New genomic toolkit set to boost Australian crop industry

The perfect commercial crop is a moving target.

To continue making the incremental gains that keep crops productive in the face of evolving plant diseases, soil conditions and climate changes, crop breeders and scientists rely on genetic tools.

When a breeder knows which beneficial genes to include in a new crop variety – say for disease resistance – the farmer can then produce a more profitable product. And a reduction in crop failure of 5 to 10 per cent, equates to millions of dollars in savings for growers.

Beyond just being the grain that brings us beer and whisky, barley plays a key role in this genetic research for crop improvement.

Owing to its small genome (its entire collection of DNA and genes) and ability to self-pollinate, barley is more convenient to study and is known as a model cereal crop. 

This means that if a gene that improves, say, drought tolerance is identified in barley, it is very likely to operate the same way in other cereals like wheat, rye, and oats as well.

Rolling revolutions

The battle for food sustainability has involved a series of scientific and technological innovations including irrigation, fertilisation and mechanised agriculture.

The science of genetics was used to enhance artificial selection programs. These programs mean humans essentially take over from natural selection by choosing to breed plants with traits we want – like higher yield, for example.

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As genetic tools become more advanced, biologists can better understand the nitty-gritty of how specific plant genes influence specific inherited traits.

This can include traits that range from the production of essential nutrients for human health, to a high tolerance of Australia’s notoriously saline soils.

This enables far more effective breeding, aided by molecular genetic tools – like genetically assisted selection and genome editing.

Currently, in barley, genetic modification is only used in research.

The genomics frontier

Our publication in Nature describes a 76-strong set of near-complete barley genome sequences known as a pangenome.

This research was conducted by an international consortium led by IPK Gatersleben in East Germany and included more than 80 researchers from 12 countries.

The importance of pangenomes can be explained with a little history.

One of the first steps in understanding the function of individual genes is to sequence them, that is, to determine the precise sequence of the DNA that makes up the gene.

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Sequencing a single gene from one individual used to take months or even years. Thanks to advances in sequencing technology, we can now sequence genes from many individuals, or even the entire genome of an individual, in a matter of days or weeks.

A critical step in whole-genome sequencing is the ability to computationally handle the data output and assemble the sequences they produce into a complete (or near-complete) genome.

To assemble a genome, we need to compare the sequence chunks, work out what's an error and then ‘stitch’ the correct chunks together into a kind of consensus sequence, which ideally represents the whole genome.

The key word there is 'ideally'.

The process is messy. Getting a good-quality genome often requires using a whole suite of sequencing techniques and software to tie them all together.

And that’s before we try to identify which parts of the sequence represent genes.

This work requires a huge amount of effort and expertise. No two genomes are quite alike, so the algorithms are complicated. And even once a genome is assembled, it requires various forms of validation to ensure the quality is fit for research purposes.

Before genome sequences, functional genetics would have felt like being a motorsports engineer trying to improve the performance of a Formula 1 car, which they were only ever allowed to access in pitch darkness.

Access to genome sequences was like flooding the workshop with light and handing over full blueprints of almost every component.

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From genomics to pangenomics

Researchers in almost every biological field now use genome sequences every day from medicine, conservation, evolution and ecology, agriculture, nutrition, and yes – even palaeontology.

Cereals have notoriously difficult genomes to sequence and, despite the comparative ease of working with barley, it took joint funding and an international consortium to generate the first few versions of a barley genome.

These early genomes were immediately adopted by the cereal improvement community to improve cereal production.

As more and more barley genomes, alongside those of other cereals, became available, researchers began to find that comparing genomes acts as a value multiplier.

After all, for genetics research to work, we can’t rely on studying just one variety with one genome – we need to study the differences between genomes and work out how they contribute to differences between the crop varieties.

And the more varieties the better.

Innovation for crop improvement

Seventy-six genome assemblies from a cereal crop this complex is epic.

One of the teams in the study highlighted how important being able to compare genomes is by demonstrating – with unprecedented ease and speed – how the repeated copying and pasting of genes involved in starch breakdown affects the malting characteristics of domesticated barley.

This is the kind of information that barley and cereal breeders around the world can integrate into their crop improvement programs.

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Helping crops survive heatwaves

While new genomic resources have immediate commercial potential, a large part of their value lies in opening pathways to explore innovative approaches that hope to outperform and supplant the status quo methods of the time.

When genomes first became available, they enabled researchers to develop predictive tools – including some that use machine learning – that breeders now use to speed up the production of better varieties. 

Now, an entirely new research direction has been opened up by the 76 genome sequences. It involves the 99 per cent of the genome that falls in between genes and how this poorly understood genetic material might produce beneficial outcomes for agriculture.

This kind of innovative exploration guarantees that science can help meet the challenge of a stable food supply well into the future.