Agronomy

The program "Genetics and Modern Technologies of Crops" (P4-0077) is carried out at the Department of Agronomy, Biotechnical Faculty in the cooperation with the Slovenian Institute of Hop Research and Brewing from Žalec, Slovenia. In 2018, the research group consists of 12 researchers, 5 young researchers and 4 technicians.

The research activities of the P4-0077 program are divided into several sets that complement or intertwine with each other and are comprised of:

• improvement of breeding procedures of agricultural plants and selected plant species through biotechnological processes, within which we explore the possibilities of genome editing in selected species from the genus Brassica by the introduction of plasmid DNA or the ribonucleoprotein complexes of the Cas9 enzyme and in vitro transcribed sgRNA. Our research is also focused on medical cannabis and we have started to develop biotechnological approaches appropriate for its breeding. In addition, we perform the breeding of hops and cabbage, where we use breeding and selection procedures using molecular markers.
• research work of biotic stress caused by the plant/pathogen interaction. In this set, we obtained a multi-layered overview of responses to the infection by Verticillium nonalfalfae in susceptible and resistant hop cultivars on transcriptome level; we study pathogenicity mechanisms of V. nonalfalfae by analyzing predicted fungal secretions and functionally characterize candidate secreted effector genes that manipulate host immunity to allow infection or trigger resistance response of the plant, and examine the impact of resistance hop genes to this fungus.
• the study of non-coding RNA sequences in plant disease states is focused on the viroid/hop interaction, where we study the role of viroid derived small RNAs in the pathogenicity mechanism of viroids and their interactions in the plant. We also perform de-novo small RNA identification in the plants and in phytopathogenic fungus V. nonalfalfae.
• diagnostic procedures; where we introduce new procedures for identifying plant pathogens based on the determination of nucleotide sequences using next generation sequencing technology (NGS). Recently, we have analyzed the virome of autochthonous cultivars of old vines, thus identifying viruses and viroids with the aim of their long-term elimination and further cultivation and clonal selection procedures. In the framework of research related to the diagnosis of the Verticillium wilt, we have developed the LAMP method for the detection and identification of specific pathotipes from the Verticillium genus. Additionally, we are simultaneously developing a PCR and quantitative PCR approach for the detection of several viroids causing severe hop stunting.
• the development of the next generation molecular markers; where we have been introducing NGS technique related methodologies for the vine and hops with the purpose to obtain a large number of data of polymorphic sites in the genome, useful for gene mapping studies, selection by the help of markers, and in the breeding in general.

Among the most important publications in the last two years (2016-2018), the following work can be highlighted: the study of the interactions of simultaneous infections of viroids in the hops (Matoušek in sod., 2017), the characterization of the hop resistance Ve1 gene (Song in sod., 2017), the transcriptomic response of hops to infection with Verticillium nonalfalfae (Progar in sod., 2017), research on the viroid-hops interaction (Pokorn in sod., 2017), labeling of plants with a DNA molecule for the purpose of cultivar protection (Ljubič Fister in sod., 2017), the study of new CRISPR enzyme variants for genome editing (Murovec in sod., 2017), diagnostic procedures for the detection of viroids (Guček in sod. 2017), identification and characterization of micro-RNA in hops (Mishra in sod., 2016), identification of new virulence-related proteins released by Verticillium nonalfalfae in the xylem of hop plants during the colonization (Flajšman in sod., 2016), the study of the hops response to the drought stress (Kolenc in sod., 2016), genomics of Verticillium nonalfalfae (Jelen in sod., 2016, Jakše in sod., 2018). During this period, the program team registered new varieties of buckwheat 'Trdinova' (Luthar in Kreft 2018), tartar buckwheat 'Zlata' (Kreft in Luthar 2018), hops 'Styrian Dragon' (Čerenak in sod., 2018), 'StyrianFox' (Čerenak in sod., 2018), 'Styrian Kolibri' (Čerenak in sod., 2017), 'Styrian Cardinal' (Čerenak in sod., 2016), 'Styrian Wolf' (Čerenak in sod., 2016) and a cabbage hybrid 'Presnik' F1 (Rudolf Pilih in sod., 2016).