Ecologically conditioned imprinting of miRNA-based profiles of Ginkgo biloba L. growing in Slovakia
DOI:
https://doi.org/10.2478/foecol-2019-0008Keywords:
Ginkgo, locality, molecular markers, SlovakiaAbstract
Ginkgo biloba L. is characterized by its high level of resistance to climatic conditions, diseases, and pests. In Slovakia, there is a rich collection of genetic resources of ginkgo consisting of 288 trees growing in 103 locations and providing valuable biological material for scientific research. There have been documented 45 trees of ginkgo older than 100 years (ranging from 112 to 242 years of age). Their dendrometrical parameters were recorded. For genomic imprinting, three types of microRNA-based markers were selected; highly conserved gb-miR160, moderately conserved gb-miR482 and the species-specific gb-miR75. The most efficient one can be considered the marker gb-miR482 with its genotype-unique miRNA profiles probably related to this marker functioning in the defence mechanisms of the ginkgo species. Unique miRNA loci were recorded in genomes of young ginkgo trees. We found that, by selecting the appropriate microRNA-based markers, it is possible to characterize the ginkgo genome in the context of microclimatic conditions.
References
Barlow, P., Kurczynska, E., 2007. The anatomy of the chi-chi of Ginkgo biloba suggests a mode of elongation growth that is an alternative to growth driven by an apical meristem. Journal of Plant Research, 120: 269–280. https://doi.org/10.1007/s10265-006-0050-3
Bartel, D.P., 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116: 281–297. https://doi.org/10.1016/S0092-8674(04)00045-5
Barvkar, V.T., Pardeshi, V.C., Kale, S.M., Qiu, S., Rollins, M., Datla, R., Kadoo, N.Y., 2013. Genome-wide identification and characterization of microRNA genes and their targets in flax (Linum usitatissimum): characterization of flax miRNA genes. Planta, 237: 1149–1151.23291876 https://doi.org/10.1007/s00425-012-1833-5
Begović, B.M., 2010. Ginkgo biloba L. 1771. All about ginkgo (or maidenhair tree). Vol. 1. Pitomača: Self-publishing. 259 p. [cit. 2018-08-09]. http://www.scribd.com/doc/74555470/Nature-s-Miracle-Ginkgo-Biloba_Book-1-Vol-1-2-B-M-Begovic-Bego
Bej, S., Basak, J., 2014. MicroRNAs: the potential bio-markers in plant stress response. American Journal of Plant Sciences, 5: 748–759. https://doi.org/10.4236/ajps.2014.55089
Benčať, F., 1982. Atlas rozšírenia cudzokrajných drevín na Slovensku a rajonizácia ich pestovania [Atlas of distribution of exotic woody species in Slovakia and zoning of their cultivation]. Bratislava: Veda. 368 p.
Fan, X.X., Shen, L., Zhang, X., Chen, X.Y., Fu, Ch.X., 2004. Assessing genetic diversity of Ginkgo biloba L. (Ginkgoaceae) populations from China by RAPD markers. Biochemical Genetics, 42: 7–8. 269–278. https://doi.org/10.1023/B:BIGI.0000034431.15308.57
Ferezliev, A., 2017. Relationship between particular dendrobiometrical indicators of natural European beech (Fagus sylvatica L.) dendrocenoses in Central Balkan Range. Folia Oecologica, 44 : 69–77. https://doi.org/10.1515/foecol-2017-0009
Fu, D., Ma, B., Mason, A.S., Xiao, M., Wei, L. An, Z., 2013. MicroRNA-based molecular markers: a novel PCR-based genotyping technique in Brassica species. Plant Breeding, 132: 375–381. https://doi.org/10.1111/pbr.12069
Ganie, S.A., Mondal, T.K., 2015. Genome-wide development of novel miRNA-based microsatellite markers of rice (Oryza sativa) for genotyping applications. Molecular Breeding, 35: 1–12. https://doi.org/10.1007/s11032-015-0207-7
Garcia-Vallve, S., Palau, J., Romeu, A., 1999. Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis. Molecular Biology and Evolution, 16: 1125–1134.10486968 https://doi.org/10.1093/oxfordjournals.molbev.a026203
Han, S., Wu, Z., Jin, Y., Yang, W., Shi, H., 2015. RNA-Seq analysis for transcriptome assembly, gene identification, and SSR mining in ginkgo (Ginkgo biloba L.). Tree Genetics and Genomes, 11: 37. https://doi.org/10.1007/s11295-015-0868-8
He, B., Gu, Y., Xu, M., Wang, J., Cao, F., Xu, L., 2015. Transcriprome analysis of Ginkgo biloba kernels. Frontiers in Plant Science, 6: 819.459386426500663 https://doi.org/10.3389/fpls.2015.00819
Hlavačková, L., Nôžková, J., Porokhovinova, E., Brutch, N., Shelenga, T., Bjelková, M. Ražná, K., 2016. Analysis of miRNA polymorphism during the selected developmental processes of flax. Journal of Central European Agriculture, 17: 707–724. https://doi.org/10.5513/JCEA01/17.3.1767
Hrubík, P., Kollár, J., Rovná, K., Tkáčová, S., Mňahončáková, E., 2011. Kvalitatívna inventarizácia, klasifikácia a hodnotenie zdravotného stavu drevín pre účely záhradno-architektonickej a krajinárskej tvorby [Qualitative inventory, classification and assessment of health state of woody plants with purpose of their use in garden and landscape design prosome]. Nitra: Slovenská poľnohospodárska univerzita. 99 p.
Jones-Rhoades, M. W., Bartel, D. P., Bartel, B., 2006. MicroRNAs and their regulatory roles in plants. Annual Review of Plant Biology, 57:19–53.16669754 https://doi.org/10.1146/annurev.arplant.57.032905.105218
Kolařík, J., Martinková, M., Čermák, M., Gebauer, R., Špinlerová, Z., Dienstbier, F., Horáček, P., Praus, L., Cudlín, P., Krejčiřík, P., Reš, B., Romanský, M., Jankovský, L., Beránek, J., Lička, D., Wessolly, L., 2010. Péče o dřeviny rostoucí mimo les [Cultivation of woody plants growing outside forest stands]. 2nd vol. Vlašim: ČSOP. 720 p.
Kruszka, K., Pieczynski, M., Windels, D., Bielewicz, D., Jarmolowski, A., Szweykowska-Kulinska, Z., Vazquez, F., 2012. Role of microRNAs and other sRNAs of plants in their changing environments. Journal of Plant Physiology, 169: 1664–1672.22647959 https://doi.org/10.1016/j.jplph.2012.03.009
Li, G.P., Zhang, C.Q., Cao, F.L., 2013. An efficient approach to identify Ginkgo biloba cultivars by using random amplified polymorphic DNA markers with a manual cultivar identification diagram strategy. Genetics and Molecular Research, 12 (1): 175–182.23408404 https://doi.org/10.4238/2013.January.24.10
Li, Y.Y., Zhang, L.P., Chen, X.Y. 2009. Development of polymorphic microsatellite markers for Ginkgo biloba L. by database mining. Conservation Genetics Resources, 1:81–83. https://doi.org/10.1007/s12686-009-9019-6
Liao, L., Liu, J., Dai, Y., Li, X., Xie, M., Chen, Q., Yin, H., Qiu, G., Liu, X., 2009. Development and application of SCAR markers for sex identification in the dioecious species Ginkgo biloba L. Euphytica. 169 (1): 49–55. https://doi.org/10.1007/s10681-009-9913-8
Lin, X., Zhang, J., Li, Y., Luo, H., Wu, Q., Sun, CH., Song, J., Li, X., Wei, J., Lu, A., Qian, Z., Khan, I.A., Chen, S., 2011. Functional genomics of a living fossil tree, Ginkgo, based on next-generation sequencing technology. Physiologia Plantarum, 143: 207–218.21834857 https://doi.org/10.1111/j.1399-3054.2011.01500.x
Mei, Z., Khan, M. A., Zeng, W., Fu, J., 2014. DNA fingerprints of living fossil Ginkgo biloba by using ISSR and improved RAPD analysis. Biochemical Systematics and Ecology, 57: 332–337. https://doi.org/10.1016/j.bse.2014.09.007
Mohanta, T.K., 2012. Advances in Ginkgo biloba research. Genomics and metabolomics perspectives. African Journal of Biotechnology. 11: 15936–15944. https://doi.org/10.5897/AJB12.627
Mondal, T.K., Ganie, S.A., 2014. Identification and characterization of salt responsive miRNA-SSR markers in rice (Oryza sativa). Gene, 535: 204–209.24315823 https://doi.org/10.1016/j.gene.2013.11.033
Neutelings, G., Fénart, S., Lucau-Danila, A., Hawkins, S., 2012. Identification and characterization of miRNA and their potential targets in flax. Journal of Plant Physiology, 169: 1754–1766.22841625 https://doi.org/10.1016/j.jplph.2012.06.011
Padmalatha, K., Prasad, M.N.V., 2006. Optimization of DNA isolation and PCR protocol for RAPD analysis of selected medicinal and aromatic plants of conservation concern from Peninsular India. African Journal Biotechnology, 5: 230–234.
Ražná, K., Hrubík, P., 2016. Ginkgo dvojlaločné (Ginkgo biloba L.) – genomická štúdia a kultúrne rozšírenie na Slovensku [Ginkgo biloba L. – genomic study and cultural area of expansion in Slovakia]. Nitra: Slovenská poľnohospodárska unvierzita. 92 p.
Ražná, K., Hrubík, P., Žiarovská, J., Kollár, J., Kullačová, D., Pavel, J., Štefúnová, V., 2014. Kultúrne rozšírenie ginka dvojlaločného (Ginkgo biloba L.) na Slovensku a hodnotenie jeho variability pomocou DNA markérov [Cultural area of expansion of Ginkgo biloba L. in Slovakia and assessments of this species variability with using DNA markers]. Nitra: Slovenská poľnohospodárska univerzita. 95 p.
Ražná, K., Nôžková, J., Hlavačková, L., Brutch, N., Porokhovinova, E., Shelenga, T., Pavlov, A., 2015. Geno-typing of flax genetic resources by miRNA-based molecular markers and morphology. Agriculture, 61: 129–138. https://doi.org/10.1515/agri-2015-0018
Šmarda, P., Horová, L., Knápek, O., Dieck, H., Dieck, M., Ražná, K., Hrubík, P., Orlóci, L., Papp, L., Veselá, K., Veselý, P., Bureš, P., 2018. Multiple haploids, triploids, and tetraploids found in modern-day “living fossil” Ginkgo biloba. Horticulture Research, 5: 55.616584530302259 https://doi.org/10.1038/s41438-018-0055-9
Šmarda, P., Veselý, P., Šmerda, J., Bureš, P., Knápek, O., Chytrá, M., 2016. Polyploidy in a “living fossil” Ginkgo biloba. New Phytologist, 212: 11–14.27265838 https://doi.org/10.1111/nph.14062
Van Beek, T. A. (eds), 2000. Ginkgo biloba. Amsterdam: Taylor and Francis e-Library. 523 p. ISBN 0-203-34306-9
Uhrin, P., Supuka, J., Billiková, M. 2018. Adaptability of Norway maple (Acer platanoides L.) to urban environment. Folia Oecologica, 45: 33–45. https://doi.org/10.2478/foecol-2018-0004
Zhang, Q., Li, J., Sang, Y., Xing, S., Wu, Q., Liu, X., 2015. Identification and characterization of MicroRNAs in Ginkgo biloba var. epiphylla Mak. PLoS ONE, 10 (5): e0127184.443326625978425 https://doi.org/10.1371/journal.pone.0127184
Zittlau, J. 2007. Liečivo ginkgo [Medicinal product ginkgo]. Bratislava: Noxi. 96 p.
Wang, L., Zhao, J., Zhang, M., Weixin, L., Luo, K., Lu, Z., Zhang, CH., Jin, B., 2015. Identification and characterization of microRNA expression in Ginkgo biloba L. leaves. Tree Genetics & Genomes, 11: 76. https://doi.org/10.1007/s11295-015-0897-3
Wang, M., Wang, Q., Wang, B., 2012. Identification and characterization of microRNAs in Asiatic cotton (Gossypium arboreum L.). Plos One, 7: 4.332089422493671 https://doi.org/10.1371/journal.pone.0033696
Yadav, C.B.Y., Muthamilarasan, M., Pandey, G., Prasad, M., 2014. Development of novel microRNA-based genetic markers in foxtail millet for genotyping applications in related grass species. Molecular Breeding, 34: 2219–2224. https://doi.org/10.1007/s11032-014-0137-9
Yan, X.L., Chen, Y.Y., Guan, B. C., Fu, Ch. X., 2009. Eleven novel microsatellite markers developed from the living fossil Ginkgo biloba L. (Ginkgoaceae). Conservation Genetics, 10: 1277–1279. https://doi.org/10.1007/s10592-008-9706-y
Yan, X.F., Lian, C.L., Hogetsu, T., 2006. Development of microsatellite markers in ginkgo (Ginkgo biloba L.). Molecular Ecology Notes, 6: 301–302. https://doi.org/10.1111/j.1471-8286.2006.01134.x
Yang, H., Gan, S.M., Yin, G.T., Xu, H.C., 2005. Identification of random amplified polymorphic DNA markers linked to sex determination in Calamus simplicifolius C. F. Wei. Journal of Integrative Plant Biology, 47 (10): 1249–1253. https://doi.org/10.1111/j.1744-7909.2005.00113.x
Downloads
Published
Issue
Section
License
This journal provides immediate open access to its content under the Creative Commons BY-NC-ND 4.0 license. Authors who publish with this journal retain all copyrights except for commercial rights (transfer of commercial rights) and agree to the terms of the above-mentioned CC BY-NC-ND 4.0 license.
