The World’s oldest living grapevine specimen and its genetic relationships

The Old Vine from Lent (Maribor, Slovenia) which belongs to the ‘Modra Kavčina’ group (i.e. ‘Blauer Kölner’ in the Vitis International Variety Catalogue and ‘Žametovka’ in the official varietal list of Slovenia) is considered to be the oldest living specimen of cultivated grapevine (at least 400 years old). The aim of our study was to determine the genetic relationships among different accessions of the ‘Žametovka’ group, the position the Old Vine within this group, and the relationship between the Old Vine and other red varieties grown in Slovenia and neighbouring countries. The molecular genetic analysis was based on microsatellite data. The study shows that the ‘Žametovka’ group is genetically completely different from other red varieties studied. Among these genetically distant varieties, in our study, ‘Chasselas red’ appears to be the closest. The ‘Žametovka’ group is genetically highly homogenous, and half of the studied accessions probably belong to the same clone. The ‘Old vine’ cannot be considered as a significantly different genotype. The minor differences detected by microsatellite markers are probably due to mutations accumulated over a long period of time and possibly to epigenetic changes.

Characteristics and empiric antimicrobial therapy of urinary tract infections in patients treated at the Departement of Infectious Diseases, General Hospital »Dr. Josip Benčević« in Slavonski Brod

Infekcije mokraćnog sustava (IMS) jedan su od najčešćih razloga traženja liječničke pomoći, pa stoga i među najčešćim razlozima propisivanja antibiotika. Istaknuta je analiza najčešćih uzročnika IMS u našoj sredini, uočavanje stupnja rezistencije na pojedine antibiotike, te ocjena uspješnosti ordinirane empirijske antimikrobne terapije. Retrospektivno su obrađeni podaci o bolesnicima liječenim na Odjelu za zarazne bolesti Opće bolnice »Dr. Josip Benčević« u Slavonskom Brodu, zbog akutnih infekcija mokraćnog sustava, tijekom 2004. godine. Najčešći je uzročnik IMS bila Escherichia coli, premda je u muškaraca s kompliciranim IMS bio najčešći uzročnik Pseudomonas aeruginosa. Obzirom da je 45 % izoliranih bakterija Escherichia coli bilo rezistentno na amoksicilin, a 35 % na kotrimoksazol, ovi antibiotici se u našoj sredini ne mogu upotrebljavati u empirijskoj antimikrobnoj terapiji IMS. Čak 65 % izoliranih bakterija Pseudomonas aeruginosa nije bilo osjetljivo na gentamicin, a 45 % na ciprofloksacin. Najčešći neuspjeh empirijske antimikrobne terapije zabilježen je u muškaraca s kompliciranim IMS, pa bi nam bio najbolji izbor empirijskog antimikrobnog liječenja ovih bolesnika kombinacija piperacilina s tazobaktamom, karbapenemi ili cefepim.Urinarv tract infections (UTI) are one of the most common reasons for seeking medical consultation and therefore are among the most frequent reasons for antibiotic prescription. The purpose of this paper is the analvsis of the most common etiologic agents of UTI in our environment, registration of the degree of bacterial resistance, and evaluation of empiric antibiotic therapv success. Retrospectively data of patients, hospitalized during year 2004, at the Departement of Infectious Diseases, General Hospital »Dr. Josip Benčević« in Slavonski Brod, due to acute urinarv tract infections, were analysed. The most common cause of UTI was Escherichia coli, although in male patients with complicated UTI, the most common cause was Pseudomonas aeruginosa. Since 45% of Escherichia coli were amoxicillin resistant, and 35% trimethoprim-sulfamethoxazole resistant, these antimicrobials can\u27t be used as empiric therapy drugs in our environment. As much as 65% of Pseudomonas aeruginosa were gentamicin and 45% ciprofloxacin resistant. The most frequent empiric antibiotic therapy failure was observed in male patients with complicated UTI, so the best empiric drug choice for these patients, in our situation, would be piperacillin/tazobactam, carbapenems or cefepime

Genetic diversity and structure of Slovenian native germplasm of plum species (P. domestica L., P. cerasifera Ehrh. and P. spinosa L.)

Slovenia has particular climatic, soil, geographic and historical conditions that lead to long tradition of plum cultivation and use. In this work, a set of 11 SSR and three universal cpDNA markers, as well as flow cytometry, were used to (1) evaluate the genetic diversity of 124 accessions of the three Prunus species (P. domestica L., P. cerasifera Ehrh., and P. spinosa L.), (2) investigate the possible involvement of P. cerasifera and P. spinosa species in P. domestica origin, (3) study the genetic relationships and variability among the most typical P. domestica accessions present in Slovenia. Ten haplotypes of cpDNA were identified and clustered into three groups according to the Neighbor-Joining analysis (NJ). All 11 SSR primer pairs were polymorphic, revealing 116 unique genotypes. A total of 328 alleles were detected with an average value of 29.82 alleles per locus, showing relatively high diversity. Bayesian analysis of genetic structure was used to identify two ancestral populations in the analyses of all three species as well as in a separate set consisting of P. domestica material only. Principal Coordinate Analysis (PCoA) showed that accessions clustered largely in agreement with Bayesian analysis. Neighbor-Joining analysis grouped 71 P. domestica accessions into three clusters with many subgroups that exhibited complex arrangement. Most accessions clustered in agreement with traditional pomological groups, such as common prunes, mirabelle plums and greengages. In this study, the analyses revealed within P. domestica pool valuable local landraces, such as traditional prunes or bluish plums, which seem to be highly interesting from a genetic point of view. Moreover, complementary approaches allowed us to distinguish between the three species and to gain insights into the origin of plum. The results will be instrumental in understanding the diversity of Slovenian plum germplasm, improving the conservation process, recovering local genotypes and enriching existing collections of plant genetic resources

First TILLING Platform in Cucurbita pepo: A New Mutant Resource for Gene Function and Crop Improvement

Although the availability of genetic and genomic resources for Cucurbita pepo has increased significantly, functional genomic resources are still limited for this crop. In this direction, we have developed a high throughput reverse genetic tool: the first TILLING (Targeting Induced Local Lesions IN Genomes) resource for this species. Additionally, we have used this resource to demonstrate that the previous EMS mutant population we developed has the highest mutation density compared with other cucurbits mutant populations. The overall mutation density in this first C. pepo TILLING platform was estimated to be 1/133 Kb by screening five additional genes. In total, 58 mutations confirmed by sequencing were identified in the five targeted genes, thirteen of which were predicted to have an impact on the function of the protein. The genotype/phenotype correlation was studied in a peroxidase gene, revealing that the phenotype of seedling homozygous for one of the isolated mutant alleles was albino. These results indicate that the TILLING approach in this species was successful at providing new mutations and can address the major challenge of linking sequence information to biological function and also the identification of novel variation for crop breeding.Financial support was provided by the Spanish Project INIA (Instituto Nacional de Investigacion y Tecnologia Agraria y Almentaria) RTA2011-00044C02-01, the ANR MELODY (ANR-11-BSV7-0024), the European Research Council (ERCSEXYPARTH), FEDER, and FSE funds. NVD has been awarded a grant by the Andalusian Institute of Agronomy Research IFAPA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Vicente-Dolera, N.; Troadec, C.; Moya, M.; Río-Celestino, MD.; Pomares-Viciana, T.; Bendahmane, A.; Picó Sirvent, MB.... (2014). First TILLING Platform in Cucurbita pepo: A New Mutant Resource for Gene Function and Crop Improvement. PLoS ONE. 9(11):112743-112743. https://doi.org/10.1371/journal.pone.0112743S112743112743911Paris, H. S., Yonash, N., Portnoy, V., Mozes-Daube, N., Tzuri, G., & Katzir, N. (2002). Assessment of genetic relationships in Cucurbita pepo (Cucurbitaceae) using DNA markers. Theoretical and Applied Genetics, 106(6), 971-978. doi:10.1007/s00122-002-1157-0Parry, M. A. J., Madgwick, P. J., Bayon, C., Tearall, K., Hernandez-Lopez, A., Baudo, M., … Phillips, A. L. (2009). Mutation discovery for crop improvement. Journal of Experimental Botany, 60(10), 2817-2825. doi:10.1093/jxb/erp189Gilchrist, E., & Haughn, G. (2010). Reverse genetics techniques: engineering loss and gain of gene function in plants. Briefings in Functional Genomics, 9(2), 103-110. doi:10.1093/bfgp/elp059McCallum, C. M., Comai, L., Greene, E. A., & Henikoff, S. (2000). Targeting Induced LocalLesions IN Genomes (TILLING) for Plant Functional Genomics. Plant Physiology, 123(2), 439-442. doi:10.1104/pp.123.2.439Colbert, T., Till, B. J., Tompa, R., Reynolds, S., Steine, M. N., Yeung, A. T., … Henikoff, S. (2001). High-Throughput Screening for Induced Point Mutations. Plant Physiology, 126(2), 480-484. doi:10.1104/pp.126.2.480Wang, T. L., Uauy, C., Robson, F., & Till, B. (2012). TILLINGin extremis. Plant Biotechnology Journal, 10(7), 761-772. doi:10.1111/j.1467-7652.2012.00708.xDong, C., Dalton-Morgan, J., Vincent, K., & Sharp, P. (2009). A Modified TILLING Method for Wheat Breeding. The Plant Genome Journal, 2(1), 39. doi:10.3835/plantgenome2008.10.0012Uauy, C., Paraiso, F., Colasuonno, P., Tran, R. K., Tsai, H., Berardi, S., … Dubcovsky, J. (2009). A modified TILLING approach to detect induced mutations in tetraploid and hexaploid wheat. BMC Plant Biology, 9(1), 115. doi:10.1186/1471-2229-9-115Kumar, A. P., Boualem, A., Bhattacharya, A., Parikh, S., Desai, N., Zambelli, A., … Bendahmane, A. (2013). SMART -- Sunflower Mutant population And Reverse genetic Tool for crop improvement. BMC Plant Biology, 13(1), 38. doi:10.1186/1471-2229-13-38Kurowska, M., Daszkowska-Golec, A., Gruszka, D., Marzec, M., Szurman, M., Szarejko, I., & Maluszynski, M. (2011). TILLING - a shortcut in functional genomics. Journal of Applied Genetics, 52(4), 371-390. doi:10.1007/s13353-011-0061-1Rigola, D., van Oeveren, J., Janssen, A., Bonné, A., Schneiders, H., van der Poel, H. J. A., … van Eijk, M. J. T. (2009). High-Throughput Detection of Induced Mutations and Natural Variation Using KeyPoint™ Technology. PLoS ONE, 4(3), e4761. doi:10.1371/journal.pone.0004761González, M., Xu, M., Esteras, C., Roig, C., Monforte, A. J., Troadec, C., … Picó, B. (2011). Towards a TILLING platform for functional genomics in Piel de Sapo melons. BMC Research Notes, 4(1). doi:10.1186/1756-0500-4-289Elias, R., Till, B. J., Mba, C., & Al-Safadi, B. (2009). Optimizing TILLING and Ecotilling techniques for potato (Solanum tuberosum L). BMC Research Notes, 2(1), 141. doi:10.1186/1756-0500-2-141Dahmani-Mardas, F., Troadec, C., Boualem, A., Lévêque, S., Alsadon, A. A., Aldoss, A. A., … Bendahmane, A. (2010). Engineering Melon Plants with Improved Fruit Shelf Life Using the TILLING Approach. PLoS ONE, 5(12), e15776. doi:10.1371/journal.pone.0015776Boualem, A., Fleurier, S., Troadec, C., Audigier, P., Kumar, A. P. K., Chatterjee, M., … Bendahmane, A. (2014). Development of a Cucumis sativus TILLinG Platform for Forward and Reverse Genetics. PLoS ONE, 9(5), e97963. doi:10.1371/journal.pone.0097963Blanca, J., Cañizares, J., Roig, C., Ziarsolo, P., Nuez, F., & Picó, B. (2011). Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics, 12(1). doi:10.1186/1471-2164-12-104Esteras, C., Gomez, P., Monforte, A. J., Blanca, J., Vicente-Dolera, N., Roig, C., … Pico, B. (2012). High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping. BMC Genomics, 13(1), 80. doi:10.1186/1471-2164-13-80Vicente-Dólera, N., Pinillos, V., Moya, M., Del Río-Celestino, M., Pomares-Viciana, T., Román, B., & Gómez, P. (2014). An improved method to obtain novel mutants in Cucurbita pepo by pollen viability. Scientia Horticulturae, 169, 14-19. doi:10.1016/j.scienta.2014.01.045Martín, B., Ramiro, M., Martínez-Zapater, J. M., & Alonso-Blanco, C. (2009). A high-density collection of EMS-induced mutations for TILLING in Landsberg erecta genetic background of Arabidopsis. BMC Plant Biology, 9(1), 147. doi:10.1186/1471-2229-9-147Wienholds, E. (2003). Efficient Target-Selected Mutagenesis in Zebrafish. Genome Research, 13(12), 2700-2707. doi:10.1101/gr.1725103Dalmais, M., Schmidt, J., Le Signor, C., Moussy, F., Burstin, J., Savois, V., … Bendahmane, A. (2008). UTILLdb, a Pisum sativum in silico forward and reverse genetics tool. Genome Biology, 9(2), R43. doi:10.1186/gb-2008-9-2-r43Triques, K., Sturbois, B., Gallais, S., Dalmais, M., Chauvin, S., Clepet, C., … Bendahmane, A. (2007). Characterization of Arabidopsis thaliana mismatch specific endonucleases: application to mutation discovery by TILLING in pea. The Plant Journal, 51(6), 1116-1125. doi:10.1111/j.1365-313x.2007.03201.xTaylor, N. E. (2003). PARSESNP: a tool for the analysis of nucleotide polymorphisms. Nucleic Acids Research, 31(13), 3808-3811. doi:10.1093/nar/gkg574Ng, P. C. (2003). SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Research, 31(13), 3812-3814. doi:10.1093/nar/gkg509Obrero, Á., González-Verdejo, C. I., Die, J. V., Gómez, P., Del Río-Celestino, M., & Román, B. (2013). Carotenogenic Gene Expression and Carotenoid Accumulation in Three Varieties of Cucurbita pepo during Fruit Development. Journal of Agricultural and Food Chemistry, 61(26), 6393-6403. doi:10.1021/jf4004576Cosio, C., Vuillemin, L., De Meyer, M., Kevers, C., Penel, C., & Dunand, C. (2009). An anionic class III peroxidase from zucchini may regulate hypocotyl elongation through its auxin oxidase activity. Planta, 229(4), 823-836. doi:10.1007/s00425-008-0876-0Sisko, M. (2003). Genome size analysis in the genus Cucurbita and its use for determination of interspecific hybrids obtained using the embryo-rescue technique. Plant Science, 165(3), 663-669. doi:10.1016/s0168-9452(03)00256-5Campa A (1991) Biological roles of plant peroxidases: known and potential function. In Peroxidases in Chemistry and Biology Vol. II. (Everse, J., Everse, K.E. & Grisham, M.B., eds), pp. 25–50, CRC Press, Boca Raton, FL.Schuller, D. J., Ban, N., van Huystee, R. B., McPherson, A., & Poulos, T. L. (1996). The crystal structure of peanut peroxidase. Structure, 4(3), 311-321. doi:10.1016/s0969-2126(96)00035-4Stephenson, P., Baker, D., Girin, T., Perez, A., Amoah, S., King, G. J., & Østergaard, L. (2010). A rich TILLING resource for studying gene function in Brassica rapa. BMC Plant Biology, 10(1), 62. doi:10.1186/1471-2229-10-62Suzuki, T., Eiguchi, M., Kumamaru, T., Satoh, H., Matsusaka, H., Moriguchi, K., … Kurata, N. (2007). MNU-induced mutant pools and high performance TILLING enable finding of any gene mutation in rice. Molecular Genetics and Genomics, 279(3), 213-223. doi:10.1007/s00438-007-0293-2Chantreau, M., Grec, S., Gutierrez, L., Dalmais, M., Pineau, C., Demailly, H., … Hawkins, S. (2013). PT-Flax (phenotyping and TILLinG of flax): development of a flax (Linum usitatissimum L.) mutant population and TILLinG platform for forward and reverse genetics. BMC Plant Biology, 13(1), 159. doi:10.1186/1471-2229-13-159Rawat, N., Sehgal, S. K., Joshi, A., Rothe, N., Wilson, D. L., McGraw, N., … Gill, B. S. (2012). A diploid wheat TILLING resource for wheat functional genomics. BMC Plant Biology, 12(1), 205. doi:10.1186/1471-2229-12-205Minoia, S., Petrozza, A., D’Onofrio, O., Piron, F., Mosca, G., Sozio, G., … Carriero, F. (2010). A new mutant genetic resource for tomato crop improvement by TILLING technology. BMC Research Notes, 3(1). doi:10.1186/1756-0500-3-69Markiewicz, P., Kleina, L. G., Cruz, C., Ehret, S., & Miller, J. H. (1994). Genetic Studies of the lac Repressor. XIV. Analysis of 4000 Altered Escherichia coli lac Repressors Reveals Essential and Non-essential Residues, as well as «Spacers» which do not Require a Specific Sequence. Journal of Molecular Biology, 240(5), 421-433. doi:10.1006/jmbi.1994.1458Carpin, S., Crèvecoeur, M., Greppin, H., & Penel, C. (1999). Molecular Cloning and Tissue-Specific Expression of an Anionic Peroxidase in Zucchini. Plant Physiology, 120(3), 799-810. doi:10.1104/pp.120.3.799Welinder, K. G., Justesen, A. F., Kjaersgård, I. V. H., Jensen, R. B., Rasmussen, S. K., Jespersen, H. M., & Duroux, L. (2002). Structural diversity and transcription of class III peroxidases from Arabidopsis thaliana. European Journal of Biochemistry, 269(24), 6063-6081. doi:10.1046/j.1432-1033.2002.03311.

Prognoziranje granice razvlačenja betonskih čelika temeljem poznatog kemijskog sastava

This research is based on both, theoretical and experimental work and aims to assessment the yield point of concrete steels, based on the known alloy chemical composition. The experimental portion of the work was performed at the Split steelmaking factory, which produces concrete steels from the waste iron. The theoretical portion of this study involves mathematical modelling carried out using the software package MATLAB. The work presented here provides both a scientific and practical contribution to the field. By using mathematical modelling, the accuracy of the estimation of the yield point is improved by 8,5%. Using this correlation enables the reduction of the concrete steel production costs because it is possible to reduce the use of expensive tests for the characterization of strength and mechanical properties.Ovo istraživanje je teorijsko eksperimentalnog karaktera, a obrađuje procjenu granice razvlačenja betonskih čelika na temelju kemijskog sastava slitina. Eksperimentalni dio istraživanja realiziran je u željezari Split koja proizvodi betonske čelike iz otpada ili starog čelika. Teorijski dio rada - matematičko modeliranje realizirano je korištenjem softverskog paketa MatLab. Istraživanje je rezultiralo znanstvenim i praktičnim doprinosom. Matematičkim modeliranjem poboljšana je točnost do sada poznate početne korelacije određivanja granice razvlačenja za 8,5 %. Korištenjem ove korelacije omogućit će se smanjenje troškova proizvodnje betonskih čelika, jer je moguće smanjiti opseg skupih ispitivanja čvrstoće i mehaničkih svojstava vlačnom probom

Genetic diversity and structure of Slovenian native germplasm of plum species (P. domestica L., P. cerasifera Ehrh. and P. spinosa L.)

Slovenia has particular climatic, soil, geographic and historical conditions that lead to long tradition of plum cultivation and use. In this work, a set of 11 SSR and three universal cpDNA markers, as well as flow cytometry, were used to (1) evaluate the genetic diversity of 124 accessions of the three Prunus species ( P. domestica L., P. cerasifera Ehrh., and P. spinosa L.), (2) investigate the possible involvement of P. cerasifera and P. spinosa species in P. domestica origin, (3) study the genetic relationships and variability among the most typical P. domestica accessions present in Slovenia. Ten haplotypes of cpDNA were identified and clustered into three groups according to the Neighbor-Joining analysis (NJ). All 11 SSR primer pairs were polymorphic, revealing 116 unique genotypes. A total of 328 alleles were detected with an average value of 29.82 alleles per locus, showing relatively high diversity. Bayesian analysis of genetic structure was used to identify two ancestral populations in the analyses of all three species as well as in a separate set consisting of P. domestica material only. Principal Coordinate Analysis (PCoA) showed that accessions clustered largely in agreement with Bayesian analysis. Neighbor-Joining analysis grouped 71 P . domestica accessions into three clusters with many subgroups that exhibited complex arrangement. Most accessions clustered in agreement with traditional pomological groups, such as common prunes, mirabelle plums and greengages. In this study, the analyses revealed within P. domestica pool valuable local landraces, such as traditional prunes or bluish plums, which seem to be highly interesting from a genetic point of view. Moreover, complementary approaches allowed us to distinguish between the three species and to gain insights into the origin of plum. The results will be instrumental in understanding the diversity of Slovenian plum germplasm, improving the conservation process, recovering local genotypes and enriching existing collections of plant genetic resources

Changes in the trophic level of an Alpine lake, Jezero v Ledvici (NW Slovenia), induced by earthquakes and climate change

Despite relatively high nutrient levels, the Slovenian Alpine lake Jezero v Ledvici (1824 m a.s.l.; max. depth 15 m) is oligotrophic, with high transparency and low chlorophyll concentrations (<1 μg l-1). Daily mean air temperatures at the lake are estimated to vary between –15.4 °C and +18.8 °C. Low air temperatures combined with the blocking of incident solar radiation by the local topography result in the lake being ice-covered for over six months of the year, suggesting that the effects of climate on the ecology of the lake may be mediated by the timing of the ice cover. Sediment cores taken in 1996 were dated by 210Pb and 137Cs and analysed for DW, LOI, cladoceran and diatom remains, pigments, C, N and S. A total of 50 diatom taxa and 4 cladoceran taxa were found. The base of the unsupported 210Pb record at 17.4 cm was dated to 1825 AD ± 25 y. An abrupt change in DW and LOI was observed at a depth of 17 cm, coinciding with a change in the cladoceran community and in C and N concentrations. From a depth of 12 cm (83 ± 4 y BP) upward, a sharp change in S and plant pigment concentrations were recorded, followed by an increase in diatom abundance at a depth of about 10 cm (63 ± 4 y BP). The timing of quantitative changes in the physical and chemical properties of the sediment, and in the community structure of diatoms and Cladocera, coincides with the occurrence of three earthquakes in the 19th century. Changes in the diatom and cladoceran record were compared with a tree-ring width index based on Larix decidua from the shore of the lake over the last 136 years, and with reconstructed air temperatures from 1781 – 1996. With a 4-y lag, a weak positive correlation exists between the tree-ring width index and the air temperatures. Although diatom abundance generally shows no correlation with the tree-ring width index, a negative correlation was found in the case of Fragilaria pinnata and Amphora lybica, interrupted only between 1942 and 1955. A similar pattern to this latter was also observed in the case of the Cladocera. During the last 250 y, anthropogenic influence on the lake catchment area has been confined mainly to limited sheep grazing. The main cause of changes occurring in the lake itself is likely to be eutrophication resulting from the input of allochthonous material from landslides triggered by earthquakes. During the last three decades, however, the main factor influencing biotic change appears to have been the increase in mean air temperature, possibly acting via ice cover

Table_1_Genetic diversity and structure of Slovenian native germplasm of plum species (P. domestica L., P. cerasifera Ehrh. and P. spinosa L.).xlsx

Slovenia has particular climatic, soil, geographic and historical conditions that lead to long tradition of plum cultivation and use. In this work, a set of 11 SSR and three universal cpDNA markers, as well as flow cytometry, were used to (1) evaluate the genetic diversity of 124 accessions of the three Prunus species (P. domestica L., P. cerasifera Ehrh., and P. spinosa L.), (2) investigate the possible involvement of P. cerasifera and P. spinosa species in P. domestica origin, (3) study the genetic relationships and variability among the most typical P. domestica accessions present in Slovenia. Ten haplotypes of cpDNA were identified and clustered into three groups according to the Neighbor-Joining analysis (NJ). All 11 SSR primer pairs were polymorphic, revealing 116 unique genotypes. A total of 328 alleles were detected with an average value of 29.82 alleles per locus, showing relatively high diversity. Bayesian analysis of genetic structure was used to identify two ancestral populations in the analyses of all three species as well as in a separate set consisting of P. domestica material only. Principal Coordinate Analysis (PCoA) showed that accessions clustered largely in agreement with Bayesian analysis. Neighbor-Joining analysis grouped 71 P. domestica accessions into three clusters with many subgroups that exhibited complex arrangement. Most accessions clustered in agreement with traditional pomological groups, such as common prunes, mirabelle plums and greengages. In this study, the analyses revealed within P. domestica pool valuable local landraces, such as traditional prunes or bluish plums, which seem to be highly interesting from a genetic point of view. Moreover, complementary approaches allowed us to distinguish between the three species and to gain insights into the origin of plum. The results will be instrumental in understanding the diversity of Slovenian plum germplasm, improving the conservation process, recovering local genotypes and enriching existing collections of plant genetic resources.</p

DataSheet_1_Genetic diversity and structure of Slovenian native germplasm of plum species (P. domestica L., P. cerasifera Ehrh. and P. spinosa L.).pdf

Slovenia has particular climatic, soil, geographic and historical conditions that lead to long tradition of plum cultivation and use. In this work, a set of 11 SSR and three universal cpDNA markers, as well as flow cytometry, were used to (1) evaluate the genetic diversity of 124 accessions of the three Prunus species (P. domestica L., P. cerasifera Ehrh., and P. spinosa L.), (2) investigate the possible involvement of P. cerasifera and P. spinosa species in P. domestica origin, (3) study the genetic relationships and variability among the most typical P. domestica accessions present in Slovenia. Ten haplotypes of cpDNA were identified and clustered into three groups according to the Neighbor-Joining analysis (NJ). All 11 SSR primer pairs were polymorphic, revealing 116 unique genotypes. A total of 328 alleles were detected with an average value of 29.82 alleles per locus, showing relatively high diversity. Bayesian analysis of genetic structure was used to identify two ancestral populations in the analyses of all three species as well as in a separate set consisting of P. domestica material only. Principal Coordinate Analysis (PCoA) showed that accessions clustered largely in agreement with Bayesian analysis. Neighbor-Joining analysis grouped 71 P. domestica accessions into three clusters with many subgroups that exhibited complex arrangement. Most accessions clustered in agreement with traditional pomological groups, such as common prunes, mirabelle plums and greengages. In this study, the analyses revealed within P. domestica pool valuable local landraces, such as traditional prunes or bluish plums, which seem to be highly interesting from a genetic point of view. Moreover, complementary approaches allowed us to distinguish between the three species and to gain insights into the origin of plum. The results will be instrumental in understanding the diversity of Slovenian plum germplasm, improving the conservation process, recovering local genotypes and enriching existing collections of plant genetic resources.</p