Digital Agriculture Alyssa Weirman, Business Manager, High Resolution Plant Phenomics Centre July 2013.

Digital Agriculture

Alyssa Weirman,Business Manager, High Resolution Plant Phenomics CentreJuly 2013

Introduction

• 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

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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.

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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:– 3D imaging– infrared imaging – fluorescence imaging– spectral reflectance.

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The Australian Plant Phenomics Facility

The Plant Accelerator™ Adelaide

High Resolution Plant Phenomics CentreCanberra

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.

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The Plant Accelerator

• A high-tech glasshouse contains plant conveyor systems, and imaging, robotic and computing equipment.

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Controlled environment growth cabinets

High Resolution High Throughput: automated plant analysis

2000 plants per day

High Throughput Plant Biology

Field technology The Phenomobile in action

2000 plants per day

High Throughput Plant Biology

An entire field per day

An integrated 3-D multi-sensing tool to analyse plant performance

PlantScan

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 lab.

• Sensors include: – far infrared thermometer– weather station– soil moisture sensor– thermistor (soil

temperature)

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Multicopter

• 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.

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Camera and images

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Thermal images of Arabidopsis RGB and Fluorescence images of Brachypodium

Far Infrared Imaging

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• Cooler plants have better root systems and take up more water.

Spectral reflectance

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• Spectral reflectance is the fraction of light reflected by a non-transparent surface.

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 plant.

Research – Improving Crop Yields

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• 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

‘Supercharging’ photosynthesis

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• Plants have two major photosynthetic mechanisms: C3 and C4. Phenomics researchers want to replace the C3 pathway of rice with a more efficient C4 mechanism.

• 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.

Brachypodium – the cereal ‘lab rat’

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• 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

wheat. • Researchers are studying root

formation in Brachypodium to speed up understanding of wheat roots.

Research: crops to cope with climate change

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• 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

Plant Phenomics Teacher Resource

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Why do we need more agricultural scientists

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• 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.

Battle of the Plants

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Registrations close 31st July

Why Brachypodium?

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• Small• Short lifecycle (6-8 weeks)• Simple growth

requirements• Model research plant

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

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Battle of the plants – The Growth Pack

• The Growth Pack contains:– Seeds– Pots– Competition instructions– Image analysis instructions

• Brachypodium growth requirements– Growing medium– Sowing the seeds– Water– Light

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Battle of the plants – Taking Digital Photos

• You will need to take a digital photo in the 5th and 8th week after sowing.

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Battle of the plants – Analysis Software

• The image analysis software used in the competition can be downloaded for free at http://rsbweb.nih.gov/ij/download.html

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Any questions?

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Thank you

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