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

• 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

Types of Resistance

≈ Race-specific

≈ Major genes

≈ Hypersensitive

Monogenic

(Boom & Bust)

Pyramiding

≈ Race-nonspecific

≈ Minor genes

≈ Slow rusting/ Partial

Polygenic

(Durable)

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

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

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

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

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

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

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

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

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

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

PBW343 X Kingbird

1A 3BS

5B

7AL 7DS

PBC

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

PBW343 X Kiritati

3BS 7DS

5BS2D

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

PBW343 X Juchi

2BS 3BS 4AS

5BL6BS

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

Avocet X Pavon 76

2BS1BL 3BS

3D6BS

5A

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

PBW343 X Hurivis#1

3BS2BS

5D PBC5BL

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

2BS 3BS

5BL

PBW343 X MUU

Inconsistent QTLs

2A-Kingbird2D-Kiritati

5A-Pavon

5DS-Hurivis#1

4BS-Kingbird

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”

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

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