The document describes Pedimap software, which is a tool for visually presenting pedigree relationships. It can be used to clarify genetic structures in breeding germplasm and inheritance patterns. The software allows input of pedigree data along with optional phenotypic trait or marker genotype data. It provides different view types, including overviews, names only, names with phenotypic values, and names with marker genotypes. Pedimap is freely available and helps breeding programs validate parentage, true-to-type status of germplasm, and understand the origin and introgression of chromosome segments.

1. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
PBA workshop, MSU JUNE’ 10 1
Eric van de Weg
Fruit Breedomics, stakeholders day Feb 11 2014, Zurich
PEDIMAP software:
Visual presentation of Pedigrees
To clarify genetic structure in breeding germplasm &
to clarify inheritance patterns
Eric van de Weg
Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18

2. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Pedimap software: Introduction
 Tool to present pedigree relationships
 Useful to present / clarify:
1. Genetic structures in breeding germplasm
2. Inheritance patterns
 Easy in use: Graphical User Interface

3. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Input file
 Simple to generate & manage
 Required: Targeted individual & its parents
 Example: Florina & its Progenitors
Name Parent1 Parent2 TypeGermp Availabel
Florina PRI612-1 Jonathan 1 1
PRI612-1 Delicious PRI14-126 1 1
Delicious - - 1 1
PRI14-126 GoldenDel F2_26829-2-2 1 1
GoldenDel - - 0 1
F2_26829-2-2 - - 0 1
Jonathan EsopSpitz F_Jonathan 1 1

4. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Input file
 Simple to generate & manage
 Required: Targeted individual & its parents
 Optional: Traits, Nuisances
 Example: Florina & its Progenitors
Name Parent1 Parent2 TypeGermp Availabel
Florina PRI612-1 Jonathan 1 1
PRI612-1 Delicious PRI14-126 1 1
Delicious - - 1 1
PRI14-126 GoldenDel F2_26829-2-2 1 1
GoldenDel - - 0 1
F2_26829-2-2 - - 0 1
Jonathan EsopSpitz F_Jonathan 1 1

5. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Pedimap software: Type of Views
 Different Type of graphs <> different goals
1. Overview
2. Names only
3. Names + Phenotypic trait
4. Names + Marker genotypes
5. Names + IBD probabilities
 Examples on applications
PBA workshop, MSU JUNE’ 10 5

6. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Type 1: Overview
 Founders that contributed to the targeted individual
 Florina, which are its Progenitors ?
GoldenDel
F2_26829-2-2
Delicious
PRI14-126
PRI612-1
Jonathan
Florina

7. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Type 2: Names only
 Founders that contributed to the targeted individual
 Florina, which is its Offspring?
Florina
X-6820
X-6564
Galarina
X-6683
12_F02
I_BB02
12_O03
12_E001
I_M12
I_W10

8. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Type 3: Names only + “phenotypic”values
Florina
X-6820
X-6564
Galarina
X-6683
12_F02
I_BB02
12_O03
12_E001
I_M12
I_W10
 Starting point
 Full sib Families
 Selections
 Cultivars
 Design of genetic experiments
 Type of offspring?
 Color name-boxes:

9. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
3. Names only + “phenotypic” values
 Tree  Not Available: lost
 Tree & NA
 Type of offspring?
 Color name-boxes:
 Design of genetic experiments
Florina
X-6820
X-6564
Galarina
X-6683
12_F02
I_BB02
12_O03
12_E001
I_M12
I_W10

10. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
3. Names only + Phenotypes, Limited # classes
PBA workshop, MSU JUNE’ 10 10
 Winter hardiness 4x garden rose
Unknown
 Inheritance patterns ?
 Color name-boxes according to phenotypic value
 Limited  x Limited   Better 

11. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
3. Names only + Phenotypes, continuous scale
Fuji X-3143X-6564 Galarina X-3263
X-3318
12_F13 12_F41 12_J16 12_J28 12_J29 I_J44 I_J50 I_J56
Very firm
Soft
Quite
soft
Firm
Intermediate
Quite
softSoft
 Firmness-QTL pyramid along successive generations
 Fruit firmness of apple
 Inheritance patterns ?
 Color name-boxes

12. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
4. Names + Marker genotypes
 Parentage & DNA sample True To Type?
2 homologs
4 loci
(SSR)
Delicious
229202
120116
152143
null 99
Cox
212 212
116 122
143 null
97 75
KidsOrRed
229212
120116
152143
null 75
Delicious
229202
120116
152143
null 99
Cox
212 212
116 122
143 null
97 75
KidsOrRed
229212
120116
152143
null 75
 Manual analyses: Pedigree records & DNA’s are OK

13. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
B. Names + Identity By Descent (IBD) probabilities
 Marker alleles coloured
according to origin (founder)
 Based on IBD data as coming
from the FlexQTLTM software
 Chromosome fragments:
 where do they come from?
 Where do they go to?
Delicious
229 202
120 116
152 143
null99
Cox
212 212
116 122
143 null
97 75
GoldenDel
229 214
116 116
152 143
79 99
KidsOrRed
229 212
120 116
152 143
null75
Gala
212 229
116 116
143 152
75 79
IngMarie
212 218
122 116
null 143
97 95
Elstar
229 218
116 116
152 143
99 97
F_IngMarie
218 999
116 122
143 null
95 999
Rubens
229 229
116 116
143 152
75 99
 Rubens: Top segment homozygous
for Golden Delicious’s Homologe-1
 Homozygous through IBD !

14. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Use:
 Validation of parentages
 Validation TTT germplasm
 Origin / introgression chromosome segments
FounderHomolog with important
gene & position locus
F2_26829-2-2
PRI14-126 PRI14-152 PRI54-12
OR38T16 PRI672-3 PRI672-1 PRI612-1 PRI612 Priam PRI370-15 Liberty
Jolana X-6799 Florina PRI1661-2 PRI1661-1 Judeline X-2773 Primula X-4638 B3F12-040 Judaine Melodie
Katka Rosana Vanda Baujade X-6820 X-6564 Galarina X-6064 Enterprise X-4337 Odra Sawa U6_36 U633 U641 U1065 X-6808 Dorianne X-6688
Rajka Topaz X-3305
1. Successful
introgression
2. Little linkage drag

15. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
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
Locus10
Locus25
Locus310
Locus415
Locus520
Was de-activated in previous
slide except for the targeted
locus
Previous slide: only targeted founder-
haplotype was coloured, all others
were set at grey

16. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Use:
 Validation of parentages
 Validation TTT germplasm
 Origin/introgression chrom. segments
 Founder composition of modern cvs
Delicious GoldenDel F2_26829-2-2 Jonathan Cox
PRI14-126 KidsOrRed
PRI612-1 Gala
Florina
Galarina
Florina
Galarina
F2-26829-2-2
Golden
Delicious
Golden
Delicious
Delicious
Cox

17. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Pedimap & Breeding decissions
Heading for maximum diversity, which
would be the best parent to combine
with Galarina?
X-6564 PRI1661-2 RosanaPRI1661-2 RosanaX-6564 PRI1661-2 Rosana
Florina
Galarina

18. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Reminder
 Pedimap is on visualisation,
 No statistical or genetic analyses
 No data manipulation
 Identity By Descent data come from the FlexQTLTM software
For apple, SNP & IBD data are coming public available for few hundred
cultivars & breeding selections through the FruitBreedomics
website/data base (spring 2016?)

19. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Conclusion
 Functionality
 Pedimap supports visual presentation of Pedigrees
 Including phenotypic values & marker genotypes
 Use: clarifies
 Genetic structures in breeding germplasm
 Inheritance patterns
Delicious GoldenDel F2_26829-2-2 Jonathan Cox
PRI14-126 KidsOrRed
PRI612-1 Gala
Florina
Galarina
Delicious GoldenDel F2_26829-2-2 Jonathan
PRI14-126
PRI612-1
Florina
Florina
X-6820
X-6564
Galarina
X-6683
12_F02
I_BB02
12_O03
12_E001
I_M12
I_W10
Delicious
229 202
120 116
152 143
null99
Cox
212 212
116 122
143 null
97 75
KidsOrRed
229 212
120 116
152 143
null75

20. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Generation Views
 Views simple to generate & manage
 Interface, user-friendly
 Manual & Additional documentation

21. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Availability & Operation
 Freeware
 Software link includes manual & examples
 Operation: Windows
Developper Dr.
Roeland Voorrips
 Download from:
http://www.wageningenur.nl/en/show/Pedimap.htm
 2 links: Software & License file request
• License generated instantly, sent by email

22. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Documentation & use
 Additional documentation
 Presentations & vimeos at the FruitBreedomics website
• www.fruitbreedomics.com
 Videos from a 1 day FruitBreedomics workshop
• http://www.fruitbreedomics.com/index.php/media-
center/learning-material-training-sessions/156-use-of-pedimap-
software-in-breeding

23. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Video’s FB-Pedimap workshop
PBA workshop, MSU JUNE’ 10 23

24. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Documentation & use
 Additional documentation
 Presentations & vimeos at the FruitBreedomics website
 Publication in J Heredity
• Voorrips et al. 2012, 103:903-907, DOI 10.1093/jhered/ess060
 Examples through scientific publications
 Rosyara et al. 2013, Mol. Breed DOI 10.1007/s11032-013-9916-y
 Bink et al. 2014, Theor Appl Genet. 127:1073-1090
 Van Dijk et al. 2014, BMC Pl Biol 14:55. doi:10.1186/1471-2229-14-55
 Soriano et al. 2014, Mol Breeding DOI 10.1007/s11032-014-0159-3

25. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Acknowledgements
 Developer: Dr. Roeland Voorrips
 Wageningen UR
PBA workshop, MSU JUNE’ 10 25
 Projects
 EU-HiDRAS : Software & Manual
 USDA-SCRI RosBREED: Scientific paper

26. Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Questions?
Thanks
Delicious GoldenDel F2_26829-2-2 Jonathan Cox
PRI14-126 KidsOrRed
PRI612-1 Gala
Florina
Galarina
Delicious GoldenDel F2_26829-2-2 Jonathan
PRI14-126
PRI612-1
Florina
Florina
X-6820
X-6564
Galarina
X-6683
12_F02
I_BB02
12_O03
12_E001
I_M12
I_W10
Delicious
229 202
120 116
152 143
null99
Cox
212 212
116 122
143 null
97 75
KidsOrRed
229 212
120 116
152 143
null75