About half of Australia’s arable lands are acidified, which causes significant reductions in crop yields. This poses a challenge for the expansion of chickpea production, as pulse crops are particularly sensitive to soil acidity.

A majority of acid soils’ negative effects on crop yields are attributable to trivalent aluminium (Al³⁺), which is solubilised and becomes dominant in the soil solution as soil pH decreases. Al³⁺ is directly toxic to plants, reducing both root biomass and function, while also reducing soil fertility by decreasing the availability of key nutrients such as phosphorus.

Importantly, low soil pH in agricultural systems can be the consequence of crop management practices, in particular overuse of inorganic nitrogen fertilisers. As inorganic nitrogen is oxidised (called “nitrification”) by soil microbes, protons are released to the soil, pH drops and aluminium becomes soluble and toxic.

Crop management practices – for example liming – can mitigate low soil pH, but developing crops that can tolerate low pH and aluminium is a more-sustainable and cost-effective solution.

Although chickpeas and other pulses are especially sensitive to the effects of low soil pH and aluminium, paradoxically they might also be part of the solution. Through their capacity for biological nitrogen fixation, chickpeas return organic nitrogen to the soil, which is a form of nitrogen that is less readily nitrified. As a consequence, legumes enhance soil productivity and lower the risk of acidification compared to inorganic nitrogen fertilisers.

Crop wild relatives have frequently been the source of novel agricultural traits, but their use has been haphazard and intermittent. Previous investments by GRDC, in partnership with US government agencies, identified and conserved a diverse collection of the wild relatives of chickpeas.

Recently, in a collaborative project with scientists at the University of California-Davis (UC Davis), a single gene that confers tolerance to low pH and aluminium has been discovered in a wild chickpea relative – a wild species, Cicer reticulatum. In parallel to trait discovery, the UC Davis scientists have developed genomic tools for morerapid and precise trait breeding into elite Australian chickpea varieties.

From trait identification to breeding Australian cultivars

With GRDC investment, the UC Davis team developed a synthetic soil system in which aluminium concentration can be varied under conditions of low pH. This moderate-throughput greenhouse assay was used to quantify the response of thousands of individual plants, focusing on genetic populations of wild species crossed with cultivated species that were purpose-bred to identify wild traits of agronomic value.

Two distinct sources of aluminium tolerance were identified; one involving the crop’s immediate wild progenitor species (Cicer reticulatum), and one in a more-distant wild relative (Cicer echinospermum). Although both species are cross-fertile with cultivated varieties, the genome of C. reticulatum has greater genetic compatibility and thus the C. reticulatum trait has been the primary focus.

By combining quantitative data about aluminium tolerance with high-throughput genotyping data, a single region in the C. reticulatum genome was identified as the source of the trait. Through a series of increasingly detailed molecular tests, the UC Davis group narrowed the trait to a region containing approximately 0.03 per cent of the genome and 25 candidate genes.

As a prelude to more-detailed studies, the UC Davis group conducted field trials to compare a series of chickpea lines that either contained or lacked the wild aluminium tolerance gene. Tests were conducted in soils with a history of intensive fertiliser use that created low pH and aluminium toxicity.

Figure 1: Root growth tolerance to aluminium conferred by a single gene from wild chickpea. Top and bottom panels: glasshouse experiments comparing cultivated chickpea to a tolerant hybrid. Middle panel: experiments in agricultural fields comparing plants with (tolerant) and without (sensitive) the wild aluminium tolerance gene. Root length is expressed as the per cent growth of treated (aluminium stress) versus untreated (no aluminium stress) plants of the same genotype. Under field conditions, tolerant plants have approximately 50 per cent growth stimulation in the presence of aluminium stress.

Credit: UC Davis

Plants were sown into these aluminium-toxic soils, as well as into comparable control soils that were treated with calcium carbonate (lime) to eliminate acidity in agricultural fields. Excitingly, the researchers discovered that plants carrying the wild gene were not only uninhibited by acidic soils, but that their growth was stimulated in the acidic soils (Figure 1). By contrast, plants carrying the sensitive (cultivated) gene were significantly inhibited for growth in the presence of aluminium.

Armed with knowledge that the trait confers aluminium tolerance in agricultural fields, the UC Davis team is crossing the causal gene into the elite Australian chickpea variety CBA Captain . Developed by breeders in the NSW Department of Primary Industries, CBA Captain (PBR) has a suite of grower-preferred traits but is sensitive to aluminium. The goal is a modified CBA Captain variety that is tolerant to aluminium which may be available for growers by mid-2024.

To facilitate breeding, the UC Davis team used a new technology known as PacBio Revio to determine the complete genome sequence of CBA Captain . Computational scientists at UC Davis then converted the genome data into a toolbox of genetic markers that will simultaneously select for the wild aluminium tolerance gene, while retaining CBA Captain identity throughout all other portions of the genome.

In the longer term, researchers envision that genome-assisted breeding efforts will be used to breed the wild aluminium tolerance trait into other chickpea varieties preferred by Australian chickpea growers. Moreover, the wild germplasm collection appears to contain other genes for aluminium tolerance, raising the prospect of developing successive generations of Australian chickpeas with increasingly greater tolerance to acid soils and aluminium.

Delivery to Australia

Hundreds of characterised chickpea genotypes, including aluminium-tolerant accessions, were imported through the Australian Grains Genebank and are now in the hands of Australian scientists including Professor Chengdao Li’s team at Murdoch University. Full sequences of chickpea genomes and hundreds of validated molecular markers, including those linked to the aluminium tolerance trait, were deposited to GRDC databases and are available to Australian bio-informaticians and breeders. By 2024, a grower-preferred chickpea variety with the aluminium tolerance gene will be in Australia for local field trials and seed increase.

More information: Professor Douglas Cook, [email protected]