Species-specific real-time PCR for nine Colletotrichum species causing apple bitter rot in Mid-Atlantic USA

Apple bitter rot causes pre- and postharvest fruit losses ranging from 2 to 100%. In the USA losses are estimated between $ 300 to 400 million annually.
In the Mid-Atlantic this disease is caused by nine Colletotrichum species: C. fructicola, C. chrysophilum, C. noveboracense, C. siamense, C. theobromicola, C. henanense, C. gloeosporioides sensu stricto (s.s.), C. fioriniae and C. nymphaeae. Classic methods to identify the Colletotrichum species are severely limited in accuracy and effectiveness while multilocus sequence typing for delineating species is costly, time-intensive, and requires higher analysis expertise.
In this work, species-specific hydrolysis probe real-time (RT)-PCR assays were developed for the nine Colletotrichum species causing bitter rot in the Mid-Atlantic USA. These resulted from meticulous searching for polymorphisms in 14 essential gene loci and designing primers and probes in five of them for these species: ladA, GAPDH, ApMat, β-tubulin and calmodulin.
Our RT-PCR assays showed that as little as 0.5 pg of target DNA was detectable and will provide rapid and reliable identification of key Colletotrichum species infecting apples for future studies aiming to elucidate their biology, epidemiology, fungicide resistance and management on apple.

VII International Symposium on Postharvest Pathology: Next Frontiers for Improved Knowledge and Management of Postharvest Disease

S.G. Aćimović, N. Boeckman, M.C. Borba

pathogen diagnostics, identification assays, development, optimization, primer-probe design, species detection, rapid detection

https://doi.org/10.17660/ActaHortic.2026.1451.10