New strategies and technologies in breeding for durable stripe (yellow)

rust resistance in wheat

2nd International Wheat Stripe Rust Symposium, 28th April -1st May 2014,

Izmir, Turkey

Dr Lesley A. Boyd, Research Group Leader, National Institute of Agricultural Botany (NIAB), Cambridge, UK

Informed resistance breedingThe plant recognises universal, common factors produced by the pathogen: PAMPS

Pathogen produces unique effectors that modify the plant environment and suppress plant defence

Disease

Effector-triggered immunity-ETI

Some effectors become Avir genes, recognised by the plant’s R-genes

Pattern-Recognition

Receptor (PRR)

R-gene

PTI and ETI lead to the induction of common defence processes, which include the genes that confer durable, partial, adult plant resistance

PAMP-triggered immunity -PTI

Boyd et al Trends in Genetics 2013

PRR

Informed resistance breedingNon-Host resistance and PTI

ERA-PG project: TritNONHOST (2009-2012) and ERA-CAP project: DURESTrit (2014-2017)

Co-ordinator Dr Patrick Schweizer, IPK, Gatersleben, Germany

TritNONHOST team Patrick’s group

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pIPKTA

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TaPERO

BAC

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F23

BAC

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x (

%) Barley-Bgh Wheat-Bgt

Expression of HvRNR8 confers partial resistance in wheat but has no effect in barley

Informed resistance breeding: RNR8 story

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control chitin 60' chitin 180' Control noninfiltrated

TaRNR8 chitin induced

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control 60 Flag 60 Flag180

TaRNR8 flagellin induced

TaRNR8 transcript levels in the wheat cv Renan

Non-Host Resistance summary:

RLKs are a complex group of proteins that potentially play different roles in host- and nonhost interactions

RLKs such as RNR8 may encode upstream components of NHR that escape effector suppression

It may therefore be possible to select or engineer non-host-like pathogen resistance into crops such as wheat

Transgenic wheat lines o/e HvRNR8 and silenced for TaRNR8 will be tested for resistance towards muliple pathogens

Within DURESTrit we have 3 more LRR_RLK with similar transient phenotypes

Identification and exploitation of natural variation in disease resistance

The BBSRC wheat pre-breeding program is divided into 4 pillars (Landraces, Synthetics, Alien Introgression, Elite Wheat) and 2 themes (Phenotyping and Genotyping).

PILLAR 1

Landraces

PILLAR 2

Synthetics

PILLAR 3

Wild

relative

PILLAR 4

Elite

Genotyping

Phenotyping

BBSRC Funded Wheat

breeders

Identification and exploitation of natural variation in disease resistance

• Historically new sources of R-gene resistance have been identified from the 1O, 2O and often the 3O wheat gene pool.

• Within the WISP project, Ian and Julie King at Nottingham University have made over 17,000 crosses between hexaploid wheat and diploid relative.

• At NIAB we have created synthetic hexaploid wheats from crossing tetraploid wheat to Ae. tauschii accessions first characterised by FIGS (Focused Identification of Germplasm Strategy) to identify environmental selection diversity and by DNA markers to determine genetic diversity.

• Simon Griffiths, NRP, Norwich is exploring the 1o gene pool within the Watkin’s landrace collection. e.g. Yr51 (Bariana et al TAG 2013)

• Keith Edwards at Bristol University has developed both SNP array and SNP markers using KASPar technology that support the genomic identification of valuable genetic regions.

•Working with UK wheat breeders these materials are crossed back to elite UK winter wheats.

Informed resistance breeding

In wheat over 60 stripe rust resistance loci have been assigned a Yr designation, while

some 140 QTL for stripe rust resistance have been reported in the literature, located to 49 chromosomal regions

through consensus mapping

(Wellings et al 2013, Rosewarne et al TAG 2013)

Identification and exploitation of natural variation in disease resistance: QTL

How do we identify the Lr34/Yr18/Pm38 complex-like genes, i.e. those that restrict

pathogen invasion, growth and reproduction?

Objective of TritNONHOST

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wheat

barley

powdery mildew

Blumeria graminis f. sp. triticihost: wheat, nonhost: barley

Blumeria graminis f. sp. hordeihost: barley, nonhost: wheat

rust

Puccinia triticinahost: wheat, nonhost: barley

Puccinia hordeihost: barley, nonhost: wheat

blast

Magnaporthe oryzaehost: wheat and barley

new Magnaporthe speciesnonhost: wheat and barley

Jam

es K

olm

er,

USD

A A

RS

General pathogen-regulated genes

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wheatbarley

Blumeria5570

Magnaporthe3252

Puccinia3763

Blumeria4811

Magnaporthe2777

Puccinia10756

The general response of wheat and barley against different pathogen species utilizes common pathways

PAMP-triggered immunity

functional categories in MapMan functional categories in MapMan

1276

1573

Identification and exploitation of natural variation in disease resistance: QTL

MAGIC populations

An innovative approach to dissecting the genetic control

of complex traits in wheat

Alison Bentley, P Howell, J Cockram, G Rose, T Barber, R Horsnell, N Gosman, P Bansept, M

Scutari, A Greenland and I Mackay

Mapping in multi-founder experimental populations

MAGIC

Multi-parent Advanced Genetic InterCross

• Genetically diverse population, bringing-in multiple alleles and allowing for multiple recombination events.

• Good for identifying multiple interacting genetic loci and traits.

• Allows for greater precision in mapping of QTL.

28210315 descendants of Founder 1

The NIAB Elite MAGIC populationFocus on mapping QTL segregating in current elite UK germplasm

Variety Reason for inclusion

Alchemy Yield, disease resistance, soft feed

Brompton 1BL/1RS, hard feed type, OWBM resistance

Claire Slow apical development, soft biscuit/distilling type

Hereward High quality benchmark Gp1 bread making type

Rialto 1BL/1RS, Gp2 moderate bread making type

Robigus High yielding, soft biscuit/distilling type, OWBM resistance

Soissons Early flowering French Gp2 bread making type

Xi19 Facultative, high quality Gp1 bread making type

90K SNP array NIAB Elite MAGIC population

allele freqs in lines

(AAm * 2 + ABm)/((AAm + ABm + BBm) * 2)

Fre

qu

en

cy

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02

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00

Potential frequency of an allele in the MAGIC population

Yellow rust resistance in NIAB MAGIC population

22nd August 2011 ‘Warrior’ Pst race

Yellow rust resistance in NIAB MAGIC population

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Yellow rust glasshouse seedling test using the ‘Warrior’ race

MAGIC line means

BLUP (log2)

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cy

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Parent 1 Hereward

Parent 2 Robigus

Resistant progeny

Yellow rust resistance in NIAB MAGIC populationYellow rust glasshouse seedling tests– distribution of disease scores

BLUP (log2 adjusted scores)

Freq

ue

ncy

Yellow rust resistance in NIAB MAGIC population

Yellow rust field assessment – natural infection

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Glasshouse and field (yellow rust) disease scores

field yellow rust

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Field YR scores

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MAGIC lines showing more yellow rust resistance in the seedling tests than the most resistant founder parent, cultivar Hereward, also showed higher levels of resistance in the field

Yellow rust resistance in NIAB MAGIC populationMapping hits – Yellow rust seedling and field tests

Gp 1 Gp 2 Gp 3 Gp 4 Gp 5 Gp 6 Gp 7 unlinked

-lo

g 10(P

)

Gp 1 Gp 2 Gp 3 Gp 4 Gp 5 Gp 6 Gp 7 unlinked

-lo

g 10(P

)

Seedling resistance

Field resistance

Yellow rust resistance in NIAB MAGIC population

3 large effects observed

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.51

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RAC875_c50347_258

genotype class

log

2 y

ello

w r

ust

Estimates(Intercept) 1.0283SNP 1 0.6476SNP 2 0.4223SNP 3 0.4069

SNP 1

SNP 1: “0” allele is associated with lower levels of yellow rust infection, i.e. resistant allele

Favourable alleles are dispersed

Yellow rust resistance in NIAB MAGIC population

Lines showing transgressivesegregation for yellow rust resistance.

Informed resistance breeding: Summary

• There is still potential for the identification of new sources of R-gene resistance with the 1O, 2O and the 3O

wheat gene pool.

• In addition, a better understanding of the primary interaction between pathogen and host (PTI and NHR) could lead to novel targets for resistance breeding.

• While the plant gene targets of effectors and the genetic pathways responsible for resistance provide targets for genetic modification.

Acknowledgements

TritNONHOST team:• Dr. Patrick Schweizer• Jeyaraman Rajaraman

• Dr. Lesley Boyd• Dr. Graham McGrann• Dr. Francesca Stefanato

• Dr. Rients Niks• Dr. Reza Aghnoum• Dr. Sajid Rehman

• Dr. Ulrich Schaffrath• Rhoda Delventhal

Additional collaborators:• Dr. Pete Hedley• Dr. Björn Usadel• Dr. Pamela Abbruscato

Wheat MAGIC population:• Alison Bentley• Phil Howell • James Cockram • Gemme Rose • Toby Barber • Richard Horsnell• Nick Gosman • Pauline Bansept • M Scutari • Andy Greenland • Ian Mackay

Pyramiding disease resistance QTLs:• Mike Grimmer• Sara Clarke • Neil Paveley

PAMP-Triggered Immunity:• Chris Ridout• Hank-jan Schoonbeek

SCPRID team:• Prof. Sakkie Pretorius• Dr . Renee Prins• Dr. Gloudi Agenbag• Dr. Peter Njau• Dr. Godwin Macharia• Dr. Ruth Wanyera• Ms. Ngina Waweru