Hi-C contact maps and synteny of the 8-1 and 8-3 chromosomes. a) Hi-C contact maps of isolates 8-1 and 8-3 show 2 distinct nuclear compartments. b) Dot plots show that the chromosomes of the isolates are highly syntenic. c) Gene density and repeat densities (10Kb bins) are shown in yellow and blue, respectively, for one haplotype of AG8-1 and AG8-3. d) Annotated CAZyme content for the 2 isolates and their haplotypes shows uniformity in enzymatic gene content for the 2 haplotypes (AAs: auxiliary activities; CEs: carbohydrate esterases; GHs: glycoside hydrolases; GTs: glycosyl transferases; PLs: polysaccharide lyases). Credit: G3: Genes, Genomes, Genetics (2025). DOI: 10.1093/g3journal/jkaf252

Researchers from CSIRO, Australia’s national science agency, have unlocked the most detailed genetic blueprint yet of a major soil-borne crop pathogen—an advance that paves the way for better crop disease management in Australian agriculture.

For the first time, researchers have sequenced and assembled a chromosome-level genome for the fungal pathogen Rhizoctonia solani AG-8, revealing its complex genetic structure. The research is published in the journal G3: Genes, Genomes, Genetics.

The fungus causes bare patch disease in wheat, barley and legume crops across Australia, resulting in over $150 million in crop losses each year.

Dr. Jonathan Anderson, Principal Research Scientist at CSIRO, said the fungus has long been a challenge for farmers because there are no resistant crop varieties and fungicides often don’t work reliably.

"Using new sequencing technology, we discovered that Rhizoctonia solani AG-8 is what’s known as dikaryotic—meaning it carries two separate sets of genetic material, called haplotypes, some of which are highly genetically diverse," Dr. Anderson said.

In simpler terms, the fungus has two distinct genetic blueprints, which could help explain why it’s so hard to control.

"By studying how genes in each haplotype behave when infecting different crops, we found that the two genetic sets may play different roles in how the fungus attacks wheat," Dr. Anderson explained. "This new level of genetic insight into the fungus gives us a powerful foundation to transform how to manage the destructive diseases it causes in the paddock."

The findings lay the foundation for nationwide studies of Rhizoctonia solani populations across Australia’s grain growing regions—research that was previously limited by uncertainty around the relationship between the fungus’ two genetic sets.

The new genome sequence also supports further research into how the fungus causes bare patch disease in different crops and guides the development of smarter crop management strategies to reduce its impact.

Publication details

Jana Sperschneider et al, The fungal pathogen Rhizoctonia solani AG-8 has 2 nuclear haplotypes that differ in abundance, G3: Genes, Genomes, Genetics (2025). DOI: 10.1093/g3journal/jkaf252

Citation: Unlocking genetic code of crop-damaging fungus paves way for better disease control (2026, January 21) retrieved 21 January 2026 from https://phys.org/news/2026-01-genetic-code-crop-fungus-paves.html

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