25% by 2025? Genetic technologies contributing to improved crop performance

CSIRO PLANT INDUSTRY

Greg Rebetzke

What are the pieces andhow efficiently assembled?

Productivity gains due to genetics of around 0.5% per annum for wheat

Selection for yield, quality and disease (potentially ‘000s of genes)

Two complementary approaches –

trait-based breeding (disease, adaptation and WUE) and

quantitative (‘numbers game’ - many lines and environments, and good knowledge of pedigrees)

Public to private –

Six breeding companies all of whom are linked to large multinational companies (as shareholders)

Genetic technology transfer from maize to wheat readily facilitated

Genetics ‘State of the nation?’ Wheat as an example

(Tony Fischer)

Drivers of yield progress? Improving adaptation

WA wheat cultivars

Thermal time (oC d) to floral initiation

400 500 600 700 800 900 1000

Gra

in y

ield

(kg

ha-1

)

800

1000

1200

1400

1600

1800 1978

1982 1960

19451946

1894

1979

1929

1915

1860

Adapted from Richards (1991)

Targeting drivers of performance under water-

limited conditions

100 200 300 400 500

0

1

2

3

4

Water use (mm)

Gra

in y

ield

(t/h

a)5

Potential22 kg grain/ha/mm

Beyondphysiological

limits

French and Schultz (1984)Sadras and Angus (2006)

District average

Agronomic innovations…..

Canola in the rotation

Wheat after Wheat Wheat after Canola

*** Reduce soil-borne diseases(take-all, crown rot, CCN, root-

lesion nematodes)

(Kirkegaard et al.)

Salt-tolerance genes

(James et al.)

Agronomy

Subsoil toxicities e.g. acid tolerance genes – malat e exudation

(Ryan et al.)

There is so much genetic diversity. What do we sele ct?

?

Maximising water use

Rainfall = Transpiration + Evaporation + Run-off + Drainage + [storage]

Aim: Capture, store and use as much of the rainfall as possible

Run-offEvaporation

Transpiration Rainfall

Drainage

Infiltration

Uptake

Maximising water use using agronomy

Fertilitytreatment

Yield(t/ha)

Water use(mm)

Evaporation(mm)

Transpiration(mm)

High63N, 20P

5.6 366 173 193

Low8N, 10P

2.8 363 259 104

(from David Hall, DAFWA)

Esperance 2001, 380 mm in-crop rainfall

Yield response in wheat to selection for greater early

vigour (BC2-derived sibs)

LAI @ 50 DAS

Final Biomass

(g.m -2)

Grain Yields

(g.m -2)

Harvest Index

Wongan Hills 1999 (453mm)

High Vigour 0.37 678 337 0.49

Low Vigour 0.32 573 293 0.49

* ** *** ns

Merredin 1999 (274 mm)

High Vigour 0.39 634 266 0.41

Low Vigour 0.30 574 247 0.43

** ** ** ns

(Botwright et al. 2002)

Must have the genetic variation! Importance of maintaining genetic resources

High vigour germplasm with greater leaf area

cv. Annuello Cycle 1 vigour selection

Cycle 4 vigour selection

0 0.05 0.1 0.15 0.2 0.25

37-6

38-19

50-4

28-14

70-22

119-4(2)

92-11(2)

Beecher

V18

Yitpi

CM18

Wyalkatchem

Annuello

Westonia

Janz

Root mass in tubes (g)

Early generation

Later generation

= Australian cvs= barley

= CSIRO recurrent selections

Cycle 1 Cycle 4

Other potential benefits….greater root growth

EGA Burke

Carazinho

Vigour 18

C4_[Vig 37-6]

C4_[Vig 119-4]

C4_[Vig 92-11]

C4_[Vig 38-19]

Gro

wth

res

pons

e in

P-li

miit

ng c

ondi

tons

(%

EG

A B

urke

)

0

20

40

60

80

100

120

140

160

180

Increased nutrient uptake/use-efficiency with greater

early growth – phosphorous and nitrogen

(R James et al.)

Shoot biomass (g)

0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6 1.8 2.0

N u

pta

ke (

mg

)

10

20

30

40

50

60

70

80

(J Palta et al.)

Wyalkatchem + vigourAxeAnnuello

+ vigour

Improved performance after dry sowing? Rapid root growth? (Bob French, MEF)

New semi-dwarf , high vigour lines in the field

YitpiYitpi + vigour

Mean grain yield(relative to comm. parents):

Without weeds-+ Up to 20%

With weeds-+ Up to 50%

(G. Gill Uni Adel.P. Newman DAFWA)

Need for quality phenotyping - controlled ‘managed’

environments (Managed Environment Facilities – ‘MEF’)

In Australia - three sites with two-three irrigation regimes

Climate characteristics of six locations in the Australian wheatbelt: mean monthly rainfall and temperature (data for 1889-2010)

ACT

NSW

NT

QLD

SA

TAS

VIC

WA

0 500 km

Rai

n (m

m)

0

50

100

Jan

Mar

May Ju

lS

ep

Nov

Dalby

10

20

30

Tem

p. (°C)

Rai

n (m

m)

0

50

100

Jan

Mar

May Ju

lS

ep

Nov

Geraldton

10

20

30

Tem

p. (°C)

Rai

n (m

m)

0

50

100

Jan

Mar

May Ju

lS

ep

Nov

Horsham

10

20

30

Tem

p. (°C)

Rai

n (m

m)

0

50

100

Jan

Mar

May Ju

lS

ep

Nov

Merredin

10

20

30

Tem

p. (°C)

Rai

n (m

m)

0

50

100

Jan

Mar

May Ju

lS

ep

Nov

Narrabri

10

20

30

Tem

p. (°C)

Rai

n (m

m)

0

50

100

Jan

Mar

May Ju

lS

ep

Nov

Yanco

10

20

30

Tem

p. (°C)

The Managed Environment Facility sites of Merredin,

Narrabri and Yanco are indicated(Karine Chenu QAFFI)

Phenomobile proximal sensing rig

Three LiDAR sensors

Head number (L) and fractional ground cover (R) with LiDAR

Above the clouds measuring canopy temperature

Airborne thermal mosaic – ready for analysisLegend [deg C]

~600 m

• Capture 3 images / second

• One pass of the field ~10 sec (3 passes required)

• Time to image entire field ~4 min

• Ideal: Simultaneous measurements at nearly a single point in time

Mean canopy temperature (ºC)

15.6 15.8 16.0 16.2 16.4 16.6 16.8 17.0 17.2

CID

(‰

)

19.5

20.0

20.5

21.0

21.5

22.0

22.5

Batavia

Halberd

CranbrookGlenlea

Westonia

Sunco

QG225

BaxterJanz

Quarrion

Chara

Tasman

Diamondbird

Kukri

CD87

EgretSunstate

y = 38.0 - 1.03x (r2 = 0.61, P<0.01)

Canopy temperature is correlated with

transpiration efficiency Surrogates for use in early generation selection

o = WW15-related crossbreds; ● = random crossbreds

The massive and complex wheat genome

WheatWheat

Human

Arabidopsis

Rice

Cotton

Barley

Huge

Polyploid

Repetitive

Which is the next Mace or Wyalkatchem? Looking for a needle in a haystack!

Genotyping Tools – Molecular markers

• Removes the potential for misclassification through phenotyping

• Used to enrich populations in early stages of a breeding cycle (with particular focus on difficult-or expensive-to-measure traits)

• Cost is reducing significantly by the day!

Moving from high -throughput to mega-throughput (Wheat seed DNA chipper)

Robotic wheat seed chipperRobotic wheat seed chipper

Chipped seedChipped seed

(Tress Walmsley Intergrain)

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Enhancing collaboration | ELP Team 3 | Page ‹#›

(Cavanagh et al.)

1 2 3 4 5 6 7

Genetic dissection of coleoptile length†

Integration of multi-population, multi-environment mapping

A B D

Group

(C/H = Cranbrook/Halberd, MAGIC = Baxter/Chara/Westonia/Yitpi)

Cranbrook/Halberd MAGIC (4-way)

† QTL common at two or soil temperatures

1 2 3 4 5 6 7

Genetic dissection of coleoptile length†

Integration of multi-population, multi-environment mapping

A B D

Group

(C/H = Cranbrook/Halberd, MAGIC = Baxter/Chara/Westonia/Yitpi)

Cranbrook/Halberd MAGIC (4-way)

† QTL common at two or soil temperatures

Yitpi +13mm Baxter +5mm

Baxter +6mmWestonia +6mm

Chara +7mmYitpi +6mm

Westonia +7mm

Ludhiana, India at 15cm sowing depth

Management and genotypes for early sowing

Long coleoptileAlternative dwarfing gene germplasm

Moisture-seeking tine

Identifying the synergies in coupling targeted bree ding with management?

(Courtesy James Hunt)

Management synergies and new genetics

Intervention Mean Yield (t/ha)

Additive effect Singular effect

No-till 1.84 1.84

Fallow weed control 2.80 2.37

Pea break crop 3.45 1.76

Sow early (from 25 April) 4.01 2.10

New genotype (long coleoptile) 4.54 1.45

Kirkegaard and Hunt (2010)

Baseline Scenario (Kerang, Victorian Mallee)

Continuous wheat, grazed fallow, burn/cultivate, sow after 25 May (1980s)

Mean yield = 1.6 t/ha

Yield progress in breeding US maize hybrids

(Donald Duvick)

Hybrid wheat? Potential to increase yield and rapidly integrate new genetic diversity

B73 (left) and Mo17 (right) produce the hybrid F1(centre) (source: Plant Science Inst Iowa St Univ)

Complementary gene action –- contribution to hybrid vigour- shorter time to commercial

release- new diversity readily

incorporated- IP protection

Issues –- development of heterotic gene

pools- cost of seed production- male-sterility systems

(apomixes?)

Genetic engineering

All other organisms

• unlimited genes

• precise expression

Interspecific hybridisation

Somatic fusion

Related plant species

Domestication

Hybridisation & selection

Induced mutation

Crop species

Solutions found by nature in

any species can inspire

improvements to crops

Global adoption of GM crops (2011)

Source: International Service for the Acquisition of Agribiotech Applications (2012)

Global adoption of GM crops (millions ha in 2011)

Source: International Service for the Acquisition of Agribiotech Applications (2012)

Evolving GM capabilities

1. Insert single gene (incl. unadapted sources)

2. Silence endogenous genes (RNAi)

3. Insert multiple genes (e.g. pathways)

4. Target gene to specific locations

5. Introduce gene groups (mini-chromosomes/

gene cassettes)

• Increasing crop productivity (yield potential)

• Bringing hybrid vigour to non-hybrid crops

• Pure-breeding hybrids (apomixis)

• Improving photosynthesis (C4 energy capture)

• Increasing input-use efficiency (water & nutrients)

• Improving stress tolerance (e.g. Al-tolerant barley)

“Step changes” through gene technology The First Wave – Input Traits

How and when will the biotechnology be deployed to 2050?

Maintaining/understanding genetic diversity will continue to deliver new traits for improving productivity in rainfed systems

Quality, robust phenotyping is becoming the weak link in the system (managed environments?)

Agronomic understanding is needed to provide direction in traits conferring adaptation over the next decades

Biotechnology via markers will increasingly deliver greater efficiency and lower costs in selection of simple and complex traits

GM winter cereals are coming but will likely focus on high return traits initially

Summary

CSIRO Plant IndustryGreg Rebetzke

t +61 2 6246 5153e Greg.Rebetzke@csiro.auw www.csiro.au/

CSIRO PLANT INDUSTRY

Thank you

Ian Longson, DAFWA and update organisers,and to those who contributed slides and ideas

• Promotes competition

• Promotes rapid uptake (and importantly feedback) on delivered pre-breeding outputs

• Provides access to new technologies from overseas private companies

� Access to new germplasm (disease, quality, yield etc.)

� Access to new methodologies (seed chipper, GS etc.) from research investment in wheat and other crops incl. maize

Benefits in commercialisation

Breeders have many objectives…

RustsCCNPrats

SeptoriaYLS

BoronAl

Grain conformationFlour yieldWater abs.

ProteinColour

Hardnessetc.

Agronomic type-Straw strengthFloweringEarly vigourEstablishmentMn, Zn efficiencyP uptake

Summary of wheat breeding objectives SA (Hollamby 2002)

Theme 1041

Global food security crisis‘in the next 50 years we will need to produce as much food as has been consumed over our entire human history’ (Megan Clark, 2009)

1 petacalorie = 4.2 x 1015 joules

Alternative uses – animal feed, biofueld etc.

Water-limited yield potential – the concept.

Grain Yield = [Water used] x [Transpiration Efficie ncy] x [Harvest Index]

Passioura (1977)

Amount of water (mm)transpired by the crop

Biomass producedper mm of water transpired (kg/mm)

Proportion of total biomassthat is harvestable grain

kg/ha = [mm] x [(kg/ha) /mm] x [kg/kg]

Breeders make genetic gain for complex traits

Year of release

1840 1860 1880 1900 1920 1940 1960 1980 2000

Gra

in y

ield

(t/h

a)

1.0

1.2

1.4

1.6

1.8

2.0

2.2

2.4

WA cultivars - mean of six experiments(Perry and D’Antuono 1989)

SA/WA cultivars – three locations(Sadras and Lawson 2011)

1950 1960 1970 1980 1990 2000 2010

Year of release