1. Association Mapping in European Winter Wheat

2. Wheat in Germany
Wheat is the most important crop plant in Germany with more than 3 million hectares (mainly winter wheat)
Yields have been stagnating and fluctuating at high levels over the last years and wheat is getting less competitive compared to other crops
Major factors for wheat production in Germany are diseases (e.g. Fusarium, Septoria) and environmental factors (such as drought, cold, etc.)

3. Association Mapping (AM) Improvement of varieties through breeding
The WHEAT association study
1975
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
372 wheat varieties
Phenotypic data
Genotypic data
Field evaluation of 372 wheat varieties for many traits ( 2 years x 4 locations x 2 replications), field evaluation of major diseases (Fusarium, Septoria, etc.)
- Molecular markers (SSRs and SNPs)
Candidate genes
Marker/Trait
Association Mapping (AM)
Identification of molecular markers associated with traits that are important for wheat breeding
Filed evaluation for F resistance were carried out for 372 wheat varieties, replicated in 2 years and 2 locations ；
For genotyping part , 2 sets of molecular markers were used. One set is multi-alles systems , which includes 732 SSR makers cover the whole 21 wheat chromosomes and the other is a bi-allelic system, snp marker, which dereved from a novel illumina XXX chip. More details about the cihp were well described in a newly published paper “Title” in XX journal 2014.
The AM statistical analysis part in this study we used the statistical software package Genstat. The 14th edition was used in this study. Through this study , we try to generate our knowledge about …
? 最后是 backcrossing
Improvement of varieties through breeding

4. Phenotyping Yield, yield components, France (SYNGENTA):
quality parameters
France (SYNGENTA):
Saultain 2010
Janville 2010
Andelu |2010
GERMANY
(KWS LOCHOW):
Wohlde |2010
Seligenstadt 2009|2010
Disease resistance
(Fusarium, Septoria, Drechslera)
Traits measured in all eight environments
Heading date - Specific weight
Protein content - Thousand kernel weight
Plant height - Zeleny volume
Plot yield

5. Genotyping - 971 SSR markers for analysis of population structure
- SNP arrays
12K wheat Infinium array
90K wheat Infinium array
35K wheat Affymetrix array
>20 candidate genes (e.g.ppd, rht)
SSR
12k
90k
35k
sum
number
971
9655
81587
35143
127356
polymorphic
781
5242
21200
20052
47275
mapped
412
3005
11676
13346
28439

6. Linkage disequilibrium
LD in
material
Between one and several cM
90k data

7. Haplotype structure and SNPs
Total number of haplotypes based on SNP marker analysis
16608
Arrays are in part complementary

8. SNPs and association studies
Summary
The data are complementary and the 90K and 35K arrays provide together a very useful marker set

9. Marker/trait associations for Fusarium
resistance using molecular markers
and candidate genes
Rht-1D
SSR system

10. The VALID study General
In association studies, there are often many marker-trait associations (MTAs) identified which later cannot be confirmed and such MTAs are not useful for breeding
Goals of the VALID project
- Analysis of additional wheat material that is relevant for wheat breeding for the investigated traits in order to confirm the identified MTAs on other material
- Validation of identified MTAs in specifically developed populations
- Analysis of the wheat varieties for abiotic traits (e.g drought)

11. Validation of effects in more recent breeding material
WHEAT Panel
372 unique genotypes
European varieties mainly from 2000 to 2008
TROST
Drought stress
Panel
184 unique genotypes
VALID Panel
133 unique genotypes
European varieties mainly from 2007 to 2010
20 overlapping genotypes
Field tests
2013/2014
Field tests
2009/2010
Field tests
2013/2014

12. Principal component analysis for all 518 wheat varieties (10,000 SNPs)
* = WHEAT panel
V = VALID panel
Only very weak population structure in the entire material (breeder, type and origin)
No significant subpopulation differences between the WHEAT and VALID panel
Material is well-suited for association studies

13. Examples for specific traits:
Fusarium (FHB) resistance plant height (PH)
heading date HD

14. Phenotypic data for FHB, PH and HD
Kosack
Tuscan
Phenotypic variation in the material
Heritability is high in the material
Candidate genes analyzed
Kosack is the most resistant variety in all the 4 enviroments.

15. Candidate genes in the data sets
HD and PH
Heading Date in WHEAT Heading Date in TROST (13) Heading Date in VALID (13/14)
Plant Height in WHEAT Plant Height in TROST (13) Plant Height in VALID (13/14)

16. MTA validation analysis
Comparison MTAs for FHB between WHEAT and VALID
Limited validation between both studies
Loci
 Validated loci
Trait 
VALID_BLUEs* MTA>=2.3 
VALID_BLUEs MTA>=2.3
WHEAT >=3.0 PH 31
10(32%) HD 63
15(24%)
Heritability
WHEAT
TRAIT h²
PH 0,98
HD 0,98
Level of validation depends on heritability
Preliminary data show the validation rate for yield is significantly lower (<10%)

17. Genetic validation approaches

18. Development of DH lines for yield
2 populations with fixed major genes (ppd, rht) were developed that were segregating for 2 or 3 identified QTLs each.
Lines were identified by marker analysis with all possible QTL combinations and grown in the field.

19. Introgression of major MTAs into another line via MAS
Goal: Pyramiding of additional QTLs in an already good line
6 QTLs were selected for backcrossing (4 crosses)
Backcross of 1-2 QTLs into a high yield elite line
Both lines are fixed for major genes (rht, ppd) and many other QTLs
MAS with genome-wide marker set
BC2S2 => more than 95% recurrent
parent, trait fixed

20. Development of BC lines for Septoria and FHB
Locus 1
Locus 2
Donor
Donor
Locus 1
Donor
Donor

21. Summary and next steps
A comprehensive phenotypic evaluation of European winter wheat material was performed over several years
A detailed molecular marker analysis (SNPs, SSRs, candidate genes) of European wheat material was performed
MTAs for important traits (disease resistance, yield and yield components, quality, drought) were identified
Known candidate genes and first confirmed MTAs indicate that the approach produces useful data for breeding however the validation rate is relatively low (<30 to <10%) even for traits with high and intermediate heritability
Mapping populations and introgression lines will further validate specific loci and open the door for using confirmed MTAs in wheat breeding
Map-based cloning of confirmed and mendelized MTAs will be possible in the future

22. Acknowledgments Thank your for your attention! Erhard Ebmeyer
Viktor Korzun
Sonja Kollers
Marion Röder
Jie Ling
Christine Zanke
Gunther Stiewe
Odile Argillier
Maike Hinze
Andrea Jansen
Thomas Zschäckel
Bernd Rodemann (BS)
Christiane Balko (GLW)
Frank Ordon (QLB)
Martin Ganal
Jörg Plieske
Jana Lemm
Thank your for your attention!
? Frank ordon