Development of diagnostic molecular markers to differentiate sharp eyespot and Fusarium crown rot isolates collected from common wheat fields in China

Soil-borne fungal diseases are always a threat to wheat production. Developing molecular markers is helpful in early diagnosis and precautionary treatment of these diseases. In this study, a total of 42 Rhizoctonia isolates and 11 Fusarium isolates were obtained from 84 samples of diseased wheat plants collected from 11 locations in China. Rhizoctonia cerealis (Rc) and Fusarium pseudograminearum (Fpg) were the most abundant species in the majority of the sampling regions, accounting for 77.4% and 11.3% of the total isolates, respectively. Eight internal transcribed spacer (ITS) types of Rc were defined based on ITS sequencing identification, among which the ITS type I was the most predominant types isolated in all test regions. Based on the ITS sequences of all isolates, two specific markers were developed to distinguish Rc, Rhizoctonia solani (Rs) and three species of Fusarium at the DNA level. These markers were used to successfully detect 53 isolates of Rc, Rs and Fusarium collected in the study. Identification results by markers developed in this work were further confirmed by ITS sequencing. These markers could be used to detect the specific infective pathogen in diseased wheat seedlings or soil residues in fields, which would then be useful for early prevention and treatment of diseases sharp eyespot (SE) and Fusarium crown rot (FCR).