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Določevanje odpornosti rastlin na povzročitelje gospodarsko pomembnih bolezni kot so npr. uvelost, rja in ožig, pomeni velik napredek za uspešno kmetijsko pridelavo. Identifikacija odpornih rastlin je danes hitrejša in bolj zanesljiva. Uporaba biotehnoloških pristopov, predvsem molekularnih markerjev na osnovi PCR, omogoča analizo genoma in posledično prisotnost genov za odpornost na določeno bolezen. Markerji, ki ločujejo med posameznimi genotipi na podlagi polimorfizmov služijo kot indikatorji prisotnosti gena za odpornost, če so v njegovi neposredni bližini. Odpornost leče (Lens culinaris Medik.) na uvelost je pogojena s Fw genom. V njegovi bližini 10,8 cM oddaljen, je RAPD marker OP-K15900. Tesnejšo povezavo so odkrili preko SSR in AFLP markerjev SSR59-2B je od Fw gena oddaljen 8,0 cM, p17m30710 pa 3,5 cM. Odpornost na rjo je determinirana z genom R, katerega prisotnost najbolje določata dva SSR markerja, LcSSR606 in LcSSR440. Njuna oddaljenost od R gena je 8,3 cM in 8,1 cM. Odpornost na uvelosti in rjo je determinirana z dominantnim genom. Ožig, ki je prav tako kot uvelost in rja posledica okužbe z glivo, nima enotnega vira odpornosti. Do zdaj je bil odkrit dominanten gen AbR1, kateremu sta najbližje RAPD markerja RB18 in RV01, ki sta oddaljena 14 cM oz. 6 cM. Poleg AbR1 je dominanten gen za odpornost tudi Ral2, recesivno pogojen pa je ral2. Crops resistant to economically important diseases such as fusarium wilt, rust and Ascochyta blight are essential for agricultural production. Identification of resistant plants is now faster and more reliable. The use of biotechnological methods, especially molecular markers based on PCR, enables the analysis of the genome and thus the presence of genes for disease resistance. Markers that differentiate between genotypes based on DNA polymorphisms serve as indicators of a resistance gene when located in its immediate vicinity. Wilt resistance in lentil (Lens culinaris Medik.) is caused by the Fw gene. The latter has a RAPD marker OP-K158900 in the proximity of 10,8 cM. A stronger association was detected with SSR marker SSR59-2B and AFLP marker p17m30710 at distances of 8,0 and 3,5 cM, respectively. Rust resistance is regulated by the R gene, which is flanked by two SSR markers LcSSR606 and LcSSR440 at distances 8,3 and 8,2 cM, respectively. Resistance to rust and wilt is determined by a dominant gene, in contrast to blight, which has two known dominant genes that determine resistance. Ascochyta blight has two RAPD markers, RB18 and RV01, near the AbR1 gene of 14 and 6 cM, respectively. Ral2 is another dominant gene, while ral2 is recessive.

Olive is considered one of the oldest and the most important cultivated fruit trees in Albania. In the present study, the genetic diversity and structure of Albanian olive germplasm is represented by a set of 194 olive genotypes collected in-situ in their natural ecosystems and in the ex-situ collection. The study was conducted using 26 microsatellite markers (14 genomic SSR and 12 Expressed Sequence Tag microsatellites). The identity analysis revealed 183 unique genotypes. Genetic distance-based and model-based Bayesian analyses were used to investigate the genetic diversity, relatedness, and the partitioning of the genetic variability among the Albanian olive germplasm. The genetic distance-based analysis grouped olives into 12 clusters, with an average similarity of 50.9%. Albanian native olives clustered in one main group separated from introduced foreign cultivars, which was also supported by Principal Coordinate Analysis (PCoA) and model-based methods. A core collection of 57 genotypes representing all allelic richness found in Albanian germplasm was developed for the first time. Herein, we report the first extended genetic characterization and structure of olive germplasm in Albania. The findings suggest that Albanian olive germplasm is a unique gene pool and provides an interesting genetic basis for breeding programs.

Namen diplomske naloge je predstavitev molekularnih markerjev in različnih modernih tehnik žlahtnjenja rastlin z njihovo uporabo. Podrobneje je prikazana uporaba teh metod pri žlahtnjenju pšenice (Triticum aestivum) na odpornost proti rumeni rji (Puccinia striiformis). Žlahtnjenje z napredkom genomskih tehnologij in novimi dognanji zelo napreduje in je v agronomiji postopek izboljšanja rastlin, ki se izvaja že odkar smo ljudje pričeli s kmetijstvom. Z žlahtnjenjem lahko pozitivno vplivamo na različne agronomske lastnosti kmetijskih rastlin, poleg tega pa lahko tudi povečamo odpornost rastlin na povzročitelje bolezni. Pšenica je med najbolj razširjenimi gojenimi rastlinami na svetu in je zaradi svoje prehranske vrednosti izjemno pomembna. Rumena rja je bolezen pšenice, ki jo povzroča obligatni parazit Puccinia striiformis iz kraljestva gliv. Tega je možno zatirati z uporabo fitofarmacevtskih sredstev, a ta onesnažujejo okolje. Pri pšenici je bila odkrita skupina Yr genov, ki kodirajo proteine za odpornost proti rumeni rji. Proučevanje teh genov in žlahtnjenje na odpornost je s pomočjo molekularnih markerjev veliko lažje in omogoča hitrejši razvoj odpornih sort pšenice. Yr15 gen izvira iz divjega sorodnika pšenice Triticum turgidum ssp. diccocoides in je dandanes pomemben vir odpornosti velikega števila sort pšenice. The aim of this thesis is to present molecular markers and different modern plant breeding techniques using them. The focus is on the application of these methods to the breeding of wheat (Triticum aestivum) for resistance to yellow rust (Puccinia striiformis). Plant breeding is advancing rapidly with advances in genomic technology and new knowledge and is a very important method in agronomy that has been practiced since humans began to cultivate plants. Breeding can positively influence many agronomic traits of cultivated species and can also increase the resistance of plants to pathogens. Wheat is one of the most widely cultivated crops in the world and, because of its nutritional composition, is of great importance. Yellow rust is a disease of wheat caused by the obligate fungal parasite Puccinia striiformis. It can be controlled with use of fungicides, but these pollute the environment. In wheat, a group of Yr genes has been identified that encode proteins for resistance to yellow rust. Studying these genes, as well as breeding for resistance is much easier with the help of molecular markers, which allows faster development of resistant wheat varieties. The Yr15 gene originates from a wild relative of wheat, Triticum turgidum ssp. diccocoides, and nowadays, it is an important source of resistance in a large number of wheat cultivars.

The Fagopyrum genus includes two cultivated species, namely common buckwheat (F. esculentum Moench) and Tartary buckwheat (F. tataricum Gaertn.), and more than 25 wild buckwheat species. The goal of breeders is to improve the properties of cultivated buckwheat with methods of classical breeding, with the support of biotechnological methods or a combination of both. In this paper, we reviewed the possibility to use transcriptomics, genomics, interspecific hybridization, tissue cultures and plant regeneration, molecular markers, genetic transformation, and genome editing to aid in both the breeding of buckwheat and in the identification and production of metabolites important for preserving human health. The key problems in buckwheat breeding are the unknown mode of inheritance of most traits, associated with crop yield and the synthesis of medicinal compounds, low seed yield, shedding of seeds, differential flowering and seed set on branches, and unknown action of genes responsible for the synthesis of buckwheat metabolites of pharmaceutical and medicinal interest.

Zelje predstavlja eno najpomembnejših zelenjadnic na svetu. Klasično žlahtnjenje in pridobivanje novih sort zelja je zelo zamudno, saj je zelje dvoletnica. Samoinkompatibilnost je lastnost nekaterih cvetočih rastlin, ki bi lahko znatno skrajšala postopek žlahtnjenja. V ta namen je bil zasnovan poskus, v katerem smo 114 čistim linijam belega zelja iz pomnoženih DNA fragmentov določili inkompatibilnostni razred na osnovi markerjev SRK (S-lokus receptor kinaza) gena, ki je ženska domena (se izrazi v pestiču). Na začetku smo uporabili 9 začetnih oligonukleotidov, ki pomnožujejo različne domene SRK gena, v nadaljevanju poskusa pa smo jih 6 izločili, ker niso delovali pravilno ali pa so bili kontaminirani. Ugotovili smo, da 33,3 % čistih linij pripada razredu I. S pomočjo sekvenčne reakcije smo določili zaporedje 66 čistim linijam in jih razvrstili v podrazrede. V razredu I smo dobili 4 različne podrazrede, v razredu II pa 2. Na 12 različnih lokacijah po Sloveniji smo v parih posadili po eno rastlino belega zelja in eno rastlino rdečega zelja za poskus križanja. Seme smo pridobili samo na dveh lokacijah. Iz semena smo vzgojili sadike in na nivoju fenotipa ter s pomočjo mikrosatelitnih markerjev preverili, ali je prišlo do samooprašitve ali križanja. Delež samooprašitve je bil v inkompatibilnostnem razredu I visok, kar pomeni, da se je kljub močni samoinkompatibilnosti oprašilo veliko število rastlin, zato bi morali poskus ponoviti v bolj optimalnih pogojih. Cabbage is one of the most important vegetables in the world. It is a biennial plant. Therefore the classical breeding procedure for new cabbage varieties is very time-consuming. Selfincompatibility is a characteristic of some flowering plants that could significantly shorten the breeding process. For this reason, the incompatibility class of 114 inbred lines of white cabbage from amplified DNA fragments using SRK-specific primers (S-locus receptor kinase) was determined. SRK gene is a female determinant and it is expressed in the pistil. Initially, we used 9 SRK-specific primers that amplify different domains of the SRK gene, and in the further experiment, 6 of them were eliminated because they did not function properly or were contaminated. We found out that 33.3% of the inbred lines belonged to class I. Using the sequence analysis, we analyzed the sequence of 66 inbred lines and classified them into subclasses. In class I, 4 different subclasses, and in class II, 2 subclasses were identified. At different locations across Slovenia, we planted a white cabbage plant together with a red cabbage plant for test-crossing. Seeds were obtained in only two locations. Seedlings were tested for self-pollination on the phenotypic level and with molecular markers. The percentage of self-pollination was very high in incompatibility class I, meaning that despite the strong selfincompatibility, a large number of plants were self-pollinated. Further research under more optimal conditions would be appropriate.

Hop (Humulus lupulus L.) is grown mostly as flavouring and bittering ingredient for beer and is also appreciated in the herbal and cosmetic industry, as well as in pharmacology. Among several diseases that damage hop growing, the most devastating in European hop production is verticillium wilt, caused by the soil-borne fungal pathogen Verticillium nonalfalfae. Colonization pattern and differential expression of selected genes after artificial infection of susceptible and resistant hop cultivars with V. nonalfalafae in stems and roots have been analysed recently Švara et al., 2019. Here, we present the dataset related to verification of plant samples infections after artificial inoculation (fungi- and mock-inoculated). After inoculation plant samples were tested for the positive infection by PCR amplification of the V. nonalfalfae ITS DNA region with species specific primers developed and optimised for this purpose. For more insight please see the article “Temporal and spatial assessment of defence responses in resistant and susceptible hop cultivars during infection with Verticillium nonalfalfae”. Keywords: Verticilium nonalfalfae, Hop, Artificial infection rate, Molecular markers, ITS primers

The main challenge associated with genotyping based on conventional length polymorphisms is the cross-laboratory standardization of allele sizes. This step requires the inclusion of standards and manual sizing to avoid false results. Capillary electrophoresis (CE) approaches limit the information to the length polymorphism and do not allow the determination of a complete marker sequence. As an alternative, high-throughput sequencing (HTS) offers complete information regarding marker sequences and their flanking regions. In this work, we investigated the suitability of a semi-quantitative sequencing approach for microsatellite genotyping using Illumina paired-end technology. Twelve microsatellite loci that are well established for grapevine CE typing were analysed on 96 grapevine samples from six different countries. We redesigned primers to the length of the amplicon for short sequencing (~100 bp). The primer pair was flanked with a 10 bp overhang for the introduction of barcodes on both sides of the amplicon to enable high multiplexing. The highest data peaks were determined as simple sequence repeat (SSR) alleles and compared with the CE dataset based on 12 reference samples. The comparison showed that HTS SSR genotyping can successfully replace the CE system in further experiments. We believe that, with next-generation sequencing, genotyping can be improved in terms of its speed, accuracy, and price.

Primordialne zarodne celice so embrionalni prekurzorji gamet in imajo ogromen pomen na področju razvojne in varstvene biologije ter akvakulture. Splošne raziskave teh celic prinesejo s seboj razvoj same vede biologije kot tudi aplikativne dosežke. Seveda primordialne zarodne celice nudijo tudi vpogled v mehanizme migracij in proliferacij celic v zgodnjem embrionalnem razvoju. Ksenotransplantacija primordialnih zarodnih celic ogroženih vrst rib v široko razširjene recipiente in krioprezervacija predstavljata enega izmed pomembnejših pristopov k ohranjanju genetskega materiala ogroženih vrst. Kopičenje znanja na modelnih vrstah rib - cebrici in medaki je pomenilo razvoj metod ksenotransplantacije in kriporezervacije tudi pri komercialno zanimivejših vrstah (npr. salmonidih). Primordial germ cells are embryonic precursors of gametes and have enormous importance in the fields of developmental and conservation biology and aquaculture. Researching these cells meant development of applied science and science from a basic point of view. Primordial germ cells offer an insight into mechanisms of cell migration and proliferation during early embryonic development. One of the main objectives in preserving genetic material of endangered species is xenotransplantation. This means transplantation of endangered fish primordial germ cells into wide-spread recipients. Cryopreservation is the other objective in preservation of endangered genetic material. With development of basic knowledge on model fish species - zebrafish and medaka, development of method such as xenotransplantation and cryopreservation has been introduced in commercially more interesting species (e.g. Salmonidae).

This book provides a comprehensive description and assessment of the use of marker-assisted selection for increasing the rate of genetic gain in crops, livestock, forestry and farmed fish, including the related policy, organizational and resource considerations. It continues FAO's tradition of dealing with issues of importance to agricultural and economic development in a multidisciplinary and cross-sectoral manner. As such it is hoped that the information and options presented and the suggestions made will provide valuable guidance to scientists and breeders in both the public and private sectors, as well as to government and institutional policy and decision-makers.