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Spring Bread Wheat Improvement for Irrigated Environments. Ravi Singh, Julio Huerta, Sybil Herrera, Pawan Singh, Govindan Velu , Sukhwinder Singh and Sridhar Bhavani. Wheat Breeding at CIMMYT . Mexico based Irrigated spring bread wheat improvement Rainfed spring bread wheat improvement

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spring bread wheat improvement for irrigated environments
Spring Bread Wheat Improvement for Irrigated Environments

Ravi Singh, Julio Huerta, Sybil Herrera, Pawan Singh, Govindan Velu, Sukhwinder Singh and Sridhar Bhavani

wheat breeding at cimmyt
Wheat Breeding at CIMMYT

Mexico based

  • Irrigated spring bread wheat improvement
  • Rainfed spring bread wheat improvement
  • Durum and triticale improvement
  • Germplasm enhancement

Regional based

  • Turkey-CIMMYT-ICARDA winter and facultative wheat improvement for CWANA region
  • CAAS-CIMMYT winter and facultative wheat improvement for China
spring wheat mega environments
Spring wheat mega-environments
  • ME1: Irrigated (36.1% area) Temperate

1. High yield potential, lodging tolerance

2. Water and nutrient use efficiency

3. Resistance to three rusts

4. Large white grain with leavened and flat bread quality

spring wheat mega environments4
Spring wheat mega-environments
  • ME2: High rainfall >500 mm (8.5% area) Temperate

1. High yield potential, lodging tolerance

2. Resistance to three rusts, septoria tritici and fusarium head blight

3. Large red grain with leavened bread quality

spring wheat mega environments5
Spring wheat mega-environments
  • ME5: Irrigated or High rainfall (7.1% area) Warmer

1. High yield potential with early maturity, lodging tolerance

2. Heat tolerance

3. Resistance to rusts and spot blotch for low rainfall areas

Resistance to rusts and fusarium head blight for high rainfall areas

4. Large white or red grain with leavened and flat bread quality or noodle quality depending on the country

irrigated spring bread wheat improvement program targeted area 45 m ha
Irrigated Spring Bread Wheat Improvement Program- Targeted area: 45 m ha
  • Irrigated Mega-environment 1:China, North-western India, Pakistan, Afghanistan, Iran, Turkey, Egypt, Mexico and Chile:30 m ha
  • Irrigated (Warmer) Mega-environment 5:North-eastern, Central and Peninsular India, Tarai of Nepal, Bangladesh, Southern Pakistan, Sudan:10 m ha
  • High rainfall Mega-environment 2:West Asia and North Africa, Highlands of East Africa:5 m ha
breeding priorities
Breeding Priorities
  • High and stable yield potential
  • Durable disease resistance
    • Rusts- Stem (Ug99), Stripe and Leaf
    • Fusarium – Scab and myco-toxins
    • Septoria leaf blight, Spot Blotch, Tan Spot
    • Karnal bunt
  • Water use efficiency/Drought tolerance
  • Heat tolerance
  • Appropriate end-use quality
  • Enhanced Zn and Fe concentration
  • Adaptation in conservation Agriculture
  • Human Resource Development
ciudad obregon toluca el batan shuttle breeding backbone of cimmyt wheat improvement
Ciudad Obregon-Toluca/El Batan “Shuttle Breeding”: Backbone of CIMMYT Wheat Improvement
  • Hot-spot screening- Ecuador (YR), Kenya (SR)
  • International testing through yield & screening nurseries

Cd. Obregón 39 m,

High yield (irrigated)

Drought tolerance

Leaf rust, stem rust

El Batán 2249 m

Leaf rust, Fusarium



Toluca 2640 m

Yellow rust

Septoria tritici


zero tillage with maize stubble

why increase yield potential
Why increase yield potential?
  • Necessary to meet the increasing demand (2% annual) due to population increase
  • Increased production must come from the existing or reducing land resources
  • Increased yield potential is reflected in yield increases in farmers’ field even though the management remains the same
how to protect gains in yield potential
How to protect gains in yield potential?
  • Resistance to important diseases and pests (biotic stresses)
  • Tolerance to drought, heat, salinity, etc (abiotic stresses)
  • Resistance and tolerance to stresses in a variety has no cost to farmers
yield stability
Yield stability
  • Capacity of a genotype (variety) to perform well under a range of environments under existing biotic and abiotic stresses
  • Environment at a location fluctuates annually
  • Easiest way to determine yield stability is to evaluate yield performance under a range of environments (wide adaptation)
type of crosses
Type of Crosses
  • Simple, three-way and four-way crosses: an attempt to create new combinations of desirable genes (creation of a distinct genotype)
  • Backcross: adds a genes or few genes from a source into an existing genotype
  • Single-backcross: maintains most characteristics of a variety but still allows selection for several new genes
the single backcross strategy
The Single-backcross Strategy
  • Increases the possibility of maintaining and reselecting desirable genes of the recurrent parent
  • Multiple genes or characters can be transferred simultaneously
  • Additional genes or characters from the donor parents can also be selected

Grain yields of wheat lines developed through traditional (Simple and 3-way crosses) and single-backcross approach

0.8% > Check

10.7% > Check

Cd. Obregon 2004-2005

crossing details
Crossing details
  • Approximately 600 targeted simple crosses, 500 single- backcross or three-way crosses per crop season
  • Approximately 300 F2 populations from simple crosses and 400 from single-backcross and three-way crosses
  • High emphasis to incorporate durable stem rust resistance in a range of germplasm carrying high yield potential, durable LR and YR resistance and quality characteristics
selection schemes
Selection Schemes
  • Various selection schemes can be applied
  • Selection schemes commonly used: pedigree, unselected-bulk, selected-bulk, modified pedigree or bulk
  • Our preferred strategy: selected-bulk
Selection Method:Selected Bulk(Harvest and thresh one spike from each of the selected plants of a population as bulk)
  • Permits selection of unlimited number of plants that have good agronomic features and desired level of resistance
  • Increases possibility to identify transgressive segregants due to larger population sizes
  • Field operation is easy, fast and economic

Genetic gain in yield from Selected Bulk is 3.3% higher than Modified Pedigree(Source: Simulation studies- J. Wang and M. van Ginkel, Crop Science)

Selected bulk retained 25% more crosses in the final selected population (Source: Simulation studies- J. Wang and M. van Ginkel)
selection strategy in segregating populations
Selection Strategy in Segregating Populations
  • Selected bulk from F1BC1/F1Top until F4/F5
  • Population sizes: Space sown 400 plants in F1BC1/F1Top and F3-F5; 1200 plants in F2 (2 million plants/season with an average selection frequency of about 7-10%)
  • Alternate segregating generations (F2-F5) under zero-tillage with maize stubble in Toluca and normal tillage in Cd. Obregon
  • Shuttling of stem rust resistance breeding F3 and F4 populations with Njoro, Kenya; grown in off-season and then main season as F4 and F5. F5 and F6 at Obregon.
  • Grain selection for size (45 mg and above) and plumpness in each generation through sieving
  • Selected plants harvested individually (or one spike harvested in Toluca) in F5 and F6 generations and plants/spikes with good grain characteristics retained
handling of advanced lines
Handling of Advanced Lines
  • Advanced lines (F6) from individual spikes in F5 populations harvested in Toluca planted in Cd. Obregon as small plots. Selected plots planted in Toluca and El Batan as PC. Selected lines form yield trials in Cd. Obregon.
  • Advanced lines (F5 or F6) from individual plants harvested in Cd. Obregon planted as F6/F7 at El Batan and Toluca in small plots and selected lines form yield trials in Cd. Obregon.
  • Yield trials-1st year (alpha-lattice design, 3 reps) sown on raised bed system in Cd. Obregon, and sets of PC are grown in Cd. Obregon (leaf rust)
  • Best lines selected based on yield and other traits and grain from Cd. Obregon used for quality analysis and for further disease and agronomic evaluations at Toluca, El Batan and Njoro (Kenya); and also multiplied in El Batan as Candidates for International Yield and Screening Nurseries (ESWYT, IBWSN, HRWYT, HRWSN)
  • 2nd year of yield trials in Cd. Obregon for selected lines conducted under five environments and seed multiplied in Mexicali for International Nursery. Simultaneous stem rust, yellow rust and leaf rust testing conducted in Kenya, Ecuador and cd. Obregon, respectively.
  • All data combined and used in selecting lines for International Yield Trials and Screening Nurseries
yield testing of advanced lines at cd obregon mexico 2009 2010 season
Yield testing of advanced lines at Cd. Obregon, Mexico2009-2010 season
  • 1st year yield trials or YT (5000 entries including checks): 30 entries/trial, 3 reps, alpha-lattice design
    • raised bed 5-irrigations

(small plots or PC planted for seed)

  • 2nd year yield trials or EYT (500 entries including checks): 30 entries/trial on beds (20 entries trial on Flat), 3 reps, alpha-lattice design
    • Raised bed, zero tillage-5 irrigations (>8 t/ha)
    • Flat-5 irrigations (>8 t/ha)
    • Raised bed-2 irrigations (4-5 t/ha)
    • Raised bed- drip irrigation (2.5-3 t/ha)
    • Raised bed-Late (85 days delay) sown- (>4 t/ha)

(small plots or EPC planted for seed)

characterization of epc entries
Characterization of EPC entries
  • Diseases:
    • Leaf rust- seedling and field (El Batan and Cd. Obregon)
    • Yellow rust- seedling and field (Toluca and Ecuador)
    • Stem rust- seedling and field: off- and main-seasons (Kenya)
    • Septoria tritici- Toluca
    • Fusarium- El Batan
    • Karnal Bunt- Cd. Obregon
    • Tan (yellow) spot- El Batan greenhouse
    • Stagnospora nodorum blotch- El Batan greenhouse
    • Spot blotch- Aguas Frias
  • Various quality traits including grain weight
  • Agronomic traits: height, heading, maturity, lodging
Progress in grain-yield potential of new breeding lines after one 5-year cycle of selection (Cd. Obregon 2004-05 and 2009-2010)

Breeding is science, art, passion, hard work & number game

12% yield gain


4814 entries


4956 entries




Shifting towards larger kernelsKernel weight of 1254 entries selected from 2009-2010 1st year yield trials at Cd. Obregon, Mexico





CIMMYT 1990s

CIMMYT 2000s

Accumulation of favorable alleles of High Molecular Weight (HMW) glutenins



high frequency of poor LMW glutenins

high frequency of good LMW glutenins

Quality profiles of newer CIMMYT wheats

Changing profiles of high and low molecular weight glutenins in CIMMYT wheats for bread making quality as well as reduction of 1BL.1RS translocation

Source: R.J. Peña

predicted expansion of heat stressed wheat me5 mega environment in india
Predicted expansion of heat-stressed wheat ME5 mega-environment in India

Current 2050

future gains in yield potential and yield stability under climate change
Future Gains in Yield Potential and Yield Stability under Climate Change
  • Targeted improvement of high yielding, widely adapted wheats: Identifying superior transgressive segregates
  • Wide incorporation of white floured 7DL.7Ag alien segment carrying Lr19/Sr25 genes: quantum jump of 10-12% in yield potential
  • Utilization of genetic resources, e.g. synthetic wheats
  • Shifting maturity towards earliness and selecting under heat-stress at hot-spot sites
  • Application of physiological tools in selection
  • Variety mixtures must be explored as an alternative strategy in heat and other stressed environments

Future Challenges- The Population Monster

Countries with highest population in 2050 and change relative to 2009

620 million more people just in South Asia by 2050 =

Population of USA and Brazil in 2009


Future challenges- Wheat Yields: 2008

Average by 2020 to produce 760 mlln tons

World average 2008

UN/FAO production goal for wheat 4 tons/ha by 2020


Rust menace- continued fight with an old enemy

Brown (leaf) rustPuccinia triticina

Yellow (stripe) rustPuccinia striiformis

Black (stem) rustPuccinia graminis


Dr. Roy Johnson (1935-2002)

Durable Resistance

Resistance, which has remained effective in a cultivar during its widespread cultivation for a long sequence of generations or period of time in an environment favourable to a disease or pest.

Types of Resistance

  • Monogenic ≈ Race-specific ≈ Major genes ≈ Hypersensitive (Boom & Bust)
  • Polygenic ≈ Race-nonspecific ≈ Minor genes ≈ Slow rusting/ Partial(Durable)
durable resistance to rust diseases why
Durable Resistance to Rust Diseases: Why?
  • Numerous races of rust pathogens
  • Mutating and migrating nature of rust pathogens
  • Annual virulence analysis and monitoring required
  • Most known race-specific genes ineffective in one or more wheat growing regions
  • Slow variety turnover in many countries
  • Opportunity to break-out of “Boom-and-Bust” cycles and focus breeding for other important traits
genes involved in durable slow rusting resistance to rust diseases
Genes involved in durable, slow rusting resistance to rust diseases
  • Minor genes with small to intermediate effects
  • Gene effects are additive
  • Resistance does not involve hypersensitivity
  • Genes confer slow disease progress through:

1. Reduced infection frequency

2. Increased latent period

3. Smaller uredinia

4. Reduced spore production

pleiotropic slow rusting genes lr34 yr18 pm38 and lr46 yr29 pm39 lr67 yr46 pm

With Lr46 Without Lr46

Pleiotropic Slow Rusting Genes:Lr34 /Yr18/Pm38 and Lr46/Yr29/Pm39Lr67/Yr46/Pm?
  • Components of slow rusting are under pleiotropic genetic control, i.e., the same resistance mechanism controls all components
  • Formation of cell wall appositions, instead of hypersensitivity
leaf tip necrosis and slow rusting resistance
Leaf tip necrosis and slow rusting resistance
  • Lr34/Yr18/Pm38, Lr46/Yr29/Pm39 and Lr67/Yr46/Pm? linked to some level of leaf tip necrosis expression
  • Slow rusting resistance without leaf tip necrosis also known

Leaf tip necrosis associated with Lr46



identification and characterization of slow rusting resistance
Identification and characterization ofslow rusting resistance
  • High or susceptible infection type in the seedling growth stage
  • Lower disease severity or rate of disease progress in the field compared to susceptible check
    • Brown rust: High (compatible) infection type in the field
    • Yellow rust: Infection type not a reliable criteria due to systemic growth habit
    • Stem rust: Variable size of pustules- bigger near nodes

Genetic basis of durable resistance to rust diseases of wheat

% Rust




1 to 2 minor genes



2 to 3 minor genes


4 to 5 minor genes








Days data recorded

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

advances in molecular mapping of slow rusting resistance genes
Advances in Molecular Mapping of Slow Rusting Resistance Genes
  • Several Genomic locations (QTLs) known
  • Developing and characterizing mapping populations that segregate for single resistance genes
    • Single gene based populations for 2 or 3 undesignated genes now available at CIMMYT
    • Very difficult to characterize populations segregating for minor genes that have relatively small effects
  • Gene-based markers for relatively larger effect slow rusting genes becoming reality
    • Gene Lr34/Yr18/Pm38 cloned and gene-based marker available
    • Significant progress made towards cloning of Lr46/Yr29/Pm39

Durable pleiotropic resistance gene Lr34/Yr18/Pm38

Perfect marker for Lr34

-veLr34sp & +veLr34spA


ABC (ATP Binding Cassette) transporter of PDR (Pleiotropic Drug Resistance) subfamily

1 2 3 4 5 6

Cloning of Lr34/Yr18/Pm38

  • Single gene based fine mapping populations
  • Gamma-ray induced deletion stocks
  • Azide-induced mutations
  • Precision phenotyping
  • Partnership (CIMMYT, CSIRO and Univ. of Zurich)
  • Lalbahadur
  • Lalbahadur+Lr34
  • Thatcher
  • RL6058 (Thatcher+Lr34)
  • Chinese Spring (+Lr34)
  • Lr34 deletion mutant

Krattinger et al. Science 2009

advances in breeding for slow rusting resistance to brown and yellow rusts at cimmyt
Advances in breeding for slow rusting resistance to brown and yellow rusts at CIMMYT
  • 1970s: Wheat lines with intermediate levels of slow rusting resistance selected.
  • 1990s: Wheat lines with near-immune level of resistance developed through intercrossing diverse sources of resistance followed by selection of transgressive segregants.
  • 2000s: Targeted introgression of resistance into adapted cultivars and genotypes resulting in high-yielding wheats with high levels of resistance.

Controlled field epidemics remain the best tool

for selecting slow rusting resistance

Adult plant leaf rust responses of 144 race-specific gene carrying and 360 seedling susceptible new elite entries in El Batan, Mexico 2009

Susceptible checks = 100% severity

0-15% severity

variation in resistance to yellow rust in 504 new elite entries tested during 2009
Variation in resistance to yellow rust in 504 new elite entries tested during 2009

Severity of susceptible checks =100S (N)

ug99 migration and evolution current status




Ug99: 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








why ug99 is a threat to wheat producing countries
Why Ug99 is a threat to wheat producing countries?
  • Historical importance of stem rust
  • Span of susceptible wheat varieties on >80% area
  • Favorable environment (dew/rain and temperatures)
  • Mountains and other areas for off-season survival
  • Continued evolution
  • Early epidemics can cause >70% losses
  • If measures not taken, estimated 10% losses in production in South Asian countries alone can be worth approx. US$1.5 billion and will provoke sharp increases in wheat prices

Planning for the Threat of Emerging Wheat Rust Variants

Advocating and Coordinating Global Cooperation

Tracking Wheat Rust Pathogens

Supporting Critical Rust Screening Facilities in East Africa

Breeding to Produce Rust Resistant Varieties

Developing and Optimizing Markers for Rust Resistance

Reducing Linkage Drag

Discovering New Sources of Rust Resistance

Exploring Rice Immunity to Rust

Borlaug Global Rust Initiative

A multi-institutional partnership for systematically reducing vulnerability of global wheat crop to wheat rusts

  • Durable Rust Resistance in Wheat Project- Objectives
methodology used for identifying adult plant resistance to ug99 in current wheat materials
Methodology used for identifying adult plant resistance to Ug99 in current wheat materials
  • Field evaluation of advanced breeding lines in Kenya/Ethiopia
  • Greenhouse seedling tests for susceptibility to Ug99 at USDA-ARS Lab. in St. Paul, Minnesota, US
  • Characterization of pseudo-black chaff phenotype and application of Sr2 molecular marker
  • Identified APR Sources:Kingbird, Kiritati, Juchi, Pavon, Parula, Picaflor, Danphe, Chonte

Kingbird-the best source of APR


Pseudo black-chaff

Durable adult-plant resistance (APR) to stem rust

  • Sr2-Complex
  • (Sr2 and other minor genes)
  • Sr2 transferred to wheat from ‘Yaroslav’ emmer in 1920s by McFadden
  • Sr2 is linked to pseudo-black chaff
  • Sr2 confers only moderate levels of resistance (about 30% reduction in disease severity)
  • Adequate resistance achieved when Sr2 combined with other unknown genes
  • Essential to reduce/curtail the evolution of Ug99 in East Africa and other high risk areas

Sr2 present

Sr2 absent


Breeding for durable, adult-plant resistance at CIMMYTMexico (Cd. Obregon-Toluca/El Batan)- Kenya International Shuttle Breeding: a five-year breeding cycle)

Cd. Obregón 39 masl

High yield (irrigated), Water-use efficiency, Heat tolerance, Leaf rust, stem rust (not Ug99)

Njoro, Kenya 2185 masl

Stem rust (Ug99 group)

Yellow rust

El Batán 2249 masl

Leaf rust, Fusarium

Toluca 2640 masl

Yellow rust

Septoria tritici


Zero tillage

  • Shuttle breeding between Mexico and Kenya initiated in 2006
  • >1000 F3/F4 populations undergo Mexico-Kenya shuttle
  • High yielding, resistant lines from 1st cycle of Mexico-Kenya shuttle under seed multiplication for international distribution in 2010

Grain yield performance comparison: Mexico Shuttle vs. Mexico-Kenya Shuttle Breeding, Cd. Obregon 2009-2010

Mexico shuttle


Mexico-Kenya shuttle


8-9% entries


No effect of selection in Kenya on grain yield performance

alternative approaches
Alternative approaches
  • Use effective race-specific resistance genes in combinations aided by molecular markers (short-term): few useful genes with markers
  • Develop cassettes of durable or unutilized race-specific resistance genes- GMO solution (long-term): need a strong collaborative cloning effort

Diversity and utilization race-specific resistance genes effective to Ug99 group of races

Seeding infection types

  • About 20 resistance genes have potential (Sr13, 14, 22, 25, 26, 27, 28, 29, 33, 35, 39, 40, 43, 44, 45, Tmp, 1A.1R, Sha7 and a few more)
  • Virulence known in other races for seven genes (Sr13, 14, 27, 25, 28, Tmp, 1A.1R)
  • Immediate value: Sr22, 26, 35, Huw234, Sha7;and Sr13, 14, 25, 1A.1R and Tmp for use in combinations
  • Translocations being shortened to reduce the negative effects and new genes being searched
  • Molecular markers essential for selecting gene combinations




Ug99 Stem Rust Resistance in 728 new CIMMYT wheat lines developed after one cycle of breeding (2006-2010)


Grain-yield performance of 298 entries with APR (NIR and R categories) to Ug99 stem rust compared with all 728 lines retained after one 5-year-breeding-cycle (Cd. Obregon 2009-2010)





About 90% lines also highly resistant to leaf rust and yellow rust and resistance of about 60% lines based on APR

acknowledging agencies supporting bread wheat improvement rust research
Acknowledging agencies supporting bread wheat improvement & rust research

Bill and Melinda Gates Foundation through:

DRRW Project

CSISA Project

Harvest Plus Project

Syngenta Foundation


ICAR, India



SDC, Switzerland

ACIAR, Australia

Farmers’ organizations:

Agrovegetal, Spain

Cofupro, Mexico

GRDC, Australia

Patronato-Sonora, Mexico

Thank you