ARS | Publication request: Real-time PCR discrimination of the southern and common corn rust pathogens Puccinia polysora and P. sorghi

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 5, 2010
Publication Date: June 5, 2011
Citation: Crouch, J., Szabo, L.J. 2011. Real-time PCR discrimination of the southern and common corn rust pathogens Puccinia polysora and P. sorghi. Plant Disease. 95(6):624-632.

Interpretive Summary: Outbreaks of southern corn rust (SCR) disease caused by the fungus Puccinia polysora have increased in incidence and severity in the U.S. over the past several years, and may have a substantial impact on corn production. SCR is currently diagnosed through the visual examination of disease symptoms and the size, shape and location of fruiting structures produced by the fungal pathogen. However, these features are similar to those produced by the "common" corn rust fungus P. sorghi, making SCR difficult to accurately diagnose visually. To overcome these limitations, a DNA-based method to quickly and accurately discriminate between the corn rust diseases caused by P. polysora and P. sorghi was developed. The assay makes use of technology that uniquely detects a cluster of small, but diagnostic differences in the DNA sequences of each of the fungal pathogens. This method provides definitive, highly sensitive discrimination between the DNA of the two corn rust fungi in less than an hour, even when only minute quantities of the fungal pathogens are present. This assay can be routinely performed by plant diagnostic facilities or other laboratories, and will ensure rapid and accurate diagnosis of SCR for scientist and plant health practitioners involved in disease monitoring, risk assessment and breeding for resistance.

Technical Abstract: Over the past several years, Southern corn rust (SCR) outbreaks caused by the fungus Puccinia polysora have become increasingly problematic for corn growers in the U.S. SCR is currently diagnosed through the visual examination of disease symptoms including size, shape and location of fruiting structures produced by the fungal pathogen. However, these characteristics are similar to those produced by the common corn rust fungus P. sorghi, confounding accurate visual diagnosis of SCR. Here we report the development of a real-time PCR assay that discriminates between P. polysora and P. sorghi. Sequences of the rDNA internal transcribed spacer (ITS) region were determined for P. polysora and P. sorghi. FAM-labeled hydrolysis probes that differed at 14-nt between the species were developed from these data and used to screen DNA extracted directly from rust-infected corn leaves. Species-specific, reproducible identifications of the pathogens were made from as little as 3 pg of DNA within 30 min, and were reliably performed from both recent collections and herbarium specimens. This assay will be useful for rapid and accurate diagnosis of SCR, and could serve as a tool to monitor the distribution and incidence of the disease in the U.S.