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Pedimap Workshop, June 12 2014
PBA workshop, MSU JUNE’ 10 1
Workshop
‘Use of Pedimap software in Breeding’
June 12 Wageningen (Rhenen),The Netherlands
Eric van de Weg
Wageningen UR Plant Breeding
Pedimap Workshop, June 12 2014
Fruit Breedomics
Workshop offered by FruitBreedomics
European Framework Project
Aim: Increase breeding efficiency in apple and peach Markers for resistance released for use in Marker Assisted Breeding
Discovery of new markers for fruit quality
Germplasm with pyramided resistances available to breeders
New phenotyping procedures for complex traits
Tools: New SNP arrays, DataBase, software for QTL analyses
Duration: 2011 March 2015 –August
Dissemination: Approaches & tools (to wider audience)
PBA workshop, MSU JUNE’ 10 2
Pedimap Workshop, June 12 2014
Acknowledgements
EU-HiDRAS Development Software
Manual
SSR – data set
USDA-SCRI-RosBREED Training material
Technical paper J. Heridity
EU-Fruit Breedomics Training material
PBA workshop, MSU JUNE’ 10 3
Pedimap Workshop, June 12 2014
Aim of workshop
At the end of the workshop, Participants are:
Able to
Prepare an Pedimap input file
Select subsets of relevant germplasm
Customise / Format Views according to their needs
Aware of a series of tricks in the use of the software
PBA workshop, MSU JUNE’ 10 4
Pedimap Workshop, June 12 2014
Program of the day
Welcome + House keeping messages 08.15
Introduction Partiticants & Workshop 08.25
Lectures & Exercises 08.40
Coffee Break 10.00
Lectures & Exercises 10.20
Lunch 12.15
Lectures & Exercises 13:15
Coffee Break 15:00
Lectures & Exercises 15:30
Round Table 16:45
Closure 17:00
Dinner 18:00 PBA workshop, MSU JUNE’ 10 5
Pedimap Workshop, June 12 2014
Training Material
Reader:
hard copy of ppt presentations
Exercises
Manual Pedimap
Technical paper
Electronic
Documentation: pdf files <> content of the above reader
Software
Exercises & their data input files
All in the Folder: PedimapWrkShp_2014
Pedimap Workshop, June 12 2014
Organization Electronic material
Folder: PedimapWrkShp_2014
Place this folder in the root of your C (or D) drive:
C:\ PedimapWrkShp_2014
D:\ PedimapWrkShp_2014
Only for the duration of this workshop
Purposes:
Ease of communication among us
Short path:
• easy to keep overview, not too much mouse-clicking
Pedimap Workshop, June 12 2014
Software - Pedimap folder
Folder holds various files
Options.ini -> default settings
Manual
Executable
License
Examples
Content License file: User Eric Van de Weg Affiliation PRI Software Pedimap Version 1.x Valid until indefinite 5853xxxxxxxxxxxxxx
Pedimap Workshop, June 12 2014
PBA workshop, MSU JUNE’ 10 9
Pedimap: Easy access through short cut
Create a shortcut
Explorer: Go to Pedimap folder
Right-click on “Pedimap.exe”
Create shortcut
Drag shortcut to the task-bar
Pedimap Workshop, June 12 2014
Printkey2000
Freeware
Screenshots
Selected sections of screen
Fast & Easy: excellent for documentation
Create short-cut
Place short-cut on task-bar
PBA workshop, MSU JUNE’ 10 10
Pedimap Workshop, June 12 2014
PBA workshop, MSU JUNE’ 10 11
First use
Explorer: Go to C:\ PedimapWrkShp_2014
Contains a ready to go project file:
Start.pmp
Right click this file
Select: Always use the selected program……
Click OK
The project file is opened
A view pops up
Software is in place
Pedimap Workshop, June 12 2014
Topics workshop
0. Introduction to Pedimap
1. Preparation of data input files
2. Preparation of a Pedimap project
3. Selection of individuals and their pedigrees
4. Visualization of phenotypic data
5. Visualization of marker data (true marker alleles, Identity By Descent probabilities)
6. Customising the look of views
7. Management of the Pedimap project
8. Ways to insert Pedimap views into Word & PPT
Pedimap Workshop, June 12 2014
Introduction to participants First Name Last Name Organization City Country
Annemarie Auwerkerken Better3fruit Rillaar Belgium
Jorge Urrestarazu CITA Zaragoza Spain
Alisea Sartori CRA Rome Italy
Helen Cockerton EMR Kent United Kingdom
Isabelle Baumgartner EVD Wädenswil Switzerland
Simone Schütz EVD Wädenswil Switzerland
Bert Meulenbroek Fresh Forward Breeding
Eck en Wiel Netherlands
Pieter Blauw Goossens Flevoplant
Ens Netherlands
Valérie Fouillet IFO Seiches sur le loir France
Mehdi Al Rifaï INRA BEAUCOUZE France, Metropolitan
Joan Bonany IRTA La Tallada Spain
Henryk Flachowsky JKI Dresden Germany
Ali liaqat liaqat corp Gujranwala Pakistan
Omar Carrillo-Mendoza
Royal San Jose de La Rinconada
Spain
Franco Capocasa Univ Politecnica delle Marche
Ancona Italy
Pedimap Workshop, June 12 2014
Introduction to Pedimap
Use of Pedimap in Breeding
• About the software
Pedimap Workshop, June 12 2014
Intro to Pedimap
Visual presentation of Pedigrees
● intuitive, easier to discover relations
Selection germplasm based on family relationships
Delicious GoldenDel F2_26829-2-2 Jonathan
PRI14-126
PRI612-1
Florina
Example: Progenitors of Florina
Pedimap Workshop, June 12 2014
Selection based on family relationships
Offspring of Florina
Florina
X-6820
Galarina
X-6564
X-6398
X-6683
12_O03
12_F02
I_BB02
I_W01
12_E001
I_M01
Pedimap Workshop, June 12 2014
Intro to Pedimap
Fuji X-3143 X-6564 Galarina X-3263
X-3318
12_F13 12_F41 12_J16 12_J28 12_J29 I_J44 I_J50 I_J56
Visual presentation of Pedigrees
● Selection germplasm based on family relationships
Supports visualization of phenotypic values
Example: Quantitative trait - Fruit firmness of apple
Very firm Intermediate
Pedimap Workshop, June 12 2014
Visualization of phenotypic
Example: Qualitative trait as Vf-Resistance to scab
Vf-present
Vf-lacking
Pedimap Workshop, June 12 2014
Intro to Pedimap
Visual presentation of Pedigrees
● Selection germplasm based on family relationships
Supports visualization of phenotypic values
Supports visualization of marker genotypes
Pedimap Workshop, June 12 2014
Visualization of marker genotypes
SNP marker for Vf-resistance to apple scab
B-allele predicts resistance
● Prediction is reliable
Delicious
A A
GoldenDel
A A
F2_26829-2-2
B A
Jonathan
A A
PRI14-126
A B
PRI612-1
A B
Florina
B A
Vf-present
Vf-lacking
Pedimap Workshop, June 12 2014
Visualization of marker genotypes
SNP marker for Vf-resistance to apple scab
B-allele predicts resistance
● Prediction is reliable
Delicious
A A
GoldenDel
A A
F2_26829-2-2
B A
Jonathan
A A
PRI14-126
A B
PRI612-1
A B
Florina
B A
Vf-present
Vf-lacking
Pedimap Workshop, June 12 2014
Use to breeding
Helpful to clarify
Genetic structures in breeding germplasm
Breeding strategy / history
Inheritance
Genetic background of CVS & selections
Pedimap Workshop, June 12 2014
Structure breeding germplasm
All crosses of a specific year
Esopus_Spitzenburg
Wagener
Grimes_Golden_?
Golden_Reinette_?
Ribston_Pippin
Blenheim_Orange
Priscilla-NL
P22-R24-A8
Minister_von_Hammerstein
Baumanns_Renette
Braeburn
F2-26829-2-2
McIntosh
Wealthy
Starr
Red_Rome_Beauty
D3
Antonovka_34-16
Schone_van_Boskoop
Golden_Pearmain
M.kaido
Koningszuur
Renette_Clochard
X2039
X3174
Red_Delicious
Kovalenkovskoye
Jonathan
Golden_Delicious
Cox's_Orange_Pippin
Geheimrat_Dr.Oldenburg
Melba
NJ_130_(old_series)
1971-071-006
1000-121-001
TN_R10-A8
Idared
Ingrid_Marie
Septer
Blushing_Golden
Alkmene
Clivia
PRI_0014-510
NJ_117637
NJ_12
Z190
Frumos_de_Voinesti
1000-122-001
X6963
Kidd's_Orange_Red
1955-044-220
Elstar
Elise
Pinova
NJ_123249
Fiesta
1980-001-010
Generos
Gala
Delblush
Bellida
Santana
Prima
1972-010-033
1994-107-170
1995-002-039
1995-002-209
1995-023-064
1995-023-113
1973-001-041
1987-035-066
2006-006
2007-046
2007-000
2007-047
Civni
2007-048
Kanzi
2006-001
2007-044
Scifresh
2006-002
2007-043
2006-045
1993-005-016
1993-005-025
1993-010-008
1984-015-017
1980-015-025
1980-015-047
Fresco
1989-007-066
2007-003
2007-004
2007-011
2007-012
2007-001
2007-002
2007-005
2007-006
2007-009
2007-010
2007-013
2007-014
2007-029
2007-030
2007-035
2007-036
2000-006-031
2000-006-034
2000-007-016
2000-007-024
2000-008-001
2000-008-006
2000-008-017
2000-008-020
1993-018-037
1993-008-009
1990-022-159
1990-045-055
1990-045-262
2007-031
2007-032
2007-037
2007-038
2005-023
2006-050
2007-042
2006-052
2007-041
2007-049
2007-050
2007-051
2007-052
2007-053
2007-054
2007-055
2007-056
2007-025
2007-026
2007-027
2007-028
2005-019
2006-016
2007-040
2005-020
2006-015
2007-039
2007-033
2007-034
2007-023
2007-024
2007-007
2007-008
2007-015
2007-016
2007-017
2007-018
2007-019
2007-020
2007-021
2007-022
Pedimap Workshop, June 12 2014
Structure breeding germplasm
Overview crosses & selections DLO-PRI
● Per year
● Series of years
Pedimap Workshop, June 12 2014
Structure
- 16 Antonovka_34 - 16 Z180
Z190
Z180
Z190
1995 - 002 - 030
1995 - 002 - 039
1995 - 002 - 062
1995 - 002 - 075
1995 - 002 - 112
1995 - 002 - 209
1995 - 002 - 357
1995 - 002 - 367
1995 - 002 - 030
1995 - 002 - 039
1995 - 002 - 062
1995 - 002 - 075
1995 - 002 - 112
1995 - 002 - 209
1995 - 002 - 357
1995 - 002 - 367
1995 002
2002 - 003
2002 - 006
2006 - 009
2006 - 010
2007 - 029
2007 - 030
2007 - 033
2007 - 034
2007 - 031
2007 - 032
2006 - 011
2006 - 012
2006 - 013
2006 - 014
2002 - 001
2002 - 005
2005 - 019 2006 - 016 2007 - 040
2005 - 020 2006 - 015 2007 - 039
2007 - 035
2007 - 036
2007 - 037
2007 - 038
2006 - 017
2006 - 018
2002 - 004
2002 - 003
2002 - 006
2006 - 009
2006 - 010
2007 - 029
2007 - 030
2007 - 033
2007 - 034
2007 - 031
2007 - 032
2006 - 011
2006 - 012
2006 - 013
2006 - 014
2002 - 001
2002 - 005
2005 - 019 2006 - 016 2007 - 040
2005 - 020 2006 - 015 2007 - 039
2007 - 035
2007 - 036
2007 - 037
2007 - 038
2006 - 017
2006 - 018
2002 - 004
Crosses descending from a source for resistance
● Antonovka
Selections
Breeding families
Pedimap Workshop, June 12 2014
Breeding strategy / history
- 16 Antonovka_34 - 16 Z180
Z190
Z180
Z190
1995 - 002 - 030
1995 - 002 - 039
1995 - 002 - 062
1995 - 002 - 075
1995 - 002 - 112
1995 - 002 - 209
1995 - 002 - 357
1995 - 002 - 367
1995 - 002 - 030
1995 - 002 - 039
1995 - 002 - 062
1995 - 002 - 075
1995 - 002 - 112
1995 - 002 - 209
1995 - 002 - 357
1995 - 002 - 367
1995 002
2002 - 003
2002 - 006
2006 - 009
2006 - 010
2007 - 029
2007 - 030
2007 - 033
2007 - 034
2007 - 031
2007 - 032
2006 - 011
2006 - 012
2006 - 013
2006 - 014
2002 - 001
2002 - 005
2005 - 019 2006 - 016 2007 - 040
2005 - 020 2006 - 015 2007 - 039
2007 - 035
2007 - 036
2007 - 037
2007 - 038
2006 - 017
2006 - 018
2002 - 004
2002 - 003
2002 - 006
2006 - 009
2006 - 010
2007 - 029
2007 - 030
2007 - 033
2007 - 034
2007 - 031
2007 - 032
2006 - 011
2006 - 012
2006 - 013
2006 - 014
2002 - 001
2002 - 005
2005 - 019 2006 - 016 2007 - 040
2005 - 020 2006 - 015 2007 - 039
2007 - 035
2007 - 036
2007 - 037
2007 - 038
2006 - 017
2006 - 018
2002 - 004
Re-gaining high fruit quality for several successive generations
1991-21-110
1990-22-159
1982-109-006
Goldrush
1990-45-133
Followed by R-gene pyramiding
Antonovka + Vf resistance
Vf
Selections
Breeding families
Pedimap Workshop, June 12 2014
Inheritance
Unknown
Winter hardiness in 4x garden rose
Limited x Limited Better
Pedimap Workshop, June 12 2014
Genetic background of CVS & selections
Pedigree of CV Rubens
Marker scores 4 SSR-loci
● Chromosome 10
● Region for fruit firmness
● Digits – marker alleles
● Font color: parental origin
Delicious
229 202 120 116 152 143 null 99
Cox
212 212 116 122 143 null 97 75
GoldenDel
229 214 116 116 152 143 79 99
F_IngMarie
218 999 116 122 143 null 95 999
KidsOrRed
229 212 120 116 152 143 null 75
IngMarie
212 218 122 116 null 143 97 95
Gala
212 229 116 116 143 152 75 79
Elstar
229 218 116 116 152 143 99 97
Rubens
229 229 116 116 143 152 75 99
Rubens – chromosome 10
Contains DNA from Golden Delicious & Cox
Partly homozygous for GD-haplotype
Pedimap Workshop, June 12 2014
Conclusion
Functionality
● Supports visual presentation of Pedigrees
● Including phenotypic values & marker genotypes
Use: clarifies
Genetic structures in breeding germplasm
Inheritance patterns
Pedimap Workshop, June 12 2014
Introduction to Pedimap
• Use of Pedimap in Breeding
About the software
Pedimap Workshop, June 12 2014
Availability
Freeware
Extensive manual available
To download from: http://www.wageningenur.nl/en/show/Pedimap.htm
• 2 links: Software & License file request • License generated instantly, sent by email.
Pedimap Workshop, June 12 2014
About the software
Visualization! , no statistics / calculations
● Visualization <> like PPT, “No Excel”
History
● Developed within the EU-HiDRAS project
● Embraced by the USDA, SCRI-RosBREED project
● A must for Pedigree Based genetic studies
Developer
● Dr. Roeland Voorrips
● Wageningen UR Plant Breeding
● Geneticist, breeder, programmer
Pedimap
Graphical presentation on genetic information in pedigrees
Roeland Voorrips, Software development & QTL analysisEric van de Weg, PBA Team Leader
Pedimap Workshop, June 12 2014
Documentation
Manual
● Website
● Downloaded with the executable
Publication Journal of Heredity
Pedimap Workshop, June 12 2014
Preparation of data input files
Pedimap Workshop, June 12 2014
Pedimap: Make use of 3 files
User defined files
1. Data file: Content: Holds the input data
Name: *.txt, *.prn, *.dat, *.ped
Origin: Created by Excel / a text editor / FlexQTL
2. Project file: Content: Holds the settings of the views/images
Name: *. pmp = PediMap Project
Origin: Created with Pedimap
File created by Pedimap 3. *.bmp = Binary data file,
Reduces loading time in following events
Created while loading a data file.
Pedimap Workshop, June 12 2014
Example data input file: Start.ped
POPULATION = Pedigree1
UNKNOWN = -
NULLHOMOZ = $
CONFIRMEDNULL = $$
PLOIDY = 2
PEDIGREE
NAME PARENT1 PARENT2 Gen DNA R Size
Cox - - 0 3 0 3.225
Delicious - - 0 5 0 3.828
F2-26829 - - 0 2 1 -
GoldenDelicious - - 0 3 0 3.549
Jonathan - - 0 3 0 3.161
Weisse_Winter_Glockenapfel - - 0 1 0 -
Gloster Weisse_Winter_Glockenapfel Delicious 1 7 0 3.950
IngridMarie Cox - 1 3 0 3.658
Melrose Jonathan Delicious 1 3 0 3.992
PRI14-126 GoldenDelicious F2-26829 1 0 1 -
Septer Jonathan GoldenDelicious 1 3 0 3.949
Elstar GoldenDelicious IngridMarie 2 3 0 3.554
PRI612-1 PRI14-126 Delicious 2 4 1 -
Elise Septer Cox 2 3 0 4.741
Florina PRI612-1 Jonathan 3 3 1 3.580
81015-045 Elstar Elise 3 3 0 -
C:\ PedimapWrkShp_2014\Start.ped
Pedimap Workshop, June 12 2014
Structure *.ped (*.dat) file
1. Header
2. Pedigree Pedigree
Additional data
Nuisance data
Phenotypic scores
3. Marker data Linkage map
Marker scores
4. IBD probabilities
Pedimap Workshop, June 12 2014
Example data file: Header
POPULATION = Pedigree1
UNKNOWN = -
NULLHOMOZ = $
CONFIRMEDNULL = $$
PLOIDY = 2
PEDIGREE
NAME PARENT1 PARENT2 Gen DNA R Size
Cox - - 0 3 0 3.225
Delicious - - 0 5 0 3.828
F2-26829 - - 0 2 1 -
GoldenDelicious - - 0 3 0 3.549
Jonathan - - 0 3 0 3.161
Weisse_Winter_Glockenapfel - - 0 1 0 -
Gloster Weisse_Winter_Glockenapfel Delicious 1 7 0 3.950
IngridMarie Cox - 1 3 0 3.658
Melrose Jonathan Delicious 1 3 0 3.992
PRI14-126 GoldenDelicious F2-26829 1 0 1 -
Septer Jonathan GoldenDelicious 1 3 0 3.949
Elstar GoldenDelicious IngridMarie 2 3 0 3.554
PRI612-1 PRI14-126 Delicious 2 4 1 -
Elise Septer Cox 2 3 0 4.741
Florina PRI612-1 Jonathan 3 3 1 3.580
81015-045 Elstar Elise 3 3 0 -
Header section
Pedimap Workshop, June 12 2014
Header
POPULATION = Pedigree1
UNKNOWN = -
NULLHOMOZ = $
CONFIRMEDNULL = $$
PLOIDY = 2
POPULATION Defines source of data -> Any Name
UNKNOWN Defines symbol for missing values
● Multiple symbols can be used simultaneously
● ? - OP
● Separated by a blank
● Recommended not to use the symbol * nor ?
● Wildcard with Microsoft <> Find & Replace X
● Recommendation: -
● Look before you leap ! [1]
Pedimap Workshop, June 12 2014
Header
POPULATION = Pedigree1
UNKNOWN = -
NULLHOMOZ = $
CONFIRMEDNULL = $$
PLOIDY = 2
POPULATION Defines source of data -> Any Name
UNKNOWN Defines symbol for missing values
NULLHOMOZ Symbol used for specific marker scores
● A locus may show just one marker, e.g. 230
– 230 230 = 230 homozygous
– 230 null = 230 heterozygous null
● Data entered as 230 $! Not as 230 230
● Look before you leap ! [2]
Pedimap Workshop, June 12 2014
Header
POPULATION = Pedigree1
UNKNOWN = -
NULLHOMOZ = $
CONFIRMEDNULL = $$
PLOIDY = 2
POPULATION Defines source of data -> Any Name
UNKNOWN Defines symbol for missing values
NULLHOMOZ Symbol used for specific marker scores
CONFIRMEDNULL Symbol to indicate null-alleles of markers
● Confirmed null-alleles are indicated by $$
– 230 230 = 230 homozygous
– 230 $ = 230 230 or 230 null
– 230 $$ = 230 null
Pedimap Workshop, June 12 2014
Header
POPULATION = Pedigree1
UNKNOWN = -
NULLHOMOZ = $
CONFIRMEDNULL = $$
PLOIDY = 2
POPULATION Defines source of data -> Any Name
UNKNOWN Defines symbol for missing values
NULLHOMOZ Symbol used for specific marker scores
CONFIRMEDNULL Symbol to indicate null-alleles of markers
PLOIDY Number to indicate the ploidy level
Pedimap Workshop, June 12 2014
Header
POPULATION = Pedigree1
UNKNOWN = -
NULLHOMOZ = $
CONFIRMEDNULL = $$
PLOIDY = 2
POPULATION Defines source of data -> Any Name
UNKNOWN Defines symbol for missing values
NULLHOMOZ Symbol used for specific marker scores
CONFIRMEDNULL Symbol to indicate null-alleles of markers
PLOIDY Number to indicate the ploidy level
NALLELES Number of founder alleles
Relevant only in presence of IBD data
IBD: Pedimap.ped is generated by FlexQTL
Parameter is entered by FlexQTL
Pedimap Workshop, June 12 2014
Example data file: Pedigree section
POPULATION = Pedigree1
UNKNOWN = -
NULLHOMOZ = $
CONFIRMEDNULL = $$
PLOIDY = 2
PEDIGREE
NAME PARENT1 PARENT2 Gen DNA R Size
Cox - - 0 3 0 3.225
Delicious - - 0 5 0 3.828
F2-26829 - - 0 2 1 -
GoldenDelicious - - 0 3 0 3.549
Jonathan - - 0 3 0 3.161
Weisse_Winter_Glockenapfel - - 0 1 0 -
Gloster Weisse_Winter_Glockenapfel Delicious 1 7 0 3.950
IngridMarie Cox - 1 3 0 3.658
Melrose Jonathan Delicious 1 3 0 3.992
PRI14-126 GoldenDelicious F2-26829 1 0 1 -
Septer Jonathan GoldenDelicious 1 3 0 3.949
Elstar GoldenDelicious IngridMarie 2 3 0 3.554
PRI612-1 PRI14-126 Delicious 2 4 1 -
Elise Septer Cox 2 3 0 4.741
Florina PRI612-1 Jonathan 3 3 1 3.580
81015-045 Elstar Elise 3 3 0 -
Pedigree section
Pedimap Workshop, June 12 2014
Pedigree
The pedigree section requires three columns
● NAME, PARENT1, PARENT2
● Plants: Parent1 = mother
● Parents have to be present in the NAME column
Adding of PRI612-1 would thus not be accepted
• PRI14-126 not being defined
Pedimap Workshop, June 12 2014
Pedigree
Pedimap accepts one of the parents being unknown
● Ingrid Marie = Cox open pollinated
● Father unknown -> “-”
● Use of OP -> unfavourable following software: various cvs will have “OP” as common parent
Future use by FlexQTLTM: IngridMarie = Cox F_IngridMarie
Look before you leap ! [3]
● Here: no perfect dataset -> more work later
Pedimap Workshop, June 12 2014
Names
Accession names are case sensitive
● Cox cox
Names allowed to contain blanks when in between “ ”
● “Weisse Winter Glockenapfel”
● Use is to be discouraged
To avoid blanks & underscores: start 2nd part with Capital
● IngridMarie
Pedimap Workshop, June 12 2014
Mutants
Mutants can be defined as such
● Parent 1 = Original cultivar
● Parent 2 = code for mutants: *MUT
Molecular marker studies:
● At marker level, mutants are identical to original cv
● Pedigree based QTL mapping: One name for all
● Phenotypic data: color related traits -> make mv
● Look before you leap [4]
Pedimap Workshop, June 12 2014
Pedigree section: Additional data
POPULATION = Pedigree1
UNKNOWN = -
NULLHOMOZ = $
CONFIRMEDNULL = $$
PLOIDY = 2
PEDIGREE
NAME PARENT1 PARENT2 Gen DNA R Size
Cox - - 0 3 0 3.225
Delicious - - 0 5 0 3.828
F2-26829 - - 0 2 1 -
GoldenDelicious - - 0 3 0 3.549
Jonathan - - 0 3 0 3.161
Weisse_Winter_Glockenapfel - - 0 1 0 -
Gloster Weisse_Winter_Glockenapfel Delicious 1 7 0 3.950
IngridMarie Cox - 1 3 0 3.658
Melrose Jonathan Delicious 1 3 0 3.992
PRI14-126 GoldenDelicious F2-26829 1 0 1 -
Septer Jonathan GoldenDelicious 1 3 0 3.949
Elstar GoldenDelicious IngridMarie 2 3 0 3.554
PRI612-1 PRI14-126 Delicious 2 4 1 -
Elise Septer Cox 2 3 0 4.741
Florina PRI612-1 Jonathan 3 3 1 3.580
81015-045 Elstar Elise 3 3 0 -
Pedimap Workshop, June 12 2014
Pedigree: additional data
The Pedigree section may include additional data
● Nuisance data
● Availability of DNA, Generation in pedigree
● Phenotypic scores of traits
● Resistance to a disease, Size of fruit
Data entered in additional columns
● Integers or letters
● Missing values: any symbol
● Empty cells not allowed !
Pedimap Workshop, June 12 2014
Structure Data file
1. Header
2. Pedigree Pedigree
Additional data
Nuisance data
Phenotypic scores
3. Marker data Linkage map
Marker scores
4. IBD probabilities
Later
Just Presented
Pedimap Workshop, June 12 2014
Setting up of a Pedimap project
Pedimap Workshop, June 12 2014
Pedimap: Makes use of 3 files
User defined files
1. Data file: Content: Holds the input data Name: *.txt, *.prn, *.dat, *.ped Origin: Created by Excel / a text editor / FlexQTL
2. Project file: Content: Holds the settings of the views/images Name: *. pmp = PediMap Project Origin: Created with Pedimap
File created by Pedimap 3. *.bmp = Binary data file,
Only when marker data are present
Reduces loading time in following events
Created automatically while loading a data file.
Pedimap Workshop, June 12 2014 PBA workshop, MSU JUNE’ 10 54
Exercise 1: Create Pedimap project starting with Pedimap_Ex1.xlsx
Excel file in the folder */PedimapWrkShp_2014/Exercises/01
Process described in detail in a pdf document (same folder)
Pedimap Workshop, June 12 2014
Exercise 1: Starting a Pedimap project
Dataset: Pedimap_Ex1.xlsx
Save as txt/ped file
Import in PediMap
Pedimap Workshop, June 12 2014
Exercise-1: Save *.xlsx as *.txt
Open the file in Excel
Save the file in text format
● Tab delimited
Import the just saved file in PediMap
Pedimap Workshop, June 12 2014
Exercise-1: import file into Pedimap
Open Pedimap
Click “File”
Click “Import data file”
Select directory & targeted file
Click the targeted file
Click “Save”
A view pops up
Click
Examine the tabs
Save the project
Pedimap Workshop, June 12 2014
Exercise 2: Prepare an input file
Folder: Exercises/02
Documentation/Instruction in Exercise_02.....pdf
Related electronic files
Pedimap Workshop, June 12 2014
Selection of individuals and their pedigrees
Pedimap Workshop, June 12 2014
Selection germplasm: Approaches
1. General Instructions
a) Starts with central individual
b) Defines number of generations
● Ancestors & Offspring
2. Manual, for
1. Fine tuning result from “general instructions”
2. Starting de novo selection of specific individuals
Both approaches start with the tab “Individuals”
Pedimap Workshop, June 12 2014
Selection of germplasm
Select Tab individuals
● Lists content pedigree section
● Content can be sorted by any column
Pedimap Workshop, June 12 2014
General instructions
1. Select individual from Tab “Individuals”
left click individual, e.g. Elstar
2. Define instruction
● Tab Select” : Click
● Enter # desired Ancestor
generations: #10
● Click: OK
● Selection highlights
3. Consolidate selection
● Click
Pedimap Workshop, June 12 2014
Result selection Elstar + ancestors
New sub-node is generated
● Its view contains Elstar’s ancestors
● as far as known
● Up to 10 generations
Pedimap Workshop, June 12 2014
Edit names of nodes
Initial name: Header, population = ...
Adjust name:
● Left-click targeted node
● Activated: blue selection
area less in size
● Can now be edited: Elstar
Pedimap Workshop, June 12 2014
Germplasm: Jonathan + Offspring
1. Select individual from Tab “Individuals”
● Start at the Source Node
● Tab Individuals
● Select individual of interest
● Click
2. Define settings
● 10 Progeny generations
● Click OK
3. Consolidate selection:
4. Rename new node: Jonathan
Pedimap Workshop, June 12 2014
New node: Jonathan + offspring
New node
Overview is generated by default, an not be edited
5. Proceed: create a view that can be edited: Click
Pedimap Workshop, June 12 2014
View: Jonathan + offspring
All descendants from Jonathan presented
● Maternal and paternal line
Simple, easy to interpret view
Latest generation: selection 81015-045
● 2nd parent?
Jonathan
Septer Melrose Florina
Elise
81015-045
Pedimap Workshop, June 12 2014
Germplasm: Offspring Jonathan + 2nd parent
1. Select Individual of interest
● Source-Node, Tab Individuals
● Select Jonathan
2. Define settings
● 10 Progeny generations
● Include progeny parents
● Click OK
3. Consolidate selection:
4. Rename new node: Jonathan-2
Pedimap Workshop, June 12 2014
New node: Jonathan + offspring
New node
5. Proceed: create a view that can be edited:
Pedimap Workshop, June 12 2014
View: Jonathan + offspring + 2nd parent
Both parents presented for any offspring of Jonathan
More complex view
Pedimap Workshop, June 12 2014
Selection germplasm: Approaches
1. General Instructions
a) Starts with central individual
b) Defines number of generations
● Ancestors & Offspring
2. Manual, for
1. Fine tuning result from “general instructions”
● Removal of some specific individuals
2. Starting de novo selection of specific individuals”
Pedimap Workshop, June 12 2014
View: Jonathan + offspring + 2nd parent
Assume: no interest for Melrose
● Melrose 1st generation descendant Jonathan
● Discard Melrose & its 2nd parent Delicious
Pedimap Workshop, June 12 2014
Views: Removal of individuals
1. Go to targeted Node, Tab ‘Individuals”
● Node “Jonathan-2”
2. Select all Individuals
● Left-click 1st individual
● Keep “Shift” pressed
● left click final individual
3. De-select to remove individuals
● Keep “Ctrl” pressed
● Left-click targeted individuals
4. Consolidate selected germplasm
● Make view:
Pedimap Workshop, June 12 2014
Manual removal individuals: Result
More simple view
Individuals filtered through tab “Individuals”
Alternative: Filter individuals through “View”
GoldenDelicious Jonathan PRI612-1
Elstar Septer Cox Florina
Elise
81015-045
Pedimap Workshop, June 12 2014
Removal germplasm through “Views”
1. Check selection-settings on
● “De-select” activated
2. Prepare de-selection
● Go to targeted list of individuals ● Select all available individuals
3. Select the to remove individuals
● Go to Tab “View” of node of interest
● Note color outline boxes: Dark blue, all individuals being selected
● Keep “Ctrl” pressed
● Left-click targeted individuals
● Color outlines changes
● Latest selected: Red; Previous: grey
4. Consolidate selection
Pedimap Workshop, June 12 2014
Selection germplasm: Approaches
1. General Instructions
a) Starts with central individual
b) Defines number of generations
● Ancestors & Offspring
2. Manual, for
1. Fine tuning result from “general instructions”
2. Starting de novo selection of specific individuals
3. Combining available views
Pedimap Workshop, June 12 2014
Combining nodes: Intro
View obtained by “Jonathan + Offspring + parents”
Need: more knowledge on the parentage of Elstar
Approach: Combine nodes “Jonathan-2” & “Elstar”
GoldenDelicious Jonathan PRI612-1
Elstar Septer Cox Florina
Elise
81015-045
Pedimap Workshop, June 12 2014
Combine info from multiple nodes
1. Select all nodes of interest
● left-click while keeping the Ctrl button pressed
2. Combine these nodes
● Right click within highlighted area
● Left-click “Combine subpops”
● A new node is generated
3. Re-name the node
4. Inspect the view
Pedimap Workshop, June 12 2014
Combining nodes
GoldenDelicious Cox F_IngridMarie Jonathan PRI612-1
IngridMarie Septer Florina
Elstar Elise
81015-045
GoldenDelicious Jonathan PRI612-1
Elstar Septer Cox Florina
Elise
81015-045
Note: compared to previous
slides, parentage of IngridMarie
has been extended from (Cox, -
) to (Cox, F_IngridMarie)
Cox F_IngridMarie
GoldenDelicious IngridMarie
Elstar
+
Pedimap Workshop, June 12 2014
Summary I
1. Germplasm selection
a) General Instructions
● # Generations of Ancestors & Offspring
b) Manual, for
● Fine tuning result from “general instructions”
● Starting de novo selection of specific individuals
● Combining available views
2. Organization of Pedimap Projects
a) Input data: *.ped, *.dat
b) Settings of the views/images; Project file *.pmp
Break
Pedimap Workshop, June 12 2014
Content *.pmp file
Project file: Holds the settings of the views/images
Dynamic way:
● Recalls the Instruction of germplasm selection
● Example: our 1st node: Elstar
● Updates on pedigree information
are automatically got through
[SUBPOP 1 ] Name Elstar Ordering 1 LastSub 0 Flag 0 Origin 0 SelLines 1 0 1 Elstar 10 0 0 0 2
10 generations !
Pedimap Workshop, June 12 2014
Content *.pmp file
Project file holds the settings of the views/images
Dynamically:
● Recalls the Instruction of germplasm selection
● Example: our 1st node: Elstar
● Updates on pedigree information
are automatically got through
Fixed
● Manual derived lists of germplasm
● Example: “Combination derived” views
[SUBPOP 5 ] Name Combination_1 Ordering 1 LastSub 0 Flag 0 Origin 0 SelLines 1 12 1 Cox Delicious GoldenDelicious Jonathan IngridMarie Melrose Septer Elstar PRI612-1 Elise Florina 81015-045
Pedimap Workshop, June 12 2014
Content *.pmp file
Project file holds the settings of the views/images
Dynamically:
● Recalls the Instruction of germplasm selection
● Example: our 1st node: Elstar
● Updates on pedigree information
are automatically got through
Fixed
● Specific lists of germplasm
● Example: “Combination derived” views
Color & size settings
● For each view separately
Pedimap Workshop, June 12 2014
Visualization of phenotypic data
Pedimap Workshop, June 12 2014
Visualization of phenotypic data
Presentation through the fill-color of boxes
Delicious
A A
GoldenDel
A A
F2_26829-2-2
B A
Jonathan
A A
PRI14-126
A B
PRI612-1
A B
Florina
B A
Vf-present
Vf-lacking
Pedimap Workshop, June 12 2014
Visualization of phenotypic data
Presentation through the fill-color of boxes
Formatting through “View Options” , Tab “Individuals”
1. Select “Based on trait”
2 & 3. Choose trait
4. Define color settings
1 2
3
4
Pedimap Workshop, June 12 2014
Qualitative trait
5. For changing current colors
● Current example Vf based
resistance to the scab-disease in
apple
● 1=Yes, 0=No
6. Finalizing this action
7. Finalizing next action, result:
5
6
7
GoldenDelicious Cox F_IngridMarie Jonathan PRI612-1
IngridMarie Septer Florina
Elstar Elise
81015-045
Pedimap Workshop, June 12 2014
Qualitative trait
Adjust color settings?
● E.g.
● Favourable = green
● Unfavourable = orange
Click “1”, Click “Change current”, Select desired color, click OK
Click “0”, same process -> orange
Click OK, Click OK
2
1
3
GoldenDelicious Cox F_IngridMarie Jonathan PRI612-1
IngridMarie Septer Florina
Elstar Elise
81015-045
Pedimap Workshop, June 12 2014
Quantitative trait
Select a quantitative trait
● “Size”
Set color settings
Pedimap Workshop, June 12 2014
Adjustment format missing values
GoldenDelicious Cox Jonathan Delicious
IngridMarie Septer PRI612-1 Melrose
Elstar Elise Florina
81015-045
GoldenDelicious Cox Jonathan Delicious
IngridMarie Septer PRI612-1 Melrose
Elstar Elise Florina
81015-045
Pedimap Workshop, June 12 2014
Format & updates on input data I
Errors in phenotypic data ?!
Input data may be changed without impact on format settings
Procedure:
● Adjust data in input file *.ped
● Save *.ped (same name)
● Save active project
● Re-open project
● Examine targeted “View”
Exercise: In Start.ped,
Change R-score of F_IngridMarie
● from “0“ to “-” (Vf-susceptible -> unknown !)
Pedimap Workshop, June 12 2014
Format & updates on input data II
Previous edit was within the existing range of data
Range extending edits devastate formats
New knowledge: R-cvs vary in intensity of their response
● 1: strong hypersensitive response
● 2: some chlorosis and some sporulation
Assume phenotypic value PRI612-1: 2 rather than 1
● Input data file to be adjusted
● New data file entered into existing project (*.pmp)
All color settings are gone: A lot of re-editing required!
Pedimap Workshop, June 12 2014
Exercise 3: Color settings qualitative trait
Available: 3 input files
● Start.ped
● Start_Dummy.ped Dummy added
● Start_Dummy_R-012.ped Scale extended
● Current project file Start.pmp
Step 1: Start with Start.pmp,
● Make a View for the basic node
● Set color settings for trait R, save project (Start.pmp)
Step 2: Save Sart.pmp once more, now as Start_test1.pmp
● Import Start_Dummy_R-012.ped, Examine relevant View
Step 3: Re-open Start.pmp, save as Start_test2.pmp,
● set color settings for trait R, Save project, import
Start_Dummy_R-012.ped, examine targeted View
Pedimap Workshop, June 12 2014
Updated data file I: “Sart_Dummy.ped” POPULATION = Pedigree1
UNKNOWN = -
NULLHOMOZ = $
CONFIRMEDNULL = $$
PLOIDY = 2
PEDIGREE
NAME PARENT1 PARENT2 Gen DNA R Size
Cox - - 0 3 0 3.225
Delicious - - 0 5 0 3.828
F_IngridMarie - - 0 0 0 -
F2-26829 - - 0 2 1 -
GoldenDelicious - - 0 3 0 3.549
Jonathan - - 0 3 0 3.161
Weisse_Winter_Glockenapfel - - 0 1 0 -
Gloster Weisse_Winter_Glockenapfel Delicious 1 7 0 3.950
IngridMarie Cox F_IngridMarie 1 3 0 3.658
Melrose Jonathan Delicious 1 3 0 3.992
PRI14-126 GoldenDelicious F2-26829 1 0 1 -
Septer Jonathan GoldenDelicious 1 3 0 3.949
Elstar GoldenDelicious IngridMarie 2 3 0 3.554
PRI612-1 PRI14-126 Delicious 2 4 1 -
Elise Septer Cox 2 3 0 4.741
Florina PRI612-1 Jonathan 3 3 1 3.580
81015-045 Elstar Elise 3 3 0 -
Dummy - - 9 9 9 -
POPULATION = Pedigree1
UNKNOWN = -
NULLHOMOZ = $
CONFIRMEDNULL = $$
PLOIDY = 2
PEDIGREE
NAME PARENT1 PARENT2 Gen DNA R Size
Cox - - 0 3 0 3.225
Delicious - - 0 5 0 3.828
F_IngridMarie - - 0 0 0 -
F2-26829 - - 0 2 1 -
GoldenDelicious - - 0 3 0 3.549
Jonathan - - 0 3 0 3.161
Weisse_Winter_Glockenapfel - - 0 1 0 -
Gloster Weisse_Winter_Glockenapfel Delicious 1 7 0 3.950
IngridMarie Cox F_IngridMarie 1 3 0 3.658
Melrose Jonathan Delicious 1 3 0 3.992
PRI14-126 GoldenDelicious F2-26829 1 0 1 -
Septer Jonathan GoldenDelicious 1 3 0 3.949
Elstar GoldenDelicious IngridMarie 2 3 0 3.554
PRI612-1 PRI14-126 Delicious 2 4 1 -
Elise Septer Cox 2 3 0 4.741
Florina PRI612-1 Jonathan 3 3 1 3.580
81015-045 Elstar Elise 3 3 0 -
Dummy - - 9 9 9 -
POPULATION = Pedigree1
UNKNOWN = -
NULLHOMOZ = $
CONFIRMEDNULL = $$
PLOIDY = 2
PEDIGREE
NAME PARENT1 PARENT2 Gen DNA R Size
Cox - - 0 3 0 3.225
Delicious - - 0 5 0 3.828
F_IngridMarie - - 0 0 0 -
F2-26829 - - 0 2 1 -
GoldenDelicious - - 0 3 0 3.549
Jonathan - - 0 3 0 3.161
Weisse_Winter_Glockenapfel - - 0 1 0 -
Gloster Weisse_Winter_Glockenapfel Delicious 1 7 0 3.950
IngridMarie Cox F_IngridMarie 1 3 0 3.658
Melrose Jonathan Delicious 1 3 0 3.992
PRI14-126 GoldenDelicious F2-26829 1 0 1 -
Septer Jonathan GoldenDelicious 1 3 0 3.949
Elstar GoldenDelicious IngridMarie 2 3 0 3.554
PRI612-1 PRI14-126 Delicious 2 4 1 -
Elise Septer Cox 2 3 0 4.741
Florina PRI612-1 Jonathan 3 3 1 3.580
81015-045 Elstar Elise 3 3 0 -
Dummy - - 9 9 9 -
Pedimap Workshop, June 12 2014
Updated data file II: Sart_Dummy_R-012.ped
POPULATION = Pedigree1
UNKNOWN = -
NULLHOMOZ = $
CONFIRMEDNULL = $$
PLOIDY = 2
PEDIGREE
NAME PARENT1 PARENT2 Gen DNA R Size
Cox - - 0 3 0 3.225
Delicious - - 0 5 0 3.828
F_IngridMarie - - 0 0 0 -
F2-26829 - - 0 2 1 -
GoldenDelicious - - 0 3 0 3.549
Jonathan - - 0 3 0 3.161
Weisse_Winter_Glockenapfel - - 0 1 0 -
Gloster Weisse_Winter_Glockenapfel Delicious 1 7 0 3.950
IngridMarie Cox F_IngridMarie 1 3 0 3.658
Melrose Jonathan Delicious 1 3 0 3.992
PRI14-126 GoldenDelicious F2-26829 1 0 1 -
Septer Jonathan GoldenDelicious 1 3 0 3.949
Elstar GoldenDelicious IngridMarie 2 3 0 3.554
PRI612-1 PRI14-126 Delicious 2 4 1 -
Elise Septer Cox 2 3 0 4.741
Florina PRI612-1 Jonathan 3 3 1 3.580
81015-045 Elstar Elise 3 3 0 -
Dummy - - 9 9 9 -
POPULATION = Pedigree1
UNKNOWN = -
NULLHOMOZ = $
CONFIRMEDNULL = $$
PLOIDY = 2
PEDIGREE
NAME PARENT1 PARENT2 Gen DNA R Size
Cox - - 0 3 0 3.225
Delicious - - 0 5 0 3.828
F_IngridMarie - - 0 0 0 -
F2-26829 - - 0 2 1 -
GoldenDelicious - - 0 3 0 3.549
Jonathan - - 0 3 0 3.161
Weisse_Winter_Glockenapfel - - 0 1 0 -
Gloster Weisse_Winter_Glockenapfel Delicious 1 7 0 3.950
IngridMarie Cox F_IngridMarie 1 3 0 3.658
Melrose Jonathan Delicious 1 3 0 3.992
PRI14-126 GoldenDelicious F2-26829 1 0 1 -
Septer Jonathan GoldenDelicious 1 3 0 3.949
Elstar GoldenDelicious IngridMarie 2 3 0 3.554
PRI612-1 PRI14-126 Delicious 2 4 1 -
Elise Septer Cox 2 3 0 4.741
Florina PRI612-1 Jonathan 3 3 1 3.580
81015-045 Elstar Elise 3 3 0 -
Dummy - - 9 9 9 -
POPULATION = Pedigree1
UNKNOWN = -
NULLHOMOZ = $
CONFIRMEDNULL = $$
PLOIDY = 2
PEDIGREE
NAME PARENT1 PARENT2 Gen DNA R Size
Cox - - 0 3 0 3.225
Delicious - - 0 5 0 3.828
F_IngridMarie - - 0 0 0 -
F2-26829 - - 0 2 1 -
GoldenDelicious - - 0 3 0 3.549
Jonathan - - 0 3 0 3.161
Weisse_Winter_Glockenapfel - - 0 1 0 -
Gloster Weisse_Winter_Glockenapfel Delicious 1 7 0 3.950
IngridMarie Cox F_IngridMarie 1 3 0 3.658
Melrose Jonathan Delicious 1 3 0 3.992
PRI14-126 GoldenDelicious F2-26829 1 0 1 -
Septer Jonathan GoldenDelicious 1 3 0 3.949
Elstar GoldenDelicious IngridMarie 2 3 0 3.554
PRI612-1 PRI14-126 Delicious 2 4 2 -
Elise Septer Cox 2 3 0 4.741
Florina PRI612-1 Jonathan 3 3 1 3.580
81015-045 Elstar Elise 3 3 0 -
Dummy - - 9 9 9 -
2 PR
I6
12
-1
Phenotypic score 612-1 adjusted from “1” to “2”
Pedimap Workshop, June 12 2014
Exercise 3: Color settings qualitative trait
Available: 3 input files
● Start.ped
● Start_Dummy.ped Dummy added
● Start_Dummy_R-012.ped Scale extended
● Current project file Start.pmp
Step 1: Start with Start.pmp,
● Make a View for the basic node
● Set color settings for trait R, save project (Start.pmp)
Step 2: Save Sart.pmp once more, now as Start_test1.pmp
● Import Start_Dummy_R-012.ped, Examine relevant View
Step 3: Re-open Start.pmp, save as Start_test2.pmp,
● set color settings for trait R, Save project, import
Start_Dummy_R-012.ped, examine targeted View
Pedimap Workshop, June 12 2014
Look before you leap [5]:
When preparing an input file, add a dummy-individual
● Parents unknown
● All qualitative traits: score beyond current range: 9
● Any new value between 0 – 9 is now excepted without changes in color settings
Pedimap Workshop, June 12 2014
Customising the look of views I
Pedimap Workshop, June 12 2014
Formatting views -Basics
GoldenDelicious Cox Jonathan F2-26829 Delicious Weisse_Winter_Glockenapfel
IngridMarie Septer PRI14-126 Gloster Melrose
Elstar Elise PRI612-1
81015-045 Florina
Pedimap is meant to easily give insight in pedigree information
through visualization
Frequently, initial views will not be very helpful
Too much information
Hard to read due to for instance a too small font
Pedimap puts all info on a single screen
we may consider to reduce the level of info
we can play around with the format.
Pedimap Workshop, June 12 2014
Formatting views: Orientation
GoldenDelicious
Cox
Jonathan
F2-26829
Delicious
Weisse_Winter_Glockenapfel
IngridMarie
Septer
PRI14-126
Gloster
Melrose
Elstar
Elise
PRI612-1
81015-045
Florina
GoldenDelicious Cox Jonathan F2-26829 Delicious Weisse_Winter_Glockenapfel
IngridMarie Septer PRI14-126 Gloster Melrose
Elstar Elise PRI612-1
81015-045 Florina
Amount of info already very limited
What else could we do to make a major difference ?
Pedimap Workshop, June 12 2014
Acronyms
GoldenDel Cox Jonathan F2-26829 Delicious WeisWintG
IngridMar Septer PRI14-126 Gloster Melrose
Elstar Elise PRI612-1
81015-045 Florina
GoldenDelicious
Cox
Jonathan
F2-26829
Delicious
Weisse_Winter_Glockenapfel
IngridMarie
Septer
PRI14-126
Gloster
Melrose
Elstar
Elise
PRI612-1
81015-045
Florina
Name-boxes are uniform in size
Adjusted to the longest name in the data set
Use Acronyms
Look before you leap [6]
Pedimap Workshop, June 12 2014
Orientation + Acronyms
GoldenDel
Cox
Jonathan
F2-26829
Delicious
WeisWintG
IngridMar
Septer
PRI14-126
Gloster
Melrose
Elstar
Elise
PRI612-1
81015-045
Florina
Format options:
Tab “Layout”
1. Distances between families &
sibs
2. Orientation of the view
● Top to bottom <> Left
to right
3. Distances between
generations
Tab “Individuals”
● Option: “Name font”
4. Font type
5. Font size
1
2
3
4
5
Pedimap Workshop, June 12 2014
Exercise-4: Examine basic format options
Continue on a project file of Ecercise 3
Experience the several options by following the instucitons
for Exercise-4 as reported in the pdf document.
C:\ PedimapWrkShp_2014\exercises\04
Adjusted
Pedimap Workshop, June 12 2014
Obtained capabilities, Example on current use:
Rosyara et al. 2013: Cherry germplasm
Pedimap Workshop, June 12 2014
Obtained capabilities, Example on current use:
Overview germplasm breeding program
Crosses & selections DLO-PRI
● Per year of origin
● Series of years
Pedimap Workshop, June 12 2014
Marker data
Input data file & Visualization
Pedimap Workshop, June 12 2014
Marker Data: Example data set
Example data set: Marker.ped
Import this file into existing project
● Open Start.pmp
● Save as Marker.pmp
● Import Marker.ped
● Save
Note: This example file lacks a dummy individual!
‘Look before you leap’ violation!
Pedimap Workshop, June 12 2014
Marker data: Input data file
1. Header 2. Pedigree
Pedigree
Additional data
Nuisance data
Phenotypic scores
3. Marker data Linkage map
Allowed Marker alleles
Marker scores
4. IBD probabilities
Pedimap Workshop, June 12 2014
Input file: Section Marker Data
Header
Pedigree
Locus (~ markers)
Pedimap Workshop, June 12 2014
Structure Marker section
- Identifier linkage group: 1
- Identifier linkage group: 2
Pedimap Workshop, June 12 2014
Structure Marker section
- Identifier linkage group: 1
Map section identifying all loci of
this LG & their map position (cM)
Loci in ascending position
* Locus ~ marker
- Identifier linkage group: 2
Pedimap Workshop, June 12 2014
Structure Marker section
- Identifier linkage group: 1
- Identifier linkage group: 2
Map section identifying all loci of
this LG & their map position (cM)
Loci in ascending position
For each locus: identification of
the allowed marker alleles
(Supports data consistency)
* Locus ~ marker
Pedimap Workshop, June 12 2014
Structure Marker section
- Identifier linkage group: 1
Same type of info as for LG 1
Same info follows for all other LG
* Locus ~ marker
Map section identifying all loci of
this LG & their map position (cM)
Loci in ascending position
For each locus: identification of
the allowed marker alleles
(Supports data consistency)
Pedimap Workshop, June 12 2014
Structure Marker section
Marker scores for all genotyped individuals
All loci in succession According to the above order
* Locus ~ marker
NOTE: Not all accessions of the PEDIGREE section have to be mentioned
Pedimap Workshop, June 12 2014
Allele names: Allowed marker alleles
Allele
size
# Obser-
vations
Allele
size
# Obser-
vations
176 3 188 75
177 1 JonGrimes 189 1
178 13 193 3
179* 3 PRI14126-DCA, Winston-BAZ, Z190 194 47
180 151 196 2
181 2 X4209-INRA 198 13
182 68 200 21
Have to be defined: tool for quality control
SSR with a 2bp repeat.
Alleles with 1 bp difference scored
All at low frequency
Erroneous sizing?
Scores need re-examination
Pedimap Workshop, June 12 2014
Allele section (follows Locus section)
ALLELES CHVF1
Cox 140 0 140 0
Delicious 168 0 174 0
F2-26829 160 0 162 0
F_IngridMar - 5 - 5
GoldenDel 140 0 174 0
Jonathan 140 0 174 0
IngridMar 140 0 140 0
Melrose 174 0 174 0
PRI14-126 140 0 160 0
Septer 174 0 140 0
Elise 174 0 140 0
Elstar 140 0 140 0
PRI612-1 160 0 174 0
Florina 160 0 174 0
81015-045 - 5 - 5
SSR Marker scores
2 alleles/locus/indi-vidual
Pedimap Workshop, June 12 2014
Allele section (follows Locus section)
ALLELES CHVF1
Cox 140 0 140 0
Delicious 168 0 174 0
F2-26829 160 0 162 0
F_IngridMar - 5 - 5
GoldenDel 140 0 174 0
Jonathan 140 0 174 0
IngridMar 140 0 140 0
Melrose 174 0 174 0
PRI14-126 140 0 160 0
Septer 174 0 140 0
Elise 174 0 140 0
Elstar 140 0 140 0
PRI612-1 160 0 174 0
Florina 160 0 174 0
81015-045 - 5 - 5
Font color codes
SSR Marker scores
2 alleles/locus/indi-vidual
Pedimap Workshop, June 12 2014
Allele section (follows Locus section)
ALLELES CHVF1
Cox 140 0 140 0
Delicious 168 0 174 0
F2-26829 160 0 162 0
F_IngridMar - 5 - 5
GoldenDel 140 0 174 0
Jonathan 140 0 174 0
IngridMar 140 0 140 0
Melrose 174 0 174 0
PRI14-126 140 0 160 0
Septer 174 0 140 0
Elise 174 0 140 0
Elstar 140 0 140 0
PRI612-1 160 0 174 0
Florina 160 0 174 0
81015-045 - 5 - 5
Font color codes
c cc
c c
SSR Marker scores
2 alleles/locus/indi-vidual
Column may be incomplete
Pedimap Workshop, June 12 2014
Allele section (follows Locus section)
ALLELES CHVF1
Cox 140 0 140 0
Delicious 168 0 174 0
F2-26829 160 0 162 0
F_IngridMar - 5 - 5
GoldenDel 140 0 174 0
Jonathan 140 0 174 0
IngridMar 140 0 140 0
Melrose 174 0 174 0
PRI14-126 140 0 160 0
Septer 174 0 140 0
Elise 174 0 140 0
Elstar 140 0 140 0
PRI612-1 160 0 174 0
Florina 160 0 174 0
81015-045 - 5 - 5
Font color codes
c cc
c c
SSR Marker scores
2 alleles/locus/indi-vidual
Column can be incomplete
Not allowed: 2 code- columns
should be balanced
Pedimap Workshop, June 12 2014
Visualization markers
Indicate wish to present
marker data
● View Options
● Tab Individuals:
● Option: Show Name &
marker scores (1)
Define the to present markers
● Tab Markers (2)
1
2
Pedimap Workshop, June 12 2014
Define the to include
markers
● Tab Markers
● Select markers (3)
● All 5 of LG10
● Click OK
3
Pedimap Workshop, June 12 2014
Pedigree
Light blue: size + $
● 143 $
● 143 143 or 143 null
● unresolved
Purple: size + null
● 220 null, null confirmed
● See 81015-045 – null 232
● 232 from Elise
● Elstar 220 $, no 232
● Null-> concordance
GoldenDel
180 188149 149235 221121 121220 232
Cox
180 194143 $219 219121 127230 230
F_IngridMar
* ** ** ** ** *
Jonathan
182 202177 177237 231121 125230 232
IngridMar
194 180143 149219 225127 121230 null
Septer
202 188177 149231 221125 121232 232
Elstar
180 180149 149235 225121 121220 null
Elise
202 180177 143221 219121 121232 230
81015-045
180 202149 143225 221121 121null 232
Pedimap Workshop, June 12 2014
Colors markers
Procedure:
Tab “Markers”
Select the to adjust color (1,2)
Click “change (3)
Select color (4)
Click OK
1
2
3 4
Pedimap Workshop, June 12 2014
GoldenDel
180 188149 149235 221121 121220 232
Cox
180 194143 $219 219121 127230 230
F_IngridMar
* ** ** ** ** *
Jonathan
182 202177 177237 231121 125230 232
IngridMar
194 180143 149219 225127 121230 null
Septer
202 188177 149231 221125 121232 232
Elstar
180 180149 149235 225121 121220 null
Elise
202 180177 143221 219121 121232 230
81015-045
180 202149 143225 221121 121null 232
Result:
● Color adjusted
● Data easier to read
Pedimap Workshop, June 12 2014
Pedimap visualizes codes for consistency
Output from FlexQTLTM software
maternal paternal
CH04c06 0.0
CH02b07 7.4
CH02a10 25.6
CH02c11 37.3
CH03d11 43.5
COL 62.9
LG10
Jonathan
157 169 202 182 177 $ 231 237 125 121 232 230
Golden
* * 188 180 149 149 221 235 121 $ 232 222
Septer
157 169 202 182 177 149 231 221 125 121 232 232
Cox
169 $ 180 192 143 $ 219 $ 121 127 230 230
Elise
157 169 202 180 177 143 221 219 121 121 232 230
Jonathan
157 169 202 182 177 $ 231 237 125 121 232 230
Golden
* * 188 180 149 149 221 235 121 $ 232 222
Septer
157 169 202 182 177 149 231 221 125 121 232 232
Cox
169 $ 180 192 143 $ 219 $ 121 127 230 230
Elise
157 169 202 180 177 143 221 219 121 121 232 230
Helpful in data scrutinizing
Pedimap Workshop, June 12 2014
Markers – Origin of alleles by IBD
Concept, Input data file & Visualization
Pedimap Workshop, June 12 2014
IBD concept
IBD: Identity By Descent
Cultivar alleles are expressed in terms of founder alleles
IBD: The chance that a marker allele in a cultivar is identical to an allele of a founder due to inheritance
Pedimap Workshop, June 12 2014
Concept: Pedigree Elise & scores of 3 SSR of LG10
x Golden
Septer x Cox
Elise
Jonathan
231 221 219 125 121 127 121 232 232 230 230
221 219 121 121
232! 230
219
221 235 121 0 232 222
231 237 125 121 232 230
0.0
7.4
22.225.627.2
38.9
4350.2
55.4
63
E34M50-300-1
E35M52-243-4
E34M59-314-1E32M47-126-9
E34M47-105-11
E32M47-171-6
E35M52-224-5
E35M48-159-7
E34M54-82-1770.4
CH04c06
CH02c11
COL
CH03d11
CH02a10
CH02b07
37
Pedimap Workshop, June 12 2014
Concept: Pedigree Elise, origin of 221-marker
x Golden
Septer x Cox
Elise
Jonathan
231 221 219 125 121 127 121 232 232 230 230
221 219 121 121
232! 230
219
221 235 121 0 232 222
231 237 125 121 232 230 Elise-221 from Septer & Golden
100% Identical By Descent (IBD)
Pedimap Workshop, June 12 2014
Concept: Pedigree Elise, origin of 221-marker
x Golden
Septer x Cox
Elise
Jonathan
231 221 219 125 121 127 121 232 232 230 230
221 219 121 121
232! 230
219
221 235 121 0 232 222
231 237 125 121 232 230
Elise - 232 from Golden or
- 232 from Jonathan ?
Elise-221 from Septer & Golden
100% Identical By Descent (IBD)
Pedimap Workshop, June 12 2014
Concept: Pedigree Elise, origin of 221-marker
Consider marker-block (haplotype)
x Golden
Septer x Cox
Elise
Jonathan
231 221 219 125 121 127 121 232 232 230 230
221 235 121 0 232 222
231 237 125 121 232 230
221 219 121 121
232! 230
219 Elise - 232 from Golden or
- 232 from Jonathan ?
Elise-221 from Septer & Golden
100% Identical By Descent (IBD)
Pedimap Workshop, June 12 2014
Concept: Pedigree Elise, origin of 221-marker
x Golden
Septer x Cox
Elise
Jonathan
231 221 219 125 121 127 121 232 232 230 230
221 235 121 0 232 222
231 237 125 121 232 230
Elise - 232 from Golden or
- 232 from Jonathan ?
221 219 121 121
232! 230
219
Consider marker-block (haplotype)
Identity by Descent:Elise-232 = ± 80% GD, ± 20% Jo
IBD: probability parameter
Elise-221 from Septer & Golden
100% Identical By Descent (IBD)
Account for recombination
0.0
7.4
22.225.627.2
38.9
4350.2
55.4
63
E34M50-300-1
E35M52-243-4
E34M59-314-1E32M47-126-9
E34M47-105-11
E32M47-171-6
E35M52-224-5
E35M48-159-7
E34M54-82-1770.4
CH04c06
CH02c11
COL
CH03d11
CH02a10
CH02b07
37
20cM
Pedimap Workshop, June 12 2014
IBD: Integrated analyses, extendable in time
Effect of 232 can be studied by
crosses with Jonathan
Septer
232-Jo
Jonathan x Golden
231 237 I 221 235
125 121 I 121 0
232 230 I 232 222
Septer x Cox
231 221 I 219
125 121 I 121 127
232 232 I 230 230
Elise
221 219
121 121
232! 230
Effect of 232 region can be studied by combining crosses with Golden Septer Elise
232-GD
81015-045
Golden x Ingrid Marie
221 235 I 219 225
121 0 I 127 121
232 222 I 230 0
Elstar
235 225
0 121
222 0
81015-045
225 221
121 121
0 232!
x
I
I
I
Statistics:
Regression: ANOVA, factorial design
Bayesian approaches
Alleles of founders as factors
232-GD, 232-Jo
Weighted by their IBD value
Elise: 232 = 80% 232-GD
integrated analysis on multiple
crosses, selections & cultivars
232
232
Pedimap Workshop, June 12 2014
IBD: Origin of data
Based on marker data & pedigrees
Probabilities estimated by other software, e.g. FlexQTL TM
Each locus: large sized table: effects ease of data handling
Hidras: >600MB txt file
Text editor: Notepad++, Ultra-edit
Pedimap: *.ped -> *.pmb
increases speed loading data file
135
Pedimap Workshop, June 12 2014
IBD Table: Interpretation
IBD: describes the flow of alleles over generations
Pedimap Workshop, June 12 2014
Scored markers IBD probabilities of founder alleles Most probable IBD alleles
Visualization IBD: Colors alleles/haplotypes
Pedimap Workshop, June 12 2014
IBD probabilities: explanation
Linkage group inherited from
mother father
Color indicates founder from
which allele is inherited
Locus positions
Width indicates probability of
founder alleles
Elise Locus1 0
Locus2 5
Locus3 10
Locus4 15
Locus5 20
Pedimap Workshop, June 12 2014
Scored markers IBD probabilities of founder alleles Most probable IBD alleles
Visualization IBD: Colors alleles/haplotypes
Pedimap Workshop, June 12 2014
Phenotypic trait values:
Background color of boxes
Golden D
Elstar Septer
Elise
81015-045
Qualitative
Quantitative
Pedimap Workshop, June 12 2014
IBD data: Input data file
1. Header
2. Pedigree
Pedigree
Additional data
● Nuisance data ● Phenotypic scores
3. Marker data
Linkage map
Allowed Marker alleles
Marker scores
4. IBD probabilities
Locus section
Pedigree section
Header section
Pedimap Workshop, June 12 2014
IBD data: Various sections adjusted
1. Header
2. Pedigree
Pedigree
Additional data
● Nuisance data ● Phenotypic scores
3. Marker data
Linkage map
Allowed Marker alleles
Marker scores
4. IBD probabilities
NALLELES = 12
Pedigree
Pedigree
Additional data
Nuisance data Phenotypic scores
FOUNDERALLELES
FOUNDERALLELES
IBDPOSITIONS
Marker scores
IBD Tables
Pedimap Workshop, June 12 2014
Header
POPULATION Defines source of data -> Any Name
UNKNOWN Defines symbol for missing values
NULLHOMOZ Symbol used for specific marker scores
CONFIRMEDNULL Symbol to indicate null-alleles of markers
PLOIDY Number to indicate the ploidy level
NALLELES Number of founder alleles
Relevant only in presence of IBD data
IBD: Pedimap.ped is generated by FlexQTL
Parameter is entered by FlexQTL
POPULATION = Pedigree1
UNKNOWN = -
NULLHOMOZ = $
CONFIRMEDNULL = $$
PLOIDY = 2
NALLELES = 12
Pedimap Workshop, June 12 2014
Locus section:
LINKAGEGROUP 1
MAP
CHVF1 56.000
X 70.000
LOCUS CHVF1 (1)
ALLELENAMES 140 160 162 168 174
FOUNDERALLELES 140 140 168 174 160 162 -
- 140 174 140 174
LOCUS x (2)
ALLELENAMES x x x
FOUNDERALLELES x x x x x x
IBDPOSITIONS 56.000 70.000
For each locus: ALLELENAMES For each LG: IBD POSITIONS
Pedimap Workshop, June 12 2014
IBD section: Table for each locus
Pedimap Workshop, June 12 2014
Visualization IBD: marker alleles
Define type of IBD presentation
● View Options
● Tab Individuals:
● Two options
● Select one
● Links automaticly to
tab “IBD” l
Define the to present Linkage
Group (LG), see next slide
2
Pedimap Workshop, June 12 2014
Visualization IBD
Define the to present Linkage Group (LG)
● Click ‘filter’ (1)
● Select LG: 10 (2)
● Click OK (3)
Result:
1
2
3
GoldenDel
180 188149 149235 221121 121220 232
Cox
180 194* *
219 219121 127230 230
F_IngridMar
* ** ** ** ** *
Jonathan
182 202177 177237 231121 125230 232
IngridMar
194 ** *
219 *127 *230 *
Septer
202 188177 149231 221125 121232 232
Elstar
180 *149 *235 *121 *220 *
Elise
202 180177 *221 219121 121232 230
81015-045
* 202* ** 221* 121* 232
Pedimap Workshop, June 12 2014
Visualization IBD
Values hard to read
● Light color type fonts
Default color settings: Founders not well differentiated
Adjust color settings !
GoldenDel
180 188149 149235 221121 121220 232
Cox
180 194* *
219 219121 127230 230
F_IngridMar
* ** ** ** ** *
Jonathan
182 202177 177237 231121 125230 232
IngridMar
194 ** *
219 *127 *230 *
Septer
202 188177 149231 221125 121232 232
Elstar
180 *149 *235 *121 *220 *
Elise
202 180177 *221 219121 121232 230
81015-045
* 202* ** 221* 121* 232
Pedimap Workshop, June 12 2014
Set colors founder alleles
Procedure
● Tab IBD
● Select founder haplotype (1)
● Click Set (2)
● Select color
● Click OK
Same procedure for each relevant founder haplotype
3
2
1
1
Pedimap Workshop, June 12 2014
Color founder alleles
Suggestions
● Same color type for both haplotypes of a founder
● Dark – Less Dark
● Use “Custom colors”
GoldenDel
180 188149 149235 221121 121220 232
Cox
180 194* *
219 219121 127230 230
F_IngridMar
* ** ** ** ** *
Jonathan
182 202177 177237 231121 125230 232
IngridMar
194 ** *
219 *127 *230 *
Septer
202 188177 149231 221125 121232 232
Elstar
180 *149 *235 *121 *220 *
Elise
202 180177 *221 219121 121232 230
81015-045
* 202* ** 221* 121* 232
Pedimap Workshop, June 12 2014
Defining Custom colors
Procedure:
Tab IBD, “Set color for selected haplotype”
Select founder allele, click : “Set” -> color
scheme pops up
Custom color section: Target one of the
available ‘black-boxes’ (1)
● Not upper left, as this one is at risk
to become lost / ‘over-written’
Select one of the default colors (2)
Use “define Custom Colors>>’ to increase
‘lightness’ by moving the arrow up (3)
Click “Add to Custom Colors” (4)
Custom color available for re-use
2
3
1
1
4
Pedimap Workshop, June 12 2014
Visualization IBD: Marker Haplotypes
Define type of IBD presentation
● View Options
● Tab Individuals:
● Two options
● Select one
● Links automatically
to tab “IBD” l
Define the to present Linkage
Group (LG), see next slide
Pedimap Workshop, June 12 2014
Visualization IBD: Marker Haplotypes
Change of Color scheme follows same procedure as for marker alleles
Presented loci & size of boxes can be set by tab “IBD”
GoldenDel Cox F_IngridMar Jonathan
IngridMar Septer
Elstar Elise
81015-045
Pedimap Workshop, June 12 2014
IBD: Tracing specific founder haplotypes
Marker SSR-COL-232 from Golden linked to high fruit firmness
Same marker from Jonathan linked to low firmness.
How are these haplotypes represented in modern cvs?
Give all founders the same color
Then re-define haplotypes of interest
GoldenDel Cox F_IngridMar Jonathan
IngridMar Septer
Elstar Elise
81015-045
Pedimap Workshop, June 12 2014
Customising views II
Pedimap Workshop, June 12 2014
Transferring formats of a single View
Formats of any View can be copy/pasted to any other View
● Within a node & Between nodes
Procedure:
● Right-click View-header (1)
● Select: Copy View Options (2)
● Go to targeted node/View
● Right-click targeted View header
● Select: Paste View Options
Use
● Completed, will thought through format can be re-used anywhere -> time efficient
● IBD marker alleles : template for Haplotypes views
● Quick start in generating set of alternative views
1
2
Pedimap Workshop, June 12 2014
Transferring series of views to other nodes
Various Views have been made for individual 81015-045
All formats transferred to any other node by 4x clicking!
Procedure:
● Right click node having desired views
● Click “Set as view source”
● Right-Click targeted new node
● Click: Add Views from source
Look before you leap! [7] May save much time
Pedimap Workshop, June 12 2014
Exercise: Adjustment Max # individuals/view
limitation to the size of the
(sub)populations for which Views
are drawn: 1000 individuals
(default).
Computation time (Drawing)
Pedimap may freeze (Memory)
This limit can be changed
Right-click shortcut to Pedimap
Click properties, adjust
“C:\Program Files\Pedimap.exe
/DL=1000 to e.g. /DL=1500”.
Test procedure: /DL=5
Pedimap Workshop, June 12 2014
Management of the Pedimap project
Pedimap Workshop, June 12 2014
Management of Nodes: Sorting
Nodes can be sorted
● Alphabetically, date of origin
● Blanks are considered
● Useful to create sub-sets
Procedure: Right-click on source-Node
Pedimap Workshop, June 12 2014
Management of Nodes: Documentation
Nodes can keep additional documentation
● Text
Procedure:
● Right-click Targeted Node
● Select “Info” -> Tab sheet pops up
● Add Text to lower plane
● Close
Notes
● No marks for presence documentation
● Upper plane reports origin of node
Pedimap Workshop, June 12 2014
Management of Nodes: Highlighting
Nodes can be marked/flagged by the “!” symbol (4 colours)
● Nodes of high importance
● Nodes containing additional text
Procedure:
● Right-click Targeted Node
● Select “Info” -> Tab sheet pops up
● Click the flag-arrow , select a flag,
● Close
Pedimap Workshop, June 12 2014
Management of Nodes: Template Node
Introduce Node having the template formats for all your favourite type of views
On top of Node Tree
● Make any selection
● Few blanks in front of name
● “ Template”
● Sort Alphabetically
Look before you leap [8]
Pedimap Workshop, June 12 2014
Exercise: Play around with several settings
Selection of generations
(De)Selection of specific individuals
Sorting by Nuisance
Views: Individual names, Marker scores, IBD
IBD – set colors – founders!
Color box: Trait, Dummy trait = 9
Copy View options
Set as Views Source
Combine Subpops
Export Charts
Sort populations (use of spaces & dots!)
Flags
Pedimap Workshop, June 12 2014
Ways to insert Pedimap views/charts into
Word and PowerPoint documents
Pedimap Workshop, June 12 2014
Export Chart
Copy Chart
Word: Text Box; Crop
PPT : Size & position; Crop; Ungroup
Pedimap Workshop, June 12 2014
A few more exempels on the use of Pedimap
Pedimap Workshop, June 12 2014
Delicious by maternal line
Maternal line: cytoplasm inheritance
Pedimap Workshop, June 12 2014
Bink et al. 2014: Offspring of two sources for
scab resistance included in a project on fruit
quality (EU-HiDRAS)
F2_26829-2-2
114 118
162 160
179 164
Discovery
150 150
174 164
177 182
PRI14-126
110 118
140 160
179 164
PRI14-510
110 114
174 162
179 179
PRI14-152
110 118
174 160
179 164
PRI668-100
114 118
174 160
* 164
PRI612-1
114 118
174 160
179 179
Prima
114 118
160 174
179 179
PRI672-3
118 116
160 174
164 179
Priam
118 116
160 174
164 179
X-2771
118 114
174 174
179 *
Florina
118 116
160 174
179 179
X-3177
118 114
140 160
* 179
X-3191
150 110
140 174
* 179
X-6799
116 *
160 *
164 179
X-4638
* 118
140 160
* 164
U1165
114 118
* 160
182 164
DiPr_001
150 114
174 174
182 179
DiPr_002
150 118
174 160
177 179
DiPr_003
150 114
164 174
182 179
DiPr_004
150 118
174 160
177 179
DiPr_005
150 114
164 174
182 179
DiPr_006
150 118
174 174
177 179
DiPr_008
150 118
174 160
177 179
DiPr_009
150 118
164 174
182 179
DiPr_012
150 118
174 174
177 179
DiPr_013
150 114
174 160
177 179
DiPr_014
150 114
164 174
182 179
DiPr_016
150 114
164 174
177 179
DiPr_018
150 114
174 160
177 179
DiPr_019
150 118
164 174
177 179
DiPr_023
150 114
164 174
182 179
DiPr_024
150 114
174 174
177 179
DiPr_026
150 114
164 174
182 179
DiPr_028
150 118
174 160
177 179
DiPr_030
150 118
164 160
182 179
DiPr_031
150 118
164 160
182 179
DiPr_032
150 118
174 162
177 179
DiPr_033
150 114
164 174
182 179
DiPr_034
150 118
164 160
182 179
DiPr_037
150 118
164 160
182 179
DiPr_038
150 114
174 174
177 179
DiPr_039
150 114
164 174
182 179
DiPr_040
150 118
164 160
182 179
DiPr_041
150 114
164 174
177 179
DiPr_042
150 114
164 174
182 179
DiPr_043
150 114
164 174
182 179
DiPr_044
150 114
164 174
182 179
DiPr_045
150 114
164 174
182 179
DiPr_047
150 118
164 160
182 179
DiPr_048
150 118
164 160
182 179
DiPr_049
150 114
174 174
177 179
DiPr_050
150 116
164 174
177 179
DiPr_052
150 114
174 160
177 179
DiPr_053
150 114
174 160
182 179
DiPr_054
150 118
164 174
182 179
DiPr_055
150 114
164 174
182 179
DiPr_056
150 118
164 160
182 179
DiPr_057
150 118
164 160
182 179
DiPr_058
150 114
174 160
177 179
DiPr_059
150 118
164 174
182 179
DiPr_061
150 114
164 160
182 179
DiPr_062
150 114
174 174
182 179
DiPr_063
150 118
164 160
177 179
DiPr_064
150 114
174 174
177 179
DiPr_065
150 118
174 160
177 179
DiPr_066
150 118
174 174
177 179
DiPr_067
150 114
164 174
182 179
DiPr_068
150 114
164 174
182 179
DiPr_069
150 118
164 160
182 179
DiPr_070
150 118
164 174
182 179
DiPr_072
150 114
174 174
177 179
DiPr_073
150 114
174 160
177 179
DiPr_074
150 114
174 174
177 179
DiPr_076
150 114
164 174
182 179
DiPr_078
150 114
164 174
182 179
DiPr_080
150 118
164 160
182 179
DiPr_083
150 114
164 174
182 179
DiPr_084
150 114
164 174
182 179
DiPr_089
150 114
164 174
182 179
DiPr_090
150 114
164 174
177 179
DiPr_091
150 114
164 160
177 179
DiPr_093
150 114
164 160
182 179
DiPr_097
150 114
164 174
177 179
DiPr_099
150 114
174 160
177 179
DiPr_101
150 118
174 174
182 179
DiPr_102
150 114
174 174
177 179
DiPr_103
150 114
164 174
182 179
DiPr_108
150 114
174 174
177 179
DiPr_109
150 114
174 174
177 179
DiPr_111
150 114
174 174
177 179
DiPr_113
150 114
164 160
182 179
DiPr_116
150 118
164 160
182 179
DiPr_118
150 118
164 160
182 179
DiPr_119
150 118
164 160
182 179
DiPr_120
150 118
174 160
177 179
DiPr_130
150 114
164 174
182 179
DiPr_131
150 118
174 160
182 179
DiPr_133
150 114
174 160
177 179
DiPr_135
150 114
174 174
177 179
X-3143
* 114
* 174
182 *
X-6564
118 116
160 140
179 179
Galarina
118 114
160 140
179 182
X-6820
116 116
160 *
179 179
X-6681
150 114
174 160
182 179
Baujade
* 114
160 *
164 205
RedWinterX3177
116 114
174 160
179 179
X-6808
116 118
140 160
179 164
Dorianne
116 118
140 160
179 *
Sa11_01
118 114
160 *
164 182
Sa11_02
118 118
174 160
182 164
Sa11_03
118 118
174 160
182 164
Sa11_04
118 118
160 160
164 164
Sa11_05
118 114
160 *
164 182
Sa11_06
118 118
174 160
182 164
Sa11_08
118 118
160 160
164 164
Sa11_09
118 114
160 *
164 182
Sa11_10
118 118
174 160
182 182
Sa11_11
118 118
160 160
164 164
Sa11_12
118 114
174 160
182 164
Sa11_13
118 118
174 160
182 164
Sa11_14
118 114
160 *
164 182
Sa11_15
118 118
174 160
182 164
Sa11_16
118 118
160 *
164 182
Sa11_17
118 114
160 160
164 164
Sa11_18
118 118
174 160
164 164
Sa11_19
118 118
174 160
182 164
Sa11_20
118 114
160 *
164 182
Sa11_21
118 118
174 160
182 164
Sa11_22
118 118
160 *
182 182
Sa11_23
118 118
160 160
182 164
Sa11_24
118 118
160 160
164 164
Sa11_25
118 118
174 160
182 164
Sa11_26
118 118
160 *
164 182
Sa11_27
118 114
174 160
182 164
Sa11_28
118 114
174 160
182 164
Sa11_29
118 114
160 *
164 182
Sa11_30
118 118
160 160
182 164
Sa11_31
118 118
160 160
182 182
Sa11_32
118 114
174 160
182 164
Sa11_33
118 118
174 160
182 164
Sa11_34
118 118
160 *
164 182
Sa11_35
118 118
160 *
164 182
Sa11_36
118 118
160 160
164 164
Sa11_37
118 114
174 160
182 164
Sa11_38
118 114
174 160
182 164
Sa11_39
118 118
174 160
182 164
Sa11_40
118 114
160 *
164 182
Sa11_41
118 114
160 *
182 182
Sa11_42
118 118
174 160
182 164
Sa11_43
118 118
160 *
164 182
Sa11_44
118 114
160 *
164 182
Sa11_45
118 114
160 *
164 182
Sa11_47
118 118
160 160
182 164
Sa11_48
118 114
160 160
164 164
Sa11_49
118 118
160 160
182 164
Sa11_50
118 118
160 160
164 164
Sa11_51
118 118
174 160
182 164
Sa11_53
118 118
160 *
164 182
Sa11_54
118 114
160 *
182 182
X-3318
116 118
* 174
179 182
X-6683
114 116
138 *
* 179
X-6398
118 112
160 *
179 164
X-3305
116 *
140 160
179 164
I_BB02
110 116
140 160
179 179
I_BB03
118 118
138 160
179 179
I_BB04
118 118
140 160
179 179
I_BB05
118 118
138 160
182 179
I_BB11
110 116
140 160
179 179
I_BB12
118 118
140 160
179 179
I_BB15
110 118
138 160
182 179
I_BB16
118 116
138 160
182 179
I_BB20
118 118
138 160
182 179
I_BB22
110 118
140 160
179 179
I_BB23
118 118
138 160
182 179
I_BB24
110 116
138 160
182 179
I_BB27
110 116
140 160
179 179
I_BB28
118 116
138 160
182 179
I_BB29
110 116
138 160
182 179
I_BB30
110 118
138 160
182 179
I_BB31
110 116
140 160
179 179
I_BB32
110 116
140 160
182 179
I_BB34
110 116
140 160
179 179
I_BB35
110 116
138 160
182 179
I_BB36
110 116
140 160
182 179
I_BB37
110 118
140 160
179 179
I_BB39
110 118
140 160
179 179
I_BB40
118 116
140 160
179 179
I_BB41
118 118
138 160
182 179
I_BB42
110 118
140 160
179 179
I_BB45
110 118
140 160
179 179
I_BB46
110 116
140 160
182 179
I_BB47
110 118
138 160
182 179
I_BB49
110 118
140 160
179 179
I_BB50
110 116
138 160
182 179
I_BB52
110 118
140 160
182 179
I_BB53
118 118
138 160
179 179
I_BB55
110 118
140 160
179 179
I_BB56
118 118
138 160
182 179
I_BB57
118 118
140 160
179 179
I_BB58
110 118
138 160
182 179
I_BB59
118 118
138 160
182 179
I_BB60
110 116
140 160
179 179
I_BB62
110 118
138 160
182 179
I_BB66
118 118
138 160
182 179
I_BB67
110 116
140 160
179 179
I_BB68
118 118
140 160
179 179
I_BB69
118 116
138 160
182 179
I_BB70
110 118
138 160
182 179
I_BB71
118 116
140 160
182 179
I_BB73
110 118
138 160
182 179
I_BB76
118 116
138 160
182 179
I_BB78
118 116
138 160
182 179
I_BB79
110 118
138 160
182 179
12_O03
114 114
160 160
179 179
12_O04
114 118
160 160
179 182
12_O05
114 118
160 160
179 179
12_O06
114 114
160 140
179 182
12_O10
114 118
160 160
179 179
12_O11
116 114
174 160
179 179
12_O12
114 114
160 140
179 182
12_O13
116 114
174 160
179 179
12_O14
116 118
160 140
179 182
12_O15
116 118
174 160
179 179
12_O16
114 118
160 160
179 179
12_O17
116 118
160 160
179 179
12_O18
116 118
174 160
179 179
12_O22
116 114
174 160
179 179
12_O24
116 118
160 160
179 179
12_O25
116 114
160 140
179 182
12_O26
114 118
160 160
179 179
12_O27
114 114
174 160
179 179
12_O28
116 114
174 160
179 179
12_O33
116 118
174 160
179 179
12_O35
116 114
174 160
179 179
12_O41
116 114
160 140
179 182
12_O42
114 118
160 140
179 182
12_O43
116 114
160 140
179 182
12_O46
114 114
160 140
179 182
12_O48
114 118
160 160
179 182
12_O51
116 118
174 160
179 179
12_O52
114 114
160 140
179 182
12_O53
116 118
160 140
179 182
12_O56
114 114
160 140
179 182
12_O58
114 118
160 160
179 179
12_O59
114 118
160 160
179 179
12_O60
116 118
174 160
179 179
12_O61
116 114
160 140
179 182
12_O63
114 118
160 160
179 179
12_O65
114 118
160 160
179 182
12_O68
114 118
160 140
179 182
12_O69
116 114
160 140
179 182
12_O70
116 118
174 160
179 179
12_O71
116 114
174 140
179 182
12_O72
116 114
174 160
179 182
12_O73
116 114
174 140
179 182
12_O74
116 114
160 140
179 179
12_K_Fake1
116 116
160 140
164 179
12_K_Fake3
116 116
174 140
164 179
12_K_Fake4
116 116
174 140
164 179
12_K01
116 116
160 160
164 164
12_K02
116 116
174 160
164 179
12_K04
116 116
174 160
179 164
12_K07
116 116
160 160
164 164
12_K08
116 116
174 160
179 164
12_K09
116 116
174 160
179 164
12_K10
114 116
160 140
179 179
12_K11
114 118
160 160
164 164
12_K14
116 118
174 160
179 164
12_K16
116 116
160 160
164 164
12_K17
114 116
160 140
164 179
12_K18
116 116
174 160
179 164
12_K19
114 116
160 140
164 179
12_K20
114 116
160 140
164 179
12_K22
116 118
174 160
179 164
12_K23
116 118
174 160
179 164
12_K24
116 116
160 140
164 179
12_K25
114 116
160 160
164 164
12_K26
114 116
160 140
164 179
12_K27
114 118
174 160
179 164
12_K28
116 118
174 160
179 164
12_K29
114 116
160 140
164 179
12_K30
116 116
174 160
179 164
12_K31
116 118
174 160
179 164
12_K35
116 116
160 140
164 179
12_K36
116 118
174 160
179 164
12_K40
114 116
174 160
164 164
12_K42
114 116
160 160
164 164
12_K43
114 118
174 160
179 164
12_K44
116 116
160 160
164 164
12_K45
114 118
160 160
164 179
12_K46
116 118
174 160
164 164
12_K47
114 118
160 140
164 179
12_K48
116 116
160 160
164 164
12_K49
116 116
160 140
164 179
12_K50
116 116
174 160
179 164
12_K52
116 118
174 160
179 164
12_K53
114 118
160 140
164 179
12_K54
116 118
174 160
179 164
12_K56
114 116
160 140
179 179
12_K58
116 116
160 160
164 164
12_K60
114 116
160 140
164 179
12_K61
114 118
160 140
164 179
12_K62
116 116
174 140
164 179
12_K63
116 116
160 160
164 164
12_K64
116 118
174 160
179 164
12_K65
116 116
174 160
179 164
12_K67
116 118
174 160
179 164
12_K68
114 118
160 140
164 179
12_K69
114 118
160 140
164 179
I_CC03
114 116
160 140
164 179
I_CC04
114 116
160 160
179 *
I_CC05
116 116
160 160
179 *
I_CC06
114 116
174 140
179 179
I_CC07
116 118
174 160
179 *
I_CC08
116 118
174 160
179 *
I_CC09
116 118
174 160
179 *
I_CC15
114 116
160 140
164 179
I_CC19
116 116
160 160
179 *
I_CC20
116 118
174 160
164 *
I_CC22
114 118
174 160
179 *
I_CC23
114 118
174 160
179 *
I_CC25
114 116
160 140
164 179
I_CC26
114 118
160 160
179 *
I_CC27
116 116
174 160
179 *
I_CC28
116 116
160 160
179 *
I_CC31
114 118
160 160
179 *
I_CC34
116 118
174 160
179 *
I_CC35
116 116
160 140
164 179
I_CC36
114 118
160 160
179 *
I_CC37
116 116
174 160
179 *
I_CC38
116 116
174 160
179 *
I_CC40
114 118
174 160
179 *
I_CC41
114 118
174 160
179 *
I_CC43
114 118
160 140
164 179
I_CC44
114 118
160 140
164 179
I_CC45
116 116
160 160
179 *
I_CC46
114 116
160 160
179 *
I_CC48
114 118
174 160
179 *
I_CC50
116 118
174 160
179 *
I_CC51
116 116
160 160
164 *
I_CC52
116 116
160 160
179 *
I_CC54
116 116
160 160
179 *
I_CC55
116 116
160 160
179 *
I_CC57
114 116
160 160
179 *
I_CC59
116 116
160 140
164 179
I_CC60
116 118
174 160
179 *
I_CC62
114 118
174 160
179 *
I_CC63
116 116
160 160
179 *
I_CC64
116 116
160 140
164 179
I_CC66
114 118
174 160
179 *
I_CC67
116 118
174 160
179 *
I_CC68
116 118
174 160
179 *
I_CC69
116 118
174 160
179 *
I_CC70
116 116
174 160
179 *
I_CC71
116 116
160 160
179 *
I_CC75
114 118
174 160
179 *
I_CC76
114 118
174 160
179 *
I_CC78
114 118
160 140
164 179
I_CC79
114 116
160 140
164 179
12_F01
118 116
174 160
182 179
12_F02
118 118
* 160
179 179
12_F03
116 118
* 160
179 179
12_F04
118 116
174 140
182 179
12_F05
118 116
174 140
182 179
12_F06
118 118
* 160
179 179
12_F07
116 118
* 160
179 179
12_F08
118 118
174 160
182 179
12_F09
118 118
174 140
182 179
12_F10
118 118
174 160
179 179
12_F11
118 118
* 160
179 179
12_F13
116 116
174 140
182 179
12_F14
116 116
174 160
182 179
12_F15
118 118
* 160
179 179
12_F16
118 118
174 160
182 179
12_F18
116 116
174 140
182 179
12_F19
118 116
174 140
182 179
12_F20
116 116
* 160
179 179
12_F21
118 118
* 160
179 179
12_F22
116 116
174 140
182 179
12_F23
118 118
174 160
182 179
12_F24
116 118
* 160
179 179
12_F29
116 118
* 160
179 179
12_F30
118 116
174 140
182 179
12_F31
116 116
* 160
179 179
12_F33
118 118
174 160
182 179
12_F35
116 118
* 160
179 179
12_F36
118 118
174 160
182 179
12_F37
116 116
174 160
182 179
12_F40
118 116
174 140
182 179
12_F41
118 118
174 160
182 179
12_F42
118 118
174 160
182 179
12_F43
118 116
174 140
182 179
12_F44
116 116
174 160
182 179
12_F45
116 116
* 160
179 179
12_F46
118 118
* 160
179 179
12_F48
116 116
174 140
182 179
12_F49
118 116
174 160
182 179
12_F50
118 116
174 140
182 179
12_F52
116 118
* 160
179 179
12_F53
116 118
* 160
179 179
12_F54
116 116
174 160
182 179
12_F55
116 116
* 160
179 179
12_F56
116 116
174 140
182 179
12_F57
118 118
174 140
182 179
12_F58
118 116
174 160
182 179
12_F59
118 116
174 160
182 179
12_F60
118 116
174 140
182 179
12_F61
118 118
174 160
179 179
12_F62
116 116
* 160
179 179
12_F64
116 118
* 160
179 179
12_J01
118 118
* 160
179 179
12_J04
118 114
174 140
179 182
12_J06
118 114
174 160
182 179
12_J07
116 118
* 160
182 182
12_J09
118 114
174 160
182 179
12_J10
116 114
* 160
179 182
12_J11
116 118
174 160
182 179
12_J13
118 118
174 160
182 179
12_J14
116 118
* 160
179 179
12_J15
116 114
* 160
179 179
12_J16
116 114
* 160
179 182
12_J18
116 114
* 160
179 179
12_J19
118 118
* 160
179 179
12_J20
118 118
174 160
182 179
12_J22
118 114
174 140
182 182
12_J23
116 114
174 140
182 182
12_J25
118 118
174 160
182 179
12_J27
118 118
174 160
182 179
12_J28
118 114
174 140
182 182
12_J29
116 118
* 160
179 179
12_J30
118 118
* 160
179 179
12_J31
118 114
174 140
179 182
12_J33
118 114
174 160
182 179
12_J45
116 118
174 140
182 182
I_J01
118 114
174 140
182 182
I_J03
118 116
174 160
182 179
I_J04
118 116
174 140
179 182
I_J05
116 114
174 160
182 179
I_J06
116 114
* 160
179 179
I_J07
116 114
174 160
179 179
I_J12
118 116
174 140
182 182
I_J13
116 116
174 140
182 182
I_J14
118 114
174 140
182 182
I_J16
116 114
* 160
179 182
I_J17
118 116
174 140
179 179
I_J18
118 116
174 140
182 179
I_J19
118 116
174 140
179 182
I_J20
116 116
174 140
182 182
I_J21
116 116
174 140
182 182
I_J24
118 116
* 140
179 179
I_J25
118 116
174 140
182 179
I_J27
118 116
174 162
182 179
I_J28
116 116
174 160
182 179
I_J30
116 116
174 140
182 182
I_J31
118 114
174 160
182 182
I_J32
118 114
174 140
182 182
I_J33
118 116
* 160
179 179
I_J35
116 116
174 140
182 182
I_J36
118 116
174 140
182 182
I_J42
116 114
174 160
182 179
I_J43
116 114
* 160
179 182
I_J44
118 114
174 160
182 182
I_J45
116 116
* 160
179 179
I_J46
118 116
* 160
179 179
I_J48
118 114
174 160
182 179
I_J49
118 114
174 160
179 179
I_J50
116 116
174 140
182 179
I_J51
118 116
174 174
182 179
I_J52
116 114
* 160
179 179
I_J54
116 114
174 160
182 179
I_J56
118 116
174 140
182 182
I_J57
118 116
174 140
182 182
I_J59
118 116
174 160
182 179
I_J60
118 116
174 160
179 179
I_J61
116 114
* 160
179 179
I_J62
116 114
174 160
182 182
I_J63
118 116
174 140
179 182
I_J64
116 114
* 160
179 179
I_J65
118 114
* 160
179 179
I_J66
116 114
174 140
182 182
I_J67
116 116
174 160
182 179
I_J68
118 114
174 140
182 182
I_J69
116 116
174 140
182 182
I_J70
116 116
174 160
182 179
I_M01
116 110
* 174
179 179
I_M02
114 150
138 160
179 179
I_M03
114 110
138 174
* 179
I_M04
116 114
* 160
* 179
I_M05
114 114
138 160
179 179
I_M07
114 150
138 160
179 179
I_M09
114 150
* 174
* 182
I_M12
114 110
138 174
* 179
I_M13
116 114
138 160
179 179
I_M14
116 114
* 160
* 179
I_M15
116 150
* 174
* 182
I_M17
116 114
138 160
179 179
I_M18
114 114
138 162
* 179
I_M19
116 150
* 174
* 182
I_M21
114 114
138 174
* 179
I_M22
116 114
* 160
* 179
I_M23
116 114
* 160
* 179
I_M24
116 150
* 174
179 182
I_M25
116 114
138 160
179 179
I_M26
114 114
138 160
179 179
I_M27
114 114
138 174
179 179
I_M29
114 150
* 174
* 182
I_M31
114 150
138 160
179 179
I_M32
114 114
138 160
179 179
I_M33
116 114
* 174
* 182
I_M34
114 114
138 174
* 179
I_M35
116 150
* 174
* 182
I_M36
114 114
138 160
179 179
I_M37
116 114
* 174
* 182
I_M43
116 114
* 160
179 179
I_M44
114 114
* 162
179 179
I_M47
116 114
138 160
179 179
I_M48
116 114
* 160
* 179
I_M49
116 110
* 160
179 179
I_M50
116 114
* 174
* 182
I_M51
116 114
* 160
179 179
I_M52
116 114
* 160
* 179
I_M53
116 114
* 160
* 179
I_M54
114 110
138 162
* 179
I_M55
116 114
138 162
* 179
I_M56
116 114
* 174
* *
I_M58
114 150
138 160
179 179
I_M60
114 150
138 160
179 179
I_M61
114 150
* 160
* 179
I_M62
114 114
* 160
* 179
I_M63
116 110
* 174
179 179
I_M64
114 110
138 162
* 179
I_M65
116 114
* 160
179 179
I_M66
116 114
* 160
* 179
I_M68
116 150
* 174
* 182
I_W01
118 114
160 *
164 *
I_W02
118 114
160 *
164 *
I_W03
112 116
* *
164 179
I_W04
112 116
* *
164 179
I_W05
118 114
* *
164 179
I_W06
112 114
* *
164 *
I_W07
112 116
* *
164 179
I_W08
112 116
* *
164 179
I_W09
118 116
160 *
179 179
I_W10
118 114
160 *
164 *
I_W11
118 116
160 *
164 *
I_W12
112 116
160 138
179 *
I_W13
118 114
160 138
179 179
I_W14
112 114
* *
164 179
I_W15
112 114
160 *
164 *
I_W16
112 116
* *
164 179
I_W17
118 114
160 *
164 *
I_W18
118 114
160 *
164 *
I_W20
118 116
160 *
164 *
I_W21
118 116
160 *
164 179
I_W22
112 116
160 *
164 *
I_W23
118 116
160 *
179 179
I_W29
118 114
160 138
164 *
I_W31
118 116
160 138
179 179
I_W34
118 114
160 138
179 *
I_W35
118 116
160 *
164 179
I_W36
118 116
160 138
179 *
I_W37
118 114
160 *
164 179
I_W38
118 116
160 *
164 *
I_W39
118 114
160 138
179 *
I_W40
118 116
160 138
179 *
I_W41
118 116
160 *
164 179
I_W42
112 116
160 *
164 *
I_W43
112 114
* 138
164 179
I_W44
112 114
* 138
164 *
I_W45
112 114
160 138
179 *
I_W46
112 114
* *
164 *
I_W47
112 114
160 138
179 *
I_W48
112 116
* *
164 179
I_W49
118 116
160 138
179 *
I_W50
112 114
160 138
179 *
I_W54
112 116
160 *
164 179
I_W55
118 116
160 *
164 179
I_W57
112 114
* *
164 179
I_W58
112 116
* *
179 179
I_W59
118 114
160 138
179 *
I_W62
112 114
* *
164 179
I_W63
112 116
160 *
164 *
I_W64
118 114
160 138
179 *
12_N_Fake1
116 116
140 140
179 179
12_N_Fake2
116 116
140 140
179 179
12_N01
116 106
140 160
179 164
12_N02
116 116
140 160
179 164
12_N03
116 116
160 160
164 164
12_N06
116 106
140 160
179 179
12_N08
* 106
160 140
164 179
12_N09
* 106
160 160
164 164
12_N10
* 116
160 160
164 164
12_N12
* 116
160 140
164 179
12_N13
116 106
140 160
179 164
12_N14
116 106
140 160
179 179
12_N15
* 116
160 140
164 179
12_N16
* 106
140 160
179 164
12_N18
116 106
140 160
179 164
12_N19
116 116
140 160
179 164
12_N20
116 106
160 160
164 164
12_N21
* 116
160 160
164 164
12_N22
* 116
160 140
164 179
12_N24
116 106
160 160
164 164
12_N27
116 106
140 160
179 164
12_N29
* 116
160 140
164 179
12_N30
116 106
140 160
179 179
12_N32
116 116
160 160
164 164
12_N33
116 106
140 160
179 164
12_N34
* 116
160 140
164 179
12_N35
* 106
160 140
164 179
12_N36
116 106
140 160
179 164
12_N37
116 116
140 140
179 179
12_N39
* 106
160 160
164 164
12_N40
116 116
160 140
179 179
12_N41
116 106
140 160
179 164
12_N42
116 106
140 160
179 164
12_N46
* 106
160 140
164 179
12_N47
* 116
160 140
164 179
12_N48
116 106
140 160
179 164
12_N49
116 106
140 160
179 164
12_N50
* 116
160 160
164 164
12_N52
* 106
160 160
164 164
12_N53
116 116
160 140
164 179
12_N54
116 116
160 140
179 179
12_N55
116 116
160 160
164 164
12_N56
* 106
140 160
179 164
12_N57
116 106
140 160
179 164
12_N58
* 106
140 160
179 164
12_N59
116 116
160 140
179 179
12_N60
116 106
140 160
179 164
12_N63
116 116
160 140
164 179
12_N64
116 116
160 140
164 179
12_P_Fake1
150 116
140 140
179 179
12_P_Fake2
150 116
140 140
179 179
12_P01
150 *
174 160
179 164
12_P02
110 *
174 160
179 164
12_P03
110 *
174 160
179 164
12_P04
150 *
174 160
179 164
12_P05
110 *
140 160
179 164
12_P06
110 *
140 160
179 164
12_P08
110 116
174 140
179 179
12_P09
150 116
174 160
179 164
12_P10
150 *
140 160
179 164
12_P12
110 116
174 160
179 179
12_P15
110 *
174 160
179 164
12_P16
110 *
140 160
179 164
12_P17
110 *
174 160
179 164
12_P18
150 116
174 160
179 164
12_P20
110 *
174 160
179 164
12_P21
110 *
140 160
179 164
12_P22
110 *
174 160
179 164
12_P23
110 *
174 160
179 164
12_P24
110 116
174 160
179 164
12_P25
110 116
174 160
179 164
12_P26
110 *
140 160
179 164
12_P27
110 *
174 160
179 164
12_P28
110 116
174 160
179 164
12_P29
150 *
140 160
179 164
12_P30
110 116
174 160
179 164
12_P31
150 *
140 160
179 164
12_P32
150 116
140 160
179 164
12_P33
150 *
140 160
179 164
12_P34
110 116
174 140
179 179
12_P35
110 116
174 140
179 179
12_P36
110 *
140 160
179 164
12_P38
150 *
140 160
179 164
12_P39
110 *
140 160
179 164
12_P40
150 *
140 160
179 164
12_P42
150 116
174 160
179 164
12_P43
110 116
174 160
179 164
12_P44
110 *
174 160
179 164
12_P45
150 *
140 160
179 164
12_P46
110 *
174 160
179 164
12_P47
110 116
174 160
179 164
12_P48
110 *
174 160
179 164
12_P50
110 *
140 160
179 164
12_P51
150 *
140 160
179 164
12_P52
150 *
174 160
179 164
12_P54
150 *
140 160
179 164
12_P55
110 116
174 160
179 164
12_P56
150 116
140 160
179 164
12_P57
110 *
140 160
179 164
12_P58
110 *
140 160
179 164
12_P60
110 *
174 160
179 164
Beauty of BathM.Floribunda 821↓ ↓
F2-26829-2-2 Discovery
↓
Pedimap Workshop, June 12 2014
Polyploidy: SSR marker genotypes in 4x cherry
English-Morello
115 125 135 140 * * * *
Crisana
115 125 135 140 * * * *
Serbian-Pie-1
115 125 135 140 * * * *
Ujfehertoi-Furtos
115 125 135 140 * * * *
II-8-(16)
115 125 135 140 * * * *
Northstar
115 125 135 140 * * * *
Kansas-Sweet
115 125 135 140 * * * *
25-14-(42)
115 125 135 140 * * * *
I-13-(61)
115 125 135 140 * * * *
I-63-(05)
115 125 135 140 * * * *
26e-17-(29)
115 125 135 140 * * * *
Montmorency
115 125 135 140 * * * *
27-27-(44)
120 140 160 180 * * * *
CLS-7
115 125 135 140 * * * *
CLS-3
120 140 160 180 * * * *
CLS-6
115 125 135 140 * * * *
Courtesy to Dr Amy Iezzoni
Pedimap Workshop, June 12 2014
Mutants
RedDelicious Delicious *MUT
Ralls_Janet Delicious
Red_Delicious
Fuji
Ralls_Janet Delicious
Red_Delicious
Fuji
Mutant symbol replaces ‘x’.
When X-symbol is switched off:
“mutant origin” not evident anymore
Summary/Questions / Discussion
Pedimap Workshop, June 12 2014
Look before you leap
1. Symbol for missing values: -, never * nor ?
2. Symbol for homozygous/null: $
3. Semi-founders: name 2nd parent: F_Accession –name
4. Synonyms, Mutants : Pedimap: *MUT
● FlexQTLTM : originating cultivar, no new accession
5. Enter a Dummy individual with a ‘9-score’ - for each qualitative Nuisance variables
6. Acronyms
7. IBD Colour of favourite founders
8. Template node: series of defined IBD Views
● (e.g. one for each linkage group)
Pedimap Workshop, June 12 2014
Topics workshop
0. Introduction to Pedimap
1. Preparation of data input files
2. Preparation of a Pedimap project
3. Selection of individuals and their pedigrees
4. Visualization of phenotypic data
5. Visualization of marker data (true marker alleles, Identity By Descent probabilities)
6. Customising the look of views
7. Management of the Pedimap project
8. Ways to insert Pedimap views into Word & PPT
Pedimap Workshop, June 12 2014 PBA workshop, MSU JUNE’ 10 175
Workshop
‘Use of Pedimap software in Breeding’
June 12 Wageningen (Rhenen),The Netherlands
Eric van de Weg
Wageningen UR Plant Breeding