Pros and cons of utilizing major, race-specific resistance genes versus partial

resistance in breeding rust resistant wheat

R. P. Singh2012 BGRI Technical WorkshopBeijing, China

Resistance in wheat to rust pathogens Highly variable: immunity to small reduction in

host reaction or severity

Race-specific genes (R-genes) large to small effect Seeding and adult plant effective Diverse hypersensitive host reactions Various genes; those with large and intermediate

effects characterized

Partial or slow rusting genes (PR-genes) Intermediate to small effects More effective in post seedling growth stages Compatible host reactions for LR & SR (chlorosis &

necrosis in stripes for YR) Associated with slower disease progress due to

longer latent period, lower infection frequency, pustule size and spore production

Only a few genes characterized

Seedling reactions- stem rust

Seedling reactions- yellow rust

Seedling reactions- leaf rust

Pro and cons debate Not new and debated for almost 50 years since the

publication of famous book of van der Plank in 1963

Both types of resistance have played important role commercially

Enhancing the resistance longevity or durability- main concern

Significantly enhanced knowledge of the genetic basis should help in implementing better breeding and deployment strategies

A successful variety must possesses various traits- rust resistance is just one of them

Breeding PrioritiesCore traits (ideally should be present in all CIMMYT wheats) High and stable yield potential Durable resistance to Rusts-

Stem (Ug99), Stripe and Leaf Water use efficiency/Drought

tolerance Heat tolerance Appropriate end-use quality

Additional traits for specific mega-environments Durable resistance to diseases and

pestsSeptoria leaf blight (ME2)Spot Blotch (ME5)Tan Spot (ME4)Fusarium – head scab and myco-

toxins (ME2/4/5)Karnal bunt (ME1)Root rots and nematodes (ME2)

Enhanced Zn and Fe concentration (ME1/5)

Most traits have complex inheritance

Utilization of R-genes in breeding: Pros Simpler to utilize:

High frequency of resistant plants with appropriate agronomic characteristics in segregating populations

Large effects and low host reactions eases selection under poor epidemics in field

Selection of seedlings in greenhouse possible- advantage for SSD method

Preferred targets for MAS, especially when located on alien chromosome segments

Large number of advanced lines likely possess them even if no selection carried out in segregating generations

“Boom-and-Bust”: Race-Specific Genes for leaf rust resistance in Northwestern Mexico

    Year  

Variety Resistance genes Released Breakdown Race

Bread Wheat:

Yecora 70 Lr1, 13 1970 1973 ?

Tanori 71 Lr13, 17 1971 1975 ?

Jupateco 73 Lr17, 27+31 1973 1977 TBD/TM

Genaro 81 Lr13, 26 1981 1984 TCB/TB

Seri 82 Lr23, 26 1982 1985 TCB/TD

Baviacora 92 Lr14b, 27+31 1992 1994 MCJ/SP

Durum Wheat:

Altar 84 LrAlt 1984 2001 BBG/BN

Jupare 2001 LrAlt, 27+31 2001 2007 BBG/BP

“Boom-and-Bust” phenomenon Evolution and selection for virulence is often rapid: 3-5

years or less in many areas Longer resistance remains effective greater the

effect of “bust” in farmers’ fields (large area or several varieties) and on breeding programs (large proportion of breeding materials)

Continuous and relevant monitoring of avirulence/virulence to R-genes necessary in country where deployed and in the region (often worldwide)

Long distance, unpredicted migration of new races more common- globalization effect

Good communication amongst scientists of different disciplines necessary

Utilization of R-genes in breeding: Cons

Coping with “boom-and-bust” by breeding programs

Breeding materials must contain sufficient diversity for R-genes

Availability of only a few R-genes at a given time for utilization

Continuous search for new sources of resistance in wheat and related species and genera

Alien R-genes usually associated with undesirable traits due to linkage drag & available in poorly adapted backgrounds

Introduction in adapted backgrounds through backcrossing is necessary to promote utilization of new genes

Utilization of R-genes in breeding: cons

Avoiding losses in farmers’ fields Continuous releases, seed multiplication and

distribution of new varieties with diverse R-genes Retrieving older varieties, when a new virulent

race detected in significant frequency, not possible due to large seed volumes and farmers’ saved seed

Slow adoption rates of new resistant varieties in most countries

Post-epidemic demands for seed of resistant varieties is higher and this unexpected demand is hardly met

Deployment of R-genes: Cons

All public and private breeding programs in a region must follow it if same R-genes are being utilized

No legislation to stop releases of varieties with single R-gene

Molecular markers necessary for pyramiding multiple R-genes

Markers based selection could lead to a reduction in latent genetic diversity (less selection in field and increased reliance on genes with markers)

Real life- rarely practiced & less likely to be practiced as wheat breeding programs worldwide are managed with limited resources

Better strategy: utilize effective R-genes in combinations to enhance resistance longevity

Breeding for high levels of durable resistance to rust diseases

Susceptible

1 to 2 minor genes

2 to 3 minor genes

4 to 5 minor genese.g. Kingbird

% Rust

Disease progress over time (days)

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

Near-immunity (trace to 5% severity) can be achieved even under high disease pressure by combining 4-5 additive genes

Utilization of PR genes in breeding: challenges Small to intermediate effects of individual genes

Dispersed presence of genes in different varieties and germplasm

Field selection environment lacking uniform and high disease pressure

Need for growing larger population sizes for selection

Necessity of pyramiding 3-5 genes to achieve adequate to high resistance levels

Presence of race-specific genes in parents used in crossing programs

Difficulty in distinguishing small effect race-specific genes from slow rusting genes (especially for resistance to yellow rust)

Higher G x E interaction on the expression and effectiveness of slow rusting genes

Slow progress in identifying linked molecular markers if MAS to be used

Despite numerous challenges, significant progress was made at CIMMYT for resistance to all three rusts

Ug99 stem rust resistance in 464 wheat lines derived from crosses made in 2006 and distributed worldwide through various CIMMYT

international trials and nurseries in 2011/2012

76% entries distributed internationally possess high to adequate adult-plant resistance & another 16% carry diverse race-specific resistance genes

Adult plant resistance Stem rust Entries Race-specific Entries

Category severity (%) No. % genes No. %

Near-Immune Resistant 1 85 18 Sr25 10 2Resistant 1-10 116 25 Sr26 7 2Resistant- Mod. Res. 15-20 121 26 SrHuw234 1 0Moderately Resistant 30 35 8 SrSha7 14 3

SrTmp 35 8Mod. Res.- Mod. Sus. 40 22 5 Sr? 3 1

Mod. Sus.- Susceptible 50-100 (dead plants) 14 3

Adult plant resistance (APR): PR- and R-genes

Not all APR is based on PR-genesRace-specific APR genes with major, intermediate and

small effects are commonTrue PR-genes likely associated with multi-pathogen

resistanceDelineating PR-genes from small to moderate effect APR

R-genes difficult for yellow rust due to similar host reactions

Combinations of PR-genes and small/int. effect R-genes can lead to high levels of longer lasting resistance

Interaction of moderately effective R-gene Lr42 and two PR- genes in enhancing the resistance of Avocet

x Quaiu3 RILs

PR geneLr46/Yr29

R-geneLr42

Lr/Yr PR QTL

Lr42+Lr46/Yr29+Lr/Yr QTL on 3D

Source: Bhoja Basnet (PhD thesis)

Release of varieties with moderate but adequate resistance is challenging in some countries where regulations require releases of clean or highly resistant varieties only

Small disease in field can be alarming and will require educating extension agencies and farmers

More PR-genes will need to be bred together to achieve near-immune levels of resistance

Deployment of PR-genes in breeding: Cons

Breeding program Breeding for yield and other important traits becomes

easier once key parental materials enriched with multiple PR-genes

Avoiding losses in farmers’ fields Resistance is expected to be durable or long lasting-

change of varieties necessary only when a better variety available

Farmers can continue using their saved seed Emergency chemical control strategies not necessary Planned multiplication, distribution and promotion of

new varieties

Deployment of PR-genes in breeding: Pros

Conclusions and future outlook● Both R- and PR-genes offer opportunities to achieve durable control of

wheat rusts if utilized properly● “Boom-and-bust” experiences are unlikely to change in the near-future● Use of complex PR-gene resistance, or combinations of small effect R-

and PR- genes, should be a more attractive strategy● High yielding wheat germplasm with complex APR to three rusts being

distributed by CIMMYT should enhance the release and deployment of varieties with durable resistance

● New PR-genes are expected to be characterized due to an increased research focus in recent years

● New selection strategies, e.g. genome-wide selection, could be beneficial in pyramiding multiple R- and PR-genes

● Development of multiple R- and PR-genes cassettes and acceptance of GM wheat can simplify breeding for durable resistance

Thank you