pedimap worlshop 20140612

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


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)



Acknowledgements

EU-HiDRAS Development Software

Manual

SSR – data set

USDA-SCRI-RosBREED Training material

Technical paper J. Heridity

EU-Fruit Breedomics Training material



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



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


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


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


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: 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


Printkey2000

Freeware

Screenshots

Selected sections of screen

Fast & Easy: excellent for documentation

Create short-cut

Place short-cut on task-bar




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


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


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


Introduction to Pedimap

Use of Pedimap in Breeding

• About the software


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


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


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


● Selection germplasm based on family relationships

Supports visualization of phenotypic values

Example: Quantitative trait - Fruit firmness of apple

Very firm Intermediate


Visualization of phenotypic

Example: Qualitative trait as Vf-Resistance to scab

Vf-present

Vf-lacking


Intro to Pedimap


● Selection germplasm based on family relationships

Supports visualization of phenotypic values

Supports visualization of marker genotypes


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


Use to breeding

Helpful to clarify

Genetic structures in breeding germplasm

Breeding strategy / history

Inheritance

Genetic background of CVS & selections


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


Structure breeding germplasm

Overview crosses & selections DLO-PRI

● Per year

● Series of years


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


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


Inheritance

Unknown

Winter hardiness in 4x garden rose

Limited x Limited Better


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


Conclusion

Functionality

● Supports visual presentation of Pedigrees

● Including phenotypic values & marker genotypes

Use: clarifies

Genetic structures in breeding germplasm

Inheritance patterns


Introduction to Pedimap

• Use of Pedimap in Breeding

About the software


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.


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


Documentation

Manual

● Website

● Downloaded with the executable

Publication Journal of Heredity


Preparation of data input files


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.


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


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


Example data file: Header


UNKNOWN = -

NULLHOMOZ = $

CONFIRMEDNULL = $$

PLOIDY = 2

PEDIGREE


Cox - - 0 3 0 3.225

Delicious - - 0 5 0 3.828

F2-26829 - - 0 2 1 -


Jonathan - - 0 3 0 3.161











81015-045 Elstar Elise 3 3 0 -

Header section


Header


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]


Header


UNKNOWN = -

NULLHOMOZ = $

CONFIRMEDNULL = $$

PLOIDY = 2



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]


Header


UNKNOWN = -

NULLHOMOZ = $

CONFIRMEDNULL = $$

PLOIDY = 2




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


Header


UNKNOWN = -

NULLHOMOZ = $

CONFIRMEDNULL = $$

PLOIDY = 2





PLOIDY Number to indicate the ploidy level


Header


UNKNOWN = -

NULLHOMOZ = $

CONFIRMEDNULL = $$

PLOIDY = 2






NALLELES Number of founder alleles

Relevant only in presence of IBD data

IBD: Pedimap.ped is generated by FlexQTL

Parameter is entered by FlexQTL


Example data file: Pedigree section


UNKNOWN = -

NULLHOMOZ = $

CONFIRMEDNULL = $$

PLOIDY = 2

PEDIGREE


Cox - - 0 3 0 3.225

Delicious - - 0 5 0 3.828

F2-26829 - - 0 2 1 -


Jonathan - - 0 3 0 3.161











81015-045 Elstar Elise 3 3 0 -

Pedigree section


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


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


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


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]


Pedigree section: Additional data


UNKNOWN = -

NULLHOMOZ = $

CONFIRMEDNULL = $$

PLOIDY = 2

PEDIGREE


Cox - - 0 3 0 3.225

Delicious - - 0 5 0 3.828

F2-26829 - - 0 2 1 -


Jonathan - - 0 3 0 3.161











81015-045 Elstar Elise 3 3 0 -


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 !


Structure Data file

1. Header

2. Pedigree Pedigree

Additional data

Nuisance data

Phenotypic scores


Marker scores


Later

Just Presented


Setting up of a Pedimap project


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)


Exercise 1: Starting a Pedimap project

Dataset: Pedimap_Ex1.xlsx

Save as txt/ped file

Import in PediMap


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


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


Exercise 2: Prepare an input file

Folder: Exercises/02

Documentation/Instruction in Exercise_02.....pdf

Related electronic files


Selection of individuals and their pedigrees


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”


Selection of germplasm

Select Tab individuals

● Lists content pedigree section

● Content can be sorted by any column


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


Result selection Elstar + ancestors

New sub-node is generated

● Its view contains Elstar’s ancestors

● as far as known

● Up to 10 generations


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


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


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


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


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


New node: Jonathan + offspring

New node

5. Proceed: create a view that can be edited:


View: Jonathan + offspring + 2nd parent

Both parents presented for any offspring of Jonathan

More complex view







2. Manual, for


● Removal of some specific individuals

2. Starting de novo selection of specific individuals”


View: Jonathan + offspring + 2nd parent

Assume: no interest for Melrose

● Melrose 1st generation descendant Jonathan

● Discard Melrose & its 2nd parent Delicious


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:


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


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







2. Manual, for


2. Starting de novo selection of specific individuals

3. Combining available views


Combining nodes: Intro

View obtained by “Jonathan + Offspring + parents”

Need: more knowledge on the parentage of Elstar

Approach: Combine nodes “Jonathan-2” & “Elstar”



Elise

81015-045


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


Combining nodes

GoldenDelicious Cox F_IngridMarie Jonathan PRI612-1

IngridMarie Septer Florina

Elstar Elise

81015-045



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

+


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


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 !


Content *.pmp file

Project file holds the settings of the views/images

Dynamically:





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


Content *.pmp file

Project file holds the settings of the views/images

Dynamically:





Fixed

● Specific lists of germplasm

● Example: “Combination derived” views

Color & size settings

● For each view separately


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



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


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



Elstar Elise

81015-045


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



Elstar Elise

81015-045


Quantitative trait

Select a quantitative trait

● “Size”

Set color settings


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


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 !)


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!


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


Updated data file I: “Sart_Dummy.ped” POPULATION = Pedigree1

UNKNOWN = -

NULLHOMOZ = $

CONFIRMEDNULL = $$

PLOIDY = 2

PEDIGREE


Cox - - 0 3 0 3.225

Delicious - - 0 5 0 3.828

F_IngridMarie - - 0 0 0 -

F2-26829 - - 0 2 1 -


Jonathan - - 0 3 0 3.161



IngridMarie Cox F_IngridMarie 1 3 0 3.658








81015-045 Elstar Elise 3 3 0 -

Dummy - - 9 9 9 -


UNKNOWN = -

NULLHOMOZ = $

CONFIRMEDNULL = $$

PLOIDY = 2

PEDIGREE


Cox - - 0 3 0 3.225

Delicious - - 0 5 0 3.828


F2-26829 - - 0 2 1 -


Jonathan - - 0 3 0 3.161











81015-045 Elstar Elise 3 3 0 -

Dummy - - 9 9 9 -


UNKNOWN = -

NULLHOMOZ = $

CONFIRMEDNULL = $$

PLOIDY = 2

PEDIGREE


Cox - - 0 3 0 3.225

Delicious - - 0 5 0 3.828


F2-26829 - - 0 2 1 -


Jonathan - - 0 3 0 3.161











81015-045 Elstar Elise 3 3 0 -

Dummy - - 9 9 9 -


Updated data file II: Sart_Dummy_R-012.ped


UNKNOWN = -

NULLHOMOZ = $

CONFIRMEDNULL = $$

PLOIDY = 2

PEDIGREE


Cox - - 0 3 0 3.225

Delicious - - 0 5 0 3.828


F2-26829 - - 0 2 1 -


Jonathan - - 0 3 0 3.161











81015-045 Elstar Elise 3 3 0 -

Dummy - - 9 9 9 -


UNKNOWN = -

NULLHOMOZ = $

CONFIRMEDNULL = $$

PLOIDY = 2

PEDIGREE


Cox - - 0 3 0 3.225

Delicious - - 0 5 0 3.828


F2-26829 - - 0 2 1 -


Jonathan - - 0 3 0 3.161











81015-045 Elstar Elise 3 3 0 -

Dummy - - 9 9 9 -


UNKNOWN = -

NULLHOMOZ = $

CONFIRMEDNULL = $$

PLOIDY = 2

PEDIGREE


Cox - - 0 3 0 3.225

Delicious - - 0 5 0 3.828


F2-26829 - - 0 2 1 -


Jonathan - - 0 3 0 3.161











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”


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


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


Customising the look of views I


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.


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


81015-045 Florina

Amount of info already very limited

What else could we do to make a major difference ?


Acronyms

GoldenDel Cox Jonathan F2-26829 Delicious WeisWintG

IngridMar Septer PRI14-126 Gloster Melrose


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]


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


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


Obtained capabilities, Example on current use:

Rosyara et al. 2013: Cherry germplasm


Obtained capabilities, Example on current use:

Overview germplasm breeding program

Crosses & selections DLO-PRI

● Per year of origin

● Series of years


Marker data

Input data file & Visualization


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!


Marker data: Input data file

1. Header 2. Pedigree

Pedigree

Additional data

Nuisance data

Phenotypic scores


Allowed Marker alleles

Marker scores



Input file: Section Marker Data

Header

Pedigree

Locus (~ markers)


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









For each locus: identification of

the allowed marker alleles

(Supports data consistency)

* Locus ~ marker




Same type of info as for LG 1

Same info follows for all other LG

* Locus ~ marker




For each locus: identification of

the allowed marker alleles

(Supports data consistency)



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


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


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



ALLELES CHVF1

Cox 140 0 140 0


F2-26829 160 0 162 0

F_IngridMar - 5 - 5




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




ALLELES CHVF1

Cox 140 0 140 0


F2-26829 160 0 162 0

F_IngridMar - 5 - 5




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


Column may be incomplete



ALLELES CHVF1

Cox 140 0 140 0


F2-26829 160 0 162 0

F_IngridMar - 5 - 5




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


Column can be incomplete

Not allowed: 2 code- columns

should be balanced


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


Define the to include

markers

● Tab Markers

● Select markers (3)

● All 5 of LG10

● Click OK

3


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


Colors markers

Procedure:

Tab “Markers”

Select the to adjust color (1,2)

Click “change (3)

Select color (4)

Click OK

1

2

3 4


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 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


Markers – Origin of alleles by IBD

Concept, Input data file & Visualization


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


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


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)



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




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






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


221 219 121 121

232! 230

219

Consider marker-block (haplotype)

Identity by Descent:Elise-232 = ± 80% GD, ± 20% Jo

IBD: probability parameter



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


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


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


IBD Table: Interpretation

IBD: describes the flow of alleles over generations


Scored markers IBD probabilities of founder alleles Most probable IBD alleles

Visualization IBD: Colors alleles/haplotypes


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


Scored markers IBD probabilities of founder alleles Most probable IBD alleles

Visualization IBD: Colors alleles/haplotypes


Phenotypic trait values:

Background color of boxes

Golden D

Elstar Septer

Elise

81015-045

Qualitative

Quantitative


IBD data: Input data file

1. Header

2. Pedigree

Pedigree

Additional data

● Nuisance data ● Phenotypic scores

3. Marker data

Linkage map


Marker scores


Locus section

Pedigree section

Header section


IBD data: Various sections adjusted

1. Header

2. Pedigree

Pedigree

Additional data

● Nuisance data ● Phenotypic scores

3. Marker data

Linkage map


Marker scores


NALLELES = 12

Pedigree

Pedigree

Additional data

Nuisance data Phenotypic scores

FOUNDERALLELES

FOUNDERALLELES

IBDPOSITIONS

Marker scores

IBD Tables


Header






NALLELES Number of founder alleles

Relevant only in presence of IBD data

IBD: Pedimap.ped is generated by FlexQTL

Parameter is entered by FlexQTL


UNKNOWN = -

NULLHOMOZ = $

CONFIRMEDNULL = $$

PLOIDY = 2

NALLELES = 12


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


IBD section: Table for each locus


Visualization IBD: marker alleles

Define type of IBD presentation

● View Options


● Two options

● Select one

● Links automaticly to

tab “IBD” l

Define the to present Linkage

Group (LG), see next slide

2


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


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


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


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


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


Visualization IBD: Marker Haplotypes

Define type of IBD presentation

● View Options


● Two options

● Select one

● Links automatically

to tab “IBD” l

Define the to present Linkage

Group (LG), see next slide


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


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


Customising views II


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


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


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


Management of the Pedimap project


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


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


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


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]


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


Ways to insert Pedimap views/charts into

Word and PowerPoint documents


Export Chart

Copy Chart

Word: Text Box; Crop

PPT : Size & position; Crop; Ungroup


A few more exempels on the use of Pedimap


Delicious by maternal line

Maternal line: cytoplasm inheritance


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

↓


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


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


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)


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

pedimap worlshop 20140612

Science

pedimap workshop

aim of workshop

software pba workshop

workshop purposes

fruit breedomics workshop

taskbar pba workshop

wider audience pba workshop

pedimap folder right