Sequence-based uniformity and mating type distribution of Berkeleyomyces rouxiae causing a pandemic black root rot disease in cotton in New South Wales, Australia

Black root rot (BRR) caused by a soilborne Berkeleyomyces rouxiae is a pandemic disease on cotton seedlings in Australia. BRR of cotton was reported for the first time in northern New South Wales (NSW), Australia in 1990. Now, the disease is widespread across cotton growing regions in NSW. Much research has focused exclusively on control management; however, relatively little work has been conducted to understand the BRR pathogen population for their temporal and spatial distributions. A total of 294 B. rouxiae isolates that were freshly collected across NSW over five cropping seasons (2017-2022) were assessed for their genetic diversity based on sequences of the nuclear ribosomal DNA internal transcribed spacer, mini-chromosome maintenance complex component 7, translation elongation factor 1-alpha and RNA polymerase II second largest subunit. Additionally, these isolates were subjected to a specific duplex PCR assay for mating type determinations. Multiple sequence alignments revealed that the prevailing cotton-B. rouxiae was 100% identical; however, the population can be divided into two subgroups based on the presence of mating idiomorphs. The MAT1-1 type was predominant and accounted for 62.2% of the population. A total of 25/77 fields were confirmed to harbour both MAT1-1 and MAT1-2 isolates. However, we failed observe sexual structures in crossing experiments. Based on the sequence uniformity of the cotton-B. rouxiae population, we suggest that the pathogen has spread from one field to another. Therefore, stricter farm hygiene practices should be enforced to minimise a further spreading risk.