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2nd International Wheat Stipe Rust Symposium Izmir, Turkey, May 2014

H-J Braun, RP Singh, J Huerta-Espino, SA Herrera-Foessel, C Lan & BR Basnet

Global status of yellow rust on wheat and strategies for its short and long term control

Trace to 100% yield losses depending on the time of the epidemic initiation, susceptibility of variety & climatic conditions

Selection of virulence for resistance genes Yr9and Yr27 associated with epidemics in the last 25 years in Africa, Middle East and Asia

Worldwide spread of aggressive, temperature tolerant races and their further evolution:

new areas, initiation of epidemics at earlier growth stages and higher severity

Fungicide application becoming a routine in some countries

Global status of yellow rust

The good news:

More productive spring, facultative and winter

wheat germplasm, resistant to current yellow

rust (and other rusts) populations has been

distributed through various international yield

trials and nurseries, and also developed by

various National Programs during past years

Various yellow rust resistant varieties released

in different countries

Immediate action points:

Reduce the area sown to susceptible varieties

by promoting new varieties with diverse

resistance

Release and seed multiplication of resistant

varieties in countries lagging behind

Release and promotion of additional varieties

with complex resistance base

If not done then in 3rd YR conference we will assemble & discuss the same again

Long-term R4D for a sustainable yellow rust control (1)

Surveillance of pathogen population for a timely detection

of new virulences of relevance

Trap nurseries (NILs and varieties)

Race characterization (GRC-Denmark, Turkey/ICARDA in Izmir,

India, Pakistan, Iran, China, Mexico, USA, Australia, etc.)

Information on the resistance genes present in commercial

varieties and important breeding materials

Gene postulation, molecular mapping- robust diagnostic

markers

High-throughput markers assays

Long-term R4D for a sustainable yellow rust control (2)

Identification of new resistance genes and their utilization

Race-specific genes- large & small effect; seedling & adult-plant

Slow rusting, pleiotropic adult-plant resistance genes

Breeding more productive wheat varieties

Utilizing race-specific effective resistance genes in combinations

(preferably 3 genes per combination)

Strong molecular breeding approaches for a forward breeding

Utilizing multiple minor, slow rusting genes, or their combination

with small/intermediate effect race-specific genes

Field based selection in conjunction with other traits

Fungicides are part of the solution

Reality with the utilization of large effect race-specific genes

● Most often end up being used as a single gene –stewardship / stacking

● Molecular breeding being practiced only in some programs but often results in non-competitive varieties

● Few effective genes with reliable molecular markers available at present

● Stronger emphasis required for marker assisted pyramiding of genes together with forward breeding approaches including genomic selection

Breeding minor, slow-rusting genes based adult plant resistance in combination with small/intermediate effect race-specific resistance genes for achieving near-immune resistance

from seedling growth stages

● Resistance based on 4-5 slow rusting APR genes is usually adequate in areas where yellow rust infection initiates from stem elongation stages onwards (APR genes are already functioning by then)

● However, with the aggressive races of yellow rust- infection in some areas initiates as early as tillering stage when APR genes still not fully functional

● Utilize combinations of slow rusting APR genes with small/intermediate effect race-specific resistance genes that have enhanced expression due to additive effects

Pleiotropic multi-pathogen resistance: a subclass of adult plant resistance genes

● Lr34 [ Syn. = Yr18=Sr57=Pm38 =Ltn1=Sb1= Bdv1]

chromosome 7DS

(leaf rust, yellow rust, stem rust, powdery mildew, leaf tip necrosis, spot blotch, barley yellow dwarf virus )

● Lr46 [ Syn.= Yr29=Sr58=Pm39=Ltn2=Ts?]

chromosome 1BL

● Lr67 [Syn.= Yr46=Sr55=Pm46=Ltn3]

chromosome 4DL

Formation of cell wall appositions (instead of hypersensitivity with race-specific genes)

Start0.0

Xgwm49769.7XksuH9c70.4XksuG34b72.5

End131.4

start0.0Xwmc1474.8

Centromere99.5

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Xgwm34983.6Xgwm30192.0Xgwm320 End95.0

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End213.5

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End170.1

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Centromere29.2

gwm742 gwm83288.2gwm16088.9End103.2

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End70.7

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glk42459.1Centromere60.9barc15185.3Vrn197.2Xfbb209.1105.0Xabg391110.0gwm126117.7End133.5

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Start gwm4590.0gwm3343.8

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Centromere75.0

bcd1510120.4ksuD27134.8End149.5

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End207.0

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Chromosome 1A

Chromosome 7DChromosome 6DChromosome 5DChromosome 4DChromosome 3D

Chromosome 7BChromosome 6BChromosome 5BChromosome 4BChromosome 3BChromosome 2B

Chromosome 7AChromosome 6AChromosome 5AChromosome 4AChromosome 3A

Chromosome 2D

Chromosome 2A

Chromosome 1D

Chromosome 1BStart0.0Xpsr94943.0Centromere45.1Xgwm60454.4Xgwm18a55.3Xgwm1160.8Xgwm27361.7glk48363.2Xgwm13168.5Xgwm268117.4Xwmc44159.5Xgwm793173.0

Lr46/Yr29/Sr58/Pm39

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End227.0

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Lr67/Yr46/Sr55/Pm46

Lr34/Yr18/Sr57/Pm38

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Sr2/Yr30

Diversity for Yellow Rust QTL (marked in yellow): > 35 regions through consensus maps(Rosewarne et al. TAG 2013, 126:2427-2449 )

Examples of small/moderate effect race-specific resistance genes characterized recently at CIMMYT and

their interaction with slow rusting genes

● Yr54 in Quaiu3 on 2DL

● YrF in Francolin on 2BS

● YrSuj in tall variety Sujata on 7BL

● Yr60 in Lalbahadur on 4AL

Contrasting example: A race-specific gene with minor effect in seedlings but immunity in adult plants:

● YrKK in tall variety Kenya Kudu on 2BS

APR QTL interaction in enhancing yellow rust resistance of Avocet x Quaiu3 RILs

Yr29 Yr30

Yr54

Minor QTL

Yr29+Yr30+3D QTL

Yr29+Yr30+3D QTL+Yr54

Source: Basnet et al. Plant Dis. 2013

Moderately effective race-specific gene YrF on 2BS and slow rusting genes

together confer a high level of YR resistance in Francolin#1

Other APR genes/QTL• Lr46/Yr29 on 1BL• Yr30/Sr2 on 3BS• Two additional minor QTL

PVE: 10.3–21.1%

Source: Lan et al. (2014) Mol. Breed. DOI 10.1007/s11032-014-0075-6

Francolin#1 is an improved CIMMYT semidwarf & shows high level of resistance to yellow rust- 50% severity when YrF present alone

Race-specific gene YrSuj on 7BL and slow rusting APR genes together

confer a high level of resistance in Avocet/Sujata mapping population

Other APR genes/QTLLr46/Yr29 (PVE:5.6-6.2%)Lr67/Yr46 (PVE: 6.9-10.7%)QYrLr.cim-7BL (PVE: 11.7-20.9%)QYr.cim-1AS (PVE: 5.7-8.9%)QYr.cim-3DS (PVE: 6.3-8.2%)

Sujata is an improved tall variety from India & shows high level of resistance to yellow rust- 40% severity when YrSuj present alone

Source: Lan et al. (unpublished)

Future: GM intervention to achieve resistance durabilityGene Cassettes- multiple resistance genes inherited as a single unit:

simplifying breeding and enhancing resistance durability

Lr34/Yr18 Yr36 Lr21

SynR1 SynR2 SynR3

Natural gene cassette(currently developed)

Synthetic gene cassette(future possibility)

Natural gene cassettes currently in the pipeline at CSIROLr34/Yr18/Sr57 +Lr67/Yr46/Sr55 +Lr21 +Yr36

• Cloning many resistance genes for diversity

• Technology for insertion of large DNA “packages” – gene expression

• Synthetic R genes?

• Cisgenic vs Transgenic crops

Scientific/Commercialisation Challenges

Source: CSIRO-GRDC Triple Rust Initiative

Conclusions Sustainable yellow rust control will require growing resistant

varieties in disease prone areas around the world

Wheat varieties should be enriched with multiple pleiotropic APR genes, representing a novel class of resistance to rusts and other wheat pathogens, to curtail/slow down pathogen evolution

Although near-immune level of durable resistance to all three rusts can be achieved through field selection, molecular markers can aid better utilization & diversity

New approaches, such as “resistance gene cassettes” could further expedite breeding for durable rust resistance

Fungicides should be part of the rust control strategy