Grains Research and Development

Date: 29.08.2016

National genebank a regional R&D powerhouse

Author: Dr Gio Braidotti

Key points

  • The way grain germplasm is exploited to sustain agricultural productivity in Australia was rationalised in 2014 with the establishment of the Australian Grains Genebank at the Grains Innovation Park in Horsham, Victoria
  • Ongoing investment now allows rapid screening of germplasm for valuable traits using automated high-throughput technology in the recently opened Plant Phenomics Victoria facility
  • The Horsham site also houses the Victorian Government’s Plant Breeding Centre, along with private breeding companies 

The decision to nationalise Australia’s grain genetic resources is paying off as the site chosen for the Australian Grains Genebank becomes a regional innovation hub with world-class capability

Photo of wheat varieties at the Australian Grains Genebank

Wheat varieties at the Australian Grains Genebank.

PHOTO: Tom Bicknell

Each year, the Global Genebank Partnership meets to decide crop conservation strategies globally and advance the use of conserved genetic diversity to drive gains in crop yield and resilience. In 2015, the Annual Genebank Meeting was hosted by the Aegean Agricultural Research Institute in Izmir, Turkey.

This year, in November, it will be hosted by the Grains Innovation Park in Horsham, Victoria. That the world’s genebank curators – including those from centres comprising the Consultative Group on International Agricultural Research (CGIAR) – are gathering at Horsham marks the rise of this regional R&D precinct first to national and, now, to international prominence.

The innovation park’s rise did not occur by accident, but rather reflects strategic consolidation of Australian R&D capability to better address pressing challenges facing the grains industry here. This included substantial investment by the GRDC and the Victorian Department of Economic Development, Jobs, Transport and Resources (DEDJTR; formerly the Victorian Department of Primary Industries).

The consolidation strategy is typified by the $6-million Australian Grains Genebank (AGG) facility, which is managed by Dr Sally Norton. Opened in 2014, the AGG now holds the nation’s grains genetic resources, organises missions to collect outstanding genetic diversity – especially indigenous wild crop relatives – and conducts research to make it easier for breeders to use novel genetic traits conserved in the collection.

The creation of the Australian genebank consolidated formerly fragmented seed collections at several underfunded state facilities into a centralised, modernised and securely funded facility for the first time in Australian history.

Dr Norton says Horsham was an excellent choice for the national grain collection. The facility is adjacent to the research infrastructure that will be needed to optimise trait discovery, to rapidly incorporate new traits into breeding programs and deliver new varieties alongside best-practice agronomy packages.

Targeted in this trait-discovery pipeline are important traits, such as water and nitrogen use efficiency, frost and cold tolerance, and disease resistance.

The opening in 2016 of the $7-million Plant Phenomics Victoria centre at Horsham, headed by Dr Surya Kant, is now set to further accelerate trait discovery rates. This new centre makes it possible to apply advanced imaging technology to compare the growth response to various stresses within genetically diverse grain populations, both in field trials and in an automated glasshouse. Promising genetic material can then be tested at the DEDJTR Plant Breeding Centre Farm.

Commercial breeding companies at Horsham include NuSeed and Cargill. The growing importance of Horsham as a research and breeding facility was further highlighted when Bayer CropScience located its new $14 million wheat and oilseed breeding centre adjacent to the AGG. The precinct also hosts one of Australia’s largest plant pathology regional groups and world-leading research into grain quality, alongside research into soils, agronomy and climate variability.

An adjacent field trials site allows wheat, barley and pulse varieties developed by international breeding programs and imported into Australia by the GRDC-funded CIMMYT-Australia-ICARDA Germplasm Evaluation (CAIGE) project to be tested under local conditions.

The trial sites also include state-of-the-art irrigation systems. This integrated capability means that the genebank possesses a complete grain R&D pipeline that encompasses not just trait discovery and the development of higher-performing varieties and agronomy practices, but also more efficient farming systems that can mitigate for climate change and foster higher profit potential from better grain quality.

The Australian Grain Genebank

Photo of Dr Sally Norton

Dr Sally Norton examines plant material at the Australian Grains Genebank.

PHOTO: Tom Bicknell

The AGG’s creation has, for the first time, allowed the consolidation of Australian grain genetic resources. The facility contains more than 2.7 kilometres of shelf space able to hold 200,000 packets of seed and more than 2000 different crop species. These are stored at minus 20ºC.

Currently the collection holds 124,000 different seeds (or accessions) covering temperate pulses and oilseeds, the winter cereals (wheat, barley, oats), and tropical crops (including oilseeds such as sunflower and soybeans, legumes, and cereals such as sorghum and maize). The collection is growing at a rate of about 3000 accessions a year and each year it distributes about 25,000 packets of seed to researchers and breeders in Australia and overseas.

The genebank employs nine staff at Horsham and one in Queensland, who is needed to regenerate seed of the tropical crops that do not grow well at Horsham.

Dr Norton, who heads the team, says the genebank is much more than a passive conservation project. There are several streams of genebank-related activities based around collection missions, evaluating conserved material, extending its usability to researchers and breeders, and finally ensuring that a new generation has the opportunity to acquire the many skills required to become curators.

“We also work with the international community to ensure information about Australian genetic resources is uploaded into the international database, Genesys PGR,” she says.

There are several collection missions underway to secure important native relatives to agricultural crops, including wheat and rice. Dr Norton says that Australia has been identified by a global gap analysis as one of the highest priority sites in the world where continued conservation of wild crop relatives is needed. There are collection agreements in place with 15 countries, including Australia, to close these gaps.

“Australia has a large number of native crop relatives, particularly for the tropical crops that are genetically quite closely related to cultivated plants,” Dr Norton says. “We have a good collection of some of the cereals and legumes from around northern Australia at the genebank already and we have an active program to expand that collection. We are also looking at the more distantly related temperate crop species such as indigenous wild wheat relatives.”

Real-world bridge

A focus moving forward is to acquire the kind of information on the conserved material that allows it to find many more real-world applications.

Dr Norton says today’s technology makes it easier to mass-screen germplasm and obtain useful information, particularly about agriculturally important genes and measurable plant traits (or phenotypes). The inclusion of native wild relatives in this program means that commercial grain varieties may one day acquire the survival skills of indigenous species.

“The first two years of the genebank’s operation were about consolidating and amalgamating the genebank and its computer system,” Dr Norton says. “This year we are using the high-throughput, robotic phenotyping capability at Plant Phenomics Victoria to look at parts of the collection for various traits of interests to breeders.”

This marks a transition of data evaluation processes to the needs of today, aligning to the needs of researchers and breeders.

“We want to change the genebank’s usage baseline by providing more relevant information framed in today’s technologies, be it genomics or phenomics,” Dr Norton says.

For trait discovery work, this can include compiling ‘best bet’ material likely to contain the looked-for traits sought by breeders based on agro-climatic conditions at the collection site.

“Plant Phenomics Victoria is going to be excellent for critical evaluation of samples and (will) help us quantify differences within the plants grown under stressed conditions in the field,” she says. “The automated imaging platforms mean we can obtain a lot of reliable, quantified data, quickly.”

Plant Phenomics Victoria

Photo of Dr Surya Kant at Plant Phenomics Victoria

Dr Surya Kant at Plant Phenomics Victoria.

PHOTO: Tom Bicknell

The ability to observe and measure differences in physiology, growth, morphology and resilience within a population of plants is called ‘phenotyping’.

Historically, phenotyping has been the most important yet challenging aspect of breeding. It typically required harvesting and manually dissecting the plants before making measurements, running biochemical tests or visually rating plant characteristics.

Phenomics is the technology platform that makes high-throughput, automated and reliable characterisation of living plants possible, allowing hundreds of plants to be rapidly phenotyped to identify lines with enhanced capabilities in desirable traits.

The new Plant Phenomics Victoria facility in Horsham allows plants to be phenotyped both within the controlled environment of an automated glasshouse and in field sites equipped with automated rainout shelters and phenotyping instruments.

“The differences we are particularly targeting are in traits such as nitrogen use efficiency, water use efficiency, frost tolerance, cold tolerance, disease resistance and boron tolerance,” Dr Kant says.

“The new phenomics facility lets us quantify differences between plants in these traits far more stringently.”

At the heart of phenomics are cameras and sensors that produce data in the form of digital images across visible, near infrared and far infrared ranges of the spectrum.

Analysis of these images has been carefully correlated to provide information about plant height, biomass, leaf number, chlorophyll content, nitrogen content, maturity and some biochemical parameters, such as carbohydrate, anthocyanin, protein and moisture content.

Since the plants are scanned rather than harvested to make the measurements, changes in these properties over time – and in relation to constraints in growth conditions, such as water stress – can be rapidly assessed.

“The overall aim is to use this data to more efficiently increase yield and productivity of crop varieties,” Dr Kant says.

Automated sensing

Within the glasshouse, there is bench space where 600 pots can be planted and prepared for analysis. A conveyor belt moves a further 600 potted plants between automated watering, weighing and imaging stations.

Dr Kant explains that Plant Phenomics Victoria has two imaging booths. One uses a digital colour camera to obtain a top view and side views as the pot is rotated. These images provide data that allow plant biomass and plant area estimates, and estimates of biomass and yield at maturity.

The second ‘hyperspectral’ sensor scans the plant through infrared wavelengths and is used to derive up to 50 different vegetative indices, such as changes in chlorophyll and anthocyanin content that is correlated to stress.

“The scans on living plants replace analytical chemistry on dead plant tissue,” Dr Kant says. “Now we can observe the impact of stresses, such as water shortage within the controlled environment of the glasshouse or in field sites equipped with rainout shelters.”

The use of imaging data to characterise plants and predict biomass and yield have been carefully checked, benchmarked and validated. At present, the facility is being used for two research projects, one targeting nitrogen use efficiency in wheat and the other seeking to improve water use efficiency in lentils, with Dr Kant describing early findings as encouraging.

At the field sites, the imaging technology is mounted on an unmanned ground vehicle called the PhenoScan and an unmanned aerial vehicle. Included on these mobile units are a high-resolution colour camera, infrared thermometer to measure canopy temperature, and near-infrared sensors to estimate different vegetative, growth and stress indices.

For WUE studies, the field sites rely on a new type of rainout shelter conceptualised by Dr Kant. The Horsham shelters are portable, constructed on rails that allow the rainout shelter to move from a parked position to cover experimental plots within two minutes of rain triggering automatic sensors. Surveillance cameras also relay information remotely to the researchers’ computers and phones.

There are three rainout shelters operating, each 20 metres long and 10m wide. They can withstand wind gusts of 153km per hour. Gusts of 107km/h have been recorded in Horsham. 

“The facility has the capacity to analyse and compare plant performance within both the controlled environment of the glasshouse and the field sites that are open to gene-by-environment effects,” Dr Kant explains. “That is important because we do see divergence in the data from the glasshouse and field for the same plants but our set-up means that we can assess which traits vary depending on growing conditions.”

The centre is open to outside research teams and to breeding companies. For example, AGT has already made use of the facility to phenotype its varieties and more screening is scheduled in the future. Also, the AGG intends to start characterising parts of the genebank collection phenotypically, with information about the agro-climatic conditions at the collection site informing trait discovery work.

“Horsham is emerging as an important grain research centre,” Dr Kant says. “Our centre adds extra capability in characterising germplasm and making use of material with enhanced performance for targeted traits.

“I am motivated and really excited to see the early results come through the phenomics facility and our phenotyping field trials on canola and wheat where we tested thousands of varieties. It will be interesting to see in the coming years how the data we generate translate into useful traits and new varieties with accelerated development times.”

Recently, the GRDC announced the Grains Innovation Park in Horsham is the recipient of a five-year, $60.5 million co-investment between the GRDC and Agriculture Victoria to develop the next generation of pulse crops. 

More information:

Leah Heinrich, regional media and communications officer, Victorian DEDJTR
leah.heinrich@ecodev.vic.gov.au

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