Gene variants are being transferred into Australian canola varieties to overcome a common and costly shortfall in the crop’s performance

Australian paddocks are among the most difficult environments for canola (Brassica napus L.) establishment, setting up a particular challenge for pre-breeders such as CSIRO’s Dr Matthew Nelson.

CSIRO estimates have 40 to 60 per cent of canola seed sown in Australian paddocks failing to establish. A trend towards sowing costly hybrid seed earlier, into hotter and drier soils,
is further exacerbating the problem.

A decade ago, CSIRO’s Dr Greg Rebetzke noted a similar challenge in wheat – one he helped solve through an ingenious use of a genetic trait.

Dr Rebetzke identified genes that increase the length of the first emergent shoot – the coleoptile – allowing for deeper sowing. This combination of changes in genetics and agronomy proved successful. When sown deep, the trait provides the seed with more reliable access to stored soil moisture and protection from high temperatures near the surface.

Curious to know if the approach could be replicated in canola, CSIRO researchers examined a broad range of past and present canola varieties.

“We found that Australian varieties uniformly put out short hypocotyls, which is the stem between the root and the first leaves of the seedlings, the cotyledons.” Dr Nelson says.

“In contrast, overseas varieties have a wide range of hypocotyl lengths. Importantly, we noted that those with long hypocotyls emerge better from deeper sowing.”

Seeing the potential for a step change in canola crop performance, CSIRO and GRDC in 2019 co-invested in two projects to test and transfer long hypocotyl genetics into Australian canola.

The second project (now underway) is also generating the knowledge needed to incorporate the new trait into Australian farming systems.

Trait discovery

The scope of the project hinges on the ability to reliably measure and compare hypocotyl length across a genetically divergent canola population. This is not as straightforward as it may seem.

Unlike wheat, canola does not produce a straw-like tube through which the seedling can grow. Instead, delicate hypocotyls have to push the seed-encased leaves through the soil.

As such, canola does not punch through soil as readily as wheat coleoptiles. The observed length of the hypocotyl will, therefore, vary with differences in soil density.

More challenging still, the hypocotyl stops growing once it is exposed to light.

To gauge the true genetic potential for hypocotyl length, CSIRO grows its seedlings in the dark for two weeks. The seed is sown shallow into peat pots in an environment of humid air. This allows full expression of the hypocotyl’s genetic potential to elongate.

What typically emerges is a long, lanky stem that is agronomically undesirable, but whose length is reliably consistent across experiments.

“This proved to be a reliable and high-throughput way to score canola varieties for their genetic potential for hypocotyl length,” Dr Nelson says.

Using this assay, Australian canola varieties were compared with international germplasm. A total of 255 varieties were tested that included 100 historical Australian (non-hybrid) varieties, with a further 30 current hybrids and 11 current non-hybrids used as a comparison.

Hypocotyl lengths in these experiments were found to vary between nine and 23 centimetres in the international germplasm. Current Australian varieties fell within a narrower range, averaging 15cm.

When a subset of 20 lines was subsequently grown in field trials, a strong correlation was detected between hypocotyl length and the ability to emerge when sown deep.

“Long hypocotyl varieties can be found in all other growing regions outside Australia, with the longest hypocotyls detected in varieties from Canada, France, Japan and Czech Republic,” Dr Nelson says.

Four were selected for further pre-breeding work. The selected material has hypocotyl lengths that ranged from 20.9 to 23.4cm when dark-grown at 15°C for 15 days.

“These varieties cover a diverse range of breeding histories, grain qualities and maturity types, so we are confident that each will have distinct genes for long hypocotyls that can be targeted for breeding in Australia,” Dr Nelson says.

Trait transfer

The four selected varieties were backcrossed to one of two high-vigour, open-pollinated Australian varieties. These Australian varieties have short hypocotyls, ranging from 12.6 to 14.7cm.

Now that backcrossing has been completed, rounds of self-pollination are being used to develop recombinant inbred lines (RILs). These will express the long hypocotyl trait but in a mostly Australian-adapted genetic background.

On average, these RILs are expected to have 87.5 per cent of their genomes from their Australian parent. The remaining 12.5 per cent is from the long hypocotyl donors.

When the work is completed in 2026, these populations will be used to map the genes that control hypocotyl length.

While the work is in progress, one important finding has already been made. Unlike wheat – where the long coleoptile trait requires variation in just the one gene – the long hypocotyl trait in canola involves several genes.

Additionally, variation in early vigour is being observed independently of the long hypocotyl trait. This could result in the project ultimately delivering two traits – long hypocotyls and early vigour – to breeders.

The mapping work will be completed in 2026. Dr Nelson expects that the team will not get its first impression of how the RILs fare in the paddock until the end of that year.

CSIRO’s Dr Matthew Nelson says that the long hypocotyl trait in canola involves several genes. Photo: Evan Collis

System benefits measured

Also underway is research to understand the benefits to farming systems of the new hypocotyl and vigour traits. Included are physiological experiments led by Dr Rebetzke to delineate the impact of temperature on the expression of the hypocotyl length trait.

“We are also adopting groundbreaking experimental approaches developed by agronomist Dr John Kirkegaard and his team in a parallel agronomic management project led by Dr Andrew Fletcher,” Dr Nelson says. “We are using these approaches to understand the impact of long hypocotyls on emergence in different kinds of soils, soil compactions and moisture contents, and how these interact with soil temperature and seed size.”

With the field work, the aim is to understand the value of deeper sowing to growers.

The challenges of adaptation

Throughout this work, the team faces a daunting challenge. Seed used in these experiments needs to all be produced the same way at the same time and place.

This is due to a quirk in canola in which the environmental conditions experienced by the mother plant greatly affect the early growth characteristics of the seedling. This is called the ‘maternal effect’, a biological mechanism that occurs across plant and animal species.

“Ensuring that the difference we see in hypocotyl length is primarily due to genetic differences is hugely challengingly,” Dr Nelson says. “With this project, a lot of effort went towards ensuring we could measure and compare hypocotyl length accurately. This helps ensure that differences in length we observe are due to genetic differences and not, for example, differences in how seed was generated via the maternal effect.”

That such foundational efforts are needed when it comes to canola crop performance does not surprise the CSIRO researcher.

“Canola has only been a sizeable crop in Australia for less than 40 years,” he says. “A lot of things still need to happen to adapt this European plant to Australian growing conditions.”

The genetics that enable canola to be sown deep even in dry, warm soils amounts to one of the most needed adaptations.

Dr Nelson adds that the project is a collaboration with the Biometry Hub at the University of Adelaide, which is supported by GRDC’s Analytics for the Australian Grains Industry initiative.

The Australian varieties used in this project were contributed by Nuseed and Australian Grains Technologies. Overseas long hypocotyl varieties were sourced from the Australian Grains Genebank and the University of Giessen.

More information: Matthew Nelson, matthew.nelson@csiro.au

See also: GroundCover™ story – Understanding canola establishment to optimise yields