Journal of Agronomy and Field Innovations

Background: Endophytic fungi are present in all parts of a plant without showing symptoms and aid the host in growth, nutrient uptake, and resistance against different stresses. In rice (Oryza sativa L.), being one of the major food crops of the world, analyzing these communities is important for sustainability in agriculture.  
Objective: The study was aimed at studying the diversity, richness, and composition of fungal endophyte communities as present in the root, stem, and leaf of the rice plant using DNA barcoding techniques.  
Method: The sterilized root, stem, and leaf samples were collected from the rice plants grown in the fields (n = 5 biological replicates per tissue). The fungal regions of ITS1 and ITS2 were PCR amplified and sequenced on the Illumina MiSeq platform.
Results: The worked yielded a total of 612,340 quality reads, producing 486 fungal ASVs from five phyla. Ascomycota (68.4%) and Basidiomycota (21.7%) are present in all tissues. The genera that were most common include Fusarium, Trichoderma, and Curvularia. The highest level of alpha diversity was exhibited by root tissues, with rapidly evolving debris, whereas the beta diversity showed a significant clustering specific to the tissues (PERMANOVA, p < 0.05).
Conclusion: The ITS metabarcoding method used helped establish the presence of an endophytic fungal community in the rice plants with the ability to promote the growth of plants and control diseases.