Breeding maize, rice and wheat for highly variable abiotic stress

environments

Marianne Bänziger CIMMYTGary Atlin IRRI => CIMMYTRichard Trethowan CIMMYT => University of Sydney

Question

You can breed maize, rice and wheat for highly variable abiotic stress environments ....

…. But can you make progress?

600

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1200

1979 1980 198 1 1 982 1983 19 84 1985 1986 1 987 1988 1989 1990

Year

Rai

nfa

ll (m

m)

1.0

1.2

1.4

1.6

1.8

2.0

Mai

ze y

ield

(t/

ha)

Rainfall

Maize yield

Africa - The extreme example for a highly variable abiotic stress environment

Rainfall and maize yields E&S Africa

Rainfall 1988 - 1998

Maize growing environments in Africa

GxE analysis RainfallTmaxN supplyLow pH

Other factors:Biotic stressesLittle use of fertilizer and other inputs

Setimela et al (2005)

Abiotic stresses

Grain yield variability by country

0%

10%

20%

30%

40%

50%

60%

70%

80%

0.00 2.00 4.00 6.00 8.00 10.00 12.00

Grain yield (t/ha)

Tren

d ad

just

ed C

V

Africa

Asia

Latin America

US & Canada

Europe

FAOSTAT, 2006

Breeding for highly variable abiotic stress environments – The history

Abiotic stress environmentsLow heritabilityLarge GxELow genetic variance, small potential gainsComplex, polygenic tolerance mechanisms - large GxG

How to make progress?

Spring wheat data from Australia (Bänziger and Cooper, 2001)

The Abiotic Stress Breeder

Given that few people want to fight wind mills …

=> Breeding under high potential conditions

=> Genotype + Inputs=> A Green Revolution that

bypassed stress prone and low input environments0

2

4

6

8

10

1 2 3 4 5 6 7 8

Variety 1 Variety 2

stressed unstressed

Mean yield of the environment (t/ha)

Yiel

d of

the

varie

ty (t

/ha)

“There is one way of getting high yield, 10,000 ways of getting low yields – hence I select under optimal conditions to not have to bother with GxE …”

Perceptions

“Traditional approaches to breeding crop plants with improved abiotic stress tolerances have so far met limited success” (Richards, 1996).

One of the most frequently used sentences in grant proposals.

FYI, it’s quite suitable to justify most research …

But is it true ?

Duvick, 1997

Yield gain under favorable conditions

84 kg ha-1 yr-1

Yield gain under mild drought stress

53 kg ha-1 yr-1

Breeding progress or US hybrids selected between 1930s and 1990s

Breeding progress under abiotic stress conditions in the US

Interpretation by the seed industry (Bruce et al., 2002)

Use of nurseries with no available irrigationUse of high densityLarge scale (>1000 locations) broad area testing combined with stability analysisConsistent feed-back from sales figures to breeding

=> Steady increase in maize grain yields under abiotic stress conditions in the US

More recent investments (Löffler et al., 2005)

E

G

Use of responsive GIS/crop simulation to characterize the target population of environmentsEvaluation of 100 to >1000 genotypes at 100 to >1000 locationsWeigh G based on the importance of E across yearsSelect the best

Progress: h * rG * i * σG

Requisite: $$,$$$,$$$

Pioneer, 2006

Breeding for individual abiotic stresses

CIMMYTStarted in the 1970s to improve maize for individual abiotic stresses such as drought, low N, low pHIntroduced the concept of managed stress environments■ NOT to simulate a farmers field■ BUT to simulate a stress that is highly relevant in farmers’ fields

0.0

0.2

0.4

0.6

0.8

0.30.40.50.60.70.80.9

Yield reduction under low N

Gen

etic

cor

rela

tion

low

N -

high

N

Bänziger et al., 1997

Concept of managed abiotic stress environments

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0.8

0.30.40.50.60.70.80.9

Yield reduction under low N

Gen

etic

cor

rela

tion

low

N -

high

N

Bänziger et al., 1997

Concept of managed abiotic stress environments

Stress management for drought tolerance screening in maize

Germination Pre-flowering Flowering Post-flowering

Plant number ***

Leaf area *** *

Leaf senescence * ** ***

ASI * ***

Ear number ***

Grain number per ear

***

Kernel size ***

Yield *** * *** **

Breeding progress * ** *** ***

0

2

4

6

8

10

12

0 1 2 3 4 5 6 7 8

Grain yield (t ha-1)

Fre

qu

ency

(%

)

drought tolerance conventional

severedrought intermediate

droughtwell-watered

La Posta

Selection

((EdmeadesEdmeades et al., 1996;)et al., 1996;)

Breeding for individual abiotic stresses

Breeding for individual abiotic stresses

Research on Drought, low N, low pHAverage breeding progress for target stress: ~100 kg ha-1 yr-1

What farmers grow today

Drought tolerant

What changed?

Bänziger et al. 1999; 2002; Bolaños & Edmeades, 1993a; 1993b; Bolaños et al., 1993; Edmeades et al., 1999; Lafitte & Edmeades, 1994a; 1994b; 1994c

Minor changesBiomassWater uptakeNutrient uptake

Large changesHarvest index Internal use of resources

Water upt

ake

WUE

Osmotic adju

stment

Roots

Stress literature

Reproductive structures

C7C4C2C1 C5C3 C6 C10C9C8

Genetic basis for maize drought stress tolerance (Ribaut et al)

Question

Progress for individual abiotic stresses is possibleWhat is the impact in a highly variable stress prone environment?

Hypothesis: “Mega trait-based index selection“

1. Prioritize abiotic and biotic stresses in the target environment

2. Manage those stresses on the experiment station

3. Apply index selection to large numbers of G

4. Progress = h * rG * i * σG

Mega trait-based index selection by CIMMYT in southern Africa

Management Season Sites Selection criteria Selection pressure

Recommended input application / high rainfall

Main 1-2 Yield, MSV, GLS, Et, Ps, ear rots, lodging, husk cover

Yield, ASI, leaf senescence, ears per plant, ear rots

Yield, ASI, leaf senescence, ears per plant

Managed low N Main 1

1

1

Managed drought Dry 1 1

Location: Zimbabwe, 1-2 years; 3000+ genotypes per year

Weigh various traits based on their (assumed) importance in the target environment (= southern and eastern Africa)

Sam

e ge

n oty

p es

SILINE AVG YP LOWN DRT ASI EPO RL SL HC PS ET TEX[K64R/CML444]-B-40-#-1-1 0.89 0.89 1.04 0.72 1.9 50.4 18.8 3.3 7.7 2.3 1.2 2.5ZM621A-10-1-1-3-1-BB 0.84 0.62 0.60 1.31 2.3 49.6 7.4 1.6 14.1 2.8 1.2 3.2ZM621A-10-1-1-1-2-BB 0.80 0.81 0.88 0.72 2.3 50.2 9.0 0.8 12.2 1.8 1.3 3.1ZM423A-8-1-1-1 0.54 -0.79 1.56 0.85 1.4 51.1 15.0 1.5 13.3 2.4 1.0[CML198/ZSR923S4BULK-2-2-X-X-X- 0.54 0.67 0.53 0.41 3.2 48.6 4.3 1.3 14.6 2.0 1.2 3.0[CML445/ZM621B]-2-1-2-3-1-BB 0.51 0.37 0.43 0.74 3.5 50.1 9.9 1.9 12.0 2.1 1.2 3.0[CML198/LPSC3H144-1-2-2-2-2-#-BB 0.21 -0.01 0.23 0.41 3.6 49.8 10.3 1.3 10.5 2.0 1.0 2.6[CML441/CML444]-B-7-#-1-3 0.19 0.65 -0.04 -0.03 4.7 53.2 8.0 2.0 10.6 2.2 1.1 3.0ZM623A-95-2-1 0.18 0.59 0.93 -0.97 3.1 51.9 15.3 3.1 6.6 1.5 1.0 2.8ZM521B-52-1-1-1-1-BB 0.05 0.44 -0.52 0.23 3.8 50.9 8.7 4.6 11.2 2.7 1.4 2.4ZM623B-45-1-1-3 0.04 0.84 -0.33 -0.39 5.5 50.3 11.8 1.1 10.1 3.2 1.3 3.298SADVIB-37-2-3-3-1 0.03 -0.07 0.18 -0.03 3.8 51.1 19.6 1.9 11.1 2.5 1.1 3.0ZM523A-38-1-1-1 -0.02 -0.79 -0.59 1.33 2.4 50.3 10.6 5.6 9.5 1.3 1.698SADVIB-37-2-1-2-1 -0.03 -0.52 1.08 -0.65 2.6 53.0 22.1 0.5 11.7 1.9 1.0 2.9ZM523B-126-1-1-2 -0.07 0.96 -0.87 -0.30 3.0 47.0 5.2 2.1 12.9 1.8 1.3[EEDMRSR/ZM523B]-64-2-1-2 -0.13 0.12 0.55 -1.06 1.8 51.7 13.1 2.7 17.4 1.9 1.398SADVIB-37-2-3-2-2 -0.14 0.42 -0.54 -0.30 5.4 54.0 10.1 5.7 8.7 2.8 1.3 3.098SADVIB-37-2-2-2-3 -0.29 -0.04 -0.62 -0.20 4.4 53.0 16.2 1.7 11.7 2.2 1.4 2.8ZM623B-103-2-1-2 -0.29 0.26 -0.57 -0.57 5.0 47.9 8.1 2.5 13.5 2.4 1.0 3.0[P1/P2]RIL203-1-6-B -0.38 -0.53 -0.49 -0.12 3.2 53.3 11.3 2.6 12.9 2.7 1.0 3.0[CML441/CML444]-B-7-#-1-2 -0.38 0.10 -0.70 -0.54 4.9 52.1 7.2 1.2 11.5 2.4 1.1 3.2[P1/P2]RIL247-2-3-B -0.87 -0.48 -1.29 -0.84 5.1 50.2 8.8 1.1 15.0 3.3 1.0 3.8[P1/P2]RIL146-1-1-B -0.88 -0.31 -1.46 -0.86 3.7 50.3 7.6 2.1 8.8 2.6 1.3 3.1[H16/K64R]F3-1638-2-1-B -0.92 -1.58 -0.64 -0.54 4.8 56.8 17.9 1.6 15.1 3.2 1.3 3.0[P1/P2]RIL247-2-4-B -1.11 -0.05 -1.80 -1.47 8.5 48.7 6.2 2.2 8.4 3.6 1.0 4.1

INDIVIDUAL TRAITS

Are we just fighting windmills?

Evaluation of stress breeding approach

Stress breeding approach:Yield potentialDisease resistanceDrought toleranceLow N tolerance

=> 42 hybrids from CIMMYT

All hybrids ever evaluated in regional trials

Classical breeding approach:Yield potentialDisease resistanceExtensive multi-loationtesting

=> 41 hybrids from the private seed sector (Monsanto, Pannar, Pioneer, Seed-Co, ZamSeed)

Evaluation in S&E Africa• 42 experimental hybrids

• 41 private company checks

• 36-65 trials, 3 years

Percentage yield increase of experimental hybrids (n=42) over checks (n=41)

0%

5%

10%

15%

20%

25%

0-1 1-2 2-3 3-4 4-5 5-6 6-7 7-8 8-9 >9

Average trial yie ld (t/ha)

Yie

ld in

crea

se o

ver

chec

ks

+

+* * ***

*** ***

*** ***

***

Trial #: 18 41 38 48 31 27 21 22 20 7

Note: no maturity differences between experimental hybrids and checks (Bänziger et al., 2006)

Conclusion

Proof that a focused and relative inexpensive breeding approach can deliberately increase maize yields in a highly

variable stress-prone environment

3-4 managed selection environments in Zimbabwe sampling 2 abiotic and 5 biotic stresses

15-20% yield increase under random stress in S&E Africa across all genotypes ever selected

Best genotypes: 100% yield increase under stress

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arie

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/ha)

Experimental Checks

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Variety 1 Variety 2

unstressed

Mean yield of the environment (t/ha)

Yie

ld o

f the

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iety

(t/h

a)

stressed

Effect of different breeding strategies

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Variety 1 Variety 2Variety 3Variety 4

unstressed

Mean yield of the environment (t/ha)

Yie

ld o

f the

var

iety

(t/h

a)

stressed

Effect of different breeding strategies

What about other crops? - Drip irrigation to stress wheat nurseries in NW Mexico

Sowing into dry soil: germinated with 40mm of

water

Stress is monitored and irrigation applied as required

Brazil Spain Algeria Bolivia

Pakistan

No sites

Saudi Arabia Argentina

South Africa Egypt

Canada

Zimbabwe Iran

Pakistan

Nepal Brazil Pakistan

Iran Canada

Gravity continuous

stress

Drip Terminal

stress

Gravity No

Stress

Drip Continuous

stress

Heat and terminal moisture

stress

Drip Moisture

stress pre-flowering

Iran Bangladesh Saudi Arabia

Spain Afghanistan

Stress generated in Mexico

International Sites

Group

Gravity terminal stress

1 2 3 4 5 6 7

No sites

Associations among managed stress environments, irrigation systems and international test sites (spring bread wheat)

Synthetic derivative

High yielding recurrent parent

Selection of synthetic wheat under managed drought stress

Synthetic wheat: AB+D (T. durum + T. tauschii)

Percentage of wheat synthetic derivative lines significantly higher yielding than the best locally adapted cultivars in dry

environments in Australia (19 sites) and Mexico (CIANO across 3 years)

01020304050607080

CIANO

AUS1

AUS2

AUS3

AUS4

AUS5

CIANO

AUS6

AUS7

AUS8

AUS9

AUS1

0AU

S11

AUS1

2AU

S13

CIANO

AUS1

4AU

S15

AUS1

6AU

S17

AUS1

8AU

S19

Per

cent

age

Number of derivatives tested = 156Source: Dreccer et al.

Raipur, 2003Raipur, 2002

Rainfed rice environments are highly variable across seasons

Selection for drought tolerance in rice

Selection for drought tolerance in rice

Average seasonal field water stress

1.0 1.5 2.0 2.5 3.0

Gra

in y

ield

(t h

a-1 )

0

1

2

3

4

5

Thailand 2003-04, Haefele et al.

Managed stress screening for rice

Variance component

Water regime Genotype Genotype x year

Error H

Full irrigation

Reproductive-stage drought

262,360

441,810

95,700

81,272

364,040

369,498

.74

.84

Variance components and broad sense heritability (H) within water regimes: IRRI dry season 2003/04

G x Y not greater in managed stress trials; H similar in stress and non-stress trials

Yield (kg/ha) of short-duration lines from the IRRI-India Drought Breeding Network: Raipur 2005

Designation Severe Stress

Moderate Stress

Control

DGI 75 2117 3648 4146

IR74371-78-1-1 1769 2927 4013

Lalmati (trad.) 1669 2049 2927

Ramjiyawan (trad.) 1542 2411 2411

IR 64 454 2679 3903

IR 36 227 1334 3729

LSD 510 790 846

Drought-selected lines DGI 75 and IR74371 out-yield IR64 and IR36 under stress and are more responsive than traditional varieties

Component EstimateVariance of QTL 28,120Residual genetic variance 29,890QTL x year 3,670Residual genetic variance x year 14,250Plot residuals 62,640H 0.70R2 0.34

Variance component analysis for drought yield QTL on chromosome 12 in Vandana/Way Rarem

In many tolerant x susceptible crosses, one or two QTLs appear to account for much of the variation in yield under stress or aerobic conditions

Drought yield QTL for Vandana/Way Rarem

A single QTL on chromosome 12 accounted for more than 50% of yield variation under severe upland stress over two years (Bernier et al., in press)

Allele more than doubles the mean yield under stress (from approximately 0.2 to 0.6 t ha-1)

Drought tolerant allele originates from the less tolerant parent, Way Rarem => epistasis

Conclusions

Selection using managed abiotic stress environments enables significant breeding progress in highly variable abiotic stress environments

These yield increases are greater than those currently reported for transgenic drought tolerance (100% vs 25%)

Some surprises - major gene effects in rice

Use of wide crosses in wheat

Methods and Genetics

Managed environment research site at Pioneer (Albertsen, 2006)

Rewriting the history of breeding for abiotic stress tolerance

Breeding: low heritability and genetic variance under abiotic stress, large GxE

1975 => “No point to breed under abiotic stress”+ Physiology: As many physiologists – as many suggestions what breeders should do

1985 => Little impact on applied stress breeding+ GxE analysis + IT + cross-disciplinary collaboration

1995 => Emerging (understanding of) impact on stress breeding+ Biotech + High throughput systems

2005 => Transgenic technologies=> Increasing progress from non-transgenic abiotic stress breeding

Abiotic stress breeding in 2015

It may all be about news coverage …“Drought resistant crops are on the way” (Pioneer and Monsanto, August 2005)“Farm News - Drought tolerant corn” (Oct 2005)“Monsanto develops drought tolerance” (Nov 2005)“2-Plants: BASF planning biotech potato and drought-tolerant corn”(April 2006)

… and investment

Time from discovery to client - transgenics: US$ 100 millionCIMMYT’s investment discovery to client (1 million ha) in southern Africa: US$ 3.5 million

The future

ConventionalPolygenic, some major gene

effects

(Progress 50 – >100 %)

TransgenicsSingle gene effects

(Progress 15 – 25%)

Wider application of managed stress environments by more breeders

Search for major gene effects, exploitation of epistasis

Use of molecular markers (example - common SNP platform for maize drought tolerance targeted at Africa)

For both approaches, GxG and GxE will remain important => investments in bioinformatics

+

Acknowledgements

Great number of colleagues at CIMMYT and IRRI, in NARS and the private seed sector in Africa, India, Australia and the US

Financial supporters: SDC, the Rockefeller Foundation, GRDC

Breeding maize, rice and wheat for highly variable abiotic stress environmentsQuestionMaize growing environments in AfricaGrain yield variability by countryBreeding for highly variable abiotic stress environments – The historyThe Abiotic Stress BreederGiven that few people want to fight wind mills …PerceptionsBut is it true ?Breeding progress under abiotic stress conditions in the USMore recent investments (Löffler et al., 2005)Breeding for individual abiotic stressesStress management for drought tolerance screening in maizeBreeding for individual abiotic stressesBreeding for individual abiotic stressesWhat changed?QuestionMega trait-based index selection by CIMMYT in southern AfricaAre we just fighting windmills?Evaluation of stress breeding approachPercentage yield increase of experimental hybrids (n=42) over checks (n=41)ConclusionBest genotypes: 100% yield increase under stressEffect of different breeding strategiesEffect of different breeding strategiesPercentage of wheat synthetic derivative lines significantly higher yielding than the best locally adapted cultivars in dry enSelection for drought tolerance in riceYield (kg/ha) of short-duration lines from the IRRI-India Drought Breeding Network: Raipur 2005Drought yield QTL for Vandana/Way RaremManaged environment research site at Pioneer (Albertsen, 2006)Rewriting the history of breeding for abiotic stress toleranceAbiotic stress breeding in 2015The futureAcknowledgements