Spatial genetic structure and clonal diversity in an alpine population of Salix herbacea (Salicaceae)

BACKGROUND AND AIMS: Many alpine plant species combine clonal and sexual reproduction to minimize the risks of flowering and seed production in high mountain regions. The spatial genetic structure and diversity of these alpine species is strongly affected by different clonal strategies (phalanx or guerrilla) and the proportion of generative and vegetative reproduction. METHODS: The clonal structure of the alpine plant species Salix herbacea was investigated in a 3 x 3 m plot of an alpine meadow using microsatellite (simple sequence repeat; SSR) analysis. The data obtained were compared with the results of a random amplified polymorphic DNA (RAPD) analysis. KEY RESULTS: SSR analysis, based on three loci and 16 alleles, revealed 24 different genotypes and a proportion of distinguishable genotypes of 0.18. Six SSR clones were found consisting of at least five samples, 17 clones consisting of more than two samples and seven single genotypes. Mean clone size comprising at least five samples was 0.96 m(2), and spatial autocorrelation analysis showed strong similarity of samples up to 130 cm. RAPD analysis revealed a higher level of clonal diversity but a comparable number of larger clones and a similar spatial structure. CONCLUSIONS: The spatial genetic structure as well as the occurrence of single genotypes revealed in this study suggests both clonal and sexual propagation and repeated seedling recruitment in established populations of S. herbacea and is thus suggestive of a relaxed phalanx strategy.     

Comparisons of alfalfa somaclonal and sexual derivatives from the same genetic source

Summary Tetraploid alfalfa (Medicago sativa L.) clones were derived from the same diploid genetic background by four different methods. A phenotypically superior clone was selected from each method and compared for herbage yield and fertility. The four methods and their best clones were: a) In vitro somatic chromosome doubling of one diploid hybrid (HG2-4x); b) selection within a two allele tetraploid synthetic population derived from HG2-4x (HAG); c) somaclonal variant selection from cell suspension culture of the diploid hybrid (NS1); and d) sexual polyploidization of a sibling hybrid (HXG). Clones HG2-4x, HAG, and NS1 were likely diallelic or monoallelic at all loci. Clone HXG was probably tetrallelic or triallelic at most loci. Experiments measured fertility, clonal herbage yield, and herbage yield of test cross progeny for each selected clone. Fertility rankings were HXG = HAG > NS1 > HG2-4x. Clonal herbage yield rankings were HXG = HAG > NS1 > HG2-4x. Test cross progeny herbage yield rankings varied depending on the tester, but, in general, HXG HAG NS1 HG2-4x. Overall the best clones from the sexual methods exceeded the best somaclonal variant which, in turn, was better than the chromosome doubled clone.     

Use of RAPD markers to screen somatic hybrids between Solanum tuberosum and S. brevidens

Summary The identification of somatic hybrids between Solanum tuberosum and S. brevidens can be carried out using polymerase chain reaction (PCR) and arbitrary 10-mer primers to generate random amplified polymorphic DNA (RAPD) markers. Five commercial primers have been tested. Each primer directed the amplification of a genome-specific fingerprint for the fusion parents and S. brevidens. The size of the amplified DNA fragments ranged from 100 to 1800 base pairs. The somatic hybrids showed a combination of the parental banding profiles with four of the five primers surveyed, whereas regenerants from one of the parents had the same or a similar banding pattern to that of the parent. Thus RAPD markers provide a quick, simple and preliminary screening method for putative somatic hybrids.Abbreviations EDTA ethylenediaminetetraacetic acid, - PCR polymerase chain reaction - RAPD random amplified polymorphic DNA - RFLP restriction fragment length polymorphisms - TBE Tris-borate-EDTA buffer - Tris trizma base     

Apparent “in situ” clone of cytogenetically marked ataxia-telangiectasia lymphocytes

Summary Six adjacent metaphases, each with the same cytogenetic aberration of a group D chromosome, most probably a No. 14, were observed in a field of a slide from a 96-hour culture of lymphocytes from an individual with ataxia-telangiectasia (AT). None of the 304 orther metaphases examined from this or other simultaneous cultures of this individual showed such an aberration. It seems most likely that an in situ marked clone has been observed and this supports interpretation of consistent cytogenetic abnormalities in those with AT as having clonal origin. The method of slide preparation employed which involves placing, rather than dropping, the cell suspension on the slide may facilitate detection of in situ clones.     

Clonal diversity and structure of the invasive aquatic plant Eichhornia crassipes in China

The information on diversity and spatial distribution of clones of an invasive clonal plant is crucial for the understanding of its clonal structure and invasive history. In this paper, random amplified polymorphic DNA (RAPD) markers were used to explore the clonal diversity and clonal structure of Eichhornia crassipes (Mart.) Solms in natural populations, and their possible effects on the plant success as an invader are also discussed. Five populations covering the entire distribution area in China were studied, sampling 43 individuals per population at an interval of 1 m in a sampling plot. Twelve RAPD primers produced 69 reproducible bands, with 22 being polymorphic. Only five RAPD phenotypes (clones) were detected in these five populations, but each population consisted of at least three clones, contrary to the traditional expectations that E. crassipes populations should be monoclonal. The diversity of clones within populations is thought to be mainly resulted from multiple introductions by humans. The evenness of distribution of clones varied slightly and most clones were widespread, suggesting clonal growth is the predominant mode of regeneration in all the populations. A single clone dominated each population and this clone might be the first one introduced into China or the genotype with a higher phenotypic plasticity, which could survive and reproduce via clonal growth in various habitats. The clones in each population were highly intermixed, especially in river populations, suggesting this species has a guerilla clonal structure which can be facilitated by water current.     

Use of random amplified polymorphic DNA (RAPD) markers in the discrimination and verification of genotypes in Eucalyptus

We carried out four separate studies using random amplified polymorphic DNA (RAPD) markers to analyse samples of Eucalyptus supplied by several different organisations. The objective was to examine the reproducibility of the RAPD technique and its ability to discriminate between individual genotypes for verification of clonal identities. We found that RAPD profiles that are unique to a genotype can be generated reliably and simply and that even closely related genotypes can be distinguished. In addition, in each of the four studies, we detected cases where the plant material studied had been mis-sampled or mis-labelled (i.e. the RAPD profiles were not consistent with the identification numbers): (1) ramets of a Eucalyptus grandis clone were found to be derived from 2 different clones; (2) ramets labelled as 2 different Eucalyptus hybrid clones were found to be the same clone, owing to a mis-planted clonal hedge; (3) samples supplied as a single progeny of a controlled E. nitens cross were derived from two crosses involving different pairs of parents; (4) mis-labelling was detected for ramets of 4 of a set of 10 clones of E. grandis and E. camaldulensis. For three of the four studies, the detection of genotype mis-identifications was unexpected, suggesting that labelling or sampling errors during the handling of plant material are a frequent occurrence, with potentially serious economic consequences.     

Stochastic simulation of clonal growth in the tall goldenrod,Solidago altissima

Summary As clonal plants grow they move through space. The movement patterns that result can be complex and difficult to interpret without the aid of models. We developed a stochastic simulation model of clonal growth in the tall goldenrod, Solidago altissima. Our model was calibrated with field data on the clonal expansion of both seedlings and established clones, and model assumptions were verified by statistical analyses.When simulations were based on empirical distributions with long rhizome lengths, there was greater dispersal, less leaf overlap, and less spatial aggregation than when simulations were based on distributions with comparatively short rhizome lengths. For the field data that we utilized, variation in rhizome lengths had a greater effect than variation for either branching angles or rhizome initiation points (see text). We also found that observed patterns of clonal growth in S. altissima did not cause the formation of fairy rings. However, simulations with an artificial distribution of branching angles demonstrate that fairy rings can result solely from a plant's clonal morphology.Stochastic simulation models that incorporated variation in rhizome lengths, branching angles, and rhizome initiation points produced greater dispersal and less leaf overlap than deterministic models. Thus, variation for clonal growth parameters may increase the efficiency of substrate exploration by increasing the area covered and by decreasing the potential for intraclonal competition. We also demonstrated that ramet displacements were slightly, but consistently lower in stochastic simulation models than in random-walk models. This difference was due to the incorporation of details on rhizome bud initiation into stochastic simulation models, but not random-walk models. We discuss the advantages and disadvantages of deterministic, stochastic simulation, and random-walk models of clonal growth.     

Genetic mapping of turnip mosaic virus resistance in Lactuca sativa

Presence of the dominant Tu gene in Lactuca sativa is sufficient to confer resistance to infection by turnip mosaic virus (TuMV). In order to obtain an immunological assay for the presence of TuMV in inoculated plants, the TuMV coat protein (CP) gene was cloned by amplification of a cDNA corresponding to the viral genome using degenerate primers designed from conserved potyvirus CP sequences. The TuMV CP was overexpressed in Escherichia coli, and polyclonal antibodies were produced. To locate Tu on the L. sativa genetic map, F₃ families from a cross between cvs Cobbham Green (resistant to TuMV) and Calmar (susceptible) were genotyped for Tu. Families known to be recombinant in the region containing Tu were infected with TuMV and tested by the indirect enzyme-linked immunosorbent assay (ELISA) using the anti-CP serum. This assay placed Tu between two random amplified polymorphic DNA (RAPD) markers and 3.2 cM from Dm5/8 (which confers resistance to Bremia lactucae). Also, bulked segregant analysis was used to screen for additional RAPD markers tightly linked to the Tu locus. Five new markers linked to Tu were identified in this region, and their location on the genetic map was determined using informative recombinants in the region. Six markers were identified as being linked within 2.5 cM of Tu.     

Molecular cloning and expression of multiple cellulase genes of Ruminococcus flavefaciens strain 186 in Escherichia coli

Summary Cellulase genes of the ruminant micro-organism Ruminococcus flavefaciens strain 186 have been cloned and expressed in Escherichia coli using the bacteriophage vector NM1149. Twenty-six clones showed expression of endo--1,4-d-glucanases and were divided into four groups according to their insert sizes of approximately 2, 3, 4 or 9 kilobases (kb). Two of the clones with 4 kb inserts also showed exo--1,4-d glucanase activity while two clones with 9 kb inserts showed -glucosidase activity. One of the clones with 9 kb inserts (M903) showed the activities of all three cellulase activities. In addition, two of the 4 kb-insert clones and one 9 kb-insert clone degraded Avicel (PH101).     

The complete primary structure of the T -Cell receptor genes from an alloreactive cytotoxic human T-lymphocyte clone

The complete primary structure of the cDNAs encoding the and chains of the T-lymphocyte receptor for antigen from a human alloreactive, cytotoxic T-cell clone, L17, is presented. Sequence analysis of these genes reveals that both are related to immunoglobulins and are composed of variable, diversity (at least in the case of the Ti clone), joining, and constant region sequences. Comparison of the sequence of the -chain cDNA to that of previously sequenced mouse and human cDNAs suggests the presence of human T-cell receptor D-region sequences. Southern blot analysis confirms the finding that these cDNAs represent the functional receptor genes expressed by the L17 cytotoxic T-cell clone. The availability of these full-length T-cell receptor cDNA clones from a human T-lymphocyte clone of known antigen specificity should allow an analysis of the relationship between T-cell receptor structure and function.     

Differential response of Daphnia genotypes to oxygen stress: respiration rates,hemoglobin content and low-oxygen tolerance

Summary Laboratory respiration rate experiments using three electrophoretically identified clones of the fresh water, planktonic cladoceran, Daphnia pulex, from an eutrophic farm pond, indicated that clones acclimated to both low and high oxygen levels, regulated oxygen consumption across a wide range of oxygen concentrations (1.0–9.0 mg· liter^-1). A threshold oxygen level of 0.5–1.0 mg·liter^-1 was reached, where animals succumbed to oxygen stress, regardless of hemoglobin content. No significant clonal differences in respiration rates were found. These data suggest that members of this Daphnia population are able to regulate oxygen metabolism across a wide range of ambient oxygen concentrations, and indicate a well-adapted respiratory system.Low-oxygen tolerance experiments and hemoglobin measurements indicated further that physiological differences indeed exist between clones; one clone produced the lowest amount of hemoglobin and was least tolerant of low oxygen levels. These data imply that spatial and temporal changes in dissolved oxygen concentration may be an important selective force influencing the clonal (genotypic) composition of natural cladoceran populations.     

Fine specificity and T-cell receptor β-chain gene rearrangements of five H-2Db-specific cytotoxic T-cell clones

A panel of cytotoxic T lymphocyte clones that recognize H-2^b target cells has been established. Six different clones were distinguished according to the following criteria. First, the fine specificity of the clones was determined by testing proliferation and cytotoxicity on target cells of recombinant mice. Clone 221 recognized H-2K^b, and five other clones recognized H-2D^b. Clone 433 distinguished itself from the other five D^b-specific clones by cross-reacting with an antigen on H-2^k cells. Second, the presence of an idiotypic determinant as defined by the 3179 clone-specific monoclonal antibodies was investigated in cytotoxicity inhibition experiments. One of the D^b-specific clones, 653, was inhibited by these antibodies and was therefore clearly different from the other D^b-specific clones. The third criterion involved the rearrangement pattern of the DNA coding for the chain of the T-cell receptor. Southern blot analysis showed that each clone had a unique pattern. Interestingly, clone 653 , which expresses the same idiotypic determinant as clone 3F9, had deleted the C 1 gene cluster, whereas this gene is functionally expressed in clone 3179.Abbreviations used in this paper C constant gene segment - Con A concanavalin A - CTLs cytotoxic T lymphocytes - D diversity gene segment - ³H-dThd tritiated thymidine - J joining gene segment - kb kilobase pairs - LPS lipopolysaccharide - MHC major histocompatibility complex - MLC mixed lymphocyte culture - SDS sodium dodecyl sulfate - V ariable gene segment     

Origin and relationships of New Zealand chestnut (Castanea sp.Fagaceae) selections reflect patterns of graft failure

Graft failure that occurs in the clonal propagation of chestnuts is a practical problem which has arisen in recent years. Several hypotheses have been put forward to explain reasons for the failure but none have focused on origin and relationships of cultivars. This study was carried out to determine whether relationships of New Zealand chestnut selections and their origin reflect patterns of graft failure within the selections. Two different character data sets, random amplified polymorphic DNA (RAPD) and morpho-nut, were employed for the analyses of the relationships between the chestnut selections. Four different analyses were done to generate trees depicting the relationships of the selections. These were: morpho-nut character, RAPD character, taxonomic congruence (combination of morpho-nut and RAPD trees), and character congruence (combination of morpho-nut and RAPD data sets). When graft failure data were mapped onto the majority rule consensus tree constructed from character congruence analysis, it was found that self graft incompatibility was reflected in the origin and relationships of the chestnut selections. Information on the affinities of the chestnut selections to introduced chestnut species showed that the selections that were mostly implicated in graft failure which are from the North Island had affinities with theCastanea crenata species. But the selections (from the South Island) that were placed withCastanea sativa as well as hybrids (1002 and 1007 from the North Island) ofCastanea mollissima andC. crenata had no failed grafts. This finding indicates that graft failure in New Zealand chestnut selections does not occur by chance but is dependent on the origin and/or evolutionary history of the selections.     

Isolation of molecular markers for tomato (L. esculentum) using random amplified polymorphic DNA (RAPD)

Summary A new DNA polymorphism assay was developed in 1990 that is based on the amplification by the polymerase chain reaction (PCR) of random DNA segments, using single primers of arbitrary nucleotide sequence. The amplified DNA fragments, referred to as RAPD markers, were shown to be highly useful in the construction of genetic maps (RAPD mapping). We have now adapted the RAPD assay to tomato. Using a set of 11 oligonucleotide decamer primers, each primer directed the amplification of a genome-specific fingerprint of DNA fragments. The potential of the original RAPD assay to generate polymorphic DNA markers with a given set of primers was further increased by combining two primers in a single PCR. By comparing fingerprints of L. esculentum, L. pennellii, and the L. esculentum chromosome 6 substitution line LA1641, which carries chromosome 6 from L. pennellii, three chromosome 6-specific RAPD markers could be directly identified among the set of amplified DNA fragments. Their chromosomal position on the classical genetic map of tomato was subsequently established by restriction fragment length polymorphism (RFLP) linkage analysis. One of the RAPD markers was found to be tightly linked to the nematode resistance gene Mi.     

珠芽蓼种群克隆多样性及克隆结构的初步研究

珠芽蓼(Polygonum viviparum)是青藏高原东缘广泛分布的克隆植物,具有有性和无性(根状茎和珠芽)两种生殖方式。该研究采用RAPD技术对分布于不同海拔的珠芽蓼7个自然种群进行了克隆结构和克隆多样性(是单克隆种群还是多克隆种群)以及克隆多样性与海拔因子之间的相关性研究,为了解高山克隆植物对环境的适应性策略及揭示克隆植物的繁殖和分布特点提供科学依据。研究结果表明:1)采用13条RAPD引物对珠芽蓼7个种群共140个样本进行扩增分析,共扩增到117个位点,其中多态性位点84个,多态位点百分率PPL达到71.79%,检测到43个基因型,且全部为局限型基因型;2)与Ellstrand和Roose(1987)总结的克隆植物的克隆多样性平均值相比(PD=0.17,D=0.62),珠芽蓼种群克隆多样性水平稍高,Simpson指数平均为0.639,基因型比率PD平均为0.307;3)克隆结构分析表明,珠芽蓼种群内克隆之间的镶嵌明显,这可能与珠芽蓼过渡型的克隆构型有关。研究中珠芽蓼种群的构型有游击型、密集型以及这两者之间的过渡类型;4)采用SPSS软件对珠芽蓼种群的克隆多样性与海拔高度进行相关性分析,结果显示它们之间并无明显的相关性。     

Molecular characterization of RAPD and SCAR markers linked to the Tm-1 locus in tomato

We have cloned and sequenced six RAPD fragments tightly linked to the Tm-1 gene which confers tomato mosaic virus (ToMV) resistance in tomato. The terminal ten bases in each of these clones exactly matched the sequence of the primer for amplifying the corresponding RAPD marker, except for one in which the 5-endmost two nucleotides were different from those of the primer. These RAPD clones did not cross-hybridize with each other, suggesting that they were derived from different loci. From Southern-hybridization experiments, five out of the six RAPD clones were estimated to be derived from middle- or high-repetitive sequences, but not from any parts of the ribosomal RNA genes (rDNA), which are known to be tightly linked with the Tm-1 locus. The remaining clone appeared to be derived from a DNA family consisting of a few copies. These six RAPD fragments were converted to sequence characterized amplified region (SCAR) markers, each of which was detectable using a pair of primers having the same sequence as that at either end of the corresponding RAPD clone. All pairs of SCAR primers amplified distinct single bands whose sizes were the same as those of the RAPD clones. In four cases, the SCAR markers were present in the line with Tm-1 but absent in the line without it, as were the corresponding RAPD markers. In the two other cases, the products of the same size were amplified in both lines. When these SCAR products were digested with different restriction endonucleases which recognize 4-bp sequences, however, polymorphisms in fragment length were found between the two lines. These co-dominant markers are useful for differentiating heterozygotes from both types of homozygote.     

Field and genetic studies testing optimal outcrossing in Agave schottii,a long-lived clonal plant

In thisstudy we combine field experiments, designed to test the predictions of optimal outcrossing theory in Agave schottii, with molecular genetic studies, using RAPD (random amplified polymorphic DNA), polymerase chain reaction to assess the underlying genetic hypothesis of optimal outcrossing theory. Initially, 48 females of A. schottii were hand-pollinated with pollen collected from 1 m, 10 m, 100 m, and 2500 m distances. Each female received all four distance treatments. Additionally, a subset of the focal females and their pollen donors were used in an analysis of genetic similarity across the four distances. Results of hand-pollinations showed that crosses of 1 m had significantly lower seed set than 10 m and 100 m crosses. Crosses of 2500 m had intermediate seed set. Combined relative fitness was significantly lower for 1 m crosses compared to 10 m crosses, while 100 m and 2500 m crosses were intermediate. Thus, A. schottii experiences inbreeding depression and a trend toward outbreeding depression. Genetic analyses showed a similar pattern: individuals 1 m apart had on average higher genetic similarity (proportion of bands shared) than individuals separated by greater distances, with a trend toward lower genetic similarity for plants located 2500 m distant. The observed spatial genetic patterns are likely maintained by the combined effects of clonal reproduction, clone longevity, limited seed dispersal and the substantial number of inbred progeny produced, counteracting distant allele transfer which tends to reduce population genetic structure. The correspondence between our ecological and genetic results indicates that RAPD markers are useful tools for assessing ecological phenomena.     

Micropropagation and field evaluation of micropropagated plants of turmeric

A protocol was developed for in vitro propagation of turmeric cv `elite' using young vegetative buds from sprouting rhizomes. The shoot buds produced multiple shoots when cultured on MS solid medium supplemented with benzyladenine and 1-naphthalene acetic acid. The effect of various cytokinins on shoot multiplication was studied by culturing the shoot tips on MS liquid medium supplemented with benzyladenine, benzyladenine riboside, kinetin, kinetin riboside, zeatin, 6-,-dimethylallylaminopurine, adenine, adenine sulfate or metatopolin each at 10 M in combination with 1-naphthalene acetic acid (1 M). Significant differences were observed between the treatments. Liquid medium was more favourable than agar medium for shoot multiplication. Among the various concentrations of agar tested, 0.4% and 0.6% were the best and produced the highest number of shoots per explant. Among the different carbohydrates tested, sucrose, fructose, glucose, sugar cubes, maltose, levulose and market sugar were found to be equally effective for shoot multiplication and xylose, rhamnose, lactose and soluble starch were inhibitory. Ninety five percent of the micropropagated plants survived in sterilized soil in paper cups and all of them survived in the field. Among 48 plants, two plants showed variegated leaves on the tillers. The micropropagated plants showed a significant increase in shoot length, number of tillers, number and length of leaves, number of fingers and total fresh rhizome weight per plant when compared with conventionally propagated plants. RAPD analysis of 11 regenerated plants using sixteen 10-mer primers did not show any polymorphism.     

Studies on the nature of the Li locus in Trifolium repens L. II. The effect of genotype on enzyme activity and properties

Various reagents which prevent enzyme inhibition by phenolic compounds were tested in attempts to improve the medium used to extract the Li-controlled enzyme activities from white clover leaves. The addition of 50 mm diethyldithiocarbamate to the extraction medium gave a fivefold increase in the enzyme activity of LiLi white clover extracts against p-nitrophenyl -d-glucoside, linamarin-lotaustralin, and p-nitrophenyl -d-galactoside. These three substrates were used in tests on the effect of genotype on enzyme activity. An absence of dominance at the Li locus was demonstrated, with a dosage effect of Li alleles on enzyme activity. A new Li allele was identified in the Lili clone, C11, which had low levels of enzyme activity. In crosses with two lili clones, Li(C11)li progeny were produced with activity levels similar to those of the C11 parent. Inhibition and heat-inactivation tests suggest that the lili clone, D4, produces an altered form of -glucosidase which may also be present in LiLi plants. The nature of the Li locus is discussed.     

Growth dynamics and population development in an alpine grassland under elevated CO2

Leaf expansion, population dynamics and reproduction under elevated CO₂ were studied for two dominant and four subdominant species in a high alpine grassland (2500 above sea level, Swiss Central Alps). Plots of alpine heath were exposed to 335 l l^-1 and 680 l l^-1 CO₂ in open-top chambers over three growing seasons. Treatments also included natural and moderately improved mineral nutrient supply (40 kg N ha^-1 year^-1 in an NPK fertilizer mix). Seasonal dynamics of leaf expansion, which was studied for the dominant graminoid Carex curvula only, were not affected by elevated CO₂ during two warm seasons or during a cool season. Improved nutrient supply increased both the expansion rate and the duration of leaf growth but elevated CO₂ did not cause any further stimulation. Plant and tiller density (studied in all species) increased under elevated CO₂ in the codominant Leontodon helveticus and the subdominant Trifolium alpinum, remained unchanged in two other minor species Poa alpina and Phyteuma globulariifolium, and decreased in Carex curvula. In Potentilla aurea elevated CO₂ compensated for a natural decline in shoot number. By year 3 the number of fertile shoots in Leontodon and individual seed weight in Carex were slightly increased under elevated CO₂, indicating CO₂ effects on sexual reproduction in these two dominant species. The results suggest that the effects of elevated CO₂ on the population dynamics of the species studied were not general, but species-specific and rather moderate effects. However, the reduction of tiller density in Carex curvula, in contrast to the increases observed in Leontodon helveticus and Trifolium alpinum, indicates that elevated CO₂ may negatively affect the abundance of the species most characteristic of this alpine plant community.