, j) = "GG"
ElseIf Cells(i, j) = "T" Then
Cells(i + row_last + 1, j) = "TT"
ElseIf Cells(i, j) = "U" Then
Cells(i + row_last + 1, j) = "NN"
ElseIf Cells(i, j) = "H" Then
Cells(i + row_last + 1, j) = Cells(i, 2)
Else
Cells(i + row_last + 1, j) = "error"
End If
Next j
Next i
End Sub
Excel file with the SNP data of
Single letter and the
VB code to transfer
To diploid type.
Please run it!
Text (.txt) file with
the VB code

7. QTL Mapping Data Format Procedure
2. F1 true/false and selfing testing
(1) One [A/C] SNP for example
P1 x P2 F1 AA CC AC
Female
male F1
True (T)
False (F)
Selfing (S) C T S F Y
IUPAC nucleotide code
Base A
Adenine C
Cytosine G
Guanine
T (or U)
Thymine (or Uracil) R
A or G Y
C or T S
G or C W
A or T K
G or T M
A or C B
C or G or T D
A or G or T H
A or C or T V
A or C or G N
any base
. or -
gap
Y = A/C

8. Progeny Testing I. F1 true/false and selfing:
One [A/C] SNP for example
Female
male F1
True (T)
False (F)
Selfing (S)
Unknown C T S F Y - U
Y=A/C; ‘-’ = missing data

9. Progeny Testing Female male F1 True (T) False (F) Selfing A T S B F H
I. F1 true/false and selfing:
2. One SNP with ABH format
Female
male F1
True (T)
False (F)
Selfing A T S B F H
H=A/B

10. Progeny Testing I. F1 true/false and selfing:
2. One SNP with ABHM format
Female
male F1
True (T)
False (F)
Unknown
Selfing A T S B F H M U
H=A/B; M=‘missing’

11. Progeny Testing Female male F2 or above True (T) False (F) Selfing (S)
II. F2 or above true/false and selfing:
1. One SNP [C/T] format
Female
male
F2 or above
True (T)
False (F)
Selfing (S)
Maybe (P) C T S F Y P

12. Progeny Testing Female male F2 True (T) False (F) Selfing Maybe (P) A
II. F2 or above true/false and selfing:
2. One SNP with ABH format
Female
male F2
True (T)
False (F)
Selfing
Maybe (P) A T S B F H P
H=A/B; M=‘missing’

13. F2 True/false or selfing
VB code
F2_plantID
M042843
M018895
M029431 ……
M038631 7 AG TT GG 8 AA 10 12
………
…….
626 CG
Female_N095
Male_P5678 CC
F2 ABH and ratio testing
With VB codes
F2 Ratio Testing
P1 x P2 F1 F2
AA AC CC AA CC AC
1 2 1
F2_plantID
Female_N095
Male_P5678 7 8 10 12 ……
626
M042843 GG AA AG
………
M018895 TT
…….
M029431
M050787 CC AC
M054083 CG

14. WinQTLCart, QGene, and QTLNetwork
Download the Windows QTL Cartographer 2.5 User Manual  or view manual or view online help how to use the WinQTLCart HERE!
Download QGene Manual at view QGene 4.3 user manual online!
Download QTLNetwork User Manual and the article or view them online!
Article examples: 1|
Online web sites are:
WinQtlCart user manual at or download it from
Qgene user manual at or Download QGene Manual at
QTLNetwork uaer manual at or or

15. WinQTLCart, QGene, and QTLNetwork
Below attached the excel file (QTL_example_formatQgene_QTLCart_Network.xlsb) shows how to make .mcd, .qdf, .txt + .map files to run tools, which are also attached below: PMR16_for_WinQtlCart.mcd for WINQTLCart; PMR16_forQGene.qdf for Qgene; and PMR16_forQtlNetwork.txt + PMR16_for_QTLNetwork_Map.map for QTLNetwork.
Two files:
.txt and .map
For running
QTLNetwork
Excel file for data format
To run WinQTLCart,
Qgene, and QtlNetwork
MCD file format for
running WinQTLCart
QDF file format for
running QGene

16. QTL Mapping Procedure
Draw QTL mapping
figures by Mapchart