2. The general objective of WP1
… is to develop more efficient breeding programs
applying MAB.
To reach this goal WP1 will design and develop:
• Selection strategies and schemes to be tested in
pilot studies
• SNP markers tightly linked to selected genes will
be developed
• Cost efficient MAB pipelines will be identified and
used to genotype the plant material of the pilot
studies
3. State of progress of the ongoing tasks
(in a nutshell)
• Task 1.1: Breeding strategies (AIM: understand how apple & peach a breed and develop better breeding strategies
– First deliverable of the WP (D1.1: description of ideotypes and breeding schemes) submitted at M18
– Applicability of GWS in apple and peach as been studied and found to be possible (see also experiments at PFR)
• Task 1.2: development/identification of SNP markers for genes mapped before the start of the project
– Apple: SNP makers identified for 12 out 18 loci
– Peach SNP makers identified for 7 out 12 loci
• Task 1.3: Pilot studies (AIM: demonstrate the power of MAS)
– Prepared list of PSP for both apple and peach, for peach final list in preparation
– GWS for apple planned (peach in consideration): populations identified, genotyping with 384 SNPs is sufficient;
genotyping approach and company identified, financing is possible within partner own budget!
• Task 1.4: Genotyping pipeline (AIM: apply MAS using T.1.2 SNPs to PSP)
– In the process of finalizing MAB protocol (deadline M24!)
– In collaboration FEM (WP6) offers from genotyping companies have been collected and a company with a good
offer has been identified
• Task 1.5: Specification list of breeder-interface (AIM: develop an breeder-friendly interface to query the DB)
– No much progresses have been made in this task. As deadline (M30!) is approaching activities have to start
during this meeting and continue until September
4. (Main) results achieved so far
• Task 1.1: Breeding strategies
– Thanks two stakeholder surveys we were able to figure out how apple
and peach are currently selected and which are the traits most
important for apple and peach breeders
• Apple results: see François talk of the stakeholder day 2012
• Peach results: see Thierry talk (in few minutes)
• Task 1.2: SNP markers
– Apple (12/18); SNP makers identified for: Rvi2 (Vh2), Rvi4 (Vh4), Rvi5
(Vm), Rvi6 (Vf), Rvi11 (Vbj), Rvi13 (Vdurello), Rvi15 (Vr2), QTLs LG17
Fiesta and Discovery, FB-MR5, FB-E and Pl2 (nearly finish Rvi12 (Vb))
• Examples of the results and surprises: see Melanie Jänsch (talk in few
minutes)
– Peach (7/12); SNP markers identified for: Rm2, Vr2, D, S, G, Y and F
5. Publications
• 1 published scientific paper:
• Kumar et al. 2012: Genomic Selection for Fruit
Quality Traits in Apple(Malus x domestica Borkh.).
PLoSONE 7(5): e36674.
• But in 2013 (M28) we have D1.4 which is
composed by the submitted manuscripts
reporting the fine mapping and development of
SNP markers for selected major genes and QTLs
(output of T1.2)
6. Main challenges for 2013
ALL Deliverables and milestones to be done in the next 6 months
(chronological order):
• D1.4 (M28): submitted manuscripts on fine mapping of selected major
genes and QTLs (output of T1.2)
• D1.2 (M30): Evaluation of breeding strategies used in other crops (GWS
included) (output of T1.1)
• MS4 (M24 not 28): markers tightly linked to the loci of interest (report)
• MS5 (24) Optimized MAB protocol (report)
• MS3 (M30): Evaluation of breeding strategies used in other crops
(review)
• MS6 (M30): Specifications of breeder interface defined (report)
7. Action Plan for the coming year
WHAT WHO HOW DEADLINE
T1.1 submit D1.2 “Evaluation of
breeding strategies used in other crops
(GWS included)”
DLO According
partner’s strategy
M30
T1.2 finish SNP identification and submit
D1.3 (MS on fine mapping of selected
major genes and QTLs)
EVD, DCA, JKI, IRTA,
UMIL, INRA
According
partner’s
strategies
M28
T1.3 perform MAB in apple and peach;
Perform GWS in apple
MAB: Apple and
peach breeders
involved in the
task;
GS: B3F, Novadi
with the support of
INRA and DLO
Breeders make
plant material
available;
Statistical
support for GWS
by INRA/DLO
If feasible
before
harvest in
order to
identify the
material to
phenotype
T1.4 Test genotyping platform
Genotype pilot studies populations
Partners involved
and selected
company
According
protocols
M25
M30
T1.5 specification list breeder-interface ALL Being active and
reactive to DCA
requests
M30
8. Interactions between WP1 and the
rest of the project
• Interactions planned with WP3, 4 and 7
(breeder interface)
• Interactions planned with the stakeholders:
– None planned
9. Selected short talks
• Melanie Jänsch
Rvi2, Rvi4 and Rvi11: SNP markers and surprises
• Thierry Pascal
Peach part of Deliverable 1.1
10. Rvi2, Rvi4, Rvi11: SNP markers and surprises
Melanie Jänsch, Juliane Weger, Giovanni Broggini, Vincent Bus, Sue Gardiner,
Heather Bassett and Andrea Patocchi
11. Objectives
1. Identification of 5 single nucleotide polymorphisms
(SNPs) within an interval of 1 cM
2. Check for level of polymorphism of SNPs in 8 founders
3. Focus of this talk: apple scab resistance genes Rvi 11
(Vbj), Rvi 2 (Vh2) and Rvi 4 (Vh4)
(Bus et al., 2011)
12. repeat
Method – SNP development
or reject region
BLAST
available flanking markers on GD sequence
Primer Design + PCR
SEQ and SNP analysis
SNP found
SNP confirmation of map position
with subset of resistant , susceptible and
recombinant individuals closest to the gene
SNP polymorphism
test with 8 founders
SNP identified and validated
ok
ok
ok
ok
reject region
reject region
15. Rvi2 (Vh2)
• Plant material: GD x X2250, 146 plants
• 44 regions tested
• In 8 regions SNPs identified
• Vh2 SNPs mapped between 0.7 and 2.8 cM
• 61 SNPS found in total
• Intense study and verification of the first
mapping to define the correct map position
(Bus et al., 2005)
CH02b10
CH2-Z13SCAR
SNP_region_53(8)
SNP_region_41(1)
CH05e03
SNP_region_20.4(1)
CH-Vbj2
SNP_region_21(15)
SNP_region_23(5)
Rvi2
SNP_region_27(21)
L19SCAR
SNP_region_34.3(6)
SNP_region_36(4)
CH03d01
0.7
0.7
0.7
0.7
1.4
Rvi2
18. Rvi4 vs. Rvi15
• Indication that Rvi4 and Rvi15 may
derive from the same region
• Allelic?
• Phenotype of the two genes is the
same (PPP)
• Rvi4 symptoms visible after 3-4
days, Rvi15 after 7 days
• Difference due to difference level of
enhancement of the resistance
cascade?
005
Hi22d06
SNP_region_TNL1(20)
SNP_region_3(2)
SNP_region_10(1)
SNP_region_Vr2_3(3)
Rvi4
SNP_region_ARGH37(1)
CH02c02a
Hi02a07
S22_SCAR
2.1
0.4
1.3
Rvi4
CH02f06
ARGH37
Rvi15
ARGH17
CH02c02a
2.9
1.2
0.3
1.7
Rvi15
(Bus et al., 2011)
19. Conclusion
• SNP markers for resistance genes most used in breeding
will be soon available.
• This will simplify marker assisted selection (MAS) and will
allow a reduction of its costs .
• The precise mapping of the genes increases the precision of
MAS and indicates the possible allelism of:
– Rvi2 and Rvi11
– Rvi4 and Rvi15
