Molecular characterization of Sclerotium rolfsii causing collar rot disease in soybean using ISSR markers

Abstract

Soybean (Glycine max [L.] Merrill) is a vital oilseed crop being cultivated globally. Its productivity in India remains below potential, partly due to the threat of soil-borne diseases like collar rot caused by Sclerotium rolfsii. This study aimed to assess the genetic diversity among S. rolfsii isolates collected from soybean-growing regions of Maharashtra using Inter Simple Sequence Repeat (ISSR) markers. A total of fifteen isolates were collected from Marathwada, Vidarbha, and Western Maharashtra and confirmed as S. rolfsii through ITS-based molecular identification. Seven ISSR primers were used for DNA fingerprinting analysis and generated 587 total amplicons, of which 337 were polymorphic, resulting in an overall polymorphism rate of 83.91%. Primers UBC-811 delineated 100% polymorphism and the highest PIC values (0.365), indicated high discriminatory power. UPGMA-based clustering grouped isolates based on moderate geographic association, revealing both inter- and intra-regional diversity. These results highlighted the effectiveness of ISSR markers in detecting genetic variability within S. rolfsii. The findings would help to provide a molecular basis for developing targeted breeding and disease management strategies to control collar rot in soybean across Maharashtra’s key production zones.