High-density mapping of a resistance gene to Ug99 from the ...
Mapping of durable adult plant stem rust resistance to Ug99 and its races
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Transcript of Mapping of durable adult plant stem rust resistance to Ug99 and its races
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Mapping of durable adult plant stem rust resistance to Ug99 and
its races
S. Bhavani, R. P. Singh, S. Singh, J. Huerta, O. Argillier, S. Brun, S. Lacam, N. Desmouceaux, P. Njau and R. Wanyera
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• Wide virulence range and highly aggressive
• Threat to significant proportion of global wheat germplasm > 80% susceptible
• New races in Ug99 (TTKSK) lineage
Ug99+Sr24 Virulence (2006)-TTKST
Ug99+Sr36 Virulence (2007)-TTTSK
Other races-TTKSF,TTKSP, PTKSK,
PTKST
Chart Title
Ineffective (32 genes)
Effective (20 genes)
Sr5, 6, 7a, 7b, 8a, 8b, 9a, 9b, 9d, 9e, 9f, 9g, 10, 11, 12, 15, 16, 17 18, 19, 20, 21, 23, 30, 31,
34, 38, 41, 42 ,Wld-1
,Sr13, 14, 22, 24, 25 ,33 ,32 ,29 ,28 ,26,27 ,43 ,40 ,39 ,37 ,36 ,351a.1R, Tmp ,45 ,44
Virulence spectrum of Ug99 (TTKSK)
Ug99-Global threat
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Types of Resistance
≈ Race-specific
≈ Major genes
≈ Hypersensitive
Monogenic
(Boom & Bust)
Pyramiding
≈ Race-nonspecific
≈ Minor genes
≈ Slow rusting/ Partial
Polygenic
(Durable)
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Focus towards durable resistance? Multiple races of rust pathogens
Mutating and migrating nature of rust pathogens
Several race-specific genes ineffective in one or
more wheat growing regions
Maintaining host genetic diversity
Preventing epidemics – reducing yield losses
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Characteristics of slow rusting resistance Minor genes with small to intermediate effects
Gene effects are usually additive
Resistance does not involve hypersensitivity
Susceptibility at seedling stage
Genes confer slow disease progress through:
Reduced infection frequency- Receptivity
Lower disease severity, Increased latent period
Small to large compatible pustules on stems
Reduced spore production
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Accumulating minor genes - Near immunity
Susceptible
1 to 2 minor genes
2 to 3 minor genesMunal, Picaflor,Francolin, Pauraque
4 to 5 minor genesKingbird
% Rust
Days data recorded
100
80
60
40
20
00 10 20 30 40 50
Relatively few additive genes, each having small to intermediate effects, required for satisfactory disease control
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Sr2-Complex for durable APR
(Sr2 + other minor genes for durable resistance to stem
rust) Sr2 transferred to wheat from ‘Yaroslav’ emmer in 1920s by McFadden and linked to pseudo-black chaff (~ 90years)
Sr2 still provides moderate levels of resistance in Kenya (~30% reduction in disease severity)
Seedling and APR genes with intermediate effects in combination with Sr2 produce enhanced levels of resistance
Formed the basis of durable resistance historically in some CIMMYT wheats
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Stem rust severities of SrTmp (n=125) and SrSha7 (n=66) possessing wheat lines in Kenya 2010
1 5 10 15 20 30 40 50 600
5
10
15
20
25
30
35
40
SrTmp
SrSha7
Stem rust severity (%)
No
. en
trie
s (%
)
APR genes enhance the expression of moderately
effective race-specific genes
Pyramiding-APR+ Major genes
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Identifying materials with adult plant resistance to Ug99
Greenhouse seedling tests -USDA-ARS Lab. in St. Paul, Minnesota, USA
Field evaluations-Kenya/Ethiopia
Characterization of PBC phenotype and Sr2 linked molecular markers
Identified APR Sources: Kingbird, Kiritati, Juchi, Pavon, Huirivis#1, Muu, Kenya Swara, Kenya Kudu, Parula, Picaflor, Danphe, Chonte
Kingbird
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Mapping of Adult Plant Resistance to Stem Rust
15 RIL mapping populations developed and phenotyped in Kenya for at least 2 seasons
Genetic studies suggest the involvement of 3 or 4 minor genes in each resistant parent
Initial molecular mapping of six populations completed
Other populations being assigned to graduate students
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Methodology Phenotyping conducted in 2009, 2010 field
seasons Artificial epidemics with Ug99+Sr24 (TTKST) SR severity recorded when 80-100% disease on
most susceptible RILs- Modified Cobb scale
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DArT and SSR markers Inclusive Composite Interval Mapping
(ICIM), Q-gene, QTL Cartographer
ICIM- http://www.isbreeding.net/
Increased power of detection Additive and Epistatic Effects LOD Scores>2.5, Probability in step wise
regression 0.001 User friendly
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PBW343 X Kingbird
0-5 5-10% 10-15% 15-20% 20-30% 30-40% 40-50% 50-60% 60-70%05
101520253035404550
2009
2010
Disease severity
Nu
mb
er o
f lin
es
Year ChromosomeMarker Position Left Marker Right Marker LOD PVE(%) Est. Add R2
2009, 10 1A 251 XwPt-0128 XwPt-4987 6.9 17.5 -11.2
3BS 21 XwPt-3921 XwPt-2757 21 41.5 11.0
5B 191 XwPt-2607 XwPt-1733 4.4 13.7 5.6 51.2
7AL 1201 XwPt-8670 XwPt-744574 3.2 10.1 -5.4
7DS 0 XwPt-1859 XwPt-731810 3.4 9.3 -31.8
Kingbird PBW343
No. of Polymorphic DArT Markers 736No. of Informative DArT Markers 508
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PBW343 X Kingbird
1A 3BS
5B
7AL 7DS
PBC
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PBW343 X Kiritati
Year ChromosomeMarker Position Left Marker Right Marker LOD PVE(%) Est.ADD R2
2009, 10 2D 20 Xbarc095 Xwmc503 3.6 N/A -3.7 6.0
3BS 30 SW58 Xbarc133 17.3 N/A 7.6 25.0
5BS 76 Xwms371 Xbarc109 5 N/A 3 8.0
7DS 36 Lr34-linked Xbarc092 7 N/A 5.3 12.0
0-5 5-10% 10-15% 15-20% 20-30% 30-40% 40-50% 50-60% 60-70% 70-80%0
5
10
15
20
25
30
35
40
45
2009 2010N
umbe
r of l
ines
Disease severity
Kiritati PBW343
No. of Polymorphic DArT Markers 271No. of Informative DArT Markers 271
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PBW343 X Kiritati
3BS 7DS
5BS2D
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PBW343 X Juchi
Year ChromosomeMarker Position Left Marker Right Marker LOD PVE(%) Est. Add R2
2009, 10 2BS 152 XwPt-7829 XwPt-2266 4.6 16.6 7.5
3BS 28 XwPt-8056 XwPt-800213 5.4 8.3 5.1
4AS 123 XwPt-5124 XwPt-6390 3.7 12.8 6.9 42.4
5BL 472 XwPt-0750 XwPt-5896 2.3 16.5 -7.5
6BS 21 XwPt-5480 XwPt-9532 4.3 23.5 8.5
0-5% 5-10% 10-20% 20-30% 20-40% 40-50% 50-60% 60-70% 70-80% 80-90% 90-100%
0
10
20
30
40
50
60
2009
2010
Num
ber o
f lin
es
Disease severity
JuchiPBW343
No. of Polymorphic DArT Markers 734
No. of Informative DArT Markers 371
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PBW343 X Juchi
2BS 3BS 4AS
5BL6BS
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Avocet X Pavon 76 (RILs without Sr26)
10 20 30 40 50 60 70 80 900
10
20
30
40
50
60
70
Mean disease severity 2007
Mean Disease severity 2009
Disease Severity (%)
Nu
mb
er o
f L
ines
Year ChromosomeMarker Position Left Marker Right Marker LOD PVE(%) Est.ADD R2
2007, 09, 10 1BL 278 XwPt-1560 XwPt-7486 2.1 23.8
N/A 3BS 52 XwPt-8093 XwPt-7212 11 18.9
N/A 68.9
5A 8 XwPt-6048 XwPt-4249 2.2 6.3 N/A
6BS 8 XwPt-1541 XwPt-0171 11 13.4 3.2
Pavon 76
No. of Polymorphic DArT Markers 510No. of Informative DArT Markers 359
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Avocet X Pavon 76
2BS1BL 3BS
3D6BS
5A
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PBW343 X Huirivis#1
Year ChromosomeMarker Position
Left Marker
Right Marker LOD PVE(%) Est. Add R2
2009,10 2BS 0 Xwmc257 Xwmc154 4 N/A 4.7 6.8
3BS 0 SW3648 Xwms533B 6.0 N/A 9.0 16.0
5BL N/A Xwms371 NW2012ND 3.9 49.2 -1.1 23.0
7B N/A N/A NW3109ND 2.5 N/A 5.3 6.9
0-5 5-10% 10-15% 15-20% 20-30% 30-40% 40-50% 50-60% 60-70% 70-80% 80-90%0
5
10
15
20
25
30
35
2009
2010
Disease severity
Num
ber o
f lin
es
Huirvis#1 PBW343
No. of Polymorphic DArT Markers 268No. of Informative DArT Markers 268
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PBW343 X Hurivis#1
3BS2BS
5D PBC5BL
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PBW343 X MUU
0-5 5-10% 10-15% 15-20% 20-30% 30-40% 40-50% 50-60% 60-70% 70-80%0
5
10
15
20
25
30
35
2009
2010
Disease severity
Num
ber o
f lin
es
Year ChromosomeMarker Position Left Marker Right Marker LOD PVE(%) Est. Add R2
2009,10 2BS 340 XwPt-744022 XwPt-1964 4.9 10.4 -4.2
3BS 41 XwPt-666139 XwPt-3921 15.8 36.5 10.7 46.0
5BL 353 XwPt-6014 XwPt-3661 9 9.1 -4.7
Muu PBW343
No. of Polymorphic DArT Markers 630No. of Informative DArT Markers 452
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2BS 3BS
5BL
PBW343 X MUU
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Inconsistent QTLs
2A-Kingbird2D-Kiritati
5A-Pavon
5DS-Hurivis#1
4BS-Kingbird
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QTLs summary In total 9 consistent and 5 inconsistent QTLs detected in six
mapping populations
QTL on chromosome 3BS in all parents is linked to resistance gene Sr2 & PBC
QTL on chromosome 7DS in Kingbird and Kiritati confirms the involvement
of Lr34 in reducing stem rust severity (Lr46/Yr29/Pm39 )
QTL on chromsome 1BL in Pavon 76 and PBW343 suggests the involvement of Lr46 in reducing stem rust severity (Lr34/Yr18/Pm38)
7 new QTLs identified on chromosomes 1A, 2B, 3D, 4A, 5B, 6B and 7A
5 inconsistent QTLs identified on chromosomes 2A, 2D, 4B, 5A and 5D
These QTLs in combination with Sr2 form the “Sr2-Complex”
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Future outlook Saturating genomic regions with additional
markers for fine mapping
Development of PCR based assays for flanking markers
Pyramiding APR + major genes using markers
Cloning for resistance gene cassettes
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Acknowledgements
Agencies supporting rust research:
Bill and Melinda Gates Foundation through:
DRRW Project
• Syngenta Foundation
• Grain Research and Development Corporation (GRDC), Australia
• Kenya Agricultural Research Institute
THANK YOU