Agriculture in the bioeconomy fast lane

Scientist looking at growth in a Petri dish.

Specialist writer Dr Giovana Braidotti joined the Ground Cover team after a successful international career as a molecular biologist, her comment being she now wanted a broader view than that from a microscope. The Australian grains industry has certainly provided this, as Gio has gained a wide following among growers and researchers for her insightful and accessible articles on the developments in grains biotechnology. Here she takes stock of the rapid advances being made in the biosciences that are now driving many of farming’s production gains.

Australia’s farms are spearheading innovations in both productivity and sustainability, and making agriculture the essential foundation of the bioeconomy

It is not just about food, feed and fibre production anymore. Farms are where biotechnology’s potential has been most fully realised in the past two decades, even overtaking medicine in the Organisation for Economic Cooperation and Development’s estimates of profitability within the bioeconomy. The scale and scope of changes have been extraordinary.

Agricultural science is making it possible to produce higher yields from a greater variety of crops while using less inputs, water and, all the while, tolerating greater environmental and seasonal extremes.

Integrated weed and pest management systems – including the GM option – have reduced chemical use and lifted farming’s environmental performance. Desirable traits that only a few years ago looked beyond reach, such as regionally suited varieties with drought resistance or tolerance to transient salinity, are now in the hands of pre-breeding researchers.

Such traits will be added to stand-out grain quality and disease-resistant germplasm for incorporation into farming systems.

We are also seeing whole new cropping systems being developed, such as plant-based biofuels and crops that can replace petroleum-based feedstocks for industrial products as diverse as plastics, lubricants and hydraulic fluid.

What is extraordinary about this progress is that it combines gains in efficiency and productivity that sustain economic growth yet improve environmental sustainability, even in the face of an increasingly unpredictable climate.

While there have been critical advances in agronomy and resource management, the unique aspect of the past two decades is the coming of age of the biological sciences.

Important breakthroughs have been achieved across biology and its support disciplines – genetic resources, bioinformatics and equipment development. The effects have been felt all the way through from research laboratories to the supermarket shelf. And this is before one of the tools offering potentially the greatest gains, genetic modification (GM), has delivered even a single trait applicable to cereals.

Over the years Ground Cover has reported on biotechnology advances, especially in its pre-breeding stages. A notable example was the recent delivery of a commercially viable salt-tolerance trait to breeders – the achievement of its development was reported in Ground Cover in a series of articles beginning in 2009.

Essential to all pre-breeding success has been step-changes in researchers’ ability to objectify a plant’s genetics, biochemistry and physiology – to start with abstract concepts and come up with real possibilities. This has required developing tools and analytical methods to better ‘see’ (or distinguish) individual components within a plant’s integrated physical and physiological processes.

These new capabilities have played out through various R&D themes. There was a reductionist gene-centric approach (which came to be known as functional genomics) through to a more ecologically minded stream that views genes, environment and seasons as one integrated – but malleable and improvable – unit (the phenotyping approach).

Research equipment in a field.

Solving the measurement challenge in the 21st
century as researchers learn to screen vast reserves
of genetic biodiversity for ever more complex traits
needed to boost performance of commercial cereal
varieties. 'Machine vision' sensors built by the High
Resolution Plant Phenomics Centre to study variation
in plant physiology have been mounted onto tractors
and blimps.

Given the collaborative nature of the Australian pre-breeding community, additional progress has been achieved through synergistic interactions across the range of approaches. So, for instance, as Australia invested in its plant functional genomics capability, the R&D took a form that stressed the need to routinely venture into the paddock to phenotype plants to validate genomic hypothesis and trait associations.

Conversely, the impressive series of breakthroughs made by the more paddock-centric phenotyping approach did not prevent researchers looking into the genetics that underlie a valuable trait and make gene and molecular marker discoveries.

Researchers have retained strong links to farms, talked to each other, exchanged material in ways that made the most of the strengths of individual laboratories, and also actively drawn on international agricultural research resources and infrastructure.

The result is a pre-breeding R&D system, strongly supported by the GRDC, that has come to be envied, studied and emulated in countries that take pride in their agricultural productivity, including Canada and the US.

A case in point: a no-till paddock in Western Australia growing a GM canola variety to better manage weeds in a rotation that includes more drought-tolerant and vigorous wheat varieties. Adjacent rows of mallee trees help manage dryland salinity while providing a renewable feedstock for biofuel production, soon to be harvested using machinery custom-designed in Australia.

This is biotechnology, agronomy and resource-management technology synchronised to take a profitable and sustainable bioeconomy from concept to reality.

Solving the complexity puzzle

The progress is all the more remarkable given that the pool of readily available, simple gene traits – those driven by single genes that do not interact too strongly with other genes, the environment or seasonal variability – have more or less been exhausted.

The ‘products’ of greatest interest to farmers – drought, salt, heat and frost-tolerance, for instance – require mastering much more complex gene combinations, or traits missing from the commercial gene pool all together, as proved to be the case with CSIRO’s new salt-tolerance trait.

Mastering these complex associations has required new concepts, technologies and analytical tools. It has also required new ways of screening genes to benefit from the genetic diversity that exists within the world’s genebanks.

With phenotypic selection, researchers must also explore a plant’s physiology within a realistic growing environment and develop an objective measure with which to select for improvements. Once a phenotypic measure has been validated, it allows researchers to screen for complex traits for transferring into commercial varieties. It lays the groundwork for gene and marker discoveries, and makes more efficient use of genetic resources.  

This is the approach used by Dr Richard Richards, from CSIRO Plant Industry, to identify wheat traits that make the most of limited soil moisture during droughts.

“One of the really big advances we’ve made in the past 15 years is to go from a nebulous idea of drought resistance to disassembling it into components like transpiration efficiency, fast early growth, longer coleoptiles, tiller number and early sowing,” Dr Richards explains.

“We can now understand the importance of different traits in different growing regions, and how to select the most useful variants for agriculture from various genetic resources.”

Work is now underway on ways to optimise root architecture in relation to terminal droughts.

“Phenotyping is the most important aspect of selection in breeding and currently its biggest bottleneck – even to gene discovery and marker development,” Dr Richards says.

New capabilities

The past five years have seen significant investment in phenotyping R&D infrastructure in Australia, culminating in the establishment of the Australian Plant Phenomics Centre. New capabilities are under development in ‘high throughput’ phenotyping of plants grown in glasshouses and more importantly, the paddock.

“Even to get good molecular markers, we need to phenotype plants under realistic growing conditions,” Dr Richards says. “So the more we can understand a plant’s physiology and how this correlates to yield, quality, and stress resistance, the more efficient we can be.”

Besides phenotyping, Dr Richards notes two additional issues where new progress will be critical to future productivity gains. The first is to return to a complex trait of fundamental importance to farmers and to global food security: yield.

“In a global sense we haven’t made much progress in the past decade in terms of grain yield,” Dr Richards says. “We are seeing yields plateau off. So we have to start to work out why that is happening and how we can start to make more genetic progress.

“I think the approach we used for drought is worth trying for yield: disassembling it into its component traits.”

The second issue involves greater efficiency in the way new traits are delivered to the restructured Australian breeding sector.

“Breeders are very lean. They don’t have a lot of flexibility or the resources and expertise to phenotype a lot of traits,” Dr Richards says. “The push I would be making is try to get the pre-breeding people to go a little bit further and make their material more breeder-friendly so that uptake by the companies is made easier.”

It is a view that shows the importance of collaboration across disciplines, of knowledge-sharing for the greater good of grain growers. In much the same way as phenotyping has taken genetics into the realities of a paddock, bioscience is increasingly going to overlap bioeconomics.

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