Investment

Pulses are a vital component of Australia's cereal-based cropping systems. They contribute to soil nitrogen and reduce the impact of cereal diseases, resulting in improved yield, quality and profitability. In addition, pulses such as chickpea can be a highly valuable cash crop. Most (>70%) of Australia's chickpeas are grown in the Northern Region, with the remainder in the Southern Region (only 1% in the Western Region).

Plant diseases are estimated to cause an annual loss of $24 million or $81/ha to the Australian chickpea industry (Murray and Brennan, 2012). This represents 16% of the average annual value of the crop. Of these diseases, Phytophthora root rot (PRR) is by far the most important, costing Australian chickpea growers on average $8.2 million a year. This is almost twice the cost of Ascochyta blight, recently estimated at $4.8 million per year. Although more prevalent in the Northern Region, the PRR pathogen, Phytophthora medicaginis, occurs throughout eastern Australia.

There are two features of the disease that make Phytophthora particularly difficult to manage:

1. once a plant is infected it usually dies
2. unlike Ascochyta, which is readily controlled with fungicides, once a plant/crop is infected with Phytophthora, there is nothing a grower can do.

These features mean PRR can be managed only by pre-sowing decisions using an integrated approach based on assessing the PRR risk of the individual paddock and selecting the variety best suited to that risk.

Currently, there are several chickpea varieties - e.g. Yorker - growers can use in paddocks with a low to moderate PRR risk. However, no current variety will survive realisation of high-risk PRR situations. Even Yorker will die under conditions highly favourable to the disease. Clearly, there is a need for chickpea varieties with greatly-improved resistance to PRR. The development of such varieties will, in combination with other management tools, provide growers with a resilient integrated disease management package and thus increase grower confidence and profitability.

This project aims to mitigate the impact of Phytophthora root rot in eastern Australia by:

1. Identifying, in wild relatives of chickpea, novel sources of resistance to Phytophthora that offer robust protection against the disease.
2. Incorporating this resistance into new chickpea varieties using innovative breeding technology to speed up varietal development.
3. Expanding our knowledge of the pathogen to ensure that the breeding process matches and/or surpasses pathogen variability.
4. Constructing improved grower guides for managing PRR that incorporate the applied research outcomes from this project.

This work will involve plant breeders, molecular biologists and pathologists based at Adelaide, Tamworth, Toowoomba, Wagga and Warwick.

Key activities planned in the project are:

1. Validate PRR resistance in wild relatives of chickpea and in crosses between wild relatives and chickpea.
2. Sample chickpea paddocks in northern NSW, southern Queensland, southern NSW, Victoria and central Queensland to determine geographical extent of the disease and assemble a collection of pathogen isolates.
3. Determine variability within the pathogen population by testing isolates against a differential set of chickpea varieties and lines (genotypes).
4. Update relevant grower management guides in conjunction with industry.
5. Seed-increase recombinant inbred lines (RILs) and collect basic agronomic data. A RIL is the progeny of genetically-distant parents that have been stabilised through inbreeding (self-fertilisation).
6. Screen (= phenotype) mapping populations with diverse sources of PRR resistance for reaction to PRR. Mapping populations are families of RILs.
7. Using phenotypic data, identify superior individuals from RILs and cross into elite, locally-adapted chickpea germplasm.
8. Determine the genetic make-up (genotype) of PRR RIL population individuals.
9. Generate linkage maps (to identify the location of genes in relation to each other) and undertake quantitative trait loci (QTL) analysis to link genes to PRR screening data. QTL analysis helps identify markers.
10. Identify markers associated with PRR resistance. Markers are molecular 'tags' that tell breeders if they have found a source of PRR resistance or have successfully transferred it into a plant.
11. Identify elite RILs following QTL analysis for use in a marker-assisted backcrossing strategy.
12. Utilise markers in marker-assisted back-crossing strategy to incorporate, and if applicable pyramid, alternative QTL for PRR resistance.
13. Validate PRR marker/s in the chickpea breeding program and implement marker use as a routine breeding strategy.

These activities will help fast-track new PRR-resistant chickpea varieties and thus support growers in developing resilient farming systems better placed to minimise losses from the key diseases in the region.