Digital Agriculture
Alyssa Weirman,
Business Manager, High Resolution Plant Phenomics Centre
July 2013
• What is Plant Phenomics and the High Resolution Plant Phenomics Centre (HRPPC)?
– Why was the centre founded?
– Technology
– What research does the centre do? What is going on in modern plant science
• Plant Phenomics Teacher Resource
– How can you use it in the classroom?
• Introduction to the Battle of the Plants Competition
– Why use Brachypodium?
– Timing the experiment
– The growth pack and Brachypodium growth requirements
– Taking digital photos
– Analysis software
• The Battle of the Plants practical
2 |
What is Plant Phenomics?
Phenome = Genome X Environment
What is Plant Phenomics?
• A plant’s genotype is all of its genes.
• A plant’s phenotype is how it looks and performs:
– a plant’s phenotype is a combination of its genotype and the environment it
grows in
– plants with the same genotype can have different phenotypes.
• Phenotyping is analysing a plant’s phenotype.
• Phenomics is a way of speeding up phenotyping using high-tech imaging systems
and computing power.
4 |
What does plant phenomics involve?
• Phenomics borrows imaging techniques from medicine to allow researchers to
study the inner workings of leaves, roots or whole plants.
• Some phenomics techniques are:
5 |
3D imaging
infrared imaging
fluorescence imaging
spectral reflectance.
The Australian Plant Phenomics
The Plant Accelerator™
High Resolution Plant Phenomics Centre
Highly cross disciplinary bringing engineering, machine vision, robotics,
high performance computing and plant biology together
High Resolution Plant Phenomics Centre
• The Centre’s researchers
develop new ways to discover
the function of genes and to
screen plant varieties for useful
agricultural traits.
• Researchers can grow plants in
growth cabinets or in the field.
7 |
The Plant Accelerator
• A high-tech glasshouse contains plant conveyor systems, and imaging,
robotic and computing equipment.
8 |
High Throughput Plant Biology
Controlled environment growth
High Resolution High Throughput:
automated plant analysis
2000 plants per day
High Throughput Plant Biology
Field technology
An entire field per day
The Phenomobile in action
2000 plants per day
An integrated 3-D multi-sensing tool to analyse plant performance
Xavier Sirault CSIRO
Phenonet Sensor Network
• A network of data loggers
collects information from a
field of crops and sends it
through the mobile phone
network to researchers at the
• Sensors include:
12 |
far infrared thermometer
weather station
soil moisture sensor
thermistor (soil
• The Multicopter can take
infrared and colour images of
a field from just a few
centimetres above the
ground to a height of up to
100 metres.
13 |
Camera and images
Thermal images of Arabidopsis
14 |
RGB and Fluorescence images
of Brachypodium
Far Infrared Imaging
• Cooler plants have better root
systems and take up more water.
15 |
Spectral reflectance
• Spectral reflectance is the fraction of
light reflected by a non-transparent
Researchers can use spectral
reflectance to tell if a plant is
stressed by saline soil or drought,
well before it can be seen by eye.
A hyperspectral camera measures
all wavelengths of light that are
either reflected or absorbed by a
16 |
Research – Improving Crop Yields
• Yearly crop yield gains have slowed to the point
of stagnation.
• Population growth + lack of suitable land +
competition from biofuel crops + fertiliser costs
+ lack of water + climate change = potential
global food crisis.
• Phenomics projects:
– ‘Supercharging’ photosynthesis
– Improving wheat yield
– Brachypodium – the cereal ‘lab rat
17 |
‘Supercharging’ photosynthesis
• Plants have two major photosynthetic
mechanisms: C3 and C4. Phenomics
researchers want to replace the C3
pathway of rice with a more efficient C4
• C4 plants can concentrate carbon dioxide
inside the leaf, and photosynthesise
more efficiently than C3 plants,
especially under:
– higher temperatures
– drought conditions
– limited nitrogen supplies.
18 |
Brachypodium – the cereal ‘lab rat’
• Phenomics researchers are using a
small wild grass called Brachypodium
distachyon as a wheat ‘lab rat’.
• Its entire genome is known
• It has many genes in common with
• Researchers are studying root
formation in Brachypodium to speed
up understanding of wheat roots.
19 |
Research: crops to cope with climate change
• Climate change is predicted to make crop growing conditions tougher in
the future.
• Phenomics researchers are developing:
– drought-tolerant wheat
– salt-tolerant wheat and barley
– non-food biofuel crops
20 |
Plant Phenomics Teacher Resource
21 |
Why do we need more agricultural scientists
• By 2050, 9.1 billion people will populate the planet.
• We will need to produce 70 per cent more food to feed them, under tougher
climate conditions.
• This is one of humanity’s greatest challenges.
• How can we do it?
• Three of the possible ways to help:
– Improve crop yields
– Breed crops that can cope with climate change
– Develop biofuel crops that don’t compete with food crops.
22 |
Battle of the Plants
Registrations close 31st July
23 |
Why Brachypodium?
• Small
• Short lifecycle (6-8 weeks)
• Simple growth
• Model research plant
24 |
Battle of the plants - Timing
• Timing the experiment, choose any 8 week period during the
official competition period according to your class schedule.
• The official competition period:
24th June to 25th October 2013
25 |
Battle of the plants – The Growth Pack
• The Growth Pack contains:
Competition instructions
Image analysis instructions
• Brachypodium growth requirements
26 |
Growing medium
Sowing the seeds
Battle of the plants – Taking Digital Photos
• You will need to take a digital photo in the 5th and 8th week after
27 |
Battle of the plants – Analysis Software
• The image analysis software used in the competition can be
downloaded for free at
28 |
Any questions?
29 |
Thank you
30 |

Phytotron : A Journey from Physiology to Phenomics (via Genomics)