Introduction

The Genetic laboratory was established in 1998 at the Agricultural Institute of Slovenia under the leadership of assoc. prof. dr. Vladimir Meglič at the Crop and Seed Science Department. Today, the genetic laboratory is part of the Crop Science Department (ORP). The head of the laboratory is dr. Barbara Pipan, who is as well responsible for the ORP laboratory work. Within the Genetic laboratory, we also have the Laboratory for tissue culture and the Laboratory for ecophysiology and crop evaluation.

The genetic laboratory are using researchers from the ORP, Plant Protection Department (OVR) and the Animal Production Department (OŽ).

From OVR side, the work in the laboratory is coordinated by dr. Irena Mavrič Pleško. For OŽ, dr. Ajda Moškrič, is responsible for coordinatin laboratory work.

The genetic laboratory facilities enable us to perform wide arrays of analyses in the field of molecular biology, genetics, population genetics of plants and animals, environmental genetics, diagnostics and to conduct general genetic analyses using different types of marker systems (biochemical, molecular). The major research equipment in our laboratory is:

  • tissueLyser, (Qiagen),
  • automated system for preparing reagent mixtures QIAgility (Qiagen),
  • flow cytometer CyFlow (Partec/Sysmex),
  • automated system for the extraction of nucleic acids (KingFisher and MagMax, Thermo Fisher Scientific),
  • QIAxcel Advanced capillary electrophoresis (Qiagen),
  • analyzer of nucleic acids and proteins (Agilent),
  • various types of cyclic thermostats (ABI Veriti, SureCycler Agilent, ABI9700), including RT-PCR (ABI7500 with fast and HRM upgrade), fluorometer (Qubit 3.0),
  • heat shaker (for macroarray, GeneTop Biotech),
  • horizontal electrophoresis with a gel imaging system (Biometra, GeneGenius),
  • additional equipment available on CFGBC/MF (Nanodrop) and BF (Genetic analyzer ABI3500, 2D-gel electrophoresis) for sharing with Agricultural institute of Slovenia as a member of the consortium.

Within the Laboratory for ecophysiology and crop evaluation we have:

  • Portable photosynthesis system (LI-COR 6400XT),
  • leaf area meter (LI3100C),
  • leaf canopy meter (LAI220C)
  • 845X UV-Visible spectrofotometer (Agilent Technologies),
  • NIR (near-infrared) Infratec™ NOVA (FOSS Analytical A/S),
  • HPLC 1260 Infinity (Agilent Technologies).

Scientific and expert publications related to genetic laboratory research results are available at the Agrobiodiversity research program site.

ORP (Crop Science Department) research conducted in the genetic laboratory

ORP research conducted in the genetic laboratory

Current programmes, research, projects, public services and other activities, related to work within the Genetic laboratory

  1. PG Agrobiodiversity P4-0072
  2. Bilateral projects: SLO-MAC, SLO-CRO, SLO-HUN, SLO-BiH
  3. ARRS L4-1840 »New management practices for mitigating abiotic and biotic stresses in maize under changing climate conditions«
  4. FWF ARRS project PlasticGrape
  5. CRP V4―1806 »Establishment of a system for the use of DNA markers for genetic identification and verification of varietal authenticity and purity of major cereals and brasicas as a basis for the quality production of seeds, food and feed«
  6. CRP V4-2007 »Development of testing protocols and establishment of official testing systems for organic varieties and heterogeneous material of selected field crops and vegetables»
  7. Public Service in Agronomy (potatoes, clovers, bucwheat)
  8. Public Service Vegetables and Herbs (common bean)
  9. PRP Osnovni opis in vrednotenje ter genetska analiza izbranih RGV, ki se v rastlinski genski banki hranijo ex situ
  10. ECPGR EUGrainLeg: Lathyrus diversity: available resources with relevance to crop improvement – progress reviews and relationship with AEGIS
  11. ECPGR EUBRASWILD: Capturing Brassica Wild Relatives Diversity in the South Eastern Europe
  12. ERA-NET ARIMNet2 projekta MedVitis: Protecting the Diversity of Mediterranean Vitis in a Changing Environment
  13. PRIMA BrasExplor: Wide exploration of genetic diversity in Brassica species for sustainable crop production
  14. H2020 projekt ECOBREED: Increasing the efficiency and competitiveness of organic crop breeding
  15. H2020 projekt INCREASE: Intelligent Collections of Food Legumes Genetic Resources for European Agrofood Systems
  16. Mentorship of the doctoral students (young researchers)
  17. Mentorship of MSc students
  18. Mentorship of the project work within object “Biotechnology” in High School
  19. Mentorship of the student practice
  20. Service (support for the Service of Official Certification; indirectly related with inspection services)

Research areas

  1. Genotyping, analysis of genetic structure and parameters of genetic for agronomically important plant species (common bean, runner bean, potato, corn, sweet potato, buckwheat, cereals, species from Brassicaceae family, clovers, grapevine, apple trees, ambrosia, dandelions, sesame).
  2. Wide association studies and mapping of quantitative trait loci (QTL) enable identification of loci, genes and genetic markers associated with the traits of interest.
  3. Molecular marker assisted selection enables precise characterization of breeding materials, facilitates the breeding process by speeding up the selection process and enables creation of superior genotypes by gene pyramiding (MAS in common bean, potato, buckwheat).
  4. Studies of crop plant responses to biotic and abiotic stress (biochemical and physiological levels and at the level of gene expression).
  5. Preparation of the target molecules for NGS-based applications.
  6. Plant tissue culture as a complement to conventional breeding methods, micropropagation of virus-free plants, when a large number of plants can be grown over a relatively short period of time; virus elimination of  infected plants; saving of inheritance (gene bank: in vitro plants and microtubers); it is about feeding autochthonous varieties and all the materials we need in raising new varieties and research.
  7. Ecophysiological assessment under protected conditions and on the field.
  8. Biochemical and nutritional analyses of plant material and crops.

Selected publications

 

OVR (Plant Protection Department) research conducted in the genetic laboratory

Genetic variability of plant pathogens and pests

 

The damage to plants caused by pests including viruses, bacteria, fungi, nematodes, insects and mites causes great yield losses and economic damage in agricultural production. Plants and pests identify and react to each other at the molecular level. With molecular biology tools genes and the gene products involved in plant-pest interaction can be identified. Even small differences in these key molecules, both in plants and in pests, can be the basis for plant resistance or virulence of pests. At Plant Protection Department we are identifying characteristics of these key molecules:

 

Nematology:

Identification of tropical root knot nematodes (Meloidogyne spp.) is challenging due to hybrid origin of these parthenogenetic species. We evaluated the suitability of different regions of DNA for molecular markers.

 

Like other pathogens, plant parasitic nematodes employ effector proteins to alter plant cellular functions and successfully infect their hosts. We have assessed molecular variability of cell wall-modifying protein (expansins and pectate lyases) in potato cyst nematodes Globodera rostochiensis and G. pallida.

 

Entomology:

With molecular typing based on mtDNA and microsatellite markers we can track the origin of the western corn rootworm Diabrotica virgifera virgigera, an economically important pest of maize in Northern America and Europe including Slovenia.

 

Bacteriology:

We explored the presence of Agrobacterium spp., a causative agent of the crown gall disease. Based on a recA allele sequence analysis isolated strains of Agrobacterium species complex were assigned to genomic species G1 and G4, and new alleles were recognized.

 

Virology:

Potato spindle tuber viroid (PSTVd) can be transmitted with ornamental plants. Sequence analysis of PSTVd revealed new variants in samples from Slovenia.

 

Selected publications

GERIČ STARE, Barbara, STRAJNAR, Polona, SUSIČ, Nik, UREK, Gregor, ŠIRCA, Saša. 2017. Reported populations of Meloidogyne ethiopica in Europe identified as Meloidogyne luci. Plant disease, vol. 101, no. 9, str. 1627-1632. https://apsjournals.apsnet.org/doi/10.1094/PDIS-02-17-0220-RE

ALI, Shawkat, MAGNE, Maxime, CHEN, Shiyan, CÔTE, Olivier, GERIČ STARE, Barbara, OBRADOVIC, Natasa, JAMSHAID, Lubna, WANG, Xiaohong, BÉLAIR, Guy, MOFFETT, Peter. 2015. Analysis of putative apoplastic effectors from the nematode, Globodera rostochiensis, and identification of an expansin-like protein that can induce and suppress host defenses. PloS one, ISSN 1932-6203. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115042

ŠTRUKELJ, Melita, MODIC, Špela, SEDLAR, Aleš, WINTER, Stephan, RAZINGER, Jaka. The use of microsatellite markers as a tool for distinction between western corn rootworm (Diabrotica virgifera virgifera [Coleoptera: Chrysomelidae]) populations. V: TRDAN, Stanislav (ur.). Zbornik predavanj in referatov 13. slovenskega posvetovanja o varstvu rastlin z mednarodno udeležbo, Rimske Toplice, 7.-8. marec 2017 = Lectures and papers presented at the 13th Slovenian Conference on Plant Protection with International Participation, Rimske Toplice, March 7-8, 2017. Ljubljana: Društvo za varstvo rastlin Slovenije: = Plant Protection Society of Slovenia. 2017, str. 358-365. http://www.dvrs.bf.uni-lj.si/spvr/2017/zbornik_2017.html

LAMOVŠEK, Janja, GERIČ STARE, Barbara, UREK, Gregor. 2014. Isolation of non-pathogenic Agrobacterium spp. biovar 1 from agricultural soils in Slovenia. Phytopathologia Mediterranea, vol. 53, no. 1, str. 130-139. http://fupress.net/index.php/pm/article/view/12706

VIRŠČEK MARN, Mojca, MAVRIČ PLEŠKO, Irena, GERIČ STARE, Barbara. 2013. Variability of potato spindle tuber viroid isolates from ornamental hosts in Slovenia. Journal of plant pathology, vol. 95, no. 2, str. 411-415. http://www.sipav.org/main/jpp/index.php/jpp/article/view/2830

 

OŽ (Animal Production Department) research conducted in the genetic laboratory

Genetic analysis in cattle

 

In the genetic laboratory, we perform analyses for verification of origin, using a standard ISAG set (12 microsatellites).

 

Determining recessive genetic traits (mutations)

CVM – Complex Vertebral Malformation

BLAD - Bovine Leucocyte Adhesion Deficiency

RF - Red factor

Pedigree testing in cattle

We are verifying cattle pedigrees with genetic markers and software within the information system Cattle at the Agricultural Institute of Slovenia.

Method STR (Microsatellites)

We check the origin of cattle with microsatellites. We are involved in the ISAG international comparison test, where we are among the most reliable laboratories (certificate).

 

 

SNP method (genotyping with SNP chip)

We are accredited by ICAR for verification of origin using SNP data.

 

Selected publications

 

LOGAR, Betka, KAVAR, Tatjana, MEGLIČ, Vladimir. Detection of recessive mutations (CVM, BLAD and Red Factor) in Holstein bulls in Slovenia = Določanje recesivnih mutacij (CVM, BLAD in alel za rdečo barvo) pri bikih črno-bele pasme v Sloveniji. Journal of central european agriculture : JCEA, ISSN 1332-9049. [Online ed.], 2008, vol. 9, no. 1, str. 101-106, graf. prikazi. http://www.agr.hr/jcea/issues/jcea9-1/index.php

 

OPARA, Andreja, RAZPET, Andrej, LOGAR, Betka. Breed assignment test of Slovenian cattle breeds using microsatellites. V: PETRIČ, Nežika (ur.). Livestock production as a technological and social challenge, (Acta agriculturae slovenica, ISSN 1854-4800, Supplement, 2012, 3). Ljubljana: Biotechnical Faculty. 2012, suppl. 3, str. 167-170. http://aas.bf.uni-lj.si/zootehnika/supl/3-2012/PDF/3-2012-167-170.pdf

 

OPARA, Andreja. Monogenske napake pri črno-beli, rjavi in lisasti pasmi goveda = Monogenic errors in Holstein, Brown and Simmental cattle breeds. V: ČEH, Tatjana (ur.), KAPUN, Stanko (ur.). Zbornik predavanj = Proceedings of the 26th International Scientific Symposium on Nutrition of Farm Animals [being] Zadravec-Erjavec Days 2017, 9th and 10th November 2017. Murska Sobota: Kmetijsko gozdarska zbornica Slovenije, Kmetijsko gozdarski zavod. 2017, str. 167-174

 

OPARA, Andreja. Uporaba DNK označevalcev za preverjanje porekla pri govedu. Govedorejec : glasilo Govedorejskega društva, mar. 2010, št. 18, str. 17, ilustr. [COBISS.SI-ID 3287912] http://www.kmetijskizavod-celje.si/images/upload/2010/254_gov_2010_web_optimal.pdf

 

OPARA, Andreja, RAZPET, Andrej, LOGAR, Betka, BABNIK, Drago. Določitev pasme goveda na podlagi mikrosatelitnih označevalcev = Determining cattle breeds on the rasis of microsatellite markers. V: ČEH, Tatjana (ur.). Zbornik predavanj = Proceedings of the 21st International Scientific Symposium on Nutrition of Farm Animals : [being] Zadravec-Erjavec Days 2012, Radenci, November 8th and 9th, 2012, 21. mednarodno znanstveno posvetovanje o prehrani domačih živali, Zadravčevi-Erjavčevi dnevi 2012. Murska Sobota: Kmetijsko gozdarska zbornica Slovenije, Kmetijsko gozdarski zavod Murska Sobota. 2012, str. 115-118. https://www.govedo.si/files/janezj2/ZED_2012/dolocitev_pasme_goveda_na_podlagi_mikrosatelitnih_oznacevalcev.pdf

 

OPARA, Andreja, RAZPET, Andrej. Population studies for 6 cattle breeds and 11 microsatellite loci. V: ARCHIBALD, Alan (ur.). 32nd Conference of the International Society for Animal Genetics, 26th - 30th July 2010, Edinburgh, Scotland : Programme and Abstract Book. [Edinburgh]: [s. n.]. 2010, str. 60

 

OPARA, Andreja. Preverjanje porekla in določanje genetske pripadnosti osebkov trem glavnim pasmam goveda v Sloveniji : magistrsko delo = Pedigree testing and assignment test in three main cattle breeds in Slovenia : M. Sc. thesis. Ljubljana: [A. Opara], 2016. IX, 59 f., ilustr. http://www.digitalna-knjiznica.bf.uni-lj.si/podiplomski_studij/md_opara_andreja.pdf

 

OBŠTETER, Jana, LOGAR, Betka, OPARA, Andreja, JENKO, Janez. Parentage verification using imputed microsatellite and SNP data in Slvoenian brown swiss population. V: Proceedings of the 2016 Interbull Meeting, Puerto Varas, Chile, October 24 - 28, 2016, (INTERBULL Bulletin, ISSN 2001-340X, No. 50, 2016). [Uppsala: Interbull Centre. 2016], str. 108-110. https://journal.interbull.org/index.php/ib/article/view/1398

 

 

Molecular analyses in apiculture

 

In the Apiculture group, we explore the options for routine genotyping of honey bee queens origin and genetic determination of the entomological signatures as a tool to detect the counterfeit honey and other products that are stated to contain honey bee resources.

Selected publications

 

MOŠKRIČ, Ajda, MOLE, Katarina, DOVČ, Peter, PREŠERN, Janez. Izolacija dednine iz neinvazivnih bioloških virov pri maticah kranjske čebele (Apis mellifera carnica) = Isolation of genomic dna from non-invasive samples of carniolan honey bee queens (Apis mellifera carnica). V: SMODIŠ ŠKERL, Maja Ivana (ur.), MOŠKRIČ, Ajda (ur.). Zbornik referatov = Book of proceedings, 3. Znanstveno posvetovanje o čebelah in čebelarstvu [tudi] Poklukarjevi dnevi, Ljubljana, 4.-5. oktober 2018 = 3rd Scientific Symposium on Bees and Beekeeping [being] Poklukar's Days, in Ljubljana, 4th-5th October 2018. Ljubljana: Slovensko akademsko čebelarsko društvo: Kmetijski inštitut Slovenije. 2018, str. 85-92. http://www.kis.si/f/docs/Poklukarjevi_dnevi_2018/ZBORNIK_PRISPEVKOV_PD_2018.pdf.