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PubMed2005

Clone identification and clonal structure of the European aspen (Populus tremula).

The European aspen (Populus tremula) is thought to reproduce mostly asexually. Thus aspen forms clones, in which several ramets belong to one genetically defined genet. We compared the clonal structure of aspen in old-growth and managed forests in southern and northeastern Finland. Clones were identified using morphological characters and nine microsatellite loci originally developed for Populus tremuloides. There were more clones identified by microsatellites than morphotypes both in old-growth and managed forest. The average size of the clones was only 2.3 ramets and most clones (70%) consisted of just one ramet. The size of the clones showed no difference between managed and old-growth forests or between northeastern and southern Finland. The small size of the clones suggests that most of them are relatively young. Therefore, sexual reproduction may be more common than previously thought. There was an aggregated spatial genetic structure as measured by Moran's I (0-10 m) and by co-ancestry (rho(ij), 0-20 m). Low level of co-ancestry can be explained by relatively unrestricted gene flow, the important role of disturbance in reproduction, and/or local selection.

Age Factors↗

PubMed2006

Genomics of hybrid poplar (Populus trichocarpax deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect-induced defences in poplar.

As part of a genomics strategy to characterize inducible defences against insect herbivory in poplar, we developed a comprehensive suite of functional genomics resources including cDNA libraries, expressed sequence tags (ESTs) and a cDNA microarray platform. These resources are designed to complement the existing poplar genome sequence and poplar (Populus spp.) ESTs by focusing on herbivore- and elicitor-treated tissues and incorporating normalization methods to capture rare transcripts. From a set of 15 standard, normalized or full-length cDNA libraries, we generated 139,007 3'- or 5'-end sequenced ESTs, representing more than one-third of the c. 385,000 publicly available Populus ESTs. Clustering and assembly of 107,519 3'-end ESTs resulted in 14,451 contigs and 20,560 singletons, altogether representing 35,011 putative unique transcripts, or potentially more than three-quarters of the predicted c. 45,000 genes in the poplar genome. Using this EST resource, we developed a cDNA microarray containing 15,496 unique genes, which was utilized to monitor gene expression in poplar leaves in response to herbivory by forest tent caterpillars (Malacosoma disstria). After 24 h of feeding, 1191 genes were classified as up-regulated, compared to only 537 down-regulated. Functional classification of this induced gene set revealed genes with roles in plant defence (e.g. endochitinases, Kunitz protease inhibitors), octadecanoid and ethylene signalling (e.g. lipoxygenase, allene oxide synthase, 1-aminocyclopropane-1-carboxylate oxidase), transport (e.g. ABC proteins, calreticulin), secondary metabolism [e.g. polyphenol oxidase, isoflavone reductase, (-)-germacrene D synthase] and transcriptional regulation [e.g. leucine-rich repeat transmembrane kinase, several transcription factor classes (zinc finger C3H type, AP2/EREBP, WRKY, bHLH)]. This study provides the first genome-scale approach to characterize insect-induced defences in a woody perennial providing a solid platform for functional investigation of plant-insect interactions in poplar.

Animals↗

PubMed2006

Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa.

Abstract Ecotilling was used as a simple nucleotide polymorphism (SNP) discovery tool to examine DNA variation in natural populations of the western black cottonwood, Populus trichocarpa, and was found to be more efficient than sequencing for large-scale studies of genetic variation in this tree. A publicly available, live reference collection of P. trichocarpa from the University of British Columbia Botanical Garden was used in this study to survey variation in nine different genes among individuals from 41 different populations. A large amount of genetic variation was detected, but the level of variation appears to be less than in the related species, Populus tremula, based on reported statistics for that tree. Genes examined varied considerably in their level of variation, from PoptrTB1 which had a single SNP, to PoptrLFY which had more than 23 in the 1000-bp region examined. Overall nucleotide diversity, measured as (Total), was relatively low at 0.00184. Linkage disequilibrium, on the other hand, was higher than reported for some woody plant species, with mean r2 equal to 0.34. This study reveals the potential of Ecotilling as a rapid genotype discovery method to explore and utilize the large pool of genetic variation in tree species.

Canada↗

PubMed2006

Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis.

Stems and branches of angiosperm trees form tension wood (TW) when exposed to a gravitational stimulus. One of the main characteristics of TW, which distinguishes it from normal wood, is the formation of fibers with a thick inner gelatinous cell wall layer mainly composed of crystalline cellulose. Hence TW is enriched in cellulose, and deficient in lignin and hemicelluloses. An expressed sequence tag library made from TW-forming tissues in Populus tremula (L.) x tremuloides (Michx.) and data from transcript profiling using microarray and metabolite analysis were obtained during TW formation in Populus tremula (L.) in two growing seasons. The data were examined with the aim of identifying the genes responsible for the change in carbon (C) flow into various cell wall components, and the mechanisms important for the formation of the gelatinous cell wall layer (G-layer). A specific effort was made to identify carbohydrate-active enzymes with a putative function in cell wall biosynthesis. An increased C flux to cellulose was suggested by a higher abundance of sucrose synthase transcripts. However, genes related to the cellulose biosynthetic machinery were not generally affected, although the expression of secondary wall-specific CesA genes was modified in both directions. Other pathways for which the data suggested increased activity included lipid and glucosamine biosynthesis and the pectin degradation machinery. In addition, transcripts encoding fasciclin-like arabinogalactan proteins were particularly increased and found to lack true Arabidopsis orthologs. Major pathways for which the transcriptome and metabolome analysis suggested decreased activity were the pathway for C flux through guanosine 5'-diphosphate (GDP) sugars to mannans, the pentose phosphate pathway, lignin biosynthesis, and biosynthesis of cell wall matrix carbohydrates. Several differentially expressed auxin- and ethylene-related genes and transcription factors were also identified.

Cell Wall↗

PubMed2006

Genetical metabolomics of flavonoid biosynthesis in Populus: a case study.

Genetical metabolomics [metabolite profiling combined with quantitative trait locus (QTL) analysis] has been proposed as a new tool to identify loci that control metabolite abundances. This concept was evaluated in a case study with the model tree Populus. Using HPLC, the peak abundances were analyzed of 15 closely related flavonoids present in apical tissues of two full-sib poplar families, Populus deltoides cv. S9-2 x P. nigra cv. Ghoy and P. deltoides cv. S9-2 x P. trichocarpa cv. V24, and correlation and QTL analysis were used to detect flux control points in flavonoid biosynthesis. Four robust metabolite quantitative trait loci (mQTL), associated with rate-limiting steps in flavonoid biosynthesis, were mapped. Each mQTL was involved in the flux control to one or two flavonoids. Based on the identities of the affected metabolites and the flavonoid pathway structure, a tentative function was assigned to three of these mQTL, and the corresponding candidate genes were mapped. The data indicate that the combination of metabolite profiling with QTL analysis is a valuable tool to identify control points in a complex metabolic pathway of closely related compounds.

Chromatography, High Pressure Liquid↗

PubMed2005

Jasmonic acid induces rapid changes in carbon transport and partitioning in Populus.

Here, we tested whether rapid changes in carbohydrate transport and partitioning to storage organs would be induced by jasmonic acid (JA), a plant-produced signal of herbivore attack known to induce resistance. Carbon-11, introduced as (11)CO(2), was used to track real-time carbohydrate transport and partitioning nondestructively in Populus species before and 12 h after application of JA to a single leaf. Jasmonic acid resulted in more rapid [(11)C]-photosynthate export from both local and systemic leaves, as well as greater partitioning of [(11)C]-photosynthate to the stem and roots. In Populus tremuloides, following JA treatment, leaf starch decreased, but there was no change in photosynthetic rates or leaf soluble sugar concentration, indicating that recent photosynthate was diverted from starch accumulation in the leaf to other plant organs. Increasing the supply of photosynthate to roots and stems may shield resources from folivorous predators, and may also facilitate both storage and nutrient uptake, and ultimately lead to greater tolerance, either by enhancing regrowth capacity or by replacing nutrients consumed by herbivores.

Biological Transport↗

PubMed2006

Arbuscular mycorrhizal fungi associated with Populus-Salix stands in a semiarid riparian ecosystem.

This study examined the activity, species richness, and species composition of the arbuscular mycorrhizal fungal (AMF) community of Populus-Salix stands on the Verde River (Arizona, USA), quantified patterns of AMF richness and colonization along complex floodplain gradients, and identified environmental variables responsible for structuring the AMF community. Samples from 61 Populus-Salix stands were analyzed for AMF and herbaceous composition, AMF colonization, gravimetric soil moisture, soil texture, per cent organic matter, pH, and concentrations of nitrate, bicarbonate phosphorus and exchangeable potassium. AMF species richness declined with stand age and distance from and elevation above the channel and was positively related to perennial species cover and richness and gravimetric soil moisture. Distance from and elevation above the active channel, forest age, annual species cover, perennial species richness, and exchangeable potassium concentration all played a role in structuring the AMF community in this riparian area. Most AMF species were found across a wide range of soil conditions, but a subset of species tended to occur more often in hydric areas. This group of riparian affiliate AMF species includes several not previously encountered in the surrounding Sonoran desert.

Arizona↗

PubMed2005

Gene expression and metabolite profiling of Populus euphratica growing in the Negev desert.

BACKGROUND: Plants growing in their natural habitat represent a valuable resource for elucidating mechanisms of acclimation to environmental constraints. Populus euphratica is a salt-tolerant tree species growing in saline semi-arid areas. To identify genes involved in abiotic stress responses under natural conditions we constructed several normalized and subtracted cDNA libraries from control, stress-exposed and desert-grown P. euphratica trees. In addition, we identified several metabolites in desert-grown P. euphratica trees. RESULTS: About 14,000 expressed sequence tag (EST) sequences were obtained with a good representation of genes putatively involved in resistance and tolerance to salt and other abiotic stresses. A P. euphratica DNA microarray with a uni-gene set of ESTs representing approximately 6,340 different genes was constructed. The microarray was used to study gene expression in adult P. euphratica trees growing in the desert canyon of Ein Avdat in Israel. In parallel, 22 selected metabolites were profiled in the same trees. CONCLUSION: Of the obtained ESTs, 98% were found in the sequenced P. trichocarpa genome and 74% in other Populus EST collections. This implies that the P. euphratica genome does not contain different genes per se, but that regulation of gene expression might be different and that P. euphratica expresses a different set of genes that contribute to adaptation to saline growth conditions. Also, all of the five measured amino acids show increased levels in trees growing in the more saline soil.

Desert Climate↗

PubMed2004

Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae).

Populus is an important model organism in forest biology, but levels of nucleotide polymorphisms and linkage disequilibrium have never been investigated in natural populations. Here I present a study on levels of nucleotide polymorphism, haplotype structure, and population subdivision in five nuclear genes in the European aspen Populus tremula. Results show substantial levels of genetic variation. Levels of silent site polymorphisms, pi(s), averaged 0.016 across the five genes. Linkage disequilibrium was generally low, extending only a few hundred base pairs, suggesting that rates of recombination are high in this obligate outcrossing species. Significant genetic differentiation was found at all five genes, with an average estimate of F(ST) = 0.116. Levels of polymorphism in P. tremula are 2- to 10-fold higher than those in other woody, long-lived perennial plants, such as Pinus and Cryptomeria. The high levels of nucleotide polymorphism and low linkage disequilibrium suggest that it may be possible to map functional variation to very fine scales in P. tremula using association-mapping approaches.

Genes, Plant↗

PubMed2005

Clinal variation in phyB2, a candidate gene for day-length-induced growth cessation and bud set, across a latitudinal gradient in European aspen (Populus tremula).

The initiation of growth cessation and dormancy represents a critical ecological and evolutionary trade-off between survival and growth in most forest trees. The most important environmental cue regulating the initiation of dormancy is a shortening of the photoperiod and phytochrome genes have been implicated in short-day-induced bud set and growth cessation in Populus. We characterized patterns of DNA sequence variation at the putative candidate gene phyB2 in 4 populations of European aspen (Populus tremula) and scored single-nucleotide polymorphisms in an additional 12 populations collected along a latitudinal gradient in Sweden. We also measured bud set from a subset of these trees in a growth chamber experiment. Buds set showed significant clinal variation with latitude, explaining approximately 90% of the population variation in bud set. A sliding-window scan of phyB2 identified six putative regions with enhanced population differentiation and four SNPs showed significant clinal variation. The clinal variation at individual SNPs is suggestive of an adaptive response in phyB2 to local photoperiodic conditions. Three of four SNPs showing clinal variation were located in regions with excessive genetic differentiation, demonstrating that searching for regions of high genetic differentiation can be useful for identifying sites putatively involved in local adaptation.

Crosses, Genetic↗

PubMed2004

[Effect of insect pest on activated oxygen metabolism in lanceolate leaves of Populus euphratica under different water condition].

This paper studied the effect of insect pest on the activities of protective enzymes SOD and CAT and the contents of H2O2 and O2*- in lanceolate leaves of Populus euphratica under different soil water conditions. The results showed that soil water deficiency did not increase SOD and CAT activities and H2O2 and O2*- contents in lanceolate leaves, but under this condition, insect pest increased them. When soil water was abundance, insect pest couldn't increase the activities of SOD and CAT and the contents of H2O2 and O2*- in lanceolate leaves. It's concluded that insect pest had an important role in death of Populus euphratica under soil water deficiency.

Animals↗

PubMed2005

[Seasonal variation of Tamarix ramosissima and Populus euphratica water potentials in southern fringe of Taklamakan Desert].

The measurement of the seasonal and diurnal variations of Tamarix ramosissima and Populus euphratica water potentials in the southern fringe of Taklamakan Desert indicated that there was no apparent water stress for the two species during their growth period, with little change of predawn water potential and some extent decrease of midday water potential. Irrigation once or thinning had no significant effects on the water status of the plants, while groundwater appeared to be a prerequisite for the survival and growth of these species. It is very important to ensure a stable groundwater table for the restoration of Tamarix ramosissima and Populus euphratica in this area.

China↗

PubMed2005

Degradation of Populus euphratica community in the lower reaches of the Tarim River, Xinjiang, China.

To investigate the relationships between the degradation of plant community and groundwater level in the lower reaches of the Tarim River, nine monitored sections were set along the main stream, where there had been no runoff for nearly 30 years. The characteristics of plant communities were analyzed. It was found that the coverage of trees gradually decreased along the groundwater depth gradient, while the coverage of shrubs slightly increased rather than decreased at first and then gradually decreased, and the coverage of herbs steadily decreased at the beginning and then quickly decreased. The species diversity and species richness of both herbs and woody plants showed obvious degrading trends, while the variations in species evenness were slight. The degrading sequences of species were related to their physiological and ecological characteristics, especially their sensitivity to changes of groundwater table. The herbs with shallow roots first degenerated or disappeared when the groundwater table fell, and then did the deep-rooted herbs, and finally the trees and shrubs with strong tolerance to drought degenerated. The Populus euphratica communities showed typical degrading characteristics, namely the dominant species Populus euphratica remained its dominant status during the degradation. Overall, the existence of strongly tolerant-drought species was the obvious indication of plant species degradation; while simplification of community structure and the decrease of species richness were the obvious indication of plant community degradation.

China↗

PubMed2006

[Physiological-ecological effects of Populus davidiana--Quercus liaotungensis mixed forest in Ziwuling forest area].

This paper studied the soil physical- properties under Populus davidiana, Quercus liaotungensis, and Populus davidiana--Quercus liaotungensis mixed forest in the Ziwuling forest area of Loess Plateau, and the leaf photosysthetic characteristics of these three types of forests. The results showed that soil moisture content in 0 - 300 cm layer was the highest under P. davidiana forest, and obviously increased below 200 cm in depth under P. davidiana--Q. liaotungensis mixed forest, which was 10.5% - 19.76% higher than that under Q. liaotungensis forest. In 0 - 60 cm layer, P. davidiana forest showed the highest soil bulk density and the lowest soil porosity, while P. davidiana--Q. liaotungensis mixed forest presented the lowest soil bulk density and the highest soil porosity, and both of these indices surpassed their corresponding values under pure forests, which indicated that the mixed forest could make effective use of water in deep soil, and obviously improved soil physical and chemical properties. P. davidiana and Q. liaotungensis had a higher content of leaf chlorophyll than P. davidiana--Q. liaotungensis mixed forest, and Q. liaotungensis presented the highest leaf chlorophyll content. Q. liaotungensis had the highest photosynthetic rate and stomatal conductance, followed by P. davidiana, and by P. davidiana--Q. liaotungensis mixed forest. The water use efficiency of the forests ranked in the decreasing order of Q. liaotungensis in pure forest, Q. liaotungensis in mixed forest, P. davidiana in mixed forest, and P. davidiana in pure forest. Q. liaotungensis in mixed forest presented the highest F(v)/F(m) and F(v)/F(o), and did not remarkably differ from those in pure forest, but in the mixed forest, the F(v)/F(m) and F(v)/F(o) of P. davidiana were markedly lower than those of P. davidiana in pure forest. Both the q(p) and NPQ of P. davidiana and Q. liaotungensis in pure forests were higher than those in mixed forest, respectively. In Ziwuling forest area, Q. liaotungensis in Q. liaotungensis--dominant climax community tended to be more stable, and grew better than Q. liaotungensis in P. davidiana--Q. liaotungensis mixed forest, and P. davidiana would be gradually replaced. Compared with P. davidiana in pure forest, P. davidiana in its mixed forest was at a disadvantage in its growth.

China↗

PubMed1999

Purification and spectroscopic studies on catechol oxidases from Lycopus europaeus and Populus nigra: evidence for a dinuclear copper center of type 3 and spectroscopic similarities to tyrosinase and hemocyanin.

We purified two catechol oxidases from Lycopus europaeus and Populus nigra which only catalyze the oxidation of catechols to quinones without hydroxylating tyrosine. The molecular mass of the Lycopus enzyme was determined to 39,800 Da and the mass of the Populus enzyme was determined to 56,050 Da. Both catechol oxidases are inhibited by thiourea, N-phenylthiourea, dithiocarbamate, and cyanide, but show different pH behavior using catechol as substrate. Atomic absorption spectrosopic analysis found 1.5 copper atoms per protein molecule. Using EPR spectroscopy we determined 1.8 Cu per molecule catechol oxidase. Furthermore, EPR spectroscopy demonstrated that catechol oxidase is a copper enzyme of type 3. The lack of an EPR signal is due to strong antiferromagnetic coupling that requires a bridging ligand between the two copper ions in the met preparation. Addition to H2O2 to both enzymes leads to oxy catechol oxidase. In the UV/Vis spectrum two new absorption bands occur at 345 nm and 580 nm. In accordance with the oxy forms of hemocyanin and tyrosinase the absorption band at 345 nm is due to an O2(2-) (pi sigma *)-->Cu(II) (dx2 - y2) charge transfer (CT) transition. The absorption band at 580 nm corresponds to the second O2(2)- (pi v*)-->Cu(II) (dx2 - y2) CT transition. The UV/Vis bands in combination with the resonance Raman spectra of oxy catechol oxidase indicate a mu-eta 2:eta 2 binding mode for dioxygen. The intense resonance Raman peak at 277 cm-1, belonging to a Cu-N (axial His) stretching mode, suggests that catechol oxidase has six terminal His ligands, as known for molluscan and arthropodan hemocyanin.

Binding Sites↗

PubMed1994

Chronic ozone exposure increases the susceptibility of hybrid Populus to disease caused by Septoria Musiva.

Rooted cuttings of hybrid Populus (DN34, Populus deltoides X nigra) were grown outdoors in pots in open-top chambers at Ithaca, NY (74.5 degrees W, 42.5 degrees N), during 1988 and 1989 (Experiment 1) and during 1989 and 1990 (Experiment 2). Ambient air was passed through charcoal filters to produce a 0.5 times ambient ozone treatment, and ozone generated from oxygen was added to produce one and two times ambient ozone treatments. In Experiment 1, treatments were applied for 8-12 h each day for 112 days of the 1988 growing season; then the plants were grown outdoors with ambient ozone in 1989. In Experiment 2, treatments were applied for 9 h each day for 98 days of the 1989 growing season; then the plants were grown outdoors with ambient ozone in 1990. Shallow wounds were made into the bark tissue and inoculated with either an aqueous suspension of conidia of Mycosphaerella populorum or sterile water on 1 and 2 September 1988 (Experiment 1) or 16 and 17 August 1989 (Experiment 2). In Experiment 1, wounds were inoculated either 0, 7, or 14 days after wounding. In Experiment 2, wounds were inoculated either 0, 3, or 6 days after wounding. Canker development was measured after harvest on 16 and 17 July 1989 (Experiment 1) and 28 May 1990 (Experiment 2). In both experiments, chronic exposure to ozone significantly increased the incidence of canker formation in inoculated wounds, and no cankers formed in wounds that received only sterile water. In Experiment 1, cankers formed only on plants inoculated the same day as wounding. No cankers formed on plants inoculated either 7 or 14 days after wounding. In Experiment 2, cankers formed on plants inoculated on the same day as wounding, and on a few plants inoculated 3 days after wounding. No cankers formed on plants inoculated 6 days after wounding. Additionally, in Experiment 2, exposure to increased concentrations of ozone caused a significantly higher number of plants to die during the subsequent winter. Analysis of partial correlation coefficients among plant growth and plant disease variables suggested that the observed ozone-induced increase in the susceptibility of the plants to disease was not mediated by alterations in plant growth.

Journal Article↗

PubMed1994

Chronic ozone exposure alters the growth of leaves, stems and roots of hybrid Populus.

Rooted cuttings of hybrid Populus (DN34, Populus deltoides x nigra) were grown outdoors in pots in open-top chambers at Ithaca, NY (74.5 degrees W, 42.5 degrees N), during 1988 and 1989 (experiment 1) and during 1989 and 1990 (experiment 2). Ambient air was passed through charcoal filters to produce a 0.5 times ambient ozone treatment, and ozone generated from oxygen was added to produce one and two times ambient ozone treatments. In experiment 1, treatments were applied for 8-12 h each day for 112 days of the 1988 growing season, then the plants were grown outdoors with ambient ozone in 1989. In experiment 2, treatments were applied for 9 h each day for 98 days of the 1989 growing season, then the plants were grown outdoors with ambient ozone in 1990. Chronic exposure to ozone caused the following changes (statistically significant in one or both experiments at p<0.05): (1) earlier leaf abscission, (2) decreased stem basal diameter, (3) decreased stem mass, (4) decreased internode length, (5) decreased shoot height p=0.005, and (6) decreased leaf size in the growing season following ozone treatment. There was also strong evidence that ozone increased the number of leaves produced p=0.055. Finally, there was some evidence that ozone increased the ratio of shoot mass to root mass p=0.093.

Journal Article↗

PubMed2002

Gibberellins in shoots and developing capsules of Populus species.

Extracts of stems of growing shoots of Populus deltoides and P. trichocarpa, and developing capsules of P. deltoides were analysed for gibberellins (GAs) by gas chromatography-mass spectrometry. The following known GAs were identified by comparison of their Kovats retention indices (KRIs) and mass spectra with those of standards: GA1, GA8, GA9, GA19, GA20, 16 beta,17-dihydro-17-hydroxy GA20, GA23, GA28, GA29, GA34, GA44, and GA97. Several of these have not been previously reported from Populus. In addition, two new GAs were identified as 12 beta-hydroxy GA53 (GA127) and 16 beta,17-dihydro-17-hydroxy GA53 and their structures were confirmed by partial synthesis. Evidence was found of 16,17-dihydro-16,17-dihydroxy GA9, 16,17-dihydro-16,17-dihydroxy GA12, 12-hydroxy GA14, and GA34-catabolite by comparison of mass spectra and KRIs with published data. Several putative GAs (hydroxy- and dihydroxy-GA12-like) were also found. The catabolites of active GAs or of key precursors, hydroxylated at C-2 in stems and either C-2, C-12, C-17, or C-16,17 in capsules, were the major proportion of the GAs.

Gas Chromatography-Mass Spectrometry↗