0
Pedimap

Announcement of a training session

Eric van de Weg
PBA workshop, MSU JUNE’ 10

1

Fruit Breedomics, stakeholders...
Announcement

What:
One day workshop on Pedimap software
For whom
Plant Breeders & their affiliates

When
2014 June 12 (Th...
Intro to Pedimap



Visual presentation of Pedigrees




Selection germplasm based on family relationships

Example: Pr...
Selection based on family relationships



Offspring of Florina

X-6820
Florina

Galarina
X-6564

X-6398
X-6683
12_O03
12...
values Intro to Pedimap



Visual presentation of Pedigrees


Selection germplasm based on family relationships



Supp...
Visualization of phenotypic



Example: Qualitative trait as Vf-Resistance to scab




PBA workshop, MSU JUNE’ 10
FB-AM...
Intro to Pedimap



Visual presentation of Pedigrees






Selection germplasm based on family relationships

Supports...
Visualization of marker genotypes




SNP marker for Vf-restistance to apple scab
B-allele predicts resistance


Predic...
Visualization of marker genotypes




SNP marker for Vf-restistance to apple scab
B-allele predicts resistance


Predic...
Use to breeding

Helpful to clarify
 Genetic structures in breeding germplasm


Breeding strategy / history



Inherita...
Structure


All crosses of a specific year
2007-049

Esopus_Spitzenburg

Bellida

Grimes_Golden_?

1955-044-220

Jonathan...
Structure: Pedimaps interface



Overview crosses DLO-PRI breeding program



Per year
Series of years

PBA workshop, M...
Structure



Crosses descending from
a source for resistance


Antonovka
1995 002
1995-002-030
1995-002-039
Z180
-16
Ant...
Breeding strategy / history





Re-gaining high fruit quality for
several successive generations
Followed by R-gene pyr...
Inheritance



Winter hardines in 4x garden rose


Limited  x Limited   Better 

PBA workshop, MSU JUNE’ 10

FB-AM3 ...
Genetic background of CVS & selecions





Pedigree of CV Rubens
Marker scores 4 SSR-loci







Chromosome 10
Regi...
Conclusion



Functionality





Supports visual presentation of Pedigrees
Including phenotypic values & marker genoty...
Availability






Freeware
Extensive manual available

Download from:
http://www.wageningenur.nl/en/show/Pedimap.htm

...
Announcement workshop

What:
One day workshop on Pedimap software

For whom
Plant Breeders & their affiliates
When
2014 Ju...
Thanks

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

20
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Transcript of "10 pedimap wan de weg eric"

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