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Barley breeding lines gain crown rot resistance

A field day at Gatton in Queensland where Dr Chunji Liu (centre) introduced visitors to barley lines containing genetics that protect against crown rot disease.
Photo: CSIRO

Management of crown rot in barley will likely undergo a transformation in the near future as lines containing genetic-based disease resistance make their way to commercial breeders.

The resistance was identified by Dr Chunji Liu and his team at CSIRO Agriculture and Food in Queensland. The genetics were discovered in a diverse collection of barley material sourced from around the world.

In the first instance, Dr Liu combined three different genetic sources of resistance into Australian-adapted barley. The top 30 performing lines underwent field trials starting in 2019 in each of the major grain growing regions.

Dr Liu says lines containing three sources of crown rot resistance demonstrated reduced stem browning, a 37.7 per cent average reduction in kernel yield loss and competitive grain yield potential when compared to commercial varieties. “Some of these 30 lines yielded as well – or even better – than the local varieties in both infected and non-infected conditions,” Dr Liu says.

In addition, a fourth source of crown rot resistance has since been identified and lines containing all four genetic elements have been developed. The top 30 performing lines in that mapping population will undergo field assessment in the coming season.

“The goal now is to backcross all four sources of resistance into varieties from each of the three wheat growing regions, with that work currently well underway,” Dr Liu says. “Meanwhile, the search for novel sources of genetic resistance continues, with the analysis of another 420 highly diverse barley genotypes now completed and the top three novel sources of resistance undergoing genetic mapping.”

This pre-breeding development work was made possible through consecutive GRDC investments. Included in the development work is the creation of diagnostic DNA markers to help commercial breeders select the resistance genes.

How it was done

The CSIRO team used a rapid high-throughput test to screen for crown rot resistance in barley germplasm. This work was performed on seedlings using a highly aggressive Fusarium pseudograminearum isolate (CS3096) in a glasshouse and controlled-environment facilities.

Dr Liu initially screened more than 1000 genetically diverse barley genotypes. Genetic analysis was undertaken to identify chromosomal regions that are co-inherited with crown rot resistance (which are called quantitative trait loci or QTLs).

Three such QTLs were identified from two of the starting barley germplasm. These QTLs were mapped to the chromosome arms called 1HL, 3HL and 4HL.

“We incorporated these QTLs into elite commercial varieties through backcrossing using DNA markers developed in the mapping study,” Dr Liu says. “However, the level of genetic resolution of these DNA markers was too coarse to reliably use them in a breeding program as they may bring over non-desirable genes due to linkage drag.”

This is a real possibility given that strong interactions between crown rot severity and agronomically important traits – such as flowering time and plant height – are known to exist. For example, the crown rot resistance gene on 3HL was found to co-locate genes that control plant height and spike structure.

In response, Dr Liu opted to use technology that allows for a clean transfer of resistance into elite Australian cultivars and the development of tightly linked and diagnostic DNA markers. This involved generating near-isogenic lines (NILs), in which genetically identical lines are created that vary only for the presence or absence of crown rot resistance.

In a NIL population, DNA recombination during reproduction creates novel genetic variation only at the chromosomal regions implicated in crown rot resistance. This results in a population with a diverse set of genetics underlying the resistance, including lines with the disease resistance but no other linked traits.

Gene expression analysis, including DNA sequencing, helped to further delineate the source of disease resistance and improved the quality of the DNA markers to diagnostic standard for the 1HL and 6HL sources of resistance.

The findings

For the 6HL form of crown rot resistance, five pairs of NILs (with contrasting crown resistance and susceptibility) were assessed in 2019 at four field trial sites at Tosari and Gatton in Queensland, Narrabri in New South Wales, and Merredin in Western Australia. Results from the field inoculation trials found that the presence of the 6HL resistance genetics:

  • reduced stem browning an average of 45.7 per cent;
  • reduced yield losses an average of 55.9 per cent;
  • increased the number of fertile tillers on average by 55.4 per cent; and
  • produced no difference in kernel weight between the NILs that varied for the presence or absence of the 6HL resistance allele.

“The chromosome 6 resistance basically reduced crown rot yield losses by maintaining larger numbers of fertile tillers,” Dr Liu says.

The 2019 crop season also produced data for 30 advanced lines containing a combination of the 1HL, 3HL and 4HL resistance genetics. The combination of these genes was associated with:

  • reduced kernel loss by an average of 32.8 per cent at Narrabri, 47.8 per cent at Tosari and 32.5 per cent at Merredin (with an average of 37.7 per cent);
  • reduced stem browning by an average 52.2 per cent at Narrabri and 49.8 per cent at Tosari; and
  • kernel yields of the top lines were competitive (or even higher) than the commercial control varieties under both the non-inoculated and inoculated conditions.

“The top two lines containing three sources of crown rot resistance have been provided to breeders,” Dr Liu says.

Efforts to combine four sources of resistance are under way and are targeting elite Australian barley lines such as Commander, Fleet, Flinders, Baudin and Franklin.

“Barley is known to show more severe crown rot symptoms and accumulate higher concentrations of Fusarium mycelium at every stage of crown infection compared to other cereals, including wheat,” Dr Liu says.

“With genetic resistance identified as the best strategy for controlling this disease, we want to ensure that the material we develop is ideally suited for uptake into breeding programs, including through the use of diagnostic markers to aid selection.”

More information: Chunji Liu,

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