Development of ISSR-Derived SCAR marker for detection of Fusarium oxysporum responsible for corm rot of saffron

Abstract

Corm rot of saffron is the deadliest disease of saffron and a major bottleneck in its successful cultivation in Jammu and Kashmir, India. To date, only limited information has been made available for the monitoring, surveillance, and detection of plant pathogens associated with corm rot of saffron in this region. Incidence and severity of corm rot caused by multiple pathogens, viz., Fusarium oxysporum, Fusarium solani, Aspergillus niger, Penicillium corymbiferum, Rhizoctonia solani, and Macrophomina phaseolina, was assessed in saffron growing regions based on multiple field surveys conducted at the farmer’s fields in Kishtwar district of Jammu and Kashmir, during June-July 2021 and 2022. Corm rot was prevalent in all the surveyed prefectures of the saffron growing region, with a maximum disease incidence (62.02%) and severity (43.68%) at Lower Pochhal. The disease manifested as yellowing, drooping, and wilting of shoots during flowering, resulting in dying of the foliage which subsequently led to rotting of corms. Association of six fungal species viz., Fusarium oxysporum, Fusarium solani, Aspergillus niger, Penicillium corymbiferum, Rhizoctonia solani and Macrophomina phaseolina was recorded from the infected saffron corms based on morphological characteristics. Out of these, F. oxysporum was the predominant pathogen, and was present in all the surveyed locations. Species specific SCAR (Sequence Characterized Amplified Region) primers (FO-SCAR-FP and FO-SCAR-RP) were designed for effective detection and diagnosis of F. oxysporum, as it emerged as the major pathogen. Results of the present study may provide new insights into the monitoring of the corm rot and the deployment of an effective disease management strategy that will enhance the production, and productivity of saffron. This being the first comprehensive survey in the region, it provides basic information regarding the occurrence of disease, the distribution of various pathogens associated with it and also about the detection and monitoring of F. oxysporum.