Molecular characterization of Alternaria burnsii causing blight of cumin using random amplified polymorphic DNA (RAPD) markers

Ten isolates of the cumin blight pathogen (Alternaria burnsii) were obtained from the major cumingrowing regions of Rajasthan state in India during the Rabi seasons of 2019-20 and 2020-21.The isolates were molecularly characterized using genomic DNA and random amplified polymorphic DNA (RAPD) analysis with five decamer primers from the OPA and OPE series.A total of ten isolates were chosen from the major cumin-growing areas of Rajasthan, and out of the ten RAPD primers used initially, only five were chosen based on their repeatability.The RAPD analysis showed 100% polymorphism, indicating genetic diversity among the isolates.Dendrogram analysis was performed to group the isolates based on their genetic relatedness, resulting in two major clusters designated C1 and C2.Cluster C1 contained nine subclusters, including Ab-RSR, Ab-OSN, Ab-BLR, Ab-BHML, Ab-RNIW, Ab-KKR, Ab-KSG, Ab-NKH, and Ab-BCWL, while cluster C2 had only one isolate, Ab-BLTR.The similarity matrix showed that Ab-BCWL had a higher similarity coefficient value of 1.000, indicating greater genetic similarity among the isolates in this subcluster, while Ab-BLTR had a lower similarity coefficient value of 0.222, indicating less genetic similarity with the other isolates.The similarity coefficient represents the degree of genetic similarity between the isolates, and its variation among the isolates provides insight into the genetic diversity of the cumin blight pathogen population in Rajasthan.The genetic diversity analysis provides crucial insights into the pathogen's population structure.This understanding of genetic clusters and sub-clusters will be essential for recognizing different virulent strains or variations that could influence disease severity and resistance patterns, ultimately leading to the development of more effective management strategies for cumin blight.