Adapting Crops to Climate

Change
Patrick S. Schnable

National Press Foundation

Kansas City
25 September 2018

PSS has IP and equity interests in Data2Bio, Dryland Genetics, DecisionPx & EnGeniousAg
 Some Terminology
• Model Species: A species with attributes that make
it particularly suitable for scientific investigations.
• Maize: the most important model species that is
also a crop
• Corn: the most important global crop which also
happens to be a model species

Mazola TV commercial from the 1970s 2

 Agricultural Successes and
Challenges
$2B/yr

• Increasing demands for food, feed, fiber and fuel;

decreasing amount of arable land
• Agricultural inputs: increasing costs (e.g., nitrogen),
reduced availability (e.g., water), and undesirable
ecological impacts
• Achieving yield stability challenging due to climate
change: droughts/floods, temperature extremes, and
 Yield Trends by Species

Why is rate of yield increase for maize higher than for wheat and
soybean?
• Biological differences (cross-pollinated vs. self-pollinated?
C4? Genetic diversity?); if so, how to explain rice?
• Greater R&D investment? (driven by ability to capture
investment via sales of hybrid seed) 4
Heterosis (Hybrid Vigor)

Genotypes: B73, F1, Mo17

 Harry Stine

Plant Breeding 101

• Plants vary in their appearance (traits/phenotypes)
• Some of the differences in traits/phenotypes
among plants are the consequence of DNA
differences among these plants
• During sexual reproduction genetic material
derived from parents is shuffled
• Consequently, intercrossing plants with desirable
Cycles Evaluate traits/phenotypes is likely to produce progeny with
Progeny
superior performance
• During traditional breeding phenotypes are used
to select parents from among progeny produced
Select
Intercross Best
via sexual reproduction
Lines
Methods to Increase Genetic Gain
per Year
• Faster breeding cycle (drive
faster)
– Winter nurseries (multiple
generations per year)
– Doubled haploid (DH)
technology
– Genomic Selection (GS)
• enables identification of superior
parents without waiting for
phenotypic evaluation
tGBS®

8
 A Single Illumina HiSeq 2000
Paired-End LaneHP LaserJet P4015
Illumina HiSeq 2000 Letter Size Paper Black & White Printer
Paired-End Lane: Letter Size Paper: Printer:
180 x 106 Reads 1” margins ~50 pages/min
2 x 100 bp reads 12 pt font size (single sided)
36 x 109 bp Times New Roman

11 inches
8 days ~2,500 character Cartridge:
(UPPERCASE) ~24,000 pages

36GB
data
Sequencing Cost 8.5 inches
<$3,000

How much paper is needed to print data from 1 paired-end lane of HiSeq?

1 ream = 500 pages 1 case = 10 reams

Or Or And

36x 109 bp / 2.5 x 103 = 14.4 x 106 pages 14.4 x 106 / 500 = 28,800 reams 28,8000 / 10 = 2,880 cases (12” x 10” x 18”) 1 printer + 600 cartridges + 200 days
A pile of cases 12 ft x 12 ft x 12ft (x2)
Supply Cost:

2,880 cases @ $40/each + 600 cartridges @ $300/each = ~$300,000 http://www.data2bio.com

 Genomic Selection (GS)

Genotype &
Evaluate with
GS Model

Intercross/ Select Best

Recombine Lines

How much milk will his

daughters produce?
• GS uses thousands of genetic (DNA sequence) markers to
more quickly and more accurately identify superior
individuals to inform breeding decisions, even though
these individuals have not themselves been phenotyped,
thereby resulting in more genetic gain per year.
 #1: Engineering Haploid Induction to Speed Up
Breeding Cycle and Increase Rate of Genetic Gain

Evaluate
Progeny

Intercross/ Select Best

Recombine Lines

11
#2: Genome Editing: Targeted Editing of
the Genetic Code

12
#3: Increasing Efficiency & Speed of Transformation
(meanwhile its reducing genotype dependency)

13
Consolidation in the Seed/Breeding
Industry

More Recently:

• China Chem
purchased
Syngenta
• DuPont & Dow
merged ->Corteva
• Bayer purchased
Monsanto

14
 Overcoming Challenges in Crop
$32M
Production
B73 Reference Genome NGS data in NCBI SRA (Oct 2016)

40
35
Tera (1012) Bases
SAM Parents Resequencing

30
Maize Pan-genome and

25
Pan-transcriptome

20
Maize HapMap2
CAU Resequencing

15
ISU Zeanome (RNA-Seq)

10
Maize
HapMap CAAS Resequencing

5
Ames Diversity Panel
IBM RILs RNA-Seq

0
2009 2010 2011 2012 2013 2014 2015 2016

15
Schnable, Ware et al, Science, 2009
 The Promise
of Predictive Statistical Models
Given sufficient genotyping, phenotyping and
environmental data we can use the approaches of Big
Data to develop statistical models that enable the
prediction of traits/phenotypes based on genotypes and
environmental data
. Phenotype (P) = Genotype (G) + Environment (E)* + GxE

*Includes crop management

 Predictive Models Will:
• Improve accuracy of selection in plant breeding programs,
thereby increasing rate of genetic gain per year
• Enhance our ability to efficiently breed crops to withstand
the increased weather variability associated with global
climate change
• Improve our ability to provide farmers with evidence-based
recommendations for the appropriate varieties to plant in a
given field, under a particular management practice in a
given year, leading to increased yields and enhanced yield
stability
• Enable daily national and global yield predictions, thereby
facilitating early responses to food emergencies and
avoiding market failures

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 What’s Required?

• Data (phenotypes, genotypes and

environment/management practices)
• New phenotyping technologies (e.g., sensors, robots
and UAVs)
• New methods of data analysis
• An enhanced understanding of how diverse factors
(genotype, environment, and GxE interactions)
influence phenotype
9/26/18 18
 Weather Varies from Location to Location within
a Year and from Year to Year at the same location
U .S . D r o u g h t M o n ito r O c to b e r 1 , 2 0 1 3
(R e l e a s e d T h u r s d a y , O c t . 3 , 2 0 1 3 )
V a lid 7 a .m . E D T

SL
S

S
L S
L
SL S S

SL S
L
D ro u g h t Im p a c t T y p e s :
L SL SL D e lin e a t e s d o m in a n t im p a c ts
S = S h o r t- T e r m , ty p ic a lly le s s th a n
L 6 m o n th s ( e .g . a g r ic u lt u r e , g r a s s la n d s )
L = L o n g - T e r m , ty p ic a lly g r e a te r t h a n
6 m o n th s ( e .g . h y d r o lo g y , e c o lo g y )
L I n t e n s i ty :
A u th o r : D 0 A b n o r m a lly D r y
D a v id M i s k u s D 1 M o d e ra te D r o u g h t
N O A A /N W S /N C E P /C P C D 2 S e v e re D ro u g h t
D 3 E x tre m e D ro u g h t
D 4 E x c e p t io n a l D r o u g h t

T h e D r o u g h t M o n it o r f o c u s e s o n b r o a d -
S S s c a le c o n d i tio n s . L o c a l c o n d it io n s m a y
L v a r y . S e e a c c o m p a n y i n g te x t s u m m a r y f o r
S S
L SL
f o r e c a s t s ta te m e n t s .

S S S
SL SL
SL L
L SL
h t t p : / / d r o u g h t m o n i t o r .u n l .e d u /
L
L
L
SL

SL
S L

Phenotype (P) = Genotype (G) + Environment (E)* + GxE

 Genomes to Fields Initiative:
Multi-State G X E Project
Executive Committee:
• Pat Schnable (Iowa State Univ), co-
lead
• Natalia DeLeon (Univ of WI), co-
lead
• Ed Buckler (USDA/Cornell),
• Shawn Kaeppler (Univ of WI)
• Jonathan Lynch (Penn State Univ)
• Nathan Springer (Univ of MN)
• David Ertl, Iowa Corn Growers’
Association
 Value of New Tools

"If you really want to change a discipline, invent some new

technology that will let you go beyond what people have
seen before,” the late William J. Dreyer (Caltech), as quoted
by Lee Hood

“Science is informed by what it is possible to measure, and it

takes a great leap forward when we can measure something
new” -Isaac Kohane, Harvard Medical School, Nature (2015)

21
 Automated Phenotyping Systems:
(some) Design Considerations

• Would like to phenotype plants at multiple time

points, allowing us to study not only on end-
point traits (such as yield) but also on dynamic
traits such as rates of development and plant
responses to the environment
• Must be able to phenotype entries in multiple
environments (E and GxE)
• For maize, much of the exciting action is only
visible from the side
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High-Throughput Field-Based Phenotyping
Systems
– Field-based systems
with large fixed sensor
infrastructure, e.g.,
gantry or rail systems
– Sensors mounted on
field-deployed
robots/UAVs
– Inexpensive, stationary
field-based sensors

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 HTP Time-Lapse
Photography

James Schnable Srikant

Univ of NE Srinivasan
Why We Want to Phenotype Over Time:
Dynamic Responses to Drought
26
2016-2017

Colton
McNinch Stefan Hey

Yield Trials
Irrigated

Camera Yield Trials

Non-Irrigated Non-Irrigated

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28
700,000
Per Mo 5.6Tb
Per Mo
 Identifying Features in
Image Data via Using AI
and HTP Computing
Baskar Ganapathysubramanian

30
 Amazon Turking Plant Height
Dan
Baskar
Nettleton
Ganapathysubramanian

Baseline: line
connecting where
plants grow out of the
soil (yellow)

Red: Look for the

highest point of a plants
and draw a line, parallel
to the stalk down to the
baseline
Zhou et al., (2018) Crowdsourcing Image Analysis for Plant Phenomics to Generate
Ground Truth Data for Machine Learning. PLOS Computational Biology, in press 31
 Seeking a Proxy Trait for Drought Tolerance

Growth rates vary: Blue and Orange Genotypes

• among genotypes within a location at two locations:
• between locations within a given
genotype
• Evidence for GxE for growth rate
 CREAMED COFEE*:
Turbocharged “Shovelomics”

Lisa Coffey

*Core Root Excavation using Compressed-air

& Core Root Feature Extraction 33
Substantial Variation for Root Architecture
(N=380 inbreds)

Zihao Zheng
( 郑子豪 )
Root
Angle

Shallow Steep
Huyu Liu
( 刘祜宇 ) Root
CAU
Volume

Yu Yang Small Large

( 杨宇 )
CAU
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 Plant “Tattoos”: Detecting RH at
leaf surface

Liang Dong
 N Application is a Goldilocks Problem
• Under application -> yield losses
• Over application -> wasted input costs & environmental impact

Optimum N Input
• Nitrogen is 2nd most expensive input for rain
fed corn (after seed)
• Selecting appropriate N application rates is
complicated by substantial year-to-year
variation in N production from soil organic
matter and field losses of N
• Predicting the optimal level of Nitrogen is
currently difficult to impossible
• 35% of fields exhibit NO response to N
• $1.67B of wasted N fertilizer per year
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 In Planta Nitrate Sensors

Plant sensor

Liang Dong Mike

Castellano

0
2000
60
600 120
180

Sensor Measurement
240
500 300

ppm nitrate-N
400

300

200

100

0
0 100 200 300 400 500 600 2000

Conventional Measurement
ppm nitrate-N
Faster, smarter breeding
of naturally water
efficient crops

James Schnable
co-founder
Problem 1: Long-term increase in
global demand for grain

Population Meat Ethanol

39
Problem 2: Exponential Investments in Breeding Major Crops
Produce only Linear Yield Increases

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 Problem 3: Water is limiting factor
in agricultural production

Competition for Water (Irrigated Corn) Competition for Water (Rain fed Corn)

• In many areas total available water is fully committed

• Cities are competing with agriculture for water
• No surplus capacity to expand corn production into new acres
• Potential for major failures in years with below average rainfall
• Aquifers are being depleted

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 Dryland Genetics
is developing improved varieties of Proso
millet

42
 DLG’s Breeding Strategy: Incorporate
Global Genetic Diversity into US Germplasm

Evaluate
Progeny

Select
Intercross Best
Lines

43
Examples of DLG’s New Varieties from 2018
Yield Trials
 Impact

• Goal is 20+% yield increase

• Longer-term, we anticipate that improved (higher
yielding) varieties will encourage increased
planting of Prosa
TurboCharging Global GeneBanks

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