McHenry, Diana J.Aćimović, Srđan G.2024-05-242024-05-242024-04-27McHenry, D.J.; Aćimović, S.G. New Species-Specific Real-Time PCR Assays for Colletotrichum Species Causing Bitter Rot of Apple. Microorganisms 2024, 12, 878.https://hdl.handle.net/10919/119102Bitter rot of apple is an economically important worldwide disease caused by different <i>Colletotrichum</i> species, depending on many factors such as climate, geography, other hosts, and crop management practices. Culture, morphology, and single-locus sequencing-based methods for identifying the <i>Colletotrichum</i> species are severely limited in effectiveness, while the multilocus sequence typing methods available for delineating species are costly, time-intensive, and require high expertise. We developed species-specific hydrolysis probe real-time PCR assays for the following nine <i>Colletotrichum</i> species causing bitter rot in the Mid-Atlantic U.S.A.: <i>C. fructicola</i>, <i>C. chrysophilum</i>, <i>C. noveboracense</i>, <i>C. gloeosporioides</i> s.s., <i>C. henanense</i>, <i>C. siamense</i> and <i>C. theobromicola</i> from the <i>C. gloeosporioides</i> species complex, and <i>C. fioriniae</i> and <i>C. nymphaeae</i> from the <i>C. acutatum</i> species complex. After searching 14 gene regions, we designed primers and probes in 5 of them for the nine target species. Four primer&ndash;probe set pairs were able to be duplexed. Sensitivity tests showed as little as 0.5 pg DNA were detectable. These real-time PCR assays will provide rapid and reliable identification of these key <i>Colletotrichum</i> species and will be critically important for studies aiming to elucidate their biology, epidemiology, and management on apples as the number one produced and consumed tree fruit in the U.S.A.application/pdfenCreative Commons Attribution 4.0 InternationalColletotrichumapple bitter rotreal-time PCRpathogen diagnosticsrapid detectionArticle - Refereed2024-05-24https://doi.org/10.3390/microorganisms12050878