Dr Mia Haoyu Lou (left) and Associate Professor Bettina Berger at the X-ray computed tomography (CT) imaging station at the Plant Accelerator in Adelaide. Photo: Australian Plant Phenomics Facility

Materials from some of Australia’s most-important breeding and pre-breeding programs are, for the first time, undergoing a novel kind of analysis at the Australian Plant Phenomics Facility at the University of Adelaide.

The analysis involves the use of advanced imaging technology made possible by GRDC investment in the acquisition of an X-ray computed tomography (CT) scanner.

The scanner is housed at the Plant Accelerator in Adelaide, where Associate Professor Bettina Berger serves as scientific director.

Associate Professor Berger says X-ray CT scanners are commonly used in medicine but the machine in Adelaide was specifically designed for use in plant research.

It innovates the ability to analyse cereal spikes by producing high-resolution 3D images of the spike and grains within.

“The imaging station is set up to allow for high-throughput, non-destructive, automatic analysis of traits related to seed number, seed volume and seed morphology,” she says. “This provides fundamental knowledge about how crops maximise yield through different floral architecture as well as important insights about the tolerance of different genotypes to stresses, such as heat, drought and frost.”

Late in 2021, the facility put out an open call to breeders and pre-breeders who were interested in testing the new imaging technology as part of a program of pilot projects. The aim is to test and maximise opportunities for using the scanner to benefit the grains industry.

Work on these pilot projects has been underway throughout 2022.

Leading the delivery of these projects is an accomplished postdoctoral fellow, Dr Mia Haoyu Lou. Dr Lou was jointly trained during her PhD at the University of Adelaide and the Hounsfield Facility at the University of Nottingham, which is one of the world’s most advanced facilities when it comes to using X-ray sources for image-based analysis of plants.

Dr Lou says the pilot projects break down into two categories:

• those designed to scan the spike of cereal crops (with efforts underway to also include legumes); and
• those more-exploratory efforts to understand whether the imaging technology can be applied to examine root structure within different soil types.

“The majority of the projects are looking at spike phenotypes in wheat, barley and oat crops,” Dr Lou says.

“The root work is more preliminary as we are still learning how to distinguish the roots – which are basically small water columns – from the denser soil material. That will also involve characterising soil types, including soil moisture, in order to ultimately link back to the influence soil has on root architecture.”

Participating in these pilot projects are an impressive group of partners who have developed important breeding populations designed to solve key production challenges.

Project partners

INVITA – Innovations in Variety Testing in Australia

Headed by Professor Scott Chapman at the University of Queensland, INVITA is the Australian arm of a European initiative designed to maximise the use of remote sensing technology (drone, satellites and paddock-based sensors or cameras) and data analytics for use in agricultural applications and in variety testing.

Working closely with the South Australian Research and Development Institute as the local partner, the goal here is to use the X-ray scanner to provide detailed yield-related traits that can feed into the INVITA analysis and modelling, especially information about grain size and morphology.

InterGrain

The Australian breeding company InterGrain is supplying 25 genotypes to Dr Lou from each of its barley, wheat and oat breeding field testing programs.

Dr Lou says the new imaging technology could potentially open up new traits to target during breeding and cites an important example in oats. “With oat florets containing two seeds, one seed is typically smaller than the other,” she says. “A three-dimensional reconstruction of seed size provides an opportunity to detect and select for genotypes that tend to produce more similarly sized seeds, thereby potentially improving yield.”

South Australian Grain Industry Trust (SAGIT)

A key focus for a SAGIT-funded project lead by Associate Professor Matthew Tucker (University of Adelaide) is to examine whether the application of plant growth regulators (PGR) on genetically diverse barley lines can affects peduncle structure, and thereby suppress head loss in crops.  The aim is to identify gene-by-management associations that could help to select for stronger peduncle strengths, thereby minimising yield losses.

Australian Research Data Commons (ARDC) OzBarley

The aim of the OzBarley project is to develop a publicly available data asset that links genetic diversity (genotypes) to changes in crop characteristics (phenotypes) that is specifically designed by (and for) Australian researchers and breeders.

For this project, Dr Lou has scanned the spikes of 223 elite barley varieties to provide data about spike and seed morphology, which will be published as part of the OzBarley project.

The wheat micronutrient initiative

Collaborators at the University of Melbourne and University of South Australia are working to increase the iron and zinc content of wheat grain, with the goal of reducing the world’s most significant micronutrient deficiencies. The project is led by Associate Professor Alex Johnson (School of BioSciences, University of Melbourne) and focuses on field-grown biofortified wheat material.

Previously, the collaborators have processed seeds at a synchrotron in a bid to map where iron and zinc are located within wheat seed. Now, Dr Lou is helping to identify where in the spike those seeds where located. This involves first scanning the spikes at the Plant Accelerator before the seed is analysed at the Australian Synchrotron.

“The aim here is to identify differences in zinc and iron distribution within the spike as part of broader efforts to boost dietary levels of these important micronutrients in targeted breeding programs, including the use of transgenic methods,” Dr Lou says.

Mutant wheat panel

A team at the University of Adelaide led by ARC Future Fellow Dr Scott Boden has developed a highly diverse wheat population to test a novel way to increase wheat yields. Currently, wheat produces three to four seeds per spikelet. The novel wheat population is being screened to determine whether that number can be increased. This is a project that benefits enormously from being able to see inside the spikes and allows the population to be directly phenotyped.

Looking ahead

Dr Lou adds that exciting additional applications are possible, citing a project in which the X-ray CT scanner was used to peer inside bee hotels in order to image the larvae of native bees and understand bee nest contents. This work is part of conservation efforts to halt the decline of these ecologically important pollinators.

In addition, a pilot project is being developed with Dr Judith Atieno (South Australian Research and Development Institute) and Dr Judith Lichtenzveig (University of Western Australia) to explore the potential of using the scanner to monitor seed development inside the pods of pulse crops.

“In making the CT scanner technology available to the grains-based research community, our focus is to get the most benefit we can from image data,” Dr Lou says. “So, while we want to push forward with grains-related applications, we also want to scope what is possible.”

The Australian Plant Phenomics Facility is funded by the Australian Government’s National Collaborative Research Infrastructure Strategy (NCRIS).

More information: Bettina Berger, bettina.berger@adelaide.edu.au; Mia Haoyu Lou, haoyu.lou@adelaide.edu.au