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High-value forms of Crown rot resistance identified

Members of the CSIRO Crown rot resistance team, from left to right, Dr Jonathan Powell, Dr Zhi Zheng, Dr Mumta Chhetri, Ms Caritta Eliasson, and Professor Chunji Liu.
Photo: Darius Koreis

Crown rot resistance in commercial wheat varieties bested by new pre-breeding lines.

The moderate level of Crown rot resistance currently available in Australian wheat varieties has been superseded by pre-breeding lines, following efforts to genetically map new sources of resistance.

At the 2019 Plant Breeding Assembly, CSIRO's Dr Jonathan Powell reported up to 30 per cent gains in resistance compared to current best varieties, such as Sunguard (PBR), with the improved resistance translating into higher yields in the paddock.

Already, the newly developed germplasm is making its way to wheat breeding companies thanks to CSIRO's accelerated pre-breeding technique, with more resistant material due in coming years.

DNA-based markers are also being developed for the new sources of resistance. This will enable Australian wheat breeding companies to routinely select for and enrich genetic regions that encode for resistance and increase Crown rot resistance levels within their breeding programs.

The enhanced level of resistance is the product of work undertaken by CSIRO Agriculture & Food and was made possible with GRDC investment.

The team at CSIRO is led by Professor Chunji Liu, with Dr Mumta Chhetri driving the marker development work, Dr Jonathan Powell and Caritta Eliasson working on the GRDC wheat project and Dr Zhi Zheng and Rosalie Sabburg working on a GRDC project to improve genetic resistance to Fusarium Crown rot in barley (CFF00010).

Dr Powell says the CSIRO wheat team works within a larger GRDC initiative that is co-ordinated by Dr Philip Davies, of the Plant Breeding Institute (PBI) at the University of Sydney. Dr Davies was previously awarded the 2016 GRDC Emerging Leader Award for his Crown rot pre-breeding work.

The parallel efforts involve:

  • The University of Sydney attempting to boost resistance by combining all known sources of Crown rot resistance within Australian germplasm and testing different combinations in large-scale field trials across Australia - with the aim of delivering pre-breeding lines to wheat breeders.
  • Efforts at the University of Southern Queensland, led by Dr Cassy Percy, to develop more reliable and efficient ways to score for Crown rot resistance - such as refining stem-browning assessment and novel applications for high-throughput imaging technology.

Know your enemy

Dr Jonathan Powell at the CSIRO glasshouses in St Lucia, Brisbane. PHOTO Darius Koreis

Dr Jonathan Powell at the CSIRO glasshouses in St Lucia, Brisbane. Photo: Darius Koreis

The intensive focus on the genetics of Crown rot resistance is necessary, as management techniques only provide partial control of F. pseudograminearum inoculum levels in the paddock and existing fungicides are ineffective in controlling the disease.

Importing resistance from elite material bred overseas is not effective, as Crown rot is a particular problem in Australian production systems - with the pathogen only recently emerging as a pathogen of consequence internationally.

We have shown that we can use quick, high-throughput laboratory platforms to find new sources of resistance that are relevant in the paddock and that consistently beat the resistance levels of Sunguard (PBR) - which was our key objective. - CSIRO researcher Dr Jonathan Powell

Three factors are thought to create the undesirable affinity for Australian paddocks:

  • as the pathogen can persist in soils on stubble, it particularly affects farming systems that are reliant on no-till for water conservation;
  • seasonal conditions that promote Crown rot and drive up yield losses - typically a hot, dry finish - are common in Australia's cereal cropping regions and are made worse by drought; and
  • F. pseudograminearum has a wide host range - affecting bread wheat, barley and even some native grasses (but without causing symptoms in the grasses). But it causes particularly severe symptoms in durum wheat, which can then increase the severity of Crown rot issues in that paddock's rotation.

"I've heard researchers refer to Crown rot as a biologically induced drought because it blocks or otherwise damages the plant's vascular tissue, which then exacerbates the impact of dry conditions on grain filling," Dr Powell says.

"The result is shrivelled grain and white head formation where the grain head has died off and, at last estimate in 2009, causing yield losses costing the Australian industry in excess of $80 million in an average year."

Currently, growers are advised to monitor their soil early in the season for Crown rot using methods such as PreDicta® B testing to help with management decisions, including reducing the inoculum load through stubble burning and rotating into non-host crops.

However, growers are warned that pathogen testing requires a dedicated sampling strategy, rather than a simple add-on to a soil nutrition test.

New sources of resistance

Sitting within a larger, national Crown rot initiative, the CSIRO team targets genetic gain and is headed by Professor Chunji Liu. PHOTO Darius Koreis

Sitting within a larger, national Crown rot initiative, the CSIRO team targets genetic gain and is headed by Professor Chunji Liu.
Photo: Darius Koreis

Unlike some fungal foliar diseases, such as rusts and mildews that can be thwarted for a time with a single resistance gene, the genetics of Crown rot resistance is complex, involving the concerted effect of hundreds (if not thousands) of different genes - each with a relatively small effect in isolation.

The sources of resistance used in the current project, however, are fundamentally different - with just four quantitative trait loci (QTL) able to provide up to 30 per cent more resistance compared to Sunguard (PBR).

Of these QTL, two (located on chromosomes 5DS and 2DL) were sourced from EGA Wiley and the others from Sunco (2B) and a spelt wheat accession (CSCR6) (3BL).

The method used to detect these QTL involves screening genetically diverse wheat germplasm using a seedling assay developed by CSIRO, genetically mapping the new sources of resistance and introgressing the new QTL to produce pairs of lines that are essentially identical except for the presence or absence of the resistance locus.

This allows testing the effect of the resistance gene in isolation and is essential to ensure that the resistance is not simply due to differences in traits which influence resistance, such as plant height or flowering time.

Developing breeding lines

These so-called near-isogenic lines (NILs) are then subjected to intensive field testing to ensure the resistance locus increases resistance in the paddock before being transferred and combined into adapted Australian wheat varieties.

The pipeline involves a considerable number of crosses and taking the resulting populations through many generations. This might otherwise require a decade to complete but for the development at CSIRO of a fast-breeding technique that uses stress to curtail the vegetative phase and accelerate flowering.

This technique allows for six generations in a year when combined with embryo rescue from immature seed. In this manner, the researchers can go from an initial cross to fixed pre-breeding lines ready for the field within a year.

"We have shown that we can use quick, high-throughput laboratory platforms to find new sources of resistance that are relevant in the paddock and that consistently beat the resistance levels of Sunguard (PBR), which was our key objective," Dr Powell says.

"In addition, we are using RNA-Seq technology to leverage information about differences in gene expression (between resistant and susceptible NILs) to refine the search for the underlying resistance genes."

The four newly discovered QTL are now being combined and moved into five Australian wheat varieties suited to different growing regions across Australia. This material has been undergoing field testing since 2016.


This effective and rapid trait discovery platform is now being deployed on additional germplasm, with screening underway of the Vavilov collection, Focused Identification of Germplasm Strategy (FIGS), CIMMYT Australia ICARDA Germplasm Evaluation (CAIGE) and other material from the Australian Grains Genebank that was selected to capture wide genetic diversity and known resistance to other soil-borne fungal diseases.

"We think we have found additional strong sources of resistance in material sourced from a variety of countries," Dr Powell says.

"The plan going forward is for all the new forms of resistance to be brought together to create entirely new standards of Fusarium Crown rot resistance in Australian cultivars."

To that end, the pre-breeders are working closely with commercial breeding companies.

The University of Sydney released several of their lines in 2017 and have continued to release germplasm annually to breeding companies.

Of the CSIRO material, one line containing three of the four QTL and expressing high yield potential was provided to breeders in 2018 - with further lines showing great promise and scheduled for release to companies in 2020.

"Our understanding is that breeding companies have started making their own crosses with the lines we provided in order to bring the resistance into their breeding lines," Dr Powell says.

"That means we could see the new crown rot resistance sources hit the paddock in the not-too-distant future."

Markers for all four QTL are due for delivery to breeders in 2020.

GRDC Research Code US00075

More information: Jonathan Powell, CSIRO,

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