| Summary: | <i>Microdochium nivale</i> is a progressive and devastating phytopathogen that causes different types of cereal crop and grass diseases that are poorly characterized at the molecular level. Although rye (<i>Secale cereale</i> L.) is one of the most resistant crops to most of the phytopathogens, it is severely damaged by <i>M. nivale</i>. The recent high-quality chromosome-scale assembly of rye genome has improved whole-genome studies of this crop. In the present work, the first transcriptome study of the <i>M. nivale</i>-infected crop plant (rye) with the detailed functional gene classification was carried out, along with the physiological verification of the RNA-Seq data. The results revealed plant reactions that contributed to their resistance or susceptibility to <i>M. nivale</i>. Phytohormone abscisic acid was shown to promote plant tolerance to <i>M. nivale</i>. Flavonoids were proposed to contribute to plant resistance to this pathogen. The upregulation of plant lipase encoding genes and the induction of lipase activity in <i>M. nivale</i>-infected plants revealed in our study were presumed to play an important role in plant susceptibility to the studied phytopathogen. Our work disclosed important aspects of plant-<i>M. nivale</i> interactions, outlined the directions for future studies on poorly characterized plant diseases caused by this phytopathogen, and provided new opportunities to improve cereals breeding and food security strategies.
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