| Summary: | During last few years, seedling blight and black lesions along culm of rice seedlings have been appearing frequently in nurseries. Identification of the causal organism was the objective of this research. The identification was done based on morpho-pathological characteristics and Internal Transcribed Spacer (ITS) region sequencing analysis. The pathogen effects on germination and development of rice seedlings were studied under laboratory and greenhouse conditions. Based on the morphological examination, 10 isolates were identified as Cochliobolus carbonum fungus. This organism recorded different levels of pathogenicity, and most of the isolates showed high virulence, up to 56% as seedling infection with isolate ECC-5. The germination percentage was reduced to 73% for cultivar Sakha 101. Sakha 101 recorded highest infected seedlings percentage (44%) under artificial inoculation. The isolates’ reaction was more variable on seedlings than on leaves of Egyptian rice cultivars. Infection severity on leaves of isolate ECC-5 recorded highest average for infection, while isolate ECC-3 did not exhibit any infection. Most of C. carbonum isolates were induced severe infection on rice seedlings. Therefore, the identified isolates were recorded as a novel pathogen causing seedling blight disease on rice. Soaking in crude extract filtrate of C. carbonium isolates culture reduced germination percentage to 1.55% with Sakha101 and inhibit the shoots and roots growth. The molecular variation using ISJ markers reflected a high level of genetic variation between isolates. The ITS region sequencing of two isolates ECC-7 and ECC-9 was successfully analyzed, and alignment with 19 isolates of Bipolaris zeicola worldwide with 97% identity. Phylogenetic analyses of sequences resulted in a well-resolved phylogeny. The data suggested that ITS region analysis was a potential tool for phylogenetic reconstruction of the new isolates and as was DNA barcode for identification of the fungal species. It confirmed that this organism is a rice seed-borne pathogen that causes seedling blight disease. Keywords: C. carbonum, Rice seedling blight, Internal Transcribed Spacer (ITS) region sequencing analysis
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