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Abstract Red clover (Trifolium pratense) is an important forage legume crop that suffers like most perennial crops from attacks by soil‐borne pathogens. Fusarium root rot is one of the most serious diseases and at the same time problematic to identify resistance because of its hidden life in the soil. Current screening methods are laborious and hampered by limited reproducibility. To remedy this situation, we aimed to establish a simple and reliable hydroponics‐based screening system to facilitate studies of red clover–Fusarium avenaceum interactions. First, the fungal spore concentrations were balanced toward the development of red clover plants grown hydroponically. We found that the optimum concentration was 30,000 spores in 2 L of hydroponic medium to ensure infection during the plant growth period in this system. The procedure was scaled‐up to screen plants from 25 populations to identify red clover individuals with the improved resistance to F. avenaceum. Susceptible plants had approximately two‐fold higher amounts of fungal DNA than resistant plants, demonstrating a correlation between the disease readings of the plants and pathogen DNA. We foresee this screening procedure meeting the needs of both applied breeding work and in‐depth molecular studies of responses between this pathogen and its host plant. This method could be applied for the screening of other plant species for resistance to Fusarium spp. or to other root microbes.

Abstract Endophytes, both of bacterial and fungal origin, are ubiquitously present in all plants. While their origin and evolution are enigmatic, there is burgeoning literature on their role in promoting growth and stress responses in their hosts. We demonstrate that a salt-tolerant endophyte isolated from salt-adapted Pokkali rice, a Fusarium sp., colonizes the salt-sensitive rice variety IR-64, promotes its growth under salt stress and confers salinity stress tolerance to its host. Physiological parameters, such as assimilation rate and chlorophyll stability index were higher in the colonized plants. Comparative transcriptome analysis revealed 1348 up-regulated and 1078 down-regulated genes in plants colonized by the endophyte. Analysis of the regulated genes by MapMan and interaction network programs showed that they are involved in both abiotic and biotic stress tolerance, and code for proteins involved in signal perception (leucine-rich repeat proteins, receptor-like kinases) and transduction (Ca2+ and calmodulin-binding proteins), transcription factors, secondary metabolism and oxidative stress scavenging. For nine genes, the data were validated by qPCR analysis in both roots and shoots. Taken together, these results show that salt-adapted Pokkali rice varieties are powerful sources for the identification of novel endophytes, which can be used to confer salinity tolerance to agriculturally important, but salt-sensitive rice varieties.