Inma

Brande

Lucy

Cintia Matt M Jan

Phon

The Sainsbury Laboratory 2 Blades Group

Andrew

Marie Sue

Matt G

Shuzhen

Guotai Burkhard

Antony

$0.09/Mb

2

Cost of DNA sequencing

Bacterium Fungus/

Oomycete

Haustorium

Effector

PAMP

receptor

Immunity

Effector

Resistance protein

Immunity

PAMPs

Plant Cell

Dodds & Rathjen 2010

Principles of plant-microbe interactions

3

Find

germplasm;

make mapping

populations

Map genes

with next-

generation

genetics

Identify and

test

candidate

genes

Generic Strategy

Pyrami

d

4

No linkage drag R genes cannot be separated Durable?

• Ensure cloning R genes with distinct specificities

• Confirm function of R transgenes

Identify matching effectors

Clone and pyramid R genes

5

Black rust Stem rust Puccinia graminis f. sp. tritici

Yellow rust Stripe rust Puccinia striiformis var. striiformis

Brown rust Leaf rust Puccinia triticina

The three rusts of wheat

6

Norman Borlaug

7

Spread of African stem rust

Ug99

2007 sr31 sr36 2006 sr31 sr24

1999 sr31

2005

2008

2007 sr31 sr24

8

9

“The new wheat has been created by inserting

genes that confer resistance to […] Ug99.”

It’s also “highly drought resistant” and “fixes nitrogen!”

30 October 2011

Seed drying to break dormancy

Seed peeling: Peeled => 95% germination

Non-peeled => 60% germination

Bagging to prevent cross-pollination

6-8 months from seed to seed

7.5 Gb genome

Diploid

Ae. sharonensis – a model “non-model”

N. Champouret

P. Green

I. Hernandez-Pinzon

S. Jiang

J. Song

S. Banfield

G. Cox 10

Biosafety Level 3 Containment Facility

University of Minnesota

Jamie Kaufman 11

Aegilops sharonensis reaction to Ug99

12

Reaction of 107 accessions to Ug99

Resistant 69%

Susceptible 13%

Intermediate/Heterogenous 18%

P. Olivera,

J. Kaufman,

B. Steffenson

Uni. Minnesota

0; ; 1; 1+ 2- 2+3 3 3+4

Resistant Susceptible

Ae. sharonensis population development

6 different susceptible

13

F1 F2 F2:3 … F5:6

Ae. sharonenesis 97 68 6 2

43 key resistant accessions

97 crosses

R genes TTKSK TRTTF TTTTF

1 (2) 3 1 2 3

3 2 Unclear 10

Segregation in F2 or F2:3

N. Champouret

J. Kaufman

P. Olivera

E. Millet

B. Steffenson

G. Yu

ABD ABd AbD Abd aBD aBd abD abd

AB

D AABBDD AABBDd AABbDD AABbDd AaBBDD AaBBDd AaBbDD AaBbDd

ABd AABBDd AABBdd AABbDd AABbdd AaBBDd AaBBdd AaBbDd AaBbdd

AbD AABbDD AABbDd AAbbDD AAbbDd AaBbDD AaBbDd AabbDD AabbDd

Abd AABbDd AABbdd AAbbDd AAbbdd AaBbDd AaBbdd AabbDd Aabbdd

aBD AaBBDD AaBBDd AaBbDD AaBbDd aaBBDD aaBBDd aaBbDD aaBbDd

aBd AaBBDd AaBBdd AaBbDd AaBbdd aaBBDd aaBBdd aaBbDd aaBbdd

abD AaBbDD AaBbDd AabbDD AabbDd aaBbDD aaBbDd aabbDD aabbDd

abd AaBbDd AaBbdd AabbDd Aabbdd aaBbDd aaBbdd aabbDd aabbdd

Non-segregating (intermediate), Segregating

Non-segregating (resistant)

Non-segregating (susceptible)

* 10:53:1

1644 x 2189 F2.3 Obs Exp* χ2

22 21 0.04

110 112 0.03

3 2 0.38

Segregation of resistance to Ug99 in 1644 × 2189 F2:3

14

1Ssh 2Ssh 3Ssh 4Ssh 5Ssh 6Ssh 7Ssh

Chromosome

group

1 2 3 4 5 6 7

1. 1644 x 1193

3. 1644 x 2232

2. 1644 x 2189

1 2 3 1 2 3 1 2 3 1 2 3 1 2 3 1 2 3 1 2 3

Integrated DArT and SNP gene-based genetic map

Moscou, Champouret, Hernández-Pinzón, Bouyioukos, Olivera, Steffenson

1644 x 1193 1644 x 2232 1644 x 2189 Consensus

F2 population 182 177 175 534

Total cM 885 972 888 1115

DArT markers 495 791 750 1598

Gene SNP markers 0 49 40 52

SSR markers 15 0 0 15

15

Relative LOD

1Ssh

2Ssh

3Ssh

4Ssh

5Ssh

6Ssh

7Ssh

QTL mapping of Ug99 resistance in 1644 × 2189

M. Moscou

N. Champouret

S. Flipo

G. Yu

A

B

F2 genotyping

F2:3 phenotyping F3:4 genotyping

F3:4 phenotyping

3:1

3:1 5.5 cM in barley

37 cM in barley

16

Wheat stripe rust severity (2000-2009)

Wellings et al. (2010) BGRI Workshop

5% yield

loss

10% yield loss

Molecular Basis of Non-host Resistance to

Wheat Stripe Rust in Barley

11

Maize

Sorghum

Wheat

Brachypodium

Rice

36

47

53

MYA

Barley

12 Sitopsis

2-6

Matt Moscou

Why are most barley

genes for resistance to

barley stripe rust recessive?

Do barley stripe rust

resistance genes function

against wheat stripe rust in

barley?

Can we exploit a molecular

understanding of this

interaction to make wheat

resistant to wheat stripe

rust?

Host to barley stripe rust Marginal host to wheat stripe rust

Stripe rust on Barley

Morex Steptoe HOR 1428 Trumpf

Full lifecycle Varying degrees of

colonisation Penetration

Little colonisation

Matt Moscou

HOR 1428 x Morex F2 population inoculated with Pst 08/501

0.0 1.0 2.0 3.0

0

20

40

30

10

Chlorosis

Fre

quency

Morex

HOR 1428

Morex

Matt Moscou

HOR 1428

HOR 1428 x Morex F2 population inoculated with Pst 08/501

SNP Genotyping - Illumina GoldenGate Oligo Pooled Assay

Matt Moscou

Composite interval mapping on the

HOR 1428 x Morex F2 population inoculated with Pst 08/501

QTL 1

QRpst-1H

QTL 2

spst1

QTL 3

QRpst-6H

Chlo

rosis

M

icro

scopy

S R R R R

Resistant Resistant parent

HOR 1428

Matt Moscou

QTL 3

Morex Het HOR

1428

13.0%

6.6%

QTL 2

Morex Het HOR

1428

49.1%

45.3%

QTL 1

Morex Het HOR

1428

0

0.5

1.0

1.5

0

1.0

2.0

3.5 12.5%

2_01451_02081_0409

1_1345

1_0490

1_0113 1_07382_05571_0223

1_1199

2_0210 1_01322_0302

2_0680 2_1418 2_0777

2_13971_0793

2_1490 2_09391_0261 1_1405 2_02691_0093 1_0942 1_0028

1_10421_1114 2_0289

1_1244 2_0610 1_08811_0262

2_0482 2_0472 2_0363 2_0412 2_1481 2_03612_14001_0509

2_0723 2_0453 2_1087 2_0062 2_1273 1_12071_0010 1_0606

1_04671_1500 1_1004 2_1353

2_06701_0724

2_0689 1_07232_01781_13981_05882_03842_08382_12431_12922_05152_04541_0510

1_0334 2_1111

1_01231_0712

1_1299 2_0701 2_1035

2_0007

2_0272

2_0013

0

5

10

15

20

25

30

35

40

45

50

55

60

65

70

75

80

85

90

95

100

105

110

115

120

CH

L

pIN

F

mIN

F

4H

4H

Mlo

0 1 2 3 4

05

10

15

Fre

quency

Infection phenotype

Bgh CC148

Segregation for resistance in a HOR

1428 x Morex F2 population

HOR 1428 F1 Morex

23

Not Mla

Not mlo

Colocalization of race-specific and species specificity

resistance loci to multiple pathogens

Mla

mlo

Mlf

Rpst1

spst

Rpst2

Mlsp

MlLa

Mlg Rmo1 QRmo

QRmo

QRmo

Barley powdery mildew

Wheat stripe rust

Rice blast

Rmo2

QRpst

QRpst-6H

QRpst-5H-2

QRpst-3H

QRpst-4H

mlo

Barley stripe rust rps2

Rps-5H

Rps-3H

Ml?

QRpst-5H-1

Black Sigatoka of banana Banana

4th most important crop after wheat, rice, maize

Staple for 400m people in the tropics

90% of bananas are grown on small farms and eaten locally

Export worth $5 billion a year

Cladosporium fulvum

Tomato leaf mold ECP2 Avr4

ECP6

v

Can C. fulvum R gene host range be extended?

Bolton et al. 2008

Stergiopoulos et al. 2010

Marshall et al. 2011

Mycosphaerella fijiensis

Black Sigatoka of banana

Mycosphaerella graminicola

Septoria leaf blotch

Stagonospora nodorum

Glume blotch

Pyrenophora tritici-repentis

Tan spot

Alternaria brassicicola

Brassica dark leaf spot

v v v

Cf-Ecp6

Cf-Ecp2

Cf-4

?

?

?

27

~40 Kb in Heinz

11G (110 Kb)

7B (117 Kb)

4B (140 Kb)

M1 M2 M4 M5

Cf-Ecp2

Mutant 1

Mutant 2

Cf-Ecp2 map interval in tomato

M3

✓

✗

✓ ✓ ✓

✓ ✓ ✓

✓ ✓ ✓ ✗

✓

✓

✓

✓

✓

✓

28

Collaborations

Ayele Badebo, Debre Zeit Agricultural Research Center, Ethiopia

Brian Steffenson, University of Minnesota1, USA

Colwyn Thomas, UEA, UK

Cristobal Uauy, JIC, UK

Diane Saunders, Sophien Kamoun, TSL, UK

Eitan Millet, Tel Aviv University, Israel

Graham Moore, JIC, UK

Jesse Poland, USDA-ARS, Manhattan, KS, USA

John Doonan, University of Aberystwyth, UK

John Rathjen, Australian National University, Australia

Jorge Dubcovsky, UC Davis, USA

Klaus Mayer, MIPS, Munich, Germany

Manash Chatterjee, BenchBio, Gujarat, India

Mario Caccamo, TGAC, UK

Mick Ayliffe1, CSIRO, Australia

Mogens Hovmøller, Aarhus University, Denmark

Nick Talbot, University of Exeter, UK

Parveen Chhuneja, Punjab Agricultural University, India

Paul Nicholson, JIC, UK

Pavel Bartoš, Prague

Peter Dodds1, CSIRO, Australia

Rients Niks, Wageningen, Netherlands

Robbie Waugh, JHI, UK

Robbie Waugh, JHI, UK

Robert Park, University of Sydney, Australia

Rosemary Bayles, NIAB, Cambridge

Ruth Waynera, Kenyan Agricultural Research Institute, Kenya

Wendy Harwood, JIC, UK

Wolfgang Spielmeyer, CSIRO, Australia

Xianming Chen, USDA-ARS, Pullman, WA, USA

Zakkie Pretorius, University of Freestate, South Africa

2Blades Group

Sue Banfield

Jan Bettgenhaeuser

Andrew Dawson

Matthew Gardiner

Phon Green

Inma Hernández-Pinzón

Georgina Cox

Shuzhen Jiang

Cintia Kawashima

Lucy McCann

Matthew Moscou

Jing Song

Burkhard Steuernagel

Marie Westergaard

Brande Wulff

Guotai Yu

Alumni: Costas Bouyioukos

Nicolas Champouret

Stephen Cranwell

John Ferguson

Gopal Jha

Eric Ward

Acknowledgements