fruitbreedomics 1st stakeholder day meeting 20120207 most used founders in different breeding...

Evaluation of the genetic diversity in EU breeding programs

Eric van de Weg

DLO , Wageningen-UR,

The Netherlands

IntroductionIntroduction

• Aim: Understanding the genetic diversity exploited in breeding• Background:

• The genetic base in breeding is thought to be narrow• EU-commission considers this a limiting factor• Commercial cultivars have indeed a narrow base

• Questions• Also true for breeding programs as a whole?• How diverse is the genetic base EU-wide?

• What are the main founders?• What is their contribution to the genetic composition?• Use & impact of genetically distinct germplasm:?

Approach

• Survey among breeders EU-wide

• Examines genetic origin current breeding germplasm• Pedigrees, • Genome-wide inbreeding coefficients

• Audience: offer results to all breeders, policy makers,...

• Organization & analyses: • Apple: DLO (Wageningen-UR)• Peach: IRTA• Only permanent staff – Confidentiality of data

Results for Wageningen-UR (apple)

• 5 founders contributed 62% of the genetic composition

• 38% delivered by 86 founders• 7% for scab resistance• Distinct origin

46

35

4

410 EU

USRussiawildOther

Narrow framework enriched with genetic distinct material

Example apple: Conclusion

• Genetic base Wageningen-UR breeding program:– Narrow framework (62%)– Considerably enriched with genetic distinct material (38%)– Usually for specific purposes

• Resistance to diseases• Resistance to abiotic stress•Taste attributes

• For breeders: an open door• For the community ......

Results INRA-Angers (apple)

• 5 founders contributed 52% of the genetic composition• Golden Delicious most used

• 48% delivered by 64 founders

Narrow framework enriched with genetic distinct material

27

87

55

48

Founder contribution to the INRA breeding program

Golden Delicious

Jonathan

Delicious

F2_26829-2-2

Winesap

Other

27

87

55

48

Founder contribution to the INRA breeding program

Golden Delicious

Jonathan

Delicious

F2_26829-2-2

Winesap

Other

Comparison among programs

27

87

55

48

Founder contribution to the INRA breeding program

Golden Delicious

Jonathan

Delicious

F2_26829-2-2

Winesap

Other

27

87

55

48

Founder contribution to the INRA breeding program

Golden Delicious

Jonathan

Delicious

F2_26829-2-2

Winesap

Other

INRADLO

Common: Golden & Jonathan

Contribution framework decreased

Diversity increases !

Activities coming six months

Extend analyses to all collaborating programs

ARC S-Africa Kenn TobuttB3F Belgium Anne Marie AuverkerkenCRA Belgium Marc LateurDLO Netherlands Ton den NijsEVD The Swiss Markus KellerhalsINRA France François LaurensRSL Italy Walter Guerra

Colla

bora

tors

Frui

tBre

edom

ics

Graminor Norway Dag Roen IFO France Emmanuel Delapparent IVAI Gunars LacisKOB Germany Cerny / Mayr SERIDA Spain Enrique DapenaSUL Sweden Hilde NybomTUM Germany Neumueller

Current collaborators (Apple)

Impact

• Knowledge on the genetic diversity used in breeding• Including effect of

• Climatic zones• Age of the breeding program

• Offered to all EU breeders and policy makers • In support to breeding decisions • In support to policies

• Starting point for genetic studies on collaborating programs • Marker-Trait validation• Discovery of genes/alleles specific for your program

Changes

• Interested breeding programs can still join

• Returns• Ability to position your program in a EU context

• Data files on your breeding program• With completed pedigrees

• based on public and your own data only

• Ready to go for PediMap software

• Training in the use of Pedimap (May 2013)

• Option to participate in subsequent genetic studies

Need

• Simple• For current breeding germplasm

• Excel file• Name Genotype• Name two parents

Individual Mother FatherSelection-X Selection Y Golden DeliciousSelection Y Delicious Cox

Evaluation of the genetic diversity in EU breeding programs

Eric van de Weg

THANKS

27

87

55

48

Founder contribution to the INRA breeding program

Golden Delicious

Jonathan

Delicious

F2_26829-2-2

Winesap

Other

Example apple: Setup

• Wageningen-UR (DLO) breeding program• Germplasm as present in the orchard inventoried• Pedigrees collected up to the founder level

Delicious Cox

Golden DeliciousKids Orange Red

Gala

Example apple: Setup

• Wageningen-UR (DLO) breeding program• Germplasm as present in the orchard inventoried• Pedigrees collected up to the founder level• Data put together

Individual Mother FatherGolden Delicious ? ?Cox ? ?Kids Orange Red Delicious CoxGala Kids Orange Red Golden Delicious

Example apple: Setup

• Wageningen-UR (DLO) breeding program• Inventory of germplasm as present in the orchard• Collecting pedigrees up to the founder level

Delicious Cox

Golden DeliciousKids Orange Red

Gala

Example apple: Setup

• Wageningen-UR (DLO) breeding program• Germplasm as present in the orchard inventoried• Pedigrees collected up to the founder level• Data put together• Contribution of founders calculated

• Gala = 25% Delicious + 25%Cox + 50% Golden Delicious

Individual Mother FatherGolden Delicious ? ?Cox ? ?Kids Orange Red Delicious 0.5 Cox 0.5Gala Kids Orange Red0.5 Golden Delicious 0.5

Example apple: Setup

• Wageningen-UR (DLO) breeding program• Inventory of germplasm as present in the orchard• Collecting pedigrees up to the founder level

Delicious Cox

Golden DeliciousKids Orange Red

Gala