2016 Michigan Wheat Program What’s the Future of Wheat Research? March 9, 2016

Steve JoehlNAWG Research Director

Topics: Wheat Research Update

• Genetic Engineering Effort Summary - Wheat

• Wheat Genome Sequencing Update

• High Throughput Phenotyping Program – Department of Energy

• Major Pest Targets for Wheat

• Research Priorities for Wheat

If GMO’s were banned from the United States…….

Purdue University’s Professor of Agricultural Science Wally Tyner

• “We lose quite a bit,” said Tyner. “We’d have higher food costs around the world. We’d have more poverty. We’d have more pesticide use, and more harmful pesticides. And we’d have higher greenhouse gas emission so more contribution to global warming.”

• The research shows without GMOs, U.S. consumers would pay somewhere between $14 and $24 billion more per year for food

• Urge leaders in science and agriculture & farmers to push back against those attacking GMO crops.

• Study shows stopping GMO seeds would cut U.S. corn yields by more than 11 %. Soybean yields would fall by 5 percent.

• Farmers would have to convert about 250,000 acres of pasture/forest land into cropland in the U.S. and 3 million acres worldwide.

February 26, 2016

Biotechnology Traits in Wheat at Early Stage of Pipeline

advanced productDEVELOPMENT PRE-LAUNCH LAUNCHearly product

DEVELOPMENTproof of

CONCEPTDISCOVERY

MANY PROJECTS DO NOT MAKE IT TO LAUNCH

1-5 years 1-5 years 1-3years 1-3 years 1-3 years

Most traits are in “Discovery Stage”.

Investments in Biotech Wheat Research ContinuesUSDA Permits requested by

numerous research organizations

• Arcadia Biosciences (Limagrain)• Bayer CropScience• Biogemma (Limagrain)• Betaseed Inc• Donald Danforth Plant Science Center• Limagrain• Monsanto• Montana State University• Pioneer• Rutgers University• Southern Ill University, Carbondale• Syngenta• United States Department of Agriculture• University of Minnesota• University of Nebraska Lincoln• University of North Texas• Washington State University

Biotech wheat research across industry, academia and non-profit research laboratories is focused on solutions to grower challenges

05

1015202530354045

2009 2010 2011 2012 2013 2014 2015

USDA Release Permits for GM Wheat Trials

Herbicide Tolerance Yield Stress QualityFungal Resistance Insect Resistance Other

GE Crops with Non Regulated Status in US – as of 11/2015

Alfalfa – HT

Canola – HT, AP, PQ

Corn – HT, IR, AP, PQ

Cotton – HT, IR

Papaya – VR

Soybean – HT, IR, AP, PQ

Sugar Beet – HT

Rose – PQ

HT – herbicide tolerant

IR – Insect Resistant

VR – Virus Resistant

AP – Agronomic Properties

PQ – Product Quality

Squash – VR

Tobacco – PQ

Potato – IR, VR, PQ

oApple – PQ

oChicory – AP

oFlax – HT

oPlum – VR

oRice – HT

oTomato – PQ

Major Commercial Production

Minor Commercial Production

o No Commercial Production

USDA - BRS

Wheat Genome Sequencing

Understanding “The Bread Wheat Genome”

• Project of the International Wheat Genome Sequencing Consortium

• Five times larger than the human genome

– Three genomes combined into one

– Three sets of 7 chromosomes

– 110,000 to 150,000 genes

– 16 billion total base pairs of DNA — far more than other significant staple crops like rice and corn.

• Of the 3 main cereals (wheat, rice, corn) only wheat is without a complete sequence

• Recent announced breakthrough: Whole genome assembly discovered!

• “We have been waiting for a number of years to have a high quality whole genome sequence assembly that would complement our chromosome based strategy and accelerate the delivery of the sequence.” Kellye Eversole, Exec Director IWGSC

Goal• Lay a foundation to accelerate wheat improvement• Increase profitability throughout the industry

Vision

• High quality annotated genome sequence, comparable to rice genome sequence

• Physical map‐based, integrated and ordered sequence

www.wheatgenome.org

Understanding “The Bread Wheat Genome”International Wheat Genome Sequencing Consortium

IWGSC v1 by 2016, GoldStandard by 2017

High Through Put Phenotyping – Dept. Of Energy

Demand Doubles 2o C 9.9 GtC 70% H20 2300 GtC

Department of Energy Interest in AgricultureSustainable, Economical, Renewable Feedstocks

FOOD – FUEL – FEED - FIBER

Agriculture has the capacity and scale to contribute solutions. However, the industry is significantly behind its productivity pathway. Increased yield and sustainability can be achieved through breeding,

BUT- Breeding is slow and inefficient

- Investment in crop development is sub-optimal- Small stakeholders are disadvantaged from the development pipeline

Food Security

Energy Security

Climate Change

GHGEmissions

Water Availability

Soil Carbon

Environment Natural Resources

Global Context:Development

Food

Energy Climate Greenhouse Gas Fresh Water Soil Carbon

SelectThe major breeding objectives include high yield, composition quality, disease and insect resistance

and tolerance to abiotic stresses include moisture, heat and cold tolerance.

Harvest

Genetic Gain

Crop Improvement Process… 8-10 yearsPhenotyping is the Bottleneck for Trait Discovery and Variety Improvement

Crop Breeding CyclePhenotype = Genotype × Environment × Management

(P = G × E × M)Cultivar

Advanced

Parent Crossing

Field Evaluations

Manual - ExpensiveLow Throughput

Unreliable

PHENOTYPES

Phenotypes• Yield• Agronomic• Pest Resistance• Grain Quality

Seed Chipper

Genetic Markers

Automated - Economical High Throughput

Precise

GENOTYPESDNA tags keep track

of an individual

1

Non-destructive

20th Century Crop Phenotyping State of the Art

2

Cutting-Edge Plant ImagingData to quantify genotype by phenotype by environmental interactions

Cameras capture signal from visible and infrared spectrum of light.

• VIS cameras detect light in the visible range from∼400 to 700 nm to measure morphological, geometric, and color properties of plants .

• Infrared (IR) cameras detect near-infrared (NIR) light for night imaging.

• NIR cameras detect NIR and short-wave infrared (SWIR) light useful for detecting leaf water content.

• Thermal infrared (TIR) cameras detect long-wave infrared (LWIR) light that is emitted by leaves in a temperature-dependent intensity.

• Hyperspectral cameras detect hundreds of spectral bands with nm-level resolution between 350 and 2500 nm to detect plant stress.

• Specialized imaging systems measure chlorophyll fluorescence after excitation.

High-throughput plant phenotyping; Noah Fahlgren, Malia A Gehan, Ivan Baxter; Plant Biology Volume 24, April 2015, Pages 93–99

7

Improve and Accelerate Yield Gains by developingnew tools that improve accuracy of variety selection

8

Segment Height- Lidar returns

Jianfeng Zhou, Washington State

Mea

sure

men

tPr

oces

sed

Dat

a Line BLine A#

ofpl

ants

Plant height

Accession Height Lodging (%)

Line A 2.5 80Line B 2.25 20

9

Transportation Energy Resources from Renewable Agriculture (TERRA)Robotic Platforms are Diverse and Data Rich

National Robotics Engineering CenterMobile Deployable Field Gantry

Carnegie Mellon, UIUC, Purdue Mobile Ground Vehicles

Near Earth, Purdue, KSU, Blue River Mobile Aerial Vehicles

Danforth Center, USDA, Lemna TecStationary Reference Field Gantry

Reference Field Gantry (20 x 200 m)

Sensor Hood

PerformanceComparison

Current Breeding

Manual

TERRAGround &

Aerial Vehicles

# Breeder Plots 1,000 1,000

# Phenotypes 10’s 1000’s

Resolution 1 m 1 cm

Bandwidth (nm) 400-700 100-2500

Data Collection Bytes Terabytes

Cycle Time Days Min - UAVHrs - AGV

Reference Field Gantry Sensors:•Hyperspectral i350-2500 nm • Height Scanner•Thermal infrared • 8 MP RGB down camera•Dedicated NDVI sensor • 2 side looking cameras•Dedicated PRI • Active reflectance in-field(photochemical reflectance) • Fluorescence

•PAR sensor • Environmental temperature,•Color sensor humidity, rainfall, wind, CO2

http://cals-mac.arizona.edu/precision-agriculture

AG’sHubble

RGB Image Head Blight Index (~670λ-560λ)

Red – diseased Green – Healthy

Platforms Can Be Scaled Across Crops

• Unit cost of UAV’s enables wide deployment.

• Optimized sensor package learned from TERRA higher resolution gantry.

• Potential to screen breeding populations for disease resistance or nutrient stress over wide number of accessions and geographies

11**Baurigel et al, Computers and Electronics in Agriculture 75(2):304

Deployable and EconomicalHyperspectral imaging distinguishes Fusarium infected ears**

(whe

atex

ampl

e)

12TERRA Performer Portfolio(6 Integrated Systems Teams: Plant Biology, Robotic Sensors, Computer Science)

PUBLIC REFERENCE DATA TEAM FULL SYSTEM TEAMS

College of Agriculture and Life Sciences

COLLEGE OF AGRICULTURE, COLLEGE OF BIOLOGICAL ENGINEERING,

COLLEGE OF AERONAUTICS

Australia Plant Phenomics: Commonwealth Scientific and Industrial Research Organization

“COMPONENT” FOCUS SYSTEMS TEAMS

ROOT × SOIL × ENVIRONMENT(SOIL RESOURCE OPTIMIZATION)

OBJECTIVES:1. CARBON ASSIMILATION (CO2 EMISSIONS MITIGATION – SOM DEPOSITION)

2. NUTRIENT ACQUISITION (N2O EMISSIONS REDUCTION – FERTILIZER EFFICIENCY)

3. WATER PRODUCTIVITY (RESOURCE EFFICIENCY)

UPCOMING 2016 ARPA-E PROGRAMTERRESTRIAL GHG BIOSEQUESTRATION

VISION: REDUCE NET GHG BY INCREASING SOILORGANIC CARBON AND REDUCING N2O EMISSIONS

BY CREATING A MULTIDISCIPLINARY SENSING, COMPUTATIONAL, AND ANALYTIC TOOLKIT TO:• SCREEN ROOT PHENOTYPES;• BREED ROOT IDEOTYPES; AND• SELECT IMPROVED CROP CULTIVARS

(DESIGN, BUILD, AND TEST)

Improved Tolerance To Pests Would Improve Yields

Important Wheat Pests

• Weeds• Resistant species increasing

• Fungi– Fusarium Head Blight (SCAB)– Rusts

• Insects– Wheat stem sawfly– Hessian fly– Aphids

• Viruses– Barley yellow dwarf virus– Wheat streak mosaic virus

Wheat Stem Sawfly

Stripe (Yellow) Rust

List of Research Priorities to Achieve Yield Improvement

1. Genome Sequence Completed

– Increased gene marker development will follow to identify genes of interest

2. More genotyping capacity to analyze genes of interest in progeny of a cross

– USDA Quality Labs need investment upgrade

3. More breeding crosses

– Crosses per breeder, more breeders

4. Development of selection technology

– Screen lines faster, sooner

– Reduces costly plots & weather variability associated with them

Industry Goal is 1.5-2.0% genetic gain for wheat

Global Population Growth & Estimates

World Population Milestones (US Census Bureau estimates)

Population (B) 1 2 3 4 5 6 7 8 9Year 1804 1927 1960 1974 1987 1999 2012 2027 2046

Years Elapsed --- 123 33 14 13 12 13 15 19

Steve arrives to the party

Steve gets out of college

Doubles2 boys enter

college. TriplesSteve turns 93

Steve’s Family Expands by 2

Reese turns 32

Thank you!

The Weed Resistance challenge worldwide Considered the single biggest threat to agriculture

• The total losses to weeds worldwide are estimated at 13.2% of agricultural production, worth more than $61.3 billion a year

• Without herbicides

– 1/3 of yields would be lost

• As of August, 2015

– 459 unique cases of herbicide resistant weeds globally

Our role is to create conversation and raise awareness of the need for new innovation & technology

The Basics of Resistance

• Resistant individuals are naturally present in the weed population (at very low frequency)

• Application of herbicide “selects” for these naturally resistant individuals

• Resistant individuals pass resistance to offspring

• Over time, continued application of herbicide increases the frequency of resistant individuals in the population

Forecasting Glyphosate Resistant Weeds in the U.S.

0

10

20

30

40

50

60

70

2000 2002 2004 2006 2008 2010 2012 2014 2016 2018 2020

Infested ha (millions)

Infested ha (millions)

• The rate of resistance spread continues to increase.• By 2020, almost ALL U.S. Row Crop acres will be infested with glyphosate

resistant weeds (66.7 m ha)

Number of Herbicide Resistant Weeds By Crop (Top 10) Worldwide

71

61

51

47

32 31

29

27

21

18

NUMBER OF RESISTANT SPECIES

HT = HERBICIDE TOLERANT CROPWheat Corn Rice Soybean Winter Wheat Roadsides Barley Orchards Canola Cotton

HT

HT

HTHT

2015 Weedscience.org – Dr. Ian Heap 4/2015

Summary

• Sole reliance on herbicides (or any practice) will eventually lead to

resistance

• The only way to sustain the efficacy of herbicides is to:

– Limit herbicides to smallest number of applications as possible

– Apply herbicides to smallest number of weeds as possible

– Use herbicides in mixture whenever possible

• Nonchemical weed management techniques can reduce the abundance of weeds and reduce the number of herbicide applications that are necessary

• Integrating nonchemical weed management techniques is the only way to sustain the efficacy of herbicides

……..but there is light ahead!

The Law of Competitive Balance

There exists in the world a negative momentum, which acts constantly to reduce the differences between strong teams and weak teams, teams which are ahead and teams which are behind, or good players and poor players. “Moneyball”, by Michael Lewis

The corollaries are:

• Every form of strength covers one weakness and creates another, and therefore every form of strength is also a form of weakness and every weakness a strength.

• The balance of strategies always favors the team which is behind

• Psychology tends to pull the winners down and push the losers upwards

Renewed Interest in Wheat Research

• Public and Private• International Wheat Yield Partnership (IWYP)

• Aims to lift wheat yield 50% over 20 years

• Australia announced Dec 8, eight new wheat projects

• USDA commits $3.4 M through NIFA toward IWYP (Dec 14th)

• United Soybean Board• Double Crop Initiative

• Unified recognition wheat needs yield growth at 1.7%/year

• To satisfy demand from population growth

• Current genetic gain - .5%/year

• Gene editing shows promise

• Private Investment Increases

– Arcadia (biotech)

– Bayer (breeding) (biotech) (hybrids)

– Dupont (breeding) (hybrids)

– KWS (breeding)

– Limagrain (breeding) (biotech)

– Monsanto (breeding) (biotech)

– Syngenta (breeding) (hybrids)

2014/2015 U.S. Wheat Planted AcresBy Class

Hard Red Spring

Hard Red Winter

Soft & HardWhite

Soft Red Winter Durum

30.3 M 1.4 M8.4 M11.9 M 4.5 M

56.5M Acres in U.S.

Source: ERS.USDA.GOV

Weed Resistance: Considered the Single Biggest Threat to Agriculture

• The total losses to weeds worldwide are estimated at 13.2% of agricultural production, worth more than $61.3 billion a year

• Without herbicides

– 1/3 of yields would be lost

• As of August, 2015

– 459 unique cases of herbicide resistant weeds globally

Our role is to create conversation and raise awareness of the need for new innovation & technology