FB-AM3 Stakeholders day, Feb 11 2014

PBA workshop, MSU JUNE’ 10 1

Pedimap

Announcement of a training session

Eric van de WegFruit Breedomics, stakeholders day Feb 11 2014,

Zurich

FB-AM3 Stakeholders day, Feb 11 2014

Announcement

What:One day workshop on Pedimap software

For whomPlant Breeders & their affiliates

When2014 June 12 (Thursday)

WhereWageningen

PBA workshop, MSU JUNE’ 10 2

FB-AM3 Stakeholders day, Feb 11 2014

Intro to Pedimap

Visual presentation of Pedigrees Selection germplasm based on family relationships

PBA workshop, MSU JUNE’ 10 3

Delicious GoldenDel F2_26829-2-2 Jonathan

PRI14-126

PRI612-1

Florina

Example: Progenitors of Florina

FB-AM3 Stakeholders day, Feb 11 2014

Selection based on family relationships

Offspring of Florina

PBA workshop, MSU JUNE’ 10 4

Florina

X-6820

Galarina

X-6564

X-6398

X-6683

12_O03

12_F02

I_BB02

I_W01

12_E001

I_M01

FB-AM3 Stakeholders day, Feb 11 2014

values Intro to Pedimap

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

Visual presentation of Pedigrees Selection germplasm based on family relationships

Supports visualization of phenotypic values

Example: Quantitative trait - Fruit firmness of apple

Very firmIntermediate

FB-AM3 Stakeholders day, Feb 11 2014

Visualization of phenotypic

Example: Qualitative trait as Vf-Resistance to scab

PBA workshop, MSU JUNE’ 10 6

Vf-present Vf-lacking

FB-AM3 Stakeholders day, Feb 11 2014

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 7

FB-AM3 Stakeholders day, Feb 11 2014

Visualization of marker genotypes

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

Prediction is reliable

PBA workshop, MSU JUNE’ 10 8

Delicious

A A

GoldenDel

A A

F2_26829-2-2

B A

Jonathan

A A

PRI14-126

AB

PRI612-1

AB

Florina

B A

Vf-present Vf-lacking

FB-AM3 Stakeholders day, Feb 11 2014

Visualization of marker genotypes

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

Prediction is reliable

PBA workshop, MSU JUNE’ 10 9

Delicious

A A

GoldenDel

A A

F2_26829-2-2

B A

Jonathan

A A

PRI14-126

AB

PRI612-1

AB

Florina

B A

Vf-present Vf-lacking

FB-AM3 Stakeholders day, Feb 11 2014

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 10

FB-AM3 Stakeholders day, Feb 11 2014

Structure

All crosses of a specific year

PBA workshop, MSU JUNE’ 10 11

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

FB-AM3 Stakeholders day, Feb 11 2014

Structure: Pedimaps interface

Overview crosses DLO-PRI breeding program Per year Series of years

PBA workshop, MSU JUNE’ 10 12

FB-AM3 Stakeholders day, Feb 11 2014

Structure

PBA workshop, MSU JUNE’ 10 13

-16Antonovka_34 -16Z180

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

2007-0302007-033

2007-034

2007-031

2007-032

2006-011

2006-012

2006-013

2006-014

2002-001

2002-005

2005-0192006-0162007-040

2005-0202006-0152007-039

2007-035

2007-036

2007-037

2007-038

2006-017

2006-0182002-004

2002-003

2002-006

2006-009

2006-010

2007-029

2007-0302007-033

2007-034

2007-031

2007-032

2006-011

2006-012

2006-013

2006-014

2002-001

2002-005

2005-0192006-0162007-040

2005-0202006-0152007-039

2007-035

2007-036

2007-037

2007-038

2006-017

2006-0182002-004

Crosses descending from a source for resistance Antonovka

Selections Breeding

families

FB-AM3 Stakeholders day, Feb 11 2014

Breeding strategy / history

PBA workshop, MSU JUNE’ 10 14

-16Antonovka_34 -16Z180

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

2007-0302007-033

2007-034

2007-031

2007-032

2006-011

2006-012

2006-013

2006-014

2002-001

2002-005

2005-0192006-0162007-040

2005-0202006-0152007-039

2007-035

2007-036

2007-037

2007-038

2006-017

2006-0182002-004

2002-003

2002-006

2006-009

2006-010

2007-029

2007-0302007-033

2007-034

2007-031

2007-032

2006-011

2006-012

2006-013

2006-014

2002-001

2002-005

2005-0192006-0162007-040

2005-0202006-0152007-039

2007-035

2007-036

2007-037

2007-038

2006-017

2006-0182002-004

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

FB-AM3 Stakeholders day, Feb 11 2014

Inheritance

PBA workshop, MSU JUNE’ 10 15 Unknown

Winter hardines in 4x garden rose Limited x Limited Better

FB-AM3 Stakeholders day, Feb 11 2014

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

PBA workshop, MSU JUNE’ 10 16

Delicious229 202120 116152 143null 99

Cox212 212116 122143null97 75

GoldenDel229 214116 116152 14379 99

F_IngMarie218 999116 122143null95 999

KidsOrRed229 212120 116152 143null 75

IngMarie212 218122 116null 14397 95

Gala212 229116 116143 15275 79

Elstar229 218116 116152 14399 97

Rubens229 229116 116143 15275 99

Rubens – chromosome 10 Contains DNA from Golden

Delicious & Cox Partly homozygous for GD-

haplotype

FB-AM3 Stakeholders day, Feb 11 2014

Conclusion

Functionality Supports visual presentation of Pedigrees Including phenotypic values & marker genotypes

PBA workshop, MSU JUNE’ 10 17

Use: clarifies Genetic structures in breeding germplasm Inheritance patterns

FB-AM3 Stakeholders day, Feb 11 2014

Availability

Freeware Extensive manual available

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

PBA workshop, MSU JUNE’ 10 18

2 links: Software & License file request License generated instantly, sent by email.

FB-AM3 Stakeholders day, Feb 11 2014

Announcement workshop

What:One day workshop on Pedimap software

For whomPlant Breeders & their affiliates

When2014 June 12 (Thursday)

WhereWageningen

PBA workshop, MSU JUNE’ 10 19

Thanks Questions?

FB-AM3 Stakeholders day, Feb 11 2014

PBA workshop, MSU JUNE’ 10 20

Thanks