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Botanical Journal of the Linnean Society, 2009, 159, 237–244.

With 4 figures

Genetic diversity among genotypes of Eryngium

viviparum (Apiaceae): a plant threatened throughout
its natural range
Department of Plant Physiology, University of Santiago de Compostela, 15782 Santiago de
Compostela, Spain
Department of Botany, Faculty of Biology, University of Santiago de Compostela, 15782 Santiago de
Compostela, Spain

Received 22 May 2006; accepted for publication 27 June 2008

Eryngium viviparum (Apiaceae) is an endangered aquatic plant, listed as threatened in several European
documents. The genotypes are distributed patchily in various wetlands in the north-west of Spain and one is
located in north-west France. The study of the genetic diversity of a small population of a rare species is important
for conservation and studies aimed at recovery programmes. Random amplified polymorphic DNA (RAPD) markers
were used to assess the genetic diversity among five Spanish and one French genotype. This technique has
contributed to the knowledge of the genetic diversity in E. viviparum, showing a greater genetic distance between
the Spanish cluster formed by S1, S4 than the second cluster formed by S2, S3, S5 and the French genotype.
Mantel testing did not show a significant correlation between genetic and geographical distances, but a significant
correlation was found between altitude, habitat and genetic distance. The French genotype showed the highest
level of polymorphism (28.16) and the highest percentage of exclusive markers (32%). One of these was isolated,
purified, cloned and sequenced, revealing a high homology to a protein mainly expressed in roots. This could
represent, for the F genotype, an adaptation to a specific habitat near the sea compared with the Spanish genotypes
which grow inland. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159,

ADDITIONAL KEYWORDS: conservation biology – endangered plant – habitat fragmentation – RAPD –


INTRODUCTION This species is an Atlantic region endemic, with a

disjointed and fragmented distribution in the north-
Eryngium viviparum Gay (Apiaceae) is an endan-
west of Spain and France (Brittany) (Fig. 1), and was
gered aquatic plant, growing in flat and depressed
previously present in north-west Portugal (Dupont,
areas subjected to seasonal flooding for about 7–9
1962). At the present time, there is a single known
months of the year. It is listed as a threatened plant
population in France (Annezo, Lesouef & Riviere,
in most European publications [see Annex I of the
1995) and the remaining examples (more than 93% of
Berne Convention, 1979, and the Habitats Directive
E. viviparum of the world) are all located in north-
92/43/EEC (Annex II and IV)], and is considered as a
west Spain (Romero & Rubinos, 2003; Romero, Ramil
priority species in the World Conservation Union
& Rubinos, 2004).
guide, where it has been classified as Vulnerable
Human activities in the landscape, such as drain-
(Anonymous, 1983, 1997).
age or transformation into agricultural systems, have
an immediate and clear impact on populations, which
are either eliminated or fragmented into isolated
*Corresponding author. E-mail: small-scale patches. All these events contribute

© 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159, 237–244 237

12 8 4 0 4 8 14




S5 S1


Figure 1. Location of the collected genotypes of Eryngium viviparum included in the study (see Table 1 for sample

towards the loss of plant biodiversity (Heywood & required. In comparison with microsatellite analysis,
Iriondo, 2003). there are some limitations and shortcomings of
Biological conservation, assessing and maintaining RAPD, such as marker allele dominance (Lynch &
genetic diversity in both nature and germplasm Milligan, 1994) and sometimes low reproducibility,
banks, is an important task in saving endangered which may have discouraged many investigators from
plants. In spite of the interest in the maintenance of using RAPD. However, under carefully controlled
the genetic resources in E. viviparum, its exact dis- reaction conditions, reproducible and interpretable
tribution and the nature of its genetic variability are RAPD banding patterns can be obtained (Sun &
unknown. Wong, 2001; Jover et al., 2003). Potentially, this tech-
Random amplified polymorphic DNA (RAPD) nique is useful in the conservation context for rare
methods aid in this assessment, and are useful in and endangered species, such as E. viviparum,
studies of natural plant populations (Bussell, 1999; because only small quantities of biological material
Nybom & Bartish, 2000). RAPD analysis has certain are required (Rossetto, Weaver & Dixon, 1995;
advantages: it can potentially provide a large number Cotrim, Chase & Pais, 2003).
of reproducible marker loci and high levels of poly- The aim of this study was to examine the genetic
morphism, costs much less, and is faster and easier to variations among six E. viviparum genotypes by the
perform than microsatellite analysis, because no prior RAPD technique. The sample size was limited by the
DNA sequence information for the target species is actual size of the natural populations. Similar prob-

© 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159, 237–244

Table 1. Origin and location of plant materials collected for random amplified polymorphic DNA (RAPD) survey in
Eryngium viviparum

Latitude Longitude Altitude

Country Province Site of collection (N) (W) (m) Code

Spain (NW of Iberian Peninsula)

Ayoó de Vidriales, Congosta 42°8′ 6°7′ 905 S1
A Espiñeira, Lagoa de Cospeito 43°10′ 7°32′ 380 S2
Melide 42°53′ 7°59′ 449 S3
Otero de Bodas 41°56′ 6°11′ 810 S4
S. Martín de Lamas, Veiga das Insuas 43°15′ 7°32′ 400 S5
France (Brittany)
Brest 47°34′ 3°15′ 12–15 F

lems with this size of sample were found by Sun & the samples were amplified using 35 cycles (94 °C,
Wong (2001), Thomas, Sreejayan & Kuriachan (2001) 15 s; 34 °C, 2 min; 72 °C, 2 min), followed by a final
and Ghany & Zaki (2003). extension of the PCR products for 5 min at 72 °C.

MATERIAL AND METHODS Amplification products were resolved electrophoreti-
PLANT MATERIAL cally on 1% agarose gels, run at 60 V for 210 min in
Eryngium viviparum plants were obtained from six 1 ¥ Tris-acetate-EDTA (TAE) buffer, and visualized by
genotypes of this species: five were located in Spain staining with ethidium bromide. Lambda DNA
and one in France. The Spanish samples were col- digested with EcoRI and HindIII, ranging from 500 to
lected in the north-west of the Iberian Peninsula and 21 000 bp, was used as a size marker.
one sample was obtained from the only French geno- Imaging gel bands were captured by a Versadoc
type located in Brittany (Table 1). Each Spanish plant scanner (BioRad) and the sizes of all RAPD fragments
was collected in the field and chosen at random from were estimated using Quantity One Software
the small group of plants. The French sample was (BioRad). Only those bands consistently reproduced
obtained from a micropropagated plant, which was in different analyses were considered. Each RAPD
derived from seeds supplied by the Conservatoire reaction was performed at least three times for each
Botanique National de Brest (France). primer.
In vitro cultures of the plants were prepared from
the seeds and grown in Murashige and Skoog (MS) CLONING AND SEQUENCING OF PCR PRODUCTS

solid medium (Murashige & Skoog, 1962). Apical buds PCR products were excised from the agarose gels and
from plantlets were cultured on MS solid medium purified using a Gel Band Purification Kit (Amer-
supplied with zeatin (23 mM) and naphthalene acetic sham Pharmacia Biotech). The purified PCR products
acid (NAA) (0.54 mM). were then cloned in pGEM-T Easy Vector (Promega)
for subsequent transformation in Escherichia coli
strain DH5a. Plasmid DNA was isolated using
DNA EXTRACTION AND AMPLIFICATION Qiaprep Spin Miniprep (Qiagen). The DNA was
Genomic DNA from both indoor and outdoor cultures sequenced with an automated ABI PRISM 3100 DNA
(0.1 g from young, fresh leaves) was extracted using Sequencer (ABI). To minimize sequencing errors, at
the method of Doyle & Doyle (1987) modified because least two independent clones of each amplified RAPD
of the small quantity of plant material available. fragment were sequenced. The multiple DNA
Polymerase chain reactions (PCRs) (Table 1) were sequence alignment was carried out using CLUST-
performed using a Techne Genius thermocycler. ALW (Thompson, Higgins & Gibson, 1994). Sequences
Primers for PCR amplification were obtained from from the E. viviparum RAPD fragments were com-
Operon Technologies and Amersham Pharmacia pared with the EBML plant database information
Biotech. Each RAPD reaction (50 mL final volume) using FASTA algorithms (Pearson & Lipman, 1988).
contained 1.66 U of Taq polymerase (Bioline), 2 mM
MgCl2, 200 mM of each deoxynucleoside triphosphate STATISTICAL ANALYSIS
(dNTP), 0.2 mM of primer, formamide 0.2% and 1 ng of Amplified fragments were scored in terms of the pres-
genomic DNA. After initial heating for 2 min at 94 °C, ence (1) or absence (0) of homologous bands, and a

© 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159, 237–244

matrix of the different RAPD phenotypes was viviparum, an endangered and rare aquatic plant
assembled. We assumed that each band showed the which survives in the north-western part of Spain and
phenotype at a single biallelic locus and that RAPD France. One or two small leaves were used for DNA
markers represented dominant alleles (Williams extraction, thus minimizing the impact on the plants,
et al., 1990). The pairwise distance matrix was com- and so RAPD is likely to be appropriate for the study
puted based on Nei’s coefficient of similarity (Nei & of populations with relatively small sample sizes
Li, 1979) using NTSYS-PC 2.1 Software (numerical (Rossetto et al., 1995; Prathepha, 2000).
taxonomy and multivariate analysis system) (Rohlf,
2000), and a dendrogram was created with the
unweighted pair group method with arithmetic aver- RAPD ANALYSIS
aging (UPGMA). The same presence/absence data One hundred and ten arbitrary primers were
matrix was used to identify the unique markers of screened and 16 (Table 2) showed a high level (up to
E. viviparum which serve to characterize a specific 65%) of polymorphism; these selected primers gener-
genotype. ated 127 consistently well-amplified bands, ranging in
In order to investigate the relationships among size from 522 to 1799 bp, and 93 were polymorphic
genetic and geographical distances and altitude and (73.22%) for the six genotypes.
genetic distance among genotypes of E. viviparum, Table 3 shows the percentage of polymorphic bands
Mantel (1967) tests were computed. All the analyses obtained from a total of 742 bands in the six geno-
were performed at least three times. types: 42.72% were polymorphic. Genotype F, corre-
sponding to the French sample, showed the highest
level of polymorphism (28.16%), and genotype S5,
corresponding to one Spanish sample (Vega das
The results show the first attempt to use RAPD Insuas, see Table 1), showed the lowest percentage of
markers to characterize the genetic variations in E. polymorphic bands (12.53%).

Table 2. Primers and sequences of random decamers, base pair range scored, total bands, polymorphic bands and
percentage of polymorphisms for amplification profiles in Eryngium viviparum genotypes

Total number Number of Polymorphic

Primer Sequence 5′ → 3′ Size (bp) of bands polymorphic bands bands (%)

E-01 CCCAAGGTCC 550–2225 9 6 66.67

E-12 TTATCGCCCC 770–2264 6 4 66.67
E-15 ACGCACAACC 536–1781 9 6 66.67
E-19 ACGGCGTATG 419–2387 13 11 84.62
K-03 CAGAGGTCCC 523–1518 7 5 71.43
K-14 ACGGGAGCAA 443–1525 8 7 87.50
K-26 TGCGAGAGTC 412–1564 8 6 75.00
K-30 ACGGATCCTG 448–2379 7 6 85.71
L-13 ACCGCCTGCT 603–1298 6 4 66.67
L-18 ACCACCCACC 541–2040 9 6 66.67
M-02 ACAACGCCTC 643–1401 5 4 80.00
M-03 GGGGGATGAG 393–1330 8 6 75.00
M-07 CCGTGACTCA 595–1616 4 3 75.00
M-16 GTAACCAGCC 545–2159 6 4 66.67
P-08 ACATCGCCCA 558–2230 15 10 66.67
P-19 GGGAAGGACA 373–1076 7 5 71.43
Total 16 127 93
Average 522–1799 73.27

Table 3. Average percentage of polymorphic bands obtained for the six genotypes of Eryngium viviparum

Sample S1 S2 S3 S4 S5 F

Polymorphic bands (%) 25.47 18.32 20.21 25.20 12.53 28.16

© 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159, 237–244

Figure 2. Dendrogram of genetic distances among six Eryngium viviparum genotypes derived from random amplified
polymorphic DNA (RAPD) marker data.


The genetic distances among the six genotypes of
E. viviparum, estimated through RAPD analysis,
showed different values for each sample. The greatest
genetic distance was obtained for the Spanish geno-
types S1 and S5 (0.289) and the closest genetic dis-
tance was obtained for S3 and S5 (0.173). The French
genotype showed intermediate values.
The dendrogram generated from the genetic dis-
tance matrix (Fig. 2) grouped all the genotypes into
two clusters: the first cluster included S1 and S4
with a genetic distance of 0.19; the second cluster
grouped the French genotype with the Spanish 982bp
samples S2, S3 and S5, which constituted a sub-
cluster inside the second cluster. These genotypes
grouped the former samples at 0.25. Thus, from the
clustering of the genotypes, it was shown that the
Spanish samples S2, S3, S5 showed less genetic dis-
tance to the French sample than to the other
Spanish samples (S1, S4).
Mantel’s test was used to observe the relationship Figure 3. Random amplified polymorphic DNA (RAPD)
between genetic and geographical distances by com- profile produced by Eryngium viviparum using the primer
paring pairwise among E. viviparum; the results L-18. The molecular size marker is phage l, and S1, S2,
revealed a nonsignificant correlation (P > 0.05) S3, S4, S5 (Spanish) and F (French) correspond to the
between RAPD and geographical distances (r = 0.233, different genotypes. The arrow indicates the size of the
P = 0.403). Similar results were obtained by Freitas & unique marker (bp) for sample F.
Brehm (2001). Mantel’s test was also useful for study-
ing the relationship between genetic distance and
altitudinal habitats. The French genotype originates and genetic distance revealed a significant correlation
from a low altitude, almost at sea level (12–15 m), (P > 0.05) between them (r = 0.535, P = 0.018). Similar
whereas the genotypes S2, S3 and S5 as a group are results were found by Thomas et al. (2001). Altitudi-
from an intermediate average altitude of 409 m, and nal habitats permitted the classification of the geno-
S1 and S4 are from a high average altitude of 857 m types into three groups, which were the same as those
(Table 1). A comparison of these altitudinal habitats obtained from the dendrogram (Fig. 2).

© 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159, 237–244













Figure 4. DNA sequence of the unique marker obtained from primer L-18 in the French (F) sample. Nucleotide
nomenclature: R = A or G; Y = C or T; K = G or T; M = A or C; S = G or C; W = A or T; N = any nucleotide.


From the 110 primers tested, 67 unique markers This study provides the first characterization of the
were detected for the six genotypes. Of these, the molecular genetic DNA diversity among genotypes
French sample showed the largest number (32%), of E. viviparum, an endangered aquatic plant, using
with genotypes S1–S4 displaying values ranging the RAPD technique. RAPD was developed in the
between 9% and 26%; S5 did not show any specific last decade of the 20th century and has become
marker. a successful tool. It has several applications, such
One of the unique markers from the French sample as the characterization of genetic resources in
(Fig. 3) was 982 bp in size. This band was isolated, plants and the identification of species when mor-
cloned and sequenced. The sequenced band was phologic characteristics are not discernible among
766 bp in size (Fig. 4). This was analysed with FASTA individuals (Transue et al., 1994; Wolff & Morgan-
software using EMBL plant database information, Richards, 1998; Nebauer, del Castillo-Agudo &
revealing that it produced high DNA sequence homol- Segura, 2000).
ogy (94%) with the gene At1g80070.1 located on chro- RAPD represents an efficient technique for the gen-
mosome 1 of Arabidopsis thaliana (L.) Heynh. The eration of molecular data with a small amount of
soluble protein encoded by this gene in Arabidopsis is biological material, which is very important in endan-
a splicing factor Prp8, related to a 278.12 kDa band, gered and rare species, such as E. viviparum. It has
located mainly in the plastids and involved in the the capacity to detect a high level of polymorphism.
mitotic cell cycle and cell cycle control. The expression Thus, the average value of the polymorphic bands
of the protein is observed in several parts of the plant, found was 73.27% (Table 2), similar to data obtained
such as the leaves, seeds, siliques and seedlings, but by other authors, including Coletta-Filho et al. (1998)
the protein is mainly expressed in the roots (16%) in mandarins (Citrus spp.), Irwin, Kaufusi & Banks
(data not shown). (1998) in taro (Colocasia esculenta) and Bekessy et al.

© 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159, 237–244

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