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Variability and structure of natural populations of Elymus caninus (L.) L. and their possible relationship with Hordelymus europaeus (L.) Jess. ex Harz as revealed by AFLP analysis
Abstract
The AFLP method was used to study the inter-population variability of eight populations of Elymus caninus (L.) L. as well as three populations of Hordelymus europaeus (L.) Jess. ex Harz. In these studies a clear distinction was found between two phenotypes of E. caninus collected in the same locality. It also appeared that two populations of E. caninus representing the “pauciflorum” morphotype were clustered together, similarly as two populations of E. caninus exhibiting morphotype “caninus”. Additionally, the populations of the “pauciflorum” type were clustered together with all
samples of H. europaeus. Furthermore, the same approach was applied to analyze the intra-population variability of E. caninus. The populations ranged from nearly uniform to as diverse as the samples collected from different localities. In some populations
of this species the presence of off-type plants was revealed. Our data indicate the predominantly self-pollinating character
of E. caninus and the possible genetic relationship between of E. caninus and H. europaeus.
... These results suggested that one genome in tetraploid H. europaeus closely related to the genome in Hordeum. A close relationship between H. europaeus populations and some populations of Elymus caninus (StH genome) was also reported in a AFLP analysis (Mizianty et al., 2006). The disagreement between all the previous studies and this one could be explained if the Hordeum copy genome in Hordelymus has been experiencing a different evolution rate between the polyploid species and its donor diploid species, which led to the failure of intergenetic crosses and chromosome pairing. ...
The origin of Hordelymus genome has been debated for years, and no consensus conclusion was reached. In this study, we sequenced and analyzed the RPB2 (RNA polymerase subunit II) gene from Hordelymus europaeus (L.) Harz, and its potential diploid ancestor species those were suggested in previous studies. The focus of this study was to examine the phylogenetic relationship of Hordelymus genomes with its potential donor Hordeum, Psathyrostachys, and Taeniatherum species. Two distinguishable copies of sequences were obtained from H. europaeus. The obvious difference between the two copies of sequences is a 24 bp indel (insertion/deletion). Phylogenetic analysis showed a strong affinity between Hordeum genome and Hordelymus with 85% bootstrap support. These results suggested that one genome in tetraploid H. europaeus closely related to the genome in Hordeum species. Another genome in H. europaeus is sister to the genomes in Triticeae species examined here, which corresponds well with the recently published EF-G data. No obvious relationship was found between Hordelymus and either Ta genome donor, Taeniatherum caput-medusae or Ns genome donor, Psathyrostachys juncea. Our data does not support the presence of Ta and Ns genome in H. europaeus, and further confirms that H. europaeus is allopolyploid.
... Absence of any intraspecific patterns in this species was also confirmed in a recent study of its genetic and morphological variability (Mizianty et al., 2007). The relationships of the genus to other taxa of the family Poaceae remain unclear (Mizianty et al., 2005Mizianty et al., , 2007). Molecular studies (based on both nuclear and chloroplast DNA analyses) suggest an autotetraploid (or segmental allotetraploid) origin most closely related to the genus Leymus (tribe Triticae) (Ellneskog-Staam et al., 2006; Bouchenak-Khelladi et al., 2008). ...
The phylogeographical structure of the European forest grass Hordelymus europaeus (Poaceae) was studied by sequencing three non-coding regions of chloroplast DNA. Forty-three populations within the entire natural distribution area were analysed. The greatest haplotype variation and divergence were revealed on Balkan and Apennine Peninsula, suggesting main glacial refugia in these regions. Among southern refugia, probably only the Balkans could have remarkably contributed to postglacial recolonisation of the northern parts of Europe. A distinctly different haplotype group found on the Crimean Peninsula and in central Italy may represent either relicts of a previously more widespread ancestor or result of long-distance dispersal. The phylogeographical pattern found in H. europaeus is to certain extent similar with that found in Fagus sylvatica. This might imply a partly common postglacial colonisation history of these ecologically narrowly tied species. Nevertheless, unlike in the case of F. sylvatica, we did not found convincing evidence for the existence of Central European glacial refugia for H. europaeus. (C) 2009 Elsevier GmbH. All rights reserved.
... It is highly reproducible and polymorphic and can be used to survey overall genetic differences in the nuclear genome in a single assay without any prior sequence knowledge (Vos et al., 1995; Jones et al., 1997). Recently, it has been applied to investigate genetic relationship among species, closely related cultivars and even clones of plants (Mizianty et al., 2006; Yoon et al., 2007; Li et al., 2008; Karimi et al., 2009). Hence, Methylation Sensitive Amplified Polymorphism (MASP) which is a modified version of AFLP may be most suitable in detecting those affected as it combines the genetic diversity evaluation with the epigenetic variation (Zhang et al., 2010). ...
Rosa rugosa is an excellent ornamental plant with important ecological, economical and medicinal values in China. Polymorphism amplifications of the genomic DNA of 5 wild R. rugosa accessions and 25 cultivars that originated from China with fluorescent amplified fragment length polymorphism molecular markers were investigated in this study to evaluate their genetic diversity and relationships. A total of 1771 clearly identifiable bands (60 ~ 500 bp), including 1704 polymorphic bands, were obtained through amplification using 10 pairs of primers. The average percentage of polymorphic locus was 96.2%, which indicated the high genetic diversity of Chinese R. rugosa germplasm resources. Different quantities of specific bands were detected by 10 pairs of primers from 24 accessions, which could be used to identify the specific R. rugosa accession. There was high similarity between Chinese R. rugosa germplasm resources, as indicated by the similarity coefficient of 30 R. rugosa accessions between 0.4977 and 0.8410, with an average of 0.624. Clustering results suggested that wild accessions from different areas of China were remotely related with the ample genetic diversity. Wild accessions and cultivars also had remote genetic relationship. However, the main Chinese R. rugosa cultivars had high similarity, low genetic differences and a narrow genetic background.
Seven populations of Hordelymus europaeus and four populations of Leymus arenarius from Poland were subjected to examination of 36 morphological characters. This study showed that both species are relatively
uniform and that morphological variation of their populations represents a continuum. Of those, three populations of either
species were selected for analysis with molecular markers – RAPDs and AFLPs. These populations differed with respect of geographical
location as well as syntaxa and habitat. RAPD-PCR was performed for individual plants and clearly grouped them according to
the population origin. For either H. europaeus or L. arenarius - the studied populations differed in degree of their intrinsic variation while none of them as a whole was significantly
different from the remaining ones. In AFLP analysis the studied populations were represented by DNA pools of several individual
plants. Also this approach allowed discrimination among the population samples of both H. europaeus and L. arenarius. Both RAPDs and AFLPs were accordant in indication that H. europaeus exceeds L. arenarius with respect to variation accumulated at the DNA level.
Abstract: The study presents the results of research on the Agropyron-Elymus complex in Poland.
The occurrence of four genera has been confirmed, namely of Agropyron Gaertn. [represented
by A. cristatum (L.) Gaertn. subsp. pectinatum (M. Bieb.) Tzvelev], Hordelymus (Jess.)
Harz [H. europaeus (L.) Jess. ex Harz], Leymus Hochst. [L. arenarius (L.) Hochst.] and Elymus L.
[E. caninus (L.) L., E. farctus (Viv.) Runemark ex Melderis subsp. boreoatlanticus (Simonet
& Guin.) Melderis, E. hispidus (Opiz) Melderis subsp. hispidus, E. hispidus (Opiz) Melderis
subsp. barbulatus (Schur) Melderis, and E. repens (L.) Gould]. The occurrence of Elymus
athericus (Link) Kerguélen, which had been given before from the Polish shores of the Baltic
Sea, has not been confirmed. Descriptions of all taxa, their chromosome numbers and distribution
have been provided. On the basis of statistical analyses of population samples, the systematic
key for determination of genera, species, and subspecies within Elymus has been prepared.
The suggested division is different from the one applied so far in Poland and it takes into account
the most up-to-date tendencies in the systematics of this critical complex.
The recombinant plasmid dpTa1 has an insert of relic wheat DNA that represents a family of tandemly organized DNA sequences with a monomeric length of approximately 340 bp. This insert was used to investigate the structural organization of this element in the genomes of 58 species within the tribe Triticeae and in 7 species representing other tribes of the Poaceae. The main characteristic of the genomic organization of dpTa1 is a classical ladder-type pattern which is typical for tandemly organized sequences. The dpTa1 sequence is present in all of the genomes of the Triticeae species examined and in 1 species from a closely related tribe (Bromus inermis, Bromeae). DNA from Hordelymus europaeus (Triticeae) did not hybridize under the standard conditions used in this study. Prolonged exposure was necessary to obtain a weak signal. Our data suggest that the dpTa1 family is quite old in evolutionary terms, probably more ancient than the tribe Triticeae. The dpTa1 sequence is more abundant in the D-genome of wheat than in other genomes in Triticeae. DNA from several species also have bands in addition to the tandem repeats. The dpTa1 sequence contains short direct and inverted subrepeats and is homologous to a tandemly repeated DNA sequence from Hordeum chilense.
Crosses ofHordelymus europaeus (2n = 4x = 28) with four genera in theTriticeae were attempted. Adult hybrids were obtained in combinations withHordeum bogdanii (2x),Hordeum depressum (4x), andSecale cereale (2x). The meiotic pairing was very low in the hybrids withH. bogdanii andSecale cereale (0.12 and 0.30 chiasmata/cell, respectively), whereas high pairing (9.90 chiasmata/cell) was found in hybrids withH. depressum due to autosyndetic pairing ofH. depressum chromosomes. The chromosome complement ofHordelymus europaeus comprised 16 metacentrics, 8 submetacentrics, and 4 SAT-chromosomes. The Giemsa C-banding patterns of the chromosomes were characterized by small to minute bands at no preferential positions. It is hypothesized thatHordelymus europaeus may genomically be closest related toTaeniatherum andPsathyrostachys spp.
A novel DNA fingerprinting technique called AFLP is described. The AFLP technique is based on the selective PCR amplification
of restriction fragments from a total digest of genomic DNA. The technique involves three steps: (i) restriction of the DNA
and ligation of oligonucleotide adapters, (ii) selective amplification of sets of restriction fragments, and (iii) gel analysis
of the amplified fragments. PCR amplification of restriction fragments is achieved by using the adapter and restriction site
sequence as target sites for primer annealing. The selective amplification is achieved by the use of primers that extend into
the restriction fragments, amplifying only those fragments in which the primer extensions match the nucleotides flanking the
restriction sites. Using this method, sets of restriction fragments may be visualized by PCR without knowledge of nucleotide
sequence. The method allows the specific co-amplification of high numbers of restriction fragments. The number of fragments
that can be analyzed simultaneously, however, is dependent on the resolution of the detection system. Typically 50—100 restriction
fragments are amplified and detected on denaturing polyacrylamide gels. The AFLP technique provides a novel and very powerful
DNA fingerprinting technique for DNAs of any origin or complexity.
Genetic diversity of 33 Elymus caninus accessions was investigated using isozyme, RAPD, and microsatellite markers. The three assays differed in the amount of polymorphism detected. Microsatellites detected the highest polymorphism. Six microsatellite primer pairs generated a total of 74 polymorphic bands (alleles), with an average of 15.7 bands per primer pair. Three genetic similarity matrices were estimated based on band presence or absence. Genetic diversity trees (dendrograms) were derived from each marker technique, and compared using Mantel's test. The correlation coefficients were 0.204, 0.267, and 0.164 between isozyme and RAPD distance matrices, RAPD and microsatellite distance matrices, and between isozyme and microsatellite distance matrices, respectively. The three methodologies gave differing views of the amount of variation present but all showed a high level of genetic variation in E. caninus. The following points may be drawn from this study whether based on RAPD, microsatellite, or isozyme data: (i) The Icelandic populations are consistently revealed by the three dendrograms. The congruence of the discrimination of this accession group by RAPD, microsatellite, and isozyme markers suggests that geographic isolation strongly influenced the evolution of the populations; (ii) The degree of genetic variation within accessions was notably great; and (iii) The DNA-based markers will be the more useful ones in detecting genetic diversity in closely related accessions. In addition, a dendrogram, which took into account all fragments produced by isozymes, RAPDs, and microsatellites, reflected better the relationships than did dendrograms based on only one type of marker.
Genetic diversity of 33 Elymus caninus accessions was investigated using isozyme, RAPD, and microsatellite markers. The three assays differed in the amount of polymorphism detected. Microsatellites detected the highest polymorphism. Six microsatellite primer pairs generated a total of 74 polymorphic bands (alleles), with an average of 15.7 bands per primer pair. Three genetic similarity matrices were estimated based on band presence or absence. Genetic diversity trees (dendrograms) were derived from each marker technique, and compared using Mantel's test. The correlation coefficients were 0.204, 0.267, and 0.164 between isozyme and RAPD distance matrices, RAPD and microsatellite distance matrices, and between isozyme and microsatellite distance matrices, respectively. The three methodologies gave differing views of the amount of variation present but all showed a high level of genetic variation in E. caninus. The following points may be drawn from this study whether based on RAPD, microsatellite, or isozyme data: (i) The Icelandic populations are consistently revealed by the three dendrograms. The congruence of the discrimination of this accession group by RAPD, microsatellite, and isozyme markers suggests that geographic isolation strongly influenced the evolution of the populations; (ii) The degree of genetic variation within accessions was notably great; and (iii) The DNA-based markers will be the more useful ones in detecting genetic diversity in closely related accessions. In addition, a dendrogram, which took into account all fragments produced by isozymes, RAPDs, and microsatellites, reflected better the relationships than did dendrograms based on only one type of marker.
Polyacrylamide gel electrophoresis was employed to study the isoenzyme variation of esterase and acid phosphatase in natural populations of Dasypyrum villosum (L.) P.Candargy, Elytrigia repens (L.) Nevski and Elymus caninus (L.) L. Four similarity indices (Sl, S. D. In) were calculated in an attempt to evaluate quantitatively genetic affinities among the species examined. Considering index D, the species D, villosum proved to be equally distant (D = 0.17 in both cases from the species pair Et. repens and El. caninus. The nearly twice lower value of D for the comparison between Et. repens and El. caninus is an indication of their stronger genetic relationship. Mean values of indices In. SI and S also indicated that D. villosum is the most distinct species within the group studied. The results were discussed in the light of chloroplast DNA sequence data, suggesting a close affinity among the genera Dasypyrum (Coss, & L.Durieu) T.Durand, Elytrigia Desv. and Elymus L. The results of the present isoenzyme study are not in congruence with cpDNA analysis. Both isoenzyme and DNA data suggest that the phylogenetic position of the genus Dasypyrum within the tribe Triticeae remains unresolved.
Of the approximately 325 species in the tribe Triticeae (= Hordeeae), about 250 are perennials that include many of the world’s important forage grasses. Although more than 75% of the species in the Triticeae are perennials, they have received far less attention from cytogeneticists and plant breeders than have the annuals, which include three major cereal crops--wheat, barley, and rye. In addition to being important in their own right as forages, the perennials form a vast genetic reservoir that might be used to improve the annual cereals.
Intergeneric hybridization between the monotypic Eurasian genus Hordelymus and species of Hordeum was performed. Hybrids were obtained in nine combinations and the meiotic pairing was analyzed in four combinations (6 families). Hordelymus europaeus is probably an alloploid with two different genomes. The very low pairing in the hybrids with H. jubatum, H. brachyantherum, and H. pusillum indicates that these species do not have any genomes in common with Hordelymus. The hybrids with H. depressum have an intermediate pairing which suggests that there is a certain homoeology in one genome.
The utilization of current nucleic acid technologies in crop improvement and phylogenetic studies require the development
and application of efficient DNA extraction procedures from plants. This paper describes efficient, reliable DNA extraction
procedures forIpomoea andMusa. These procedures are combinations and modifications of the techniques described by Murray and Thompson (1980) and Saghai-Maroof
et al. (1984) and are applicable, without further modification, to other plant genera.
Four accessions of Agropyron drobovii Nevski were introduced into the United States in 1965 from a subrange of the Tien-Shan Mountains in Uzbek Soviet Socialist Republic. A study was undertaken at Logan, Utah, to determine how A. drobovii reproduces, to describe its cytogenetic characteristics, and to determine its genomic and phylogenetic relationships with five other Agropyron species through genome analysis of their F1 hybrids. Seed set was abundant when the plants were pollinated by their own pollen, demonstrating that A. drobovii is self-fertile All plants were 2n = 42 and behaved cytologically as strict alloploids with three distinct genomes. Hybrids were easily obtained between A drobovii and the following species with known genome formulas: A. libanoticum Hack, 2n = 14, SS; A dasystachyum (Hook) Scribn, 2n = 28, SSHH; A mutabile Drob., 2n = 28, SSHH; A. ugamicum Drob., 2n = 28, SSYY; and A leptourum (Nevski) Grossh, 2n = 42, SSSSHH. Chromosome pairing in the five sets of hybrids demonstrated that A drobovii contained the S, H, and Y genomes, and its genome formula should be written as SSHHYY All hybrids were highly or totally sterile. Most hybrids were more vigorous than their parent species, and A libanoticum x A. drobovii showed genuine potential as a forage grass if fertility could be restored
Levels and distribution of genetic variation were assessed using allozymes in 54 populations of Elymus cuninus from different locations in Denmark, Finland, Iceland, Italy, Norway, Sweden, Russia, China and Pakistan in order to obtain information on the extent and nature of genetic variation in this caespitose, predominantly self-fertilising, allotetraploid and perennial grass species. Allozyme variation at the species level was high, with 71.4%) of the loci being polymorphic, an average number of alleles per locus of 2.2, and an average genetic diversity of 0.23. All 54 populations showed some level of polymorphism, which varied substantially from population to population. A high degree of population differentiation was found, with the following remarkable findings: (1) statistically significant differences were found in allele frequencies among populations for every polymorphic locus (P < 0.001), (2) 62%)of the total allozyme variation at polymorphic loci was partitioned among populations (Gst= 0.62), and (3) relatively high genetic distances between the populations were obtained (mean D = 0.16). Genetic structuring was evident among populations from different geographical areas. The Nordic populations showed the highest levels of genetic variation. Cluster and principal component analyses revealed the same genetic patterns of relationships among populations. Generally, this study indicates that E. caninus contains a high level of allozymic variation in its populations.
Amplified fragment length polymorphisms (AFLPs) were used to evaluate the capacity of discontinuous markers to reveal genetic structure within Hordeum, a challenging higher plant genus from the standpoint of natural systematics. Phylogenies of 63 accessions encompassing nine species from four Hordeum sections were inferred from polymorphisms scored at 600 loci. Phylogenies based on sequences from the nuclear internal transcribed spacer (ITS) region were constructed for comparison, but revealed severe sampling errors inherent to single genes. Although superior by virtue of providing genome-wide estimates of genetic similarity, the adoption of AFLPs in infrageneric studies requires caution. Comigrating AFLP bands studied here could be divided on the basis of band intensity variation into two types that are □ 100 % identical and < 40 % identical in DNA sequence, respectively, in infrageneric comparisons. Thus, the careful selection of AFLP bands to be analyzed bears heavily upon their phylogenetic utility. Within the H. murinum complex, which encompasses three morphologically distinct subspecies, AFLP data from 37 accessions reveal unexpected genetic differentiation between H. murinum, glaucumpopulations to the east and west of Alexandria (Egypt), suggesting the presence of allopatric speciation in the wake of human settlement.
Great variability involving 36 quantitative and 31 qualitative characters, as well as the habitats occupied has been shown in 18 populations of Elymus caninus from Poland, based on the detailed population and statistical analyses of morphological characters. The variability of these characters proves that the intraspecific units which have been distinguished on the basis of these characters do not have systematic significance. The two morphotypes of E. caninus (pauciflorum and caninus) described in this study will provide the basis for further genetic studies aimed at establishing their significance for considerations in the systematics of the species.
AFLP™ is one of the most frequently used techniques for identification of molecular markers. We have modified the procedures for
genomic DNA extraction, AFLP product generation and silver staining in order to speed up analyses and screen large numbers
of plant samples. Using this protocol, we were able to achieve an 82% reduction of costs without compromising the reliability
and quality of data gathered.
Genetic diversity in a natural Elymus caninus population from Denmark was assessed using isozyme and microsatellite markers. A total of 119 individuals from 46 maternal
plants were assayed. Microsatellite loci are shown to display higher levels of variation than isozyme loci. The mean number
of alleles per locus was 1.04 for isozymes and 1.38 for microsatellites. The percentage of polymorphic loci for isozymes and
microsatellites was 4.7% and 23.6% across the maternal plant, respectively. The genetic diversity at population level was
0.1 for isozymes, and 0.63 for microsatellites. The mean genetic diversity at maternal plant level was 0.027 for isozyme loci
and 0.117 for microsatellite loci. The average of total allozyme diversity (HT) was 0.22. The average of total microsatellite diversity was 0.56. Isozyme and microsatellite variation showed the same pattern
of differentiation between maternal plants. More than 75% total genetic diversity was found among maternal plants. About 25%
total genetic diversity was detected within maternal plants. Ten (22.7%) maternal plants produced heterozygous offspring at
allozyme loci, and 30 (68.2%) maternal plants gave heterozygous offspring at microsatellite loci. Both types of markers revealed
a relatively high genetic diversity in this population.
Creeping bentgrass (Agrostis stolonifera L.) is currently the most desirable grass for golf courses in temperate climates. In temperate climates, creeping bentgrass is highly susceptible to snow mold fungi which can cause significant injury and mortality. The objectives of this study were to survey a collection of creeping bentgrass clones for reaction to snow mold fungi (Typhula spp.), to identify clones with potential resistance to snow mold fungi, and to identify ecological factors related to necrotic reactions of creeping bentgrass clones to snow mold fungi. Three hundred sixty creeping bentgrass clones, selected from old golf courses in Wisconsin, were evaluated for necrosis reaction during incubation and recovery periods following inoculation with Typhula ishikariensis Imai or as noninoculated controls. Genotypic variation was observed for tolerance to snow mold and cold, dark (noninoculated) conditions but the two tolerances were uncorrelated with each other. Clones from fairways were more tolerant of snow mold, most likely due to long-term natural selection in the absence of fungicide applications. In a second experiment involving 72 selected clones, selection was successful in identifying divergent groups of clones, although differences between experiments indicated that future selection and breeding should make use of multiple inoculation runs. Resistance to snow mold in creeping bentgrass appears to be nonspecific with respect to race and species of snow mold isolates.
Three types of markers-isozymes, RAPDs (random amplified polymorphic DNAs), and wheat microsatellites- were tested on wheat, spelt, and four wild wheat relatives (Aegilops cylindrica, Elymus caninus, Hordeum marinum, and Agropyron junceum). The aim was to evaluate their capability to provide specific markers for differentiation of the cultivated and wild species. The markers were set up for subsequent detection of hybrids and introgression of wheat DNA into wild relatives. All markers allowed differentiation of the cultivated from the wild species. Wheat microsatellites were not amplified in all the wild relatives, whereas RAPDs and isozymes exhibited polymorphism for all species. The dendrograms obtained with RAPD and isozyme data separated Swiss wheat cultivars from those collected in Austria and England, while no difference was found between Swiss spelt and wheat. RAPD data provided a weak discrimination between English and Austrian E. caninus. The microsatellite-based dendrogram discriminated populations of Ae. cylindrica, but no clear separation of H. marinum from E. caninus was revealed. The similarity matrices based on the three different sets of data were strongly correlated. The highest value was recorded between the matrices based on RAPDs and isozymes (Mantel's test, r = 0.93). Correlations between the similarity matrix based on microsatellites and matrices based on RAPDs and isozymes were lower: 0.74 and 0.68, respectively. While microsatellites are very useful for comparisons of closely related accessions, they are less suitable for studies involving less-related taxa. Isozymes provide interesting markers for species differentiation, but their use seems less appropriate for studies of within-species genetic variation. RAPDs can produce a large set of markers, which can be used for the evaluation of both between- and within-species genetic variation, more rapidly and easily than isozymes and microsatellites.
Electrophoretic study of Elymus caninus (L.) L. and Elytrigia repens (L.) Nevski
- G Angelov
Conspectus of the Triticeae
- Löve
M 2002Use of RAPDs for assessment of genetic variation in the germplasm collection of carrot Daucus carota (in Polish)
- Combik
PHYLIP: phylogeny interference package, version 3.5. Department of Genome Sciences
- J Felsenstein
- R Guadagnuolo