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Towards an understanding of the molecular mechanisms of durable and non-durable resistance to stripe rust
1. Towards an understanding of
the molecular mechanisms
of durable and non-durable
resistance to stripe rust
Xianming Chen
USDA-ARS, Wheat Genetics, Quality, Physiology, and Disease
Research Unit, Pullman, WA and
Department of Plant Pathology, Washington State University
2. Stripe rust
damage can be
HUGE
Average 2010
3 86
0 10 20 30 40 50 60 70 80 90 100
3. Distribution of Stripe Rust in the US in 2010
Grain Yield Loss in the US
2003: 89 M. Bu (2.42 M. MT)
2005: 73 M. Bu (1.99 M. MT)
2010: 87 M. Bu (2.38 M. MT)
6. In Washington State in 2010:
•The various levels of resistance including HTAP
resistance were estimated to reduce yield loss from
potentially more than 60% to about 9%.
• The application of fungicides in more than 60% of winter
and spring wheat acreage in Washington State was
estimated to reduce yield loss further to about 3% (about
4.5 million bushels) in average.
• The total resistance in all wheat cultivars collectively was
able to save 73 million bushes ($512 million) and the
fungicide application further saved 13.7 million bushels
($96 million) at the cost of estimated over $27 million.
7. All-Stage (Seedling) Resistance:
Can be detected in seedling stage
Effective in all growth stages Yr5 AVS
High-level resistance
Easy to incorporate
into cultivars
Not durable if a single
gene is involved
8. Dr. Orville A. Vogel was the first to develop wheat
cultivars with partial resistance to stripe rust
IT and % in 2008
Pullman Mt. Vernon
Cultivar Release Flow. S. elong Head.
Brevor 1949 3 30 5 30 2 20
Omar 1955 8 90 8 60 8 100
Gaines 1960 5 50 8 60 5 60
Nugaines 1965 5 40 8 40 3 40
Luke 1970 2 10 3 15 3 5
Photo source: http://cahnrsnews.wsu.edu/reportertools/news/2007/vogel-building-2007-09.html
9. Dr. Roland F. Line
characterized high-temperature
adult-plant (HTAP) resistance as
the type of resistance expressed
at high post-inoculation
temperatures and at adult-plant
stage.
10. High-Temperature Adult-Plant Resistance
Expresses when weather is warm and
plants grow old
Low to high-level resistance
Durable
Conferred by quantitative trait loci
Relatively difficult to detect and difficult to
incorporate into cultivars
May not be adequate
11. Year
release Wheat cultivars and their possible source of HTAP resistance
1949 Brevor
Nord
1960 Gaines Desprez
1965 Nugaines
1970 Luke
1971 Hyslop
1972 Sprague
1976 Raeder McDermid Daws
1977 Stephens
1979 Walladay
1982 Lewjain
1983 Hill 81
1984 Basin John
1985 Malcolm Dusty Batum
1986 Oveson
1987 Frontana Spillman Wakanz
1988 Madsen
1990 Eltan Kmor
1991 Express Bonneville
1992 Macvicar Rod
1993 Rohde
1994 Lambert Alpowa Wawawai
1997 Boundary
1998 Weatherford Coda Hiller
2000 Edwin Cappelle Desprez Hubbard
2001 Bruehl Brundage 96 Chukar Finch Gary
2002 Tubbs
2004 Masami
2005 MDM Bauermeister Otis Louise
2006 Darwin
2007 Xerpha
12. Why is race-specific all-stage resistance
not durable and nonrace-specific HTAP
resistance durable?
13. Wheat GeneChip
55,052 probe sets
Derived from the public content
of the T. aestivum UniGene Build
#38
Probe sets consist of pairs of 11
perfect match (PM) and
mismatch (MM) 25-mer
oligonucleotides
14. Yr5 Experimental Design
Near isogenic lines (Isolines)
Yr5 AvS
Yr5 (AvSYr5NIL: resistant)
yr5 (AvS: susceptible)
Mock- and P. s. tritici-inoculation
Seedling stage (~10 days)
PST-100
Time-course sampling (6, 12, 24, 48 h)
3 biological replicates
RNA extraction, labeling and hybridization
28. Meta-analysis Design
• Custom oligonucleotide microarray
– 116 significant transcripts from Yr5 results
– 207 significant transcripts from Yr39 results
• Aim to identify common/unique gene expression
signatures involved in each resistance
29. Resistance Type Comparison
(More Genes of Races-Specific vs. Nonrace-specific)
• 8 wheat genotypes with race-specific resistance
– Yr1, Yr5, Yr7, Yr8, Yr9, Yr10, Yr15 and Yr17
• 4 genotypes with nonrace-specific resistance
– Yr18, Yr29, Yr36 and Yr39
• Mock and incompatible interaction
– Seedling and adult plant stage
30. Race-specific Resistance
• Seedling stage phenotype effect
– Combined genotype data
• 28 transcripts significant
– P <0.10 and fold change >2.0
• Compared to 116 transcripts in Yr5 response
– Meta-analysis narrowed the gene list
31. Transcript Annotation
Functional category Putative function Fold change p value
Defense Putative disease resistance protein 2.45 0.017
Defense Putative disease resistance protein 2.36 0.017
Defense - alkaloid 28 transcripts annotated
• 21 of the Reticuline oxidase 2.01 0.078
Defense - cell wall Pathogen induced WIR1A protein 2.15 0.000
– 15 (71%) involved in defense/signaling
Defense - oxidative stress Blue copper-binding protein 4.11 0.000
Defense - oxidative stress Blue copper-binding protein 2.35 0.012
Defense - oxidative stress Peroxidase 2.54 0.022
Defense - oxidative stress Peroxidase 2.71 0.089
Defense - phenylpropanoid Phenylalanine ammonia-lyase 2.13 0.004
Defense - phenylpropanoid Phenylalanine ammonia-lyase 5.43 0.001
Defense - PR protein Beta-1,3-glucanase 2.04 0.087
Defense - PR protein PR protein 10 2.01 0.003
Defense - R protein NB-ARC domain containing protein 2.66 0.024
Signal transduction Calmodulin-binding protein 2.82 0.055
Signal transduction LRR-containing extracellular glycoprotein 2.57 0.001
Transcription Transcription factor 2.40 0.000
32. Nonrace-specific resistance
• Only detectable at adult-stage
• Zero significant transcripts for nonrace-
specific resistance phenotype effect
• Directly compared race-specific resistance to
nonrace-specific resistance
– 5 transcripts significant for race-specific
resistance
– 1 transcript significant for nonrace-specific
resistance
33. Race-specific resistance
Functional Category Putative Function Fold change p value
Defense - cell wall Hydroxyproline-rich glycoprotein 10.78 0.000
Defense - R protein NB-ARC domain containing protein 2.22 0.006
Signal transduction Protein kinase 5.50 0.000
Unknown No homology 4.38 0.000
Unknown No homology 2.43 0.000
Nonrace-specific resistance
Functional category Putative function Fold change p value
Transport Nonclathrin coat protein 2.16 0.000
34. Relationships of Yr genes based on common and unique
transcripts in response to stripe rust infection
Yr1
Yr5
Yr17
Yr15
Yr8
Yr10
Yr18
Yr39
Yr9
Yr29
35. Conclusions and Perspectives
In comparison with race-specific all-stage resistance, nonrace-
specific HTAP resistance is contributed by a relatively great
number of defense-related genes, which may explain the durability
of HTAP resistance.
Genes contributing to all-stage resistance are induced fast and
their transcription levels increased dramatically in the infection
process, while those contributing to HTAP resistance are induced
more slowly and their transcription changes are less dramatic.
All-stage resistances mediated by different R genes tend to share
many common defense genes, while HTAP resistances-mediated
by different genes do not have many defense genes in common.
Transcription factors identified in these studies may play key roles
in the networks of plant defense. Further characterization of these
genes may enhance our understanding of molecular mechanisms
of different types of resistance.
37. Genes with similar sequence to Ta.6990.1.S1
Ta.6990.1.S1_at is likely a PDR
[Pleiotropic Drug Resistance]-type ABC
[ATP Binding Cassette] transporter
38. ABC Gene
associated with
Ta.6990.1.S1_at
Yr18/Lr34
Ta.6990.1.S1_at Yr18/Lr34
Size (kb) 7.4 11.8
Introns 18 24
Chromosome 7A* 7D*
• Lr34-A, a homolog of Lr34, is located on 7A, but its sequence
is dissimilar from the Ta.6990.1 associated gene.
The gene associated with the Ta.6990.1.S1 transcript is
substantially different from Yr18/Lr34 (47% similar) even
though both are PDR- type ABC transporters.