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Genome Sizes of 227 Accessions of Gagea (Liliaceae) Discriminate

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Genome Sizes of 227 Accessions of Gagea (Liliaceae) Discriminate Zonneveld et al. SpringerPlus (2015) 4:395 DOI 10.1186/s40064-015-1167-4 RESEARCH Open Access Genome sizes of 227 accessions of Gagea (Liliaceae) discriminate between the species from the Netherlands and reveal new ploidies in Gagea B J M Zonneveld1*, B te Linde2 and L‑J van den Berg2 Abstract Nuclear genome size, as measured by flow cytometry with propidium iodide, was used to investigate the relation‑ ships within the genus Gagea (Liliaceae), mainly from the Netherlands. The basic chromosome number for Gagea is x 12. The inferred ploidy in the Dutch and German accessions varies from diploid to decaploid. Consequently there is =a large range of genome sizes (DNA 2C-values) from 14.9 to 75.1 pg. Genome sizes are evaluated here in combina‑ tion with the results of morphological observations. Five species and the hybrid G. megapolitana are reported. Apart from 14 diploid G. villosa, six plants of G. villosa with an inferred tetraploidy were× found. For the 186 Dutch acces‑ sions investigated 85 turned out to be the largely sterile G. pratensis (inferred to be pentaploid). Inferred tetraploid and hexaploid G. pratensis were found in 30 and 20 localities, respectively. In one locality an inferred decaploid (10 ) plant was found that could represent a doubled pentaploid G. pratensis. An inferred decaploid G. pratensis was never× reported before. The genome size of Gagea megapolitana from Germany fitted with its origin as a cross between the two hexaploids G. pratensis and G. lutea. ×Gagea spathacea from the Netherlands was inferred to be nonaploid as was recorded from plants across Europe. The aim of the study was to use flow cytometry as a tool to elucidate the taxonomic position of the Dutch Gagea. Keywords: Gagea, The Netherlands, DNA 2C-value, Genome size, Ploidy level, New decaploid G. pratensis Background are recorded for The Netherlands and in Heukels Flora of The genus Gagea Salisb. conmprizes about 275 species. The Netherlands (van der Meijden 2005) a fifth is added. In the World Checklist for Gagea (Govaerts 2006) 594 To elucidate the relationships between Gagea species, names were listed. It is a genus of small bulbous plants the classical taxonomic traits based on morphological in the family Liliaceae, endemic to Eurasia and North characters, chromosome numbers (Peruzzi 2003, 2012) Africa. A single circumpolar species, a former Lloydia and sequencing data (Peterson et al. 2008; Zarrei et al. is now included in Gagea (Peruzzi 2012). The greatest 2009) are here supplemented with data on nuclear DNA number of species can be found in Kazakhstan in the content. From only five species genome size was deter- Tien Shan and Pamir-Alai. This coincides with the great- mined earlier (Greilhuber et al. 2000; Vesely et al. 2011; est richness of Tulipa (Zonneveld 2010). In Flora Neer- Leitch et al. 2007). Taxonomy of Gagea is rather diffi- landica (van Oostrom and Reichgelt 1964) four species cult and the main useful characters so far are: the chro- mosome numbers, the number and type of bulbils, the number and width of the leaves, the presence of red col- oration at the base of the leaf, the hairiness of the flower *Correspondence: [email protected] stalk, the shape of the petals and the number of flowers 1 NBC Naturalis, Herbarium Section, P.O. Box 9517, 2300 RA Leiden, The Netherlands on a scape. Newer investigations are also based on mor- Full list of author information is available at the end of the article pho-anatomical data (Peruzzi 2012). © 2015 Zonneveld et al. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Zonneveld et al. SpringerPlus (2015) 4:395 Page 2 of 17 186 different accessions from The Netherlands were Linde, Stichting Berglinde, Babberich and a few from L. measured in an attempt to understand the relationships Duistermaat from NCB Naturalis, Leiden, The Nether- within the Dutch gageas. These values were compared with lands. Further material came from T. Pfeiffer from the an additional 41 taxa from Germany. Nuclear DNA con- Ernst-Moritz-Arndt-University of Greifswald, Germany. tent can conveniently be measured by flow cytometry using The German plants, supplied with chromosomes counts, propidium iodide, a stoichiometric DNA stain that inter- were used to infer the ploidy of the Dutch plants. Mate- calates in the double helix. Where many species in a genus rial of known origin was used. Vouchers will be lodged in have the same chromosome number, differences in DNA the Herbarium of Naturalis Leiden (L). Figures 2, 3, 4, 5, 2C-value have proven to be very effective in delimiting 6, 7, 8 show the spread of the taxa in the Netherlands. infrageneric divisions in a number of taxa (Ohri 1998). The evolution of genome size (Greilhuber 1979) has received Flow cytometric measurement of DNA 2C‑value increased attention during recent years (Greilhuber 2005). For the isolation of nuclei, a few cm of leaf or a single The smallest angiosperm genome size reported so far is for bulbil was chopped together with a piece of Agave ameri- Genlisia margarethae Hutch. with 2C = 0.13 pg (Greilhu- cana L. ‘Aureomarginata’ or Agave attenuata L. as an ber et al. 2006). The record holders for maximum genome internal standard (see below). The chopping was done size were for eudicots Viscum album L. with 2C = 205.8 pg with a new razor blade in a Petri dish in 0.25 ml nuclei- and for monocots Paris japonica with 2C = 304.5 pg (Pel- isolation buffer to which 0.25 mg RNase/ml was added licer et al. 2010). Flow cytometry was successfully used (Zonneveld and van Iren 2001). After adding 1.75 ml to measure the 2C-value for the genera Hosta Tratt., Hel- propidium iodide solution (50 mg PI/l in isolation buffer) leborus L., Clivia Lindl., Nerine Herb., Agapanthus L’Hér., the suspension with nuclei was filtered through a 20 μm Galanthus L., Narcissus L., Gasteria Duval. Tulipa L. etc. nylon filter. The fluorescence of the nuclei at 585 nm was by Zonneveld (2001, 2003, 2008, 2009, 2010), Zonn- measured half an hour and 1 h after addition of propid- eveld and Van Iren (2001), Zonneveld and Duncan (2003, ium iodide excitation, using a BD Accuri C6 flow cytom- 2006), and Zonneveld et al. (2003, 2012). In this paper eter equiped with a 488 nm laser suitable for propidium it is shown that genome size is helpful to discriminate iodide. Data were analyzed by means of BD Accuri Cflow between the species of Gagea from The Netherlands Plus software provided by the supplier. Plots were first (Fig. 1). gated to exclude debris on a scatter diagram (Fl2-A vs Nuclear DNA content as measured by using flow cytom- FL1-A) and counted against FL2-A on a logarithmic etry may conveniently be used to produce systematic data. scale. The 2C DNA content of the sample was calculated It is applicable even in dormant bulbs or sterile plants for as the sample peak mean, divided by the Agave peak the monitoring of the trade in bulbous species. In the case mean, and multiplied with the amount of DNA of the of Gagea, it is difficult to ascribe a plant to a taxon in the Agave standard. Two different samples, with each at least often non-flowering state. Genome size is a good way to 5,000 nuclei, were measured twice for each clone. Most determine the species and their ploidy. A different genome histograms revealed a Coefficient of Variation of less than size infers usually a different ploidy or a different species. 5%. The standard deviation was calculated for the DNA However, the reverse is not true: if plants have the same content of each species, using all relevant measurements. genome size it does not automatically mean that they are the same species, it might be a coincidence. Internal standard and absolute DNA content values Based on van den Berg and te Linde (2003) and new When measuring nuclear DNA content by means of observations, morphological descriptions were given for flow cytometry, it is necessary to chop tissue from the the species, correlating it with the measured genome plant of interest together with an internal standard. weights. New ploidies were inferred for Gagea villosa This standard must be as close as possible to the plants which, apart from 14 diploids, had six plants with an of interest and not overlap with the ploidy area of inter- inferred tetraploid amount of DNA and for G. praten- est. If they are too close together the peak values inter- sis that was found to have, apart from the tetraploid, the fere with each other. Linearity is checked by comparing hexaploid and the very common pentaploid accessions, the different ploidies as found within leaves and roots also a genome size inferring decaploidy. of many plants. In this way, variation in signal inten- sities due to staining kinetics, to light absorption and Methods quenching by sample components, as well as to instru- Plant material ment and other variables, is reduced to a minimum. The plant material used in this study was collected Agave americana was chosen as internal standard for from locations across The Netherlands and Germany as Gagea. For Gagea minima and G. villosa, with 2C-val- described in Table 1. It was mainly obtained from B. te ues that more or less coincided with Agave americana, Zonneveld et al.
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