Yellow (stripe) rust Puccinia striiformis Brown (leaf) rust Puccinia triticina Black (stem) rust Puccinia graminis R.P. Singh 27 September 2011 Threat of rust pathogens, anticipating it and preparing for a long-term solution

Major worldwide threat at present: ● Stem rust race Ug99 and its derivatives  East African highlands, Southern Sudan, Zimbabwe, South Africa, Yemen and Iran ● Yellow rust race 134E16 and its derivatives: aggressive and adapted to warmer temperatures  Middle East, Asia, Europe, North America, Australasia ● Leaf rust race BBG/BN and derivatives on durum  America, Southern Europe, North Africa, Middle East Rapid migration and evolution

Ug99 stem rust: migration and evolution: current status  1988: Uganda  2002: Kenya  2003: Ethiopia  2006: Yemen and Sudan  2006: Sr24 virulent mutant-Kenya  2007: Iran  2007: Sr36 virulent mutant-Kenya  2007: Sr24 virulent mutant- caused epidemic in Kenya  2008 & 2009: Similar races found in South Africa

Stem race Ug99 and its derivatives Bad news: ● Seven variants already known and pathogen is spreading ● Initial studies indicate cooler temperature adaptation ● High susceptibility of popular varieties and breeding materials Good news: ● Major worldwide effort (BGRI: DRRW and other projects) ● Several resistance sources known for utilization (including those based on slow rusting, minor genes) and new ones being identified and transferred to wheat from alien relatives ● Opportunity to replace years old varieties with more productive new varieties (higher yields will offset the cost with high ratio)

Yellow rust race 134E16 and its derivatives Bad news: ● Several variants already known that have in 10 years added virulence for Yr1, Yr10 (Yr24/Yr26), Yr17, Yr27, Yr31, etc. ● Refuge in fungicides ● Aggressiveness and adaptation to warmer temperatures:  spread to new areas where disease was not problem before  Faster multiplication rate leads to at least one additional disease cycle  Effects of resistance genes reduced and some minor genes seem to become ineffective due to extra disease pressure Good news: ● Several resistance sources known for utilization, including those based on slow rusting, minor genes ● Varieties and germplasm combining resistance to all three rusts becoming available

Leaf rust race BBG/BN and its derivatives on durum wheat Bad news: ● Spread in Americas, Southern Europe, North Africa, Middle East ● Susceptibility of most varieties and germplasm (all Australian materials tested were susceptible) ● Various variants evolved with virulence to Lr3, Lr14a, Lr27+31 and Lr26 in a short time ● Limited research effort worldwide Good news: ● Presence in Mexico accelerates the genetic and breeding efforts ● At least 2-3 race-specific resistance genes in durum continue to be effective and can be utilized ● Germplasm with adequate levels of slow rusting APR developed at CIMMYT through intercrossing of sources that carried moderate resistance ● High-yielding lines with adequate APR under development at CIMMYT

Way forward: Safeguarding wheat from rusts while enhancing productivity gains: the basic principles 1.Pathogen monitoring and surveillance within country, region and internationally 2.Diverse and durable genetic resistance 3.Forward breeding strategy 4.Resilient seed industry ● Human capacity ● Long-term commitment- financial & scientific

Resistance and breeding ● Various resistance genes, race-specific and slow rusting, known to exist (not always designated) in wheat germplasm ● Choice of choosing the type of resistance is decision of breeding programs ● CIMMYT decision is to give high focus on slow rusting, adult plant resistance- once achieved has high long-term benefits

Race-specific resistance: challenges ● Preparedness for boom-and-bust cycles through a good pathogen monitoring system & associated response to promote new resistant varieties ● Longer resistance remains effective greater the effect of “bust” in farmers’ fields (large area or several varieties) and on breeding program (large proportion of breeding materials) ● Continuous search for new sources of resistance, their assessment and utilization in breeding program ● Identifying molecular markers tightly linked to resistance genes for their utilization in combinations

Race-specific resistance genes: deployment strategies ● Combinations of effective resistance genes (gene pyramids) lead to resistance longevity due to a negligible probability of simultaneous mutations from avirulence to virulence in the same rust spore ● Marker assisted selection for gene combinations coupled with selection for other traits (e.g. grain yield) can lead to the successful development of new varieties ● No benefit in generating combinations if the same resistance genes are also utilized/deployed singly: stepwise evolution of virulence by defeating resistance genes one at a time  NEED A STRONG AGREEMENT AMONG REGIONAL AND INTERNATIONAL SCIENTIFIC COMMUNITY ON THIS ISSUE OTHERWISE PROGESS WILL BE SHORT-LIVED

Breeding minor, slow-rusting genes based adult plant resistance: a better strategy ● Leads to resistance durability ● Higher returns from investments due to long-term effectiveness ● Significantly enhanced knowledge of the genetic basis ● High-yielding wheats with high levels of resistance to all three rusts now available ● Field based selection in conjunction with other traits ● Higher focus can be given to breed for other important traits

Slow rusting, adult plant resistance genes ● The four catalogued genes confer resistance to multiple pathogens (should become essential genes) Yr18/Lr34/Sr?/Pm38 on chromosome arm 7DS Yr29/Lr46/Sr?/Pm39 on chromosome arm 1BL Yr30/Sr2/Pm? on chromosome arm 3BS Yr46/Lr67/Sr?/Pm? on chromosome arm 4DL ● Lr68: a new slow rusting gene in chromosome arm 7BL ● APR QTLs at many other genomic locations

Slow rusting resistance: gene interactions Susceptible 1 to 2 minor genes 2 to 3 minor genes 4 to 5 minor genes % Rust Days data recorded Single, or few, genes confer inadequate resistance Combining 4-5 additive genes leads to near-immunity (trace to 5% severity) under high disease pressure

● 2005: BGRI launched & Ug99 resistance screening initiated in Kenya/Ethiopia: >80% materials with inadequate resistance ● Greenhouse seedling tests with Ug99 at USDA-ARS Lab. in St. Paul, Minnesota, USA ● Characterization of pseudo-black chaff phenotype and application of Sr2 SSR marker gwm533 ● Identified APR Sources: Kingbird, Kiritati, Juchi, Pavon, Parula, Picaflor, Danphe, Chonte Kingbird-the best source of APR Mapping & breeding slow-rusting genes based resistance: the Ug99 stem rust case

KingbirdPBW343 ChromosomeLeft MarkerRight MarkerLODPVE(%)R2R2 1AXwPt-0128XwPt BSXwPt-3921XwPt BXwPt-2607XwPt ALXwPt-8670XwPt DSXwPt-1859XwPt Source: Bhavani et al Mapping of APR to Ug99 in PBW343 X Kingbird RIL population

Mapping of APR to Ug99 in PBW343 X Kiritati RIL population KiritatiPBW343 Chromosome Marker PositionLeft MarkerRight MarkerLODR2R2 2D20Xbarc095Xwmc BS30SW58Xbarc BS76Xwms371Xbarc DS36Lr34-linkedXbarc Source: Bhavani et al. 2011

Targeted breeding to develop superior germplasm with resistance to Ug99 ● Simple crosses in 2006; BC1 and Top crosses with high-yielding parents ● Initially about 500, now 1000 segregating populations (F3 & F4) shuttled each year with Kenya ● 2 generation/per year in Mexico and Kenya (F3/F4 or F4/F5) ● Selected-bulk scheme until F5 or F6 generation to handle large numbers ● Parallel populations maintained in Mexico for comparison ● Advanced lines phenotyped for yield, resistance and other traits in 2009/10 and 2010/11 seasons ● International yield trials and nurseries for planting in 2011/12 and 2012/13 ● 200 best lines provided to Australia in Dec through CAIGE project Njoro, Oct. 2008

Yield potential phenotyping Heat tolerance phenotyping Drought tolerance phenotyping ● 1 st year yield trials: alpha-lattice design, 3 reps  raised bed 5-irrigations Yield potential ● 2 nd year yield trials: alpha-lattice design, 3 reps  Raised bed, Zero till-5 irrigations Yield Potential and adaptation under conservation agriculture  Flat-5 irrigations Yield potential  Raised bed-2 irrigations Water use efficiency  Raised bed- drip irrigation Drought tolerance  Raised bed-Late (85 days delay) sown- Heat tolerance Yield and stress tolerance phenotyping of advanced lines in Mexico

Grain-yield performance of 728 entries in three environments (irrigated) in 2009/10 and 2010/11 in Cd. Obregon, Mexico PBW entries Heading: days Maturity: days Derived from 322 crosses

Ug99 Stem Rust Resistance in 728 Wheat Lines Njoro, Kenya 2010 Adult plant resistanceStem rustEntries Categoryseverity (%)No.% R-genesNo.% Near-Immune Resistant Sr Resistant Sr Resistant- Mod. Res SrTmp496.7 Moderately Resistant SrHuw SrSha Mod. Res.- Mod. Sus SrUnknown50.7 Moderately Susceptible Mod. Sus.- Susceptible Susceptible

Yellow rust resistance of 728 bread wheats in Toluca and Kenya 2010 >90% high yielding lines immune or highly resistant with APR in about 40% lines Severity of susceptible checks =100S (N) Races in Mexico and Kenya are virulent on Yr27 and several other important resistance genes including Yr31 present in Pastor and its derivatives.

Conclusions ● New races of rust pathogens pose threat and cause losses, however they also bring opportunities to strengthen the research and development agenda ● Although both race-specific and slow-rusting resistance sources are available, the utilization of durable APR should become preferred strategy ● Investments in research, breeding, human resources and infrastructure are key for future food security ● Enhanced cooperation and exchange of germplasm and information are essential for progress