Key points

• Mapping the genomes of key Australian oat varieties as part of the international oat pan-genome initiative PanOat will lay the foundation for genomic-assisted selection for Australian oat breeding
• Using the knowledge generated from PanOat will enable Australian breeders to target specific germplasm for the Australian industry
• Tools and technology will be developed for breeders to accelerate improvement for Australian oats

Market opportunities for Australian oats are growing as consumers learn about their health benefits. However, until recently, oats have not profited from yield and quality trait improvements that are being realised for barley and wheat through the application of new breeding technologies.

Oats have a complex evolutionary history and are thought to have been domesticated more than 3000 years ago while growing as a weed in wheat, emmer and barley fields in Anatolia, Turkey. Cultivated oat (Avena sativa) is a hexaploid species; it has three complete sets of chromosomes from different varieties. In this respect it is genetically more like wheat than barley, which is diploid (it only has one set of chromosomes).

Collective effort

The genetic variability of cultivated oats and its related species has only been explored to a limited extent. Lack of genomic information and tools could be a key limiting factor that has also hampered genetic gain of adapted oat varieties.

This is about to change with the activities of an International Oat Pan Genome Consortium (PanOat), says Professor Chengdao Li from Murdoch University, who leads Australia’s effort in PanOat.

PanOat involves scientific experts from around the world, many of whom have established reputations in decoding the genetic basis of wheat and barley. Australia has joined Canada, Germany, Finland, Denmark, Poland, Spain, Sweden, the UK and the US to develop this oat genomic resource. The PanOat initiative is being led by Dr Martin Mascher from the Leibniz Institute of Plant Genetics and Crop Plant Research in Germany.

Similar ventures have been undertaken for wheat and barley using an international consortium. Oats now stand to gain from the scientific knowledge generated in these initiatives through improved efficiencies and reduced cost of the technology.

GRDC investment in partnership with the Western Crop Genetics Alliance (joint venture between Murdoch University and the Department of Primary Industries and Regional Development, Western Australia), with some recent support from the WA Processed Oat Partnership, has secured Australia’s early and ongoing involvement in PanOat and ensured inclusion of Australian oat varieties in the pan-genome initiative.

“The pan-genome represents the entire set of genes within a species, consisting of a core genome – containing sequences shared between all individuals of the species – and the ‘specialised’ genome for environmental adaptation,” Professor Li says.

“Assembling a pan-genome is a vital resource for plant breeders as it captures the extent of variation within a species beyond what traditional genotype sequencing can achieve. The ‘specialised genome’ in the pan-genome work is critical as this repertoire of genes can code for many agronomically important traits.

“The work will generate a blueprint of oat genetic diversity, which will enable breeders to accelerate the rate of genetic gain for the crop.

Essentially, breeders will be able to go prospecting for new traits and introduce new genetic diversity in breeding programs using the pan-genome information.

“The goals of PanOat include characterising core gene sets and identifying lineage-specific genes of commercial varieties in each country”, Professor Li says.

“PanOat will also catalogue structural variation in wild and domesticated oats and accumulate comparative sequence information for use in agronomic and quality trait mapping.”

Through the oat pan-genome project, an efficient and cost-effective framework will be developed that can be used to map new genome sequences, enabling new oat genomes to be assembled. This will mean that a researcher can generate useful genome sequences of specific accessions of interest for only a few thousand dollars.

Gene discovery, genome analysis and the development and application of genomics-based tools to support oat breeding will be dramatically enhanced through this resource.

Evolutionary insights

“Ultimately, PanOat hopes to undertake evolutionary genomic analyses to understand the origin and evolution of oats,” Professor Li says.

Wheat and barley have a long history of co-evolution with humans as they became crops, and growers progressively selected better-performing varieties. Oats’ domestication rode on the coat-tails of these cereals as it initially was a weed among the cereals.

Professor Li says the ability to ‘mine’ the pan-genome for oats is a way to determine what has been gained or lost within the oat genome during the course of domestication of the species for agricultural purposes.

“We will be able to ascertain how much diversity may have been lost and identify genetic traits that could be useful to recombine into commercial varieties, such as flowering time, heat tolerance, disease resistance and even quality attributes such as beta-glucan.

The PanOat initiative will provide fundamental genetic-based information to determine whether oats can be developed as a gluten-free food for people with coeliac disease.

The venture has sequenced 30 oat genomes from oat genetic resources across the world. PanOat has discovered that there are more genetic structural changes in the oat genomes than wheat, which has important implications for breeders when wanting to introgress new genes of interest. “These translocations also make oats agile in adapting to different environments.”

PanOat and Australian oats

“As part of the international consortium, four oat genomes nominated by Australia will be sequenced and assembled that cover the diversity of Australian oat varieties.”

The oat variety Bannister is representative of WA germplasm and is a long-time benchmark variety for its yield and adaptation, while Bilby is representative of South Australian germplasm and favoured for its grain quality.

Dr Pamela Zwer, retired national oat breeder, with her South Australian-bred Bilby (PBR), a line favoured for its grain quality and nominated for sequencing in the PanOat genome mapping initiative. Photo: Dr Sue Knights

A third line nominated by Australia is a Spanish variety, FM13, which contributes to international diversity. This line is adapted to Mediterranean conditions and is therefore of relevance to Australia.

Williams is the fourth variety nominated. It is a founder line of Australian oats and is favoured for its disease resistance profile.

Australian oat varieties have a very narrow genetic background, with most germplasm being drawn from cooler northern regions of Europe and North America. The Australian grains industry would benefit from expansion of the pan-genome with a focus on increased knowledge of genetic variation from germplasm adapted to warmer Mediterranean-like environments, such as Spain. To cover address this, GRDC has recently embarked on expanding the oat pan-genome efforts towards inclusion of additional accessions from environments more similar to Australian growing conditions.

“Development of the pan-genome, with unique Australian oat genetics incorporated, will help accelerate and extend the outputs of other GRDC investments in oats. These include the InterGrain breeding program, optimising oat phenology for Australia and capturing novel sources of resistance to the main oat diseases – Septoria leaf blotch and oat crown rust,” Professor Li says.

“Additionally, GRDC and WA’s Processed Oat Partnership investment in PanOat will leverage current and future outputs from the recently established OzOats diversity panel developed by CSIRO with support by GRDC. This initiative will provide a bridge between phenotypic outputs and information of genetic variation provided via the pan-genome.”

More information: Professor Chengdao Li, c.li@murdoch.edu.au