1. Pedimap
Announcement of a training session
Eric van de Weg
PBA workshop, MSU JUNE’ 10
1
Fruit Breedomics, stakeholders Feb 11 2014 11 2014, Zurich
day Feb
FB-AM3 Stakeholders day,

2. Announcement
What:
One day workshop on Pedimap software
For whom
Plant Breeders & their affiliates
When
2014 June 12 (Thursday)
Where
Wageningen
PBA workshop, MSU JUNE’ 10
FB-AM3 Stakeholders day, Feb 11 2014
2

3. Intro to Pedimap

Visual presentation of Pedigrees


Selection germplasm based on family relationships
Example: Progenitors of Florina
Delicious
GoldenDel
F2_26829-2-2
Jonathan
PRI14-126
PRI612-1
Florina
PBA workshop, MSU JUNE’ 10
FB-AM3 Stakeholders day, Feb 11 2014
3

4. Selection based on family relationships

Offspring of Florina
X-6820
Florina
Galarina
X-6564
X-6398
X-6683
12_O03
12_F02
I_BB02
PBA workshop, MSU JUNE’ 10
FB-AM3 Stakeholders day, Feb 11 2014
I_W01
12_E001
I_M01
4

5. values Intro to Pedimap

Visual presentation of Pedigrees

Selection germplasm based on family relationships

Supports visualization of phenotypic values

Example: Quantitative trait - Fruit firmness of apple
X-6564
Fuji
X-3143
Galarina
X-3263
X-3318
12_F13
12_F41
Intermediate
12_J16
12_J28
12_J29
I_J44
Very firm
FB-AM3 Stakeholders day, Feb 11 2014
I_J50
I_J56

6. Visualization of phenotypic

Example: Qualitative trait as Vf-Resistance to scab


PBA workshop, MSU JUNE’ 10
FB-AM3 Stakeholders day, Feb 11 2014
6
Vf-present
Vf-lacking

7. Intro to Pedimap

Visual presentation of Pedigrees



Selection germplasm based on family relationships
Supports visualization of phenotypic values
Supports visualization of marker genotypes
PBA workshop, MSU JUNE’ 10
FB-AM3 Stakeholders day, Feb 11 2014
7

8. Visualization of marker genotypes


SNP marker for Vf-restistance to apple scab
B-allele predicts resistance

Prediction is reliable
Delicious
GoldenDel
AA
F2_26829-2-2
AA
BA
Jonathan
AA
PRI14-126
AB
PRI612-1
AB
Florina


Vf-present
Vf-lacking
BA
FB-AM3 Stakeholders day, Feb 11 2014
PBA workshop, MSU JUNE’ 10
8

9. Visualization of marker genotypes


SNP marker for Vf-restistance to apple scab
B-allele predicts resistance

Prediction is reliable
Delicious
GoldenDel
AA
F2_26829-2-2
AA
BA
Jonathan
AA
PRI14-126
AB
PRI612-1
AB
Florina


Vf-present
Vf-lacking
BA
FB-AM3 Stakeholders day, Feb 11 2014
PBA workshop, MSU JUNE’ 10
9

10. Use to breeding
Helpful to clarify
 Genetic structures in breeding germplasm

Breeding strategy / history

Inheritance

Validation / use of marker predictions
PBA workshop, MSU JUNE’ 10
FB-AM3 Stakeholders day, Feb 11 2014
10

11. Structure

All crosses of a specific year
2007-049
Esopus_Spitzenburg
Bellida
Grimes_Golden_?
1955-044-220
Jonathan
Golden_Reinette_?
Ingrid_Marie
Santana
Elstar
Prima
Ribston_Pippin
Golden_Delicious
Septer
Priscilla-NL
Elise
1994-107-170
1995-002-039
Cox's_Orange_Pippin
Alkmene
Baumanns_Renette
NJ_123249
Fresco
1989-007-066
2007-003
2007-025
2000-008-020
2007-026
2007-027
1993-018-037
2007-028
2007-004
1993-008-009
2005-019
2007-011
2007-012
1990-022-159
2006-006
2007-001
1990-045-055
2006-015
2007-002
1990-045-262
2007-039
2007-000
2007-005
2007-031
2007-047
2007-006
2006-016
NJ_130_(old_series)
2007-033
1980-001-010
Z190
Antonovka_34-16
Civni
Schone_van_Boskoop
1971-071-006
Generos
2007-009
M.kaido
1000-121-001
Gala
Renette_Clochard
2007-010
2007-013
2007-044
2007-014
2007-029
Scifresh
X6963
X2039
2006-002
TN_R10-A8
2007-037
Delblush
2007-043
Kidd's_Orange_Red
2006-045
2007-030
2007-035
2007-036
2007-024
2007-007
2007-008
2007-038
2006-001
1000-122-001
Koningszuur
2007-048
2007-034
2007-023
2007-032
Kanzi
Frumos_de_Voinesti
2007-040
2005-020
NJ_12
Red_Rome_Beauty
Kovalenkovskoye
2007-056
2000-008-017
1973-001-041
NJ_117637
Fiesta
Red_Delicious
2007-055
2007-046
Melba
Starr
X3174
2007-054
2000-008-001
1987-035-066
PRI_0014-510
McIntosh
Golden_Pearmain
1980-015-047
Geheimrat_Dr.Oldenburg
F2-26829-2-2
D3
2007-053
Pinova
1995-023-113
Wealthy
2007-052
2000-007-024
1980-015-025
1995-023-064
Clivia
Braeburn
2007-051
2000-007-016
1984-015-017
1995-002-209
Minister_von_Hammerstein
2007-050
2000-006-034
2000-008-006
Blushing_Golden
P22-R24-A8
2000-006-031
1993-010-008
1972-010-033
Blenheim_Orange
1993-005-016
1993-005-025
Idared
Wagener
2007-015
2007-016
2005-023
2006-050
2007-017
2007-018
2007-042
2007-019
2006-052
2007-020
2007-041
2007-021
2007-022
PBA workshop, MSU JUNE’ 10
FB-AM3 Stakeholders day, Feb 11 2014
11

12. Structure: Pedimaps interface

Overview crosses DLO-PRI breeding program


Per year
Series of years
PBA workshop, MSU JUNE’ 10
FB-AM3 Stakeholders day, Feb 11 2014
12

13. Structure

Crosses descending from
a source for resistance

Antonovka
1995 002
1995-002-030
1995-002-039
Z180
-16
Antonovka_34 -16
1995-002-062
1995-002-075
Z190
1995-002-112
1995-002-209
1995-002-357


Selections
Breeding families
1995-002-367
PBA workshop, MSU
FB-AM3 Stakeholders day, Feb 11 2014
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
JUNE’ 10
2006-018
2002-004
13

14. Breeding strategy / history


Re-gaining high fruit quality for
several successive generations
Followed by R-gene pyramiding

Antonovka + Vf resistance
1982-109-006
Vf
1991-21-110
Goldrush
1990-22-159
1990-45-133
1995 002
1995-002-030
1995-002-039
Z180
-16
Antonovka_34 -16
1995-002-062
1995-002-075
Z190
1995-002-112
1995-002-209
1995-002-357


Selections
Breeding families
1995-002-367
PBA workshop, MSU
FB-AM3 Stakeholders day, Feb 11 2014
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
JUNE’ 10
2006-018
2002-004
14

15. Inheritance

Winter hardines in 4x garden rose

Limited  x Limited   Better 
PBA workshop, MSU JUNE’ 10
FB-AM3 Stakeholders day, Feb 11 2014
15
Unknown

16. Genetic background of CVS & selecions


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
Rubens – chromosome 10


Contains DNA from Golden
Delicious & Cox
Partly homozygous for GDhaplotype
Cox
212 212
116 122
143 null
97 75
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
PBA workshop, MSU JUNE’ 10
FB-AM3 Stakeholders day, Feb 11 2014
GoldenDel
229 214
116 116
152 143
79 99
16
Rubens
229 229
116 116
143 152
75 99
F_IngMarie
218 999
116 122
143 null
95 999

17. Conclusion

Functionality



Supports visual presentation of Pedigrees
Including phenotypic values & marker genotypes
Use: clarifies


Genetic structures in breeding germplasm
Inheritance patterns
PBA workshop, MSU JUNE’ 10
FB-AM3 Stakeholders day, Feb 11 2014
17

18. Availability



Freeware
Extensive manual available
Download from:
http://www.wageningenur.nl/en/show/Pedimap.htm


2 links: Software & License file request
License generated instantly, sent by email.
PBA workshop, MSU JUNE’ 10
FB-AM3 Stakeholders day, Feb 11 2014
18

19. Announcement workshop
What:
One day workshop on Pedimap software
For whom
Plant Breeders & their affiliates
When
2014 June 12 (Thursday)
Thanks
Where
Wageningen
PBA workshop, MSU JUNE’ 10
FB-AM3 Stakeholders day, Feb 11 2014
Questions?
19

20. Thanks
PBA workshop, MSU JUNE’ 10
FB-AM3 Stakeholders day, Feb 11 2014
20