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Projects / Programmes source: ARRS

Genetics and Modern Technologies of Crops

Periods
Research activity

Code Science Field Subfield
4.03.01  Biotechnical sciences  Plant production  Agricultural plants 
4.06.05  Biotechnical sciences  Biotechnology  Plant biotechnology 

Code Science Field
B006  Biomedical sciences  Agronomics 

Code Science Field
4.01  Agricultural and Veterinary Sciences  Agriculture, Forestry and Fisheries 
4.04  Agricultural and Veterinary Sciences  Agricultural biotechnology 
Keywords
targeted mutagenesis; genome editing; next generation molecular markers; biotic and abiotic stress; plant-pathogen interaction; transcriptome and proteome analysis; comparative genomics; small RNAs; non-coding RNAs; plant breeding; CRISPR/Cas9; genetic markers; marker assisted selection
Evaluation (rules)
source: COBISS
Points
10,221.62
A''
4,662.98
A'
6,778.62
A1/2
7,591.82
CI10
6,138
CImax
581
h10
30
A1
39.91
A3
34.33
Data for the last 5 years (citations for the last 10 years) on January 28, 2023; A3 for period 2016-2020
Data for ARRS tenders ( 04.04.2019 – Programme tender , archive )
Database Linked records Citations Pure citations Average pure citations
WoS  351  9,622  8,750  24.93 
Scopus  387  11,573  10,661  27.55 
Researchers (33)
no. Code Name and surname Research area Role Period No. of publications
1.  21407  PhD Sabina Berne  Biotechnology  Researcher  2019 - 2023  157 
2.  55852  Luka Bitežnik  Plant production  Junior researcher  2021 - 2023 
3.  09565  PhD Borut Bohanec  Biotechnology    2019 - 2023  592 
4.  50811  Tjaša Cesar  Plant production  Technician  2019 - 2023 
5.  18828  PhD Andreja Čerenak  Plant production  Researcher  2019 - 2023  397 
6.  51925  Maja Dobrajc  Plant production  Junior researcher  2019 - 2023  12 
7.  17787  Viktorija Dolenc    Technician  2019 - 2023 
8.  51973  Marjeta Eržen  Biotechnology  Junior researcher  2019 - 2023  25 
9.  34332  PhD Marko Flajšman  Plant production  Researcher  2019 - 2023  148 
10.  36371  PhD Tanja Guček  Plant production  Researcher  2019 - 2023  49 
11.  38323  Marinka Horvat  Biotechnology  Technician  2019 - 2020 
12.  31143  Nataša Hren    Technician  2019 - 2023 
13.  54733  Kristina Ilnikar  Plant production  Junior researcher  2020 - 2023 
14.  16379  PhD Jernej Jakše  Plant production  Principal Researcher  2019 - 2023  639 
15.  37427  PhD Taja Jeseničnik  Plant production  Researcher  2019 - 2023  29 
16.  09085  PhD Katarina Košmelj  Mathematics  Researcher  2019 - 2023  232 
17.  50528  PhD Urban Kunej  Biotechnical sciences  Researcher  2019 - 2023  48 
18.  53760  Lucija Luskar  Plant production  Junior researcher  2021 - 2023  41 
19.  05083  PhD Zlata Luthar  Biotechnology  Researcher  2019 - 2023  348 
20.  36372  PhD Kristina Marton  Biotechnology  Researcher  2019  42 
21.  53733  Matea Maruna  Biochemistry and molecular biology  Junior researcher  2019 - 2020 
22.  51860  Špela Mestinšek Mubi  Plant production  Junior researcher  2019 - 2023  20 
23.  24413  PhD Jana Murovec  Biotechnology  Researcher  2019 - 2023  160 
24.  23196  Monika Oset Luskar  Plant production  Technician  2019 - 2023  163 
25.  54401  Adriana Podržaj    Technician  2020 - 2023 
26.  20162  PhD Sebastjan Radišek  Plant production  Researcher  2019 - 2023  572 
27.  20164  PhD Katarina Rudolf Pilih  Biotechnology  Researcher  2019 - 2023  86 
28.  53626  Andrej Sečnik  Plant production  Junior researcher  2019 - 2023  14 
29.  38120  PhD Ester Stajič  Plant production  Researcher  2019 - 2023  29 
30.  54400  Sinja Svetik    Technician  2020 - 2023 
31.  19184  PhD Nataša Štajner  Plant production  Researcher  2019 - 2023  292 
32.  15577  Nevenka Valič  Plant production  Technician  2019  89 
33.  37428  PhD Helena Volk  Biotechnical sciences  Researcher  2019 - 2023  50 
Organisations (2)
no. Code Research organisation City Registration number No. of publications
1.  0416  Slovenian Institute of Hop Research and Brewing  Žalec  5051762000  4,017 
2.  0481  University of Ljubljana, Biotechnical Faculty  Ljubljana  1626914  64,297 
Abstract
Research program focuses on genetic and evolutionary mechanisms involved in adaptation to spatial or temporal heterogeneity under various stresses and selection conditions. The changing climate is affecting plants, disrupting ecosystems, affecting pathogen development, their survival rates and modify host susceptibility. The proposed research program contributes to the establishment of innovative and feasible approaches to answer aforementioned challenges that are of high importance for development of sustainable agriculture as well as scientific excellence. Program is divided into 4 interrelated modules. Module (A) Studying of plant genetic resources explores the diversity, conservation and sustainable use of genetic resources for food and agriculture using various molecular markers tools. Further prospects are linked to the utilization of NGS based genotyping technologies for high-throughput studies enabling rapid and cost-effective large-scale analyses. The expected results of this module are: identification of new molecular markers, assessment of variability and kinship relations, development of genetic maps and identification of agronomic QTLs desired for crop breeding programs. Module (B) Biotic stress response investigates host plant-pathogen interactions in two specific pathosystems: hop vs. pathogenic fungus Verticillium nonalfalfae and hop vs. viroids. Module is divided in two specific tasks; first one is focused on studies of plant defense mechanisms and second on understanding of molecular and cellular mechanisms of pathogen during infection processes. Module (C) Modern diagnostic of phytopathogens records genomic variations among different plant pathogens (fungi, viroids and viruses) with the aim of developing strain-specific molecular markers which serve for early diagnostic and pathogen identification. Module is also focused on development and optimization of modern diagnostic methods including assays for testing in the field, in soil or water. Module (D) Modern plant breeding methods aim at implementing genome editing techniques for genome manipulations of Brassica and other species. Numerous plant species are still recalcitrant to standard haploid induction techniques therefore, gene CENH3 will be edited first to induce chromosomal elimination and consequently haploid induction. In addition, we will target other traits important for plant resistance in relation to other modules of the program. In conclusion, the effects of climate change will be examined on plant pathogens and the diseases they cause using advanced methods and modern technologies. Our group has established well-developed cooperation with several foreign institutions which is of major assistance in the rapid transfer of the latest knowledge and procedures. The proposed project will address important challenges in studies of population genetics and plant breeding.
Significance for science
The program will focus on studies of the genetics and biotechnology of agricultural plants. It will cover both basic and applied sciences, with an emphasis on: Studies of plant genetic resources for food and agriculture, Studies of basic mechanisms of plant biotic stress responses, Development of tools for modern diagnostics of phytopathogens using next generation sequencing techniques, Development of modern methods for breeding of selected vegetables and field crops Conservation of genetic variability and diversity is of outmost importance for global food security and nutrition. Using NGS based genotyping technologies for rapid and cost-effective large-scale analyses, we expect to obtain new molecular markers associated with agriculturally important traits and markers linked to genetic variability and kinship relations. These will contribute to the development of genetic maps and identification of agronomic QTLs desired for crop breeding programs. Basic knowledge of infection strategies, molecular and cellular mechanisms of host-pathogen interactions and plant immune responses will significantly contribute to plant pathology research and provide support to plant protection and sustainable crop production in order to develop efficient disease control strategies without harmful effects on human health, biodiversity and the environment and for the employment of effective resistance plant breeding. The development of novel biotechnological methods for early diagnostics and reliable identification of plant pathogens is essential in the field of plant pathology to devise suitable disease control measures and prevent spreading of disease. In addition, studies of soil microbiome will stimulate the development of bio-control agents and enable sustainable agriculture. Introduction of high throughput next generation sequencing techniques and implementation of CRISPR/Cas9 genome editing system for genome modifications will modernize plant breeding methods. Furthermore, our recently patented "Method for Breeding Hybrid Plants" (US application number 15/640,096), which combines haploid induction and genetic marker analysis and was developed in our longstanding cabbage breeding program, will be upgraded with the use of genotyping by sequencing and translated into other agronomically important plant species to improve desired traits. Such an approach will significantly contribute to understanding the underlying genetic mechanisms of traits modification and will not only enable the development of efficient plant breeding methods but also advance knowledge in the field of plant genetics. In addition to the specific scientific findings, the program aims to contribute to the field of biotechnical sciences, within the wider research community and within educational processes. We expect to transfer advanced knowledge of genetics and plant breeding methods into training program for future generations to be able to carry out modern plant genetic and biotechnology research.
Significance for the country
Research into the genetics and breeding of agricultural plants has very great importance in Slovenia, because this field of research make a constant essential contribution to solving a number of accumulated problems with which agriculture is faced daily. The proposed research program is therefore focused on genetic characterization of key plant species and their pathogens and on the development of novel Slovenian varieties. We are at present particularly active in hop, grapevine, cabbage, onion, hemp and medical cannabis, buckwheat and other species, in which we have already substantially contributed in a number of ways to the characterization of varieties and their pathogens and have been active in the development of improved varieties. More specifically, we list below the sets of our activities. The need to improve crop varieties and the introduction of completely new products of plant origin has so far been achieved primarily through the use of genetic transformation but this method has gained a negative connotation, especially in the EU. We anticipate that the application of several novel techniques, such as site- directed mutagenesis might drastically change the current aversion to biotechnology techniques, thus opening tremendous opportunities for progress in this area. This has already been discussed by the regulatory authorities of the EU and other developed countries, which have issued a positive opinion. It is therefore very important that such research is carried out in our country and that students are thus provided with the latest knowledge, comparable with global trends. We will continue working closely with plant breeding companies, growers, regulatory bodies and other stakeholders in order to transfer the obtained knowledge. Hop production and hop breeding in Slovenia have a long tradition and hop has consistently been an important Slovene agricultural product, since most of the yield (99 %) is exported. Acreage of hop gardens put Slovenia on 6th place in the world, they provide significant earnings for producers because of the high value crop. The outbreak in 1997 and spread of the lethal V. nonalfalfae pathotype has become a serious threat to Slovene hop production particularly because of the prevalence of susceptible hop varieties. A similar problem, although on a larger scale, has also occurred in German hop gardens. It is therefore necessary to speed up breeding programs by marker assistant selection and thus offer to hop growers wilt resistant varieties specific for agricultural conditions, as the most effective means to control wilt disease. The results of the program will have a direct impact on the effectiveness of hop resistance breeding, since we employ a wide range of approaches to the study of plants, pathogens and their interactions and we expect to obtain enough information to develop efficient marker(s) for direct use in breeding. With the release of resistant cultivars, we would contribute to the preservation of hop cultivation and to sustainable agriculture in Slovenia. The results of the program will also have a direct impact on the formation of new strategies and guidelines for farming practice management and fighting the development of highly virulent strains of pathogens. At the same time, the development of new techniques for identification of pathogens will allow interested services in the field of plant pathology to apply faster and more cost efficient protocols in their routine. The development of a new generation of techniques of molecular markers and their generation in large numbers will allow rapid detection of linkage with agronomically important characteristics and the use of these markers in breeding applications with the help of markers (MAS), which will be implemented in breeding programs at institutes and in seed companies. Finally, the proposed research will have significant relevance in the transfer of up-to-date knowledge to educational processes at professional, undergrad
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