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fruitbreedomics

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.

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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
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
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
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
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
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
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
Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18 Type 3: Names only + phenotypicvalues 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:
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
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
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
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 & DNAs are OK
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 Deliciouss Homologe-1 Homozygous through IBD !
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
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
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
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
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?)
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
Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18 Generation Views Views simple to generate & manage Interface, user-friendly Manual & Additional documentation
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
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
Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18 Videos FB-Pedimap workshop PBA workshop, MSU JUNE 10 23
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
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
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

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19 van de weg

  • 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 + phenotypicvalues 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 & DNAs 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 Deliciouss 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 Videos 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

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