Identification and validation of novel EST-SSR markers in olives

The olive (Olea europaea L.) is a leading oil crop in the Mediterranean area. Limited information on the inheritance of agronomic significant traits hinders progress in olive breeding programs, which encourages the development of markers linked to the traits. In this study, we report on the development of 46 olive simple sequence repeat (SSR) markers, obtained from 577,025 expressed sequence tags (ESTs) in developing olive fruits generated in the framework of the Slovenian national olive transcriptome project. Sequences were de novo assembled into 98,924 unigenes, which were then used as a source for microsatellites searching. We identified 923 unigenes that contained 984 SSRs among which dinucleotide SSRs (36 %) were the most abundant, followed by tri- (33 %) and hexa- (21 %) nucleotides. Microsatellite repeat motif GA (37 %) was the most common among dinucleotides, while microsatellite repeat motif GAA was the most abundant trinucleotide SSR motif (16 %). Gene ontology annotations could be assigned to 27 % of the unigenes. A hundred and ten expressed sequence tag-derived-simple sequence repeats (EST-SSRs) with annotated genes were selected for primer designing and finally, 46 (42 %) polymorphic EST-SSRs were successfully amplified and used to validate genetic diversity among 24 olive varieties. The average number of alleles per locus, observed heterozygosity, expected heterozygosity, and polymorphic information content were 4.5, 0.649, 0.604 and 0.539, respectively. Twenty-seven EST-SSRs showed good diversity properties and were recommended for further olive genome investigation

Paternity Analysis of the Olive Variety “Istrska Belica” and Identification of Pollen Donors by Microsatellite Markers

The leading olive variety in Slovenia is “Istrska belica” (Olea europaea L.), which currently represents 70% of all olive trees in productive orchards. Paternity analysis based on microsatellite markers was used for genotyping and identification of the potential pollen donors of “Istrska belica” and for assessing the proportion of self-fertilization in monovarietal olive orchards in the Slovene Istria. Seven microsatellite loci were used for genotyping thirty-one olive embryos from “Istrska belica” trees and for all potential pollen donor varieties, which are grown in the region and could participate as pollinators. Genotyping results and allele identification were performed using the FaMoz software. The most probable pollen donor was assigned to 39% of all analyzed embryos. Among all analyzed embryos no single case of self-fertilization was confirmed. According to the present results, the variety “Istrska belica” was in all cases fertilized by foreign pollen. The results will contribute to defining the new guidelines for farmers regarding the proper management and growing practice in monovarietal olive groves

Genetička, biokemijska, hranjiva i antimikrobna svojstva šipka (Punica granatum L.) uzgojenog u Istri

This study characterises the genetic variability of local pomegranate (Punica granatum L.) germplasm from the Slovenian and Croatian areas of Istria. The bioactive components and antioxidant and antimicrobial properties of ethanol and water extracts of different parts of pomegranate fruit were also determined, along with their preliminary nutritional characterisation. Twenty-six different genotypes identified with microsatellite analysis indicate the great diversity of pomegranate in Istria. The pomegranate fruit ethanol extracts represent rich sources of phenolic compounds (mean value of the mass fraction in exocarp and mesocarp expressed as gallic acid is 23 and 16 mg/g, respectively). The ethanol extracts of pomegranate exocarp and mesocarp showed the greatest antimicrobial activity against Candida albicans, Candida parapsilosis, Rhodotorula mucilaginosa, Exophiala dermatitidis and Staphylococcus aureus, and the same water extracts against S. aureus and Escherichia coli. To the best of our knowledge, this study represents the first report of the characterisation of pomegranate genetic resources from Istria at different levels, including the molecular, chemical, antimicrobial and nutritional properties.U ovom je radu opisana genetička raznolikost germplazme šipka (Punica granatum L.) s područja slovenskog i hrvatskog dijela Istre. U etanolnim i vodenim ekstraktima različitih dijelova ploda šipka pronađeni su bioaktivni spojevi, te su ispitana njihova antioksidacijska i antimikrobna svojstva i preliminarno određena hranjiva svojstva ekstrakata. Dvadeset i šest različitih genotipova utvrđenih analizom mikrosatelita upućuju na veliku raznolikost šipka u Istri. Etanolni ekstrakti ploda šipka predstavljaju bogat izvor fenolnih spojeva (srednja vrijednost masenog udjela, izraženog kao galna kiselina, bila je 23 mg/g u egzokarpu i 16 mg/L u mezokarpu). Etanolni ekstrakti egzokarpa i mezokarpa šipka imali su snažan antimikrobni učinak na sljedeće vrste: Candida albicans, Candida parapsilosis, Rhodotorula mucilaginosa, Exophiala dermatitidis i Staphylococcus aureus, dok su vodeni ekstrakti egzokarpa i mezokarpa uspješno suzbijali rast bakterija S. aureus i Escherichia coli. Prema našim spoznajama, ovo je prva karakterizacija genetičkih izvora šipka iz Istre, koja obuhvaća molekularna, kemijska, antimikrobna i hranjiva svojstva plodova

An Integrated Characterization of Jujube (Ziziphus jujuba Mill.) Grown in the North Adriatic Region

Žižula (Ziziphus jujuba Mill.) ima dobra hortikulturna svojstva, koja uključuju prilagodbu uvjetima suše, abiotskim i biotskim stresovima, te pozitivan utjecaj na zdravlje ljudi. U ovom je istraživanju opisana genska raznolikost germplazme žižule s istarskog poluotoka, te su određeni važni kemijski spojevi, antioksidacijski, antibakterijski i protugljivični učinak ekstrakata plodova žižule te njihova hranjiva svojstva. Rezultati analize gena pokazuju da većina uzoraka s istarskog poluotoka pripada dvjema nedavno introduciranim sortama, \u27Li\u27 i \u27Lang\u27, te najrasprostranjenijoj lokalnoj sorti Domaća žižula\u27. Lokalna sorta ima sitnije plodove od sorata \u27Li\u27 i \u27Lang\u27, s tanjim i mesnatijim mezokarpom. Kemijska je analiza pokazala da su plodovi lokalne sorte vrijedan izvor vlakana ((9,7±0,6) g/100 g), te da su bogati mineralima poput kalija ((829±51) g/ 100 g suhe tvari), kalcija ((1 77±1 1 ) g/ 1 00 g suhe tvari) i fosfora ((129±19) g/ 100 g suhe tvari). Vodeni su ekstrakti imali blagu antibakterijsku aktivnost, dok su etanolni ekstrakti imali veće masene udjele fenolnih spojeva (5,8-8,7 mg/g), izražene kao ekvivalent galne kiseline (GAE), od vodenih ekstrakata, no nisu imali antimikrobnu aktivnost. Osim fenolnih spojeva, i ostali spojevi u plodu žižule mogu imati veću biološku aktivnost. Na osnovi rezultata ovih analiza smatramo da lokalna istarska sorta žižule ima potencijal za uzgoj.Jujube (Ziziphus jujuba Mill.) has favourable horticultural properties including adaptation to arid conditions, abiotic and biotic stresses, as well as positive impact on human health. The present study describes the characterization of genetic diversity of the germplasm of jujube from the Istrian peninsula, the determination of important chemical compounds, antioxidative properties in relation to antibacterial and antifungal activities of jujube fruit extracts, and the determination of nutritional properties of jujube fruit. The results of the genetic analysis showed that most of the samples from the Istrian peninsula belong to two recently introduced varieties, \u27Li\u27 and \u27Lang\u27, and the most widespread local variety \u27Navadna žižola\u27. The local variety has smaller fruit than the ‘Li’ and ‘Lang’ varieties, with thick and fleshy mesocarp. Chemical analysis indicated that fruits of the local variety contained a valuable source of dietary fibre ((9.7±0.6) g/100 g) and were rich in minerals such as (in g/100 g dry mass): potassium (829±51), calcium (177±11) and phosphorus (129±19). Aqueous extracts showed slight antibacterial activity, while ethanol extracts had higher mass fractions of phenolic compounds (expressed as gallic acid equivalents (GAE), 5.8-8.7 mg/g) than the aqueous extracts, but did not show antimicrobial activity. Compounds other than phenolic compounds in jujube fruit may be more biologically active. Based on the results of these analyses, the local Istrian jujube variety is a promising candidate for cultivation potential

Razvoj in karakterizacija funkcijskih markerjev za genetske študije oljke (Olea europaea L.)

Razvili smo nov set genskih mikrosatelitskih markerjev za genetske študije oljke (Olea europaea L.). Za identifikacijo mikrosatelitov smo pregledali 98.924 zaporedij EST razvijajočega plodu oljke. V 923 zaporedjih EST, ki so vsebovala mikrosatelite, smo odkrili skupno 984 mikrosatelitov, med katerimi so prevladovali dinukleotidi in sledili so jim trinukleotidi. Med dinukleotidi je prevladoval mikrosatelitski motiv GA in med trinukleotidi motiv GAA. Za izdelavo začetnih oligonukleotidov smo izbrali 110 anotiranih zaporedij EST-SSR, izmed katerih je bilo 46 polimorfnih. S sekvenčno reakcijo in poravnavo alelov EST-SSR oljke smo potrdili pomnoževanje predvidenih mikrosatelitskih motivov in odkrili visoko stopnjo ohranjenosti robnih območij analiziranih mikrosatelitskih lokusov. Sposobnost genskih markerjev SSR za odkrivanje genetske raznolikosti je primerljiva s predhodno razvitimi genomskimi mikrosateliti. Povprečno število alelov na lokus je bilo 4,5, vrednosti dejanske in pričakovane heterozigotnosti ter informacijska vrednost polimorfizma pa so znašale 0,649, 0,604 in 0,539. Na podlagi rezultatov genotipizacije z markerji EST-SSR oz. SSR in na osnovi Jaccardovih koeficientov podobnosti se je jasno razlikovalo vseh 24 oljčnih sort. Genetska raznolikost znotraj sort "Ascolana tenera" in "Santa Caterina" se je jasno pokazala le z genomskimi mikrosateliti. Za analizo starševstva smo uporabili 7 visoko polimorfnih markerjev EST-SSR. Izvedba starševskega testa s tremi različnimi računalniškimi programi (FAMOZ, CERVUS, PARENTE) je pokazala, da je "Istrska belica" navzkrižno kompatibilna z različnimi oljčnimi sortami. Vrednosti indeksa samonekompatibilnosti med 0,2 in 1,0 so "Istrsko belico" uvrstile med delno samonekompatibilne sorte.We developed a new set of functional microsatellite markers for genetic studies in olive (Olea europaea L.). A total of 98,924 ESTs from developing olive fruit were examined for the presence of SSRs, and 984 SSR motifs from 923 SSR containing ESTs were identified, among which dinucleotide SSRs were the most abundant, followed by trinucleotides. The motif GA was the most common among dinucleotides, while GAA was the most abundant trinucleotide SSR motif. A total of 110 EST-SSRs with annotated genes was selected for primer designing, of which 46 EST-SSRs finally showed polymorphism. The sequencing and alignment of the olive EST-SSR alleles confirmed the amplification of predicted microsatellite motifs and revealed a high degree of conservation of the SSRs flanking regions. New EST-SSRs possess genetic diversity properties comparable to previously developed genomic SSRs. The average number of alleles per locus, observed heterozygosity, expected heterozygosity, and polymorphic information content were 4.5, 0.649, 0.604 and 0.539, respectively. Cluster analysis based on EST-SSR or SSR genotyping data and Jaccard"s similarity coefficient clearly distinguished 24 olive varieties, but intra-cultivar variability in "Ascolana tenera" and "Santa Caterina" was well resolved only by genomic SSRs. Seven new EST-SSR loci with high polymorphic information content were used for paternity analysis. Paternity testing with three computer programs (FAMOZ, CERVUS, PARENTE) showed that "Istrska belica" is cross-compatible with other olive varieties. The index of self-incompatibility was between 0.2 and 1.0 and "Istrska belica" variety was classified as partly self-incompatible

Potential for using student-centred teaching and learning methods in biological subjects at UP FAMNIT

In order to successfully acquire theoretical knowledge and to gain a deeper understanding of the structure and functioning of biological structures and phenomena, theoretical lessons in biological subjects are supported by practical exercises at all levels of education. At the higher education level, the importance of practical lessons can even equal that of lectures. Student-centred learning and teaching approaches, supported by ICT, can help improve knowledge acquisition as well as provide students with digital competencies. In order to understand which teaching methods are currently being used in practical biological courses, we conducted a survey among UP FAMNIT’s teaching assistants. Only half of the respondents incorporate innovative teaching and learning methods in their lessons. Among the ICT tools we surveyed, the majority know and use the freely available virtual learning environment, Moodle. Many are familiar with other web applications but do not incorporate them into the teaching process. Most respondents are in favour of using ICT tools but do not use them due to time constraints or poor knowledge of them.Za uspešno pridobivanje teoretičnega znanja in globlje razumevanje zgradbe in delovanja bioloških struktur ter pojavov je teoretični pouk bioloških predmetov na vseh stopnjah izobraževanja podprt s praktičnimi vajami. Na visokošolski stopnji so praktične vaje pri posameznih predmetih celo bolj ali manj enakovreden del predavanjem. Na študenta osredinjeni pristopi učenja in poučevanja, podprti z orodji informacijsko-komunikacijske tehnologije (IKT), lahko pripomorejo k učinkovitejšemu razvoju znanja, izjemnega pomena pa so lahko tudi z vidika pridobivanja digitalnih kompetenc pri študentih. Na Fakulteti za matematiko, naravoslovje in informacijske tehnologije Univerze na Primorskem (UP FAMNIT) smo izvedli anketno raziskavo, v kateri smo želeli ugotoviti, kakšne metode poučevanja uporabljajo izvajalci praktičnega pouka bioloških predmetov. Rezultati so pokazali, da le slaba polovica anketiranih izvajalcev v praktični pouk vključuje inovativne metode učenja in poučevanja. Med orodji IKT, po katerih smo spraševali v anketi, več kot 80 % vprašanih pozna in uporablja prosto dostopno virtualno učno okolje Moodle. Mnogi poznajo tudi druge spletne aplikacije, vendar jih ne vključujejo v pedagoški proces. Večina vprašanih je naklonjena uporabi orodij IKT, a jih največkrat ne uporabljajo zaradi stiske s časom ali zaradi njihovega slabega poznavanja