Pathogens represent a major threat to agricultural production and it is estimated that they contribute to 15 % yield losses in major crops. The most cost effective and environmental friendly way to protect plants against pathogens is to deploy natural resistance. Since, plants have evolved together with pathogens they developed several defense pathways during this arms race we can explore. The most important of them is innate immune receptors that recognize different pathogens and trigger resistance responses. Despite the enormous agricultural importance of these resistance genes, the mechanisms regulating their expression are not well understood. In recent years, small RNA molecules emerged as an important post transcriptional gene expression regulators of various cellular processes. This project provide information to understand the role of small RNA molecules regulating resistance genes during biotic stress in plants. Understanding the molecular mechanisms of small RNA molecule based regulation of resistance genes give us important knowledge that can be adapted to crop species and used in future breeding programs. If we can apply this new knowledge it may result new type of pathogen resistant plants, which provide better protection of crop plants than the currently available methods.

Suppression of NB-LRR genes by miRNAs promotes nitrogen-fixing nodule development in Medicago truncatula

Transcriptome reprogramming in the shoot apical meristem of CymRSV-infected Nicotiana benthamiana plants associates with viral exclusion and the lack of recovery

Plants as sessile organisms continually sense and adapt to environmental conditions. The 21-24 nt small regulatory RNAs (sRNA) have recently been recognised as important gene expression regulators, which play a major role in development and adaptation. However, little is known about how they respond to ambient temperature at the genomic level. It was shown recently, that chromatin state is important to mediate thermosensory response in plants. Since sRNAs are important chromatin regulators in plants, it is plausible to hypothesize that sRNAs could have a role in temperature sensing and mediating physiological responses to different temperature. To test this hypothesis, we used of both next generation sequencing and analysis of sRNA biogenesis mutants, to globally identify expression changes of sRNAs in response to ambient temperature in Arabidopsis. This project helped to understand the role of sRNAs in temperature perception and to evaluate their role in regulating gene expression changes in response to ambient temperature. Understanding the sRNA associated molecular mechanisms of ambient temperature response of sRNAs in Arabidopsis can be adapted to crop species and used in future breeding programs.

Ambient temperature regulates the expression of a small set of sRNAs influencing plant development through NF-YA2 and YUC2

Genome-wide identification of RNA silencing-related genes and their expressional analysis in response to heat stress in barley (Hordeum vulgare l.)

The tomato genome contains four putative DML genes encoding proteins with characteristic domains of functional DNA demethylase. It was recently demonstrated that repression of the SlDML2 gene expression in transgenic tomato, inhibits fruit DNA demethylation and strongly inhibits the onset and progression of fruit ripening. This demonstrated that SlDML2 is central in mediating the promoter DNA hypomethylation necessary for ripening progression of tomato. We use CRISPR/Cas9 system targeting of cis-regulatory motifs of SlDML2 promoter to engineer fruit ripening variants of tomato. Genome editing driven mutagenesis of SlDML2 promoter creates a continuum of variation for fruit ripening. Selected SlDML2 promoter alleles with altered fruit ripening and shelf life could improve fruit quality traits that could be later used in plant breeding. The increased shelf life has an important economic and environmental protection consequence, since it is a major contributor to the reduction of post-harvest losses.