CSIRO Finds Backup Resistance Gene to Fight Cotton’s Bacterial Blight

14 September 2026, Narrabri, Australia: Scientists at Australia’s national science agency, Commonwealth Scientific and Industrial Research Organisation (CSIRO), have located a previously unused disease resistance gene in cotton that could give the crop a second line of defense against bacterial blight, a disease that has cost growers significant yield in the past. The discovery, announced in August 2026, comes from a multi-year genome mapping effort led by the CSIRO cotton breeding team and could speed the development of more durable, disease resistant cotton varieties worldwide, including in India, the world’s largest cotton growing country by area.

Bacterial blight is caused by a bacterium that infects cotton leaves, stems and bolls, causing lesions that can lead to defoliation and reduced fiber quality in warm, humid conditions. For decades, breeders controlled the disease using a small number of resistance genes bred into commercial varieties. But around 2011, a new strain of the pathogen overcame the main resistance gene used in United States cotton, causing renewed outbreaks and reminding the industry how quickly a single-gene defense can fail once a pathogen adapts.

Finding a backup gene on a different part of the genome

To find a backup option, the CSIRO team, including bioinformatician Dr Angel Popa-Báez, head cotton breeder Dr Warwick Stiller, disease resistance researcher Iain Wilson and laboratory researcher Melanie Soliveres, turned to a technique called pangenome mapping. Unlike conventional genome sequencing, which compares a crop against a single reference plant, pangenome mapping builds a composite genetic map from many individual plants, including older, wild relatives of modern cotton that are rarely used in commercial breeding. This approach captures genetic variation that a single reference genome would miss entirely, because useful genes can be present in a wild relative’s genome but absent from the elite commercial lines bred for high yield.

Cultivated cotton is what scientists call an allotetraploid, meaning its genome is actually a combination of two separate ancestral genomes, referred to as subgenomes, that fused together in the plant’s evolutionary past. The CSIRO team crossed ancestral cotton species with modern commercial lines and then used bioinformatic analysis, meaning computer based comparison of DNA sequences, to search both subgenomes for genes linked to disease resistance. They found that the gene that failed in 2011 sat on one subgenome, while a previously overlooked backup resistance gene sits on the other. As Dr Popa-Báez explained, the new resistance “sits on a chromosome from an entirely different subgenome to the original,” meaning a pathogen that has already evolved to beat the first gene would need an entirely separate adaptation to overcome the second.

Why a second subgenome matters for durability

This distinction matters because resistance genes clustered in the same genomic region, or subgenome, tend to be vulnerable to the same evolutionary shortcuts a pathogen might take. A backup gene on an unrelated part of the genome gives breeders the option to combine, or stack, both resistance sources in a single variety, a strategy plant pathologists generally consider more durable than relying on one gene alone. Stacking multiple, unrelated resistance genes forces a pathogen to acquire several independent mutations at once to overcome the crop’s defenses, which is statistically far less likely than defeating a single gene.

For now, the finding is a genetic discovery rather than a released variety. The next steps for CSIRO’s breeding program will involve confirming the gene’s effectiveness in field trials and incorporating it into breeding lines destined for commercial release, a process that typically takes several years in perennial and semi-perennial row crops like cotton. The pangenome map itself is also a resource: because it was built from multiple plants rather than one reference, it can continue to be mined for other useful traits beyond blight resistance, including tolerance to drought or other diseases.

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