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Insights into historic and genetic relationships of diverse common lilac (Syringa vulgaris) genotypes based on whole-genome profiling
Published online by Cambridge University Press: 20 December 2023
Abstract
Common lilac (Syringa vulgaris L.) is a popular landscaping plant. Our aim was to obtain a large set of single nucleotide polymorphism (SNP) markers, to reveal the precise identities of the investigated S. vulgaris accessions, and to discover genetic relationships among them. The studied plant material included local Finnish, previously unidentified accessions, known reference cultivars, and so-called historical accessions i.e., old shrubs growing in historic cultural landscapes. We intended to verify cultivar names for some valuable local common lilac accessions and to provide insights into the history of common lilac cultivation in Finland. In the analyses, we used a set of 15,007 SNP markers. First, polymorphic information contents were calculated (mean 0.190, range 0.012–0.500 per marker). Then, to investigate genetic relationships among genotypes, a phylogenetic tree was constructed, and a principal coordinate analysis was conducted. A Bayesian analysis of population structure was performed to determine the number and distribution of genetic clusters among samples. Genetic marker data combined with existing historical and phenotypic knowledge revealed novel information on the unidentified cultivars and on the genetic relationships among studied accessions and solved the arrival and early history of common lilac in Finland. Overall, such comprehensive genomic characterization and deep understanding of genetic relationships of S. vulgaris can be used when utilizing present cultivars and developing new ones in future breeding programs.
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- Copyright © The Author(s), 2023. Published by Cambridge University Press on behalf of National Institute of Agricultural Botany
References
Bastien, M, Boudhrioua, C, Fortin, G and Belzile, F (2018) Exploring the potential and limitations of genotyping-by-sequencing for SNP discovery and genotyping in tetraploid potato. Genome 61, 449–456.CrossRefGoogle ScholarPubMed
Bean, WJ (1980) Trees and Shrubs Hardy in the British Isles. vol. 4, 8th Ed. London: John Murray, 808 pp.Google Scholar
Chen, H, Lattier, JD, Vining, K and Contreras RN, R (2020) Two SNP markers identified using genotyping-by-sequencing are associated with remontancy in a segregating F1 population of Syringa meyeri ‘Palibin’ × S. pubescens ‘Penda’ Bloomerang®. Journal of the American Society for Horticultural Science 145, 104–109.CrossRefGoogle Scholar
Cheng, Y-Q, Jiang, Z-M and Cai, J (2021) Characteristic and phylogenetic analyses of chloroplast genome for Syringa komarowii C.K.Schneid. (Oleaceae) from Huoditang. China, an important horticultural plant. Mitochondrial DNA Part B 6, 1521–1522.CrossRefGoogle ScholarPubMed
Darlington, CD and Wylie, AP (1956) Chromosome Atlas of Flowering Plants. New York, NY: Macmillan.Google Scholar
de la Rosa, R, James, CM and Tobutt, KR (2002) Isolation and characterization of polymorphic microsatellites in olive (Olea europaea L.) and their transferability to other genera in the Oleaceae. Molecular Ecology Notes 2, 265–267.CrossRefGoogle Scholar
Doyle, JJ and Doyle, JL (1990) Isolation of plant DNA from fresh tissue. Focus 12, 13–15.Google Scholar
Earl, DA and von Holdt, BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4, 359–361.CrossRefGoogle Scholar
Elfving, F (1897) Anteckningar om kulturväxterna I Finland. Acta Societatis Pro Fauna et Flora Fennica 14, 1–116.Google Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14, 2611–2620.CrossRefGoogle ScholarPubMed
Fiala, JL and Vrugtman, F (2008) Lilacs. A Gardener's Encyclopedia. 2nd revised Edn. Portland, USA: Timber Press.Google Scholar
Govaerts, R (2020) World checklist of Syringa vulgaris L. Facilitated by the Royal Botanic Gardens, Kew. Available at http://wcsp.science.kew.org/ (accessed 30 May 2022).Google Scholar
Harbourne, ME, Douglas, GC, Waldren, S and Hodkinson, TR (2005) Characterization and primer development for amplification of chloroplast microsatellite regions of Fraxinus excelsior. Journal of Plant Research 118, 339–341.CrossRefGoogle ScholarPubMed
Havemeyer, TA (1917) How the modern lilac came to be. The Garden Magazine 25, 232–233.Google Scholar
Helander, V, Henttonen, S, Simons, T and Ahlqvist, R (1987) Suomenlinnan Maisema, Kunnostussuunnitelma. Helsinki: Suomenlinnan hoitokunta.Google Scholar
Ho, SS, Urban, AE and Mills, RE (2020) Structural variation in the sequencing era. Nature Reviews Genetics 21, 171–189.CrossRefGoogle ScholarPubMed
Jun, M and Wanchun, G (2006) Genetic diversity in natural populations of Syringa oblata detected by AFLP markers. Acta Horticulturae Sinica 33, 1269–1274.Google Scholar
Juntheikki-Palovaara, I, Antonius, K, Lindén, L and Korpelainen, H (2013) Microsatellite markers for common lilac (Syringa vulgaris L.). Plant Genetic Resources: Characterization and Utilization 11, 279–282.CrossRefGoogle Scholar
Kilian, A, Wenzl, P, Huttner, E, Carling, J, Xia, L, Blois, H, Caig, V, Heller-Uszynska, K, Jaccoud, D and Hopper, C (2012) Diversity arrays technology: a generic genome profiling technology on open platforms. In: Pompanon, F and Bonin, A (eds), Data Production and Analysis in Population Genomics. Methods in Molecular Biology (Methods and Protocols), vol. 888. Totowa, NJ: Humana Press, pp. 67–89.Google Scholar
Kochieva, EZ, Ryzhova, NN, Molkanova, OI, Kudriavtsev, AM, Upelniek, VP and Okuneva, IB (2004a) Syringa species: molecular marking of species and cultivars. Genetika 40, 37–40, T.Google Scholar
Kochieva, EZ, Ryzhova, NN, Molkanova, OI, Kudryavtsev, AM, Upelniek, VP and Okuneva, IB (2004b) The genus Syringa: molecular markers of species and cultivars. Russian Journal of Genetics 40, 30–32.CrossRefGoogle Scholar
Kodama, K, Yamada, T and Maki, M (2008) Development and characterization of 10 microsatellite markers for the semi-evergreen tree species, Ligustrum ovalifolium (Oleaceae). Molecular Ecology Resorces 8, 1008–1010.CrossRefGoogle ScholarPubMed
Kopelman, NM, Mayzel, J, Jakobsson, M, Rosenberg, NA and Mayrose, I (2015) Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecology Resources 15, 1179–1191.CrossRefGoogle ScholarPubMed
Lack, HW (2000) Lilac and horse-chestnut: discovery and rediscovery. Curtis's Botanical Magazine 17, 109–141.CrossRefGoogle Scholar
Lange, J (1999) Kulturplanternes Indførselshistorie I Danmark Indtil Midten af 1900-Tallet, 2nd Edn. Frederiksberg: DSR Forlag.Google Scholar
Lendvay, B, Pedryc, A and Höhn, M (2013) Characterization of nuclear microsatellite markers for the narrow endemic Syringa josikaea Jacq. fil. ex Rchb. Notulae Botanicae Horti Agrobotanici Cluj-Napoca 41, 301–305.CrossRefGoogle Scholar
Lendvay, B, Kadereit, JW, Westberg, E, Cornejo, C, Pedryc, A and Höhn, M (2016) Phylogeography of Syringa josikaea (Oleaceae): early Pleistocene divergence from East Asian relatives and survival in small populations in the Carpathians. Biological Journal of Linnean Society 119, 689–703.CrossRefGoogle Scholar
Lindén, L, Hauta-aho, L, Temmes, O and Tegel, S (2010) An inventory of old lilac and crab apple cultivars in the city of Helsinki, Finland. Acta Horticulturae 881, 1027–1030.CrossRefGoogle Scholar
Lyu, Y-Z, Dong, X-Y, Huang, L-B, Zheng, J-W, He, X-D, Sun, H-N and Jiang, Z-P (2020) SLAF-seq uncovers the genetic diversity and adaptation of Chinese elm (Ulmus parvifolia) in Eastern China. Forests 11, 80.CrossRefGoogle Scholar
Marsolais, JV, Pringle, JS and White, BN (1993) Assessment of random amplified polymorphic DNA (RAPD) as genetic markers for determining the origin of interspecific lilac hybrids. Taxon 42, 531–537.CrossRefGoogle Scholar
Martinsson, K and Ryman, S (2008) Blomboken. Bilder ur Olof Rudbecks Stora Botaniska Verk. Stockholm: Prisma.Google Scholar
Melnikova, NV, Borhert, EV, Martynov, SP, Okuneva, IB, Molkanova, OI, Upelniek, VP and Kudryavtsev, AM (2009) Molecular genetic marker-based approaches to the verification of lilac Syringa vulgaris L. in vitro germplasm collections. Russian Journal of Genetics 45, 85–90.CrossRefGoogle Scholar
Meyer, F (1952) Flieder - Ein Einblick in die Gattung Syringa für Gärtner und Gartenfreunde. Grundlagen und Fortschritte im Garten- und Weinbau, Heft, vol. 102. Stutgart: Eugen Ulmer.Google Scholar
Nikander, G (1928) Hertonäs. In Nikander, G (ed.), Herrgårdar I Finland. Helsinki: Söderström & C:o Förlagsaktiebolag, pp. 31–44.Google Scholar
Nybom, H, Weising, K and Rotter, B (2014) DNA fingerprinting in botany: past, present, future. Investigative Genetics 5, 1–35.CrossRefGoogle ScholarPubMed
Oh, S, Lee, M, Kim, K, Han, H, Won, K, Kwack, Y-N, Shin, H and Kim, D (2019) Genetic diversity of kiwifruit (Actinidia spp.), including Korean native A. arguta, using single nucleotide polymorphisms derived from genotyping-by-sequencing. Horticulture, Environment and Biotechnology 60, 105–114.CrossRefGoogle Scholar
Peakall, R and Smouse, PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics (Oxford, England) 28, 2537–2539.Google ScholarPubMed
Pettersson, L (1948) Suomenlinna arkkitehtuurin muistomerkkinä. In Sario, N and Valpasvuo, A (eds), Suomenlinna, vol. 1748–1948. Helsinki: Rannikkotykistön upseeriyhdistys, pp. 17–62.Google Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945–959.CrossRefGoogle ScholarPubMed
Royal Horticultural Society (2001) RHS Color Chart, 4th Edn. London: The Royal Horticultural Society.Google Scholar
Rzepka-Plevnes, D, Smolik, M and Tanska, K (2006) Genetic similarity of chosen Syringa species determined by the ISSR-PCR technique. Dendrobiology 56, 61–67.Google Scholar
Saitou, N and Nei, M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4, 406–425.Google Scholar
Selander, V (1939) Puutarhanhoidon alkuvaiheet Karkussa. Tyrvään seudun museo- ja kotiseutuyhdistyksen julkaisuja 11, 1–60.Google Scholar
Smolik, M, Andrys, D, Franas, A, Krupa-Małkiewicz, M and Malinowska, K (2010) Polymorphism in Syringa rDNA regions assessedby PCR technique. Dendrobiology 64, 55–64.Google Scholar
Suominen, O (1997) Syreeni, muiston tyyssija. In Pekonen, O (ed.), Elämän puu. Helsinki: WSOY, pp. 278–297.Google Scholar
Tamura, K, Stecher, G, Peterson, D, Filipski, A and Kumar, S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30, 2725–2729.CrossRefGoogle ScholarPubMed
Taylor, J (1990) Four Lemoine genera: Syringa, Philadelphus, Deutzia, Weigela. The Plantsman 11, 225–240.Google Scholar
Tomimoto, S and Satake, A (2023) Modelling somatic mutation accumulation and expansion in a long-lived tree with hierarchical modular architecture. Journal of Theoretical Biology 565, 111465.CrossRefGoogle Scholar
Venison, EP, Litthauer, S, Laws, P, Denancé, C, Fernández-Fernández, F, Durel, C-E and Ordidge, M (2022) Microsatellite markers as a tool for active germplasm management and bridging the gap between national and local collections of apple. Genetic Resources and Crop Evolution 69, 1817–1832.CrossRefGoogle Scholar
Wang, J, Tian, T, Han, X, Ye, B, Ma, X, Meng, X, Xie, J and Zhou, H (2021) The complete chloroplast genome and phylogenetic analysis of Syringa reticulata subsp. amurensis (Rupr.) P.S.Green & M.C.Chang from Qinghai Province, China. Mitochondrial DNA Part B 6, 1829–1831.CrossRefGoogle ScholarPubMed
Xinlu, C, Zhenfeng, C and Jing, H (1999) Using random amplified polymorphic DNA (RAPD) markers for lilac genetic analysis and classification of lilac cultivars. Acta Botanica Boreali-Occidentalia Sinica 19, 169–176.Google Scholar
Yang, Y, He, R, Zheng, J, Hu, Z, Wu, J and Leng, P (2020) Development of EST-SSR markers and association mapping with floral traits in Syringa oblata. BMC Plant Biology 20, 436.CrossRefGoogle ScholarPubMed
Zhang, J, Jiang, Z, Su, H, Zhao, H and Cai, J (2019) The complete chloroplast genome sequence of the endangered species Syringa pinnatifolia (Oleaceae). Nordic Journal of Botany 2019, e02201.CrossRefGoogle Scholar
Zhao, M, Zhang, Y, Xin, Z, Meng, X and Wang, W (2020) The complete chloroplast genome of Syringa oblata (Oleaceae). Mitochondrial DNA Part B 5, 2278–2279.CrossRefGoogle ScholarPubMed
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