Mike Pumphrey, Washington State University

1. Stocking the
Breeder’s
Toolbox:
An update on
the status of
Ug99 resistance
Mike Pumphrey
Sept 2, 2012
m.pumphrey@wsu.edu

2. DRRW Pre-breeding efforts:
CIMMYT
Cornell Univ.
CSIRO
EIAR
ICCI-Tel Aviv Univ.
Kansas State Univ.
Univ. of Adelaide
UC-Davis
Univ. of the Free State
Univ. of Minnesota
Univ. of Sydney
USDA-ARS
Washington State Univ.

3. Why do we need a better
toolbox?
 Speedand support replacement of rust
susceptible varieties with varieties based
on complex resistance - globally
 Increase
diversity of resistance and
promote durable resistance
 Enablestewardship of resistance sources
in a manner never before possible

4. What tools are needed?
A well-surveyed resistance gene
landscape
 Additional, useful, sources of resistance
 Effective gene pyramids
 DNA markers and supporting information
for robust selection/diagnostics
 Good germplasm

5. Deploying COMPLEX resistance
Seedling/All-stage
 3 or more
effective R genes
combined
Adult plant/Slow-
rusting
 3 or more
effective APR
genes combined

6. COMPLEX resistance
% Rust Severity
Susceptible
100
80
1 to 2 APR genes
60 or 1+ race-specific gene
40
2 to 3 APR genes
or 1+ race-specific gene
20
4 to 5 APR genes
0 or 1+ race-specific gene
0 10 20 30 3+ 40 50
Day of Epidemic
This is the goal!

7. Ug99-family Resistance Loci
(circa 2008) Red genes are translocations or show reduced recombination
Green genes are APR loci
Black genes have normal recombination
Sr1A.1R Sr27
Sr21
Sr35 Sr26 Sr22
Sr13
1A 2A 3A 4A 5A 6A 7A
Sr39
Sr2
Sr40
Sr37
Sr28
1B 2B 3B 4B 5B 6B 7B
Sr33 Sr32
Sr45 Sr42 Sr44
Sr50
Sr25
Sr29 Sr43
1D 2D 3D 4D 5D 6D 7D
Alien introgression with linkage drag

8. Ug99-family Resistance Loci
(2012) Red genes are translocations or show reduced recombination
Green genes are APR loci
Black genes have normal recombination
SrTr129
Sr1A.1R Sr27
Sr21
Sr35 QTL Sr26 Sr22
SrTm4 Sr52
QTL SrND643 Sr13 Sr15
1A 2A 3A 4A 5A 6A 7A
Sr39
Sr2
Sr40 Sr12
QTL QTL QTL
SrWeb/ Sr37
Gabo 56 QTL QTL
Sr28 Sr56
Lr46 Sr47
1B 2B 3B 4B 5B 6B 7B
Sr1662
Sr33 Sr32 Sr57
Sr45 Sr51 Sr42 Sr44
Sr46
Sr50
SrAt6D SrAt7D
Sr53
Sr25
SrSha7 Sr55 SrC Sr29 Sr43
1D 2D 3D 4D 5D 6D 7D

9. Sources of Ug99 resistance
Gene Chrom. Origin Notes
Sr2 3BS Tetraploid wheat APR
Sr12 3BS Tetraploid wheat Moderate/background eff.
Sr13 6AL Tetraploid wheat
Sr15 7AL Hexaploid wheat Moderate/background eff.
Sr22 7AL Triticum monococcum Diagnostic markers
Sr25 7DL Thinopyrum ponticum Diagnostic markers
Sr26 6AL Thinopyrum ponticum Diagnostic markers
Sr28 2BL Hexaploid wheat Linkage block, diagnostic
Sr32 2DS Aegilops speltoides New recombinants
Sr33 1DS Aegilops tauschii Linkage block, cloned
Sr35 3AL Triticum monococcum Cloned
Sr37 4B Triticum timopheevii New recombinants

10. Sources of Ug99 resistance
Gene Chrom. Origin Notes
Sr39 2BS Aegilops speltoides New recombinants
Sr40 2BS Triticum timopheevii New recombinants
Sr42 6DS Hexaploid wheat SrCad?, SrNini?
Sr43 7DL Thinopyrum elongatum New recombinants
Sr44 7DS Th. intermedium New translocation
Sr45 1DS Aegilops tauschii Linkage block
Sr46 2DS Aegilops tauschii
Sr47 2BL Aegilops speltoides New recombinants
Sr50 1DS Rye Linkage block
Sr51 3DS Aegilops searsii Recombinants underway
Sr52 6AL Dasypyrum villosum Temperature sensitive
Sr53 5DL Aegilops geniculata New recombinants

11. Sources of Ug99 resistance
Gene Chrom. Origin Notes
Sr55 4DL Hexaploid wheat APR-Lr67/Yr46
Sr56 5BL Hexaploid wheat APR
Sr57 7DS Hexaploid wheat APR-Lr34/Yr18, cloned
Lr46 1BL Hexaploid wheat APR-Yr29
Temporary Designations
SrWeb/ 2BL Hexaploid wheat Linkage block
Gabo56
Sr1662 1DS Aegilops tauschii
SrTr129 6AS
SrTm4 2A Triticum monococcum
SrAt6D 6D Aegilops tauschii
SrAt7D 7D Aegilops tauschii

12. Sources of Ug99 resistance
Gene Chrom. Origin Notes
Temporary Designations
SrSha7
SrC
SrNini 6DS
SrND643 4AL
Consistent QTL (by association mapping or bi-parental mapping)
1A, 1B, CIMMYT germplasm via
2B, 3D, bi-parental and AM
4A, 5B, approaches
6B, 7A,
7B

13. Several additional sources and
better tools are coming (from
many directions):
A few DRRW project examples

14. Discovery from wheat relatives
 Introgression,
allelism
tests, mapping
, chromosome
engineering
 Aegilops
species, wild
tetraploids, Da
sypyrum
villosum
 Association
mapping

15. Cytogenetic improvement
 Thinopyrum
intermedium- Group 2

16. Marker development
Sequencing, 9000 SNP, 90,000K SNP
platforms accelerating progress
 Consolidated/standardized/dense
90,000 SNP genotyping
 ~160 Sr resistance sources from USDA-ARS
 ~90 Lr resistance sources from USDA-ARS
 ~400 Yr resistance sources from USDA-ARS
Washington State
 Numerous populations by 9K or 90K
Map-based cloning (Sr33, Sr35, others)

17. Linkage Block Development
Recombining
linked loci to
enhance
stewardship
and breeding
ease

18. Genomic selection/prediction

19. So what?
 Therehas never been a more opportune
time for the international community to
embrace strategic deployment and
responsible stewardship of our genetic
resources for durable stem rust control …
……before we lose tools that we
can’t afford to replace.

20. Acknowledgements
 BMGF/DFID
 Cornell
University
 Collaborator
institutions
 BGRI
 IPP-CAAS