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Sample records for populus tremuloides internodes

  1. Microsatellite DNA markers in Populus tremuloides.

    PubMed

    Rahman, M H; Dayanandan, S; Rajora, O P

    2000-04-01

    Markers for eight new microsatellite DNA or simple sequence repeat (SSR) loci were developed and characterized in trembling aspen (Populus tremuloides) from a partial genomic library. Informativeness of these microsatellite DNA markers was examined by determining polymorphisms in 38 P. tremuloides individuals. Inheritance of selected markers was tested in progenies of controlled crosses. Six characterized SSR loci were of dinucleotide repeats (two perfect and four imperfect), and one each of trinucleotide and tetranucleotide repeats. The monomorphic SSR locus (PTR15) was of a compound imperfect dinucleotide repeat. The primers of one highly polymorphic SSR locus (PTR7) amplified two loci, and alleles could not be assigned to a specific locus. At the other six polymorphic loci, 25 alleles were detected in 38 P. tremuloides individuals; the number of alleles ranged from 2 to 7, with an average of 4.2 alleles per locus, and the observed heterozygosity ranged from 0.05 to 0.61, with an average of 0.36 per locus. The two perfect dinucleotide and one trinucleotide microsatellite DNA loci were the most informative. Microsatellite DNA variants of four SSR loci characterized previously followed a single-locus Mendelian inheritance pattern, whereas those of PTR7 from the present study showed a two-locus Mendelian inheritance pattern in controlled crosses. The microsatellite DNA markers developed and reported here could be used for assisting various genetic, breeding, biotechnology, genome mapping, conservation, and sustainable forest management programs in poplars. PMID:10791817

  2. Widespread Triploidy in Western North American Aspen (Populus tremuloides)

    PubMed Central

    Mock, Karen E.; Callahan, Colin M.; Islam-Faridi, M. Nurul; Shaw, John D.; Rai, Hardeep S.; Sanderson, Stewart C.; Rowe, Carol A.; Ryel, Ronald J.; Madritch, Michael D.; Gardner, Richard S.; Wolf, Paul G.

    2012-01-01

    We document high rates of triploidy in aspen (Populus tremuloides) across the western USA (up to 69% of genets), and ask whether the incidence of triploidy across the species range corresponds with latitude, glacial history (as has been documented in other species), climate, or regional variance in clone size. Using a combination of microsatellite genotyping, flow cytometry, and cytology, we demonstrate that triploidy is highest in unglaciated, drought-prone regions of North America, where the largest clone sizes have been reported for this species. While we cannot completely rule out a low incidence of undetected aneuploidy, tetraploidy or duplicated loci, our evidence suggests that these phenomena are unlikely to be significant contributors to our observed patterns. We suggest that the distribution of triploid aspen is due to a positive synergy between triploidy and ecological factors driving clonality. Although triploids are expected to have low fertility, they are hypothesized to be an evolutionary link to sexual tetraploidy. Thus, interactions between clonality and polyploidy may be a broadly important component of geographic speciation patterns in perennial plants. Further, cytotypes are expected to show physiological and structural differences which may influence susceptibility to ecological factors such as drought, and we suggest that cytotype may be a significant and previously overlooked factor in recent patterns of high aspen mortality in the southwestern portion of the species range. Finally, triploidy should be carefully considered as a source of variance in genomic and ecological studies of aspen, particularly in western U.S. landscapes. PMID:23119006

  3. Widespread triploidy in Western North American aspen (Populus tremuloides).

    PubMed

    Mock, Karen E; Callahan, Colin M; Islam-Faridi, M Nurul; Shaw, John D; Rai, Hardeep S; Sanderson, Stewart C; Rowe, Carol A; Ryel, Ronald J; Madritch, Michael D; Gardner, Richard S; Wolf, Paul G

    2012-01-01

    We document high rates of triploidy in aspen (Populus tremuloides) across the western USA (up to 69% of genets), and ask whether the incidence of triploidy across the species range corresponds with latitude, glacial history (as has been documented in other species), climate, or regional variance in clone size. Using a combination of microsatellite genotyping, flow cytometry, and cytology, we demonstrate that triploidy is highest in unglaciated, drought-prone regions of North America, where the largest clone sizes have been reported for this species. While we cannot completely rule out a low incidence of undetected aneuploidy, tetraploidy or duplicated loci, our evidence suggests that these phenomena are unlikely to be significant contributors to our observed patterns. We suggest that the distribution of triploid aspen is due to a positive synergy between triploidy and ecological factors driving clonality. Although triploids are expected to have low fertility, they are hypothesized to be an evolutionary link to sexual tetraploidy. Thus, interactions between clonality and polyploidy may be a broadly important component of geographic speciation patterns in perennial plants. Further, cytotypes are expected to show physiological and structural differences which may influence susceptibility to ecological factors such as drought, and we suggest that cytotype may be a significant and previously overlooked factor in recent patterns of high aspen mortality in the southwestern portion of the species range. Finally, triploidy should be carefully considered as a source of variance in genomic and ecological studies of aspen, particularly in western U.S. landscapes.

  4. Induced resistance in the indeterminate growth of aspen (Populus tremuloides).

    PubMed

    Stevens, Michael T; Lindroth, Richard L

    2005-09-01

    Studies of induction in trees have examined rapid induced resistance (RIR) or delayed induced resistance (DIR), but have not examined induction that occurs in leaves produced by indeterminately growing trees subsequent to, but in the same season as, damage. We refer to induction that occurs during this time period as intermediate-delayed induced resistance (IDIR). We assessed the influences of genetic and environmental factors, and their interactions, on temporal and spatial variation in induction and on tradeoffs between induced and constitutive levels of resistance in indeterminately growing saplings of aspen (Populus tremuloides). We utilized a common garden of 12 aspen genotypes experiencing two levels of defoliation and two levels of soil nutrients. We assessed concentrations of phenolic glycosides and condensed tannins in damaged leaf remnants collected 1 week after defoliation to examine rapid and local induction, and in undamaged leaves produced 8 weeks after defoliation to assess intermediate-delayed and systemic induction. In general, tannins showed RIR, while phenolic glycosides expressed IDIR. For both classes of allelochemicals, we found high estimates of broad-sense heritability and genetic variation in both induced and constitutive levels. Genetic variation may be maintained by both direct costs of allelochemicals and by costs of inducibility (phenotypic plasticity). Such costs may drive the tradeoff exhibited between induced and constitutive levels of phenolic glycosides. IDIR may be important in reducing total-season tissue loss by providing augmented resistance against late summer herbivores in trees that have experienced damage earlier in the season. Herbivore-resistant compensatory growth is especially beneficial to young trees growing in competitive environments.

  5. Naphthenic acids inhibit root water transport, gas exchange and leaf growth in aspen (Populus tremuloides) seedlings.

    PubMed

    Kamaluddin, M; Zwiazek, Janusz J

    2002-12-01

    Effects of sodium naphthenates (NAs) on root hydraulic conductivity (Lp) and gas exchange processes were examined in aspen (Populus tremuloides Michx.) seedlings grown in solution culture. Exposure of roots to NAs for 3-5 weeks significantly decreased Lp and stomatal conductance. Root-absorbed NAs also decreased leaf chlorophyll concentration, net photosynthesis and leaf growth. Short-term (< or = 2 h) exposure of excised roots to NAs significantly decreased root water flow (Qv) with a concomitant decline in root respiration. We conclude that NAs metabolically inhibited Lp, likely by affecting water channel activity, and that this inhibition could be responsible for the observed reductions in gas exchange and leaf growth.

  6. Populations of aspen (Populus tremuloides Michx.) with different evolutionary histories differ in their climate occupancy.

    PubMed

    Greer, Burke T; Still, Christopher; Howe, Glenn T; Tague, Christina; Roberts, Dar A

    2016-05-01

    Quaking aspens (Populus tremuloides Michx.) are found in diverse habitats throughout North America. While the biogeography of aspens' distribution has been documented, the drivers of the phenotypic diversity of aspen are still being explored. In our study, we examined differences in climate between northern and southwestern populations of aspen, finding large-scale differences between the populations. Our results suggest that northern and southwestern populations live in distinct climates and support the inclusion of genetic and phenotypic data with species distribution modeling for predicting aspens' distribution.

  7. Efficient shoot regeneration from internodal explants of Populus angustifolia, Populus balsamifera and Populus deltoids.

    PubMed

    Maheshwari, Priti; Kovalchuk, Igor

    2011-10-01

    In the present study, interactions between the duration of treatment with auxin and different cytokinins and their effect on shoot regeneration were evaluated with the aim to establish a rapid and efficient in vitro regeneration method applicable to a variety of Populus species. Three different species, Populus angustifolia, P. balsamifera, and P. deltoids, were chosen for that purpose. We were successful in regenerating plantlets from stem and petiole explants from all three chosen species using a four-step simple procedure. The first step was callus induction when the explants were exposed to an auxin-rich medium for 0-20 days. During the second step, they were transferred onto a cytokinin-rich medium for shoot bud induction. In the third step, the shoots regenerated were transferred onto a medium with reduced levels of cytokinins to promote shoot proliferation and elongation; finally, in the fourth step, the shoots were rooted and acclimated. A short period (6-10 days) of time of exposure to auxin was sufficient for shoot regeneration. A culture time longer than ten days in callus induction medium drastically reduced the efficiency of shoot regeneration. Besides, cytokinin type and concentration also affected the frequency of shoot induction. A 0.2 mg/l concentration of 2,4-D for callus induction followed by 0.02 mg/l of Thidiazuron for shoot formation proved to be the best treatment for adventitious shoot bud multiplication, generating a maximum of 10-13 shoots of P. balsamifera and P. angustifolia in ten weeks. In contrast, for P. deltoids, a combination of 1.1mg/l 2,4-D, 1.0mg/l NAA, 0.1mg/l zeatin for callus induction followed by a combination of 1mg/l zeatin plus 1.0mg/l BA for shoot bud induction was found to be the most effective, generating on average 15 shoots over a period of ten weeks.

  8. Differences in leaf characteristics between ozone-sensitive and ozone-tolerant hybrid aspen (Populus tremula x Populus tremuloides) clones.

    PubMed

    Häikiö, Elina; Freiwald, Vera; Julkunen-Tiitto, Riitta; Beuker, Egbert; Holopainen, Toini; Oksanen, Elina

    2009-01-01

    The authors analyzed a suite of leaf characteristics that might help to explain the difference between ozone-sensitive and ozone-tolerant hybrid aspen (Populus tremula L. x Populus tremuloides Michx.) clones. An open-field experiment comprising ambient ozone and 1.5x ambient ozone concentration (about 35 ppb) and two soil nitrogen regimes (60 and 140 kg N ha(-1) year(-1)) was conducted over two growing seasons on potted plants of eight hybrid aspen clones. Four of the clones had previously been determined to be ozone sensitive based on impaired growth in response to elevated ozone concentration. Photosynthetic rate, chlorophyll fluorescence, and concentrations of chlorophyll, protein and carbohydrates were analyzed three times during the second growing season, and foliar phenolic concentrations were measured at the end of the second growing season. Nitrogen amendment counteracted the effects of ozone, but had no effect on growth-related ozone sensitivity of the clones. Ozone-sensitive clones had higher photosynthetic capacity and higher concentrations of Rubisco and phenolics than ozone-tolerant clones, but the effects of ozone were similar in the sensitive and tolerant groups. Nitrogen addition had no effect on phenolic concentration, but elevated ozone concentration increased the concentrations of chlorogenic acid and (+)-catechin. This study suggests that condensed tannins and catechin, but not salicylates or flavonol glycosides, play a role in the ozone tolerance of hybrid aspen.

  9. Diurnal and Seasonal Patterns of Photosynthesis and Respiration by Stems of Populus tremuloides Michx. 1

    PubMed Central

    Foote, Knowlton C.; Schaedle, Michail

    1976-01-01

    The photosynthetic and respiratory rates of 5- to 7-year-old aspen stems (Populus tremuloides Michx.) were monitored in the field for 1 year to determine the seasonal patterns. The stem was not capable of net photosynthesis, but the respiratory CO2 loss from the stem was reduced by 0 to 100% depending on the time of year and the level of illumination as a result of bark photosynthesis. The monthly dark respiratory rate ranged from 0.24 mg CO2/dm2· hr in January to a maximum 7.4 mg CO2/dm2· hr in June. Individual measurements ranged from 0.02 mg CO2/dm2· hr in February to 12.3 mg CO2/dm2· hr in June. Gross photosynthesis followed a pattern similar to the dark respiratory rate. The mean monthly rate was highest in June (1.65 mg CO2/dm2· hr) and lowest in December (0.02 mg CO2/dm2· hr). Individual measurements ranged from 0.0 mg CO2/dm2· hr in winter to 5.5 mg CO2/dm2· hr in July. Winter studies showed that stem respiration continued down to −11 C, the coldest temperature during this study. Upon warning to −3 C, the dark respiratory rate showed a sudden sharp increase (7- to 12-fold) which required many hours to return to normal levels. No measurable photosynthesis occurred below −3 C. Between −3 and 0 C, the maximal photosynthetic rate was reduced to less than 50% of the respiratory rate, but increased to 89% between 5 to 10 C. On a yearly basis, bark photosynthesis in P. tremuloides reduced the stem respiratory CO2 loss by 28.7% on a daytime basis and an estimated 16 to 18% on a 24-hour basis. PMID:16659737

  10. Competition- and resource-mediated tradeoffs between growth and defensive chemistry in trembling aspen (Populus tremuloides).

    PubMed

    Donaldson, Jack R; Kruger, Eric L; Lindroth, Richard L

    2006-01-01

    Costs of defense are thought to maintain genetic variations in the expression of defense within plant populations. As with many plant species, aspen exhibits considerable variation in allocation to secondary metabolites. This study examined the independent and interactive effects of genotype, soil fertility and belowground competition on defensive chemistry and growth in trembling aspen (Populus tremuloides). Four aspen genotypes were grown with high and low soil fertility, and with and without root competition. Physiological, morphological and allocational determinants of growth were measured to identify growth-defense tradeoffs. Nutrient limitation and competition decreased growth, leaf mass ratio, leaf nitrogen concentration and photosynthesis, and increased root : shoot ratio and leaf condensed tannin concentrations. The competition treatment also resulted in increased leaf phenolic glycoside (PG) concentrations. Aspen growth was negatively correlated with PG concentrations under low fertility with competition. The relationship between growth and its major determinants was also negatively related to foliar condensed tannins expressed as a proportion of tree mass, indicating an additional indirect cost of allocation to secondary metabolites.

  11. Phenology and climate relationships in aspen (Populus tremuloides Michx.) forest and woodland communities of southwestern Colorado

    USGS Publications Warehouse

    Meier, Gretchen A.; Brown, Jesslyn F.; Evelsizer, Ross J.; Vogelmann, James E.

    2014-01-01

    Trembling aspen (Populus tremuloides Michx.) occurs over wide geographical, latitudinal, elevational, and environmental gradients, making it a favorable candidate for a study of phenology and climate relationships. Aspen forests and woodlands provide numerous ecosystem services, such as high primary productivity and biodiversity, retention and storage of environmental variables (precipitation, temperature, snow–water equivalent) that affect the spring and fall phenology of the aspen woodland communities of southwestern Colorado. We assessed the land surface phenology of aspen woodlands using two phenology indices, start of season time (SOST) and end of season time (EOST), from the U.S. Geological Survey (USGS) database of conterminous U.S. phenological indicators over an 11-year time period (2001–2011). These indicators were developed with 250 m resolution remotely sensed data from the Moderate Resolution Imaging Spectroradiometer processed to highlight vegetation response. We compiled data on SOST, EOST, elevation, precipitation, air temperature, and snow water equivalent (SWE) for selected sites having more than 80% cover by aspen woodland communities. In the 11-year time frame of our study, EOST had significant positive correlation with minimum fall temperature and significant negative correlation with fall precipitation. SOST had a significant positive correlation with spring SWE and spring maximum temperature.

  12. Stomatal Conductance and Sulfur Uptake of Five Clones of Populus tremuloides Exposed to Sulfur Dioxide 1

    PubMed Central

    Kimmerer, Thomas W.; Kozlowski, T. T.

    1981-01-01

    Plants of five clones of Populus tremuloides Michx. were exposed to 0, 0.2 or 0.5 microliter per liter SO2 for 8 hours in controlled environment chambers. In the absence of the pollutant, two pollution-resistant clones maintained consistently lower daytime diffusive conductance (LDC) than did a highly susceptible clone or two moderately resistant clones. Differences in LDC among the latter three clones were not significant. At 0.2 microliter per liter SO2, LDC decreased in the susceptible clone after 8 hours fumigation while the LDC of the other clones was not affected. Fumigation with 0.5 microliter per liter SO2 decreased LDC of all five clones during the fumigation. Rates of recovery following fumigation varied with the clone, but the LDC of all clones had returned to control values by the beginning of the night following fumigation. Night LDC was higher in the susceptible clone than in the other clones. Fumigation for 16 hours (14 hours day + 2 hours night) with 0.4 microliter per liter SO2 decreased night LDC by half. Sulfur uptake studies generally confirmed the results of the conductance measurements. The results show that stomatal conductance is important in determining relative susceptibility of the clones to pollution stress. PMID:16661807

  13. Resource availability and repeated defoliation mediate compensatory growth in trembling aspen (Populus tremuloides) seedlings

    PubMed Central

    Galvez, David A.; Zhang, Bin; Najar, Ahmed

    2014-01-01

    Plant ecologists have debated the mechanisms used by plants to cope with the impact of herbivore damage. While plant resistance mechanisms have received much attention, plant compensatory growth as a type of plant tolerance mechanisms has been less studied. We conducted a greenhouse experiment to evaluate compensatory growth for trembling aspen (Populus tremuloides) seedlings under varying intensities and frequencies of simulated defoliation, with or without nutrient enriched media. For the purpose of this study, changes in biomass production and non-structural carbohydrate concentrations (NSC) of roots and leaves were considered compensatory responses. All defoliated seedlings showed biomass accumulation under low defoliation intensity and frequency, regardless of resource availability; however, as defoliation intensity and frequency increased, compensatory growth of seedlings was altered depending on resource availability. Seedlings in a resource-rich environment showed complete compensation, in contrast responses ranged from undercompensation to complete compensation in a resource-limited environment. Furthermore, at the highest defoliation intensity and frequency, NSC concentrations in leaves and roots were similar between defoliated and non-defoliated seedlings in a resource-rich environment; in contrast, defoliated seedlings with limited resources sustained the most biomass loss, had lower amounts of stored NSC. Using these results, we developed a new predictive framework incorporating the interactions between frequency and intensity of defoliation and resource availability as modulators of plant compensatory responses. PMID:25083352

  14. Root chemistry in Populus tremuloides: effects of soil nutrients, defoliation, and genotype.

    PubMed

    Stevens, Michael T; Gusse, Adam C; Lindroth, Richard L

    2014-01-01

    Although genetic, environmental, and G x E effects on aboveground phytochemistry have been well documented in trembling aspen (Populus tremuloides), little work has focused on the same factors affecting tissues underground. Belowground plant defenses are likely important mediators of root-feeding herbivores that can strongly influence plant fitness. We used a common garden of potted aspen trees to explore the individual and interactive effects of soil nutrient availability, foliar damage, genotype, and their interactions, on concentrations of phytochemicals in aspen roots. Our common garden experiment employed 12 aspen genotypes that were planted into either low- or high-nutrient soil environments. Half of the trees were subjected to defoliation for two successive years, while the others were protected from damage. At the end of the growing season after the second defoliation, we harvested the trees to obtain root samples for which we assessed levels of phenolic glycosides, condensed tannins, nitrogen, and starch. Phenolic glycosides were most affected by genotype, while the other root phytochemicals were most responsive to soil nutrient conditions. The effects of defoliation were observed in interaction with soil nutrient environment and/or genotype. Interestingly, the effect of defoliation on phenolic glycosides was mediated by soil nutrients, whereas the effect of defoliation on condensed tannins was observed in concert with effects of both soil nutrients and genotype. Comparison of data from this study with an earlier, related study revealed that concentrations of phenolic glycosides and condensed tannins are lower in roots than leaves, and less responsive to defoliation. That soil nutrient environment affects root phytochemical concentrations is not unexpected given the intimate association of roots and soil, but the complex interactions between soil nutrients, aboveground damage, and genotype, and their effects on root phytochemistry, are intriguing

  15. Browse quality in quaking Aspen (Populus tremuloides): effects of genotype, nutrients, defoliation, and coppicing.

    PubMed

    Lindroth, Richard L; Donaldson, Jack R; Stevens, Michael T; Gusse, Adam C

    2007-05-01

    The consequences of interactions among genetic, ontogenetic, and environmental factors for the quality of winter-dormant tissues as food for browsing herbivores is poorly understood. We conducted two sequential common garden studies to assess the impacts of intraspecific genetic variation, nutrient availability, prior defoliation, and ontogenetic stage on the chemical quality of winter-dormant tissue in quaking aspen (Populus tremuloides Michx.). In the first study, saplings of 12 aspen genotypes were grown under low and high soil nutrient conditions, with or without two successive seasons of defoliation. Quantity and quality of current year's twig growth were assessed. Twig production varied among genotypes and declined under low nutrient availability, but showed little response to prior defoliation. Chemical quality of sapling twigs varied substantially among genotypes, and in response to nutrient availability and prior defoliation. Overall, browse quality improved (nitrogen levels increased while phenolic glycoside and condensed tannin levels decreased) after defoliation. Growth and chemical variables exhibited low to moderate clonal repeatability (broad sense heritability) values. Our second study employed the same 12 genotypes, grown under high-nutrient conditions and with or without two seasons of defoliation. The trees were coppiced to produce root sprouts, which were chemically assessed 1 yr later. Rejuvenation via coppicing led to increased levels of nitrogen, phenolic glycosides (salicortin), and tannins in root sprouts, and the magnitude of change varied among aspen genotypes. Signatures of defoliation nearly 2 yr earlier persisted in terms of elevated levels of phenolic glycosides in root sprouts of previously defoliated trees. Aspen forests likely present browsing herbivores with chemically heterogeneous environments because of the interactions of genetic, ontogenetic, and environmental factors that vary over space and time.

  16. Genotypic differences and prior defoliation affect re-growth and phytochemistry after coppicing in Populus tremuloides.

    PubMed

    Stevens, Michael T; Gusse, Adam C; Lindroth, Richard L

    2012-03-01

    Although considerable research has explored how tree growth and defense can be influenced by genotype, the biotic environment, and their interaction, little is known about how genotypic differences, prior defoliation, and their interactive effects persist in trees that re-grow after damage that severs their primary stem. To address these issues, we established a common garden consisting of twelve genotypes of potted aspen (Populus tremuloides) trees, and subjected half of the trees to defoliation in two successive years. At the beginning of the third year, all trees were severed at the soil surface (coppiced) and allowed to regenerate for five months. Afterwards, we counted the number of root and stump sprouts produced and measured the basal diameter (d) and height (h) of the tallest ramet in each pot. We collected leaves one and two years after the second defoliation and assessed levels of phenolic glycosides, condensed tannins, and nitrogen. In terms of re-growth, we found that the total number of sprouts produced varied by 3.6-fold among genotypes, and that prior defoliation decreased total sprout production by 24%. The size (d(2)h) of ramets, however, did not differ significantly among genotypes or defoliation classes. In terms of phytochemistry, we observed genotypic differences in concentrations of all phytochemicals assessed both one and two years after the second defoliation. Two years after defoliation, we observed effects of prior defoliation in a genotype-by-defoliation interaction for condensed tannins. Results from this study demonstrate that genotypic differences and impacts of prior defoliation persist to influence growth and defense traits in trees even after complete removal of above-ground stems, and thus likely influence productivity and plant-herbivore interactions in forests affected by natural disturbances or actively managed through coppicing.

  17. Physiological Characteristics of Photosynthesis and Respiration in Stems of Populus tremuloides Michx. 1

    PubMed Central

    Foote, Knowlton C.; Schaedle, Michail

    1976-01-01

    The physiological responses of 6- to 8-year-old aspen (Populus tremuloides Michx.) stems to temperature, light, and CO2 concentration were investigated in the field throughout the year using infrared CO2 analysis. Light response studies showed that the rate of gross photosynthesis was linear from 0 to 400 ft-c (0 to 1.6 mw/cm2 of 400-700 nm) with light saturation being reached between 800 to 1400 ft-c (3.2 to 5.6 mw/cm2 of 400-700 nm). At this light intensity, the respiratory CO2 loss was reduced to 10 to 15% of dark rates. Net photosynthetic CO2 uptake was not observed even at intensities as high as 3400 ft-c (13.6 mw/cm2 of 400-700 nm). The light response curve was similar for both winter and summer stems. During summer months, the respiratory and photosynthetic rates of the aspen stem increased with temperature at a near constant rate between 5 and 35 C. For winter stems, the gross photosynthetic rate increased in a pattern similar to the dark respiratory rate as the temperature rose from 3 to 17 C. Below 0 C and above 17 C, however, the gross photosynthetic rate fell off in relation to the respiratory rate so that the per cent of CO2 reassimilated decreased from 75% to less than 50%. Measurable bark photosynthetic activity was not observed below —3 C. The gross photosynthetic rate of stems was not affected when the gas passing through the cuvette contained concentrations of CO2 ranging from 0 to 580 μl CO2/l air. PMID:16659628

  18. SHORT INTERNODES-like genes regulate shoot growth and xylem proliferation in Populus.

    PubMed

    Zawaski, Christine; Kadmiel, Mahita; Ma, Cathleen; Gai, Ying; Jiang, Xiangning; Strauss, Steve H; Busov, Victor B

    2011-08-01

    • Genes controlling plant growth and form are of considerable interest, because they affect survival and productivity traits, and are largely unknown or poorly characterized. The SHORT INTERNODES(SHI) gene is one of a 10-member SHI-RELATED SEQUENCE (SRS) gene family in Arabidopsis that includes important developmental regulators. • Using comparative sequence analysis of the SRS gene families in poplar and Arabidopsis, we identified two poplar proteins that are most similar to SHI and its closely related gene STYLISH1 (STY1). The two poplar genes are very similar in sequence and expression and are therefore probably paralogs with redundant functions. • RNAi suppression of the two Populus genes enhanced shoot and root growth, whereas the overexpression of Arabidopsis SHI in poplar reduced internode and petiole length. The suppression of the two genes increased fiber length and the proportion of xylem tissue, mainly through increased xylem cell proliferation. The transgenic modifications were also associated with significant changes in the concentrations of gibberellins and cytokinin. • We conclude that Populus SHI-RELATED SEQUENCE (SRS) genes play an important role in the regulation of vegetative growth, including wood formation, and thus could be useful tools for the modification of biomass productivity, wood quality or plant form.

  19. Scale dependence of disease impacts on quaking aspen (Populus tremuloides) mortality in the southwestern United States.

    PubMed

    Bell, David M; Bradford, John B; Lauenroth, William K

    2015-07-01

    Depending on how disease impacts tree exposure to risk, both the prevalence of disease and disease effects on survival may contribute to patterns of mortality risk across a species' range. Disease may accelerate tree species' declines in response to global change factors, such as drought, biotic interactions, such as competition, or functional traits, such as allometry. To assess the role of disease in mediating mortality risk in quaking aspen (Populus tremuloides), we developed hierarchical Bayesian models for both disease prevalence in live aspen stems and the resulting survival rates of healthy and diseased aspen near the species' southern range limit using 5088 individual trees on 281 United States Forest Service Forest Inventory and Analysis plots in the southwestern United States. We found that disease prevalence depended primarily on tree size, tree allometry, and spatial variation in precipitation, while mortality depended on tree size, allometry, competition, spatial variation in summer temperature, and both temporal and spatial variation in summer precipitation. Disease prevalence was highest in large trees with low slenderness found on dry sites. For healthy trees, mortality decreased with diameter, slenderness, and temporal variation in summer precipitation, but increased with competition and spatial variation in summer temperature. Mortality of diseased trees decreased with diameter and aspen relative basal area and increased with mean summer temperature and precipitation. Disease infection increased aspen mortality, especially in trees of intermediate size and trees on plots at climatic extremes (i.e., cool, wet and warm, dry climates). By examining variation in disease prevalence, mortality of healthy trees, and mortality of diseased trees, we showed that the role of disease in aspen tree mortality depended on the scale of inference. For variation among individuals in diameter, disease tended to expose intermediate-size trees experiencing moderate

  20. Elevated Rocky Mountain elk numbers prevent positive effects of fire on quaking aspen (Populus tremuloides) recruitment

    USGS Publications Warehouse

    Smith, David Solance; Fettig, Stephen M.; Bowker, Matthew A.

    2016-01-01

    Quaking aspen (Populus tremuloides) is the most widespread tree species in North America and has supported a unique ecosystem for tens of thousands of years, yet is currently threatened by dramatic loss and possible local extinctions. While multiple factors such as climate change and fire suppression are thought to contribute to aspen’s decline, increased browsing by elk (Cervus elaphus), which have experienced dramatic population increases in the last ∼80 years, may severely inhibit aspen growth and regeneration. Fires are known to favor aspen recovery, but in the last several decades the spatial scale and intensity of wildfires has greatly increased, with poorly understood ramifications for aspen growth. Here, focusing on the 2000 Cerro Grande fire in central New Mexico – one of the earliest fires described as a “mega-fire” - we use three methods to examine the impact of elk browsing on aspen regeneration after a mega-fire. First, we use an exclosure experiment to show that aspen growing in the absence of elk were 3× taller than trees growing in the presence of elk. Further, aspen that were both protected from elk and experienced burning were 8.5× taller than unburned trees growing in the presence of elk, suggesting that the combination of release from herbivores and stimulation from fire creates the largest aspen growth rates. Second, using surveys at the landscape level, we found a correlation between elk browsing intensity and aspen height, such that where elk browsing was highest, aspen were shortest. This relationship between elk browsing intensity and aspen height was stronger in burned (r = −0.53) compared to unburned (r = −0.24) areas. Third, in conjunction with the landscape-level surveys, we identified possible natural refugia, microsites containing downed logs, shrubs etc. that may inhibit elk browsing by physically blocking aspen from elk or by impeding elk’s ability to move through the forest patch. We did not find any

  1. Characterizing recent phenological and climate relationships in trembling aspen (Populus tremuloides)

    NASA Astrophysics Data System (ADS)

    Meier, G.; Brown, J. F.; Vogelmann, J. E.; Evelsizer, R.

    2012-12-01

    Trembling aspen (Populus tremuloides, referred hereafter as Aspen) has an especially wide geographical distribution in North America, extending from Alaska across the Canadian provinces, the U.S., and south into Mexico. This deciduous species is successional, shade intolerant, and often exists as a dominant among other species at mid-elevations. Aspen occupies wide latitudinal, elevational, and environmental gradients making it a favorable candidate for a study of phenology and climate relationships. The phenological characterization in our Aspen study is derived from a database of conterminous U.S. phenological indicators hosted by the U.S. Geological Survey (http://phenology.cr.usgs.gov/index.php). Nine satellite-derived phenological indicators are calculated from 250m resolution Moderate Resolution Imaging Spectroradiometer (MODIS) Normalized Difference Vegetation Index (NDVI). From this database, we selected start of season (SOST), end of season (EOST), maximum NDVI (MaxN) and time integrated NDVI (TIN) to characterize and analyze the seasonal patterns of Aspen over a 10-year time period (2001-2010). Areas of continuous Aspen cover (≥ 80% Aspen cover type) derived from the LANDFIRE project were then used to extract elevation, precipitation, temperature, and snow water equivalent data. In the Rocky Mountains, Aspen recently suffered from multi-year drought stress accompanied by insect and disease infestations. Numerous studies have documented the existence of Sudden Aspen Decline (SAD) in Montana, Utah, Arizona, and Colorado, indicating that Aspen may be on the edge of its environmental tolerances in some areas. The satellite-derived phenology metrics, and climate and biogeographical indicators were the basis for characterizing Aspen seasonality and assessing the environmental context of SAD. Between several Aspen study areas, there was reasonably consistent progression in the SOST timing from low elevations to higher elevations. A less obvious progression was

  2. Association of Pinus banksiana Lamb. and Populus tremuloides Michx. seedling fine roots with Sistotrema brinkmannii (Bres.) J. Erikss. (Basidiomycotina).

    PubMed

    Potvin, Lynette R; Richter, Dana L; Jurgensen, Martin F; Dumroese, R Kasten

    2012-11-01

    Sistotrema brinkmannii (Bres.) J. Erikss. (Basidiomycotina, Hydanaceae), commonly regarded as a wood decay fungus, was consistently isolated from bareroot nursery Pinus banksiana Lamb. seedlings. S. brinkmannii was found in ectomycorrhizae formed by Thelephora terrestris Ehrh., Laccaria laccata (Scop.) Cooke, and Suillus luteus (L.) Roussel. In pure culture combinations with sterile P. banksiana and Populus tremuloides Michx. seedlings, S. brinkmannii colonized root cortical cells while not killing seedlings. Colonization by S. brinkmannii appeared to be intracellular but typical endo- or ectomycorrhizae were not formed. The fungus did not decay roots, although it was shown to produce cellulase in enzyme tests. Results suggest a unique association between S. brinkmannii and seedling roots that is neither mycorrhizal nor detrimental; its exact function remains to be elucidated.

  3. Laccaria bicolor aquaporin LbAQP1 is required for Hartig net development in trembling aspen (Populus tremuloides).

    PubMed

    Navarro-RóDenas, Alfonso; Xu, Hao; Kemppainen, Minna; Pardo, Alejandro G; Zwiazek, Janusz J

    2015-11-01

    The development of ectomycorrhizal associations is crucial for growth of many forest trees. However, the signals that are exchanged between the fungus and the host plant during the colonization process are still poorly understood. In this study, we have identified the relationship between expression patterns of Laccaria bicolor aquaporin LbAQP1 and the development of ectomycorrhizal structures in trembling aspen (Populus tremuloides) seedlings. The peak expression of LbAQP1 was 700-fold higher in the hyphae within the root than in the free-living mycelium after 24 h of direct interaction with the roots. Moreover, in LbAQP1 knock-down strains, a non-mycorrhizal phenotype was developed without the Hartig net and the expression of the mycorrhizal effector protein MiSSP7 quickly declined after an initial peak on day 5 of interaction of the fungal hyphae with the roots. The increase in the expression of LbAQP1 required a direct contact of the fungus with the root and it modulated the expression of MiSSP7. We have also determined that LbAQP1 facilitated NO, H2 O2 and CO2 transport when heterologously expressed in yeast. The report demonstrates that the L. bicolor aquaporin LbAQP1 acts as a molecular signalling channel, which is fundamental for the development of Hartig net in root tips of P. tremuloides.

  4. Influence of Genotype, Environment, and Gypsy Moth Herbivory on Local and Systemic Chemical Defenses in Trembling Aspen (Populus tremuloides).

    PubMed

    Rubert-Nason, Kennedy F; Couture, John J; Major, Ian T; Constabel, C Peter; Lindroth, Richard L

    2015-07-01

    Numerous studies have explored the impacts of intraspecific genetic variation and environment on the induction of plant chemical defenses by herbivory. Relatively few, however, have considered how those factors affect within-plant distribution of induced defenses. This work examined the impacts of plant genotype and soil nutrients on the local and systemic phytochemical responses of trembling aspen (Populus tremuloides) to defoliation by gypsy moth (Lymantria dispar). We deployed larvae onto foliage on individual tree branches for 15 days and then measured chemistry in leaves from: 1) branches receiving damage, 2) undamaged branches of insect-damaged trees, and 3) branches of undamaged control trees. The relationship between post-herbivory phytochemical variation and insect performance also was examined. Plant genotype, soil nutrients, and damage all influenced phytochemistry, with genotype and soil nutrients being stronger determinants than damage. Generally, insect damage decreased foliar nitrogen, increased levels of salicinoids and condensed tannins, but had little effect on levels of a Kunitz trypsin inhibitor, TI3. The largest damage-mediated tannin increases occurred in leaves on branches receiving damage, whereas the largest salicinoid increases occurred in leaves of adjacent, undamaged branches. Foliar nitrogen and the salicinoid tremulacin had the strongest positive and negative relationships, respectively, with insect growth. Overall, plant genetics and environment concomitantly influenced both local and systemic phytochemical responses to herbivory. These findings suggest that herbivory can contribute to phytochemical heterogeneity in aspen foliage, which may in turn influence future patterns of herbivory and nutrient cycling over larger spatial scales.

  5. Hydraulic conductivity and aquaporin transcription in roots of trembling aspen (Populus tremuloides) seedlings colonized by Laccaria bicolor.

    PubMed

    Xu, Hao; Cooke, Janice E K; Kemppainen, Minna; Pardo, Alejandro G; Zwiazek, Janusz J

    2016-07-01

    Ectomycorrhizal fungi have been reported to increase root hydraulic conductivity (L pr) by altering apoplastic and plasma membrane intrinsic protein (PIP)-mediated cell-to-cell water transport pathways in associated roots, or to have little effect on root water transport, depending on the interacting species and imposed stresses. In this study, we investigated the water transport properties and PIP transcription in roots of aspen (Populus tremuloides) seedlings colonized by the wild-type strain of Laccaria bicolor and by strains overexpressing a major fungal water-transporting aquaporin JQ585595. Inoculation of aspen seedlings with L. bicolor resulted in about 30 % colonization rate of root tips, which developed dense mantle and the Hartig net that was restricted in the modified root epidermis. Transcript abundance of the aspen aquaporins PIP1;2, PIP2;1, and PIP2;2 decreased in colonized root tips. Root colonization by JQ585595-overexpressing strains had no significant impact on seedling shoot water potentials, gas exchange, or dry mass; however, it led to further decrease in transcript abundance of PIP1;2 and PIP2;3 and the significantly lower L pr than in non-inoculated roots. These results, taken together with our previous study that showed enhanced root water hydraulics of L. bicolor-colonized white spruce (Picea glauca), suggest that the impact of L. bicolor on root hydraulics varies by the ectomycorrhiza-associated tree species.

  6. Fluoride inhibits root water transport and affects leaf expansion and gas exchange in aspen (Populus tremuloides) seedlings.

    PubMed

    Kamaluddin, Mohammed; Zwiazek, Janusz J.

    2003-03-01

    The effects of sodium fluoride (0.3, 5 and 10 mM NaF) on root hydraulic conductivity, and gas exchange processes were examined in aspen (Populus tremuloides Michx.) seedlings grown in solution culture. A long-term exposure of roots to NaF significantly decreased root hydraulic conductivity (Lp) and stomatal conductance ( gs). Root absorbed NaF significantly affected electrolyte leakage in leaf tissues and substantially restricted leaf expansion. NaF did not significantly affect leaf chlorophyll contents but decreased net photosynthesis (Pn). A short-term exposure of excised roots to 5 mM NaF and KF significantly decreased root water flow (Qv) with a concomitant decline in root respiration and reduced gs when applied through intact roots or excised stems. The same molar concentration of NaCl also decreased Qv and gs in intact seedlings, but to a lesser extent than NaF or KF, and did not significantly affect root respiration. The results suggest that fluoride metabolically inhibited Qv or Lp, probably by affecting water channel activity. We suggest that the metabolic inhibition of Lp by root-absorbed fluoride affected gas exchange and leaf expansion in aspen seedlings.

  7. Hydraulic conductivity and aquaporin transcription in roots of trembling aspen (Populus tremuloides) seedlings colonized by Laccaria bicolor.

    PubMed

    Xu, Hao; Cooke, Janice E K; Kemppainen, Minna; Pardo, Alejandro G; Zwiazek, Janusz J

    2016-07-01

    Ectomycorrhizal fungi have been reported to increase root hydraulic conductivity (L pr) by altering apoplastic and plasma membrane intrinsic protein (PIP)-mediated cell-to-cell water transport pathways in associated roots, or to have little effect on root water transport, depending on the interacting species and imposed stresses. In this study, we investigated the water transport properties and PIP transcription in roots of aspen (Populus tremuloides) seedlings colonized by the wild-type strain of Laccaria bicolor and by strains overexpressing a major fungal water-transporting aquaporin JQ585595. Inoculation of aspen seedlings with L. bicolor resulted in about 30 % colonization rate of root tips, which developed dense mantle and the Hartig net that was restricted in the modified root epidermis. Transcript abundance of the aspen aquaporins PIP1;2, PIP2;1, and PIP2;2 decreased in colonized root tips. Root colonization by JQ585595-overexpressing strains had no significant impact on seedling shoot water potentials, gas exchange, or dry mass; however, it led to further decrease in transcript abundance of PIP1;2 and PIP2;3 and the significantly lower L pr than in non-inoculated roots. These results, taken together with our previous study that showed enhanced root water hydraulics of L. bicolor-colonized white spruce (Picea glauca), suggest that the impact of L. bicolor on root hydraulics varies by the ectomycorrhiza-associated tree species. PMID:26861480

  8. Polyphenol oxidase and herbivore defense in trembling aspen (Populus tremuloides): cDNA cloning, expression, and potential substrates.

    PubMed

    Haruta, Miyoshi; Pedersen, Jens A.; Constabel, C. Peter

    2001-08-01

    The biochemical anti-herbivore defense of trembling aspen (Populus tremuloides Michx.) was investigated in a molecular analysis of polyphenol oxidase (PPO; EC 1.10.3.2). A PPO cDNA was isolated from a trembling aspen wounded leaf cDNA library and its nucleotide sequence determined. Southern analysis indicated the presence of two PPO genes in the trembling aspen genome. Expression of PPO was found to be induced after herbivory by forest tent caterpillar, by wounding, and by methyl jasmonate treatment. Wound induction was systemic, and occurred in unwounded leaves on wounded plants. This pattern of expression is consistent with a role of this enzyme in insect defense. A search for potential PPO substrates in ethanolic aspen leaf extracts using electron spin resonance (ESR) found no pre-existing diphenolic compounds. However, following a brief delay and several additions of oxygen, an ESR signal specific for catechol was detected. The source of this catechol was most likely the aspen phenolic glycosides tremulacin or salicortin which decomposed during ESR experiments. This was subsequently confirmed in experiments using pure salicortin.

  9. Molecular analysis of herbivore-induced condensed tannin synthesis: cloning and expression of dihydroflavonol reductase from trembling aspen (Populus tremuloides).

    PubMed

    Peters, Darren J; Constabel, C Peter

    2002-12-01

    In order to study condensed tannin synthesis and its induction by herbivory, a dihydroflavonol reductase (DFR) cDNA was isolated from trembling aspen (Populus tremuloides). Bacterial overexpression demonstrated that this cDNA encodes a functional DFR enzyme, and Southern analysis revealed that DFR likely is a single-copy gene in the aspen genome. Aspen plants that were mechanically wounded showed a dramatic increase in DFR expression after 24 h in both wounded leaves and unwounded leaves on wounded trees. Feeding by forest tent caterpillar (Malacosoma disstria) and satin moth (Leucoma salicis) larvae, and treatment with methyl jasmonate, all strongly induced DFR expression. DFR enzyme activity was also induced in wounded aspen leaves, and phytochemical assays revealed that condensed tannin concentrations significantly increased in wounded and systemic leaves. The expression of other genes involved in the phenylpropanoid pathway were also induced by wounding. Our findings suggest that the induction of condensed tannins, compounds known to be important for defense against herbivores, is mediated by increased expression of DFR and other phenylpropanoid genes.

  10. Nutrient concentrations in coarse and fine woody debris of Populus tremuloides Michx.-dominated forests, northern Minnesota, USA

    USGS Publications Warehouse

    Klockow, Paul A.; D'Amato, Anthony W.; Bradford, John B.; Fraver, Shawn

    2014-01-01

    Contemporary forest harvesting practices, specifically harvesting woody biomass as a source of bioenergy feedstock, may remove more woody debris from a site than conventional harvesting. Woody debris, particularly smaller diameter woody debris, plays a key role in maintaining ecosystem nutrient stores following disturbance. Understanding nutrient concentrations within woody debris is necessary for assessing the long-term nutrient balance consequences of altered woody debris retention, particularly in forests slated for use as bioenergy feedstocks. Nutrient concentrations in downed woody debris of various sizes, decay classes, and species were characterized within one such forest type, Populus tremuloides Michx.-dominated forests of northern Minnesota, USA. Nutrient concentrations differed significantly between size and decay classes and generally increased as decay progressed. Fine woody debris (≤ 7.5 cm diameter) had higher nutrient concentrations than coarse woody debris (> 7.5 cm diameter) for all nutrients examined except Na and Mn, and nutrient concentrations varied among species. Concentrations of N, Mn, Al, Fe, and Zn in coarse woody debris increased between one and three orders of magnitude, while K decreased by an order of magnitude with progressing decay. The variations in nutrient concentrations observed here underscore the complexity of woody debris nutrient stores in forested ecosystems and suggest that retaining fine woody debris at harvest may provide a potentially important source of nutrients following intensive removals of bioenergy feedstocks.

  11. Influence of Genotype, Environment, and Gypsy Moth Herbivory on Local and Systemic Chemical Defenses in Trembling Aspen (Populus tremuloides).

    PubMed

    Rubert-Nason, Kennedy F; Couture, John J; Major, Ian T; Constabel, C Peter; Lindroth, Richard L

    2015-07-01

    Numerous studies have explored the impacts of intraspecific genetic variation and environment on the induction of plant chemical defenses by herbivory. Relatively few, however, have considered how those factors affect within-plant distribution of induced defenses. This work examined the impacts of plant genotype and soil nutrients on the local and systemic phytochemical responses of trembling aspen (Populus tremuloides) to defoliation by gypsy moth (Lymantria dispar). We deployed larvae onto foliage on individual tree branches for 15 days and then measured chemistry in leaves from: 1) branches receiving damage, 2) undamaged branches of insect-damaged trees, and 3) branches of undamaged control trees. The relationship between post-herbivory phytochemical variation and insect performance also was examined. Plant genotype, soil nutrients, and damage all influenced phytochemistry, with genotype and soil nutrients being stronger determinants than damage. Generally, insect damage decreased foliar nitrogen, increased levels of salicinoids and condensed tannins, but had little effect on levels of a Kunitz trypsin inhibitor, TI3. The largest damage-mediated tannin increases occurred in leaves on branches receiving damage, whereas the largest salicinoid increases occurred in leaves of adjacent, undamaged branches. Foliar nitrogen and the salicinoid tremulacin had the strongest positive and negative relationships, respectively, with insect growth. Overall, plant genetics and environment concomitantly influenced both local and systemic phytochemical responses to herbivory. These findings suggest that herbivory can contribute to phytochemical heterogeneity in aspen foliage, which may in turn influence future patterns of herbivory and nutrient cycling over larger spatial scales. PMID:26099738

  12. Disentangling herbivore impacts on Populus tremuloides: a comparison of native ungulates and cattle in Canada's Aspen Parkland.

    PubMed

    Bork, Edward W; Carlyle, Cameron N; Cahill, James F; Haddow, Rae E; Hudson, Robert J

    2013-11-01

    Ungulates impact woody species' growth and abundance but little is understood about the comparative impacts of different ungulate species on forest expansion in savanna environments. Replacement of native herbivore guilds with livestock [i.e., beef cattle (Bos taurus)] has been hypothesized as a factor facilitating trembling aspen (Populus tremuloides Michx.) encroachment into grasslands of the Northern Great Plains. We used a controlled herbivory study in the Parklands of western Canada to compare the impact of native ungulates and cattle on aspen saplings. Native ungulate treatments included a mixed species guild and sequences of herbivory by different ungulates [bison (Bison bison subsp. bison), elk (Cervus elaphus) then deer (Odocoileus hemionus); or deer, elk, then bison]. Herbivory treatments were replicated in three pastures, within which sets of 40 marked aspen saplings (<1.8 m) were tracked along permanent transects at 2-week intervals, and compared to a non-grazed aspen stand. Stems were assessed for mortality and incremental damage (herbivory, leader breakage, stem abrasion and trampling). Final mortality was greater with exposure to any type of herbivore, but remained similar between ungulate treatments. However, among all treatments, the growth of aspen was highest with exposure only to cattle. Herbivory of aspen was attributed primarily to elk within the native ungulate treatments, with other forms of physical damage, and ultimately sapling mortality, associated with exposure to bison. Overall, these results indicate that native ungulates, specifically elk and bison, have more negative impacts on aspen saplings and provide evidence that native and domestic ungulates can have different functional effects on woody plant dynamics in savanna ecosystems. PMID:23649757

  13. Disentangling herbivore impacts on Populus tremuloides: a comparison of native ungulates and cattle in Canada's Aspen Parkland.

    PubMed

    Bork, Edward W; Carlyle, Cameron N; Cahill, James F; Haddow, Rae E; Hudson, Robert J

    2013-11-01

    Ungulates impact woody species' growth and abundance but little is understood about the comparative impacts of different ungulate species on forest expansion in savanna environments. Replacement of native herbivore guilds with livestock [i.e., beef cattle (Bos taurus)] has been hypothesized as a factor facilitating trembling aspen (Populus tremuloides Michx.) encroachment into grasslands of the Northern Great Plains. We used a controlled herbivory study in the Parklands of western Canada to compare the impact of native ungulates and cattle on aspen saplings. Native ungulate treatments included a mixed species guild and sequences of herbivory by different ungulates [bison (Bison bison subsp. bison), elk (Cervus elaphus) then deer (Odocoileus hemionus); or deer, elk, then bison]. Herbivory treatments were replicated in three pastures, within which sets of 40 marked aspen saplings (<1.8 m) were tracked along permanent transects at 2-week intervals, and compared to a non-grazed aspen stand. Stems were assessed for mortality and incremental damage (herbivory, leader breakage, stem abrasion and trampling). Final mortality was greater with exposure to any type of herbivore, but remained similar between ungulate treatments. However, among all treatments, the growth of aspen was highest with exposure only to cattle. Herbivory of aspen was attributed primarily to elk within the native ungulate treatments, with other forms of physical damage, and ultimately sapling mortality, associated with exposure to bison. Overall, these results indicate that native ungulates, specifically elk and bison, have more negative impacts on aspen saplings and provide evidence that native and domestic ungulates can have different functional effects on woody plant dynamics in savanna ecosystems.

  14. Factors affecting fall down rates of dead aspen (Populus tremuloides) biomass following severe drought in west-central Canada.

    PubMed

    Ted Hogg, Edward H; Michaelian, Michael

    2015-05-01

    Increases in mortality of trembling aspen (Populus tremuloides Michx.) have been recorded across large areas of western North America following recent periods of exceptionally severe drought. The resultant increase in standing, dead tree biomass represents a significant potential source of carbon emissions to the atmosphere, but the timing of emissions is partially driven by dead-wood dynamics which include the fall down and breakage of dead aspen stems. The rate at which dead trees fall to the ground also strongly influences the period over which forest dieback episodes can be detected by aerial surveys or satellite remote sensing observations. Over a 12-year period (2000-2012), we monitored the annual status of 1010 aspen trees that died during and following a severe regional drought within 25 study areas across west-central Canada. Observations of stem fall down and breakage (snapping) were used to estimate woody biomass transfer from standing to downed dead wood as a function of years since tree death. For the region as a whole, we estimated that >80% of standing dead aspen biomass had fallen after 10 years. Overall, the rate of fall down was minimal during the year following stem death, but thereafter fall rates followed a negative exponential equation with k = 0.20 per year. However, there was high between-site variation in the rate of fall down (k = 0.08-0.37 per year). The analysis showed that fall down rates were positively correlated with stand age, site windiness, and the incidence of decay fungi (Phellinus tremulae (Bond.) Bond. and Boris.) and wood-boring insects. These factors are thus likely to influence the rate of carbon emissions from dead trees following periods of climate-related forest die-off episodes.

  15. Aspen (Populus tremuloides Michx.) intake and preference by mammalian herbivores: the role of plant secondary compounds and nutritional context.

    PubMed

    Villalba, Juan J; Burritt, Elizabeth A; St Clair, Samuel B

    2014-10-01

    Aspen (Populus tremuloides Michx.) has evolved a chemical defense system comprised of phenolic glycosides (PG), which effectively deter insect herbivory. However, much less is known about the role of PG and the nutritional quality of the associated plant community on aspen browse susceptibility to mammalian herbivores. In three successive periods during the growing season, we conducted experiments with sheep by offering leaves from two aspen stands with different concentrations of PG (LOW, HIGH) or aspen leaves vs. leaves from a forb (Utah pea, Lathyrus pauciflorus) or a grass (smooth brome, Bromus inermis Leyss.) growing in an aspen understory. Intake of aspen (19 to 35 % PG) was low in all periods (1 to 6 g/Kg(0.75) in 2 hr) supporting the notion that aspen's defense system may contribute to its ecological success. However, lambs ate larger amounts of LOW than of HIGH suggesting that sheep could discriminate between aspen stands with different concentrations of PG, even when both stands were relatively well defended. Concentration of nutrients and chemical defenses in aspen leaves remained fairly stable across the growing season, and preference for aspen increased over the growing season. In contrast, preference for the forb and the grass decreased across the growing season in concert with a decline in the nutritional quality of these plants. The data suggest that nutritional context of aspen and associated forage species drove preference more than contrasts in defense chemistry of aspen. There may be periods of "susceptibility" of aspen use by mammalian herbivores, despite high concentrations of chemical defenses, which can potentially be targeted by management to reduce aspen herbivory.

  16. Decay of aspen (Populus tremuloides Michx.) wood in moist and dry boreal, temperate, and tropical forest fragments.

    PubMed

    González, Grizelle; Gould, William A; Hudak, Andrew T; Hollingsworth, Teresa Nettleton

    2008-12-01

    In this study, we set up a wood decomposition experiment to i) quantify the percent of mass remaining, decay constant and performance strength of aspen stakes (Populus tremuloides) in dry and moist boreal (Alaska and Minnesota, USA), temperate (Washington and Idaho, USA), and tropical (Puerto Rico) forest types, and ii) determine the effects of fragmentation on wood decomposition rates as related to fragment size, forest age (and/or structure) and climate at the macro- and meso-scales. Fragment sizes represented the landscape variability within a climatic region. Overall, the mean small fragments area ranged from 10-14 ha, medium-sized fragments 33 to 60 ha, and large fragments 100-240 ha. We found that: i) aspen stakes decayed fastest in the tropical sites, and the slowest in the temperate forest fragments, ii) the percent of mass remaining was significantly greater in dry than in moist forests in boreal and temperate fragments, while the opposite was true for the tropical forest fragments, iii) no effect of fragment size on the percent of mass remaining of aspen stakes in the boreal sites, temperate dry, and tropical moist forests, and iv) no significant differences of aspen wood decay between forest edges and interior forest in boreal, temperate and tropical fragments. We conclude that: i) moisture condition is an important control over wood decomposition over broad climate gradients; and that such relationship can be non linear, and ii) the presence of a particular group of organism (termites) can significantly alter the decay rates of wood more than what might be predicted based on climatic factors alone. Biotic controls on wood decay might be more important predictors of wood decay in tropical regions, while abiotic constraints seems to be important determinants of decay in cold forested fragments. PMID:19205182

  17. Growth and photosynthesis of plants in response to environmental stress. [Raphanus sativus; Glycine max; Salix nigra; Alnus serrulata; Populus tremuloides

    SciTech Connect

    Greitner, C.S.

    1991-01-01

    Environmental stresses generally decrease photosynthetic rates and growth of plants, and alter biomass partitioning. Nutrient deficiency and drought cause root:shoot ratios to increase, whereas the air pollutant ozone (O[sub 3]) causes an opposite shift in carbon allocation. Plants in nature usually grow under suboptimal conditions; therefore plants were raised with O[sub 3] combined with other stresses to analyze the mechanisms whereby multiple stresses influence gas exchange and growth. Physiological and growth responses to stress were determined for radish (raphanus sativus), soybean (Glycine max) willow (Salix nigra), alder (Alnus serrulata) and aspen (Populus tremuloides) in laboratory and field trials. In willow, high-nutrient status plants had more visible injury, but a smaller decline in leaf area with O[sub 3] than did low-nutrient plants. Ultrastructure of host plant cells in alder root nodules was disrupted by O[sub 3], suggesting that this air pollutant can affect the ability of plants to acquire nutrients via symbiosis. Biomass and root:shoot ratios decreased with O[sub 3] in radish and soy-bean. Shifts in stable carbon isotope ratios were caused by O[sub 3], and this technique was used to integrate the effects of O[sub 3] on gas exchange over time. In aspen, O[sub 3] enhanced photosynthesis and foliar areas in young leaves of well-watered aspen, partially compensating for declines in older leaves. This effect was more pronounced in plants raised at a high nitrogen level than in N-deficient plants. Carboxylation efficiency decreased in older, but increased in younger leaves with O[sub 3]. Prior exposure to drought reduced effects of O[sub 3] on photosynthesis and leaf area.

  18. Photosynthetic acclimation of overstory Populus tremuloides and understory Acer saccharum to elevated atmospheric CO2 concentration: interactions with shade and soil nitrogen.

    PubMed

    Kubiske, Mark E; Zak, Donald R; Pregitzer, Kurt S; Takeuchi, Yu

    2002-04-01

    We exposed Populus tremuloides Michx. and Acer saccharum Marsh. to a factorial combination of ambient and elevated atmospheric CO2 concentrations ([CO2]) and high-nitrogen (N) and low-N soil treatments in open-top chambers for 3 years. Our objective was to compare photosynthetic acclimation to elevated [CO2] between species of contrasting shade tolerance, and to determine if soil N or shading modify the acclimation response. Sun and shade leaf responses to elevated [CO2] and soil N were compared between upper and lower canopy leaves of P. tremuloides and between A. saccharum seedlings grown with and without shading by P. tremuloides. Both species had higher leaf N concentrations and photosynthetic rates in high-N soil than in low-N soil, and these characteristics were higher for P. tremuloides than for A. saccharum. Electron transport capacity (Jmax) and carboxylation capacity (Vcmax) generally decreased with atmospheric CO2 enrichment in all 3 years of the experiment, but there was no evidence that elevated [CO2] altered the relationship between them. On a leaf area basis, both Jmax and Vcmax acclimated to elevated [CO2] more strongly in shade leaves than in sun leaves of P. tremuloides. However, the apparent [CO2] x shade interaction was largely driven by differences in specific leaf area (m2 g-1) between sun and shade leaves. In A. saccharum, photosynthesis acclimated more strongly to elevated [CO2] in sun leaves than in shade leaves on both leaf area and mass bases. We conclude that trees rooted freely in the ground can exhibit photosynthetic acclimation to elevated [CO2], and the response may be modified by light environment. The hypothesis that photosynthesis acclimates more completely to elevated [CO2] in shade-tolerant species than in shade-intolerant species was not supported.

  19. The influence of phosphorus availability and Laccaria bicolor symbiosis on phosphate acquisition, antioxidant enzyme activity, and rhizospheric carbon flux in Populus tremuloides.

    PubMed

    Desai, Shalaka; Naik, Dhiraj; Cumming, Jonathan R

    2014-07-01

    Many forest tree species are dependent on their symbiotic interaction with ectomycorrhizal (ECM) fungi for phosphorus (P) uptake from forest soils where P availability is often limited. The ECM fungal association benefits the host plant under P limitation through enhanced soil exploration and increased P acquisition by mycorrhizas. To study the P starvation response (PSR) and its modification by ECM fungi in Populus tremuloides, a comparison was made between nonmycorrhizal (NM) and mycorrhizal with Laccaria bicolor (Myc) seedlings grown under different concentrations of phosphate (Pi) in sand culture. Although differences in growth between NM and Myc plants were small, Myc plants were more effective at acquiring P from low Pi treatments, with significantly lower k m values for root and leaf P accumulation. Pi limitation significantly increased the activity of catalase, ascorbate peroxidase, and guaiacol-dependent peroxidase in leaves and roots to greater extents in NM than Myc P. tremuloides. Phosphoenolpyruvate carboxylase activity also increased in NM plants under P limitation, but was unchanged in Myc plants. Formate, citrate, malonate, lactate, malate, and oxalate and total organic carbon exudation by roots was stimulated by P limitation to a greater extent in NM than Myc plants. Colonization by L. bicolor reduced the solution Pi concentration thresholds where PSR physiological changes occurred, indicating that enhanced Pi acquisition by P. tremuloides colonized by L. bicolor altered host P homeostasis and plant stress responses to P limitation. Understanding these plant-symbiont interactions facilitates the selection of more P-efficient forest trees and strategies for tree plantation production on marginal soils.

  20. Intraspecific variation in root and leaf traits and leaf-root trait linkages in eight aspen demes (Populus tremula and P. tremuloides).

    PubMed

    Hajek, Peter; Hertel, Dietrich; Leuschner, Christoph

    2013-01-01

    Leaf and fine root morphology and physiology have been found to vary considerably among tree species, but not much is known about intraspecific variation in root traits and their relatedness to leaf traits. Various aspen progenies (Populus tremula and P. tremuloides) with different growth performance are used in short-rotation forestry. Hence, a better understanding of the link between root trait syndromes and the adaptation of a deme to a particular environment is essential in order to improve the match between planted varieties and their growth conditions. We examined the between-deme (genetic) and within-deme (mostly environmental) variation in important fine root traits [mean root diameter, specific root area (SRA) and specific root length (SRL), root tissue density (RTD), root tip abundance, root N concentration] and their co-variation with leaf traits [specific leaf area (SLA), leaf size, leaf N concentration] in eight genetically distinct P. tremula and P. tremuloides demes. Five of the six root traits varied significantly between the demes with largest genotypic variation in root tip abundance and lowest in mean root diameter and RTD (no significant difference). Within-deme variation in root morphology was as large as between-deme variation suggesting a relatively low genetic control. Significant relationships existed neither between SLA and SRA nor between leaf N and root N concentration in a plant. Contrary to expectation, high aboveground relative growth rates (RGR) were associated with large, and not small, fine root diameters with low SRA and SRL. Compared to leaf traits, the influence of root traits on RGR was generally low. We conclude that aspen exhibits large intraspecific variation in leaf and also in root morphological traits which is only partly explained by genetic distances. A root order-related analysis might give deeper insights into intraspecific root trait variation.

  1. Genotypic variation for condensed tannin production in trembling aspen (POPULUS TREMULOIDES, salicaceae) under elevated CO2 and in high- and low-fertility soil.

    PubMed

    Mansfield, J L; Curtis, P S; Zak, D R; Pregitzer, K S

    1999-08-01

    The carbon/nutrient balance hypothesis suggests that leaf carbon to nitrogen ratios influence the synthesis of secondary compounds such as condensed tannins. We studied the effects of rising atmospheric carbon dioxide on carbon to nitrogen ratios and tannin production. Six genotypes of Populus tremuloides were grown under elevated and ambient CO(2) partial pressure and high- and low-fertility soil in field open-top chambers in northern lower Michigan, USA. During the second year of exposure, leaves were harvested three times (June, August, and September) and analyzed for condensed tannin concentration. The carbon/nutrient balance hypothesis was supported overall, with significantly greater leaf tannin concentration at high CO(2) and low soil fertility compared to ambient CO(2) and high soil fertility. However, some genotypes increased tannin concentration at elevated compared to ambient CO(2), while others showed no CO(2) response. Performance of lepidopteran leaf miner (Phyllonorycter tremuloidiella) larvae feeding on these plants varied across genotypes, CO(2), and fertility treatments. These results suggest that with rising atmospheric CO(2), plant secondary compound production may vary within species. This could have consequences for plant-herbivore and plant-microbe interactions and for the evolutionary response of this species to global climate change.

  2. PHYTOALEXIN DEFICIENT 4 affects reactive oxygen species metabolism, cell wall and wood properties in hybrid aspen (Populus tremula L. × tremuloides).

    PubMed

    Ślesak, Ireneusz; Szechyńska-Hebda, Magdalena; Fedak, Halina; Sidoruk, Natalia; Dąbrowska-Bronk, Joanna; Witoń, Damian; Rusaczonek, Anna; Antczak, Andrzej; Drożdżek, Michał; Karpińska, Barbara; Karpiński, Stanisław

    2015-07-01

    The phytoalexin deficient 4 (PAD4) gene in Arabidopsis thaliana (AtPAD4) is involved in the regulation of plant--pathogen interactions. The role of PAD4 in woody plants is not known; therefore, we characterized its function in hybrid aspen and its role in reactive oxygen species (ROS)-dependent signalling and wood development. Three independent transgenic lines with different suppression levels of poplar PAD expression were generated. All these lines displayed deregulated ROS metabolism, which was manifested by an increased H2O2 level in the leaves and shoots, and higher activities of manganese superoxide dismutase (MnSOD) and catalase (CAT) in the leaves in comparison to the wild-type plants. However, no changes in non-photochemical quenching (NPQ) between the transgenic lines and wild type were observed in the leaves. Moreover, changes in the ROS metabolism in the pad4 transgenic lines positively correlated with wood formation. A higher rate of cell division, decreased tracheid average size and numbers, and increased cell wall thickness were observed. The results presented here suggest that the Populus tremula × tremuloides PAD gene might be involved in the regulation of cellular ROS homeostasis and in the cell division--cell death balance that is associated with wood development.

  3. PHYTOALEXIN DEFICIENT 4 affects reactive oxygen species metabolism, cell wall and wood properties in hybrid aspen (Populus tremula L. × tremuloides).

    PubMed

    Ślesak, Ireneusz; Szechyńska-Hebda, Magdalena; Fedak, Halina; Sidoruk, Natalia; Dąbrowska-Bronk, Joanna; Witoń, Damian; Rusaczonek, Anna; Antczak, Andrzej; Drożdżek, Michał; Karpińska, Barbara; Karpiński, Stanisław

    2015-07-01

    The phytoalexin deficient 4 (PAD4) gene in Arabidopsis thaliana (AtPAD4) is involved in the regulation of plant--pathogen interactions. The role of PAD4 in woody plants is not known; therefore, we characterized its function in hybrid aspen and its role in reactive oxygen species (ROS)-dependent signalling and wood development. Three independent transgenic lines with different suppression levels of poplar PAD expression were generated. All these lines displayed deregulated ROS metabolism, which was manifested by an increased H2O2 level in the leaves and shoots, and higher activities of manganese superoxide dismutase (MnSOD) and catalase (CAT) in the leaves in comparison to the wild-type plants. However, no changes in non-photochemical quenching (NPQ) between the transgenic lines and wild type were observed in the leaves. Moreover, changes in the ROS metabolism in the pad4 transgenic lines positively correlated with wood formation. A higher rate of cell division, decreased tracheid average size and numbers, and increased cell wall thickness were observed. The results presented here suggest that the Populus tremula × tremuloides PAD gene might be involved in the regulation of cellular ROS homeostasis and in the cell division--cell death balance that is associated with wood development. PMID:24943986

  4. Effects of canopy-deposition interaction on H+ supply to soils in Pinus banksiana and Populus tremuloides ecosystems in the Athabasca oil sands region in Alberta, Canada.

    PubMed

    Jung, Kangho; Chang, Scott X; Arshad, M A Charlie

    2011-05-01

    Soil acidification has been of concern in the oil sands region in Alberta due to increased acid deposition. Using the canopy budget model, and accounting for H(+) canopy leaching by organic acids, we determined sources and sinks of H+ in throughfall in jack pine (Pinus banksiana) and trembling aspen (Populus tremuloides) stands in two watersheds from 2006 to 2009. In pine stands, H+ deposition was greater in throughfall than in bulk precipitation while the opposite was true in aspen stands. The annual H+ interception deposition was 148.8-193.8 and 49.7-70.0 molcha(-1) in pine and aspen stands, respectively; while the annual H+ canopy leaching was 127.1-128.7 and 0.0-6.0 molcha(-1), respectively. The greater H+ supply in pine stands was caused by greater interception deposition of SO4(2-) and organic acids released from the pine canopy. Such findings have significant implications for establishing critical loads for various ecosystems in the oil sands region.

  5. Effects of canopy-deposition interaction on H+ supply to soils in Pinus banksiana and Populus tremuloides ecosystems in the Athabasca oil sands region in Alberta, Canada.

    PubMed

    Jung, Kangho; Chang, Scott X; Arshad, M A Charlie

    2011-05-01

    Soil acidification has been of concern in the oil sands region in Alberta due to increased acid deposition. Using the canopy budget model, and accounting for H(+) canopy leaching by organic acids, we determined sources and sinks of H+ in throughfall in jack pine (Pinus banksiana) and trembling aspen (Populus tremuloides) stands in two watersheds from 2006 to 2009. In pine stands, H+ deposition was greater in throughfall than in bulk precipitation while the opposite was true in aspen stands. The annual H+ interception deposition was 148.8-193.8 and 49.7-70.0 molcha(-1) in pine and aspen stands, respectively; while the annual H+ canopy leaching was 127.1-128.7 and 0.0-6.0 molcha(-1), respectively. The greater H+ supply in pine stands was caused by greater interception deposition of SO4(2-) and organic acids released from the pine canopy. Such findings have significant implications for establishing critical loads for various ecosystems in the oil sands region. PMID:21310518

  6. Impacts of elevated CO2 and/or O3 on leaf ultrastructure of aspen (Populus tremuloides) and birch (Betula papyrifera) in the aspen FACE experiment.

    PubMed

    Oksanen, E; Sober, J; Karnosky, D F

    2001-01-01

    Impacts of elevated atmospheric O3 and/or CO2 on three clones of aspen (Populus tremuloides Michx.) and birch (Betula papyrifera Marsh.) were studied to determine, whether or not elevated CO2 ameliorates O3-induced damage to leaf cells. The plants were exposed for 3 years at the Aspen FACE exposure site in Wisconsin (USA) prior to sampling for ultrastructural investigations on 19 June 1999. In the aspen clones, elevated CO2 increased chloroplast cover index, leaf and spongy mesophyll layer thickness, intercellular air space volume in mesophyll, amount of starch in chloroplasts and cytoplasmic lipids but decreased the number of plastoglobuli in chloroplasts. In contrast, elevated O3 decreased chloroplast cover index, starch content, and the proportion of cytoplasm and intercellular space in mesophyll, and increased the proportion of vacuoles, the amount of condensed vacuolar tannins and the number of plastoglobuli. Ozone also caused structural thylakoid injuries (dilation, distortion) and stromal condensation in chloroplasts, which was ameliorated by elevated CO2 by 5-66% in aspen clones and by 2-10% in birch. Birch ultrastructure was less affected by elevated CO2 or O3 stress compared to aspen. In the most O3-sensitive aspen clone, thinner leaves and cell walls, lower proportion of cell wall volume, and higher volume for vacuoles was found compared to more-tolerant clones.

  7. Impacts of post-harvest slash and live-tree retention on biomass and nutrient stocks in Populus tremuloides Michx.-dominated forests, northern Minnesota, USA

    USGS Publications Warehouse

    Klockow, Paul A.; D'Amato, Anthony W.; Bradford, John B.

    2013-01-01

    Globally, there is widespread interest in using forest-derived biomass as a source of bioenergy. While conventional timber harvesting generally removes only merchantable tree boles, harvesting biomass feedstock can remove all forms of woody biomass (i.e., live and dead standing woody vegetation, downed woody debris, and stumps) resulting in a greater loss of biomass and nutrients as well as more severe habitat alteration. To investigate the potential impacts of this practice, this study examined the initial impacts (pre- and post-harvest) of various levels of slash and live-tree retention on biomass and nutrient stocks, including carbon (C), nitrogen (N), calcium (Ca), potassium (K), and phosphorus (P), in Populus tremuloides Michx.-dominated forests of northern Minnesota, USA. Treatments examined included three levels of slash retention, whole-tree harvest (WTH), 20% slash retention (20SR), and stem-only harvest (SOH), factored with three levels of green-tree retention, no trees retained (NONE), dispersed retention (DISP), and aggregate retention (AGR). Slash retention was the primary factor affecting post-harvest biomass and nutrient stocks, including woody debris pools. Compared to the unharvested control, stocks of biomass, carbon, and nutrients, including N, Ca, K, and P, in woody debris were higher in all treatments. Stem-only harvests typically contained greater biomass and nutrient stocks than WTH, although biomass and nutrients within 20SR, a level recommended by biomass harvesting guidelines in the US and worldwide, generally did not differ from WTH or SOH. Biomass in smaller-diameter slash material (typically 2.5-22.5 cm in diameter) dominated the woody debris pool following harvest regardless of slash retention level. Trends among treatments in this diameter range were generally similar to those in the total woody debris pool. Specifically, SOH contained significantly greater amounts of biomass than WTH while 20SR was not different from either WTH or

  8. Will changes in root-zone temperature in boreal spring affect recovery of photosynthesis in Picea mariana and Populus tremuloides in a future climate?

    PubMed

    Fréchette, Emmanuelle; Ensminger, Ingo; Bergeron, Yves; Gessler, Arthur; Berninger, Frank

    2011-11-01

    Future climate will alter the soil cover of mosses and snow depths in the boreal forests of eastern Canada. In field manipulation experiments, we assessed the effects of varying moss and snow depths on the physiology of black spruce (Picea -mariana (Mill.) B.S.P.) and trembling aspen (Populus tremuloides Michx.) in the boreal black spruce forest of western Québec. For 1 year, naturally regenerated 10-year-old spruce and aspen were grown with one of the following treatments: additional N fertilization, addition of sphagnum moss cover, removal of mosses, delayed soil thawing through snow and hay addition, or accelerated soil thawing through springtime snow removal. Treatments that involved the addition of insulating moss or snow in the spring caused lower soil temperature, while removing moss and snow in the spring caused elevated soil temperature and thus had a warming effect. Soil warming treatments were associated with greater temperature variability. Additional soil cover, whether moss or snow, increased the rate of photosynthetic recovery in the spring. Moss and snow removal, on the other hand, had the opposite effect and lowered photosynthetic activity, especially in spruce. Maximal electron transport rate (ETR(max)) was, for spruce, 39.5% lower after moss removal than with moss addition, and 16.3% lower with accelerated thawing than with delayed thawing. Impaired photosynthetic recovery in the absence of insulating moss or snow covers was associated with lower foliar N concentrations. Both species were affected in that way, but trembling aspen generally reacted less strongly to all treatments. Our results indicate that a clear negative response of black spruce to changes in root-zone temperature should be anticipated in a future climate. Reduced moss cover and snow depth could adversely affect the photosynthetic capacities of black spruce, while having only minor effects on trembling aspen. PMID:22021010

  9. Spring leaf flush in aspen (Populus tremuloides) clones is altered by long-term growth at elevated carbon dioxide and elevated ozone concentration.

    PubMed

    McGrath, Justin M; Karnosky, David F; Ainsworth, Elizabeth A

    2010-04-01

    Early spring leaf out is important to the success of deciduous trees competing for light and space in dense forest plantation canopies. In this study, we investigated spring leaf flush and how long-term growth at elevated carbon dioxide concentration ([CO(2)]) and elevated ozone concentration ([O(3)]) altered leaf area index development in a closed Populus tremuloides (aspen) canopy. This work was done at the Aspen FACE experiment where aspen clones have been grown since 1997 in conditions simulating the [CO(2)] and [O(3)] predicted for approximately 2050. The responses of two clones were compared during the first month of spring leaf out when CO(2) fumigation had begun, but O(3) fumigation had not. Trees in elevated [CO(2)] plots showed a stimulation of leaf area index (36%), while trees in elevated [O(3)] plots had lower leaf area index (-20%). While individual leaf area was not significantly affected by elevated [CO(2)], the photosynthetic operating efficiency of aspen leaves was significantly improved (51%). There were no significant differences in the way that the two aspen clones responded to elevated [CO(2)]; however, the two clones responded differently to long-term growth at elevated [O(3)]. The O(3)-sensitive clone, 42E, had reduced individual leaf area when grown at elevated [O(3)] (-32%), while the tolerant clone, 216, had larger mature leaf area at elevated [O(3)] (46%). These results indicate a clear difference between the two clones in their long-term response to elevated [O(3)], which could affect competition between the clones, and result in altered genotypic composition in future atmospheric conditions.

  10. Will changes in root-zone temperature in boreal spring affect recovery of photosynthesis in Picea mariana and Populus tremuloides in a future climate?

    PubMed

    Fréchette, Emmanuelle; Ensminger, Ingo; Bergeron, Yves; Gessler, Arthur; Berninger, Frank

    2011-11-01

    Future climate will alter the soil cover of mosses and snow depths in the boreal forests of eastern Canada. In field manipulation experiments, we assessed the effects of varying moss and snow depths on the physiology of black spruce (Picea -mariana (Mill.) B.S.P.) and trembling aspen (Populus tremuloides Michx.) in the boreal black spruce forest of western Québec. For 1 year, naturally regenerated 10-year-old spruce and aspen were grown with one of the following treatments: additional N fertilization, addition of sphagnum moss cover, removal of mosses, delayed soil thawing through snow and hay addition, or accelerated soil thawing through springtime snow removal. Treatments that involved the addition of insulating moss or snow in the spring caused lower soil temperature, while removing moss and snow in the spring caused elevated soil temperature and thus had a warming effect. Soil warming treatments were associated with greater temperature variability. Additional soil cover, whether moss or snow, increased the rate of photosynthetic recovery in the spring. Moss and snow removal, on the other hand, had the opposite effect and lowered photosynthetic activity, especially in spruce. Maximal electron transport rate (ETR(max)) was, for spruce, 39.5% lower after moss removal than with moss addition, and 16.3% lower with accelerated thawing than with delayed thawing. Impaired photosynthetic recovery in the absence of insulating moss or snow covers was associated with lower foliar N concentrations. Both species were affected in that way, but trembling aspen generally reacted less strongly to all treatments. Our results indicate that a clear negative response of black spruce to changes in root-zone temperature should be anticipated in a future climate. Reduced moss cover and snow depth could adversely affect the photosynthetic capacities of black spruce, while having only minor effects on trembling aspen.

  11. Effects of overproduction of condensed tannins and elevated temperature on chemical and ecological traits of genetically modified hybrid aspens (Populus tremula × P. tremuloides).

    PubMed

    Kosonen, Minna; Keski-Saari, Sarita; Ruuhola, Teija; Constabel, C Peter; Julkunen-Tiitto, Riitta

    2012-10-01

    Gene transfer techniques offer new possibilities to study regulation of phenolic pathways and the defensive role of phenolics. Hybrid aspen lines (Populus tremula × tremuloides) that overexpress the PtMYB134 transcription factor were used to study the effects of condensed tannin production on plant physiology and plant defenses. The MYB134 protein activates all the known genes of the biosynthetic pathway for condensed tannins (CTs), so overexpression of MYB134 was expected to increase CT concentration in all tissues of the plants. Two out of three MYB134 overexpression lines (46 and 54) accumulated high levels of CTs and (+)-catechin, with a concomitant decrease in the levels of salicylates, but one transgenic line, MYB 61, failed to overproduce CTs. The concentrations of phenolic compounds generally were lower in the aspen leaves grown under elevated temperature than in those grown under ambient temperature. A specialist leaf beetle, Phratora vitellinae (Coleoptera: Chrysomelidae), was chosen to examine how over-expression of MYB134 and elevated temperature affect the food choice of a beetle adapted to feed on leaves rich in salicylates but containing little CT. Specialist beetles preferred the leaves grown at ambient temperatures possibly because these leaves had higher concentrations of salicylates, which are feeding stimulants. Beetles also preferred MYB line 61, which contained a normal level of CT but a slightly elevated level of salicylates. Our results show that transgenic plants are powerful tools, but that enhancing one secondary pathway may lead to unexpected effects on other pathways, and thus impact characteristics such as plant resistance against herbivores, especially under changing climatic conditions.

  12. Pre- and Post-Harvest Carbon Dioxide Fluxes from an Upland Boreal Aspen (Populus tremuloides) Forest in Western Boreal Plain, Alberta, Canada

    NASA Astrophysics Data System (ADS)

    Giroux, Kayla

    The Utikuma Region Study Area (URSA) is located in north-central Alberta, Canada, in a region where aspen (Populus tremuloides) dominate the upland vegetation of the Western Boreal Plain Due to the heterogeneity of the surficial geology as well as the sub-humid climate where the water balance is dominated by evapotranspiration, the carbon balance across this landscape is highly variable. Moreover, the upland aspen regions represent significant stores of carbon. More recently, aspen stands have become valuable commercial resources for pulp and paper processing. These stands are harvested through a clear cutting process and are generally left to regenerate on their own, a process which occurs rapidly in clonal species like aspen. Since clonal species establish very quickly following harvest, information on the key ecohydrological controls on stand carbon dioxide (CO2) exchange from the years immediately following harvest are essential to understand the successional trajectory. However, most information currently available on these interactions are obtained several years following a disturbance. Thus, to determine the effects of harvest on aspen regeneration and productivity, ecosystem level fluxes of CO2 three years before and three years after timber harvest were analyzed. Prior to harvest, the ecosystem sequestered 1216 to 1286 g CO2 m-2period-1 over the growing season. Immediately after harvest, the ecosystem became a significant source of CO2 ranging from -874 to -1183 g CO2 m -2period-1, while the second growing season ranged from -233 to -577 g CO2 m-2period-1. The third growing season resulted in a net sink (76 g CO2 m -2period-1) over the same period, but if extrapolated over the whole year, the ecosystem would remain a source of carbon. The magnitude of Gross Ecosystem Productivity (GEP) returned pre-harvest range within two growing seasons. Ecosystem respiration (RE), on the other hand, increased year over year after harvest had taken place

  13. Genetic variation in natural populations of Populus tremuloide

    SciTech Connect

    Cheliak, W.M.

    1980-01-01

    Vegetative reproduction results in a mosaic of clones throughout the extensive natural range of this species. An electrophoretic survey of 26 loci in 222 trees from seven natural populations in Alberta demonstrated great variability. Average observed population heterozygosity was 0.52 with an average of 2.3 alleles per locus; 84% of the loci were polymorphic. A model (for a finite population with neutral alleles) was developed to investigate the effects of partial vegetative reproduction on the amount of variation in a population. Results of the survey conformed to those predicted by the model for a population with a rate of sexual establishment greater than 1/N, where N is the population size. The model states that under these conditions, vegetative reproduction has no effect on the population. Therefore, the high level of observed variation is not an artifact of the mode of natural reproduction. These results support conclusions about high population variability based on phenotypic measurements and also suggest a genetic basis for this variation, rather than simply phenotypic plasticity.

  14. Slow lifelong growth predisposes Populus tremuloides trees to mortality.

    PubMed

    Ireland, Kathryn B; Moore, Margaret M; Fulé, Peter Z; Zegler, Thomas J; Keane, Robert E

    2014-07-01

    Widespread dieback of aspen forests, sometimes called sudden aspen decline, has been observed throughout much of western North America, with the highest mortality rates in the southwestern United States. Recent aspen mortality has been linked to drought stress and elevated temperatures characteristic of conditions expected under climate change, but the role of individual aspen tree growth patterns in contributing to recent tree mortality is less well known. We used tree-ring data to investigate the relationship between an individual aspen tree's lifetime growth patterns and mortality. Surviving aspen trees had consistently higher average growth rates for at least 100 years than dead trees. Contrary to observations from late successional species, slow initial growth rates were not associated with a longer lifespan in aspen. Aspen trees that died had slower lifetime growth and slower growth at various stages of their lives than those that survived. Differences in average diameter growth between live and dead trees were significant (α = 0.05) across all time periods tested. Our best logistical model of aspen mortality indicates that younger aspen trees with lower recent growth rates and higher frequencies of abrupt growth declines had an increased risk of mortality. Our findings highlight the need for species-specific mortality functions in forest succession models. Size-dependent mortality functions suitable for late successional species may not be appropriate for species with different life history strategies. For some early successional species, like aspen, slow growth at various stages of the tree's life is associated with increased mortality risk. PMID:24817158

  15. Clonal and spatial genetic structures of aspen (Populus tremuloides Michx.).

    PubMed

    Namroud, Marie-Claire; Park, Andrew; Tremblay, Francine; Bergeron, Yves

    2005-09-01

    To portray aspen clonal and spatial genetic structures, we mapped and genotyped trees in two 1-ha plots, each containing three aspen cohorts originating from fire or subsequent secondary disturbances. We used four microsatellite loci to identify aspen clones and increment core analysis to determine tree age. Clonal dimensions were measured by the maximum distance between two ramets and the number of ramets per genet. Standard normal deviate (SND) was used to assess the spatial distribution of aspen genets and cohorts, and multivariate spatial genetic autocorrelations to assess the spatial distribution of aspen genetic variation. Most aspen genets consisted of only one ramet (> 75%). Median clonal dimensions were 19 and 29 m (maxima: 104 and 72 m in the two plots). No segregation was observed between clones. Aspen cohorts were spatially segregated but trees were spatially aggregated within old and medium-aged cohorts. In contrast, trees were more randomly distributed within the youngest cohorts. This coincided with a spatial genetic autocorrelation at small scales (up to 30 m) in the older cohorts and a more random genetic distribution in the youngest ones. Our results suggest that aspen spatial genetic structuring reflects the spatial patterns produced by the regeneration of discrete cohorts at different stages of succession. Vegetative reproduction leads to aspen genetic spatial structuring at small scales (few metres) until midsuccession. However, as the stand gets older, the spatial distribution of aspen trees and genetic structure evolve from a structured pattern to a more random one under a gap disturbances regime.

  16. Microsatellite primer resource for Populus developed from

    SciTech Connect

    Yin, Tongming; Yang, Xiaohan; Gunter, Lee E; Tuskan, Gerald A; Wullschleger, Stan D; Huang, Prof. Minren; Li, Shuxian; Zhang, Xinye

    2008-01-01

    In this study, 148 428 simple sequence repeat (SSR) primer pairs were designed from the unambiguously mapped sequence scaffolds of the Nisqually-1 genome. The physical position of the priming sites were identified along each of the 19 Populus chromosomes, and it was specified whether the priming sequences belong to intronic, intergenic, exonic or UTR regions. A subset of 150 SSR loci were amplified and a high amplification success rate (72%) was obtained in P. tremuloides, which belongs to a divergent subgenus of Populus relative to Nisqually-1. PCR reactions showed that the amplification success rate of exonic primer pairs was much higher than that of the intronic/intergenic primer pairs. Applying ANOVA and regression analyses to the flanking sequences of microsatellites, the repeat lengths, the GC contents of the repeats, the repeat motif numbers, the repeat motif length and the base composition of the repeat motif, it was determined that only the base composition of the repeat motif and the repeat motif length significantly affect the microsatellite variability in P. tremuloides samples. The SSR primer resource developed in this study provides a database for selecting highly transferable SSR markers with known physical position in the Populus genome and provides a comprehensive genetic tool to extend the genome sequence of Nisqually-1 to genetic studies in different Populus species.

  17. Expansins in deepwater rice internodes

    SciTech Connect

    Cho, Hyung-Taeg; Kende, H.

    1997-04-01

    Cell walls of deepwater rice internodes undergo long-term extension (creep) when placed under tension in acidic buffers. This is indicative of the action of the cell wall-loosening protein expansion. Wall extension had a pH optimum of around 4.0 and was abolished by boiling. Acid-induced extension of boiled cell walls could be reconstituted by addition of salt-extracted rice or cucumber cell wall proteins. Cucumber expansion antibody recognized a single protein band of 24.5-kD apparent molecular mass on immunoblots of rice cell wall proteins. Expansions were partially purified by concanavalin A affinity chromatography and sulfopropyl (SP) cation-exchange chromatography. The latter yielded two peaks with extension activity (SP20 and SP29), and immunoblot analysis showed that both of these active fractions contained expansion of 24.5-kD molecular mass. The N-terminal amino acid sequence of SP20 expansion is identical to that deduced from the rice expansion cDNA Os-EXP1. The N-terminal amino acid sequence of SP29 expansion matches that deduced from the rice expansion cDNA Os-EXP2 in six of eight amino acids. Our results show that two expansions occur in the cell walls of rice internodes and that they may mediate acid-induced wall extension.

  18. Agrobacterium-Mediated Stable Genetic Transformation of Populus angustifolia and Populus balsamifera.

    PubMed

    Maheshwari, Priti; Kovalchuk, Igor

    2016-01-01

    The present study demonstrates Agrobacterium tumefaciens-mediated stable genetic transformation of two species of poplar - Populus angustifolia and Populus balsamifera. The binary vector pCAMBIA-Npro-long-Luc containing the luciferase reporter gene was used to transform stem internode and axillary bud explants. Putative transformants were regenerated on selection-free medium using our previously established in vitro regeneration method. Explant type, genotype, effect of pre-culture, Agrobacterium concentration, a time period of infection and varying periods of co-culture with bacteria were tested for the transformation frequency. The highest frequency of transformation was obtained with stem internode explants pre-cultured for 2 days, infected with Agrobacterium culture at the concentration of OD600 = 0.5 for 10 min and co-cultivated with Agrobacterium for 48 h. Out of the two genotypes tested, P. balsamifera exhibited a higher transformation rate in comparison to P. angustifolia. The primary transformants that exhibited luciferase activity in a bioluminescence assay under the CCD camera when subjected to polymerase chain reaction and Southern blot analysis revealed a stable single-copy integration of luc in their genomes. The reported protocol is highly reproducible and can be applied to other species of poplar; it will also be useful for future genetic engineering of one of the most important families of woody plants for sustainable development. PMID:27014319

  19. Agrobacterium-Mediated Stable Genetic Transformation of Populus angustifolia and Populus balsamifera

    PubMed Central

    Maheshwari, Priti; Kovalchuk, Igor

    2016-01-01

    The present study demonstrates Agrobacterium tumefaciens-mediated stable genetic transformation of two species of poplar – Populus angustifolia and Populus balsamifera. The binary vector pCAMBIA-Npro-long-Luc containing the luciferase reporter gene was used to transform stem internode and axillary bud explants. Putative transformants were regenerated on selection-free medium using our previously established in vitro regeneration method. Explant type, genotype, effect of pre-culture, Agrobacterium concentration, a time period of infection and varying periods of co-culture with bacteria were tested for the transformation frequency. The highest frequency of transformation was obtained with stem internode explants pre-cultured for 2 days, infected with Agrobacterium culture at the concentration of OD600 = 0.5 for 10 min and co-cultivated with Agrobacterium for 48 h. Out of the two genotypes tested, P. balsamifera exhibited a higher transformation rate in comparison to P. angustifolia. The primary transformants that exhibited luciferase activity in a bioluminescence assay under the CCD camera when subjected to polymerase chain reaction and Southern blot analysis revealed a stable single-copy integration of luc in their genomes. The reported protocol is highly reproducible and can be applied to other species of poplar; it will also be useful for future genetic engineering of one of the most important families of woody plants for sustainable development. PMID:27014319

  20. Agrobacterium-Mediated Stable Genetic Transformation of Populus angustifolia and Populus balsamifera.

    PubMed

    Maheshwari, Priti; Kovalchuk, Igor

    2016-01-01

    The present study demonstrates Agrobacterium tumefaciens-mediated stable genetic transformation of two species of poplar - Populus angustifolia and Populus balsamifera. The binary vector pCAMBIA-Npro-long-Luc containing the luciferase reporter gene was used to transform stem internode and axillary bud explants. Putative transformants were regenerated on selection-free medium using our previously established in vitro regeneration method. Explant type, genotype, effect of pre-culture, Agrobacterium concentration, a time period of infection and varying periods of co-culture with bacteria were tested for the transformation frequency. The highest frequency of transformation was obtained with stem internode explants pre-cultured for 2 days, infected with Agrobacterium culture at the concentration of OD600 = 0.5 for 10 min and co-cultivated with Agrobacterium for 48 h. Out of the two genotypes tested, P. balsamifera exhibited a higher transformation rate in comparison to P. angustifolia. The primary transformants that exhibited luciferase activity in a bioluminescence assay under the CCD camera when subjected to polymerase chain reaction and Southern blot analysis revealed a stable single-copy integration of luc in their genomes. The reported protocol is highly reproducible and can be applied to other species of poplar; it will also be useful for future genetic engineering of one of the most important families of woody plants for sustainable development.

  1. Can elevated CO2 and ozone shift the genetic composition of aspen (Populus tremuloides) stands?

    PubMed

    Moran, Emily V; Kubiske, Mark E

    2013-04-01

    The world's forests are currently exposed to increasing concentrations of carbon dioxide (CO2) and ozone (O3). Both pollutants can potentially exert a selective effect on plant populations. This, in turn, may lead to changes in ecosystem properties, such as carbon sequestration. Here, we report how elevated CO2 and O3 affect the genetic composition of a woody plant population via altered survival. Using data from the Aspen free-air CO2 enrichment (FACE) experiment (in which aspen clones were grown in factorial combinations of CO2 and O3), we develop a hierarchical Bayesian model of survival. We also examine how survival differences between clones could affect pollutant responses in the next generation. Our model predicts that the relative abundance of the tested clones, given equal initial abundance, would shift under either elevated CO2 or O3 as a result of changing survival rates. Survival was strongly affected by between-clone differences in growth responses. Selection could noticeably decrease O3 sensitivity in the next generation, depending on the heritability of growth responses and the distribution of seed production. The response to selection by CO2, however, is likely to be small. Our results suggest that the changing atmospheric composition could shift the genotypic composition and average pollutant responses of tree populations over moderate timescales.

  2. Growth and mortality of trembling aspen (Populus tremuloides) in response to artificial defoliation

    NASA Astrophysics Data System (ADS)

    Moulinier, Julien; Lorenzetti, François; Bergeron, Yves

    2014-02-01

    To simulate the effects of forest tent caterpillar (FTC) defoliation on trembling aspen growth and mortality, an artificial defoliation experiment was performed over three years in young aspen stands of northwestern Quebec. Defoliation plots of 15 × 15 m were established on three sites, together with associated control stands of pure trembling aspen. In 2007, root collar diameters were measured and positions of all trees were mapped prior defoliation. Severe FTC defoliation was simulated for three successive years (2007-2009) by manually removing all leaves from all but 7-10% of the trees present in the defoliation plots. Yearly surveys of growth and mortality were conducted until 2010 to evaluate defoliation effects on defoliated as well as surrounding undefoliated trees. In absence of other factors, growth and mortality of trembling aspen decreased and increased, respectively, after defoliation. Our study further revealed that small diameter trees died after one year of artificial defoliation, while larger-diameter trees died after repeated defoliations. Distributions of tree mortality tended to be aggregated at small scales (<5 m), corroborating gap patterns observed in mature stands following FTC outbreaks. This experiment revealed that trembling aspen mortality can be directly attributed solely to defoliation. Repeated defoliations during FTC outbreaks have the potential to profoundly modify stand productivity and structure by reducing tree growth and increasing tree mortality in the absence of predisposing factors.

  3. Scale dependence of disease impacts on quaking aspen (Populus tremuloides) mortality in the southwestern United States

    USGS Publications Warehouse

    Bell, David M.; Bradford, John B.; Lauenroth, William K.

    2015-01-01

    By examining variation in disease prevalence, mortality of healthy trees, and mortality of diseased trees, we showed that the role of disease in aspen tree mortality depended on the scale of inference. For variation among individuals in diameter, disease tended to expose intermediate-size trees experiencing moderate risk to greater risk. For spatial variation in summer temperature, disease exposed lower risk populations to greater mortality probabilities, but the magnitude of this exposure depended on summer precipitation. Furthermore, the importance of diameter and slenderness in mediating responses to climate supports the increasing emphasis on trait variation in studies of ecological responses to global change.

  4. Internode length in pisum: do the internode length genes effect growth in dark-grown plants?

    PubMed

    Reid, J B

    1983-07-01

    Internode length in light-grown peas (Pisum sativum L.) is controlled by the interaction of genes occupying at least five major loci, Le, La, Cry, Na, and Lm. The present work shows that the genes at all of the loci examined (Le, Cry, and Na) also exert an effect on internode length in plants grown in complete darkness. Preliminary results using pure lines were verified using either segregating progenies or near isogenic lines. The major cause of the differences was due to a change in the number of cells per internode rather than to an alteration of the cell length. Since the genes occupying at least two of these loci, Le and Na, have been shown to be directly involved with gibberellin metabolism, it appears that gibberellins are not only essential for elongation in the dark but are limiting for elongation in the nana (extremely short, na), dwarf (Na le), and tall (Na Le) phenotypes. These results are supported by the large inhibitory effects of AMO 1618 treatments on stem elongation in dwarf and tall lines grown in the dark and the fact that applied gibberellic acid could overcome this inhibition and greatly promote elongation in a gibberellin-deficient na line. It is clear that the internode length genes, and in particular the alleles at the Le locus, are not acting by simply controlling the sensitivity of the plant to light. PMID:16663081

  5. Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus).

    PubMed

    Geraldes, A; Hefer, C A; Capron, A; Kolosova, N; Martinez-Nuñez, F; Soolanayakanahally, R Y; Stanton, B; Guy, R D; Mansfield, S D; Douglas, C J; Cronk, Q C B

    2015-07-01

    All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole-genome scans that the sex-associated region in Populus trichocarpa is small and much younger than the age of the genus. This indicates that sex determination is highly labile in poplar, consistent with recent evidence of 'turnover' of sex-determination regions in animals. We performed whole-genome resequencing of 52 P. trichocarpa (black cottonwood) and 34 Populus balsamifera (balsam poplar) individuals of known sex. Genomewide association studies in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex-linked region to be ~100 kbp. All SNPs significantly associated with sex were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex-associated SNPs revealed this to be an XY sex-determining system. Estimated divergence times of X and Y haplotype sequences (6-7 Ma) are much more recent than the divergence of P. trichocarpa (poplar) and Populus tremuloides (aspen). Consistent with this, in P. tremuloides, we found no XY haplotype divergence within the P. trichocarpa sex-determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past.

  6. Internode data communications in a parallel computer

    SciTech Connect

    Archer, Charles J.; Blocksome, Michael A.; Miller, Douglas R.; Parker, Jeffrey J.; Ratterman, Joseph D.; Smith, Brian E.

    2013-09-03

    Internode data communications in a parallel computer that includes compute nodes that each include main memory and a messaging unit, the messaging unit including computer memory and coupling compute nodes for data communications, in which, for each compute node at compute node boot time: a messaging unit allocates, in the messaging unit's computer memory, a predefined number of message buffers, each message buffer associated with a process to be initialized on the compute node; receives, prior to initialization of a particular process on the compute node, a data communications message intended for the particular process; and stores the data communications message in the message buffer associated with the particular process. Upon initialization of the particular process, the process establishes a messaging buffer in main memory of the compute node and copies the data communications message from the message buffer of the messaging unit into the message buffer of main memory.

  7. Internode data communications in a parallel computer

    SciTech Connect

    Archer, Charles J; Blocksome, Michael A; Miller, Douglas R; Parker, Jeffrey J; Ratterman, Joseph D; Smith, Brian E

    2014-02-11

    Internode data communications in a parallel computer that includes compute nodes that each include main memory and a messaging unit, the messaging unit including computer memory and coupling compute nodes for data communications, in which, for each compute node at compute node boot time: a messaging unit allocates, in the messaging unit's computer memory, a predefined number of message buffers, each message buffer associated with a process to be initialized on the compute node; receives, prior to initialization of a particular process on the compute node, a data communications message intended for the particular process; and stores the data communications message in the message buffer associated with the particular process. Upon initialization of the particular process, the process establishes a messaging buffer in main memory of the compute node and copies the data communications message from the message buffer of the messaging unit into the message buffer of main memory.

  8. Alteration of PHYA expression change circadian rhythms and timing of bud set in Populus.

    PubMed

    Kozarewa, Iwanka; Ibáñez, Cristian; Johansson, Mikael; Ogren, Erling; Mozley, David; Nylander, Eva; Chono, Makiko; Moritz, Thomas; Eriksson, Maria E

    2010-05-01

    In many temperate woody species, dormancy is induced by short photoperiods. Earlier studies have shown that the photoreceptor phytochrome A (phyA) promotes growth. Specifically, Populus plants that over-express the oat PHYA gene (oatPHYAox) show daylength-independent growth and do not become dormant. However, we show that oatPHYAox plants could be induced to set bud and become cold hardy by exposure to a shorter, non-24 h diurnal cycle that significantly alters the relative position between endogenous rhythms and perceived light/dark cycles. Furthermore, we describe studies in which the expression of endogenous Populus tremula x P. tremuloides PHYTOCHROME A (PttPHYA) was reduced in Populus trees by antisense inhibition. The antisense plants showed altered photoperiodic requirements, resulting in earlier growth cessation and bud formation in response to daylength shortening, an effect that was explained by an altered innate period that leads to phase changes of clock-associated genes such as PttCO2. Moreover, gene expression studies following far-red light pulses show a phyA-mediated repression of PttLHY1 and an induction of PttFKF1 and PttFT. We conclude that the level of PttPHYA expression strongly influences seasonally regulated growth in Populus and is central to co-ordination between internal clock-regulated rhythms and external light/dark cycles through its dual effect on the pace of clock rhythms and in light signaling.

  9. Dynamics of the volatile defense of winter "dormant" balsam poplar (Populus balsamifera).

    PubMed

    Clausen, Thomas P; Chen, Janice; Bryant, John P; Provenza, Frederick D; Villalba, Juan

    2010-05-01

    6-Hydroxycylohex-2-en-1-one (6-HCH) has been reported as a major chemical defense of the winter-dormant internodes of balsam poplar (Populus balsamifera) against feeding by herbivores such as the snowshoe hare (Lepus americanus). We report that the concentration of 6-HCH in the fall internodes is triggered by a single hard frost, and then undergoes an exponential decline through volatilization over the winter that results in barely detectable quantities by early spring. We conclude that the role of 6-HCH in the defense of mature balsam poplar is more complex than simply acting as a toxin. Rather, 6-HCH's role as a defensive agent must evolve over the course of the winter from being a co-toxin to a cue for a conditioned flavor aversion (CFA) to finally having no role by late spring.

  10. Contrasting Strategies of Alfalfa Stem Elongation in Response to Fall Dormancy in Early Growth Stage: The Tradeoff between Internode Length and Internode Number

    PubMed Central

    Wang, Zongli; Sun, Qizhong

    2015-01-01

    Fall dormancy (FD) in alfalfa (Medicago sativa L.) can be described using 11 FD ratings, is widely used as an important indicator of stress resistance, productive performance and spring growth. However, the contrasting growth strategies in internode length and internode number in alfalfa cultivars with different FD rating are poorly understood. Here, a growth chamber study was conducted to investigate the effect of FD on plant height, aboveground biomass, internode length, and internode number in alfalfa individuals in the early growth stages. In order to simulate the alfalfa growth environment in the early stage, 11 alfalfa cultivars with FD ratings from one to 11 were chosen and seeded at the greenhouse, and then were transplanted into an artificial growth chamber. The experimental design was a randomized complete block in a split-plot arrangement with three replicates. Plant height, above-ground biomass, internode length, and internode number were measured in early growth stage in all individuals. Our findings showed that plant height and the aboveground biomass of alfalfa did not significantly differ among 11 different FD rated cultivars. Also, internode length and internode number positively affected plant height and the aboveground biomass of alfalfa individuals and the average internode length significantly increased with increasing FD rating. However, internode number tended to sharply decline when the FD rating increased. Moreover, there were no correlations, slightly negative correlations, and strongly negative correlations between internode length and internode number in alfalfa individuals among the three scales, including within-FD ratings, within-FD categories and inter-FD ratings, respectively. Therefore, our results highlighted that contrasting growth strategies in stem elongation were adopted by alfalfa with different FD ratings in the early growth stage. Alfalfa cultivars with a high FD rating have longer internodes, whereas more dormant alfalfa

  11. Spring leaf flush in aspen (Populus tremuloides) clones is altered by growth at elevated carbon dioxide and elevated ozone

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Early spring leaf out is important to the success of trees competing for light and space in dense forest plantation canopies. In this study, we investigated spring leaf flush and how elevated carbon dioxide concentration and elevated ozone concentration altered leaf area index development in a clos...

  12. Elevated CO2 interacts with herbivory to alter chlorophyll fluorescence and leaf temperature in Betula papyrifera and Populus tremuloides.

    PubMed

    Nabity, Paul D; Hillstrom, Michael L; Lindroth, Richard L; DeLucia, Evan H

    2012-08-01

    Herbivory can influence ecosystem productivity, but recent evidence suggests that damage by herbivores modulates potential productivity specific to damage type. Because productivity is linked to photosynthesis at the leaf level, which in turn is influenced by atmospheric CO(2) concentrations, we investigated how different herbivore damage types alter component processes of photosynthesis under ambient and elevated atmospheric CO(2). We examined spatial patterns in chlorophyll fluorescence and the temperature of leaves damaged by leaf-chewing, gall-forming, and leaf-folding insects in aspen trees as well as by leaf-chewing insects in birch trees under ambient and elevated CO(2) at the aspen free-air CO(2) enrichment (FACE) site in Wisconsin. Both defoliation and gall damage suppressed the operating efficiency of photosystem II (ΦPSII) in remaining leaf tissue, and the distance that damage propagated into visibly undamaged tissue was marginally attenuated under elevated CO(2). Elevated CO(2) increased leaf temperatures, which reduced the cooling effect of gall formation and freshly chewed leaf tissue. These results provide mechanistic insight into how different damage types influence the remaining, visibly undamaged leaf tissue, and suggest that elevated CO(2) may reduce the effects of herbivory on the primary photochemistry controlling photosynthesis.

  13. Structural characteristics of developing Nitella internodal cell walls.

    PubMed

    GREEN, P B

    1958-09-25

    The Nilella intermodal cell is formed by a division of the segment cell, the latter being a direct derivative of the shoot apical cell. The internodal cell is remarkable in that it elongates from an initial length of about 20 microns to a mature length of about 60 millimeters. The structures of the apical and segment cells, and the internodal cells in all stages of development were examined with the techniques of interference, polarization, and electron microscopy. The apical and segment cells were found to be isotropic. The upper part of the segment cell, destined to form a node, shows a curious pitted structure that was characteristic of certain node structures. The lower part of the segment cell, destined to become an internodal cell, shows a vague transverse arrangement of fibrils at the inner wall surface. The internodal cells, from the time they are first formed, show negative birefringence and a transverse arrangement of microfibrils at the inner wall surface. The elongation of the internodal cell is characterized by a rise, dip, and rise in both the optical thickness and retardation of the cell wall. The dip in both these variables coincides with the attainment of the maximum relative elongation rate. After the cessation of elongation, wall deposition continues, but the fibrils at .the inner surface of the wall are now seen to occur in fields of nearly parallel microfibrils. These fields, with varying fibrillar directions, may partly overlap each other or may merge with one another. Unlike the growing wall, this wall which is deposited after the end of elongation is isotropic.

  14. Gibberellin biosynthesis and signal transduction is essential for internode elongation in deepwater rice

    PubMed Central

    Ayano, Madoka; Kani, Takahiro; Kojima, Mikiko; Sakakibara, Hitoshi; Kitaoka, Takuya; Kuroha, Takeshi; Angeles-Shim, Rosalyn B; Kitano, Hidemi; Nagai, Keisuke; Ashikari, Motoyuki

    2014-01-01

    Under flooded conditions, the leaves and internodes of deepwater rice can elongate above the water surface to capture oxygen and prevent drowning. Our previous studies showed that three major quantitative trait loci (QTL) regulate deepwater-dependent internode elongation in deepwater rice. In this study, we investigated the age-dependent internode elongation in deepwater rice. We also investigated the relationship between deepwater-dependent internode elongation and the phytohormone gibberellin (GA) by physiological and genetic approach using a QTL pyramiding line (NIL-1 + 3 + 12). Deepwater rice did not show internode elongation before the sixth leaf stage under deepwater condition. Additionally, deepwater-dependent internode elongation occurred on the sixth and seventh internodes during the sixth leaf stage. These results indicate that deepwater rice could not start internode elongation until the sixth leaf stage. Ultra-performance liquid chromatography tandem mass-spectrometry (UPLC-MS/MS) method for the phytohormone contents showed a deepwater-dependent GA1 and GA4 accumulation in deepwater rice. Additionally, a GA inhibitor abolished deepwater-dependent internode elongation in deepwater rice. On the contrary, GA feeding mimicked internode elongation under ordinary growth conditions. However, mutations in GA biosynthesis and signal transduction genes blocked deepwater-dependent internode elongation. These data suggested that GA biosynthesis and signal transduction are essential for deepwater-dependent internode elongation in deepwater rice. Deepwater rice obtained the ability for rapid internode elongation to avoid drowning and adapt to flooded condition. How does it regulate internode elongation? Using both physiological and genetic approach, this paper shows that the plant hormone, gibberellin (GA) regulates internode elongation. PMID:24891164

  15. Role of Polyamines in Gibberellin-Induced Internode Growth in Peas

    PubMed Central

    Smith, Mary A.; Davies, Peter J.; Reid, James B.

    1985-01-01

    To determine the requirement for polyamines in gibberellin (GA) induced internode growth polyamine content was measured in internodes of peas of various internode phenotypes (slender, tall, dwarf, nana) with and without applied gibberellin (GA3) and polyamine synthesis inhibitors. Polyamines were assayed as dansyl derivatives which were separated by reverse phase high performance liquid chromatography and detected by fluorescence spectrophotometry. The amounts of polyamines in the different genetic lines of peas, which differed in internode lengths and extractable GA content, correlated with the extent of internode elongation. High polyamine concentrations were associated with young internodes and decreased with internode expansion. Extremely short internodes of nana plants without GA exhibited equal or higher amine concentrations relative to internodes of other lines of peas and GA-stimulated nana seedlings. The polyamine synthesis inhibitors, α-difluoromethylornithine and α-difluoromethylarginine, independently or in combination, inhibited polyamine accumulation and internode elongation of tall peas and GA-stimulated nana plants. Agmatine and putrescine restored growth and endogenous polyamine content to variable degrees. However, exogenous polyamines were not effective in promoting growth unless intracellular amines were partially depleted. These results suggest that polyamines do not have a role in cell elongation, but may be required to support cell proliferation. Polyamines do not mediate the entire action of GA in internode growth of peas since GA induction of growth involves both cell division and cell elongation, whereas polyamines appear to affect cell division only. Images Fig. 1 Fig. 4 PMID:16664217

  16. Role of polyamines in gibberellin-induced internode growth in peas.

    PubMed

    Smith, M A; Davies, P J; Reid, J B

    1985-05-01

    To determine the requirement for polyamines in gibberellin (GA) induced internode growth polyamine content was measured in internodes of peas of various internode phenotypes (slender, tall, dwarf, nana) with and without applied gibberellin (GA(3)) and polyamine synthesis inhibitors. Polyamines were assayed as dansyl derivatives which were separated by reverse phase high performance liquid chromatography and detected by fluorescence spectrophotometry. The amounts of polyamines in the different genetic lines of peas, which differed in internode lengths and extractable GA content, correlated with the extent of internode elongation. High polyamine concentrations were associated with young internodes and decreased with internode expansion. Extremely short internodes of nana plants without GA exhibited equal or higher amine concentrations relative to internodes of other lines of peas and GA-stimulated nana seedlings. The polyamine synthesis inhibitors, alpha-difluoromethylornithine and alpha-difluoromethylarginine, independently or in combination, inhibited polyamine accumulation and internode elongation of tall peas and GA-stimulated nana plants. Agmatine and putrescine restored growth and endogenous polyamine content to variable degrees. However, exogenous polyamines were not effective in promoting growth unless intracellular amines were partially depleted.These results suggest that polyamines do not have a role in cell elongation, but may be required to support cell proliferation. Polyamines do not mediate the entire action of GA in internode growth of peas since GA induction of growth involves both cell division and cell elongation, whereas polyamines appear to affect cell division only.

  17. The Location of Genes Governing Long First Internode of Corn

    PubMed Central

    Troyer, A. F.

    1997-01-01

    Knowing breeding behavior and cytological location of traits helps breeders. My objective was to locate dominant genes for long first internode of corn (Zea mays L.). I determined that Hopi Indian corn PI213733 (variety Komona) displayed the trait and grew well in the U.S. Corn Belt. I crossed PI213733 to 26 translocation tester stocks in Minnesota inbred A188 background, backcrossed semi-sterile plants carrying the translocation to A188 the next generation, and grew the segregating generation planted in trenches 15 cm deep with ridges of dirt 10 cm high one year, in trenches 25 cm deep the other year and also at normal (6 cm) depth. Emerged plants were classified for semi-sterility or for normal pollen. I concluded from multiple testers for each chromosome arm that dominant genes for long first internode are located (chromosome and region) on 3S, on 6 near the centromere, and on 9S; spurious associations occurred for two testers. Measurement of cell lengths indicated that PI213733 had more cells than A188 both in upper and in lower mesocotyl sections and that lower, older cells elongated sooner. I found a normal-sized kernel with twin embryos that developed two long first internode seedlings indicating that the amount of endosperm did not limit mesocotyl growth. PMID:9093865

  18. Changes in diurnal patterns within the Populus transcriptome and metabolome in response to photoperiod variation.

    PubMed

    Hoffman, Daniel E; Jonsson, Pär; Bylesjö, Max; Trygg, Johan; Antti, Henrik; Eriksson, Maria E; Moritz, Thomas

    2010-08-01

    Changes in seasonal photoperiod provides an important environmental signal that affects the timing of winter dormancy in perennial, deciduous, temperate tree species, such as hybrid aspen (Populus tremula x Populus tremuloides). In this species, growth cessation, cold acclimation and dormancy are induced in the autumn by the detection of day-length shortening that occurs at a given critical day length. Important components in the detection of such day-length changes are photoreceptors and the circadian clock, and many plant responses at both the gene regulation and metabolite levels are expected to be diurnal. To directly examine this expectation and study components in these events, here we report transcriptomic and metabolomic responses to a change in photoperiod from long to short days in hybrid aspen. We found about 16% of genes represented on the arrays to be diurnally regulated, as assessed by our pre-defined criteria. Furthermore, several of these genes were involved in circadian-associated processes, including photosynthesis and primary and secondary metabolism. Metabolites affected by the change in photoperiod were mostly involved in carbon metabolism. Taken together, we have thus established a molecular catalog of events that precede a response to winter.

  19. Lignification in rapidly elongating internodes of deep water rice as a limiting factor in growth

    SciTech Connect

    Sauter, M.; Kende, H. )

    1990-05-01

    Internodes of deep water rice are induced to elongate rapidly by partial submergence, or by treatment with ethylene or gibberellin. This growth response is based, in part, on enhanced cell elongation and an increase in the size of the internodal growing zone. For this to occur, processes that limit growth, e.g. lignification, must be delayed. We examined the activity and distribution of two enzymes of the lignin biosynthetic pathway, phenylalanine ammonia-lyase (PAL) and coniferylalcohol dehydrogenase (CAD) in rapidly growing and control internodes. CAD activity decreased in the rapidly growing region of submerged or gibberellin-treated internodes to about 25% of the activity found in air-grown control internodes. No comparable change in CAD activity was observed in the older, non-growing portions of the internodes. PAL activity changed in similar fashion upon induction of rapid growth.

  20. [The roles of microtubule in internodal cell elongation (Nitellopsis obtusa)].

    PubMed

    Yu, Rong; Yuan, Ming; Zhu, Guo Li; Wang, Xue Chen

    2004-04-01

    The relationship between cell elongation and microtubules (MTs) was investigated in characean internodal cells (Nitellops obtusa). First, we examined the immunofluorescent localization of MTs in different living stages under confocal laser scanning microscope. In young, rapidly elongating cells, MTs were predominantly transverse to the long axis of the cell. As the relative growth rate fell, transverse MTs gradually decreased, and in non-growing cells, longitudinally oriented cortical MTs became most pronounced. Moreover, cells in different living stages responded to the treatment of oryzalin (microtubule-disrupting agent) differently, young active internodal cells seemed to be more sensitive. After 40 min incubation of 10 micromol/L oryzalin, nearly all cortical MTs in the elongating cells depolymerized. However, in the old, non-growing cells, some MT fragments still remained after 3 h treatment of oryzalin. Second, we measured the cell growth rates with and without the treatment of oryzalin. In young growing cells treated with 10 micromol/L oryzalin, the elongation rates were inhibited obviously. When the oryzalin was removed, the elongation rates could be recovered to some extent. Interestingly, a time-gap existed between microtubule disassembly (40 min) and cessation of cell elongation (100 min). Our data confirmed the evidence that MTs are involved in cell elongation.

  1. Proteomics of Leaf Tissues from Populus

    SciTech Connect

    Hurst, Gregory {Greg} B; Yang, Xiaohan; Tschaplinski, Timothy J; Tuskan, Gerald A; Lankford, Patricia K; Shah, Manesh B; Jawdy, Sara; Gunter, Lee E; Engle, Nancy L

    2010-01-01

    Trees of the genus Populus are farmed commercially for wood and fiber, and are a potential bioenergy crop. As a scientific model organism, P. trichocarpa was the first forest tree for which the genome sequence has been determined. Knowledge of the Populus proteome will provide a deeper understanding of gene expression patterns in various tissues of the plant. To build on our previous profile of the proteome of xylem tissue in Populus (Kalluri et al., Proteomics 2009, 9, 4871), we are currently developing methods for studying the proteome of Populus leaves.

  2. Effect of Limb Lengthening on Internodal Length and Conduction Velocity of Peripheral Nerve

    PubMed Central

    Gillingwater, Thomas H.; Anderson, Heather; Cottrell, David; Sherman, Diane L.; Ribchester, Richard R.; Brophy, Peter J.

    2013-01-01

    The influences of axon diameter, myelin thickness, and internodal length on the velocity of conduction of peripheral nerve action potentials are unclear. Previous studies have demonstrated a strong dependence of conduction velocity on internodal length. However, a theoretical analysis has suggested that this relationship may be lost above a nodal separation of ∼0.6 mm. Here we measured nerve conduction velocities in a rabbit model of limb lengthening that produced compensatory increases in peripheral nerve growth. Divided tibial bones in one hindlimb were gradually lengthened at 0.7 mm per day using an external frame attached to the bone. This was associated with a significant increase (33%) of internodal length (0.95–1.3 mm) in axons of the tibial nerve that varied in proportion to the mechanical strain in the nerve of the lengthened limb. Axonal diameter, myelin thickness, and g-ratios were not significantly altered by limb lengthening. Despite the substantial increase in internodal length, no significant change was detected in conduction velocity (∼43 m/s) measured either in vivo or in isolated tibial nerves. The results demonstrate that the internode remains plastic in the adult but that increases in internodal length of myelinated adult nerve axons do not result in either deficiency or proportionate increases in their conduction velocity and support the view that the internodal lengths of nerves reach a plateau beyond which their conduction velocities are no longer sensitive to increases in internodal length. PMID:23467369

  3. Profile based image analysis for identification of chopped biomass stem nodes and internodes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Because of their significant variation in chemical composition, segregation of chopped biomass into nodes and internodes helps in efficient utilization of these feedstocks. Stem internodes having low ash content are a better feedstock for bioenergy and biofuel applications than nodes. However, separ...

  4. Trade-offs between xylem hydraulic properties, wood anatomy and yield in Populus.

    PubMed

    Hajek, Peter; Leuschner, Christoph; Hertel, Dietrich; Delzon, Sylvain; Schuldt, Bernhard

    2014-07-01

    Trees face the dilemma that achieving high plant productivity is accompanied by a risk of drought-induced hydraulic failure due to a trade-off in the trees' vascular system between hydraulic efficiency and safety. By investigating the xylem anatomy of branches and coarse roots, and measuring branch axial hydraulic conductivity and vulnerability to cavitation in 4-year-old field-grown aspen plants of five demes (Populus tremula L. and Populus tremuloides Michx.) differing in growth rate, we tested the hypotheses that (i) demes differ in wood anatomical and hydraulic properties, (ii) hydraulic efficiency and safety are related to xylem anatomical traits, and (iii) aboveground productivity and hydraulic efficiency are negatively correlated to cavitation resistance. Significant deme differences existed in seven of the nine investigated branch-related anatomical and hydraulic traits but only in one of the four coarse-root-related anatomical traits; this likely is a consequence of high intra-plant variation in root morphology and the occurrence of a few 'high-conductivity roots'. Growth rate was positively related to branch hydraulic efficiency (xylem-specific conductivity) but not to cavitation resistance; this indicates that no marked trade-off exists between cavitation resistance and growth. Both branch hydraulic safety and hydraulic efficiency significantly depended on vessel size and were related to the genetic distance between the demes, while the xylem pressure causing 88% loss of hydraulic conductivity (P88 value) was more closely related to hydraulic efficiency than the commonly used P50 value. Deme-specific variation in the pit membrane structure may explain why vessel size was not directly linked to growth rate. We conclude that branch hydraulic efficiency is an important growth-influencing trait in aspen, while the assumed trade-off between productivity and hydraulic safety is weak.

  5. Characean internodal cells as a model system for the study of cell organization.

    PubMed

    Foissner, Ilse; Wasteneys, Geoffrey O

    2014-01-01

    Giant internodal cells of characean green algae have been widely used for studying cellular physiology. This review emphasizes their significance for understanding cytoarchitecture and cytoplasmic reorganization. The cytoarchitecture of internodal cells undergoes pronounced, cytoskeleton-dependent changes during development and in response to environmental cues. Under bright light, internodes develop alternating bands of acid and alkaline pH at their surface that correlate with the differential size and abundance of cortical organelles and, in the genus Chara, with the size and distribution of convoluted plasma membrane domains known as charasomes. Wounding induces responses ranging from chloroplast detachment to deposition of wound walls. These properties and the possibility for mechanical manipulation make the internodal cell ideal for exploring plasma membrane domains, organelle interactions, vesicle trafficking, and local cell wall deposition. The significance of this model system will further increase with the application of molecular biological methods in combination with metabolomics and proteomics.

  6. Characean internodal cells as a model system for the study of cell organization.

    PubMed

    Foissner, Ilse; Wasteneys, Geoffrey O

    2014-01-01

    Giant internodal cells of characean green algae have been widely used for studying cellular physiology. This review emphasizes their significance for understanding cytoarchitecture and cytoplasmic reorganization. The cytoarchitecture of internodal cells undergoes pronounced, cytoskeleton-dependent changes during development and in response to environmental cues. Under bright light, internodes develop alternating bands of acid and alkaline pH at their surface that correlate with the differential size and abundance of cortical organelles and, in the genus Chara, with the size and distribution of convoluted plasma membrane domains known as charasomes. Wounding induces responses ranging from chloroplast detachment to deposition of wound walls. These properties and the possibility for mechanical manipulation make the internodal cell ideal for exploring plasma membrane domains, organelle interactions, vesicle trafficking, and local cell wall deposition. The significance of this model system will further increase with the application of molecular biological methods in combination with metabolomics and proteomics. PMID:24952921

  7. The Brassica rapa elongated internode (EIN) gene encodes phytochrome B.

    PubMed

    Devlin, P F; Somers, D E; Quail, P H; Whitelam, G C

    1997-06-01

    The elongated internode (ein) mutation of Brassica rapa leads to a deficiency in immunochemically detectable phytochrome B. Molecular analysis of the PHYB gene from ein indicates a deletion in the flanking DNA 5' of the ATG start codon, which could interfere either with PHYB transcription or processing of the PHYB transcript. Restriction fragment length polymorphisms and inverse PCR fragments generated from the PHYB gene of wild-type and ein seedlings demonstrate the deletion to be 500 bp in length. Seedlings of heterozygote, EIN/ein, contain about 50% of the level of immunochemically detectable phytochrome B of equivalent wild-type EIN/EIN seedlings. Etiolated seedlings of EIN/ein show a responsiveness to red light almost intermediate between that of ein/ein and EIN/EIN homozygotes. Furthermore, whereas the ein/ein homozygote is poorly responsive to low red/far-red ratio light, the presence of one functional allele of EIN in the heterozygote confers an elongation response intermediate between that of the homozygotes EIN/EIN and ein/ein in these light conditions. The partial dominance of ein indicates a close relationship between phytochrome B level and phenotype.

  8. Plasmalogen phospholipids protect internodal myelin from oxidative damage.

    PubMed

    Luoma, Adrienne M; Kuo, Fonghsu; Cakici, Ozgur; Crowther, Michelle N; Denninger, Andrew R; Avila, Robin L; Brites, Pedro; Kirschner, Daniel A

    2015-07-01

    Reactive oxygen species (ROS) are implicated in a range of degenerative conditions, including aging, neurodegenerative diseases, and neurological disorders. Myelin is a lipid-rich multilamellar sheath that facilitates rapid nerve conduction in vertebrates. Given the high energetic demands and low antioxidant capacity of the cells that elaborate the sheaths, myelin is considered intrinsically vulnerable to oxidative damage, raising the question whether additional mechanisms prevent structural damage. We characterized the structural and biochemical basis of ROS-mediated myelin damage in murine tissues from both central nervous system (CNS) and peripheral nervous system (PNS). To determine whether ROS can cause structural damage to the internodal myelin, whole sciatic and optic nerves were incubated ex vivo with a hydroxyl radical-generating system consisting of copper (Cu), hydrogen peroxide (HP), and ortho-phenanthroline (OP). Quantitative assessment of unfixed tissue by X-ray diffraction revealed irreversible compaction of myelin membrane stacking in both sciatic and optic nerves. Incubation in the presence of the hydroxyl radical scavenger sodium formate prevented this damage, implicating hydroxyl radical species. Myelin membranes are particularly enriched in plasmalogens, a class of ether-linked phospholipids proposed to have antioxidant properties. Myelin in sciatic nerve from plasmalogen-deficient (Pex7 knockout) mice was significantly more vulnerable to Cu/OP/HP-mediated ROS-induced compaction than myelin from WT mice. Our results directly support the role of plasmalogens as endogenous antioxidants providing a defense that protects ROS-vulnerable myelin.

  9. Energy values of nine Populus clones

    SciTech Connect

    Strong, T.F.

    1980-01-01

    This paper compares calorific values for components of nine Populus clones. The components include stem wood, stem bark, and branches. Also compared are calorific values for clones of balsam poplar and black cottonwood parentages.

  10. Wood properties of Populus and Betula in long-term exposure to elevated CO₂ and O₃.

    PubMed

    Kostiainen, Katri; Saranpää, Pekka; Lundqvist, Sven-Olof; Kubiske, Mark E; Vapaavuori, Elina

    2014-06-01

    We studied the interactive effects of elevated concentrations of CO2 and O3 on radial growth and wood properties of four trembling aspen (Populus tremuloides Michx.) clones and paper birch (Betula papyrifera Marsh.) saplings. The material for the study was collected from the Aspen FACE (free-air CO2 enrichment) experiment in Rhinelander (WI, USA). Trees had been exposed to four treatments [control, elevated CO2 (560 ppm), elevated O3 (1.5 times ambient) and combined CO2 + O3 ] during growing seasons 1998-2008. Most treatment responses were observed in the early phase of experiment. Our results show that the CO2- and O3-exposed aspen trees displayed a differential balance between efficiency and safety of water transport. Under elevated CO2, radial growth was enhanced and the trees had fewer but hydraulically more efficient larger diameter vessels. In contrast, elevated O3 decreased radial growth and the diameters of vessels and fibres. Clone-specific decrease in wood density and cell wall thickness was observed under elevated CO2 . In birch, the treatments had no major impacts on wood anatomy or wood density. Our study indicates that short-term impact studies conducted with young seedlings may not give a realistic view of long-term ecosystem responses.

  11. No Evidence of Geographical Structure of Salicinoid Chemotypes within Populus Tremula

    PubMed Central

    Keefover-Ring, Ken; Ahnlund, Maria; Abreu, Ilka Nacif; Jansson, Stefan; Moritz, Thomas; Albrectsen, Benedicte Riber

    2014-01-01

    Salicinoids are well-known defense compounds in salicaceous trees and careful screening at the population level is warranted to fully understand their diversity and function. European aspen, Populus tremula, is a foundation species in Eurasia and highly polymorphic in Sweden. We exhaustively surveyed 102 replicated genotypes from the Swedish Aspen collection (SwAsp) for foliar salicinoids using UHPLC-ESI-TOF/MS and identified nine novel compounds, bringing the total to 19 for this species. Salicinoid structure followed a modular architecture of a salicin skeleton with added side groups, alone or in combination. Two main moieties, 2′-cinnamoyl and 2′-acetyl, grouped the SwAsp population into four distinct chemotypes, and the relative allocation of salicinoids was remarkably constant between different environments, implying a highly channeled biosynthesis of these compounds. Slightly more than half of the SwAsp genotypes belonged to the cinnamoyl chemotype. A fraction synthesized the acetyl moiety alone (∼7%) or in combination with cinnamoyl (∼2%), and close to forty percent lacked either of the two characteristic moieties, and thus resemble P. tremuloides in their salicinoid profile. The two most abundant chemotypes were evenly distributed throughout Sweden, unlike geographical patterns reported for SwAsp phenology traits, plant defense genes, and herbivore community associations. Here we present the salicinoid characterization of the SwAsp collection as a resource for future studies of aspen chemical ecology, salicinoid biosynthesis, and genetics. PMID:25299342

  12. Plant regeneration capacity of callus derived from leaf, stem, and root segments of Populus alba L. x P. grandidentata Michx.

    PubMed

    Son, S H; Hall, R B

    1990-10-01

    Expiants for establishing callus cultures originated from in vitro cultured hybrid poplar (Populus alba L. X P. grandidentata Michx.). Plant regeneration was achieved from established callus cultures derived from stem internodes (SI), leaf discs (LD), and root segments (RS). Shoot regeneration from callus occurred within 4 weeks of culture on most of the media tested. Frequency of shoot formation was greatly increased by subculturing the selected organogenic calli on regeneration media. The highest rate of multiple shoot formation (an average number of 7/SI, 11/LD, and 8/RS) was obtained by using 0.05 μM IBA in combination with 22.5 μM 2iP, 22.5 μM zeatin, and 12.5 μM 2iP, respectively. Regenerated shoots were easily rooted in polyterra(™) peat plugs in transparent plastic boxes. The rooted plantlets were subsequently transferred to pots containing an artificial potting mix. PMID:24226948

  13. ptr-MIR169 is a posttranscriptional repressor of PtrHAP2 during vegetative bud dormancy period of aspen (Populus tremuloides) trees

    SciTech Connect

    Potkar, Rewati; Recla, Jill; Busov, Victor

    2013-02-15

    Highlights: ► We show a novel microRNA-mediated mechanism for control of bud dormancy in trees. ► ptr-MIR169a and PtrHAP2–5 gene showed inverse expression during dormancy period. ► The PtrHAP2–5 decline in abundance correlated with high ptr-MIR169a levels. ► PtrHAP2–5 cleavage occurred at the miR169 site during PtrHAP2–5 transcript decline. ► Our results show that miR169 attenuates PtrHAP2–5 transcript during dormancy. -- Abstract: Dormancy is a mechanism evolved in woody perennial plants to survive the winter freezing and dehydration stress via temporary suspension of growth. We have identified two aspen microRNAs (ptr-MIR169a and ptr-MIR169h) which were highly and specifically expressed in dormant floral and vegetative buds. ptr-MIR169a and its target gene PtrHAP2–5 showed inverse expression patterns during the dormancy period. ptr-MIR169a transcript steadily increased through the first half of the dormancy period and gradually declined with the approach of active growing season. PtrHAP2–5 abundance was higher in the beginning of the dormancy period but rapidly declined thereafter. The decline of PtrHAP2–5 correlated with the high levels of ptr-MIR169a accumulation, suggesting miR169-mediated attenuation of the target PtrHAP2–5 transcript. We experimentally verified the cleavage of PtrHAP2–5 at the predicted miR169a site at the time when PtrHAP2–5 transcript decline was observed. HAP2 is a subunit of a nuclear transcription factor Y (NF-Y) complex consisting of two other units, HAP3 and HAP5. Using digital expression profiling we show that poplar HAP2 and HAP5 are preferentially detected in dormant tissues. Our study shows that microRNAs play a significant and as of yet unknown and unstudied role in regulating the timing of bud dormancy in trees.

  14. ptr-MIR169 is a posttranscriptional repressor of PtrHAP2 during vegetative bud dormancy period of aspen (Populus tremuloides) trees.

    PubMed

    Potkar, Rewati; Recla, Jill; Busov, Victor

    2013-02-15

    Dormancy is a mechanism evolved in woody perennial plants to survive the winter freezing and dehydration stress via temporary suspension of growth. We have identified two aspen microRNAs (ptr-MIR169a and ptr-MIR169h) which were highly and specifically expressed in dormant floral and vegetative buds. ptr-MIR169a and its target gene PtrHAP2-5 showed inverse expression patterns during the dormancy period. ptr-MIR169a transcript steadily increased through the first half of the dormancy period and gradually declined with the approach of active growing season. PtrHAP2-5 abundance was higher in the beginning of the dormancy period but rapidly declined thereafter. The decline of PtrHAP2-5 correlated with the high levels of ptr-MIR169a accumulation, suggesting miR169-mediated attenuation of the target PtrHAP2-5 transcript. We experimentally verified the cleavage of PtrHAP2-5 at the predicted miR169a site at the time when PtrHAP2-5 transcript decline was observed. HAP2 is a subunit of a nuclear transcription factor Y (NF-Y) complex consisting of two other units, HAP3 and HAP5. Using digital expression profiling we show that poplar HAP2 and HAP5 are preferentially detected in dormant tissues. Our study shows that microRNAs play a significant and as of yet unknown and unstudied role in regulating the timing of bud dormancy in trees.

  15. Clone history shapes Populus drought responses.

    PubMed

    Raj, Sherosha; Bräutigam, Katharina; Hamanishi, Erin T; Wilkins, Olivia; Thomas, Barb R; Schroeder, William; Mansfield, Shawn D; Plant, Aine L; Campbell, Malcolm M

    2011-07-26

    Just as animal monozygotic twins can experience different environmental conditions by being reared apart, individual genetically identical trees of the genus Populus can also be exposed to contrasting environmental conditions by being grown in different locations. As such, clonally propagated Populus trees provide an opportunity to interrogate the impact of individual environmental history on current response to environmental stimuli. To test the hypothesis that current responses to an environmental stimulus, drought, are contingent on environmental history, the transcriptome- level drought responses of three economically important hybrid genotypes-DN34 (Populus deltoides × Populus nigra), Walker [P. deltoides var. occidentalis × (Populus laurifolia × P. nigra)], and Okanese [Walker × (P. laurifolia × P. nigra)]-derived from two different locations were compared. Strikingly, differences in transcript abundance patterns in response to drought were based on differences in geographic origin of clones for two of the three genotypes. This observation was most pronounced for the genotypes with the longest time since establishment and last common propagation. Differences in genome-wide DNA methylation paralleled the transcriptome level trends, whereby the clones with the most divergent transcriptomes and clone history had the most marked differences in the extent of total DNA methylation, suggesting an epigenomic basis for the clone history-dependent transcriptome divergence. The data provide insights into the interplay between genotype and environment in the ecologically and economically important Populus genus, with implications for the industrial application of Populus trees and the evolution and persistence of these important tree species and their associated hybrids. PMID:21746919

  16. Burial Depth and Stolon Internode Length Independently Affect Survival of Small Clonal Fragments

    PubMed Central

    Dong, Bi-Cheng; Liu, Rui-Hua; Zhang, Qian; Li, Hong-Li; Zhang, Ming-Xiang; Lei, Guang-Chun; Yu, Fei-Hai

    2011-01-01

    Disturbance can fragment plant clones into different sizes and unstabilize soils to different degrees, so that clonal fragments of different sizes can be buried in soils at different depths. As a short-term storage organ, solon internode may help fragmented clones of stoloniferous plants to withstand deeper burial in soils. We address (1) whether burial in soils decreases survival and growth of small clonal fragments, and (2) whether increasing internode length increases survival and growth of small fragments under burial. We conducted an experiment with the stoloniferous, invasive herb Alternanthera philoxeroides, in which single-node fragments with stolon internode of 0, 2, 4 and 8 cm were buried in soils at 0, 2, 4 and 8 cm depth, respectively. Increasing burial depth significantly reduced survival of the A. philoxeroides plants and increased root to shoot ratio and total stolon length, but did not change growth measures. Increasing internode length significantly increased survival and growth measures, but there was no interaction effect with burial depth on any traits measured. These results indicate that reserves stored in stolon internodes can contribute to the fitness of the A. philoxeroides plants subject to disturbance. Although burial reduced the regeneration capacity of the A. philoxeroides plants, the species may maintain the fitness by changing biomass allocation and stolon length once it survived the burial. Such responses may play an important role for A. philoxeroides in establishment and invasiveness in frequently disturbed habitats. PMID:21912652

  17. Tuning of Ranvier node and internode properties in myelinated axons to adjust action potential timing

    PubMed Central

    Ford, Marc C.; Alexandrova, Olga; Cossell, Lee; Stange-Marten, Annette; Sinclair, James; Kopp-Scheinpflug, Conny; Pecka, Michael; Attwell, David; Grothe, Benedikt

    2015-01-01

    Action potential timing is fundamental to information processing; however, its determinants are not fully understood. Here we report unexpected structural specializations in the Ranvier nodes and internodes of auditory brainstem axons involved in sound localization. Myelination properties deviated significantly from the traditionally assumed structure. Axons responding best to low-frequency sounds had a larger diameter than high-frequency axons but, surprisingly, shorter internodes. Simulations predicted that this geometry helps to adjust the conduction velocity and timing of action potentials within the circuit. Electrophysiological recordings in vitro and in vivo confirmed higher conduction velocities in low-frequency axons. Moreover, internode length decreased and Ranvier node diameter increased progressively along the distal axon segments, which simulations show was essential to ensure precisely timed depolarization of the giant calyx of Held presynaptic terminal. Thus, individual anatomical parameters of myelinated axons can be tuned to optimize pathways involved in temporal processing. PMID:26305015

  18. Epigenomics of Development in Populus

    SciTech Connect

    Strauss, Steve; Freitag, Michael; Mockler, Todd

    2013-01-10

    We conducted research to determine the role of epigenetic modifications during tree development using poplar (Populus trichocarpa), a model woody feedstock species. Using methylated DNA immunoprecipitation (MeDIP) or chromatin immunoprecipitation (ChIP), followed by high-throughput sequencing, we are analyzed DNA and histone methylation patterns in the P. trichocarpa genome in relation to four biological processes: bud dormancy and release, mature organ maintenance, in vitro organogenesis, and methylation suppression. Our project is now completed. We have 1) produced 22 transgenic events for a gene involved in DNA methylation suppression and studied its phenotypic consequences; 2) completed sequencing of methylated DNA from eleven target tissues in wildtype P. trichocarpa; 3) updated our customized poplar genome browser using the open-source software tools (2.13) and (V2.2) of the P. trichocarpa genome; 4) produced summary data for genome methylation in P. trichocarpa, including distribution of methylation across chromosomes and in and around genes; 5) employed bioinformatic and statistical methods to analyze differences in methylation patterns among tissue types; and 6) used bisulfite sequencing of selected target genes to confirm bioinformatics and sequencing results, and gain a higher-resolution view of methylation at selected genes 7) compared methylation patterns to expression using available microarray data. Our main findings of biological significance are the identification of extensive regions of the genome that display developmental variation in DNA methylation; highly distinctive gene-associated methylation profiles in reproductive tissues, particularly male catkins; a strong whole genome/all tissue inverse association of methylation at gene bodies and promoters with gene expression; a lack of evidence that tissue specificity of gene expression is associated with gene methylation; and evidence that genome methylation is a significant impediment to tissue

  19. The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)

    SciTech Connect

    Tuskan, Gerald A; DiFazio, Stephen P; Jansson, Bo S; Bohlmann, J.; Grigoriev, I.; Hellsten, U.; Putman, N.; Ralph, S.; Rombauts, S.; Salamov, A.; Schein, J.; Sterck, L.; Aerts, A.; Bhalerao, R. R.; Bhalerao, Rishikesh P; Blaudez, D.; Boerjan, W.; Brun, A.; Brunner, A.; Busov, V.; Campbell, M.; Larimer, Frank W; Detter, J C; Richardson, P M; Chen, Gwo-Liang; Gunter, Lee E; Kalluri, Udaya C; LoCascio, Philip F; Uberbacher, Edward C; Yin, Tongming

    2006-01-01

    We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

  20. The genome of black cottonwood, Populus trichocarpa (Torr.&Gray)

    SciTech Connect

    Tuskan, G.A.; DiFazio, S.; Jansson, S.; Bohlmann, J.; Grigoriev,I.; Hellsten, U.; Putnam, N.; Ralph, S.; Rombauts, S.; Salamov, A.; Schein, J.; Sterck, L.; Aerts, A.; Bhalerao, R.R.; Bhalerao, R.P.; Blaudez, D.; Boerjan, W.; Brun, A.; Brunner, A.; Busov, V.; Campbell, M.; Carlson, J.; Chalot, M.; Chapman, J.; Chen, G.-L.; Cooper, D.; Coutinho,P.M.; Couturier, J.; Covert, S.; Cronk, Q.; Cunningham, R.; Davis, J.; Degroeve, S.; Dejardin, A.; dePamphillis, C.; Detter, J.; Dirks, B.; Dubchak, I.; Duplessis, S.; Ehiting, J.; Ellis, B.; Gendler, K.; Goodstein, D.; Gribskov, M.; Grimwood, J.; Groover, A.; Gunter, L.; Hamberger, B.; Heinze, B.; Helariutta, Y.; Henrissat, B.; Holligan, D.; Holt, R.; Huang, W.; Islam-Faridi, N.; Jones, S.; Jones-Rhoades, M.; Jorgensen, R.; Joshi, C.; Kangasjarvi, J.; Karlsson, J.; Kelleher, C.; Kirkpatrick, R.; Kirst, M.; Kohler, A.; Kalluri, U.; Larimer, F.; Leebens-Mack, J.; Leple, J.-C.; Locascio, P.; Lou, Y.; Lucas, S.; Martin,F.; Montanini, B.; Napoli, C.; Nelson, D.R.; Nelson, D.; Nieminen, K.; Nilsson, O.; Peter, G.; Philippe, R.; Pilate, G.; Poliakov, A.; Razumovskaya, J.; Richardson, P.; Rinaldi, C.; Ritland, K.; Rouze, P.; Ryaboy, D.; Schmutz, J.; Schrader, J.; Segerman, B.; Shin, H.; Siddiqui,A.; Sterky, F.; Terry, A.; Tsai, C.; Uberbacher, E.; Unneberg, P.; Vahala, J.; Wall, K.; Wessler, S.; Yang, G.; Yin, T.; Douglas, C.; Marra,M.; Sandberg, G.; Van der Peer, Y.; Rokhsar, D.

    2006-09-01

    We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. Over 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event, with approximately 8,000 pairs of duplicated genes from that event surviving in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication and gross chromosomal rearrangement appear to proceed substantially slower in Populus relative to Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average between 1.4-1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with disease resistance, meristem development, metabolite transport and lignocellulosic wall biosynthesis.

  1. Identification of nodes and internodes of chopped biomass stems by Image analysis using profile curvature and slope

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Morphological components of biomass stems vary in their chemical composition and they can be better utilized when processed after segregation. Within the stem, nodes and internodes have significantly different compositions. The internodes have low ash content and are a better feedstock for bioenergy...

  2. Axon classes and internodal growth in the ventral spinal root L7 of adult and developing cats.

    PubMed Central

    Nilsson, I; Berthold, C H

    1988-01-01

    Internodal length, number of myelin sheath lamellae and axon diameter were estimated in samples of nerve fibres reconstructed from transverse sections (EM and LM) of the L7 ventral spinal root of adult cats, kittens and cat fetuses. The axon calibre spectrum was unimodal in the youngest fetuses, became bimodal at 47 days after mating, i.e. about 2 weeks before birth (63 days after mating) and trimodal at 1 week of postnatal age. Alpha-axons received myelin during the period 40-45 to 50-55 days after mating while gamma-axons became myelinated from 60-63 days after mating to 2-3 weeks of postnatal age. The mean length of the first completely myelinated internodes measured 139 microns and 209 microns in the alpha- and gamma-fibre group respectively. The adult mean values were 1390 microns and 640 microns respectively. The average internodal elongation was x 10 and x 3 in the two fibre groups, whereas the longitudinal growth of the whole ventral root was x 5.4 and x 3.5. A combined linlog function could be fitted to describe the regression between internodal length and axon diameter and was established from birth onwards. The separate alpha- and gamma-fibre samples were best described by linear functions, the alpha internodal length being independent of axon diameter while the gamma internodal length increased linearly with axon diameter. The amount of internodal myelin increased linearly with increasing mantle area of the internodal axon. The mean amount of internodal myelin of alpha-fibres showed two periods of intense growth; one from the start of myelination to 2 months postnatally and the other between 4 and 6 months of age. The mean length of the lamellar spiral forming the myelin sheath showed about the same increase per unit length of axon circumference (about 160:1) in both alpha- and gamma-fibre groups as long as longitudinal internodal growth persisted. PMID:3417553

  3. Terra Populus and DataNet Collaboration

    NASA Astrophysics Data System (ADS)

    Kugler, T.; Ruggles, S.; Fitch, C. A.; Clark, P. D.; Sobek, M.; Van Riper, D.

    2012-12-01

    Terra Populus, part of NSF's new DataNet initiative, is developing organizational and technical infrastructure to integrate, preserve, and disseminate data describing changes in the human population and environment over time. Terra Populus will incorporate large microdata and aggregate census datasets from the United States and around the world, as well as land use, land cover, climate and other environmental datasets. These data are widely dispersed, exist in a variety of data structures, have incompatible or inadequate metadata, and have incompatible geographic identifiers. Terra Populus is developing methods of integrating data from different domains and translating across data structures based on spatio-temporal linkages among data contents. The new infrastructure will enable researchers to identify and merge data from heterogeneous sources to study the relationships between human behavior and the natural world. Terra Populus will partner with data archives, data producers, and data users to create a sustainable international organization that will guarantee preservation and access over multiple decades. Terra Populus is also collaborating with the other projects in the DataNet initiative - DataONE, the DataNet Federation Consortium (DFC) and Sustainable Environment-Actionable Data (SEAD). Taken together, the four projects address aspects of the entire data lifecycle, including planning, collection, documentation, discovery, integration, curation, preservation, and collaboration; and encompass a wide range of disciplines including earth sciences, ecology, social sciences, hydrology, oceanography, and engineering. The four projects are pursuing activities to share data, tools, and expertise between pairs of projects as well as collaborating across the DataNet program on issues of cyberinfrastructure and community engagement. Topics to be addressed through program-wide collaboration include technical, organizational, and financial sustainability; semantic

  4. Barcoding Poplars (Populus L.) from Western China

    PubMed Central

    Shang, Huiying; Dong, Miao; Wang, Gaini; He, Xinyu; Zhao, Changming; Mao, Kangshan

    2013-01-01

    Background Populus is an ecologically and economically important genus of trees, but distinguishing between wild species is relatively difficult due to extensive interspecific hybridization and introgression, and the high level of intraspecific morphological variation. The DNA barcoding approach is a potential solution to this problem. Methodology/Principal Findings Here, we tested the discrimination power of five chloroplast barcodes and one nuclear barcode (ITS) among 95 trees that represent 21 Populus species from western China. Among all single barcode candidates, the discrimination power is highest for the nuclear ITS, progressively lower for chloroplast barcodes matK (M), trnG-psbK (G) and psbK-psbI (P), and trnH-psbA (H) and rbcL (R); the discrimination efficiency of the nuclear ITS (I) is also higher than any two-, three-, or even the five-locus combination of chloroplast barcodes. Among the five combinations of a single chloroplast barcode plus the nuclear ITS, H+I and P+I differentiated the highest and lowest portion of species, respectively. The highest discrimination rate for the barcodes or barcode combinations examined here is 55.0% (H+I), and usually discrimination failures occurred among species from sympatric or parapatric areas. Conclusions/Significance In this case study, we showed that when discriminating Populus species from western China, the nuclear ITS region represents a more promising barcode than any maternally inherited chloroplast region or combination of chloroplast regions. Meanwhile, combining the ITS region with chloroplast regions may improve the barcoding success rate and assist in detecting recent interspecific hybridizations. Failure to discriminate among several groups of Populus species from sympatric or parapatric areas may have been the result of incomplete lineage sorting, frequent interspecific hybridizations and introgressions. We agree with a previous proposal for constructing a tiered barcoding system in plants

  5. Catalyst Transport in Corn Stover Internodes: Elucidating Transport Mechanisms Using Direct Blue-I

    SciTech Connect

    Viamajala, S.; Selig, M. J.; Vinzant, T. B.; Tucker, M. P.; Himmel, M. E.; McMillan, J. D.; Decker, S. R.

    2006-04-01

    The transport of catalysts (chemicals and enzymes) within plant biomass is believed to be a major bottleneck during thermochemical pretreatment and enzymatic conversion of lignocellulose. Subjecting biomass to size reduction and mechanical homogenization can reduce catalyst transport limitations; however, such processing adds complexity and cost to the over-all process. Using high-resolution light microscopy, we have monitored the transport of an aqueous solution of Direct Blue-I (DB-I) dye through intact corn internodes under a variety of impregnation conditions. DB-I is a hydrophilic anionic dye with affinity for cellulose. This model system has enabled us to visualize likely barriers and mechanisms of catalyst transport in corn stems. Microscopic images were compared with calculated degrees of saturation (i.e., volume fraction of internode void space occupied by dye solution) to correlate impregnation strategies with dye distribution and transport mechanisms. Results show the waxy rind exterior and air trapped within individual cells to be the major barriers to dye transport, whereas the vascular bundles, apoplastic continuum (i.e., the intercellular void space at cell junctions), and fissures formed during the drying process provided the most utilized pathways for transport. Although representing only 20-30% of the internode volume, complete saturation of the apoplast and vascular bundles by fluid allowed dye contact with a majority of the cells in the internode interior.

  6. Constitutive endocytosis in characean internodal cells is independent of an intact actin cytoskeleton.

    PubMed

    Foissner, Ilse; Klima, Andreas

    2008-05-01

    We have investigated constitutive endocytosis in internodal cells of the characean green algae. The endocytic tracer FM1-43 accumulated in distinct plasma membrane domains that are probably enriched in sterol-like substances. Internalization of the dye was active but independent of an intact actin or microtubule cytoskeleton.

  7. Involvement of membrane potential in alkaline band formation by internodal cells of Chara corallina.

    PubMed

    Shimmen, Teruo; Wakabayashi, Akiko

    2008-10-01

    Internodal cells of Chara corallina form alkaline bands on their surface upon illumination via photosynthesis. In the present study, the effect of KCl on alkaline band formation was analyzed. When the extracellular KCl concentration was increased, alkaline band formation was extensively inhibited. Electrophysiological analysis unequivocally showed the need for inner negative membrane potential for alkaline band formation.

  8. Node Detection and Internode Length Estimation of Tomato Seedlings Based on Image Analysis and Machine Learning.

    PubMed

    Yamamoto, Kyosuke; Guo, Wei; Ninomiya, Seishi

    2016-01-01

    Seedling vigor in tomatoes determines the quality and growth of fruits and total plant productivity. It is well known that the salient effects of environmental stresses appear on the internode length; the length between adjoining main stem node (henceforth called node). In this study, we develop a method for internode length estimation using image processing technology. The proposed method consists of three steps: node detection, node order estimation, and internode length estimation. This method has two main advantages: (i) as it uses machine learning approaches for node detection, it does not require adjustment of threshold values even though seedlings are imaged under varying timings and lighting conditions with complex backgrounds; and (ii) as it uses affinity propagation for node order estimation, it can be applied to seedlings with different numbers of nodes without prior provision of the node number as a parameter. Our node detection results show that the proposed method can detect 72% of the 358 nodes in time-series imaging of three seedlings (recall = 0.72, precision = 0.78). In particular, the application of a general object recognition approach, Bag of Visual Words (BoVWs), enabled the elimination of many false positives on leaves occurring in the image segmentation based on pixel color, significantly improving the precision. The internode length estimation results had a relative error of below 15.4%. These results demonstrate that our method has the ability to evaluate the vigor of tomato seedlings quickly and accurately.

  9. Identification of nodes and internodes of chopped biomass stems by Image analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Separating the morphological components of biomass leads to better handling, more efficient processing as well as value added product generation, as these components vary in their chemical composition and can be preferentially utilized. Nodes and internodes of biomass stems have distinct chemical co...

  10. Modelling photo-modulated internode elongation in growing glasshouse cucumber canopies.

    PubMed

    Kahlen, Katrin; Stützel, Hartmut

    2011-05-01

    • Growing glasshouse plant canopies are exposed to natural fluctuations in light quantity, and the dynamically changing canopy architecture induces local variations in light quality. This modelling study aimed to analyse the importance of both light signals for an accurate prediction of individual internode lengths. • We conceptualized two model approaches for estimating final internode lengths (FILs). The first one is only photosynthetically active radiation (PAR)-sensitive and ignores canopy architecture, whereas the second approach uses a functional-structural growth model for considering variations in both PAR and red : far-red (R : FR) ratio (L-Cucumber). Internode lengths measured in three experiments were used for model parameterization and evaluation. • The overall trends for the simulated FILs using the exclusively PAR-sensitive model approach were already in line with the measured FILs, but they underestimated FILs at higher ranks. L-Cucumber provided considerably better FIL predictions under various light conditions and canopy architectures. • Both light signals are needed for an accurate estimation of the FILs, and only L-Cucumber is able to consider R : FR signals from the growing canopy. Yet this study highlights the significance of the PAR signal for predicting FILs as neighbour effects increase, which indicates a potential role of photosynthate signalling in internode elongation.

  11. Node Detection and Internode Length Estimation of Tomato Seedlings Based on Image Analysis and Machine Learning

    PubMed Central

    Yamamoto, Kyosuke; Guo, Wei; Ninomiya, Seishi

    2016-01-01

    Seedling vigor in tomatoes determines the quality and growth of fruits and total plant productivity. It is well known that the salient effects of environmental stresses appear on the internode length; the length between adjoining main stem node (henceforth called node). In this study, we develop a method for internode length estimation using image processing technology. The proposed method consists of three steps: node detection, node order estimation, and internode length estimation. This method has two main advantages: (i) as it uses machine learning approaches for node detection, it does not require adjustment of threshold values even though seedlings are imaged under varying timings and lighting conditions with complex backgrounds; and (ii) as it uses affinity propagation for node order estimation, it can be applied to seedlings with different numbers of nodes without prior provision of the node number as a parameter. Our node detection results show that the proposed method can detect 72% of the 358 nodes in time-series imaging of three seedlings (recall = 0.72, precision = 0.78). In particular, the application of a general object recognition approach, Bag of Visual Words (BoVWs), enabled the elimination of many false positives on leaves occurring in the image segmentation based on pixel color, significantly improving the precision. The internode length estimation results had a relative error of below 15.4%. These results demonstrate that our method has the ability to evaluate the vigor of tomato seedlings quickly and accurately. PMID:27399708

  12. The internodal axon membrane: electrical excitability and continuous conduction in segmental demyelination.

    PubMed Central

    Bostock, H; Sears, T A

    1978-01-01

    1. Longitudinal action currents were recorded from single undissected myelinated nerve fibres in intact, perfused ventral roots of normal rats and ones treated with diphtheria toxin to produce demyelination. 2. Closely spaced recording electrodes (120 micron), signal averaging and the use of a calibrating current throught the root permitted membrane currents to be determined over 240 micron lengths of nerve. Contour plotting was used to plot membrane current density as a function of space and time. 3. The previous result of Rasminsky & Sears (1972) of delayed saltation in demyelinated nerve fibres was confirmed. 4. In addition a new phenomenon of continuous conduction was observed, along distances of up to 1 1/2 times the afferent internodal distance. The continuous spatial distribution of inward current in these cases showed that electrical excitability was distributed along the internodes. 5. Internodal excitability was also revealed in demyelinated fibres by extra foci of inward current judged to be internodal on the basis of the spacing of the other (nodal) foci. 6. Continuous conduction occurred at velocities in the range of 1.1-2.3 m/sec or roughly 1/20th-1/40th of the velocities expected for normal stretches of the same fibres. 7. The continuous conduction was attributed to conduction along lengths of demyelinated axon. This was supported by estimates of 0.86 and 1.5 muF/cm2 for membrane capacity from the foot of a continuously conducted action potential. 8. The implications of internodal electrical excitability in demyelinated nerve fibres are discussed in relation to (a) recent estimates of the density of sodium channels in intact and homogenized normal nerves, (b) the pathophysiology of demyelinating disease. PMID:690876

  13. Morpho-anatomical traits of two lowest internodes related to lodging resistance in selected genotypes of Triticum

    NASA Astrophysics Data System (ADS)

    Packa, Danuta; Wiwart, Marian; Suchowilska, Elżbieta; Bieńkowska, Teresa

    2015-10-01

    The cross-sections of first and second internodes were analyzed under a light and fluorescence microscopes in six varieties of Triticum spelta, two varieties of T. polonicum, and one variety of T. aestivum. The morphometric parameters of stem cross-sections were measured. The analyzed wheats were characterized by significant differences in traits associated with lodging resistance ie: internode diameter, lumen diameter, stem wall thickness, mechanical layer thickness, area of transverse section, and area of lumen for the first and second internode and between the internodes. In all varieties, the values of internode diameter, lumen diameter, area of transverse section and area of lumen were higher for the second internode than for the first internode, whereas the reverse was reported for stem wall thickness and mechanical layer thickness The results of the principal component analysis and section modulus values revealed similarities between spring spelt Wirtas and Rubinas and between common wheat Kontesa and winter spelt Poeme and Epanis. The number of large vascular bundles varied across the studied varieties. The average number of vascular bundles in common wheat Kontesa was significantly higher than in spring spelt Rubinas and Wirtas and significantly lower than in Polish wheat Pol-3 and winter spelt Epanis and Poeme.

  14. GC-MS analysis of compounds extracted from buds of Populus balsamifera and Populus nigra.

    PubMed

    Isidorov, Valery A; Vinogorova, Vera T

    2003-01-01

    The composition of hexane and ether extracts from buds of two poplar species (Populus balsamifera and P. nigra) was investigated by GC-MS method. In hexane extracts, 54 "neutral" compounds were recorded. The greatest amounts of them are sesquiterpenes and n-alkanes. Among 56 components of ether extracts, many aliphatic acids and hydroxyacids were detected. However, the main fraction consists of phenolcarboxylic acids, substituted cinnamic acids, and their esters. It was established that chemotaxonomic differences between Populus balsamifera and P. nigra are observed in the case of both hexane and ether bud extracts.

  15. Enhancement of transpiration by ethylene is responsible for absence of internodal elongation in floating rice at low humidity.

    PubMed

    Azuma, Tetsushi; Hatanaka, Tomoko; Uchida, Naotsugu; Yasuda, Takeshi

    2003-09-01

    Internodal elongation in floating rice (Oryza sativa) is known to be enhanced by treatment with ethylene or gibberellic acid (GA3) at high relative humidity (RH). However, ethylene-induced internodal elongation is inhibited at low RH, while GA3-induced internodal elongation is hardly affected by humidity. We examined the effects of ethylene and GA3 on the rate of transpiration in stem segments incubated at 30% or 100% RH. Ethylene promoted the transpiration of stem segments at 30% RH, but not at 100% RH, while GA3 had little effect on transpiration at either 30% or 100% RH. We propose that the absence of ethylene-induced internodal elongation at low RH is due, at least in part, to ethylene-induced transpiration. PMID:14593815

  16. Simplification of a light-based model for estimating final internode length in greenhouse cucumber canopies

    PubMed Central

    Kahlen, Katrin; Stützel, Hartmut

    2011-01-01

    Background and Aims Light quantity and quality affect internode lengths in cucumber (Cucumis sativus), whereby leaf area and the optical properties of the leaves mainly control light quality within a cucumber plant community. This modelling study aimed at providing a simple, non-destructive method to predict final internode lengths (FILs) using light quantity and leaf area data. Methods Several simplifications of a light quantity and quality sensitive model for estimating FILs in cucumber have been tested. The direct simplifications substitute the term for the red : far-red (R : FR) ratios, by a term for (a) the leaf area index (LAI, m2 m−2) or (b) partial LAI, the cumulative leaf area per m2 ground, where leaf area per m2 ground is accumulated from the top of each plant until a number, n, of leaves per plant is reached. The indirect simplifications estimate the input R : FR ratio based on partial leaf area and plant density. Key Results In all models, simulated FILs were in line with the measured FILs over various canopy architectures and light conditions, but the prediction quality varied. The indirect simplification based on leaf area of ten leaves revealed the best fit with measured data. Its prediction quality was even higher than of the original model. Conclusions This study showed that for vertically trained cucumber plants, leaf area data can substitute local light quality data for estimating FIL data. In unstressed canopies, leaf area over the upper ten ranks seems to represent the feedback of the growing architecture on internode elongation with respect to light quality. This highlights the role of this domain of leaves as the primary source for the specific R : FR signal controlling the final length of an internode and could therefore guide future research on up-scaling local processes to the crop level. PMID:21642233

  17. Rose bush leaf and internode expansion dynamics: analysis and development of a model capturing interplant variability

    PubMed Central

    Demotes-Mainard, Sabine; Bertheloot, Jessica; Boumaza, Rachid; Huché-Thélier, Lydie; Guéritaine, Gaëlle; Guérin, Vincent; Andrieu, Bruno

    2013-01-01

    Rose bush architecture, among other factors, such as plant health, determines plant visual quality. The commercial product is the individual plant and interplant variability may be high within a crop. Thus, both mean plant architecture and interplant variability should be studied. Expansion is an important feature of architecture, but it has been little studied at the level of individual organs in rose bushes. We investigated the expansion kinetics of primary shoot organs, to develop a model reproducing the organ expansion of real crops from non-destructive input variables. We took interplant variability in expansion kinetics and the model's ability to simulate this variability into account. Changes in leaflet and internode dimensions over thermal time were recorded for primary shoot expansion, on 83 plants from three crops grown in different climatic conditions and densities. An empirical model was developed, to reproduce organ expansion kinetics for individual plants of a real crop of rose bush primary shoots. Leaflet or internode length was simulated as a logistic function of thermal time. The model was evaluated by cross-validation. We found that differences in leaflet or internode expansion kinetics between phytomer positions and between plants at a given phytomer position were due mostly to large differences in time of organ expansion and expansion rate, rather than differences in expansion duration. Thus, in the model, the parameters linked to expansion duration were predicted by values common to all plants, whereas variability in final size and organ expansion time was captured by input data. The model accurately simulated leaflet and internode expansion for individual plants (RMSEP = 7.3 and 10.2% of final length, respectively). Thus, this study defines the measurements required to simulate expansion and provides the first model simulating organ expansion in rosebush to capture interplant variability. PMID:24167509

  18. Brevis plant1, a putative inositol polyphosphate 5-phosphatase, is required for internode elongation in maize

    PubMed Central

    Avila, Luis M.; Cerrudo, Diego; Swanton, Clarence

    2016-01-01

    In maize (Zea mays L.), as in other grass species, stem elongation occurs during growth and most noticeably upon the transition to flowering. Genes that reduce stem elongation have been important to reduce stem breakage, or lodging. Stem elongation has been mediated by dwarf and brachytic/brevis plant mutants that affect giberellic acid and auxin pathways, respectively. Maize brevis plant1 (bv1) mutants, first identified over 80 years ago, strongly resemble brachytic2 mutants that have shortened internodes, short internode cells, and are deficient in auxin transport. Here, we characterized two novel bv1 maize mutants. We found that an inositol polyphosphate 5-phosphatase orthologue of the rice gene dwarf50 was the molecular basis for the bv1 phenotype, implicating auxin-mediated inositol polyphosphate and/or phosphoinositide signalling in stem elongation. We suggest that auxin-mediated internode elongation involves processes that also contribute to stem gravitropism. Genes misregulated in bv1 mutants included genes important for cell wall synthesis, transmembrane transport, and cytoskeletal function. Mutant and wild-type plants were indistinguishable early in development, responded similarly to changes in light quality, had unaltered flowering times, and had normal flower development. These attributes suggest that breeding could utilize bv1 alleles to increase crop grain yields. PMID:26767748

  19. Differences in Membrane Properties in Simulated Cases of Demyelinating Neuropathies: Internodal Focal Demyelinations with Conduction Block

    PubMed Central

    Daskalova, M. S.; Alexandrov, A. S.

    2006-01-01

    The aim of this study is to investigate the membrane properties (potentials and axonal excitability indices) in the case of myelin wrap reduction (96%) in one, two and three consecutive internodes along the length of human motor nerve fibre. The internodally focally demyelinated cases (termed as IFD1, IFD2 and IFD3, respectively, with one, two and three demyelinated internodes are simulated using our previous double cable model of the fibre. The progressively greater increase of focal loss of myelin lamellae blocks the invasion of the intracellular potentials into the demyelinated zones. For all investigated cases, the radial decline of the extracellular potential amplitudes increases with the increase of the radial distance and demyelination, whereas the electrotonic potentials show a decrease in the slow part of the depolarizing and hyperpolarizing responses. The time constants are shorter and the rheobases higher for the IFD2 and IFD3 cases than for the normal case. In the recovery cycles, the same cases have less refractoriness, greater supernormality and less late subnormality than the normal case. The simulated membrane abnormalities can be observed in vivo in patients with demyelinating forms of Guillain-Barré syndrome. The study provides new information about the pathophysiology of acquired demyelinating neuropathies. PMID:19669456

  20. Phosphatidylserine Synthase Controls Cell Elongation Especially in the Uppermost Internode in Rice by Regulation of Exocytosis

    PubMed Central

    Chen, Jun; Shen, Jinbo; Zhang, Baocai; Ren, Yulong; Ding, Yu; Zhou, Yihua; Zhang, Huan; Zhou, Kunneng; Wang, Jiu-Lin; Lei, Cailin; Zhang, Xin; Guo, Xiuping; Gao, He; Bao, Yiqun; Wan, Jian-Min

    2016-01-01

    The uppermost internode is one of the fastest elongating organs in rice, and is expected to require an adequate supply of cell-wall materials and enzymes to the cell surface to enhance mechanical strength. Although it has been reported that the phenotype of shortened uppermost internode 1 (sui1) is caused by mutations in PHOSPHATIDYLSERINE SYNTHASE (OsPSS), the underlying mechanism remains unclear. Here we show that the OsPSS-1, as a gene expressed predominantly in elongating cells, regulates post-Golgi vesicle secretion to intercellular spaces. Mutation of OsPSS-1 leads to compromised delivery of CESA4 and secGFP towards the cell surface, resulting in weakened intercellular adhesion and disorganized cell arrangement in parenchyma. The phenotype of sui1-4 is caused largely by the reduction in cellulose contents in the whole plant and detrimental delivery of pectins in the uppermost internode. We found that OsPSS-1 and its potential product PS (phosphatidylserine) localized to organelles associated with exocytosis. These results together suggest that OsPSS-1 plays a potential role in mediating cell expansion by regulating secretion of cell wall components. PMID:27055010

  1. Newly identified helper bacteria stimulate ectomycorrhizal formation in Populus

    SciTech Connect

    Labbe, Jessy L.; Weston, David J.; Dunkirk, Nora; Pelletier, Dale A.; Tuskan, Gerald A.

    2014-10-24

    Mycorrhiza helper bacteria (MHB) are known to increase host root colonization by mycorrhizal fungi but the molecular mechanisms and potential tripartite trophic interactions are poorly understood. Through an effort to study Populus microbiome, we isolated 21 Pseudomonas strains from native Populus deltoides roots. These bacterial isolates were characterized and screened for MHB effectiveness on the Populus-Laccaria system. Two other Pseudomonas strains (i.e., Pf-5 and BBc6R8) from existing collections were also included as reference in the screening process. We analyzed Laccaria bicolor S238N growth rate, mycelial architecture and transcriptional changes induced by the contrasting Pseudomonas strains (i.e., inhibitory, neutral and beneficial). We characterized 17 out of the 21 Pseudomonas strains from the Populus rhizosphere with positive effects on L. bicolor S238N growth, as well as on Populus root architecture and colonization by L. bicolor S238N across three Populus species. Four of seven reporter genes, Tra1, Tectonin2, Gcn5 and Cipc1, thought to be specific to the interaction with strain BBc6R8, were induced or repressed while interacting with six (i.e., GM17, GM33, GM41, GM48, Pf-5 and BBc6R8) of the tested Pseudomonas strains. GM41 promoted the highest roots colonization across three Populus species but most notably in P. deltoides, which is otherwise, poorly colonized by L. bicolor. Here we report novel MHB strains isolated from native Populus that improve roots colonization. This tripartite relationship could be exploited in nursery production for target Populus species/genotypes as a means of improving establishment and survival in marginal lands.

  2. Newly identified helper bacteria stimulate ectomycorrhizal formation in Populus

    DOE PAGESBeta

    Labbe, Jessy L.; Weston, David J.; Dunkirk, Nora; Pelletier, Dale A.; Tuskan, Gerald A.

    2014-10-24

    Mycorrhiza helper bacteria (MHB) are known to increase host root colonization by mycorrhizal fungi but the molecular mechanisms and potential tripartite trophic interactions are poorly understood. Through an effort to study Populus microbiome, we isolated 21 Pseudomonas strains from native Populus deltoides roots. These bacterial isolates were characterized and screened for MHB effectiveness on the Populus-Laccaria system. Two other Pseudomonas strains (i.e., Pf-5 and BBc6R8) from existing collections were also included as reference in the screening process. We analyzed Laccaria bicolor S238N growth rate, mycelial architecture and transcriptional changes induced by the contrasting Pseudomonas strains (i.e., inhibitory, neutral and beneficial).more » We characterized 17 out of the 21 Pseudomonas strains from the Populus rhizosphere with positive effects on L. bicolor S238N growth, as well as on Populus root architecture and colonization by L. bicolor S238N across three Populus species. Four of seven reporter genes, Tra1, Tectonin2, Gcn5 and Cipc1, thought to be specific to the interaction with strain BBc6R8, were induced or repressed while interacting with six (i.e., GM17, GM33, GM41, GM48, Pf-5 and BBc6R8) of the tested Pseudomonas strains. GM41 promoted the highest roots colonization across three Populus species but most notably in P. deltoides, which is otherwise, poorly colonized by L. bicolor. Here we report novel MHB strains isolated from native Populus that improve roots colonization. This tripartite relationship could be exploited in nursery production for target Populus species/genotypes as a means of improving establishment and survival in marginal lands.« less

  3. Predicting Plant Performance Under Simultaneously Changing Environmental Conditions-The Interplay Between Temperature, Light, and Internode Growth.

    PubMed

    Kahlen, Katrin; Chen, Tsu-Wei

    2015-01-01

    Plant performance is significantly influenced by prevailing light and temperature conditions during plant growth and development. For plants exposed to natural fluctuations in abiotic environmental conditions it is however laborious and cumbersome to experimentally assign any contribution of individual environmental factors to plant responses. This study aimed at analyzing the interplay between light, temperature and internode growth based on model approaches. We extended the light-sensitive virtual plant model L-Cucumber by implementing a common Arrhenius function for appearance rates, growth rates, and growth durations. For two greenhouse experiments, the temperature-sensitive model approach resulted in a precise prediction of cucumber mean internode lengths and number of internodes, as well as in accurately predicted patterns of individual internode lengths along the main stem. In addition, a system's analysis revealed that environmental data averaged over the experimental period were not necessarily related to internode performance. Finally, the need for a species-specific parameterization of the temperature response function and related aspects in modeling temperature effects on plant development and growth is discussed.

  4. Anthocyanins of the anthers as chemotaxonomic markers in the genus Populus L.. Differentiation between Populus nigra, Populus alba and Populus tremula.

    PubMed

    Alcalde-Eon, Cristina; García-Estévez, Ignacio; Rivas-Gonzalo, Julián C; Rodríguez de la Cruz, David; Escribano-Bailón, María Teresa

    2016-08-01

    Three main species of Popululs L. (Salicaceae) have been reported to occur in the Iberian Peninsula: Populus nigra L., Populus alba L. and Populus tremula L. The degree of pilosity of the bracts of the male catkins is a key character for their differentiation. The anthers of these poplar species possess anthocyanins that provide them a red colouration. Since these poplars are wind-pollinated and, consequently, do not need to attract pollinators, anthocyanins in the anthers might be acting as photoprotectors, shielding pollen grains from excessive sunlight. In order to verify this hypothesis, the first objective of this study was to establish if there is any relationship between the degree of pilosity of the bracts (related to the physical shading of the pollen grains) and the levels and types of anthocyanins in the anthers of these three species. This study also aimed to check the usefulness of the anthocyanins of the anthers as chemotaxonomic markers, through the study of the differences in the anthocyanin composition between these poplar species. Anthocyanins were identified from the data supplied by HPLC-DAD-MS(n) analyses. Seventeen different compounds, including mono-, di- and triglycosides and anthocyanin-derived pigments (F-A(+) dimers) have been identified. Cyanidin 3-O-glucoside was the major compound in all the samples (>60% of the total content), which may be in accordance with the photoprotective role proposed for them. However, qualitative and quantitative differences were detected among samples. Cyanidin and delphinidin 3-O-sambubiosides have been detected only in the anthers of P. tremula as well as cyanidin 3-O-(2″-O-xyloxyl)rutinoside, making them valuable chemotaxonomic markers for this species. Hierarchical Cluster and Principal Components Analyses (HCA and PCA) carried out with the anthocyanin percent composition data have allowed a separation of the samples that is in accordance with the initial classification of the samples made from the

  5. Anthocyanins of the anthers as chemotaxonomic markers in the genus Populus L.. Differentiation between Populus nigra, Populus alba and Populus tremula.

    PubMed

    Alcalde-Eon, Cristina; García-Estévez, Ignacio; Rivas-Gonzalo, Julián C; Rodríguez de la Cruz, David; Escribano-Bailón, María Teresa

    2016-08-01

    Three main species of Popululs L. (Salicaceae) have been reported to occur in the Iberian Peninsula: Populus nigra L., Populus alba L. and Populus tremula L. The degree of pilosity of the bracts of the male catkins is a key character for their differentiation. The anthers of these poplar species possess anthocyanins that provide them a red colouration. Since these poplars are wind-pollinated and, consequently, do not need to attract pollinators, anthocyanins in the anthers might be acting as photoprotectors, shielding pollen grains from excessive sunlight. In order to verify this hypothesis, the first objective of this study was to establish if there is any relationship between the degree of pilosity of the bracts (related to the physical shading of the pollen grains) and the levels and types of anthocyanins in the anthers of these three species. This study also aimed to check the usefulness of the anthocyanins of the anthers as chemotaxonomic markers, through the study of the differences in the anthocyanin composition between these poplar species. Anthocyanins were identified from the data supplied by HPLC-DAD-MS(n) analyses. Seventeen different compounds, including mono-, di- and triglycosides and anthocyanin-derived pigments (F-A(+) dimers) have been identified. Cyanidin 3-O-glucoside was the major compound in all the samples (>60% of the total content), which may be in accordance with the photoprotective role proposed for them. However, qualitative and quantitative differences were detected among samples. Cyanidin and delphinidin 3-O-sambubiosides have been detected only in the anthers of P. tremula as well as cyanidin 3-O-(2″-O-xyloxyl)rutinoside, making them valuable chemotaxonomic markers for this species. Hierarchical Cluster and Principal Components Analyses (HCA and PCA) carried out with the anthocyanin percent composition data have allowed a separation of the samples that is in accordance with the initial classification of the samples made from the

  6. Promotion by gibberellic Acid of polyamine biosynthesis in internodes of light-grown dwarf peas.

    PubMed

    Dai, Y R; Kaur-Sawhney, R; Galston, A W

    1982-01-01

    When gibberellic acid (GA(3); 5-35 micrograms per milliliter) is sprayed on 9-day-old light-grown dwarf Progress pea (Pisum sativum) seedlings, it causes a marked increase in the activity of arginine decarboxylase (ADC; EC 4.1.1.9) in the fourth internodes. The titer of putrescine and spermidine, polyamines produced indirectly as a result of ADC action, also rises markedly, paralleling the effect of GA(3) on internode growth. Ammonium (5-hydroxycarvacryl) trimethyl chloride piperidine carboxylate (AMO-1618; 100-200 micrograms per milliliter) causes changes in the reverse direction for enzyme activity, polyamine content, and growth. GA(3) also reverses the red-light-induced inhibition of ADC activity in etiolated Alaska pea epicotyls; this is additional evidence for gibberellin-light interaction in the control of polyamine biosynthesis. The enzyme ornithine decarboxylase (ODC; EC 4.1.1.17), an alternate source of putrescine arising from arginine, is not increased by GA(3) or by AMO-1618.The results support the hypothesis that ADC and polyamine content are important regulators of plant growth. PMID:16662137

  7. Gibberellin (GA) biosynthesis in elongating internodes Zea mays (maize): The 3. beta. -hydroxylase

    SciTech Connect

    Spray, C.R.; Phinney, B.O. ); Gaskin, P.; MacMillan, J. )

    1989-04-01

    The early-13-hydroxylation pathway for GA biosynthesis in maize leads to GA{sub 1}, the main GA responsible for shoot elongation. Growth response data, double-labeled feeding studies and endogenous GA levels suggest that the dwarf-1 mutant blocks the step GA{sub 20}to GA{sub 1}. We are screening for a system from maize from which we can purify the 3{beta}-hydroxylase and study its physical and biological properties. We find that diced internodal tissues will metabolize ({sup 13}C, {sup 3}H)-GA{sub 20} to ({sup 13}C, {sup 3}H)-GA{sub 1} and ({sup 13}C, {sup 3}H)-GA{sub 29} with metabolism as high as 80%. A cell free system from this material will give 5% metabolism. In a typical experiment 1g of internodal tissue is frozen in liquid nitrogen and macerated in 0.1M Tris plus cofactors. The homogenate is centrifuged at 15000 x g for 30 min at 4{degrees}C and the supernatant used for metabolic studies.

  8. Differences in Membrane Properties in Simulated Cases of Demyelinating Neuropathies: Internodal Focal Demyelinations without Conduction Block

    PubMed Central

    Daskalova, M. S.; Alexandrov, A. S.

    2006-01-01

    The membrane properties (intracellular, extracellular, electrotonic potentials, strength-duration time constants, rheobasic currents and recovery cycles), which can now be measured in healthy subjects and patients with demyelinating neuropathies, are investigated in simulated cases of focal reduction (70%) of the myelin sheath in one, two and three successive internodal segments along the length of human motor fibres. The internodally focally demyelinated cases (termed as IFD1, IFD2 and IFD3, respectively) are simulated using our previous double cable model of the fibres. The results show that the intracellular potentials are with reduced amplitude and slowed conduction velocity in the vicinity of demyelinated segments, however the segmental conduction block is not achieved. The radial decline of the extracellular potential amplitudes slightly increases with the increase of the radial distance and demyelination. In contrast, the electrotonic potentials, strength-duration time constants and rheobases are normal. In the recovery cycles, the refractoriness, supernormality and less late subnormality are close to the normal, showing that the pathology is relatively minor. The obtained abnormalities in the potentials and excitability properties provide new information about the pathophysiology of the demyelinated human motor axons and can be observed in vivo in patients with acquired demyelinating neuropathies. PMID:19669452

  9. Populus: Arabidopsis for Forestry. Do We Need a Model Tree?

    PubMed Central

    TAYLOR, GAIL

    2002-01-01

    Trees are used to produce a variety of wood‐based products including timber, pulp and paper. More recently, their use as a source of renewable energy has also been highlighted, as has their value for carbon mitigation within the Kyoto Protocol. Relative to food crops, the domestication of trees has only just begun; the long generation time and complex nature of juvenile and mature growth forms are contributory factors. To accelerate domestication, and to understand further some of the unique processes that occur in woody plants such as dormancy and secondary wood formation, a ‘model’ tree is needed. Here it is argued that Populus is rapidly becoming accepted as the ‘model’ woody plant and that such a ‘model’ tree is necessary to complement the genetic resource being developed in arabidopsis. The genus Populus (poplars, cottonwoods and aspens) contains approx. 30 species of woody plant, all found in the Northern hemisphere and exhibiting some of the fastest growth rates observed in temperate trees. Populus is fulfilling the ‘model’ role for a number of reasons. First, and most important, is the very recent commitment to sequence the Populus genome, a project initiated in February 2002. This will be the first woody plant to be sequenced. Other reasons include the relatively small genome size (450–550 Mbp) of Populus, the large number of molecular genetic maps and the ease of genetic transformation. Populus may also be propagated vegetatively, making mapping populations immortal and facilitating the production of large amounts of clonal material for experimentation. Hybridization occurs routinely and, in these respects, Populus has many similarities to arabidopsis. However, Populus also differs from arabidopsis in many respects, including being dioecious, which makes selfing and back‐cross manipulations impossible. The long time‐to‐flower is also a limitation, whilst physiological and biochemical experiments are more readily conducted in

  10. Populus: arabidopsis for forestry. Do we need a model tree?

    PubMed

    Taylor, Gail

    2002-12-01

    Trees are used to produce a variety of wood-based products including timber, pulp and paper. More recently, their use as a source of renewable energy has also been highlighted, as has their value for carbon mitigation within the Kyoto Protocol. Relative to food crops, the domestication of trees has only just begun; the long generation time and complex nature of juvenile and mature growth forms are contributory factors. To accelerate domestication, and to understand further some of the unique processes that occur in woody plants such as dormancy and secondary wood formation, a 'model' tree is needed. Here it is argued that Populus is rapidly becoming accepted as the 'model' woody plant and that such a 'model' tree is necessary to complement the genetic resource being developed in arabidopsis. The genus Populus (poplars, cottonwoods and aspens) contains approx. 30 species of woody plant, all found in the Northern hemisphere and exhibiting some of the fastest growth rates observed in temperate trees. Populus is fulfilling the 'model' role for a number of reasons. First, and most important, is the very recent commitment to sequence the Populus genome, a project initiated in February 2002. This will be the first woody plant to be sequenced. Other reasons include the relatively small genome size (450-550 Mbp) of Populus, the large number of molecular genetic maps and the ease of genetic transformation. Populus may also be propagated vegetatively, making mapping populations immortal and facilitating the production of large amounts of clonal material for experimentation. Hybridization occurs routinely and, in these respects, Populus has many similarities to arabidopsis. However, Populus also differs from arabidopsis in many respects, including being dioecious, which makes selfing and back-cross manipulations impossible. The long time-to-flower is also a limitation, whilst physiological and biochemical experiments are more readily conducted in Populus compared with the

  11. Expression of a fungal glucuronoyl esterase in Populus: effects on wood properties and saccharification efficiency.

    PubMed

    Latha Gandla, Madhavi; Derba-Maceluch, Marta; Liu, Xiaokun; Gerber, Lorenz; Master, Emma R; Mellerowicz, Ewa J; Jönsson, Leif J

    2015-04-01

    The secondary walls of angiosperms contain large amounts of glucuronoxylan that is thought to be covalently linked to lignin via ester bonds between 4-O-methyl-α-D-glucuronic acid (4-O-Me-GlcA) moieties in glucuronoxylan and alcohol groups in lignin. This linkage is proposed to be hydrolysed by glucuronoyl esterases (GCEs) secreted by wood-degrading fungi. We report effects of overexpression of a GCE from the white-rot basidiomycete Phanerochaete carnosa, PcGCE, in hybrid aspen (Populus tremula L. x tremuloides Michx.) on the wood composition and the saccharification efficiency. The recombinant enzyme, which was targeted to the plant cell wall using the signal peptide from hybrid aspen cellulase PttCel9B3, was constitutively expressed resulting in the appearance of GCE activity in protein extracts from developing wood. Diffuse reflectance FT-IR spectroscopy and pyrolysis-GC/MS analyses showed significant alternation in wood chemistry of transgenic plants including an increase in lignin content and S/G ratio, and a decrease in carbohydrate content. Sequential wood extractions confirmed a massive (+43%) increase of Klason lignin, which was accompanied by a ca. 5% decrease in cellulose, and ca. 20% decrease in wood extractives. Analysis of the monosaccharide composition using methanolysis showed a reduction of 4-O-Me-GlcA content without a change in Xyl contents in transgenic lines, suggesting that the covalent links between 4-O-Me-GlcA moieties and lignin protect these moieties from degradation. Enzymatic saccharification without pretreatment resulted in significant decreases of the yields of Gal, Glc, Xyl and Man in transgenic lines, consistent with their increased recalcitrance caused by the increased lignin content. In contrast, the enzymatic saccharification after acid pretreatment resulted in Glc yields similar to wild-type despite of their lower cellulose content. These data indicate that whereas PcGCE expression in hybrid aspen increases lignin deposition

  12. Genetic Dissection of Internode Length Above the Uppermost Ear in Four RIL Populations of Maize (Zea mays L.)

    PubMed Central

    Ku, Lixia; Cao, Liru; Wei, Xiaomin; Su, Huihui; Tian, Zhiqiang; Guo, Shulei; Zhang, Liangkun; Ren, Zhenzhen; Wang, Xiaobo; Zhu, Yuguang; Li, Guohui; Wang, Zhiyong; Chen, Yanhui

    2014-01-01

    The internode length above the uppermost ear (ILAU) is an important influencing factor for canopy architecture in maize. Analyzing the genetic characteristics of internode length is critical for improving plant population structure and increasing photosynthetic efficiency. However, the genetic control of ILAU has not been determined. In this study, quantitative trait loci (QTL) for internode length at five positions above the uppermost ear were identified using four sets of recombinant inbred line (RIL) populations in three environments. Genetic maps and initial QTL were integrated using meta-analyses across the four populations. Seventy QTL were identified: 16 in population 1; 14 in population 2; 25 in population 3; and 15 in population 4. Individual effects ranged from 5.36% to 26.85% of phenotypic variation, with 27 QTL >10%. In addition, the following common QTL were identified across two populations: one common QTL for the internode length of all five positions; one common QTL for the internode length of three positions; and one common QTL for the internode length of one position. In addition, four common QTL for the internode length of four positions were identified in one population. The results indicated that the ILAU at different positions above the uppermost ear could be affected by one or several of the same QTL. The traits may also be regulated by many different QTL. Of the 70 initial QTL, 46 were integrated in 14 meta-QTL (mQTLs) by meta-analysis, and 17 of the 27 initial QTL with R2 >10% were integrated in 7 mQTLs. Four of the key mQTLs (mQTL2-2, mQTL3-2, mQTL5-1, mQTL5-2, and mQTL9) in which the initial QTL displayed R2 >10% included four to 11 initial QTL for an internode length of four to five positions from one or two populations. These results may provide useful information for marker-assisted selection to improve canopy architecture. PMID:25538101

  13. A Populus EST resource for plant functional genomics.

    PubMed

    Sterky, Fredrik; Bhalerao, Rupali R; Unneberg, Per; Segerman, Bo; Nilsson, Peter; Brunner, Amy M; Charbonnel-Campaa, Laurence; Lindvall, Jenny Jonsson; Tandre, Karolina; Strauss, Steven H; Sundberg, Björn; Gustafsson, Petter; Uhlén, Mathias; Bhalerao, Rishikesh P; Nilsson, Ove; Sandberg, Göran; Karlsson, Jan; Lundeberg, Joakim; Jansson, Stefan

    2004-09-21

    Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide >4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (POPULUSDB) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.

  14. Is the basal area of maize internodes involved in borer resistance?

    PubMed Central

    2011-01-01

    Background To elucidate the role of the length of the internode basal ring (LIBR) in resistance to the Mediterranean corn borer (MCB), we carried out a divergent selection program to modify the LIBR using two maize synthetic varieties (EPS20 and EPS21), each with a different genetic background. We investigated the biochemical mechanisms underlying the relationship between the LIBR and borer resistance. Selection to lengthen or shorten the LIBR was achieved for each synthetic variety. The resulting plants were analyzed to determine their LIBR response, growth, yield, and borer resistance. Results In the synthetic variety EPS20 (Reid germplasm), reduction of the LIBR improved resistance against the MCB. The LIBR selection was also effective in the synthetic variety EPS21 (non-Reid germplasm), although there was no relationship detected between the LIBR and MCB resistance. The LIBR did not show correlations with agronomic traits such as plant height and yield. Compared with upper sections, the internode basal ring area contained lower concentrations of cell wall components such as acid detergent fiber (ADF), acid detergent lignin (ADL), and diferulates. In addition, some residual 2,4-dihydroxy-7-methoxy-(2H)-1,4-benzoxazin-3-(4H)-one (DIMBOA), a natural antibiotic compound, was detected in the basal area at 30 days after silking. Conclusion We analyzed maize selections to determine whether the basal area of maize internodes is involved in borer resistance. The structural reinforcement of the cell walls was the most significant trait in the relationship between the LIBR and borer resistance. Lower contents of ADF and ADL in the rind of the basal section facilitated the entry of larvae in this area in both synthetic varieties, while lower concentrations of diferulates in the pith basal section of EPS20 facilitated larval feeding inside the stem. The higher concentrations of DIMBOA may have contributed to the lack of correlation between the LIBR and borer resistance in

  15. Structure and stability of internodal myelin in mouse models of hereditary neuropathy.

    PubMed

    Avila, Robin L; Inouye, Hideyo; Baek, Rena C; Yin, Xinghua; Trapp, Bruce D; Feltri, M Laura; Wrabetz, Lawrence; Kirschner, Daniel A

    2005-11-01

    Peripheral neuropathies often result in abnormalities in the structure of internodal myelin, including changes in period and membrane packing, as observed by electron microscopy (EM). Mutations in the gene that encodes the major adhesive structural protein of internodal myelin in the peripheral nervous system of humans and mice--P0 glycoprotein--correlate with these defects. The mechanisms by which P0 mutations interfere with myelin packing and stability are not well understood and cannot be provided by EM studies that give static and qualitative information on fixed material. To gain insights into the pathogenesis of mutant P0, we used x-ray diffraction, which can detect more subtle and dynamic changes in native myelin, to investigate myelin structure in sciatic nerves from murine models of hereditary neuropathies. We used mice with disruption of one or both copies of the P0 gene (models of Charcot-Marie-Tooth-like neuropathy [CMT1B] or Dejerine-Sottas-like neuropathy) and mice with a CMT1B resulting from a transgene encoding P0 with an amino terminal myc-tag. To directly test the structural role of P0, we also examined a mouse that expresses P0 instead of proteolipid protein in central nervous system myelin. To link our findings on unfixed nerves with EM results, we analyzed x-ray patterns from unembedded, aldehyde-fixed nerves and from plastic-embedded nerves. From the x-ray patterns recorded from whole nerves, we assessed the amount of myelin and its quality (i.e. relative thickness and regularity). Among sciatic nerves having different levels of P0, we found that unfixed nerves and, to a lesser extent, fixed but unembedded nerves gave diffraction patterns of sufficient quality to distinguish periods, sometimes differing by a few Angstroms. Certain packing abnormalities were preserved qualitatively by aldehyde fixation, and the relative amount and structural integrity of myelin among nerves could be distinguished. Measurements from the same nerve over time

  16. Validation of Bayesian kriging of arsenic, chromium, lead and mercury surface soil concentrations based on internode sampling

    PubMed Central

    Aelion, C.M.; Davis, H.T.; Liu, Y.; Lawson, A.B.; McDermott, S.

    2009-01-01

    Bayesian kriging is a useful tool for estimating spatial distributions of metals; however, estimates are generally only verified statistically. In this study surface soil samples were collected on a uniform grid and analyzed for As, Cr, Pb, and Hg. The data were interpolated at individual locations by Bayesian kriging. Estimates were validated using a leave-one-out cross validation (LOOCV) statistical method which compared the measured and LOOCV predicted values. Validation also was carried out using additional field sampling of soil metal concentrations at points between original sampling locations, which were compared to kriging prediction distributions. LOOCV results suggest that Bayesian kriging was a good predictor of metal concentrations. When measured internode metal concentrations and estimated kriged values were compared, the measured values were located within the 5th – 95th percentile prediction distributions in over half of the internode locations. Estimated and measured internode concentrations were most similar for As and Pb. Kriged estimates did not compare as well to measured values for concentrations below the analytical minimum detection limit, or for internode samples that were very close to the original sampling node. Despite inherent variability in metal concentrations in soils, the kriged estimates were validated statistically and by in situ measurement. PMID:19603658

  17. Internode and petiole elongation of soybean in response to photoperiod and end-of-day light quality

    NASA Technical Reports Server (NTRS)

    Thomas, J. F.; Raper, C. D. Jr; Raper CD, J. r. (Principal Investigator)

    1985-01-01

    Elongation of main stem internodes and petioles of soybeans, Glycine max 'Ransom,' was examined in response to various photoperiod/temperature combinations and to end-of-day (EOD) light quality. Photoperiod treatments consisted of 10, 14, and 16 h in combination with day/night temperatures of 18/14, 22/18, 26/22, 30/26, and 34/30 C. The EOD treatments consisted of exposing plants to illumination from either incandescent (high far-red component, FR) or fluorescent (high red component, R) lamps during the final 0.5 h of a 10-h photoperiod. Internode elongation was not significantly promoted by the photoperiod treatments, and, in fact, under the two highest temperature regimes, internode elongation was suppressed under the longer photoperiods. Petiole elongation, however, was enhanced under the longer photoperiods at all temperatures. In the EOD light study, internode and petiole elongation was significantly greater on plants exposed to 0.5 h EOD from incandescent lamps than from fluorescent. Under the incandescent EOD treatment, plants increased dry matter production by 41% and exhibited greater partitioning of assimilates in stem and root portions than under fluorescent EOD.

  18. Investigation of Inter-Node B Macro Diversity for Single-Carrier Based Radio Access in Evolved UTRA Uplink

    NASA Astrophysics Data System (ADS)

    Kawai, Hiroyuki; Morimoto, Akihito; Higuchi, Kenichi; Sawahashi, Mamoru

    This paper investigates the gain of inter-Node B macro diversity for a scheduled-based shared channel using single-carrier FDMA radio access in the Evolved UTRA (UMTS Terrestrial Radio Access) uplink based on system-level simulations. More specifically, we clarify the gain of inter-Node B soft handover (SHO) with selection combining at the radio frame length level (=10msec) compared to that for hard handover (HHO) for a scheduled-based shared data channel, considering the gains of key packet-specific techniques including channel-dependent scheduling, adaptive modulation and coding (AMC), hybrid automatic repeat request (ARQ) with packet combining, and slow transmission power control (TPC). Simulation results show that the inter-Node B SHO increases the user throughput at the cell edge by approximately 10% for a short cell radius such as 100-300m due to the diversity gain from a sudden change in other-cell interference, which is a feature specific to full scheduled-based packet access. However, it is also shown that the gain of inter-Node B SHO compared to that for HHO is small in a macrocell environment when the cell radius is longer than approximately 500m due to the gains from hybrid ARQ with packet combining, slow TPC, and proportional fairness based channel-dependent scheduling.

  19. Rooting greenwood tip cuttings of several Populus clones hydroponically (hydroponic rooting of Populus cuttings)

    SciTech Connect

    Phipps, H.M.; Hansen, E.A.; Tolsted, D.N.

    1980-01-01

    Greenwood cuttings of several Populus clones were successfully rooted with a relatively simple hydroponic method. Indolebutyric acid and naphthaleneacetic acid at concentrations of 500 to 5000 ppM applied as a quick dip to the cutting bases, a complete nutrient solution at 20 to 40% of full strength, and a solution temperature between 27 and 30/sup 0/C generally produced the best rooting performance of most clones. Cuttings propagated by the hydroponic procedure rooted faster and generally outgrew those produced by a standard method after being transplanted to pots and grown in the greenhouse.

  20. Newly identified helper bacteria stimulate ectomycorrhizal formation in Populus

    PubMed Central

    Labbé, Jessy L.; Weston, David J.; Dunkirk, Nora; Pelletier, Dale A.; Tuskan, Gerald A.

    2014-01-01

    Mycorrhiza helper bacteria (MHB) are known to increase host root colonization by mycorrhizal fungi but the molecular mechanisms and potential tripartite interactions are poorly understood. Through an effort to study Populus microbiome, we isolated 21 Pseudomonas strains from native Populus deltoides roots. These bacterial isolates were characterized and screened for MHB effectiveness on the Populus-Laccaria system. Two additional Pseudomonas strains (i.e., Pf-5 and BBc6R8) from existing collections were included for comparative purposes. We analyzed the effect of co-cultivation of these 23 individual Pseudomonas strains on Laccaria bicolor “S238N” growth rate, mycelial architecture and transcriptional changes. Nineteen of the 23 Pseudomonas strains tested had positive effects on L. bicolor S238N growth, as well as on mycelial architecture, with strains GM41 and GM18 having the most significant effect. Four of seven L. bicolor reporter genes, Tra1, Tectonin2, Gcn5, and Cipc1, thought to be regulated during the interaction with MHB strain BBc6R8, were induced or repressed, while interacting with Pseudomonas strains GM17, GM33, GM41, GM48, Pf-5, and BBc6R8. Strain GM41 promoted the highest roots colonization across three Populus species but most notably in P. deltoides, which is otherwise poorly colonized by L. bicolor. Here we report novel MHB strains isolated from native Populus that improve L. bicolor root colonization on Populus. This tripartite relationship could be exploited for Populus species/genotypes nursery production as a means of improving establishment and survival in marginal lands. PMID:25386184

  1. Conversion of the proprietary ROLM (tm) inter-node link from multimode to singlemode operation

    NASA Technical Reports Server (NTRS)

    Boucher, Larry

    1993-01-01

    Many NASA centers have selected ROLM(TM) Computerized Branch Exchanges (CBX's) as their standard telephone exchange. The ROLM 9751 CBX Model 70 with ROLM software release 9005 can inter-communicate as a 'multi-node' system over a multimode fiber optic link of 450 to 6,000 meters. Singlemode fiber installations are not supported by ROLM. Two New Mexico-based NASA satellite ground terminals were already connected via a 6 kilometer singlemode fiber optic link. The ROLM Inter-Node Link (INL) was converted from multimode LED transmitters to singlemode laser transmitters and two ROLM CBX systems were interconnected using the modified INL. On activation, the system operated normally and has done so for six months. System testing indicates sufficient margin to drive 45 kilometers of singlemode fiber, an important benefit for widely separated facilities.

  2. Computing the Internode Certainty and Related Measures from Partial Gene Trees

    PubMed Central

    Kobert, Kassian; Salichos, Leonidas; Rokas, Antonis; Stamatakis, Alexandros

    2016-01-01

    We present, implement, and evaluate an approach to calculate the internode certainty (IC) and tree certainty (TC) on a given reference tree from a collection of partial gene trees. Previously, the calculation of these values was only possible from a collection of gene trees with exactly the same taxon set as the reference tree. An application to sets of partial gene trees requires mathematical corrections in the IC and TC calculations. We implement our methods in RAxML and test them on empirical datasets. These tests imply that the inclusion of partial trees does matter. However, in order to provide meaningful measurements, any dataset should also include trees containing the full species set. PMID:26915959

  3. Managing internode data communications for an uninitialized process in a parallel computer

    DOEpatents

    Archer, Charles J; Blocksome, Michael A; Miller, Douglas R; Parker, Jeffrey J; Ratterman, Joseph D; Smith, Brian E

    2014-05-20

    A parallel computer includes nodes, each having main memory and a messaging unit (MU). Each MU includes computer memory, which in turn includes, MU message buffers. Each MU message buffer is associated with an uninitialized process on the compute node. In the parallel computer, managing internode data communications for an uninitialized process includes: receiving, by an MU of a compute node, one or more data communications messages in an MU message buffer associated with an uninitialized process on the compute node; determining, by an application agent, that the MU message buffer associated with the uninitialized process is full prior to initialization of the uninitialized process; establishing, by the application agent, a temporary message buffer for the uninitialized process in main computer memory; and moving, by the application agent, data communications messages from the MU message buffer associated with the uninitialized process to the temporary message buffer in main computer memory.

  4. Elongating internodes of Zea mays (maize): Early steps in the GA biosynthetic pathway

    SciTech Connect

    Suzuki, Y.; Phinney, B.O. ); Gaskin, P.; MacMillan, J. )

    1989-04-01

    The early steps in the gibberellin (GA) biosynthetic pathway have yet to be defined for tissues that show a growth response to GAs. To this end we have synthesized the ({sup 13}C,{sup 3}H)-ent-kaurenoids, ent-kaurenol, ent-kaurenal ent-kaukenoic acid. We also have double-labeled ent-kaurene and double-labeled GA{sub 12}-aldehyde. We feed 1 - 10{mu}g of each substrate, individually, to 1.0g diced internodes in the appropriate buffer plus cofactors. We have observed up to 80% metabolism. We have identified (full scan GC-MS) 7{beta}-hydroxy-ent-kaurenoic acid as the major metabolite from double-labeled ent-kaurenoic acid feeds, thus defining the step ent-kaurenoic acid to 7{beta}-hydroxy-ent-kaurenoic acid.

  5. Highly Efficient Isolation of Populus Mesophyll Protoplasts and Its Application in Transient Expression Assays

    SciTech Connect

    Guo, Jianjun; Morrell-Falvey, Jennifer L; Labbe, Jessy L; Muchero, Wellington; Kalluri, Udaya C; Tuskan, Gerald A; Chen, Jay

    2012-01-01

    Background: Populus is a model woody plant and a promising feedstock for lignocellulosic biofuel production. However, its lengthy life cycle impedes rapid characterization of gene function. Methodology/Principal Findings: We optimized a Populus leaf mesophyll protoplast isolation protocol and established a Populus protoplast transient expression system. We demonstrated that Populus protoplasts are able to respond to hormonal stimuli and that a series of organelle markers are correctly localized in the Populus protoplasts. Furthermore, we showed that the Populus protoplast transient expression system is suitable for studying protein-protein interaction, gene activation, and cellular signaling events. Conclusions/Significance: This study established a method for efficient isolation of protoplasts from Populus leaf and demonstrated the efficacy of using Populus protoplast transient expression assays as an in vivo system to characterize genes and pathways.

  6. Osmotic properties of pea internodes in relation to growth and auxin action

    SciTech Connect

    Cosgrove, D.J.; Cleland, R.E.

    1983-01-01

    The water transport properties of etiolated pea (Pisum sativum L.) internodes were studied using both dynamic and steady-state methods to determine (a) whether water transport through the growing tissue limits the rate of cell enlargement, and (b) whether auxin stimulates growth in part by increasing the hydraulic conductance of the growing tissue. Measurements using the pressure probe technique showed that the hydraulic conductivity of cortical cell membranes was the same for both slowly growing and auxin-induced rapidly growing cells (membrane hydraulic conductivity, about 1.5 x 10/sup -5/ centimeters per second per bar). In a second technique which measured the rate of water movement through the entire pea internode, the half-time for radial water flow was about 60 seconds and was not altered by auxin application. These results indicate that auxin does not alter the hydraulic conductance of pea stem tissue, either at the cellular or the whole tissue level. When the growth rate was altered by various treatments, including decapitation, auxin application, cold temperature, and KCN treatment, the water potential was independent of the growth rate of the stem. We attribute the depression of the water potential in young pea stems to the presence of solutes in the cell wall free space of the tissue. From the results of these dynamic and steady-state experiments, we conclude that the internal gradient in water potential (from the xylem to the epidermis) needed to sustain cell enlargement is small (no greater than 0.5 bar). Thus, the hydraulic conductance of the tissue is sufficiently large that it does not control or limit the rate of cell enlargement. 30 references, 5 figures, 4 tables.

  7. The ERF11 Transcription Factor Promotes Internode Elongation by Activating Gibberellin Biosynthesis and Signaling.

    PubMed

    Zhou, Xin; Zhang, Zhong-Lin; Park, Jeongmoo; Tyler, Ludmila; Yusuke, Jikumaru; Qiu, Kai; Nam, Edward A; Lumba, Shelley; Desveaux, Darrell; McCourt, Peter; Kamiya, Yuji; Sun, Tai-Ping

    2016-08-01

    The phytohormone gibberellin (GA) plays a key role in promoting stem elongation in plants. Previous studies show that GA activates its signaling pathway by inducing rapid degradation of DELLA proteins, GA signaling repressors. Using an activation-tagging screen in a reduced-GA mutant ga1-6 background, we identified AtERF11 to be a novel positive regulator of both GA biosynthesis and GA signaling for internode elongation. Overexpression of AtERF11 partially rescued the dwarf phenotype of ga1-6 AtERF11 is a member of the ERF (ETHYLENE RESPONSE FACTOR) subfamily VIII-B-1a of ERF/AP2 transcription factors in Arabidopsis (Arabidopsis thaliana). Overexpression of AtERF11 resulted in elevated bioactive GA levels by up-regulating expression of GA3ox1 and GA20ox genes. Hypocotyl elongation assays further showed that overexpression of AtERF11 conferred elevated GA response, whereas loss-of-function erf11 and erf11 erf4 mutants displayed reduced GA response. In addition, yeast two-hybrid, coimmunoprecipitation, and transient expression assays showed that AtERF11 enhances GA signaling by antagonizing the function of DELLA proteins via direct protein-protein interaction. Interestingly, AtERF11 overexpression also caused a reduction in the levels of another phytohormone ethylene in the growing stem, consistent with recent finding showing that AtERF11 represses transcription of ethylene biosynthesis ACS genes. The effect of AtERF11 on promoting GA biosynthesis gene expression is likely via its repressive function on ethylene biosynthesis. These results suggest that AtERF11 plays a dual role in promoting internode elongation by inhibiting ethylene biosynthesis and activating GA biosynthesis and signaling pathways. PMID:27255484

  8. The ERF11 Transcription Factor Promotes Internode Elongation by Activating Gibberellin Biosynthesis and Signaling1[OPEN

    PubMed Central

    Zhou, Xin; Zhang, Zhong-Lin; Tyler, Ludmila; Yusuke, Jikumaru; Qiu, Kai; Lumba, Shelley; Desveaux, Darrell; McCourt, Peter; Sun, Tai-ping

    2016-01-01

    The phytohormone gibberellin (GA) plays a key role in promoting stem elongation in plants. Previous studies show that GA activates its signaling pathway by inducing rapid degradation of DELLA proteins, GA signaling repressors. Using an activation-tagging screen in a reduced-GA mutant ga1-6 background, we identified AtERF11 to be a novel positive regulator of both GA biosynthesis and GA signaling for internode elongation. Overexpression of AtERF11 partially rescued the dwarf phenotype of ga1-6. AtERF11 is a member of the ERF (ETHYLENE RESPONSE FACTOR) subfamily VIII-B-1a of ERF/AP2 transcription factors in Arabidopsis (Arabidopsis thaliana). Overexpression of AtERF11 resulted in elevated bioactive GA levels by up-regulating expression of GA3ox1 and GA20ox genes. Hypocotyl elongation assays further showed that overexpression of AtERF11 conferred elevated GA response, whereas loss-of-function erf11 and erf11 erf4 mutants displayed reduced GA response. In addition, yeast two-hybrid, coimmunoprecipitation, and transient expression assays showed that AtERF11 enhances GA signaling by antagonizing the function of DELLA proteins via direct protein-protein interaction. Interestingly, AtERF11 overexpression also caused a reduction in the levels of another phytohormone ethylene in the growing stem, consistent with recent finding showing that AtERF11 represses transcription of ethylene biosynthesis ACS genes. The effect of AtERF11 on promoting GA biosynthesis gene expression is likely via its repressive function on ethylene biosynthesis. These results suggest that AtERF11 plays a dual role in promoting internode elongation by inhibiting ethylene biosynthesis and activating GA biosynthesis and signaling pathways. PMID:27255484

  9. Identification of Dw1, a Regulator of Sorghum Stem Internode Length.

    PubMed

    Hilley, Josie; Truong, Sandra; Olson, Sara; Morishige, Daryl; Mullet, John

    2016-01-01

    Sorghum is an important C4 grain and grass crop used for food, feed, forage, sugar, and biofuels. In its native Africa, sorghum landraces often grow to approximately 3-4 meters in height. Following introduction into the U.S., shorter, early flowering varieties were identified and used for production of grain. Quinby and Karper identified allelic variation at four loci designated Dw1-Dw4 that regulated plant height by altering the length of stem internodes. The current study used a map-based cloning strategy to identify the gene corresponding to Dw1. Hegari (Dw1dw2Dw3dw4) and 80M (dw1dw2Dw3dw4) were crossed and F2 and HIF derived populations used for QTL mapping. Genetic analysis identified four QTL for internode length in this population, Dw1 on SBI-09, Dw2 on SBI-06, and QTL located on SBI-01 and SBI-07. The QTL on SBI-07 was ~3 Mbp upstream of Dw3 and interacted with Dw1. Dw1 was also found to contribute to the variation in stem weight in the population. Dw1 was fine mapped to an interval of ~33 kbp using HIFs segregating only for Dw1. A polymorphism in an exon of Sobic.009G229800 created a stop codon that truncated the encoded protein in 80M (dw1). This polymorphism was not present in Hegari (Dw1) and no other polymorphisms in the delimited Dw1 locus altered coding regions. The recessive dw1 allele found in 80M was traced to Dwarf Yellow Milo, the progenitor of grain sorghum genotypes identified as dw1. Dw1 encodes a putative membrane protein of unknown function that is highly conserved in plants. PMID:26963094

  10. Identification of Dw1, a Regulator of Sorghum Stem Internode Length

    PubMed Central

    Hilley, Josie; Truong, Sandra; Olson, Sara; Morishige, Daryl; Mullet, John

    2016-01-01

    Sorghum is an important C4 grain and grass crop used for food, feed, forage, sugar, and biofuels. In its native Africa, sorghum landraces often grow to approximately 3–4 meters in height. Following introduction into the U.S., shorter, early flowering varieties were identified and used for production of grain. Quinby and Karper identified allelic variation at four loci designated Dw1-Dw4 that regulated plant height by altering the length of stem internodes. The current study used a map-based cloning strategy to identify the gene corresponding to Dw1. Hegari (Dw1dw2Dw3dw4) and 80M (dw1dw2Dw3dw4) were crossed and F2 and HIF derived populations used for QTL mapping. Genetic analysis identified four QTL for internode length in this population, Dw1 on SBI-09, Dw2 on SBI-06, and QTL located on SBI-01 and SBI-07. The QTL on SBI-07 was ~3 Mbp upstream of Dw3 and interacted with Dw1. Dw1 was also found to contribute to the variation in stem weight in the population. Dw1 was fine mapped to an interval of ~33 kbp using HIFs segregating only for Dw1. A polymorphism in an exon of Sobic.009G229800 created a stop codon that truncated the encoded protein in 80M (dw1). This polymorphism was not present in Hegari (Dw1) and no other polymorphisms in the delimited Dw1 locus altered coding regions. The recessive dw1 allele found in 80M was traced to Dwarf Yellow Milo, the progenitor of grain sorghum genotypes identified as dw1. Dw1 encodes a putative membrane protein of unknown function that is highly conserved in plants. PMID:26963094

  11. Pleistocene speciation in the genus Populus (salicaceae).

    PubMed

    Levsen, Nicholas D; Tiffin, Peter; Olson, Matthew S

    2012-05-01

    The macroevolutionary consequences of recent climate change remain controversial, and there is little paleobotanical or morphological evidence that Pleistocene (1.8-0.12 Ma) glacial cycles acted as drivers of speciation, especially among lineages with long generation times, such as trees. We combined genetic and ecogeographic data from 2 closely related North American tree species, Populus balsamifera and P. trichocarpa (Salicacaeae), to determine if their divergence coincided with and was possibly caused by Pleistocene climatic events. We analyzed 32 nuclear loci from individuals of P. balsamifera and P. trichocarpa to produce coalescent-based estimates of the divergence time between the 2 species. We coupled the coalescent analyses with paleodistribution models to assess the influence of climate change on species' range. Furthermore, measures of niche overlap were used to investigate patterns of ecological differentiation between species. We estimated the divergence date of P. balsamifera and P. trichocarpa at approximately 75 Ka, which corresponds closely with the onset of Marine Isotope Stage 4 (∼76 Ka) and a rapid increase in global ice volume. Significance tests of niche overlap, in conjunction with genetic estimates of migration, suggested that speciation occurred in allopatry, possibly resulting from the environmental effects of Pleistocene glacial cycles. Our results indicate that the divergence of keystone tree species, which have shaped community diversity in northern North American ecosystems, was recent and may have been a consequence of Pleistocene-era glaciation and climate change.

  12. Variable Nitrogen Fixation in Wild Populus

    PubMed Central

    Doty, Sharon L.; Sher, Andrew W.; Fleck, Neil D.; Khorasani, Mahsa; Bumgarner, Roger E.; Khan, Zareen; Ko, Andrew W. K.; Kim, Soo-Hyung; DeLuca, Thomas H.

    2016-01-01

    The microbiome of plants is diverse, and like that of animals, is important for overall health and nutrient acquisition. In legumes and actinorhizal plants, a portion of essential nitrogen (N) is obtained through symbiosis with nodule-inhabiting, N2-fixing microorganisms. However, a variety of non-nodulating plant species can also thrive in natural, low-N settings. Some of these species may rely on endophytes, microorganisms that live within plants, to fix N2 gas into usable forms. Here we report the first direct evidence of N2 fixation in the early successional wild tree, Populus trichocarpa, a non-leguminous tree, from its native riparian habitat. In order to measure N2 fixation, surface-sterilized cuttings of wild poplar were assayed using both 15N2 incorporation and the commonly used acetylene reduction assay. The 15N label was incorporated at high levels in a subset of cuttings, suggesting a high level of N-fixation. Similarly, acetylene was reduced to ethylene in some samples. The microbiota of the cuttings was highly variable, both in numbers of cultured bacteria and in genetic diversity. Our results indicated that associative N2-fixation occurred within wild poplar and that a non-uniformity in the distribution of endophytic bacteria may explain the variability in N-fixation activity. These results point to the need for molecular studies to decipher the required microbial consortia and conditions for effective endophytic N2-fixation in trees. PMID:27196608

  13. Variable Nitrogen Fixation in Wild Populus.

    PubMed

    Doty, Sharon L; Sher, Andrew W; Fleck, Neil D; Khorasani, Mahsa; Bumgarner, Roger E; Khan, Zareen; Ko, Andrew W K; Kim, Soo-Hyung; DeLuca, Thomas H

    2016-01-01

    The microbiome of plants is diverse, and like that of animals, is important for overall health and nutrient acquisition. In legumes and actinorhizal plants, a portion of essential nitrogen (N) is obtained through symbiosis with nodule-inhabiting, N2-fixing microorganisms. However, a variety of non-nodulating plant species can also thrive in natural, low-N settings. Some of these species may rely on endophytes, microorganisms that live within plants, to fix N2 gas into usable forms. Here we report the first direct evidence of N2 fixation in the early successional wild tree, Populus trichocarpa, a non-leguminous tree, from its native riparian habitat. In order to measure N2 fixation, surface-sterilized cuttings of wild poplar were assayed using both 15N2 incorporation and the commonly used acetylene reduction assay. The 15N label was incorporated at high levels in a subset of cuttings, suggesting a high level of N-fixation. Similarly, acetylene was reduced to ethylene in some samples. The microbiota of the cuttings was highly variable, both in numbers of cultured bacteria and in genetic diversity. Our results indicated that associative N2-fixation occurred within wild poplar and that a non-uniformity in the distribution of endophytic bacteria may explain the variability in N-fixation activity. These results point to the need for molecular studies to decipher the required microbial consortia and conditions for effective endophytic N2-fixation in trees. PMID:27196608

  14. Characterization of DWARF14 Genes in Populus

    DOE PAGESBeta

    Zheng, Kaijie; Wang, Xiaoping; Weighill, Deborah A.; Guo, Hao-Bo; Xie, Meng; Yang, Yongil; Yang, Jun; Wang, Shucai; Jacobson, Daniel A.; Guo, Hong; et al

    2016-02-15

    Strigolactones are a new class of plant hormones regulating shoot branching and symbiotic interactions with arbuscular mycorrhizal fungi. Studies of branching mutants in herbaceous plants have identified several key genes involved in strigolactone biosynthesis or signaling. The strigolactone signal is perceived by a member of the α/β-fold hydrolase superfamily, known as DWARF14 (D14). However, little is known about D14 genes in the woody perennial plants. Here we report the identification of D14 homologs in the model woody plant Populus trichocarpa. We showed that there are two D14 homologs in P. trichocarpa, designated as PtD14a and PtD14b that are over 95%more » similar at the amino acid level. Expression analysis indicated that the transcript level of PtD14a is generally more abundant than that of PtD14b. However, only PtD14a was able to complement Arabidopsis d14 mutants, suggesting that PtD14a is the functional D14 ortholog. Amino acid alignment and structural modeling revealed substitutions of several highly conserved amino acids in the PtD14b protein including a phenylalanine near the catalytic triad of D14 proteins. Ultimately, we find this study lays a foundation for further characterization of strigolactone pathway and its functions in the woody perennial plants.« less

  15. Variable Nitrogen Fixation in Wild Populus.

    PubMed

    Doty, Sharon L; Sher, Andrew W; Fleck, Neil D; Khorasani, Mahsa; Bumgarner, Roger E; Khan, Zareen; Ko, Andrew W K; Kim, Soo-Hyung; DeLuca, Thomas H

    2016-01-01

    The microbiome of plants is diverse, and like that of animals, is important for overall health and nutrient acquisition. In legumes and actinorhizal plants, a portion of essential nitrogen (N) is obtained through symbiosis with nodule-inhabiting, N2-fixing microorganisms. However, a variety of non-nodulating plant species can also thrive in natural, low-N settings. Some of these species may rely on endophytes, microorganisms that live within plants, to fix N2 gas into usable forms. Here we report the first direct evidence of N2 fixation in the early successional wild tree, Populus trichocarpa, a non-leguminous tree, from its native riparian habitat. In order to measure N2 fixation, surface-sterilized cuttings of wild poplar were assayed using both 15N2 incorporation and the commonly used acetylene reduction assay. The 15N label was incorporated at high levels in a subset of cuttings, suggesting a high level of N-fixation. Similarly, acetylene was reduced to ethylene in some samples. The microbiota of the cuttings was highly variable, both in numbers of cultured bacteria and in genetic diversity. Our results indicated that associative N2-fixation occurred within wild poplar and that a non-uniformity in the distribution of endophytic bacteria may explain the variability in N-fixation activity. These results point to the need for molecular studies to decipher the required microbial consortia and conditions for effective endophytic N2-fixation in trees.

  16. Shotgun proteome profile of Populus developing xylem

    SciTech Connect

    Kalluri, Udaya C; Hurst, Gregory {Greg} B; Lankford, Patricia K; Ranjan, Priya; Pelletier, Dale A

    2009-01-01

    Understanding the molecular pathways of plant cell wall biosynthesis and remodeling is central to interpreting biological mechanisms underlying plant growth and adaptation as well as leveraging that knowledge towards development of improved bioenergy feedstocks. Here we report the application of shotgun tandem mass spectrometry profiling to the proteome of Populus developing xylem. Additionally, we mined public databases to obtain information in support of subcellular localization, transcript-level expression, and functional categorization of these proteins. Nearly 6000 different proteins were identified from the xylem proteome, with over 4400 proteins identified from one or more unique peptides. In addition to finding protein-level evidence of candidate wall biosynthesis genes from xylem (wood) tissue such as cellulose synthase, phenylalanine ammonia-lyase, and 4-coumarate:CoA ligase, several other potentially new candidate genes in the pathway were discovered. In order to identify low-abundance DNA-regulatory proteins from the developing xylem, a selective nuclear proteome profiling method was developed. Several putative transcription factor and chromatin remodeling proteins were identified using this method, such as LIM and NAC domain transcription factors and CHB3-SWI/SNF-related proteins. Further application of these proteomics methods will enhance understanding not only of cell wall biosynthesis in system biology modeling, but also other plant developmental and physiological pathways.

  17. Pleistocene Speciation in the Genus Populus (Salicaceae)

    PubMed Central

    Levsen, Nicholas D.; Tiffin, Peter; Olson, Matthew S.

    2012-01-01

    The macroevolutionary consequences of recent climate change remain controversial, and there is little paleobotanical or morphological evidence that Pleistocene (1.8–0.12 Ma) glacial cycles acted as drivers of speciation, especially among lineages with long generation times, such as trees. We combined genetic and ecogeographic data from 2 closely related North American tree species, Populus balsamifera and P. trichocarpa (Salicacaeae), to determine if their divergence coincided with and was possibly caused by Pleistocene climatic events. We analyzed 32 nuclear loci from individuals of P. balsamifera and P. trichocarpa to produce coalescent-based estimates of the divergence time between the 2 species. We coupled the coalescent analyses with paleodistribution models to assess the influence of climate change on species' range. Furthermore, measures of niche overlap were used to investigate patterns of ecological differentiation between species. We estimated the divergence date of P. balsamifera and P. trichocarpa at approximately 75 Ka, which corresponds closely with the onset of Marine Isotope Stage 4 (∼76 Ka) and a rapid increase in global ice volume. Significance tests of niche overlap, in conjunction with genetic estimates of migration, suggested that speciation occurred in allopatry, possibly resulting from the environmental effects of Pleistocene glacial cycles. Our results indicate that the divergence of keystone tree species, which have shaped community diversity in northern North American ecosystems, was recent and may have been a consequence of Pleistocene-era glaciation and climate change. PMID:22213709

  18. Characterization of DWARF14 Genes in Populus

    PubMed Central

    Zheng, Kaijie; Wang, Xiaoping; Weighill, Deborah A.; Guo, Hao-Bo; Xie, Meng; Yang, Yongil; Yang, Jun; Wang, Shucai; Jacobson, Daniel A.; Guo, Hong; Muchero, Wellington; Tuskan, Gerald A.; Chen, Jin-Gui

    2016-01-01

    Strigolactones are a new class of plant hormones regulating shoot branching and symbiotic interactions with arbuscular mycorrhizal fungi. Studies of branching mutants in herbaceous plants have identified several key genes involved in strigolactone biosynthesis or signaling. The strigolactone signal is perceived by a member of the α/β-fold hydrolase superfamily, known as DWARF14 (D14). However, little is known about D14 genes in the woody perennial plants. Here we report the identification of D14 homologs in the model woody plant Populus trichocarpa. We showed that there are two D14 homologs in P. trichocarpa, designated as PtD14a and PtD14b that are over 95% similar at the amino acid level. Expression analysis indicated that the transcript level of PtD14a is generally more abundant than that of PtD14b. However, only PtD14a was able to complement Arabidopsis d14 mutants, suggesting that PtD14a is the functional D14 ortholog. Amino acid alignment and structural modeling revealed substitutions of several highly conserved amino acids in the PtD14b protein including a phenylalanine near the catalytic triad of D14 proteins. This study lays a foundation for further characterization of strigolactone pathway and its functions in the woody perennial plants. PMID:26875827

  19. The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome.

    PubMed

    Sjödin, Andreas; Street, Nathaniel Robert; Sandberg, Göran; Gustafsson, Petter; Jansson, Stefan

    2009-06-01

    Populus has become an important model plant system. However, utilization of the increasingly extensive collection of genetics and genomics data created by the community is currently hindered by the lack of a central resource, such as a model organism database (MOD). Such MODs offer a single entry point to the collection of resources available within a model system, typically including tools for exploring and querying those resources. As a starting point to overcoming the lack of such an MOD for Populus, we present the Populus Genome Integrative Explorer (PopGenIE), an integrated set of tools for exploring the Populus genome and transcriptome. The resource includes genome, synteny and quantitative trait locus (QTL) browsers for exploring genetic data. Expression tools include an electronic fluorescent pictograph (eFP) browser, expression profile plots, co-regulation within collated transcriptomics data sets, and identification of over-represented functional categories and genomic hotspot locations. A number of collated transcriptomics data sets are made available in the eFP browser to facilitate functional exploration of gene function. Additional homology and data extraction tools are provided. PopGenIE significantly increases accessibility to Populus genomics resources and allows exploration of transcriptomics data without the need to learn or understand complex statistical analysis methods. PopGenIE is available at www.popgenie.org or via www.populusgenome.info.

  20. Evolutionary Quantitative Genomics of Populus trichocarpa

    PubMed Central

    McKown, Athena D.; La Mantia, Jonathan; Guy, Robert D.; Ingvarsson, Pär K.; Hamelin, Richard; Mansfield, Shawn D.; Ehlting, Jürgen; Douglas, Carl J.; El-Kassaby, Yousry A.

    2015-01-01

    Forest trees generally show high levels of local adaptation and efforts focusing on understanding adaptation to climate will be crucial for species survival and management. Here, we address fundamental questions regarding the molecular basis of adaptation in undomesticated forest tree populations to past climatic environments by employing an integrative quantitative genetics and landscape genomics approach. Using this comprehensive approach, we studied the molecular basis of climate adaptation in 433 Populus trichocarpa (black cottonwood) genotypes originating across western North America. Variation in 74 field-assessed traits (growth, ecophysiology, phenology, leaf stomata, wood, and disease resistance) was investigated for signatures of selection (comparing QST -FST) using clustering of individuals by climate of origin (temperature and precipitation). 29,354 SNPs were investigated employing three different outlier detection methods and marker-inferred relatedness was estimated to obtain the narrow-sense estimate of population differentiation in wild populations. In addition, we compared our results with previously assessed selection of candidate SNPs using the 25 topographical units (drainages) across the P. trichocarpa sampling range as population groupings. Narrow-sense QST for 53% of distinct field traits was significantly divergent from expectations of neutrality (indicating adaptive trait variation); 2,855 SNPs showed signals of diversifying selection and of these, 118 SNPs (within 81 genes) were associated with adaptive traits (based on significant QST). Many SNPs were putatively pleiotropic for functionally uncorrelated adaptive traits, such as autumn phenology, height, and disease resistance. Evolutionary quantitative genomics in P. trichocarpa provides an enhanced understanding regarding the molecular basis of climate-driven selection in forest trees and we highlight that important loci underlying adaptive trait variation also show relationship to

  1. The glutamine synthetase gene family in Populus

    PubMed Central

    2011-01-01

    Background Glutamine synthetase (GS; EC: 6.3.1.2, L-glutamate: ammonia ligase ADP-forming) is a key enzyme in ammonium assimilation and metabolism of higher plants. The current work was undertaken to develop a more comprehensive understanding of molecular and biochemical features of GS gene family in poplar, and to characterize the developmental regulation of GS expression in various tissues and at various times during the poplar perennial growth. Results The GS gene family consists of 8 different genes exhibiting all structural and regulatory elements consistent with their roles as functional genes. Our results indicate that the family members are organized in 4 groups of duplicated genes, 3 of which code for cytosolic GS isoforms (GS1) and 1 which codes for the choroplastic GS isoform (GS2). Our analysis shows that Populus trichocarpa is the first plant species in which it was observed the complete GS family duplicated. Detailed expression analyses have revealed specific spatial and seasonal patterns of GS expression in poplar. These data provide insights into the metabolic function of GS isoforms in poplar and pave the way for future functional studies. Conclusions Our data suggest that GS duplicates could have been retained in order to increase the amount of enzyme in a particular cell type. This possibility could contribute to the homeostasis of nitrogen metabolism in functions associated to changes in glutamine-derived metabolic products. The presence of duplicated GS genes in poplar could also contribute to diversification of the enzymatic properties for a particular GS isoform through the assembly of GS polypeptides into homo oligomeric and/or hetero oligomeric holoenzymes in specific cell types. PMID:21867507

  2. Genomics of Secondary Metabolism in Populus: Interactions with Biotic and Abiotic Environments

    SciTech Connect

    Chen, F.; Liu, C.; Tschaplinski, T. J.; Zhao, N.

    2009-09-01

    Populus trees face constant challenges from the environment during their life cycle. To ensure their survival and reproduction, Populus trees deploy various types of defenses, one of which is the production of a myriad of secondary metabolites. Compounds derived from the shikimate-phenylpropanoid pathway are the most abundant class of secondary metabolites synthesized in Populus. Among other major classes of secondary metabolites in Populus are terpenoids and fatty acid-derivatives. Some of the secondary metabolites made by Populus trees have been functionally characterized. Some others have been associated with certain biological/ecological processes, such as defense against insects and microbial pathogens or acclimation or adaptation to abiotic stresses. Functions of many Populus secondary metabolites remain unclear. The advent of various novel genomic tools will enable us to explore in greater detail the complexity of secondary metabolism in Populus. Detailed data mining of the Populus genome sequence can unveil candidate genes of secondary metabolism. Metabolomic analysis will continue to identify new metabolites synthesized in Populus. Integrated genomics that combines various 'omics' tools will prove to be the most powerful approach in revealing the molecular and biochemical basis underlying the biosynthesis of secondary metabolites in Populus. Characterization of the biological/ecological functions of secondary metabolites as well as their biosynthesis will provide knowledge and tools for genetically engineering the production of seconday metabolites that can lead to the generation of novel, improved Populus varieties.

  3. Assessment of Populus Wood Chemistry Following the Introduction of a Bt Toxin Gene

    SciTech Connect

    Davis, M. F.; Tuskan, G. A.; Payne, P.; Tschaplinski, T. J.; Meilan, R.

    2006-01-01

    Unintended changes in plant physiology, anatomy and metabolism as a result of genetic engineering are a concern as more transgenic plants are commercially deployed in the ecosystem. We compared the cell wall chemical composition of three Populus lines (Populus trichocarpa Torr. and A. Gray x Populus deltoides Bartr. ex Marsh., Populus trichocarpa x Populus nigra L. and Populus deltoides x Populus nigra) genetically modified to express the Cry3A or Cry3B2 protein of Bacillus thuringiensis (Bt) with the cellwall chemistry of non-transformed isogenic control lines. Three genetically modified clones, each represented by 10 independent transgenic lines, were analyzed by pyrolysis molecular beam mass spectrometry, gas chromatography/mass spectrometry and traditional wet chemical analytical methods to assess changes in cell wall composition. Based on the outcome of these techniques, there were no comprehensive differences in chemical composition between the transgenic and control lines for any of the studied clones.

  4. Assessment of Populus wood chemistry following the introduction of a Bt toxin gene

    SciTech Connect

    Tschaplinski, Timothy J; Davis, M F; Tuskan, Gerald A; Payne, M M; Meilan, R

    2006-01-01

    Unintended changes in plant physiology, anatomy and metabolism as a result of genetic engineering are a concern as more transgenic plants are commercially deployed in the ecosystem. We compared the cell wall chemical composition of three Populus lines (Populus trichocarpa Torr. & A. Gray x Populus trichocarpa Bartr. ex Marsh., Populus trichocarpa x Populus nigra L. and Populus deltoides x Populus nigra) genetically modified to express the Cry3A or Cry3B2 protein of Bacillus thuringiensis (Bt) with the cell wall chemistry of non-transformed isogenic control lines. Three genetically modified clones, each represented by 10 independent transgenic lines, were analyzed by pyrolysis molecular beam mass spectrometry, gas chromatography/mass spectrometry and traditional wet chemical analytical methods to assess changes in cell wall composition. Based on the outcome of these techniques, there were no comprehensive differences in chemical composition between the transgenic and control lines for any of the studied clones.

  5. Overexpression of a CYP94 family gene CYP94C2b increases internode length and plant height in rice

    PubMed Central

    Kurotani, Ken-Ich; Hattori, Tsukaho; Takeda, Shin

    2015-01-01

    Plant growth is controlled by intrinsic developmental programmes and environmental cues. Jasmonate (JA) has important roles in both processes, by regulating cell division and differentiation, as well as in defense responses and senescence. We report an increase in rice plant height caused by overexpression of a gene encoding a cytochrome P450 enzyme, CYP94C2b, which promoted deactivation of JA-Ile. The height increase occurred through enhanced elongation of internodes in the absence of concomitant cell elongation, unlike previous findings with coi1 knock-down plants. Thus, modulating JA metabolism can increase the number of elongated cells in an internode. Based on these and previous findings, we discuss the difference in the effects of CYP94C2b overexpression vs. coi1 knock-down. PMID:26251886

  6. Microtubule-dependent motility and orientation of the cortical endoplasmic reticulum in elongating characean internodal cells.

    PubMed

    Foissner, Ilse; Menzel, Diedrik; Wasteneys, Geoffrey O

    2009-03-01

    Motility of the endoplasmic reticulum (ER) is predominantly microtubule- dependent in animal cells but thought to be entirely actomyosin-dependent in plant cells. Using live cell imaging and transmission electron microscopy to examine ER motility and structural organization in giant internodal cells of characean algae, we discovered that at the onset of cell elongation, the cortical ER situated near the plasma membrane formed a tight meshwork of predominantly transverse ER tubules that frequently coaligned with microtubules. Microtubule depolymerization increased mesh size and decreased the dynamics of the cortical ER. In contrast, perturbing the cortical actin array with cytochalasins did not affect the transverse orientation but decreased mesh size and increased ER dynamics. Our data suggest that myosin-dependent ER motility is confined to the ER strands in the streaming endoplasm, while the more sedate cortical ER uses microtubule-based mechanisms for organization and motility during early stages of cell elongation. We show further that the ER has an inherent, NEM-sensitive dynamics which can be altered via interaction with the cytoskeleton and that tubule formation and fusion events are cytoskeleton-independent.

  7. The excitability of plant cells: with a special emphasis on characean internodal cells

    NASA Technical Reports Server (NTRS)

    Wayne, R.

    1994-01-01

    This review describes the basic principles of electrophysiology using the generation of an action potential in characean internodal cells as a pedagogical tool. Electrophysiology has proven to be a powerful tool in understanding animal physiology and development, yet it has been virtually neglected in the study of plant physiology and development. This review is, in essence, a written account of my personal journey over the past five years to understand the basic principles of electrophysiology so that I can apply them to the study of plant physiology and development. My formal background is in classical botany and cell biology. I have learned electrophysiology by reading many books on physics written for the lay person and by talking informally with many patient biophysicists. I have written this review for the botanist who is unfamiliar with the basics of membrane biology but would like to know that she or he can become familiar with the latest information without much effort. I also wrote it for the neurophysiologist who is proficient in membrane biology but knows little about plant biology (but may want to teach one lecture on "plant action potentials"). And lastly, I wrote this for people interested in the history of science and how the studies of electrical and chemical communication in physiology and development progressed in the botanical and zoological disciplines.

  8. Genome structure and primitive sex chromosome revealed in Populus

    SciTech Connect

    Tuskan, Gerald A; Yin, Tongming; Gunter, Lee E; Blaudez, D

    2008-01-01

    We constructed a comprehensive genetic map for Populus and ordered 332 Mb of sequence scaffolds along the 19 haploid chromosomes in order to compare chromosomal regions among diverse members of the genus. These efforts lead us to conclude that chromosome XIX in Populus is evolving into a sex chromosome. Consistent segregation distortion in favor of the sub-genera Tacamahaca alleles provided evidence of divergent selection among species, particularly at the proximal end of chromosome XIX. A large microsatellite marker (SSR) cluster was detected in the distorted region even though the genome-wide distribute SSR sites was uniform across the physical map. The differences between the genetic map and physical sequence data suggested recombination suppression was occurring in the distorted region. A gender-determination locus and an overabundance of NBS-LRR genes were also co-located to the distorted region and were put forth as the cause for divergent selection and recombination suppression. This hypothesis was verified by using fine-scale mapping of an integrated scaffold in the vicinity of the gender-determination locus. As such it appears that chromosome XIX in Populus is in the process of evolving from an autosome into a sex chromosome and that NBS-LRR genes may play important role in the chromosomal diversification process in Populus.

  9. Intraspecific variation in the Populus balsamifera drought transcriptome.

    PubMed

    Hamanishi, Erin T; Raj, Sherosha; Wilkins, Olivia; Thomas, Barb R; Mansfield, Shawn D; Plant, Aine L; Campbell, Malcolm M

    2010-10-01

    Drought is a major limitation to the growth and productivity of trees in the ecologically and economically important genus Populus. The ability of Populus trees to contend with drought is a function of genome responsiveness to this environmental insult, involving reconfiguration of the transcriptome to appropriately remodel growth, development and metabolism. Here we test hypotheses aimed at examining the extent of intraspecific variation in the drought transcriptome using six different Populus balsamifera L. genotypes and Affymetrix GeneChip technology. Within a given genotype there was a positive correlation between the magnitude of water-deficit induced changes in transcript abundance across the transcriptome, and the capacity of that genotype to maintain growth following water deficit. Genotypes that had more similar drought-responsive transcriptomes also had fewer genotypic differences, as determined by microarray-derived single feature polymorphism (SFP) analysis, suggesting that responses may be conserved across individuals that share a greater degree of genotypic similarity. This work highlights the fact that a core species-level response can be defined; however, the underpinning genotype-derived complexities of the drought response in Populus must be taken into consideration when defining both species- and genus-level responses.

  10. Drought induces alterations in the stomatal development program in Populus.

    PubMed

    Hamanishi, Erin T; Thomas, Barb R; Campbell, Malcolm M

    2012-08-01

    Much is known about the physiological control of stomatal aperture as a means by which plants adjust to water availability. By contrast, the role played by the modulation of stomatal development to limit water loss has received much less attention. The control of stomatal development in response to water deprivation in the genus Populus is explored here. Drought induced declines in stomatal conductance as well as an alteration in stomatal development in two genotypes of Populus balsamifera. Leaves that developed under water-deficit conditions had lower stomatal indices than leaves that developed under well-watered conditions. Transcript abundance of genes that could hypothetically underpin drought-responsive changes in stomatal development was examined, in two genotypes, across six time points, under two conditions, well-watered and with water deficit. Populus homologues of STOMAGEN, ERECTA (ER), STOMATA DENSITY AND DISTRIBUTION 1 (SDD1), and FAMA had variable transcript abundance patterns congruent with their role in the modulation of stomatal development in response to drought. Conversely, there was no significant variation in transcript abundance between genotypes or treatments for the Populus homologues of YODA (YDA) and TOO MANY MOUTHS (TMM). The findings highlight the role that could be played by stomatal development during leaf expansion as a longer term means by which to limit water loss from leaves. Moreover, the results point to the key roles played by the regulation of the homologues of STOMAGEN, ER, SDD1, and FAMA in the control of this response in poplar.

  11. Why and How Populus Became a "Model Tree"

    SciTech Connect

    Tuskan, Gerald A; Ellis, Brian; Jansson, Bo S; Strauss, S

    2010-01-01

    Although Populus was not a favored experimental system for very many plant biologists in 2000, P. trichocarpa ultimately became only the third plant species to have its genome fully sequenced. Here we examine the many different factors that came into play when this species was abruptly elevated to the status of a new 'model organism'.

  12. Effect of inhibitors of polyamine biosynthesis on gibberellin-induced internode growth in light-grown dwarf peas

    NASA Technical Reports Server (NTRS)

    Kaur-Sawhney, R.; Dai, Y. R.; Galston, A. W.

    1986-01-01

    When gibberellic acid (GA3) is sprayed on 9-day-old light-brown dwarf Progress pea (Pisum sativum) seedlings, arginine decarboxylase (ADC; EC 4.1.1.9) activity increases within 3 h and peaks at about 9 h after GA3 application. This is followed by a second lower peak at about 30 h; both peaks were higher than the corresponding peaks in the controls. In contrast, no appreciable effect of GA3 on internode length was observed until about 12 h, after which time a dramatic increase in growth rate occurred and persisted for about 12 h. Specific (DL-alpha-difluoromethylarginine) and non-specific (D-arginine and L-canavanine) inhibitors of ADC strongly inhibited ADC activity and to a lesser extent internode growth. The inhibition was reversed only slightly by the addition of polyamines. Actinomycin D and cycloheximide inhibited the rise in ADC activity induced by GA3. The half-life of the enzyme was increased by GA3 treatment. The results suggest that part of the GA3-induced increase in internode growth may result from enhanced polyamine biosynthesis through the ADC pathway. Furthermore, the GA3 induced increase in ADC activity probably requires de novo synthesis of both RNA and protein.

  13. Fluorescent phosphocholine--a specific marker for the endoplasmic reticulum and for lipid droplets in Chara internodal cells.

    PubMed

    Foissner, Ilse

    2009-12-01

    The staining pattern of 1,2-bis(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-undecanoyl)-sn-glycero-3-phosphocholine (Bodipy PC) was investigated in internodal cells of the green alga Chara corallina. Ten minutes after dye addition, Bodipy-PC-derived fluorescence appeared in lipid droplets and after 1 h in the cortical endoplasmic reticulum (ER) and in the inner ER tubes. Staining of the ER required energy but was independent of an intact actin or microtubule cytoskeleton and independent of vesicular endocytosis. The size of the lipid droplets varied between 0.25 microm in elongating cells and 3.2 microm in senescent internodes. They moved together with or along the cortical ER cisternae in a cytoskeleton-independent manner or remained immobile up to several minutes. Detachment of lipid droplets from the cortical ER or fusion of lipid droplets was never observed. The results of this study suggest that Bodipy PC is a valuable, less toxic alternative to 3,3'-dihexyloxacarbocyanine iodide (DiOC6) staining of the ER in Chara. They confirm an earlier report about microtubule-dependent cortical ER morphology and dynamics in elongating internodes and offer new perspectives for the study of organelle interactions.

  14. Microfilaments and microtubules control the shape, motility, and subcellular distribution of cortical mitochondria in characean internodal cells.

    PubMed

    Foissner, I

    2004-12-01

    The shape, motility, and subcellular distribution of mitochondria in characean internodal cells were studied by visualizing fluorescent dyes with confocal laser scanning microscopy and conducting drug-inhibitor experiments. Shape, size, number, and distribution of mitochondria varied according to the growth status and the metabolic activity within the cell. Vermiform (sausage-shaped), disc-, or amoeba-like mitochondria were present in elongating internodes, whereas very young cells and older cells that had completed growth contained short, rodlike organelles only. Mitochondria were evenly distributed and passively transported in the streaming endoplasm. In the cortex, mitochondria were sandwiched between the plasma membrane and the stationary chloroplast files and distributed in relation to the pattern of pH banding. Highest mitochondrial densities were found at the acid, photosynthetically more active regions, whereas the alkaline sites contained fewer and smaller mitochondria. In the cortex of elongating cells, small mitochondria moved slowly along microtubules or actin filaments. The shape and motility of giant mitochondria depended on the simultaneous interaction with both cytoskeletal systems. There was no microtubule-dependent motility in the cortex of nonelongating mature cells and mitochondria only occasionally travelled along actin filaments. These observations suggest that mitochondria of characean internodes possess motor proteins for microtubules and actin filaments, both of which can be used either as tracks for migration or for immobilization. The cortical cytoskeleton probably controls the spatiotemporal distribution of mitochondria within the cell and promotes their association with chloroplasts, which is necessary for exchange of metabolites during photosynthesis and detoxification.

  15. An efficient protocol for high-frequency direct multiple shoot regeneration from internodes of peppermint (Mentha x piperita).

    PubMed

    Thul, Sanjog T; Kukreja, Arun K

    2010-12-01

    A simple, repeatable and efficient protocol for direct multiple shoot regeneration from internodal explants has been defined in peppermint (Mentha x piperita var. Indus). In vitro regenerated shoots of peppermint were excised into 4 to 8 mm long internodes and cultured on Murashige and Skoog's medium supplemented with different cytokinins. In the hormonal assay, 3.0 mg L(-1) zeatin or 6-isopentenyl adenine independently supplemented to half strength MS medium exhibited multiple shoot regeneration, while thiaduzorn (0.1-3.0 mg L(-1)) showed no morphogenetic effect. A maximum of 85% in vitro cultured explants showed multiple shoot formation with an average of 7 shoots per explant on MS medium supplemented with zeatin. Multiple shoots were initiated within three weeks of cultivation. Internodes with regenerated multiple shoots were transferred to half- strength MS medium without supplementing with any plant growth hormone for shoot elongation and rhizogenesis. Rooted plants acclimatized and grew to maturity under glasshouse conditions. The plantlets developed were phenotypically identical to the parent plant and exhibited 96% survival.

  16. Effect of inhibitors of polyamine biosynthesis on gibberellin-induced internode growth in light-grown dwarf peas.

    PubMed

    Kaur-Sawhney, R; Dai, Y R; Galston, A W

    1986-01-01

    When gibberellic acid (GA3) is sprayed on 9-day-old light-brown dwarf Progress pea (Pisum sativum) seedlings, arginine decarboxylase (ADC; EC 4.1.1.9) activity increases within 3 h and peaks at about 9 h after GA3 application. This is followed by a second lower peak at about 30 h; both peaks were higher than the corresponding peaks in the controls. In contrast, no appreciable effect of GA3 on internode length was observed until about 12 h, after which time a dramatic increase in growth rate occurred and persisted for about 12 h. Specific (DL-alpha-difluoromethylarginine) and non-specific (D-arginine and L-canavanine) inhibitors of ADC strongly inhibited ADC activity and to a lesser extent internode growth. The inhibition was reversed only slightly by the addition of polyamines. Actinomycin D and cycloheximide inhibited the rise in ADC activity induced by GA3. The half-life of the enzyme was increased by GA3 treatment. The results suggest that part of the GA3-induced increase in internode growth may result from enhanced polyamine biosynthesis through the ADC pathway. Furthermore, the GA3 induced increase in ADC activity probably requires de novo synthesis of both RNA and protein. PMID:11538869

  17. Identification and characterization of the Populus sucrose synthase gene family.

    PubMed

    An, Xinmin; Chen, Zhong; Wang, Jingcheng; Ye, Meixia; Ji, Lexiang; Wang, Jia; Liao, Weihua; Ma, Huandi

    2014-04-10

    In this study, we indentified 15 sucrose synthase (SS) genes in Populus and the results of RT-qPCR revealed that their expression patterns were constitutive and partially overlapping but diverse. The release of the most recent Populus genomic data in Phytozome v9.1 has revealed the largest SS gene family described to date, comprising 15 distinct members. This information will now enable the analysis of transcript expression profiles for those that have not been previously reported. Here, we performed a comprehensive analysis of SS genes in Populus by describing the gene structure, chromosomal location and phylogenetic relationship of each family member. A total of 15 putative SS gene members were identified in the Populus trichocarpa (Torr. & Gray) genome using the SS domain and amino acid sequences from Arabidopsis thaliana as a probe. A phylogenetic analysis indicated that the 15 members could be classified into four groups that fall into three major categories: dicots, monocots & dicots 1 (M & D 1), and monocots & dicots 2 (M & D 2). In addition, the 15 SS genes were found to be unevenly distributed on seven chromosomes. The two conserved domains (sucrose synthase and glycosyl transferase) were found in this family. Meanwhile, the expression profiles of all 15 gene members in seven different organs were investigated in Populus tomentosa (Carr.) by using RT-qPCR. Additional analysis indicated that the poplar SS gene family is also involved in response to water-deficit. The current study provides basic information that will assist in elucidating the functions of poplar SS family. PMID:24508272

  18. Genome-Wide Identification of miRNAs and Their Targets Involved in the Developing Internodes under Maize Ears by Responding to Hormone Signaling

    PubMed Central

    Yang, Huili; Li, Huimin; Sun, Gaoyang; Zhao, Xiaofeng; Ding, Dong; Tang, Jihua

    2016-01-01

    Internode length is one of the decisive factors affecting plant height (PH) and ear height (EH), which are closely associated with the lodging resistance, biomass and grain yield of maize. miRNAs, currently recognized as important transcriptional/ post-transcriptional regulators, play an essential role in plant growth and development. However, their roles in developing internodes under maize ears remain unclear. To identify the roles of miRNAs and their targets in the development of internodes under maize ears, six miRNA and two degradome libraries were constructed using the 7th, 8th and 9th internodes of two inbred lines, ‘Xun928’ and ‘Xun9058’, which had significantly different internode lengths. A total of 45 and 54 miRNAs showed significant changes for each pairwise comparison among the 7th, 8th and 9th internodes of ‘Xun9058’ and ‘Xun928’, respectively. The expression of 31 miRNAs showed significant changes were common to the corresponding comparison groups of the 7th, 8th and 9th internodes of ‘Xun9058’ and ‘Xun928’. For the corresponding internodes of ‘Xun9058’ and ‘Xun928’, compared with the expression of miRNAs in the 7th, 8th and 9th internodes of ‘Xun928’, the numbers of up-regulated and down-regulated miRNAs were 11 and 36 in the 7th internode, 9 and 45 in the 8th internode, and 9 and 25 in the 9th internode of ‘Xun9058’, respectively. Moreover, 10 miRNA families containing 45 members showed significant changes at least in two internodes of ‘Xun928’ by comparing with the corresponding internodes of ‘Xun9058’. Based on the sequencing data, 20 miRNAs related to hormone signaling among the candidates, belonging to five conserved miRNA families, were selected for expression profiling using quantitative reverse-transcription polymerase chain reaction (qRT-PCR). The five miRNA families, zma-miR160, zma-miR167, zma-miR164, zma-miR169 and zma-miR393, targeted the genes encoding auxin response factor, N

  19. Uncoupling light quality from light irradiance effects in Helianthus annuus shoots: putative roles for plant hormones in leaf and internode growth.

    PubMed

    Kurepin, Leonid V; Emery, R J Neil; Pharis, Richard P; Reid, David M

    2007-01-01

    An attempt has been made to uncouple the effects of the two primary components of shade light, a reduced red to far-red (R/FR) ratio and low photosynthetically active radiation (PAR), on the elongation of the youngest internode of sunflower (Helianthus annuus) seedlings. Maximal internode growth (length and biomass) was induced by a shade light having a reduced R/FR ratio (0.85) under the low PAR of 157 micromol m(-2) s(-1). Reducing the R/FR ratio under normal PAR (421 micromol m(-2) s(-1)) gave similar growth trends, albeit with a reduced magnitude of the response. Leaf area growth showed a rather different pattern, with maximal growth occurring at the higher (normal) PAR of 421 micromol m(-2) s(-1)), but with variable effects being seen with changes in light quality. Reducing the R/FR ratio (by enrichment with FR) gave significant increases in gibberellin A(1) (GA(1)) and indole-3-acetic acid (IAA) contents in both internodes and leaves. By contrast, a lower PAR irradiance had no significant effect on GA(1) and IAA levels in internodes or leaves, but did increase the levels of other GAs, including two precursors of GA(1). Interestingly, both leaf and internode hormone content (GAs, IAA) are positively and significantly correlated with growth of the internode, as are leaf levels of abscisic acid (ABA). However, changes in these three hormones bear little relationship to leaf growth. By implication, then, the leaf may be the major source of GAs and IAA, at least, for the rapidly elongating internode. Several other hormones were also assessed in leaves for plants grown under varying R/FR ratios and PARs. Leaf ethylene production was not influenced by changes in R/FR ratio, but was significantly reduced under the normal (higher) PAR, the irradiance treatment which increased leaf growth. Levels of the growth-active free base and riboside cytokinins were significantly increased in leaves under a reduced R/FR ratio, but only at the higher (normal) PAR irradiance; other

  20. Plasma membrane domains participate in pH banding of Chara internodal cells.

    PubMed

    Schmölzer, Patric M; Höftberger, Margit; Foissner, Ilse

    2011-08-01

    We investigated the identity and distribution of cortical domains, stained by the endocytic marker FM 1-43, in branchlet internodal cells of the characean green algae Chara corallina and Chara braunii. Co-labeling with NBD C(6)-sphingomyelin, a plasma membrane dye, which is not internalized, confirmed their location in the plasma membrane, and co-labelling with the fluorescent pH indicator Lysotracker red indicated an acidic environment. The plasma membrane domains co-localized with the distribution of an antibody against a proton-translocating ATPase, and electron microscopic data confirmed their identity with elaborate plasma membrane invaginations known as charasomes. The average size and the distribution pattern of charasomes correlated with the pH banding pattern of the cell. Charasomes were larger and more frequent at the acidic regions than at the alkaline bands, indicating that they are involved in outward-directed proton transport. Inhibition of photosynthesis by DCMU prevented charasome formation, and incubation in pH buffers resulted in smaller, homogenously distributed charasomes irrespective of whether the pH was clamped at 5.5 or 8.5. These data indicate that the differential size and distribution of charasomes is not due to differences in external pH but reflects active, photosynthesis-dependent pH banding. The fact that pH banding recovered within several minutes in unbuffered medium, however, confirms that pH banding is also possible in cells with evenly distributed charasomes or without charasomes. Cortical mitochondria were also larger and more abundant at the acid bands, and their intimate association with charasomes and chloroplasts suggests an involvement in carbon uptake and photorespiration.

  1. The characean internodal cell as a model system for studying wound healing.

    PubMed

    Foissner, I; Wasteneys, G O

    2012-07-01

    This work describes the characean internodal cell as a model system for the study of wound healing and compares wounds induced by certain chemicals and UV irradiation with wounds occurring in the natural environment. We review the existing literature and define three types of wound response: (1) cortical window formation characterised by disassembly of microtubules, transient inhibition of actin-dependent cytoplasmic streaming and chloroplast detachment, (2) fibrillar wound walls characterised by exocytosis of vesicles carrying wall polysaccharides and membrane-bound cellulose synthase complexes coupled with endocytosis of surplus membrane and (3) amorphous, callose- and membrane-containing wound walls characterised by exocytosis of vesicles and endoplasmic reticulum cisternae in the absence of membrane recycling. We hypothesize that these three wound responses reflect the extent of damage, probably Ca(2+) influx, and that the secretion of Ca(2+) -loaded endoplasmic reticulum cisternae is an emergency reaction in case of severe Ca(2+) load. Microtubules are not required for wound healing but their disassembly could have a signalling function. Transient reorganisation of the actin cytoskeleton into a meshwork of randomly oriented filaments is required for the migration of wound wall forming organelles, just as occurs in tip-growing plant cells. New data presented in this study show that during the deposition of an amorphous wound wall numerous actin rings are present, which may indicate specific ion fluxes and/or a storage form for actin. In addition, we present new evidence for the exocytosis of FM1-43-stained organelles, putative endosomes, required for plasma membrane repair during wound healing. Finally, we show that quickly growing fibrillar wound walls, even when deposited in the absence of microtubules, have a highly ordered helical structure of consistent handedness comprised of cellulose microfibrils.

  2. The characean internodal cell as a model system for studying wound healing

    PubMed Central

    Foissner, I.; Wasteneys, G.O.

    2012-01-01

    Summary This work describes the characean internodal cell as a model system for the study of wound healing and compares wounds induced by certain chemicals and UV irradiation with wounds occurring in the natural environment. We review the existing literature and define three types of wound response: 1) cortical window formation characterized by disassembly of microtubules, transient inhibition of actin-dependent cytoplasmic streaming and chloroplast detachment, 2) fibrillar wound walls characterized by exocytosis of vesicles carrying wall polysaccharides and membrane-bound cellulose synthase complexes coupled with endocytosis of surplus membrane and 3) amorphous, callose- and membrane-containing wound walls characterized by exocytosis of vesicles and endoplasmic reticulum (ER) cisternae in the absence of membrane recycling. We hypothesize that these three wound responses reflect the extent of damage, probably Ca2+ influx, and that the secretion of Ca2+ - loaded ER cisternae is an emergency reaction in case of severe Ca2+ load. Microtubules are not required for wound healing but their disassembly could have a signalling function. Transient reorganization of the actin cytoskeleton into a meshwork of randomly oriented filaments is required for the migration of wound wall forming organelles, just as occurs in tip-growing plant cells. New data presented in this study show that during the deposition of an amorphous wound wall numerous actin rings are present, which may indicate specific ion fluxes and/or a storage form for actin. In addition, we present new evidence for the exocytosis of FM1-43-stained organelles, putative endosomes, required for plasma membrane repair during wound healing. Finally we show that quickly growing fibrillar wound walls, even when deposited in the absence of microtubules, have a highly ordered helical structure of consistent handedness comprised of cellulose microfibrils. PMID:22118365

  3. Physical basis for altered stem elongation rates in internode length mutants of Pisum

    SciTech Connect

    Behringer, F.J.; Davies, P.J. ); Cosgrove, D.J. ); Reid, J.B. )

    1990-09-01

    Biophysical parameters related to gibberellin (GA)-dependent stem elongation were examined in dark-grown stem-length genotypes of Pisum sativum L. The rate of internode expansion in these genotypes is altered due to recessive mutations which affect either the endogenous levels of, or response to, GA. The GA deficient dwarf L181 (ls), two GA insensitive semierectoides dwarfs NGB5865 and NGB5862 (lka and lkb, respectively) and the slender line L197 (la cry{sup s}), which is tall regardless of GA content, were compared to the wild-type tall cultivar, Torsdag. Osmotic pressure, estimated by vapor pressure osmometry, and turgor pressure, measured directly with a pressure probe, did not correlate with the differences in growth rate among the genotypes. Mechanical wall properties of frozen-thawed tissue were measured using a constant force assay. GA deficiency resulted in increased wall stiffness judged both on the basis of plastic compliance and plastic extensibility normalized for equal stem circumference. Plastic compliance was not reduced in the GA insensitive dwarfs, though lka reduced circumference-normalized plasticity. In contrast, in vivo wall relaxation, determined by the pressure-block technique, differed among genotypes in a manner which did correlate with extension rates. The wall yield threshold was 1 bar or less in the tall lines, but ranged from 3 to 6 bars in the dwarf genotypes. The results with the ls mutant indicate that GA enhances stem elongation by both decreasing the wall yield threshold and increasing the wall yield coefficient. In the GA-insensitive mutants, lka and lkb, the wall yield threshold is substantially elevated. Plants possessing lka may also possess a reduced wall yield coefficient.

  4. Rapid auxin-induced stimulation of cell wall synthesis in pea internodes

    SciTech Connect

    Kutschera, U.; Briggs, W.R.

    1987-05-01

    The effect of auxin (indole-3-acetic acid; IAA) on growth and incorporation of myo-(2-/sup 3/H(N)) inositol ((/sup 3/H)Ins) into noncellulosic polysacchharides in the cell walls of third internode sections from red light-grown pea seedlings (Pisum sativum L. cv. Alaska) was investigated. Intact section were incubated on (/sup 3/H)Ins for 4 hr to permit uptake of the tracer and then IAA was added. Growth started after a lag phase of 15 min under these conditions. The sections were removed from the tracer and separated into epidermis and cortical cylinder (cortex plus vascular tissue). In the epidermis, IAA-induced stimulation of (/sup 3/H)Ins incorporation started after a lag of 15 min. The amount of incorporation was 15% higher after 30 min and 24% higher after 2 hr than in the control. In the cortical cylinder, IAA-induced stimulation of (/sup 3/H)Ins incorporation started only approx. = 1 hr after adding IAA. The ionophore monensin (20 ..mu..M) inhibited the IAA-induced growth by 95%. Under these conditions, the IAA-induced stimulation of (/sup 3/H)Ins incorporation and the IAA-induced increase in in vivo extensibility of the sections was almost completely inhibited, although oxygen uptake was unaffected. The authors suggest that wall synthesis (as represented by (/sup 3/H)Ins incorporation) and wall loosening (increase in in vivo extensibility) are related processes. The results support the hypothesis that IAA induces growth by rapid simulation of cell wall synthesis in the growth-limiting epidermal cell layer.

  5. Physical basis for altered stem elongation rates in internode length mutants of Pisum

    NASA Technical Reports Server (NTRS)

    Behringer, F. J.; Cosgrove, D. J.; Reid, J. B.; Davies, P. J.

    1990-01-01

    Biophysical parameters related to gibberellin (GA)-dependent stem elongation were examined in dark-grown stem-length genotypes of Pisum sativum L. The rate of internode expansion in these genotypes is altered due to recessive mutations which affect either the endogenous levels of, or response to, GA. The GA deficient dwarf L181 (ls), two GA insensitive semierectoides dwarfs NGB5865 and NGB5862 (lka and lkb, respectively) and the slender' line L197 (la crys), which is tall regardless of GA content, were compared to the wild-type tall cultivar, Torsdag. Osmotic pressure, estimated by vapor pressure osmometry, and turgor pressure, measured directly with a pressure probe, did not correlate with the differences in growth rate among the genotypes. Mechanical wall properties of frozen-thawed tissue were measured using a constant force assay. GA deficiency resulted in increased wall stiffness judged both on the basis of plastic compliance and plastic extensibility normalized for equal stem circumference. Plastic compliance was not reduced in the GA insensitive dwarfs, though lka reduced circumference-normalized plasticity. In contrast, in vivo wall relaxation, determined by the pressure-block technique, differed among genotypes in a manner which did correlate with extension rates. The wall yield threshold was 1 bar or less in the tall lines, but ranged from 3 to 6 bars in the dwarf genotypes. The results with the ls mutant indicate that GA enhances stem elongation by both decreasing the wall yield threshold and increasing the wall yield coefficient. In the GA-insensitive mutants, lka and lkb, the wall yield threshold is substantially elevated. Plants possessing lka may also possess a reduced wall yield coefficient.

  6. Increasing the productivity of short-rotation Populus plantations. Final report

    SciTech Connect

    DeBell, D.S.; Harrington, C.A.; Clendenen, G.W.; Radwan, M.A.; Zasada, J.C.

    1997-12-31

    This final report represents the culmination of eight years of biological research devoted to increasing the productivity of short rotation plantations of Populus trichocarpa and Populus hybrids in the Pacific Northwest. Studies provide an understanding of tree growth, stand development and biomass yield at various spacings, and how patterns differ by Populus clone in monoclonal and polyclonal plantings. Also included is some information about factors related to wind damage in Populus plantings, use of leaf size as a predictor of growth potential, and approaches for estimating tree and stand biomass and biomass growth. Seven research papers are included which provide detailed methods, results, and interpretations on these topics.

  7. Shortened internodal length of dermal myelinated nerve fibres in Charcot–Marie-Tooth disease type 1A

    PubMed Central

    Saporta, Mario A.; Katona, Istvan; Lewis, Richard A.; Masse, Stacey; Shy, Michael E.

    2009-01-01

    Charcot–Marie-Tooth disease type 1A is the most common inherited neuropathy and is caused by duplication of chromosome 17p11.2 containing the peripheral myelin protein-22 gene. This disease is characterized by uniform slowing of conduction velocities and secondary axonal loss, which are in contrast with non-uniform slowing of conduction velocities in acquired demyelinating disorders, such as chronic inflammatory demyelinating polyradiculoneuropathy. Mechanisms responsible for the slowed conduction velocities and axonal loss in Charcot–Marie-Tooth disease type 1A are poorly understood, in part because of the difficulty in obtaining nerve samples from patients, due to the invasive nature of nerve biopsies. We have utilized glabrous skin biopsies, a minimally invasive procedure, to evaluate these issues systematically in patients with Charcot–Marie-Tooth disease type 1A (n = 32), chronic inflammatory demyelinating polyradiculoneuropathy (n = 4) and healthy controls (n = 12). Morphology and molecular architecture of dermal myelinated nerve fibres were examined using immunohistochemistry and electron microscopy. Internodal length was uniformly shortened in patients with Charcot–Marie-Tooth disease type 1A, compared with those in normal controls (P < 0.0001). Segmental demyelination was absent in the Charcot–Marie-Tooth disease type 1A group, but identifiable in all patients with chronic inflammatory demyelinating polyradiculoneuropathy. Axonal loss was measurable using the density of Meissner corpuscles and associated with an accumulation of intra-axonal mitochondria. Our study demonstrates that skin biopsy can reveal pathological and molecular architectural changes that distinguish inherited from acquired demyelinating neuropathies. Uniformly shortened internodal length in Charcot–Marie-Tooth disease type 1A suggests a potential developmental defect of internodal lengthening. Intra-axonal accumulation of mitochondria provides new insights into the

  8. Using Populus as a lignocellulosic feedstock for bioethanol.

    PubMed

    Porth, Ilga; El-Kassaby, Yousry A

    2015-04-01

    Populus species along with species from the sister genus Salix will provide valuable feedstock resources for advanced second-generation biofuels. Their inherent fast growth characteristics can particularly be exploited for short rotation management, a time and energy saving cultivation alternative for lignocellulosic feedstock supply. Salicaceae possess inherent cell wall characteristics with favorable cellulose to lignin ratios for utilization as bioethanol crop. We review economically important traits relevant for intensively managed biofuel crop plantations, genomic and phenotypic resources available for Populus, breeding strategies for forest trees dedicated to bioenergy provision, and bioprocesses and downstream applications related to opportunities using Salicaceae as a renewable resource. Challenges need to be resolved for every single step of the conversion process chain, i.e., starting from tree domestication for improved performance as a bioenergy crop, bioconversion process, policy development for land use changes associated with advanced biofuels, and harvest and supply logistics associated with industrial-scale biorefinery plants using Populus as feedstock. Significant hurdles towards cost and energy efficiency, environmental friendliness, and yield maximization with regards to biomass pretreatment, saccharification, and fermentation of celluloses and the sustainability of biorefineries as a whole still need to be overcome. PMID:25676392

  9. Using Populus as a lignocellulosic feedstock for bioethanol.

    PubMed

    Porth, Ilga; El-Kassaby, Yousry A

    2015-04-01

    Populus species along with species from the sister genus Salix will provide valuable feedstock resources for advanced second-generation biofuels. Their inherent fast growth characteristics can particularly be exploited for short rotation management, a time and energy saving cultivation alternative for lignocellulosic feedstock supply. Salicaceae possess inherent cell wall characteristics with favorable cellulose to lignin ratios for utilization as bioethanol crop. We review economically important traits relevant for intensively managed biofuel crop plantations, genomic and phenotypic resources available for Populus, breeding strategies for forest trees dedicated to bioenergy provision, and bioprocesses and downstream applications related to opportunities using Salicaceae as a renewable resource. Challenges need to be resolved for every single step of the conversion process chain, i.e., starting from tree domestication for improved performance as a bioenergy crop, bioconversion process, policy development for land use changes associated with advanced biofuels, and harvest and supply logistics associated with industrial-scale biorefinery plants using Populus as feedstock. Significant hurdles towards cost and energy efficiency, environmental friendliness, and yield maximization with regards to biomass pretreatment, saccharification, and fermentation of celluloses and the sustainability of biorefineries as a whole still need to be overcome.

  10. Blockage by gibberellic Acid of phytochrome effects on growth, auxin responses, and flavonoid synthesis in etiolated pea internodes.

    PubMed

    Russell, D W; Galston, A W

    1969-09-01

    Red light inhibits the growth of etiolated pea internodes, causes a shift toward higher indoleacetic acid (IAA) concentrations in the IAA dose-response curve of excised sections, and promotes the synthesis in intact internodes of kaempferol-3-triglucoside. Gibberellic acid (GA(3)) prevents all 3 effects, the first effect substantially and the last 2 completely. This suggests GA(3) blockage of an early or basic event initiated by the active form of phytochrome. The red light-induced shift in the IAA dose-response curve of excised sections is consistent with a light-induced increase in the activity of an IAA destruction system, since the magnitude of the red light inhibition varied with IAA concentration. The red light and GA(3) effects on growth and on flavonoid synthesis are consistent with the view that phytochrome may control growth by regulating the synthesis of phenolic compounds which act as cofactors in an IAA-oxidase system. GA(3) reversal of the red light-induced shift in the IAA dose-response curve involves both growth promotion and inhibition by GA(3) at different IAA concentrations and this, together with the GA(3) reversal of light-induced flavonoid synthesis, supports the suggested regulatory role of phenolic compounds in growth. PMID:16657193

  11. 14C/C measurements support Andreev's internode method to determine lichen growth rates in Cladina stygia (Fr.) Ahti

    SciTech Connect

    Holt, E; Bench, G

    2007-12-05

    Growth rates and the ability to date an organism can greatly contribute to understanding its population biology and community dynamics. 1n 1954, Andreev proposed a method to date Cladina, a fruticose lichen, using total thallus length and number of internodes. No research, however, has demonstrated the reliability of this technique or compared its estimates to those derived by other means. In this study, we demonstrate the utility of {sup 14}C/C ratios to determine lichen age and growth rate in Cladina stygia (Fr.) Ahti collected from northwestern Alaska, USA. The average growth rate using {sup 14}C/C ratios was 6.5 mm {center_dot} yr{sup -1}, which was not significantly different from growth rates derived by Andreev's internode method (average = 6.2 mm {center_dot} yr{sup -1}); thus, suggesting the reliability of Andreev's simple field method for dating lichens. In addition, we found lichen growth rates appeared to differ with geographic location, yet did not seem related to ambient temperature and total precipitation.

  12. Rice HOX12 Regulates Panicle Exsertion by Directly Modulating the Expression of ELONGATED UPPERMOST INTERNODE1[OPEN

    PubMed Central

    Gao, Shaopei; Fang, Jun; Xu, Fan; Wang, Wei

    2016-01-01

    Bioactive gibberellins (GAs) are key endogenous regulators of plant growth. Previous work identified ELONGATED UPPERMOST INTERNODE1 (EUI1) as a GA-deactivating enzyme that plays an important role in panicle exsertion from the flag leaf sheath in rice (Oryza sativa). However, the mechanism that regulates EUI1 activity during development is still largely unexplored. In this study, we identified the dominant panicle enclosure mutant regulator of eui1 (ree1-D), whose phenotype is caused by the activation of the homeodomain-leucine zipper transcription factor HOX12. Diminished HOX12 expression by RNA interference enhanced panicle exsertion, mimicking the eui1 phenotype. HOX12 knockdown plants contain higher levels of the major biologically active GAs (such as GA1 and GA4) than the wild type. The expression of EUI1 is elevated in the ree1-D mutant but reduced in HOX12 knockdown plants. Interestingly, both HOX12 and EUI1 are predominantly expressed in panicles, where GA4 is highly accumulated. Yeast one-hybrid, electrophoretic mobility shift assay, and chromatin immunoprecipitation analyses showed that HOX12 physically interacts with the EUI1 promoter both in vitro and in vivo. Furthermore, plants overexpressing HOX12 in the eui1 mutant background retained the elongated uppermost internode phenotype. These results indicate that HOX12 acts directly through EUI1 to regulate panicle exsertion in rice. PMID:26977084

  13. Comparative nucleotide diversity across North American and European populus species.

    PubMed

    Ismail, Mohamed; Soolanayakanahally, Raju Y; Ingvarsson, Pär K; Guy, Robert D; Jansson, Stefan; Silim, Salim N; El-Kassaby, Yousry A

    2012-06-01

    Nucleotide polymorphisms in two North American balsam poplars (Populus trichocarpa Torr. & Gray and P. balsamifera L.; section Tacamahaca), and one Eurasian aspen (P. tremula L.; section Populus) were compared using nine loci involved in defense, stress response, photoperiodism, freezing tolerance, and housekeeping. Nucleotide diversity varied among species and was highest for P. tremula (θ(w) = 0.005, π(T) = 0.007) as compared to P. balsamifera (θ(w) = 0.004, π(T) = 0.005) or P. trichocarpa (θ(w) = 0.002, π(T) = 0.003). Across species, the defense and the stress response loci accounted for the majority of the observed level of nucleotide diversity. In general, the studied loci did not deviate from neutral expectation either at the individual locus (non-significant normalized Fay and Wu's H) or at the multi-locus level (non-significant HKA test). Using molecular clock analysis, section Tacamahaca probably shared a common ancestor with section Populus approximately 4.5 million year ago. Divergence between the two closely related balsam poplars was about 0.8 million years ago, a pattern consistent with an isolation-with-migration (IM) model. As expected, P. tremula showed a five-fold higher substitution rate (2 × 10(-8) substitution/site/year) compared to the North American species (0.4 × 10(-8) substitution/site/year), probably reflecting its complex demographic history. Linkage disequilibrium (LD) varied among species with a more rapid decay in the North American species (<400 bp) in comparison to P. tremula (≫400 bp). The similarities in nucleotide diversity pattern and LD decay of the two balsam poplar species likely reflects the recent time of their divergence.

  14. Balsacones D-I, dihydrocinnamoyl flavans from Populus balsamifera buds.

    PubMed

    Simard, François; Legault, Jean; Lavoie, Serge; Pichette, André

    2014-04-01

    A phytochemical investigation of an ethanolic extract from Populus balsamifera L. buds resulted in the isolation and characterization of twelve new flavan derivatives consisting of six pairs of enantiomers. Structures of (+) and (-)-balsacones D-I were elucidated based on spectroscopic data (1D and 2D NMR, MS) and their absolute configurations were established using X-ray single crystal diffraction analysis and ECD computational calculations. Antibacterial activity and cytotoxicity of all purified enantiomers were evaluated in vitro against Staphylococcus aureus and human skin fibroblast cells, respectively.

  15. A simple shoot multiplication procedure using internode explants, and its application for particle bombardment and Agrobacterium-mediated transformation in watercress.

    PubMed

    Ogita, Shinjiro; Usui, Miki; Shibutani, Nanae; Kato, Yasuo

    2009-07-01

    A shoot multiplication system derived from internode explants was investigated with the aim of improving genetic characteristics of watercress (Nasturtium officinale R. Br.). Internodes of ca. 1 cm excised from in vitro stock shoot culture were placed on half-strength Murashige and Skoog (MS) medium supplemented with 3 muM 2,4-dichlorophenoxyacetic acid as a pre-treatment. Laser scanning microscopy indicated clearly that the first sign of meristematic cell division could be seen after 1-2 days of pre-culture, and meristematic tissues multiplied along the vascular cambium of the internode segment during 7 days of culture. Multiple shoots could be obtained from more than 90% of the pre-treated explants when they were subsequently transferred to MS medium supplemented with 1 muM thidiazuron for 3 weeks. These findings indicate that pre-treatment of the internodes for 7 days promoted their capacity for organogenesis. Using this pre-treatment, frequent generation of transgenic watercress plants was achieved by adapting particle bombardment and Agrobacterium-mediated transformation techniques with a construct expressing a synthetic green florescent protein gene. PMID:19308313

  16. A simple shoot multiplication procedure using internode explants, and its application for particle bombardment and Agrobacterium-mediated transformation in watercress.

    PubMed

    Ogita, Shinjiro; Usui, Miki; Shibutani, Nanae; Kato, Yasuo

    2009-07-01

    A shoot multiplication system derived from internode explants was investigated with the aim of improving genetic characteristics of watercress (Nasturtium officinale R. Br.). Internodes of ca. 1 cm excised from in vitro stock shoot culture were placed on half-strength Murashige and Skoog (MS) medium supplemented with 3 muM 2,4-dichlorophenoxyacetic acid as a pre-treatment. Laser scanning microscopy indicated clearly that the first sign of meristematic cell division could be seen after 1-2 days of pre-culture, and meristematic tissues multiplied along the vascular cambium of the internode segment during 7 days of culture. Multiple shoots could be obtained from more than 90% of the pre-treated explants when they were subsequently transferred to MS medium supplemented with 1 muM thidiazuron for 3 weeks. These findings indicate that pre-treatment of the internodes for 7 days promoted their capacity for organogenesis. Using this pre-treatment, frequent generation of transgenic watercress plants was achieved by adapting particle bombardment and Agrobacterium-mediated transformation techniques with a construct expressing a synthetic green florescent protein gene.

  17. Effects of lanthanum on calcium and magnesium contents and cytoplasmic streaming of internodal cells of Chara corallina.

    PubMed

    Li, Zijie; Zhang, Zhiyong; Yu, Ming; Zhou, Yunlong; Zhao, Yuliang

    2011-10-01

    Biological and environmental effects of lanthanide series of elements have received much attention recently due to their wide applications. In this study, effects of La(3+) treatments on calcium and magnesium concentrations as well as cytoplasmic streaming of internodal cells of Chara corallina were investigated. At all treatment concentrations (10, 100, and 1,000 μM), La(3+) significantly decreased calcium concentrations in the cell-wall fractions after 5-h treatments. Calcium concentrations in the cell contents and magnesium concentrations in the cell-wall fractions were reduced by 100 and 1,000 μM La(3+) treatments. However, cytoplasmic streaming as an indicator of [Ca(2+)](cyt) was only inhibited at the highest La(3+) concentration (1,000 μM). The results suggest that La(3+) may affect cellular calcium homeostasis by actions other than as a simple Ca(2+) antagonist. La(3+) could partially compensate for calcium deficiency at certain concentrations.

  18. Water use sources of desert riparian Populus euphratica forests.

    PubMed

    Si, Jianhua; Feng, Qi; Cao, Shengkui; Yu, Tengfei; Zhao, Chunyan

    2014-09-01

    Desert riparian forests are the main body of natural oases in the lower reaches of inland rivers; its growth and distribution are closely related to water use sources. However, how does the desert riparian forest obtains a stable water source and which water sources it uses to effectively avoid or overcome water stress to survive? This paper describes an analysis of the water sources, using the stable oxygen isotope technique and the linear mixed model of the isotopic values and of desert riparian Populus euphratica forests growing at sites with different groundwater depths and conditions. The results showed that the main water source of Populus euphratica changes from water in a single soil layer or groundwater to deep subsoil water and groundwater as the depth of groundwater increases. This appears to be an adaptive selection to arid and water-deficient conditions and is a primary reason for the long-term survival of P. euphratica in the desert riparian forest of an extremely arid region. Water contributions from the various soil layers and from groundwater differed and the desert riparian P. euphratica forests in different habitats had dissimilar water use strategies.

  19. Water use sources of desert riparian Populus euphratica forests.

    PubMed

    Si, Jianhua; Feng, Qi; Cao, Shengkui; Yu, Tengfei; Zhao, Chunyan

    2014-09-01

    Desert riparian forests are the main body of natural oases in the lower reaches of inland rivers; its growth and distribution are closely related to water use sources. However, how does the desert riparian forest obtains a stable water source and which water sources it uses to effectively avoid or overcome water stress to survive? This paper describes an analysis of the water sources, using the stable oxygen isotope technique and the linear mixed model of the isotopic values and of desert riparian Populus euphratica forests growing at sites with different groundwater depths and conditions. The results showed that the main water source of Populus euphratica changes from water in a single soil layer or groundwater to deep subsoil water and groundwater as the depth of groundwater increases. This appears to be an adaptive selection to arid and water-deficient conditions and is a primary reason for the long-term survival of P. euphratica in the desert riparian forest of an extremely arid region. Water contributions from the various soil layers and from groundwater differed and the desert riparian P. euphratica forests in different habitats had dissimilar water use strategies. PMID:24816539

  20. Nucleotide diversity and linkage disequilibrium in balsam poplar (Populus balsamifera).

    PubMed

    Olson, Matthew S; Robertson, Amanda L; Takebayashi, Naoki; Silim, Salim; Schroeder, William R; Tiffin, Peter

    2010-04-01

    *Current perceptions that poplars have high levels of nucleotide variation, large effective population sizes, and rapid decay of linkage disequilibrium are based primarily on studies from one poplar species, Populus tremula. *We analysed 590 gene fragments (average length 565 bp) from each of 15 individuals from different populations from throughout the range of Populus balsamifera. *Nucleotide diversity (theta(total) = 0.0028, pi = 0.0027) was low compared with other trees and model agricultural systems. Patterns of nucleotide diversity and site frequency spectra were consistent with purifying selection on replacement and intron sites. When averaged across all loci we found no evidence for decay of linkage disequilibrium across 750 bp, consistent with the low estimates of the scaled recombination parameter, rho = 0.0092. *Compared with P. tremula, a well studied congener with a similar distribution, P. balsamifera has low diversity and low effective recombination, both of which indicate a lower effective population size in P. balsamifera. Patterns of diversity and linkage indicate that there is considerable variation in population genomic patterns among poplar species and unlike P. tremula, association mapping techniques in balsam poplar should consider sampling single nucleotide polymorphisms (SNPs) at well-spaced intervals.

  1. FM dyes label sterol-rich plasma membrane domains and are internalized independently of the cytoskeleton in characean internodal cells.

    PubMed

    Klima, Andreas; Foissner, Ilse

    2008-10-01

    We applied the endocytic markers FM1-43, FM4-64 and filipin to internodal cells of the green alga Chara corallina. Both FM dyes stained stable, long-living plasma membrane patches with a diameter of up to 1 microm. After 5 min, FM dyes labeled cortical, trembling structures up to 500 nm in size. After 15 min, FM dyes localized to endoplasmic organelles up to 1 microm in diameter, which migrated actively along actin bundles or participated in cytoplasmic mass streaming. After 30-60 min, FM fluorescence appeared in the membrane of small, endoplasmic vacuoles but not in that of the central vacuole. Some of the FM-labeled organelles were also stained by neutral red and lysotracker yellow, indicative of acidic compartments. Filipin, a sterol-specific marker, likewise labeled plasma membrane domains which co-localized with the FM patches. However, internalization of filipin could not be observed. KCN, cytochalasin D, latrunculin B and oryzalin had no effect on size, shape and distribution of FM- and filipin-labeled plasma membrane domains. Internalization of FM dyes was inhibited by KCN but not by drugs which interfere with the actin or microtubule cytoskeleton. Our data indicate that the plasma membrane of characean internodal cells contains discrete domains which are enriched in sterols and probably correspond to clusters of lipid rafts. The inhibitor experiments suggest that FM uptake is active but independent of actin filaments, actin polymerization and microtubules. The possible function of the sterol-rich, FM labeled plasma membrane areas and the significance of actin-independent FM internalization (via endocytosis or energy-dependent flippases) are discussed.

  2. Photophysiology of the Elongated Internode (ein) Mutant of Brassica rapa: ein Mutant Lacks a Detectable Phytochrome B-Like Polypeptide.

    PubMed

    Devlin, P F; Rood, S B; Somers, D E; Quail, P H; Whitelam, G C

    1992-11-01

    Several phytochrome-controlled processes have been examined in etiolated and light-grown seedlings of a normal genotype and the elongated internode (ein/ein) mutant of rapid-cycling Brassica rapa. Although etiolated ein seedlings displayed normal sensitivity to prolonged far-red light with respect to inhibition of hypocotyl elongation, expansion of cotyledons, and synthesis of anthocyanin, they displayed reduced sensitivity to prolonged red light for all three of these deetiolation responses. In contrast to normal seedlings, light-grown ein seedlings did not show a growth promotion in response to end-of-day far-red irradiation. Additionally, whereas the first internode of light-grown normal seedlings showed a marked increase in elongation in response to reduced ratio of red to far-red light, ein seedlings showed only a small elongation response. When blots of protein extracts from etiolated and light-treated ein and normal seedlings were probed with monoclonal antibody to phytochrome A, an immunostaining band at about 120 kD was observed for both extracts. The immunostaining intensity of this band was substantially reduced for extracts of light-treated normal and ein seedlings. A mixture of three monoclonal antibodies directed against phytochrome B from Arabidopsis thaliana immunostained a band at about 120 kD for extracts of etiolated and light-treated normal seedlings. This band was undetectable in extracts of ein seedlings. We propose that ein is a photoreceptor mutant that is deficient in a light-stable phytochrome B-like species.

  3. Auxin-Growth Relationships in Maize Coleoptiles and Pea Internodes and Control by Auxin of the Tissue Sensitivity to Auxin

    PubMed Central

    Haga, Ken; Iino, Moritoshi

    1998-01-01

    Growth of a zone of maize (Zea mays L.) coleoptiles and pea (Pisum sativum L.) internodes was greatly suppressed when the organ was decapitated or ringed at an upper position with the auxin transport inhibitor N-1-naphthylphthalamic acid (NPA) mixed with lanolin. The transport of apically applied 3H-labeled indole-3-acetic acid (IAA) was similarly inhibited by NPA. The growth suppressed by NPA or decapitation was restored by the IAA mixed with lanolin and applied directly to the zone, and the maximal capacity to respond to IAA did not change after NPA treatment, although it declined slightly after decapitation. The growth rate at IAA saturation was greater than the rate in intact, nontreated plants. It was concluded that growth is limited and controlled by auxin supplied from the apical region. In maize coleoptiles the sensitivity to IAA increased more than 3 times when the auxin level was reduced over a few hours with NPA treatment. This result, together with our previous result that the maximal capacity to respond to IAA declines in pea internodes when the IAA level is enhanced for a few hours, indicates that the IAA concentration-response relationship is subject to relatively slow adaptive regulation by IAA itself. The spontaneous growth recovery observed in decapitated maize coleoptiles was prevented by an NPA ring placed at an upper position of the stump, supporting the view that recovery is due to regenerated auxin-producing activity. The sensitivity increase also appeared to participate in an early recovery phase, causing a growth rate greater than in intact plants. PMID:9701602

  4. Photosynthesis-dependent formation of convoluted plasma membrane domains in Chara internodal cells is independent of chloroplast position.

    PubMed

    Foissner, Ilse; Sommer, Aniela; Hoeftberger, Margit

    2015-07-01

    The characean green alga Chara australis forms complex plasma membrane convolutions called charasomes when exposed to light. Charasomes are involved in local acidification of the surrounding medium which facilitates carbon uptake required for photosynthesis. They have hitherto been only described in the internodal cells and in close contact with the stationary chloroplasts. Here, we show that charasomes are not only present in the internodal cells of the main axis, side branches, and branchlets but that the plasma membranes of chloroplast-containing nodal cells, protonemata, and rhizoids are also able to invaginate into complex domains. Removal of chloroplasts by local irradiation with intense light revealed that charasomes can develop at chloroplast-free "windows" and that the resulting pH banding pattern is independent of chloroplast or window position. Charasomes were not detected along cell walls containing functional plasmodesmata. However, charasomes formed next to a smooth wound wall which was deposited onto the plasmodesmata-containing wall when the neighboring cell was damaged. In contrast, charasomes were rarely found at uneven, bulged wound walls which protrude into the streaming endoplasm and which were induced by ligation or puncturing. The results of this study show that charasome formation, although dependent on photosynthesis, does not require intimate contact with chloroplasts. Our data suggest further that the presence of plasmodesmata inhibits charasome formation and/or that exposure to the outer medium is a prerequisite for charasome formation. Finally, we hypothesize that the absence of charasomes at bulged wound walls is due to the disturbance of uniform laminar mass streaming. PMID:25524777

  5. Photophysiology of the Elongated Internode (ein) Mutant of Brassica rapa: ein Mutant Lacks a Detectable Phytochrome B-Like Polypeptide.

    PubMed

    Devlin, P F; Rood, S B; Somers, D E; Quail, P H; Whitelam, G C

    1992-11-01

    Several phytochrome-controlled processes have been examined in etiolated and light-grown seedlings of a normal genotype and the elongated internode (ein/ein) mutant of rapid-cycling Brassica rapa. Although etiolated ein seedlings displayed normal sensitivity to prolonged far-red light with respect to inhibition of hypocotyl elongation, expansion of cotyledons, and synthesis of anthocyanin, they displayed reduced sensitivity to prolonged red light for all three of these deetiolation responses. In contrast to normal seedlings, light-grown ein seedlings did not show a growth promotion in response to end-of-day far-red irradiation. Additionally, whereas the first internode of light-grown normal seedlings showed a marked increase in elongation in response to reduced ratio of red to far-red light, ein seedlings showed only a small elongation response. When blots of protein extracts from etiolated and light-treated ein and normal seedlings were probed with monoclonal antibody to phytochrome A, an immunostaining band at about 120 kD was observed for both extracts. The immunostaining intensity of this band was substantially reduced for extracts of light-treated normal and ein seedlings. A mixture of three monoclonal antibodies directed against phytochrome B from Arabidopsis thaliana immunostained a band at about 120 kD for extracts of etiolated and light-treated normal seedlings. This band was undetectable in extracts of ein seedlings. We propose that ein is a photoreceptor mutant that is deficient in a light-stable phytochrome B-like species. PMID:16653143

  6. Photosynthesis-dependent formation of convoluted plasma membrane domains in Chara internodal cells is independent of chloroplast position.

    PubMed

    Foissner, Ilse; Sommer, Aniela; Hoeftberger, Margit

    2015-07-01

    The characean green alga Chara australis forms complex plasma membrane convolutions called charasomes when exposed to light. Charasomes are involved in local acidification of the surrounding medium which facilitates carbon uptake required for photosynthesis. They have hitherto been only described in the internodal cells and in close contact with the stationary chloroplasts. Here, we show that charasomes are not only present in the internodal cells of the main axis, side branches, and branchlets but that the plasma membranes of chloroplast-containing nodal cells, protonemata, and rhizoids are also able to invaginate into complex domains. Removal of chloroplasts by local irradiation with intense light revealed that charasomes can develop at chloroplast-free "windows" and that the resulting pH banding pattern is independent of chloroplast or window position. Charasomes were not detected along cell walls containing functional plasmodesmata. However, charasomes formed next to a smooth wound wall which was deposited onto the plasmodesmata-containing wall when the neighboring cell was damaged. In contrast, charasomes were rarely found at uneven, bulged wound walls which protrude into the streaming endoplasm and which were induced by ligation or puncturing. The results of this study show that charasome formation, although dependent on photosynthesis, does not require intimate contact with chloroplasts. Our data suggest further that the presence of plasmodesmata inhibits charasome formation and/or that exposure to the outer medium is a prerequisite for charasome formation. Finally, we hypothesize that the absence of charasomes at bulged wound walls is due to the disturbance of uniform laminar mass streaming.

  7. A cohesion/tension mechanism explains the gating of water channels (aquaporins) in Chara internodes by high concentration.

    PubMed

    Ye, Qing; Wiera, Boguslaw; Steudle, Ernst

    2004-02-01

    Isolated internodes of Chara corallina have been used to study the gating of aquaporins (water channels) in the presence of high concentrations of osmotic solutes of different size (molecular weight). Osmolytes were acetone and three glycol ethers: ethylene glycol monomethyl ether (EGMME), diethylene glycol monomethyl ether (DEGMME), and triethylene glycol monoethyl ether (TEGMEE). The 'osmotic efficiency' of osmolytes was quite different. Their reflection coefficients ranged between 0.15 (acetone), 0.59 (EGMME), 0.78 (DEGMME), and 0.80 (TEGMEE). Bulk water permeability (Lp) and diffusive permeabilities (Ps) of heavy water (HDO), hydrogen peroxide (H2O2), acetone, and glycol ethers (EGMME, DEGMME, and TEGMEE) were measured using a cell pressure probe. Cells were treated with different concentrations of osmotic solutes of up to 800 mM ( approximately 2.0 MPa of osmotic pressure). Inhibition of aquaporin activity increased with both increasing concentration and size of solutes (reflection coefficients). As cell Lp decreased, Ps increased, indicating that water and solutes used different passages across the plasma membrane. Similar to earlier findings of an osmotic gating of ion channels, a cohesion/tension model of the gating of water channels in Chara internodes by high concentration is proposed. According to the model, tensions (negative pressures) within water channels affected the open/closed state by changing the free energy between states and favoured a distorted/collapsed rather than the open state. They should have differed depending on the concentration and size of solutes that are more or less excluded from aquaporins. The bigger the solute, the lower was the concentration required to induce a reversible closure of aquaporins, as predicted by the model.

  8. Initial characterization of shade avoidance response suggests functional diversity between Populus phytochrome B genes.

    SciTech Connect

    Karve, Abhijit A; Weston, David; Jawdy, Sara; Gunter, Lee E; Allen, Sara M; Yang, Xiaohan; Wullschleger, Stan D; Tuskan, Gerald A

    2012-01-01

    Shade avoidance signaling in higher plants involves perception of the incident red/far-red (R/FR) light by phytochromes and the modulation of downstream transcriptional networks to regulate developmental plasticity in relation to heterogeneous light environments. In this study, we characterized the expression and functional features of Populus phytochrome (PHY) gene family as well as the transcriptional responses of Populus to the changes in R/FR light. Expression data indicated that PHYA is the predominant PHY in the dark grown Populus seedling whereas PHYBs are most abundant in mature tissue types. Out of three Populus PHYs, PHYA is light labile and localized to cytosol in dark whereas both PHYB1 and PHYB2 are light stable and are localized to nucleus in mesophyll protoplasts. When expressed in Arabidopsis, PHYB1 rescued Arabidopsis phyB mutant phenotype whereas PHYB2 did not, suggesting functional diversification between these two gene family members. However, phenotypes of transgenic Populus lines with altered expression of PHYB1, PHYB2 or both and the expression of candidate shade response genes in these transgenic lines suggest that PHYB1 and PHYB2 may have distinct yet overlapping functions. The RNAseq results and analysis of Populus exposed to enriched-FR light indicate that genes associated in cell wall modification and brassinosteroid signaling were induced under far red light. Overall our data indicate that Populus transcriptional responses are at least partially conserved with Arabidopsis.

  9. Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa)

    PubMed Central

    2012-01-01

    Background CCCH zinc finger proteins contain a typical motif of three cysteines and one histidine residues and serve regulatory functions at all stages of mRNA metabolism. In plants, CCCH type zinc finger proteins comprise a large gene family represented by 68 members in Arabidopsis and 67 in rice. These CCCH proteins have been shown to play diverse roles in plant developmental processes and environmental responses. However, this family has not been studied in the model tree species Populus to date. Results In the present study, a comprehensive analysis of the genes encoding CCCH zinc finger family in Populus was performed. Using a thorough annotation approach, a total of 91 full-length CCCH genes were identified in Populus, of which most contained more than one CCCH motif and a type of non-conventional C-X11-C-X6-C-X3-H motif was unique for Populus. All of the Populus CCCH genes were phylogeneticly clustered into 13 distinct subfamilies. In each subfamily, the gene structure and motif composition were relatively conserved. Chromosomal localization of these genes revealed that most of the CCCHs (81 of 90, 90 %) are physically distributed on the duplicated blocks. Thirty-four paralogous pairs were identified in Populus, of which 22 pairs (64.7 %) might be created by the whole genome segment duplication, whereas 4 pairs seem to be resulted from tandem duplications. In 91 CCCH proteins, we also identified 63 putative nucleon-cytoplasm shuttling proteins and 3 typical RNA-binding proteins. The expression profiles of all Populus CCCH genes have been digitally analyzed in six tissues across different developmental stages, and under various drought stress conditions. A variety of expression patterns of CCCH genes were observed during Populus development, of which 34 genes highly express in root and 22 genes show the highest level of transcript abundance in differentiating xylem. Quantitative real-time RT-PCR (RT-qPCR) was further performed to confirm the tissue

  10. Genome Analyses and Supplement Data from the International Populus Genome Consortium (IPGC)

    DOE Data Explorer

    International Populus Genome Consortium (IPGC)

    The sequencing of the first tree genome, that of Populus, was a project initiated by the Office of Biological and Environmental Research in DOE’s Office of Science. The International Populus Genome Consortium (IPGC) was formed to help develop and guide post-sequence activities. The IPGC website, hosted at the Oak Ridge National Laboratory, provides draft sequence data as it is made available from DOE Joint Genome Institute, genome analyses for Populus, lists of related publications and resources, and the science plan. The data are available at http://www.ornl.gov/sci/ipgc/ssr_resource.htm.

  11. Genome-wide analysis of a TaLEA-introduced transgenic Populus simonii × Populus nigra dwarf mutant.

    PubMed

    Yuan, Hong-Mei; Chen, Su; Lin, Lin; Wei, Rui; Li, Hui-Yu; Liu, Gui-Feng; Jiang, Jing

    2012-01-01

    A dwarf mutant (dwf1) was obtained among 15 transgenic lines, when TaLEA (Tamarix androssowii late embryogenesis abundant gene) was introduced into Populus simonii × Populus nigra by Agrobacterium tumefaciens-mediated transformation. Under the same growth conditions, dwf1 height was significantly reduced compared with the wild type and the other transgenic lines. Because only one transgenic line (dwf1) displayed the dwarf phenotype, we considered that T-DNA insertion sites may play a role in the mutant formation. The mechanisms underlying this effect were investigated using TAIL-PCR (thermal asymmetric interlaced PCR) and microarrays methods. According to the TAIL-PCR results, two flanking sequences located on chromosome IV and VIII respectively, were cloned. The results indicated the integration of two independent T-DNA copies. We searched for the potential genes near to the T-DNA insertions. The nearest gene was a putative poplar AP2 transcription factor (GI: 224073210). Expression analysis showed that AP2 was up-regulated in dwf1 compared with the wild type and the other transgenic lines. According to the microarrays results, a total of 537 genes involved in hydrolase, kinase and transcription factor activities, as well as protein and nucleotide binding, showed significant alterations in gene expression. These genes were expressed in more than 60 metabolic pathways, including starch, sucrose, galactose and glycerolipid metabolism and phenylpropanoids and flavonoid biosyntheses. Our transcriptome and T-DNA insertion sites analyses might provide some useful insights into the dwarf mutant formation. PMID:22489122

  12. Nanometrology of delignified Populus using mode synthesizing atomic force microscopy

    SciTech Connect

    Tetard, Laurene; Passian, Ali; Farahi, R H; Davison, Brian H; Jung, S; Ragauskas, A J; Lereu, Aude; Thundat, Thomas George

    2011-01-01

    The study of the spatially resolved physical and compositional properties of materials at the nanoscale is increasingly challenging due to the level of complexity of biological specimens such as those of interest in bioenergy production. Mode synthesizing atomic force microscopy (MSAFM) has emerged as a promising metrology tool for such studies. It is shown that, by tuning the mechanical excitation of the probe-sample system, MSAFM can be used to dynamically investigate the multifaceted complexity of plant cells. The results are argued to be of importance both for the characteristics of the invoked synthesized modes and for accessing new features of the samples. As a specific system to investigate, we present images of Populus, before and after a holopulping treatment, a crucial step in the biomass delignification process.

  13. Genome-wide profiling of Populus small RNAs

    PubMed Central

    2009-01-01

    Background Short RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale. We investigated the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the sequenced Populus trichocarpa using a concatenation strategy in combination with 454 sequencing. Results The most abundant size class of sRNAs were 24 nt. Long Terminal Repeats were particularly associated with 24 nt sRNAs. Additionally, some repetitive elements were associated with 22 nt sRNAs. We identified an sRNA hot-spot on chromosome 19, overlapping a region containing both the proposed sex-determining locus and a major cluster of NBS-LRR genes. A number of phased siRNA loci were identified, a subset of which are predicted to target PPR and NBS-LRR disease resistance genes, classes of genes that have been significantly expanded in Populus. Additional loci enriched for sRNA production were identified and characterised. We identified 15 novel predicted microRNAs (miRNAs), including miRNA*sequences, and identified a novel locus that may encode a dual miRNA or a miRNA and short interfering RNAs (siRNAs). Conclusions The short RNA population of P. trichocarpa is at least as complex as that of Arabidopsis thaliana. We provide a first genome-wide view of short RNA production for P. trichocarpa and identify new, non-conserved miRNAs. PMID:20021695

  14. Expansion and diversification of the Populus R2R3-MYB family of transcription factors.

    PubMed

    Wilkins, Olivia; Nahal, Hardeep; Foong, Justin; Provart, Nicholas J; Campbell, Malcolm M

    2009-02-01

    The R2R3-MYB proteins comprise one of the largest families of transcription factors in plants. R2R3-MYB family members regulate plant-specific processes, such as the elaboration of specialized cell types, including xylem, guard cells, trichomes, and root hairs, and the biosynthesis of specialized branches of metabolism, including phenylpropanoid biosynthesis. As such, R2R3-MYB family members are hypothesized to contribute to the emergence of evolutionary innovations that have arisen in specific plant lineages. As a first step in determining the role played by R2R3-MYB family members in the emergence of lineage-specific innovations in the genus Populus, the entire Populus trichocarpa R2R3-MYB family was characterized. The Populus R2R3-MYB complement is much larger than that found in other angiosperms with fully sequenced genomes. Phylogenetic analyses, together with chromosome placement, showed that the expansion of the Populus R2R3-MYB family was not only attributable to whole genome duplication but also involved selective expansion of specific R2R3-MYB clades. Expansion of the Populus R2R3-MYB family prominently involved members with expression patterns that suggested a role in specific components of Populus life history, including wood formation and reproductive development. An expandable compendium of microarray-based expression data (PopGenExpress) and associated Web-based tools were developed to better enable within- and between-species comparisons of Populus R2R3-MYB gene expression. This resource, which includes intuitive graphic visualization of gene expression data across multiple tissues, organs, and treatments, is freely available to, and expandable by, scientists wishing to better understand the genome biology of Populus, an ecologically dominant and economically important forest tree genus. PMID:19091872

  15. Expansion and diversification of the Populus R2R3-MYB family of transcription factors.

    PubMed

    Wilkins, Olivia; Nahal, Hardeep; Foong, Justin; Provart, Nicholas J; Campbell, Malcolm M

    2009-02-01

    The R2R3-MYB proteins comprise one of the largest families of transcription factors in plants. R2R3-MYB family members regulate plant-specific processes, such as the elaboration of specialized cell types, including xylem, guard cells, trichomes, and root hairs, and the biosynthesis of specialized branches of metabolism, including phenylpropanoid biosynthesis. As such, R2R3-MYB family members are hypothesized to contribute to the emergence of evolutionary innovations that have arisen in specific plant lineages. As a first step in determining the role played by R2R3-MYB family members in the emergence of lineage-specific innovations in the genus Populus, the entire Populus trichocarpa R2R3-MYB family was characterized. The Populus R2R3-MYB complement is much larger than that found in other angiosperms with fully sequenced genomes. Phylogenetic analyses, together with chromosome placement, showed that the expansion of the Populus R2R3-MYB family was not only attributable to whole genome duplication but also involved selective expansion of specific R2R3-MYB clades. Expansion of the Populus R2R3-MYB family prominently involved members with expression patterns that suggested a role in specific components of Populus life history, including wood formation and reproductive development. An expandable compendium of microarray-based expression data (PopGenExpress) and associated Web-based tools were developed to better enable within- and between-species comparisons of Populus R2R3-MYB gene expression. This resource, which includes intuitive graphic visualization of gene expression data across multiple tissues, organs, and treatments, is freely available to, and expandable by, scientists wishing to better understand the genome biology of Populus, an ecologically dominant and economically important forest tree genus.

  16. Comparative proteomic analysis of Populus trichocarpa early stem from primary to secondary growth.

    PubMed

    Liu, Jinwen; Hai, Guanghui; Wang, Chong; Cao, Shenquan; Xu, Wenjing; Jia, Zhigang; Yang, Chuanping; Wang, Jack P; Dai, Shaojun; Cheng, Yuxiang

    2015-08-01

    Wood is derived from the secondary growth of tree stems. In this study, we investigated the global changes of protein abundance in Populus early stems using a proteomic approach. Morphological and histochemical analyses revealed three typical stages during Populus early stems, which were the primary growth stage, the transition stage from primary to secondary growth and the secondary growth stage. A total of 231 spots were differentially abundant during various growth stages of Populus early stems. During Populus early stem lignifications, 87 differential spots continuously increased, while 49 spots continuously decreased. These two categories encompass 58.9% of all differential spots, which suggests significant molecular changes from primary to secondary growth. Among 231 spots, 165 unique proteins were identified using LC-ESI-Q-TOF-MS, which were classified into 14 biological function groups. The proteomic characteristics indicated that carbohydrate metabolism, oxido-reduction, protein degradation and secondary cell wall metabolism were the dominantly occurring biochemical processes during Populus early stem development. This study helps in elucidating biochemical processes and identifies potential wood formation-related proteins during tree early stem development. It is a comprehensive proteomic investigation on tree early stem development that, for the first time, reveals the overall molecular networks that occur during Populus early stem lignifications.

  17. Association Genetics of Populus trichocarpa or Resequencing in Populus: Towards Genome Wide Association Genetics (2011 JGI User Meeting)

    ScienceCinema

    Tuskan, Gerry

    2016-07-12

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Gerry Tuskan of Oak Ridge National Laboratory on "Resequencing in Populus: Towards Genome Wide Association Genetics" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  18. Association Genetics of Populus trichocarpa or Resequencing in Populus: Towards Genome Wide Association Genetics (2011 JGI User Meeting)

    SciTech Connect

    Tuskan, Gerry

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Gerry Tuskan of Oak Ridge National Laboratory on "Resequencing in Populus: Towards Genome Wide Association Genetics" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  19. Actin-dependent deposition of putative endosomes and endoplasmic reticulum during early stages of wound healing in characean internodal cells.

    PubMed

    Klima, A; Foissner, I

    2011-07-01

    We investigated the behaviour of organelles stained with FM1-43 (putative endosomes) and/or LysoTracker Red (LTred; acidic compartments) and of the endoplasmic reticulum (ER) during healing of puncture and UV-induced wounds in internodal cells of Nitella flexilis and Chara corallina. Immediately after puncture, wounds were passively sealed with a plug of solid vacuolar inclusions, onto which a bipartite wound wall was actively deposited. The outer, callose-containing amorphous layer consisted of remnants of FM1-43- and LTred-labelled organelles, ER cisternae and polysaccharide-containing secretory vesicles, which became deposited in the absence of membrane retrieval (compound exocytosis). During formation of the inner cellulosic layer, exocytosis of secretory vesicles with the newly formed plasma membrane is coupled to endocytosis via coated vesicles. Migration of FM1-43- and LTred-stained organelles, ER and secretory vesicles towards the cell cortex and deposition of a bipartite wound wall could also be induced by spot-like irradiation with ultraviolet light. Cytochalasin D reversibly inhibited the accumulation and deposition of organelles. Our study indicates that active actin-dependent deposition of putative recycling endosomes is required for wound healing (plasma membrane repair) and supports the hypothesis that deposition of ER cisternae helps to restore wounding-disturbed Ca(2+) metabolism.

  20. Myelinating Schwann cells determine the internodal localization of Kv1.1, Kv1.2, Kvbeta2, and Caspr.

    PubMed

    Arroyo, E J; Xu, Y T; Zhou, L; Messing, A; Peles, E; Chiu, S Y; Scherer, S S

    1999-01-01

    We examined the localization of Caspr and the K(+) channels Kv1.1 and Kv1.2, all of which are intrinsic membrane proteins of myelinated axons in the PNS. Caspr is localized to the paranode; Kv1. 1, Kv1.2 and their beta2 subunit are localized to the juxtaparanode. Throughout the internodal region, a strand of Caspr staining is flanked by a double strand of Kv1.1/Kv1.2/Kvbeta2 staining. This tripartite strand apposes the inner mesaxon of the myelin sheath, and forms a circumferential ring that apposes the innermost aspect of Schmidt-Lanterman incisures. The localization of Caspr and Kv1.2 are not disrupted in mice with null mutations of the myelin associated glycoprotein, connexin32, or Kv1.1 genes. At all of these locations, Caspr and Kv1.1/Kv1.2/Kvbeta2 define distinct but interrelated domains of the axonal membrane that appear to be organized by the myelin sheath. PMID:10739575

  1. Characterization of internodal collecting lymphatic vessel function after surgical removal of an axillary lymph node in mice.

    PubMed

    Kwon, Sunkuk; Price, Roger E

    2016-04-01

    Secondary lymphedema is an acquired lymphatic disorder, which occurs because of damage to the lymphatic system from surgery and/or radiation therapy for cancer treatment. However, it remains unknown how post-nodal collecting lymphatic vessels (CLVs) draining to the surgical wound area change in response to lymphadenectomy. We investigated functional and architectural changes of inguinal-to-axillary internodal CLVs (ICLVs) in mice after a single axillary LN (ALN) dissection using near-infrared fluorescence imaging. Our data showed no lymph flow in the ICLVs draining from the inguinal LN (ILN) at 2 days post-surgery. External compression enabled visualization of a small segment of contractile fluorescent ICLVs, but not all the way to the axillary region. At day 6, abnormal lymphatic drainage patterns, including lateral and retrograde lymph flow via vessels branching off the ICLVs were observed, which started to disappear beginning 9 days after surgery. The administration of vascular endothelial growth factor (VEGF)-C into the wound increased resolution of altered lymphatic drainage. Lymphatic drainage from the base of the tail to the ILN did not significantly change over time. These results demonstrate that lymph flow in the CLVs is dramatically affected by a LN dissection and long-term interruption of lymph flow might cause CLV dysfunction and thus contribute to chronic lymphatic disorders. PMID:27446639

  2. Spatiotemporal distribution of essential elements through Populus leaf ontogeny

    PubMed Central

    Carvalho, Mónica R.; Woll, Arthur; Niklas, Karl J.

    2016-01-01

    We examined the spatiotemporal distribution and accumulation of calcium (Ca), potassium (K), and zinc (Zn) during the growth and maturation of grey poplar (Populus tremula × alba) leaves covering plastochrons 01 through 10. This period spans the sugar sink-to-source transition and requires coordinated changes of multiple core metabolic processes that likely involve alterations in essential and non-essential element distributions as tissues mature and effect a reversal in phloem flow direction. Whole-leaf elemental maps were obtained from dried specimens using micro X-ray fluorescence spectroscopy. Additional cross-sections of fresh leaves were scanned to check for tissue specificity in element accumulation. The anatomical distribution of Zn and K remains relatively consistent throughout leaf development; Ca accumulation varied across leaf developmental stages. The basipetal allocation of Ca to the leaf mesophyll matched spatially and temporally the sequence of phloem maturation, positive carbon balance, and sugar export from leaves. The accumulation of Ca likely reflects the maturation of xylem in minor veins and the enhancement of the transpiration stream. Our results independently confirm that xylem and phloem maturation are spatially and temporally coordinated with the onset of sugar export in leaves. PMID:26985054

  3. Nucleotide diversity among natural populations of a North American poplar (Populus balsamifera, Salicaceae).

    PubMed

    Breen, Amy L; Glenn, Elise; Yeager, Adam; Olson, Matthew S

    2009-01-01

    Poplars (Populus spp.) comprise an important component of circumpolar boreal forest ecosystems and are the model species for tree genomics. In this study, we surveyed genetic variation and population differentiation in three nuclear genes among populations of balsam poplar (Populus balsamifera) in North America. We examined nucleotide sequence variation in alcohol dehydrogenase 1 (Adh1) and glyceraldehyde 3-phosphate dehydrogenase (G3pdh), two well-studied nuclear loci in plants, and abscisic acid insensitivity 1B (ABI1B), a locus coincident with timing of seasonal dormancy in quantitative trait locus (QTL) studies of hybrid poplars. We compared estimates of baseline population genetic parameters for these loci with those obtained in studies of other poplar species, particularly European aspen (Populus tremula). Average pairwise nucleotide diversity (pi(tot) = 0.00216-0.00353) was equivalent to that in Populus trichocarpa, but markedly less than that in P. tremula. Elevated levels of population structure were observed in ABI1B between the northern and southern regions (F(CT) = 0.184, P < 0.001) and among populations (F(ST) = 0.256, P < 0.001). These results suggest that geographic or taxonomic factors are important for understanding patterns of variation throughout the genus Populus. Our findings have the potential to aid in the design of sampling regimes for conservation and breeding stock and contribute to historical inferences regarding the factors that shaped the genetic diversity of boreal plant species.

  4. Detection of a variable number of ribosomal DNA loci by fluorescent in situ hybridization in Populus species.

    PubMed

    Prado, E A; Faivre-Rampant, P; Schneider, C; Darmency, M A

    1996-10-01

    Fluorescent in situ hybridization (FISH) was applied to related Populus species (2n = 19) in order to detect rDNA loci. An interspecific variability in the number of hybridization sites was revealed using as probe an homologous 25S clone from Populus deltoides. The application of image analysis methods to measure fluorescence intensity of the hybridization signals has enabled us to characterize major and minor loci in the 18S-5.8S-25S rDNA. We identified one pair of such rDNA clusters in Populus alba; two pairs, one major and one minor, in both Populus nigra and P. deltoides; and three pairs in Populus balsamifera, (two major and one minor) and Populus euroamericana (one major and two minor). FISH results are in agreement with those based on RFLP analysis. The pBG13 probe containing 5S sequence from flax detected two separate clusters corresponding to the two size classes of units that coexist within 5S rDNA of most Populus species. Key words : Populus spp., fluorescent in situ hybridization, FISH, rDNA variability, image analysis.

  5. Genome-Wide Identification, Evolutionary Expansion, and Expression Profile of Homeodomain-Leucine Zipper Gene Family in Poplar (Populus trichocarpa)

    PubMed Central

    Hu, Ruibo; Chi, Xiaoyuan; Chai, Guohua; Kong, Yingzhen; He, Guo; Wang, Xiaoyu; Shi, Dachuan; Zhang, Dongyuan; Zhou, Gongke

    2012-01-01

    Background Homeodomain-leucine zipper (HD-ZIP) proteins are plant-specific transcriptional factors known to play crucial roles in plant development. Although sequence phylogeny analysis of Populus HD-ZIPs was carried out in a previous study, no systematic analysis incorporating genome organization, gene structure, and expression compendium has been conducted in model tree species Populus thus far. Principal Findings In this study, a comprehensive analysis of Populus HD-ZIP gene family was performed. Sixty-three full-length HD-ZIP genes were found in Populus genome. These Populus HD-ZIP genes were phylogenetically clustered into four distinct subfamilies (HD-ZIP I–IV) and predominately distributed across 17 linkage groups (LG). Fifty genes from 25 Populus paralogous pairs were located in the duplicated blocks of Populus genome and then preferentially retained during the sequential evolutionary courses. Genomic organization analyses indicated that purifying selection has played a pivotal role in the retention and maintenance of Populus HD-ZIP gene family. Microarray analysis has shown that 21 Populus paralogous pairs have been differentially expressed across different tissues and under various stresses, with five paralogous pairs showing nearly identical expression patterns, 13 paralogous pairs being partially redundant and three paralogous pairs diversifying significantly. Quantitative real-time RT-PCR (qRT-PCR) analysis performed on 16 selected Populus HD-ZIP genes in different tissues and under both drought and salinity stresses confirms their tissue-specific and stress-inducible expression patterns. Conclusions Genomic organizations indicated that segmental duplications contributed significantly to the expansion of Populus HD-ZIP gene family. Exon/intron organization and conserved motif composition of Populus HD-ZIPs are highly conservative in the same subfamily, suggesting the members in the same subfamilies may also have conservative functionalities

  6. Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus

    SciTech Connect

    Yang, Xiaohan; Jawdy, Sara; Tschaplinski, Timothy J; Tuskan, Gerald A

    2009-01-01

    Protein sequences were compared among Arabidopsis, Oryza and Populus to identify differential gene (DG) sets that are in one but not the other two genomes. The DG sets were screened against a plant transcript database, the NR protein database and six newly-sequenced genomes (Carica, Glycine, Medicago, Sorghum, Vitis and Zea) to identify a set of species-specific genes (SS). Gene expression, protein motif and intron number were examined. 192, 641 and 109 SS genes were identified in Arabidopsis, Oryza and Populus, respectively. Some SS genes were preferentially expressed in flowers, roots, xylem and cambium or up-regulated by stress. Six conserved motifs in Arabidopsis and Oryza SS proteins were found in other distant lineages. The SS gene sets were enriched with intronless genes. The results reflect functional and/or anatomical differences between monocots and eudicots or between herbaceous and woody plants. The Populus-specific genes are candidates for carbon sequestration and biofuel research.

  7. [Proof of the indigenous nature of Populus alba L. in the western Mediterranean Basin].

    PubMed

    Roiron, Paul; Ali, Adam A; Guendon, Jean-Louis; Carcaillet, Christopher; Terral, Jean-Frédéric

    2004-02-01

    Around the western Mediterranean Basin, the ecological status of Populus alba, whether indigenous or introduced, is controversial. This note presents new palaeobotanical data based on analyses of leaf imprints from a travertine formation located in southern France. This travertine presents two levels with Populus alba imprints. The oldest level is dated back by 14C to the Early Holocene, i.e., 8890 +/- 70 BP. This demonstrates that Populus alba is an autochthonous species of the southern-France vegetation, removing speculations reporting that its distribution area was greatly influenced by Roman civilization. Finally, we discuss this new data in regard to other Pleistocene and Holocene deposits circum the Mediterranean Basin and in Europe, where this species was identified. PMID:15060983

  8. Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa

    SciTech Connect

    Kalluri, Udaya C; DiFazio, Stephen P; Brunner, A.; Tuskan, Gerald A

    2007-01-01

    Auxin/Indole-3-Acetic Acid (Aux/IAA) and Auxin Response Factor (ARF) transcription factors are key regulators of auxin responses in plants. A total of 35 Aux/IAA and 39 ARF genes were identified in the Populus genome. Comparative phylogenetic analysis revealed that the subgroups PoptrARF2, 6, 9 and 16 and PoptrIAA3, 16, 27 and 29 have differentially expanded in Populus relative to Arabidopsis. Activator ARFs were found to be two fold-overrepresented in the Populus genome. PoptrIAA and PoptrARF gene families appear to have expanded due to high segmental and low tandem duplication events. Furthermore, expression studies showed that genes in the expanded PoptrIAA3 subgroup display differential expression. The gene-family analysis reported here will be useful in conducting future functional genomics studies to understand how the molecular roles of these large gene families translate into a diversity of biologically meaningful auxin effects.

  9. Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding.

    PubMed

    Kersten, Birgit; Faivre Rampant, Patricia; Mader, Malte; Le Paslier, Marie-Christine; Bounon, Rémi; Berard, Aurélie; Vettori, Cristina; Schroeder, Hilke; Leplé, Jean-Charles; Fladung, Matthias

    2016-01-01

    Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x P. alba 717-1B4 (section Populus). The organization of the chloroplast genomes of both Populus clones is described. A phylogenetic tree constructed from all available complete chloroplast DNA sequences of Populus was not congruent with the assignment of the related species to different Populus sections. In total, 3,024 variable nucleotide positions were identified among all compared Populus chloroplast DNA sequences. The 5-prime part of the LSC from trnH to atpA showed the highest frequency of variations. The variable positions included 163 positions with SNPs allowing for differentiating the two clones with P. tremula chloroplast genomes (W52, 717-1B4) from the other seven Populus individuals. These potential P. tremula-specific SNPs were displayed as a whole-plastome barcode on the P. tremula W52 chloroplast DNA sequence. Three of these SNPs and one InDel in the trnH-psbA linker were successfully validated by Sanger sequencing in an extended set of Populus individuals. The complete mitochondrial genome sequence of P. tremula is the first in the family of Salicaceae. The mitochondrial genomes of the two clones are 783,442 bp (W52) and 783,513 bp (717-1B4) in size, structurally very similar and organized as single circles. DNA sequence regions with high similarity to the W52 chloroplast sequence account for about 2% of the W52 mitochondrial genome. The mean SNP frequency was found to be nearly six fold higher in the chloroplast than in the mitochondrial genome when comparing 717-1B4 with W52. The availability of the genomic information of all three DNA-containing cell organelles will allow a holistic approach in poplar molecular breeding in the future.

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

    PubMed

    Zeng, Fanjiang; Zhang, Ximing; Li, Xiangyi; Foetzki, Andrea; Runge, Michael

    2005-08-01

    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.

  11. Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding

    PubMed Central

    Mader, Malte; Le Paslier, Marie-Christine; Bounon, Rémi; Berard, Aurélie; Vettori, Cristina; Schroeder, Hilke; Leplé, Jean-Charles; Fladung, Matthias

    2016-01-01

    Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x P. alba 717-1B4 (section Populus). The organization of the chloroplast genomes of both Populus clones is described. A phylogenetic tree constructed from all available complete chloroplast DNA sequences of Populus was not congruent with the assignment of the related species to different Populus sections. In total, 3,024 variable nucleotide positions were identified among all compared Populus chloroplast DNA sequences. The 5-prime part of the LSC from trnH to atpA showed the highest frequency of variations. The variable positions included 163 positions with SNPs allowing for differentiating the two clones with P. tremula chloroplast genomes (W52, 717-1B4) from the other seven Populus individuals. These potential P. tremula-specific SNPs were displayed as a whole-plastome barcode on the P. tremula W52 chloroplast DNA sequence. Three of these SNPs and one InDel in the trnH-psbA linker were successfully validated by Sanger sequencing in an extended set of Populus individuals. The complete mitochondrial genome sequence of P. tremula is the first in the family of Salicaceae. The mitochondrial genomes of the two clones are 783,442 bp (W52) and 783,513 bp (717-1B4) in size, structurally very similar and organized as single circles. DNA sequence regions with high similarity to the W52 chloroplast sequence account for about 2% of the W52 mitochondrial genome. The mean SNP frequency was found to be nearly six fold higher in the chloroplast than in the mitochondrial genome when comparing 717-1B4 with W52. The availability of the genomic information of all three DNA-containing cell organelles will allow a holistic approach in poplar molecular breeding in the future. PMID:26800039

  12. Establishment of Populus deltoides under simulated alluvial groundwater declines

    USGS Publications Warehouse

    Segelquist, Charles A.; Scott, Michael L.; Auble, Gregor T.

    1993-01-01

    Establishment, growth, and survival of seedlings of Populus deltoides subsp. monilifera (plains cottonwood) were examined in an experimental facility simulating five rates of declining alluvial groundwater. The treatments were permanent saturation, drawdown rates of 0.4, 0.7, 2.9 cm/d and immediate drainage. The experiment was conducted outdoors in planters near Fort Collins, Colorado. Seedling survival was highest under the two slowest drawdown rates and declined significantly with faster drawdown rates. The highest growth rate was associated with the drawdown rate of 0.4 cm/d, in which mean shoot height was 2.4 cm and mean root length was 39 am 98 days after planting. Growth of shoots and roots was reduced both by saturated conditions and by the more rapid drawdown rates of 0.7 and 2.9 cm/d. No establishment was observed in the immediate drawdown treatment. Whereas maximum biomass accumulation is associated with the most gradual drawdown or saturated conditions, seedling establishing naturally under such conditions are also most likely to be removed by ice or subsequent flooding. Seedlings establishing in higher topographic positions, in contrast, are subject to increased mortality and reduced shoot growth, resulting from reduced soil moisture. Rapid root extension following establishment allows P. deltoides seedlings to grow across a wide range of groundwater drawdown rates, and thus a variety of positions across a gradient of riparian soil moisture. Our results indicate that in coarse alluvial sands of low fertility, 47% of germinating P. deltoides seeds were able to survive in associated with a drawdown rate of 2.9 cm/d and a final water table depth of 80 cm.

  13. Transcriptome Profiles of Populus euphratica upon Heat Shock stress.

    PubMed

    Chen, Jinhuan; Yin, Weilun; Xia, Xinli

    2014-10-01

    Heat stress, which strongly affects plant performance and often results in reduced vegetative growth and yields depression, has become an increasingly serious global problem. Populus euphratica Oliv. which has been considered as a tree model for the study of plant response to abiotic stresses, could be resistant to an extremely wide environmental temperature range (-40 °C to 45 °C). Previous study is mainly focused on its gene regulation upon drought and salt stress. However, little is known about gene regulation at the global transcriptome level upon heat stress. To understand the gene network controlling heat stress in P. euphratica, a transcriptome sequencing using Illumina Hiseq 2000 was performed to generate a 10 gigabases depth for each sample in the tissue of leaf. 119,573 unigeneswere generated with an average length of 474 bp. Approximately 49,605 (41.49%) unigenes exhibited significantly different expressions between two libraries. Among these unigenes, 11,165 (9.34%) were upregulated and 38,440 (32.15%) were down regulated. Heat shock proteins classified as molecular chaperones showed a significant percentage (1.13%) in the up regulated group. Heat responsive genes, such as polyubiquitins, were over expressed in heat treated sample. GO enrichment analysis revealed that the Go terms for differentially expressed unigenes were significantly enriched in hormone-mediated signal, biological process regulation and metabolic process regulation. Our data revealed a global transcriptome picture of P. euphratica in response to heat shock. The identified potential heat stress-related transcripts can be used to infer the gene regulation networks underlying the molecular mechanisms of heat response in P. euphratica.

  14. [Sexual differences in climatic response of dioecious Populus davidiana tree].

    PubMed

    Gao, Lu-Shuang; Zhao, Xiu-Hai; Wang, Xiao-Ming; Zhang, Chun-Yu

    2014-07-01

    The tree-ring width series and standardized chronologies of Populus davidiana trees in broad-leaved and Korean pine forest in Changbai Mountains were developed separately for male and female trees. Their differential radial growth and their relationship with climatic conditions were analyzed to reveal the effect of gender on radial growth and their climatic responses. It was found that there was a significant differential growth pattern before and after climate change for dioecious trees. The differential responses of the females and males to climate were also observed. The radial increment of female trees before 1980 was significantly higher than that of male trees, and the growth of female was negatively related with the monthly minimum temperature at the end of current growing season and precipitation in the previous and current growing season. The male was significantly positively related with the current growing season temperature. After 1980, the monthly temperature significantly increased, especially the monthly minimum temperature. The increment of dioecious trees decreased. The annual radial growth rate of the female was significantly lower than that of the male. Compared with the male tree, the female was more sensitive to the monthly minimum temperature. The female was significantly positively related with the spring minimum temperature and significantly negatively with the minimum temperature at the end of previous growing season. There was no significant correlation between the male and monthly minimum temperature. The monthly minimum temperature had an important impact on female P. davidiana trees in Changbai Mountains. Under the condition of stable precipitation, the increase of minimum temperature would restrain the growth of females, but lightly influenced the males' growth. PMID:25345033

  15. Lignin content in natural Populus variants affects sugar release

    PubMed Central

    Studer, Michael H.; DeMartini, Jaclyn D.; Davis, Mark F.; Sykes, Robert W.; Davison, Brian; Keller, Martin; Tuskan, Gerald A.; Wyman, Charles E.

    2011-01-01

    The primary obstacle to producing renewable fuels from lignocellulosic biomass is a plant's recalcitrance to releasing sugars bound in the cell wall. From a sample set of wood cores representing 1,100 individual undomesticated Populus trichocarpa trees, 47 extreme phenotypes were selected across measured lignin content and ratio of syringyl and guaiacyl units (S/G ratio). This subset was tested for total sugar release through enzymatic hydrolysis alone as well as through combined hot-water pretreatment and enzymatic hydrolysis using a high-throughput screening method. The total amount of glucan and xylan released varied widely among samples, with total sugar yields of up to 92% of the theoretical maximum. A strong negative correlation between sugar release and lignin content was only found for pretreated samples with an S/G ratio < 2.0. For higher S/G ratios, sugar release was generally higher, and the negative influence of lignin was less pronounced. When examined separately, only glucose release was correlated with lignin content and S/G ratio in this manner, whereas xylose release depended on the S/G ratio alone. For enzymatic hydrolysis without pretreatment, sugar release increased significantly with decreasing lignin content below 20%, irrespective of the S/G ratio. Furthermore, certain samples featuring average lignin content and S/G ratios exhibited exceptional sugar release. These facts suggest that factors beyond lignin and S/G ratio influence recalcitrance to sugar release and point to a critical need for deeper understanding of cell-wall structure before plants can be rationally engineered for reduced recalcitrance and efficient biofuels production. PMID:21444820

  16. Method and apparatus for routing data in an inter-nodal communications lattice of a massively parallel computer system by dynamically adjusting local routing strategies

    DOEpatents

    Archer, Charles Jens; Musselman, Roy Glenn; Peters, Amanda; Pinnow, Kurt Walter; Swartz, Brent Allen; Wallenfelt, Brian Paul

    2010-03-16

    A massively parallel computer system contains an inter-nodal communications network of node-to-node links. Each node implements a respective routing strategy for routing data through the network, the routing strategies not necessarily being the same in every node. The routing strategies implemented in the nodes are dynamically adjusted during application execution to shift network workload as required. Preferably, adjustment of routing policies in selective nodes is performed at synchronization points. The network may be dynamically monitored, and routing strategies adjusted according to detected network conditions.

  17. Method and apparatus for routing data in an inter-nodal communications lattice of a massively parallel computer system by employing bandwidth shells at areas of overutilization

    DOEpatents

    Archer, Charles Jens; Musselman, Roy Glenn; Peters, Amanda; Pinnow, Kurt Walter; Swartz, Brent Allen; Wallenfelt, Brian Paul

    2010-04-27

    A massively parallel computer system contains an inter-nodal communications network of node-to-node links. An automated routing strategy routes packets through one or more intermediate nodes of the network to reach a final destination. The default routing strategy is altered responsive to detection of overutilization of a particular path of one or more links, and at least some traffic is re-routed by distributing the traffic among multiple paths (which may include the default path). An alternative path may require a greater number of link traversals to reach the destination node.

  18. Method and apparatus for routing data in an inter-nodal communications lattice of a massively parallel computer system by routing through transporter nodes

    DOEpatents

    Archer, Charles Jens; Musselman, Roy Glenn; Peters, Amanda; Pinnow, Kurt Walter; Swartz, Brent Allen; Wallenfelt, Brian Paul

    2010-11-16

    A massively parallel computer system contains an inter-nodal communications network of node-to-node links. An automated routing strategy routes packets through one or more intermediate nodes of the network to reach a destination. Some packets are constrained to be routed through respective designated transporter nodes, the automated routing strategy determining a path from a respective source node to a respective transporter node, and from a respective transporter node to a respective destination node. Preferably, the source node chooses a routing policy from among multiple possible choices, and that policy is followed by all intermediate nodes. The use of transporter nodes allows greater flexibility in routing.

  19. The obscure events contributing to the evolution of an incipient sex chromosome in Populus A retrospective working hypothesis.

    SciTech Connect

    Tuskan, Gerald A; Tschaplinski, Timothy J; Chen, Jay; Labbe, Jessy L; Ranjan, Priya; DiFazio, Steven P; Slavov, Goncho T.; Yin, Tongming

    2012-01-01

    Genetic determination of gender is a fundamental developmental and evolutionary process in plants. Although it appears that dioecy in Populus is partially genetically controlled, the precise gender-determining systems remain unclear. The recently-released second draft assembly and annotated gene set of the Populus genome provided an opportunity to re-visit this topic. We hypothesized that over evolutionary time, selective pressure has reformed the genome structure and gene composition in the peritelomeric region of the chromosome XIX which has resulted in a distinctive genome structure and cluster of genes contributing to gender determination in Populus. Multiple lines of evidence support this working hypothesis. First, the peritelomeric region of the chromosome XIX contains significantly fewer single nucleotide polymorphisms than the rest of Populus genome and has a distinct evolutionary history. Second, the peritelomeric end of chromosome XIX contains the largest cluster of the nucleotide-binding site-leucine-rich repeat (NBS-LRR) class of disease resistances genes in the entire Populus genome. Third, there is a high occurrence of small microRNAs on chromosome XIX coincident to the region containing the putative gender-determining locus and the major cluster of NBS-LRR genes. Further, by analyzing the metabolomic profiles of floral bud in male and female Populus trees using a gas chromatography-mass spectrometry, we found there are gender-specific accumulations of phenolic glycosides. Taken together, these findings provide new insights into the genetic control of gender determination in Populus.

  20. Genome structure and emerging evidence of an incipient sex chromosome in Populus

    SciTech Connect

    Yin, Tongming; DiFazio, Stephen P; Gunter, Lee E; Zhang, Xinye; Sewell, Mitchell; Woolbright, Dr. Scott; Allan, Dr. Gery; Kelleher, Colin; Douglas, Carl; Wang, Prof. Mingxiu; Tuskan, Gerald A

    2008-01-01

    The genus Populus consists of dioecious woody species with largely unknown genetic mechanisms for gender determination. We have discovered genetic and genomic features in the peritelomeric region of chromosome XIX that suggest this region of the Populus genome is in the process of developing characteristics of a sex chromosome. We have identified a gender-associated locus that consistently maps to this region. Furthermore, comparison of genetic maps across multiple Populus families reveals consistently distorted segregation within this region. We have intensively characterized this region using an F1 interspecific cross involving the female genotype that was used for genome sequencing. This region shows suppressed recombination and high divergence between the alternate haplotypes, as revealed by dense map-based genome assembly using microsatellite markers. The suppressed recombination, distorted segregation, and haplotype divergence were observed only for the maternal parent in this cross. Furthermore, the progeny of this cross showed a strongly male-biased sex ratio, in agreement with Haldane's rule that postulates that the heterogametic sex is more likely to be absent, rare, or sterile in interspecific crosses. Together, these results support the role of chromosome XIX in sex determination and suggest that sex determination in Populus occurs through a ZW system in which the female is the heterogametic gender.

  1. Intercontinental divergence in the Populus-associated ectomycorrhizal fungus, Tricholoma populinum.

    PubMed

    Grubisha, Lisa C; Levsen, Nicholas; Olson, Matthew S; Taylor, D Lee

    2012-04-01

    The ectomycorrhizal fungus Tricholoma populinum is host-specific with Populus species. T. populinum has wind-dispersed progagules and may be capable of long-distance dispersal. In this study, we tested the hypothesis of a panmictic population between Scandinavia and North America. DNA sequences from five nuclear loci were used to assess phylogeographic structure and nucleotide divergence between continents. Tricholoma populinum was composed of Scandinavian and North American lineages with complete absence of shared haplotypes and only one shared nucleotide mutation. Divergence of these lineages was estimated at approx. 1.7-1.0 million yr ago (Ma), which occurred after the estimated divergence of host species Populus tremula and Populus balsamifera/Populus trichocarpa at 5 Ma. Phylogeographic structure was not observed within Scandinavian or North American lineages of T. populinum. Intercontinental divergence appears to have resulted from either allopatric isolation; a recent, rare long-distance dispersal founding event followed by genetic drift; or the response in an obligate mycorrhizal fungus with a narrow host range to contractions and expansion of host distribution during glacial and interglacial episodes within continents. Understanding present genetic variation in populations is important for predicting how obligate symbiotic fungi will adapt to present and future changing climatic conditions.

  2. Gibberellin-associated cisgenes modify growth, stature and wood properties in Populus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We studied the effects on plant growth from insertion of five cisgenes involved in gibberellic acid metabolism or signaling. We cloned intact genomic copies of GA20ox7, GA2ox2, RGL1_1, RGL1_2, and GAI1 genes from the genome sequenced Populus trichocarpa clone Nisqually-1, transformed them into Popul...

  3. Draft Genome Sequences of Four Streptomyces Isolates from the Populus trichocarpa Root Endosphere and Rhizosphere

    PubMed Central

    Klingeman, Dawn M.; Utturkar, Sagar; Lu, Tse-Yuan S.; Schadt, Christopher W.; Pelletier, Dale A.

    2015-01-01

    Draft genome sequences for four Actinobacteria from the genus Streptomyces are presented. Streptomyces is a metabolically diverse genus that is abundant in soils and has been reported in association with plants. The strains described in this study were isolated from the Populus trichocarpa endosphere and rhizosphere. PMID:26564053

  4. Draft genome sequences of four Streptomyces isolates from the Populus trichocarpa root endosphere and rhizosphere

    DOE PAGESBeta

    Klingeman, Dawn M.; Utturkar, Sagar; Lu, Tse -Yuan S.; Schadt, Christopher W.; Pelletier, Dale A.; Brown, Steve D.

    2015-11-12

    Draft genome sequences for four Actinobacteria from the genus Streptomyces are presented. Streptomyces is a metabolically diverse genus that is abundant in soils and has been reported in association with plants. The strains described in this study were isolated from the Populus trichocarpa endosphere and rhizosphere.

  5. Cryopreservation of Populus trichocarpa and Salix using dormant buds with recovery by grafting or direct rooting

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Populus trichocarpa and Salix can be successfully cryopreserved by using dormant scions as the source explants. These scions (either at their original moisture content of 48 to 60% or dried to 30%) were slowly cooled to –35 degree Celsius, transferred to the vapor phase of liquid nitrogen (LNV,-160...

  6. Environmental Influences on Wood Chemistry and Density of Populus and Loblolly Pine

    SciTech Connect

    Tuskan, G.A.

    2006-08-11

    The objectives of the study are to: (1) determine the degree to which physical and chemical wood properties vary in association with environmental and silvicultural practices in Populus and loblolly pine and (2) develop and verify species-specific empirical models in an effort to create a framework for understanding environmental influences on wood quality.

  7. Identification of quantitative trait loci and candidate genes for cadmium tolerance in Populus

    SciTech Connect

    Induri, Brahma R; Ellis, Danielle R; Slavov, Goncho T.; Yin, Tongming; Zhang, Xinye; Tuskan, Gerald A; DiFazio, Steven P

    2012-01-01

    Understanding genetic variation for the response of Populus to heavy metals like cadmium (Cd) is an important step in elucidating the underlying mechanisms of tolerance. In this study, a pseudo-backcross pedigree of Populus trichocarpa Torr. & Gray and Populus deltoides Bart. was characterized for growth and performance traits after Cd exposure. A total of 16 quantitative trait loci (QTL) at logarithm of odds (LOD) ratio 2.5 were detected for total dry weight, its components and root volume. Major QTL for Cd responses were mapped to two different linkage groups and the relative allelic effects were in opposing directions on the two chromosomes, suggesting differential mechanisms at these two loci. The phenotypic variance explained by Cd QTL ranged from 5.9 to 11.6% and averaged 8.2% across all QTL. A whole-genome microarray study led to the identification of nine Cd-responsive genes from these QTL. Promising candidates for Cd tolerance include an NHL repeat membrane-spanning protein, a metal transporter and a putative transcription factor. Additional candidates in the QTL intervals include a putative homolog of a glutamate cysteine ligase, and a glutathione-S-transferase. Functional characterization of these candidate genes should enhance our understanding of Cd metabolism and transport and phytoremediation capabilities of Populus.

  8. Genome-wide analysis of the structural genes regulating defense phenylpropanoid metabolism in Populus

    SciTech Connect

    Tschaplinski, Timothy J; Tsai, Chung-Jui; Harding, Scott A; Lindroth, richard L; Yuan, Yinan

    2006-01-01

    Salicin-based phenolic glycosides, hydroxycinnamate derivatives and flavonoid-derived condensed tannins comprise up to one-third of Populus leaf dry mass. Genes regulating the abundance and chemical diversity of these substances have not been comprehensively analysed in tree species exhibiting this metabolically demanding level of phenolic metabolism. Here, shikimate-phenylpropanoid pathway genes thought to give rise to these phenolic products were annotated from the Populus genome, their expression assessed by semiquantitative or quantitative reverse transcription polymerase chain reaction (PCR), and metabolic evidence for function presented. Unlike Arabidopsis, Populus leaves accumulate an array of hydroxycinnamoyl-quinate esters, which is consistent with broadened function of the expanded hydroxycinnamoyl-CoA transferase gene family. Greater flavonoid pathway diversity is also represented, and flavonoid gene families are larger. Consistent with expanded pathway function, most of these genes were upregulated during wound-stimulated condensed tannin synthesis in leaves. The suite of Populus genes regulating phenylpropanoid product accumulation should have important application in managing phenolic carbon pools in relation to climate change and global carbon cycling.

  9. RepPop: A Database for Repetitive Elements in Populus Trichocarpa

    DOE Data Explorer

    Zhou, Fengfeng; Xu, Ying

    The populus was selected as the first tree with the genome to be sequenced, mainly due to its small genome size, the wide deployment worldwide (30+ species), and its short juvenile period. Its rich content of cellulose, which is one of the most important source for biofuel. A female clone of P. trichocarpa was chosen to be sequenced. The current assembly of Populus genome is release 1.0, whose small insert end-sequence coverage is 7.5X, and it was released in June 2004. It consists of 22,012 sequences (including the 19 chromosomes) and the total length is 485,510,911 bps. The data was downloaded from the offical site of the Populus trichocarpa genome sequencing project. The latest version of the genome can be found at the Poplar Genome Project at JGI Eukaryotic Genomics. Duplication regions introduce significant difficulties into the correct assemblying of sequence contigs. We identified all the repetitive elements in the populus genome. We further assign each of them as different classes of repetitive elements, including DNA transposons, RNA retrotransposons, Miniature Inverted-repeat Transposable Elements (MITE), Simple Sequence Repeats (SSR), and Segmental Duplications (SD), etc. We organized the annotations into this easily browsable, searchable, and blastable database, RepPop, for the whole community.[From website for RepPop at http://csbl.bmb.uga.edu/~ffzhou/RepPop/

  10. [Sequence analysis of bacterial transposon in NHX gene of Populus euphratica].

    PubMed

    Li, Jin-Yao; Ma, Ji; Cai, Lun; Zeng, You-Ling; Mei, Xin-Di; Zhang, Fu-Chun

    2003-09-01

    The United Nations Environment Program estimates that approximately 20% of agricultural land and 50% of cropland in the world is salt-stressed. The gene NHX (Na+/H+ exchanger) encodes functional protein that catalyzes the countertransport of Na+ and H+ across membranes and may play an important role in plant salt tolerance. To clone the NHX from the wild plant Populus euphratica collected in Tarim basin and Xinjiang Wujiaqu district into a T-vector, designed primer was used to amplify 1kb NHX cDNA fragment with RT-PCR. Total RNA was extracted from Populus euphratica tissue (plant tissue was collected from Tarim basin and Xinjiang Wujiaqu district and stored in liquid nitrogen) according to the Plant RNA Mini Kits of Omega. First cDNAs were synthesized from 1 microg total RNA of Populus euphratica seedling. A pair of primers were used to perform RT-PCR. The amplified DNA fragment was purified and cloned into pMD18-T vector. However, 1kb and 2.3kb fragment were obtained from Tarim basin and Xinjiang Wujiaqu district and named as PtNHX and PwNHX, respectively. Sequence analysis reveals that the cloned PtNHX fragment of Populus euphratica contains partial NHX coding region with 98%, 86%, 84% and 80% identity comparing with Atriplex gemelini, Suaeda maritima, Arabidopsis thaliana and Oryza sativa, respectively. This analysis suggests that NHX gene would be highly conserved in terms of evolution in plant; and it also suggests that the NHX gene of Populus euphratica also would have the similarity with that of Arabidopsis. It may be of great importance in improvement of the plant salt tolerance and breed of crop. At the same time, sequence analysis shows that PwNHX gene includes a coding region about 1350bp with 99% identity comparing with transposon Tn10 IS10-left transposase of Shigella flexneri. On the one hand, the NHX gene may lose its function because it was inserted a fragment in coding region. On the other hand, its product may play a important role in salt

  11. The effect of mepiquat chloride on elongation of cotton (Gossypium hirsutum L.) internode is associated with low concentration of gibberellic acid.

    PubMed

    Wang, Li; Mu, Chun; Du, Mingwei; Chen, Yin; Tian, Xiaoli; Zhang, Mingcai; Li, Zhaohu

    2014-08-01

    The growth regulator mepiquat chloride (MC) is globally used in cotton (Gossypium hirsutum L.) canopy manipulation to avoid excess growth and yield loss. However, little information is available as to whether the modification of plant architecture by MC is related to alterations in gibberellic acid (GA) metabolism and signaling. Here, the role of GA metabolism and signaling was investigated in cotton seedlings treated with MC. The MC significantly decreased endogenous GA3 and GA4 levels in the elongating internode, which inhibited cell elongation by downregulating GhEXP and GhXTH2, and then reducing plant height. Biosynthetic and metabolic genes of GA were markedly suppressed within 2-10d of MC treatment, which also downregulated the expression of DELLA-like genes. A remarkable feedback regulation was observed at the early stage of MC treatment when GA biosynthetic and metabolic genes expression was evidently upregulated. Mepiquat chloride action was controlled by temporal translocation and spatial accumulation which regulated GA biosynthesis and signal expression for maintaining GA homeostasis. The results suggested that MC application could reduce endogenous GA levels in cotton through controlled GA biosynthetic and metabolic genes expression, which might inhibit cell elongation, thereby shortening the internode and reducing plant height. PMID:25017155

  12. The effect of mepiquat chloride on elongation of cotton (Gossypium hirsutum L.) internode is associated with low concentration of gibberellic acid.

    PubMed

    Wang, Li; Mu, Chun; Du, Mingwei; Chen, Yin; Tian, Xiaoli; Zhang, Mingcai; Li, Zhaohu

    2014-08-01

    The growth regulator mepiquat chloride (MC) is globally used in cotton (Gossypium hirsutum L.) canopy manipulation to avoid excess growth and yield loss. However, little information is available as to whether the modification of plant architecture by MC is related to alterations in gibberellic acid (GA) metabolism and signaling. Here, the role of GA metabolism and signaling was investigated in cotton seedlings treated with MC. The MC significantly decreased endogenous GA3 and GA4 levels in the elongating internode, which inhibited cell elongation by downregulating GhEXP and GhXTH2, and then reducing plant height. Biosynthetic and metabolic genes of GA were markedly suppressed within 2-10d of MC treatment, which also downregulated the expression of DELLA-like genes. A remarkable feedback regulation was observed at the early stage of MC treatment when GA biosynthetic and metabolic genes expression was evidently upregulated. Mepiquat chloride action was controlled by temporal translocation and spatial accumulation which regulated GA biosynthesis and signal expression for maintaining GA homeostasis. The results suggested that MC application could reduce endogenous GA levels in cotton through controlled GA biosynthetic and metabolic genes expression, which might inhibit cell elongation, thereby shortening the internode and reducing plant height.

  13. Regeneration Capacity of Small Clonal Fragments of the Invasive Mikania micrantha H.B.K.: Effects of Burial Depth and Stolon Internode Length

    PubMed Central

    Li, Xiaoxia; Shen, Yide; Huang, Qiaoqiao; Fan, Zhiwei; Huang, Dongdong

    2013-01-01

    The perennial stoloniferous herbaceous vine Mikania micrantha H.B.K. is among the most noxious exotic invaders in China and the world. Disturbance can fragment stolons of M. micrantha and disperse these fragments over long distances or bury them in soils at different depths. To test their regeneration capacity, single-node stolon fragments with stolon internode lengths of 0, 3, 6 and 12 cm were buried in soil at 0, 2, 5 and 8 cm depths, respectively. The fragments were growing for nine weeks, and their emergence status, growth and morphological traits were measured. The results indicated that increasing burial depth significantly decreased survival rate and increased the emergence time of the M. micrantha plants. At an 8-cm burial depth, very few fragments (2.19%) emerged and survived. Burial did not affect the total biomass and root to shoot ratio of the surviving M. micrantha plants that emerged from the 0- and 2-cm burial depths. Increasing internode length significantly increased survival rate and growth measures, but there was no interaction effect with burial depth for any traits measured. These results suggest that M. micrantha can regenerate from buried stolon fragments, and thus, disturbance may contribute to the spread of this exotic invader. Any human activities producing stolon fragments or facilitating dispersal should be avoided. PMID:24367686

  14. Transcriptomic analysis of Clostridium thermocellum Populus hydrolysate-tolerant mutant strain shows increased cellular efficiency in response to Populus hydrolysate compared to the wild type strain

    PubMed Central

    2014-01-01

    Background The thermophilic, anaerobic bacterium, Clostridium thermocellum is a model organism for consolidated processing due to its efficient fermentation of cellulose. Constituents of dilute acid pretreatment hydrolysate are known to inhibit C. thermocellum and other microorganisms. To evaluate the biological impact of this type of hydrolysate, a transcriptomic analysis of growth in hydrolysate-containing medium was conducted on 17.5% v/v Populus hydrolysate-tolerant mutant (PM) and wild type (WT) strains of C. thermocellum. Results In two levels of Populus hydrolysate medium (0% and 10% v/v), the PM showed both gene specific increases and decreases of gene expression compared to the wild-type strain. The PM had increased expression of genes in energy production and conversion, and amino acid transport and metabolism in both standard and 10% v/v Populus hydrolysate media. In particular, expression of the histidine metabolism increased up to 100 fold. In contrast, the PM decreased gene expression in cell division and sporulation (standard medium only), cell defense mechanisms, cell envelope, cell motility, and cellulosome in both media. The PM downregulated inorganic ion transport and metabolism in standard medium but upregulated it in the hydrolysate media when compared to the WT. The WT differentially expressed 1072 genes in response to the hydrolysate medium which included increased transcription of cell defense mechanisms, cell motility, and cellulosome, and decreased expression in cell envelope, amino acid transport and metabolism, inorganic ion transport and metabolism, and lipid metabolism, while the PM only differentially expressed 92 genes. The PM tolerates up to 17.5% v/v Populus hydrolysate and growth in it elicited 489 genes with differential expression, which included increased expression in energy production and conversion, cellulosome production, and inorganic ion transport and metabolism and decreased expression in transcription and cell

  15. Identification of Quantitative Trait Loci (QTL) and Candidate Genes for Cadmium Tolerance in Populus

    SciTech Connect

    Induri, Brahma R; Ellis, Danielle R; Slavov, Gancho; Yin, Tongming; Muchero, Wellington; Tuskan, Gerald A; DiFazio, Stephen P

    2012-01-01

    Knowledge of genetic variation in response of Populus to heavy metals like cadmium (Cd) is an important step in understanding the underlying mechanisms of tolerance. In this study, a pseudo-backcross pedigree of Populus trichocarpa and Populus deltoides was characterized for Cd exposure. The pedigree showed significant variation for Cd tolerance thus enabling the identification of relatively tolerant and susceptible genotypes for intensive characterization. A total of 16 QTLs at logarithm of odds (LOD) ratio > 2.5, were found to be associated with total dry weight, its components, and root volume. Four major QTLs for total dry weight were mapped to different linkage groups in control (LG III) and Cd conditions (LG XVI) and had opposite allelic effects on Cd tolerance, suggesting that these genomic regions were differentially controlled. The phenotypic variation explained by Cd QTL for all traits under study varied from 5.9% to 11.6% and averaged 8.2% across all QTL. Leaf Cd contents also showed significant variation suggesting the phytoextraction potential of Populus genotypes, though heritability of this trait was low (0.22). A whole-genome microarray study was conducted by using two genotypes with extreme responses for Cd tolerance in the above study and differentially expressed genes were identified. Candidate genes including CAD2 (CADMIUM SENSITIVE 2), HMA5 (HEAVY METAL ATPase5), ATGTST1 (Arabidopsis thaliana Glutathione S-Transferase1), ATGPX6 (Glutathione peroxidase 6), and ATMRP 14 (Arabidopsis thaliana Multidrug Resistance associated Protein 14) were identified from QTL intervals and microarray study. Functional characterization of these candidate genes could enhance phytoremediation capabilities of Populus.

  16. Aldehyde Dehydrogenase Gene Superfamily in Populus: Organization and Expression Divergence between Paralogous Gene Pairs

    PubMed Central

    Tian, Feng-Xia; Zang, Jian-Lei; Wang, Tan; Xie, Yu-Li; Zhang, Jin; Hu, Jian-Jun

    2015-01-01

    Aldehyde dehydrogenases (ALDHs) constitute a superfamily of NAD(P)+-dependent enzymes that catalyze the irreversible oxidation of a wide range of reactive aldehydes to their corresponding nontoxic carboxylic acids. ALDHs have been studied in many organisms from bacteria to mammals; however, no systematic analyses incorporating genome organization, gene structure, expression profiles, and cis-acting elements have been conducted in the model tree species Populus trichocarpa thus far. In this study, a comprehensive analysis of the Populus ALDH gene superfamily was performed. A total of 26 Populus ALDH genes were found to be distributed across 12 chromosomes. Genomic organization analysis indicated that purifying selection may have played a pivotal role in the retention and maintenance of PtALDH gene families. The exon-intron organizations of PtALDHs were highly conserved within the same family, suggesting that the members of the same family also may have conserved functionalities. Microarray data and qRT-PCR analysis indicated that most PtALDHs had distinct tissue-specific expression patterns. The specificity of cis-acting elements in the promoter regions of the PtALDHs and the divergence of expression patterns between nine paralogous PtALDH gene pairs suggested that gene duplications may have freed the duplicate genes from the functional constraints. The expression levels of some ALDHs were up- or down-regulated by various abiotic stresses, implying that the products of these genes may be involved in the adaptation of Populus to abiotic stresses. Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus ALDH gene superfamily and provide insights into the function and evolution of ALDH gene families in vascular plants. PMID:25909656

  17. Aldehyde Dehydrogenase Gene Superfamily in Populus: Organization and Expression Divergence between Paralogous Gene Pairs.

    PubMed

    Tian, Feng-Xia; Zang, Jian-Lei; Wang, Tan; Xie, Yu-Li; Zhang, Jin; Hu, Jian-Jun

    2015-01-01

    Aldehyde dehydrogenases (ALDHs) constitute a superfamily of NAD(P)+-dependent enzymes that catalyze the irreversible oxidation of a wide range of reactive aldehydes to their corresponding nontoxic carboxylic acids. ALDHs have been studied in many organisms from bacteria to mammals; however, no systematic analyses incorporating genome organization, gene structure, expression profiles, and cis-acting elements have been conducted in the model tree species Populus trichocarpa thus far. In this study, a comprehensive analysis of the Populus ALDH gene superfamily was performed. A total of 26 Populus ALDH genes were found to be distributed across 12 chromosomes. Genomic organization analysis indicated that purifying selection may have played a pivotal role in the retention and maintenance of PtALDH gene families. The exon-intron organizations of PtALDHs were highly conserved within the same family, suggesting that the members of the same family also may have conserved functionalities. Microarray data and qRT-PCR analysis indicated that most PtALDHs had distinct tissue-specific expression patterns. The specificity of cis-acting elements in the promoter regions of the PtALDHs and the divergence of expression patterns between nine paralogous PtALDH gene pairs suggested that gene duplications may have freed the duplicate genes from the functional constraints. The expression levels of some ALDHs were up- or down-regulated by various abiotic stresses, implying that the products of these genes may be involved in the adaptation of Populus to abiotic stresses. Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus ALDH gene superfamily and provide insights into the function and evolution of ALDH gene families in vascular plants.

  18. Evaluation of Populus and Salix continuously irrigated with landfill leachate I. Genotype-specific elemental phytoremediation.

    PubMed

    Zalesny, Ronald S; Bauer, Edmund O

    2007-01-01

    There is a need for the identification and selection of specific tree genotypes that can sequester elements from contaminated soils, with elevated rates of uptake. We irrigated Populus (DN17, DN182, DN34, NM2, NM6) and Salix (94003, 94012, S287, S566, SX61) genotypes planted in large soil-filled containers with landfill leachate or municipal water and tested for differences in inorganic element concentrations (P, K, Ca, Mg, S, Zn, B, Mn, Fe, Cu, Al, Na, and Cl) in the leaves, stems, and roots. Trees were irrigated with leachate or water during the final 12 wk of the 18-wk study. Genotype-specific uptake existed. For genera, tissue concentrations exhibited four responses. First, Populus had the greatest uptake of P, K, S, Cu, and Cl. Second, Salix exhibited the greatest uptake of Zn, B, Fe, and Al. Third, Salix had greater concentrations of Ca and Mg in leaves, while Populus had greater concentrations in stems and roots. Fourth, Populus had greater concentrations of Mn and Na in leaves and stems, while Salix had greater concentrations in roots. Populus deltoides x P. nigra clones exhibited better overall phytoremediation than the P. nigra x P. maximowiczii genotypes tested. Phytoremediation for S. purpurea clones 94003 and 94012 was generally less than for other Salix genotypes. Overall, concentrations of elements in the leaves, stems, and roots corroborated those in the plant-sciences literature. Uptake was dependent upon the specific genotype for most elements. Our results corroborated the need for further testing and selecting of specific clones for various phytoremediation needs, while providing a baseline for future researchers developing additional studies and resource managers conducting on-site remediation.

  19. Genome resequencing in Populus: Revealing large-scale genome variation and implications on specialized-trait genomics

    SciTech Connect

    Muchero, Wellington; Labbe, Jessy L; Priya, Ranjan; DiFazio, Steven P; Tuskan, Gerald A

    2014-01-01

    To date, Populus ranks among a few plant species with a complete genome sequence and other highly developed genomic resources. With the first genome sequence among all tree species, Populus has been adopted as a suitable model organism for genomic studies in trees. However, far from being just a model species, Populus is a key renewable economic resource that plays a significant role in providing raw materials for the biofuel and pulp and paper industries. Therefore, aside from leading frontiers of basic tree molecular biology and ecological research, Populus leads frontiers in addressing global economic challenges related to fuel and fiber production. The latter fact suggests that research aimed at improving quality and quantity of Populus as a raw material will likely drive the pursuit of more targeted and deeper research in order to unlock the economic potential tied in molecular biology processes that drive this tree species. Advances in genome sequence-driven technologies, such as resequencing individual genotypes, which in turn facilitates large scale SNP discovery and identification of large scale polymorphisms are key determinants of future success in these initiatives. In this treatise we discuss implications of genome sequence-enable technologies on Populus genomic and genetic studies of complex and specialized-traits.

  20. A re-examination of the minor role of unstirred layers during the measurement of transport coefficients of Chara corallina internodes with the cell pressure probe.

    PubMed

    Ye, Qing; Kim, Yangmin; Steudle, Ernst

    2006-05-01

    The impact of unstirred layers (USLs) during cell pressure probe experiments with Chara corallina internodes has been quantified. The results show that the hydraulic conductivity (Lp) measured in hydrostatic relaxations was not significantly affected by USLs even in the presence of high water flow intensities ('sweep-away effect'). During pressure clamp, there was a reversible reduction in Lp by 20%, which was explained by the constriction of water to aquaporins (AQPs) in the C. corallina membrane and a rapid diffusional equilibration of solutes in arrays where water protruded across AQPs. In osmotic experiments, Lp, and permeability (Ps) and reflection (sigma s) coefficients increased as external flow rate of medium increased, indicating some effects of external USLs. However, the effect was levelling off at 'usual' flow rates of 0.20-0.30 m s(-1) and in the presence of vigorous stirring by air bubbles, suggesting a maximum thickness of external USLs of around 30 microm including the cell wall. Because the diameters of internodes were around 1 mm, internal USLs could have played a significant or even a dominating role, at least in the presence of the rapidly permeating solutes used [acetone, 2-propanol and dimethylformamide (DMF)]. A comparison of calculated (diffusion kinetics) and of measured permeabilities indicated an upper limit of the contribution of USLs for the rapidly moving solute acetone of 29%, and of 15% for the less rapidly permeating DME The results throw some doubt on recent claims that in C. corallina, USLs rather than the cell membrane dominate solute uptake, at least for the most rapidly moving solute acetone.

  1. BENT UPPERMOST INTERNODE1 Encodes the Class II Formin FH5 Crucial for Actin Organization and Rice Development[W][OA

    PubMed Central

    Yang, Weibing; Ren, Sulin; Zhang, Xiaoming; Gao, Mingjun; Ye, Shenghai; Qi, Yongbin; Zheng, Yiyan; Wang, Juan; Zeng, Longjun; Li, Qun; Huang, Shanjin; He, Zuhua

    2011-01-01

    The actin cytoskeleton is an important regulator of cell expansion and morphogenesis in plants. However, the molecular mechanisms linking the actin cytoskeleton to these processes remain largely unknown. Here, we report the functional analysis of rice (Oryza sativa) FH5/BENT UPPERMOST INTERNODE1 (BUI1), which encodes a formin-type actin nucleation factor and affects cell expansion and plant morphogenesis in rice. The bui1 mutant displayed pleiotropic phenotypes, including bent uppermost internode, dwarfism, wavy panicle rachis, and enhanced gravitropic response. Cytological observation indicated that the growth defects of bui1 were caused mainly by inhibition of cell expansion. Map-based cloning revealed that BUI1 encodes the class II formin FH5. FH5 contains a phosphatase tensin-like domain at its amino terminus and two highly conserved formin-homology domains, FH1 and FH2. In vitro biochemical analyses indicated that FH5 is capable of nucleating actin assembly from free or profilin-bound monomeric actin. FH5 also interacts with the barbed end of actin filaments and prevents the addition and loss of actin subunits from the same end. Interestingly, the FH2 domain of FH5 could bundle actin filaments directly and stabilize actin filaments in vitro. Consistent with these in vitro biochemical activities of FH5/BUI1, the amount of filamentous actin decreased, and the longitudinal actin cables almost disappeared in bui1 cells. The FH2 or FH1FH2 domains of FH5 could also bind to and bundle microtubules in vitro. Thus, our study identified a rice formin protein that regulates de novo actin nucleation and spatial organization of the actin filaments, which are important for proper cell expansion and rice morphogenesis. PMID:21307285

  2. Xylan hydrolysis in Populus trichocarpa × P. deltoides and model substrates during hydrothermal pretreatment.

    PubMed

    Trajano, Heather L; Pattathil, Sivakumar; Tomkins, Bruce A; Tschaplinski, Timothy J; Hahn, Michael G; Van Berkel, Gary J; Wyman, Charles E

    2015-03-01

    Previous studies defined easy and difficult to hydrolyze fractions of hemicellulose that may result from bonds among cellulose, hemicellulose, and lignin. To understand how such bonds affect hydrolysis, Populus trichocarpa × Populus deltoides, holocellulose isolated from P. trichocarpa × P. deltoides and birchwood xylan were subjected to hydrothermal flow-through pretreatment. Samples were characterized by glycome profiling, HPLC, and UPLC-MS. Glycome profiling revealed steady fragmentation and removal of glycans from solids during hydrolysis. The extent of polysaccharide fragmentation, hydrolysis rate, and total xylose yield were lowest for P. trichocarpa × P. deltoides and greatest for birchwood xylan. Comparison of results from P. trichocarpa × P. deltoides and holocellulose suggested that lignin-carbohydrate complexes reduce hydrolysis rates and limit release of large xylooligomers. Smaller differences between results with holocellulose and birchwood xylan suggest xylan-cellulose hydrogen bonds limited hydrolysis, but to a lesser extent. These findings imply cell wall structure strongly influences hydrolysis.

  3. Cytogenetic Analysis of Populus trichocarpa - Ribosomal DNA, Telomere Repeat Sequence, and Marker-selected BACs

    SciTech Connect

    Tuskan, Gerald A; Gunter, Lee E; DiFazio, Stephen P

    2009-01-01

    The 18S-28S rDNA and 5S rDNA loci in Populus trichocarpa were localized using fluorescent in situ hybridization (FISH). Two 18S-28S rDNA sites and one 5S rDNA site were identified and located at the ends of 3 different chromosomes. FISH signals from the Arabidopsis -type telomere repeat sequence were observed at the distal ends of each chromosome. Six BAC clones selected from 2 linkage groups based on genome sequence assembly (LG-I and LG-VI) were localized on 2 chromosomes, as expected. BACs from LG-I hybridized to the longest chromosome in the complement. All BAC positions were found to be concordant with sequence assembly positions. BAC-FISH will be useful for delineating each of the Populus trichocarpa chromosomes and improving the sequence assembly of this model angiosperm tree species.

  4. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa

    SciTech Connect

    Slavov, Gancho; DiFazio, Stephen P; Martin, Joel R; Schackwitz, Wendy; Muchero, Wellington; Rodgers-Melnick, Eli; Lipphardt, Mindie; Pennacchio, Christa; Hellsten, Uffe; Pennacchio, Len; Gunter, Lee; Ranjan, Priya; Strauss, Steven; Rokhsar, Daniel; Tuskan, Gerald A

    2012-01-01

    Population genomics of forest trees provides crucial information for breeding, conservation, and bioenergy feedstock development. As part of a large-scale association study, we resequenced 16 genomes of the model tree Populus trichocarpa to an average depth of 39 . Analyses of the resulting data revealed surprisingly extensive population genetic structure and decay of linkage disequilibrium over much larger physical distances than the expected based on previous, smaller-scale studies. Rates of recombination varied widely across the genome but were largely predictable based on DNA sequence and methylation patterns. Our results suggest that genomewide association studies and accurate prediction of phenotypes from DNA data are more feasible in Populus than previously assumed, thereby laying the foundation for a step change in our understanding of tree biology.

  5. Knockdown of a laccase in Populus deltoides confers altered cell wall chemistry and increased sugar release.

    PubMed

    Bryan, Anthony C; Jawdy, Sara; Gunter, Lee; Gjersing, Erica; Sykes, Robert; Hinchee, Maud A W; Winkeler, Kimberly A; Collins, Cassandra M; Engle, Nancy; Tschaplinski, Timothy J; Yang, Xiaohan; Tuskan, Gerald A; Muchero, Wellington; Chen, Jin-Gui

    2016-10-01

    Plant laccases are thought to function in the oxidation of monolignols which leads to higher order lignin formation. Only a hand-full of laccases in plants have been functionally evaluated, and as such little is known about the breadth of their impact on cell wall chemistry or structure. Here, we describe a previously uncharacterized laccase from Populus, encoded by locus Potri.008G064000, whose reduced expression resulted in transgenic Populus trees with changes in syringyl/guaiacyl ratios as well as altered sugar release phenotypes. These phenotypes are consistent with plant biomass exhibiting reduced recalcitrance. Interestingly, the transgene effect on recalcitrance is dependent on a mild pretreatment prior to chemical extraction of sugars. Metabolite profiling suggests the transgene modulates phenolics that are associated with the cell wall structure. We propose that this particular laccase has a range of functions related to oxidation of phenolics and conjugation of flavonoids that interact with lignin in the cell wall.

  6. Biochemical basis of drought tolerance in hybrid Populus grown under field production conditions. CRADA final report

    SciTech Connect

    Tschaplinski, T.J.; Tuskan, G.A.; Wierman, C.

    1997-04-01

    The purpose of this cooperative effort was to assess the use of osmotically active compounds as molecular selection criteria for drought tolerance in Populus in a large-scale field trial. It is known that some plant species, and individuals within a plant species, can tolerate increasing stress associated with reduced moisture availability by accumulating solutes. The biochemical matrix of such metabolites varies among species and among individuals. The ability of Populus clones to tolerate drought has equal value to other fiber producers, i.e., the wood products industry, where irrigation is used in combination with other cultural treatments to obtain high dry weight yields. The research initially involved an assessment of drought stress under field conditions and characterization of changes in osmotic constitution among the seven clones across the six moisture levels. The near-term goal was to provide a mechanistic basis for clonal differences in productivity under various irrigation treatments over time.

  7. Genome-Wide Identification, Classification, and Expression Analysis of 14-3-3 Gene Family in Populus

    PubMed Central

    Tian, Fengxia; Wang, Tan; Xie, Yuli; Zhang, Jin; Hu, Jianjun

    2015-01-01

    Background In plants, 14-3-3 proteins are encoded by a large multigene family and are involved in signaling pathways to regulate plant development and protection from stress. Although twelve Populus 14-3-3s were identified based on the Populus trichocarpa genome V1.1 in a previous study, no systematic analysis including genome organization, gene structure, duplication relationship, evolutionary analysis and expression compendium has been conducted in Populus based on the latest P. trichocarpa genome V3.0. Principal Findings Here, a comprehensive analysis of Populus 14-3-3 family is presented. Two new 14-3-3 genes were identified based on the latest P. trichocarpa genome. In P. trichocarpa, fourteen 14-3-3 genes were grouped into ε and non-ε group. Exon-intron organizations of Populus 14-3-3s are highly conserved within the same group. Genomic organization analysis indicated that purifying selection plays a pivotal role in the retention and maintenance of Populus 14-3-3 family. Protein conformational analysis indicated that Populus 14-3-3 consists of a bundle of nine α-helices (α1-α9); the first four are essential for formation of the dimer, while α3, α5, α7, and α9 form a conserved peptide-binding groove. In addition, α1, α3, α5, α7, and α9 were evolving at a lower rate, while α2, α4, and α6 were evolving at a relatively faster rate. Microarray analyses showed that most Populus 14-3-3s are differentially expressed across tissues and upon exposure to various stresses. Conclusions The gene structures and their coding protein structures of Populus 14-3-3s are highly conserved among group members, suggesting that members of the same group might also have conserved functions. Microarray and qRT-PCR analyses showed that most Populus 14-3-3s were differentially expressed in various tissues and were induced by various stresses. Our investigation provided a better understanding of the complexity of the 14-3-3 gene family in poplars. PMID:25867623

  8. Identification and biochemical characterization of four wood-associated glucuronoxylan methyltransferases in Populus.

    PubMed

    Yuan, Youxi; Teng, Quincy; Zhong, Ruiqin; Ye, Zheng-Hua

    2014-01-01

    Wood is one of the promising bioenergy feedstocks for lignocellulosic biofuel production. Understanding how wood components are synthesized will help us design strategies for better utilization of wood for biofuel production. One of the major wood components is xylan, in which about 10% of xylosyl residues are substituted with glucuronic acid (GlcA) side chains. All the GlcA side chains of xylan in wood of Populus trichocarpa are methylated, which is different from Arabidopsis xylan in which about 60% of GlcA side chains are methylated. Genes responsible for methylation of GlcA side chains in Populus xylan have not been identified. Here, we report genetic and biochemical analyses of four DUF579 domain-containing proteins, PtrGXM1, PtrGXM2, PtrGXM3 and PtrGXM4, from Populus trichocarpa and their roles in GlcA methylation in xylan. The PtrGXM genes were found to be highly expressed in wood-forming cells and their encoded proteins were shown to be localized in the Golgi. When overexpressed in the Arabidopsis gxm1/2/3 triple mutant, PtrGXMs were able to partially complement the mutant phenotypes including defects in glucuronoxylan methyltransferase activity and GlcA methylation in xylan, indicating that PtrGXMs most likely function as glucuronoxylan methyltransferases. Direct evidence was provided by enzymatic analysis of recombinant PtrGXM proteins showing that they possessed a methyltransferase activity capable of transferring the methyl group onto GlcA-substituted xylooligomers. Kinetic analysis showed that PtrGXMs exhibited differential affinities toward the GlcA-substituted xylooligomer acceptor with PtrGXM3 and PtrGXM4 having 10 times higher K m values than PtrGXM1 and PtrGXM2. Together, these findings indicate that PtrGXMs are methyltransferases mediating GlcA methylation in Populus xylan during wood formation.

  9. Isolating a functionally relevant guild of fungi from the root microbiome of Populus

    DOE PAGESBeta

    Bonito, Gregory; Hameed, Khalid; Ventura, Rafael; Krishnan, Jay; Schadt, Christopher W.; Vilgalys, Rytas

    2016-05-27

    Plant roots interact with a bewilderingly complex community of microbes, including root-associated fungi that are essential for maintaining plant health. To improve understanding of the diversity of fungi in the rhizobiome of Populus deltoides, Populus trichocarpa and co-occurring plant hosts Quercus alba and Pinus taeda, we conducted field and greenhouse studies and sampled, isolated, and characterized the diversity of culturable root-associated fungi on these hosts. Using both general and selective isolation media we obtained more than 1800 fungal isolates from individual surface sterilized root tips. Sequences from the ITS and/or D1– D2 regions of the LSU rDNA were obtained frommore » 1042 of the >1800 pure culture isolates and were compared to accessions in the NCBI nucleotide database and analyzed through phylogenetics for preliminary taxonomic identification. Sequences from these isolates were also compared to 454 sequence datasets obtained directly from the Populus rhizosphere and endosphere. Although most of the ectomycorrhizal taxa known to associate with Populus evaded isolation, many of the abundant sequence types from rhizosphere and endosphere 454 datasets were isolated, including novel species belonging to the Atractiellales. Isolation and identification of key endorrhizal fungi will enable more targeted study of plant-fungal interactions. Genome sequencing is currently underway for a subset of our culture library with the aim of understanding the mechanisms involved in host-endophyte establishment and function. As a result, this diverse culture library of fungal root associates will be a valuable resource for metagenomic research, experimentation and further studies on plant-fungal interactions.« less

  10. Dendrochronological and palynological observations on Populus balsamifera in northern Alaska, USA

    SciTech Connect

    Edwards, M.E.; Dunwiddie, P.W.

    1985-01-01

    Sexual and clonal reproduction is occurring in a stand of Populus balsamifera on the Alaskan North Slope. Both even-aged and gradually expanding clones were observed. Trees attain ages in excess of 230 yr, but are slender due to slow diametrical growth (1.4 to 2.5 mm yr/sup -1/). A tree-ring chronology developed using 16 trees exhibited higher mean sensitivity (0.48) and lower first-order autocorrelation (0.43) than other high-latitude chronologies. Ring-width indices were most highly correlated with June temperature (r = 0.50). This species may be useful in expanding the array of climatically sensitive tree-ring sites in the Arctic. Moss polster samples in the vicinity of the stand indicate that although abundant Populus pollen is produced, little is found in surface samples > 30 m from the trees. It is suggested that Populus balsamifera was considerably more abundant in Beringia during the early Holocene due to warm early summer temperatures and widespread substrates favorable for its growth.

  11. Soil nitrogen limitation does not impact nighttime water loss in Populus.

    PubMed

    Howard, Ava R; Donovan, Lisa A

    2010-01-01

    Nighttime transpirational water loss from C(3) trees occurs without carbon gain and is both common and substantial. However, the magnitude of this water loss varies and a better understanding of the environmental factors driving this variation is needed. We investigated the response of nighttime conductance (g(night)) and transpiration (E(night)) to soil nitrogen limitation. We used instantaneous gas exchange measurements in greenhouse studies of Populus angustifolia James (narrowleaf cottonwood) and Populus balsamifera L. spp. trichocarpa (Torr. & A. Gray ex Hook.) Brayshaw (black cottonwood). g(night) for sufficiently watered plants ranged from 0.045 to 0.308 mol m(-2) s(-1) for P. balsamifera and 0.037 to 0.188 mol m(-2) s(-1) for P. angustifolia, which was much larger than minimum leaf conductance (g(min); up to 0.005 mol m(-2) s(-1) in the dark). Long-term nitrogen limitation sufficient to substantially reduce biomass did not affect g(night) or E(night) when potentially confounding water stress effects were eliminated. We conclude that nighttime water loss from two Populus species is large and although it is under stomatal control is not regulated at night in response to soil nitrogen availability.

  12. Metabolic profiling reveals altered sugar and secondary metabolism in response to UGPase overexpression in Populus

    SciTech Connect

    Payyavula, Raja S.; Tschaplinski, Timothy J.; Jawdy, Sara; Sykes, Robert; Tuskan, Gerald A.; Kalluri, Udaya C.

    2014-10-07

    Background: UDP-glucose pyrophopharylase (UGPase) is a sugar metabolizing enzyme (E.C. 2.7.7.9) that catalyzes a reversible reaction of UDP-glucose and pyrophosphate from glucose-1-phosphate and uridine triphosphate glucose. UDP-glucose is a key intermediate sugar that is channeled to multiple metabolic pathways. The functional role of UGPase in woody plants such as Populus is poorly understood. Results: We characterized the functional role of UGPase in Populus deltoides by overexpressing a native gene. Overexpression of the native gene resulted in increased leaf area and leaf-to-shoot biomass ratio but decreased shoot and root growth. Metabolomic analyses showed that manipulation of UGPase results in perturbations in primary as well as secondary metabolism resulting in reduced sugar and starch levels and increased phenolics such as caffeoyl- and feruloyl conjugates. While cellulose and lignin levels in the cell walls were not significantly altered, the syringyl-to-guaiacyl ratio was significantly reduced. Conclusions: These results demonstrate that UGPase plays a key role in the tightly coupled primary and secondary metabolic pathways and perturbation in its function results in pronounced effects on growth and metabolism outside of cell wall biosynthesis of Populus.

  13. Metabolic profiling reveals altered sugar and secondary metabolism in response to UGPase overexpression in Populus

    DOE PAGESBeta

    Payyavula, Raja S.; Tschaplinski, Timothy J.; Jawdy, Sara; Sykes, Robert; Tuskan, Gerald A.; Kalluri, Udaya C.

    2014-10-07

    Background: UDP-glucose pyrophopharylase (UGPase) is a sugar metabolizing enzyme (E.C. 2.7.7.9) that catalyzes a reversible reaction of UDP-glucose and pyrophosphate from glucose-1-phosphate and uridine triphosphate glucose. UDP-glucose is a key intermediate sugar that is channeled to multiple metabolic pathways. The functional role of UGPase in woody plants such as Populus is poorly understood. Results: We characterized the functional role of UGPase in Populus deltoides by overexpressing a native gene. Overexpression of the native gene resulted in increased leaf area and leaf-to-shoot biomass ratio but decreased shoot and root growth. Metabolomic analyses showed that manipulation of UGPase results in perturbations inmore » primary as well as secondary metabolism resulting in reduced sugar and starch levels and increased phenolics such as caffeoyl- and feruloyl conjugates. While cellulose and lignin levels in the cell walls were not significantly altered, the syringyl-to-guaiacyl ratio was significantly reduced. Conclusions: These results demonstrate that UGPase plays a key role in the tightly coupled primary and secondary metabolic pathways and perturbation in its function results in pronounced effects on growth and metabolism outside of cell wall biosynthesis of Populus.« less

  14. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa.

    PubMed

    Slavov, Gancho T; DiFazio, Stephen P; Martin, Joel; Schackwitz, Wendy; Muchero, Wellington; Rodgers-Melnick, Eli; Lipphardt, Mindie F; Pennacchio, Christa P; Hellsten, Uffe; Pennacchio, Len A; Gunter, Lee E; Ranjan, Priya; Vining, Kelly; Pomraning, Kyle R; Wilhelm, Larry J; Pellegrini, Matteo; Mockler, Todd C; Freitag, Michael; Geraldes, Armando; El-Kassaby, Yousry A; Mansfield, Shawn D; Cronk, Quentin C B; Douglas, Carl J; Strauss, Steven H; Rokhsar, Dan; Tuskan, Gerald A

    2012-11-01

    • Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype-genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination. • We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29,213 single-nucleotide polymorphisms. • Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r(2) dropping below 0.2 within 3-6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N(e) ≈ 4000-6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features. • Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed. PMID:22861491

  15. Genetic basis of aboveground productivity in two native Populus species and their hybrids.

    PubMed

    Lojewski, Nathan R; Fischer, Dylan G; Bailey, Joseph K; Schweitzer, Jennifer A; Whitham, Thomas G; Hart, Stephen C

    2009-09-01

    Demonstration of genetic control over riparian tree productivity has major implications for responses of riparian systems to shifting environmental conditions and effects of genetics on ecosystems in general. We used field studies and common gardens, applying both molecular and quantitative techniques, to compare plot-level tree aboveground net primary productivity (ANPP(tree)) and individual tree growth rate constants in relation to plant genetic identity in two naturally occurring Populus tree species and their hybrids. In field comparisons of four cross types (Populus fremontii S. Wats., Populus angustifolia James, F(1) hybrids and backcross hybrids) across 11 natural stands, productivity was greatest for P. fremontii trees, followed by hybrids and lowest in P. angustifolia. A similar pattern was observed in four common gardens across a 290 m elevation and 100 km environmental gradient. Despite a doubling in productivity across the common gardens, the relative differences among the cross types remained constant. Using clonal replicates in a common garden, we found ANPP(tree) to be a heritable plant trait (i.e., broad-sense heritability), such that plant genetic factors explained between 38% and 82% of the variation in ANPP(tree). Furthermore, analysis of the genetic composition among individual tree genotypes using restriction fragment length polymorphism molecular markers showed that genetically similar trees also exhibited similar ANPP(tree). These findings indicate strong genetic contributions to natural variation in ANPP with important ecological implications. PMID:19578030

  16. Polyphenol oxidase overexpression in transgenic Populus enhances resistance to herbivory by forest tent caterpillar (Malacosoma disstria).

    PubMed

    Wang, Jiehua; Constabel, C Peter

    2004-11-01

    In order to functionally analyze the predicted defensive role of leaf polyphenol oxidase (PPO; EC 1.10.3.1) in Populus, transgenic hybrid aspen (Populus tremula x P. alba) plants overexpressing a hybrid poplar (Populus trichocarpa x P. deltoides) PtdPPO1 gene were constructed. Regenerated transgenic plants showed high PPO enzyme activity, PtdPPO1 mRNA levels and PPO protein accumulation. In leaf disk bioassays, forest tent caterpillar (Malacosoma disstria) larvae feeding on PPO-overexpressing transgenics experienced significantly higher mortality and reduced average weight gain compared to larvae feeding on control leaves. However, this effect was observed only when older egg masses were used and the resulting larvae showed reduced growth and vigor. In choice tests, no effect of PPO overexpression was detected. Although PPO in poplar leaves is latent and requires activation with detergents or trypsin for full enzymatic activity, in caterpillar frass the enzyme was extracted in the fully activated form. This activation correlated with partial proteolytic cleavage, suggesting that PPO latency and activation during digestion could be an adaptive and defense-related feature of poplar PPO.

  17. Plants remember past weather: a study for atmospheric pollen concentrations of Ambrosia, Poaceae and Populus

    NASA Astrophysics Data System (ADS)

    Matyasovszky, István; Makra, László; Csépe, Zoltán; Sümeghy, Zoltán; Deák, Áron József; Pál-Molnár, Elemér; Tusnády, Gábor

    2015-10-01

    After extreme dry (wet) summers or years, pollen production of different taxa may decrease (increase) substantially. Accordingly, studying effects of current and past meteorological conditions on current pollen concentrations for different taxa have of major importance. The purpose of this study is separating the weight of current and past weather conditions influencing current pollen productions of three taxa. Two procedures, namely multiple correlations and factor analysis with special transformation are used. The 11-year (1997-2007) data sets include daily pollen counts of Ambrosia (ragweed), Poaceae (grasses) and Populus (poplar), as well as daily values of four climate variables (temperature, relative humidity, global solar flux and precipitation). Multiple correlations of daily pollen counts with simultaneous values of daily meteorological variables do not show annual course for Ambrosia, but do show definite trends for Populus and Poaceae. Results received using the two methods revealed characteristic similarities. For all the three taxa, the continental rainfall peak and additional local showers in the growing season can strengthen the weight of the current meteorological elements. However, due to the precipitation, big amount of water can be stored in the soil contributing to the effect of the past climate elements during dry periods. Higher climate sensitivity (especially water sensitivity) of the herbaceous taxa ( Ambrosia and Poaceae) can be definitely established compared to the arboreal Populus. Separation of the weight of the current and past weather conditions for different taxa involves practical importance both for health care and agricultural production.

  18. Genome-Wide Identification of the Invertase Gene Family in Populus

    PubMed Central

    Su, Xiaoxing; Rao, Pian; An, Xinmin

    2015-01-01

    Invertase plays a crucial role in carbohydrate partitioning and plant development as it catalyses the irreversible hydrolysis of sucrose into glucose and fructose. The invertase family in plants is composed of two sub-families: acid invertases, which are targeted to the cell wall and vacuole; and neutral/alkaline invertases, which function in the cytosol. In this study, 5 cell wall invertase genes (PtCWINV1-5), 3 vacuolar invertase genes (PtVINV1-3) and 16 neutral/alkaline invertase genes (PtNINV1-16) were identified in the Populus genome and found to be distributed on 14 chromosomes. A comprehensive analysis of poplar invertase genes was performed, including structures, chromosome location, phylogeny, evolutionary pattern and expression profiles. Phylogenetic analysis indicated that the two sub-families were both divided into two clades. Segmental duplication is contributed to neutral/alkaline sub-family expansion. Furthermore, the Populus invertase genes displayed differential expression in roots, stems, leaves, leaf buds and in response to salt/cold stress and pathogen infection. In addition, the analysis of enzyme activity and sugar content revealed that invertase genes play key roles in the sucrose metabolism of various tissues and organs in poplar. This work lays the foundation for future functional analysis of the invertase genes in Populus and other woody perennials. PMID:26393355

  19. Isolation and Characterization of cDNAs Encoding Leucoanthocyanidin Reductase and Anthocyanidin Reductase from Populus trichocarpa

    PubMed Central

    Lu, Wanxiang; Yang, Li; Karim, Abdul; Luo, Keming

    2013-01-01

    Proanthocyanidins (PAs) contribute to poplar defense mechanisms against biotic and abiotic stresses. Transcripts of PA biosynthetic genes accumulated rapidly in response to infection by the fungus Marssonina brunnea f.sp. multigermtubi, treatments of salicylic acid (SA) and wounding, resulting in PA accumulation in poplar leaves. Anthocyanidin reductase (ANR) and leucoanthocyanidin reductase (LAR) are two key enzymes of the PA biosynthesis that produce the main subunits: (+)-catechin and (−)-epicatechin required for formation of PA polymers. In Populus, ANR and LAR are encoded by at least two and three highly related genes, respectively. In this study, we isolated and functionally characterized genes PtrANR1 and PtrLAR1 from P. trichocarpa. Phylogenetic analysis shows that Populus ANR1 and LAR1 occurr in two distinct phylogenetic lineages, but both genes have little difference in their tissue distribution, preferentially expressed in roots. Overexpression of PtrANR1 in poplar resulted in a significant increase in PA levels but no impact on catechin levels. Antisense down-regulation of PtrANR1 showed reduced PA accumulation in transgenic lines, but increased levels of anthocyanin content. Ectopic expression of PtrLAR1 in poplar positively regulated the biosynthesis of PAs, whereas the accumulation of anthocyanin and flavonol was significantly reduced (P<0.05) in all transgenic plants compared to the control plants. These results suggest that both PtrANR1 and PtrLAR1 contribute to PA biosynthesis in Populus. PMID:23741362

  20. Genome-Wide Identification of the Invertase Gene Family in Populus.

    PubMed

    Chen, Zhong; Gao, Kai; Su, Xiaoxing; Rao, Pian; An, Xinmin

    2015-01-01

    Invertase plays a crucial role in carbohydrate partitioning and plant development as it catalyses the irreversible hydrolysis of sucrose into glucose and fructose. The invertase family in plants is composed of two sub-families: acid invertases, which are targeted to the cell wall and vacuole; and neutral/alkaline invertases, which function in the cytosol. In this study, 5 cell wall invertase genes (PtCWINV1-5), 3 vacuolar invertase genes (PtVINV1-3) and 16 neutral/alkaline invertase genes (PtNINV1-16) were identified in the Populus genome and found to be distributed on 14 chromosomes. A comprehensive analysis of poplar invertase genes was performed, including structures, chromosome location, phylogeny, evolutionary pattern and expression profiles. Phylogenetic analysis indicated that the two sub-families were both divided into two clades. Segmental duplication is contributed to neutral/alkaline sub-family expansion. Furthermore, the Populus invertase genes displayed differential expression in roots, stems, leaves, leaf buds and in response to salt/cold stress and pathogen infection. In addition, the analysis of enzyme activity and sugar content revealed that invertase genes play key roles in the sucrose metabolism of various tissues and organs in poplar. This work lays the foundation for future functional analysis of the invertase genes in Populus and other woody perennials. PMID:26393355

  1. [Effects of cadmium stress on the microbial biodiversity in purple soil and alluvial soil potted with a poplar (Populus deltoides x Populus nigra)].

    PubMed

    Wang, Ao; Wu, Fu-Zhong; Yang, Wan-Qin; Zhou, Li-Qiang; Wang, Xu-Xi; Han, Yu

    2011-07-01

    Effects of current Cd contamination levels on microbial biodiversity were studied under the typical Cd contaminated soils in the Yangtze Basin. Purple soil and alluvial soil potted with a poplar (Populus deltoides x Populus nigra) were selected, and the culturable soil microbial amounts by flat method, microbial biomass and bacterial community structure by PCR-DGGE were investigated. Cd supplies significantly increased the culturable amounts of bacteria and actinomyces in purple soil, but decreased the culturable amounts of fungi and the content of microbial biomass N. Fingerprint of DGGE also showed that bacterial community structure have obviously changed under different Cd supplies. In contrast, the lower Cd supplies slightly increased the culturable amounts of bacteria and fungi in alluvial soil, but higher Cd supply treatment decreased the culturable amounts of bacteria, actinomyces and fungi, and the content of microbial biomass N. However, only a slight change was observed under different Cd supplies by DGGE fingerprint. Additionally, there were few effects of Cd supplies on the content of microbial biomass C in both purple soil and alluvial soil. The results provided basic data to understand the effects of present Cd contamination levels on soil microbial characteristics.

  2. Common trade-offs between xylem resistance to cavitation and other physiological traits do not hold among unrelated Populus deltoides x Populus nigra hybrids.

    PubMed

    Fichot, Régis; Barigah, Têtè S; Chamaillard, Sylvain; LE Thiec, Dider; Laurans, Françoise; Cochard, Hervé; Brignolas, Franck

    2010-09-01

    We examined the relationships between xylem resistance to cavitation and 16 structural and functional traits across eight unrelated Populus deltoides x Populus nigra genotypes grown under two contrasting water regimes. The xylem water potential inducing 50% loss of hydraulic conductance (Psi(50)) varied from -1.60 to -2.40 MPa. Drought-acclimated trees displayed a safer xylem, although the extent of the response was largely genotype dependent, with Psi(50) being decreased by as far as 0.60 MPa. At the tissue level, there was no clear relationship between xylem safety and either xylem water transport efficiency or xylem biomechanics; the only structural trait to be strongly associated with Psi(50) was the double vessel wall thickness, genotypes exhibiting a thicker double wall being more resistant. At the leaf level, increased cavitation resistance was associated with decreased stomatal conductance, while no relationship could be identified with traits associated with carbon uptake or bulk leaf carbon isotope discrimination, a surrogate of intrinsic water-use efficiency. At the whole-plant level, increased safety was associated with higher shoot growth potential under well-irrigated regime only. We conclude that common trade-offs between xylem resistance to cavitation and other physiological traits that are observed across species may not necessarily hold true at narrower scales.

  3. Elucidating the evolutionary history and expression patterns of nucleoside phosphorylase paralogs (vegetative storage proteins) in Populus and the plant kingdom

    PubMed Central

    2013-01-01

    Background Nucleoside phosphorylases (NPs) have been extensively investigated in human and bacterial systems for their role in metabolic nucleotide salvaging and links to oncogenesis. In plants, NP-like proteins have not been comprehensively studied, likely because there is no evidence of a metabolic function in nucleoside salvage. However, in the forest trees genus Populus a family of NP-like proteins function as an important ecophysiological adaptation for inter- and intra-seasonal nitrogen storage and cycling. Results We conducted phylogenetic analyses to determine the distribution and evolution of NP-like proteins in plants. These analyses revealed two major clusters of NP-like proteins in plants. Group I proteins were encoded by genes across a wide range of plant taxa while proteins encoded by Group II genes were dominated by species belonging to the order Malpighiales and included the Populus Bark Storage Protein (BSP) and WIN4-like proteins. Additionally, we evaluated the NP-like genes in Populus by examining the transcript abundance of the 13 NP-like genes found in the Populus genome in various tissues of plants exposed to long-day (LD) and short-day (SD) photoperiods. We found that all 13 of the Populus NP-like genes belonging to either Group I or II are expressed in various tissues in both LD and SD conditions. Tests of natural selection and expression evolution analysis of the Populus genes suggests that divergence in gene expression may have occurred recently during the evolution of Populus, which supports the adaptive maintenance models. Lastly, in silico analysis of cis-regulatory elements in the promoters of the 13 NP-like genes in Populus revealed common regulatory elements known to be involved in light regulation, stress/pathogenesis and phytohormone responses. Conclusion In Populus, the evolution of the NP-like protein and gene family has been shaped by duplication events and natural selection. Expression data suggest that previously

  4. Transcript profiles of the cytokinin response regulator gene family in Populus imply diverse roles in plant development.

    PubMed

    Ramírez-Carvajal, Gustavo A; Morse, Alison M; Davis, John M

    2008-01-01

    Cytokinins are plant hormones that influence diverse processes of growth and development. In this study the cytokinin response regulators (RRs) were identified, annotated and characterized at the transcript level in Populus balsamifera ssp. trichocarpa genotype Nisqually 1. The Populus genome was searched for genes that exhibit high sequence identity across their receiver domains. Gene structure was determined by prediction software and, where possible, corroborated by publicly available expressed sequence tags (ESTs). Thirty-three genes belonging to the cytokinin RR gene family were identified in Populus: 11 type As, 11 type Bs and 11 pseudo-RRs. Developmental and cytokinin-responsive expression of the Populus RRs was assessed by whole-genome microarrays and semiquantitative reverse transcription polymerase chain reaction (RT-PCR). Populus RR type As and type Bs appear to be preferentially expressed in nodes, while pseudo-RRs are preferentially expressed in mature leaves. Seven type As and three type Bs were rapidly induced by exogenous cytokinin. Organ-preferred expression patterns suggest possible roles for type As and Bs in development and for pseudo-RRs in integration of environmental signals with plant function.

  5. Genome-wide identification, classification, and expression analysis of CDPK and its closely related gene families in poplar (Populus trichocarpa).

    PubMed

    Zuo, Ran; Hu, Ruibo; Chai, Guohua; Xu, Meiling; Qi, Guang; Kong, Yingzhen; Zhou, Gongke

    2013-03-01

    Calcium-dependent protein kinases (CDPKs) are Ca(2+)-binding proteins known to play crucial roles in Ca(2+) signal transduction pathways which have been identified throughout plant kingdom and in certain types of protists. Genome-wide analysis of CDPKs have been carried out in Arabidopsis, rice and wheat, and quite a few of CDPKs were proved to play crucial roles in plant stress responsive signature pathways. In this study, a comprehensive analysis of Populus CDPK and its closely related gene families was performed, including phylogeny, chromosome locations, gene structures, and expression profiles. Thirty Populus CDPK genes and twenty closely related kinase genes were identified, which were phylogenetically clustered into eight distinct subfamilies and predominately distributed across fifteen linkage groups (LG). Genomic organization analyses indicated that purifying selection has played a pivotal role in the retention and maintenance of Populus CDPK gene family. Furthermore, microarray analysis showed that a number of Populus CDPK and its closely related genes differentially expressed across disparate tissues and under various stresses. The expression profiles of paralogous pairs were also investigated to reveal their evolution fates. In addition, quantitative real-time RT-PCR was performed on nine selected CDPK genes to confirm their responses to drought stress treatment. These observations may lay the foundation for future functional analysis of Populus CDPK and its closely related gene families to unravel their biological roles.

  6. Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides

    SciTech Connect

    Brown, Steven D; Utturkar, Sagar M; Klingeman, Dawn Marie; Johnson, Courtney M; Martin, Stanton; Land, Miriam L; Lu, Tse-Yuan; Schadt, Christopher Warren; Doktycz, Mitchel John; Pelletier, Dale A

    2012-01-01

    To aid in the investigation of the Populus deltoides microbiome we generated draft genome sequences for twenty one Pseudomonas and twenty one other diverse bacteria isolated from Populus deltoides roots. Genome sequences for isolates similar to Acidovorax, Bradyrhizobium, Brevibacillus, Burkholderia, Caulobacter, Chryseobacterium, Flavobacterium, Herbaspirillum, Novosphingobium, Pantoea, Phyllobacterium, Polaromonas, Rhizobium, Sphingobium and Variovorax were generated.

  7. Functional characterization of drought-responsive aquaporins in Populus balsamifera and Populus simonii×balsamifera clones with different drought resistance strategies.

    PubMed

    Almeida-Rodriguez, Adriana M; Cooke, Janice E K; Yeh, Francis; Zwiazek, Janusz J

    2010-12-01

    We have characterized poplar aquaporins (AQPs) to investigate their possible functions in differential drought responses of Populus balsamifera and Populus simonii×balsamifera leaves. Plants were exposed to mild and severe levels of drought stress and to drought stress recovery treatment, and their responses were compared with well-watered controls. Compared with P. balsamifera, P. simonii×balsamifera used drought avoidance as the main drought resistance strategy, and rapidly reduced stomatal conductance in response to stress. This strategy is correlated with growth rate reductions. Eleven AQPs were transcriptionally profiled in leaves from these experiments and five were functionally characterized for water channel activity. PIP1;3 and PIP2;5 were among the most highly expressed leaf AQPs that were responsive to drought. Expression of PIP1;3 and five other AQPs increased in response to drought in the leaves of P. simonii×balsamifera but not in P. balsamifera, suggesting a possible role of these AQPs in water redistribution in the leaf tissues. PIP2;5 was upregulated in P. balsamifera, but not in P. simonii×balsamifera, suggesting that this AQP supports the transpiration-driven water flow. Functional characterization of five drought-responsive plasma membrane intrinsic proteins (PIPs) demonstrated that three PIP2 AQPs (PIP2;2, PIP2;5, PIP2;7) functioned as water transporters in Xenopus laevis oocytes, while the two PIP1 AQPs (PIP1;2 and PIP1;3) did not, consistent with the notion that they may be functional only as heterotetramers.

  8. Hydraulic efficiency and coordination with xylem resistance to cavitation, leaf function, and growth performance among eight unrelated Populus deltoidesxPopulus nigra hybrids.

    PubMed

    Fichot, Régis; Chamaillard, Sylvain; Depardieu, Claire; Le Thiec, Didier; Cochard, Hervé; Barigah, Têtè S; Brignolas, Franck

    2011-03-01

    Tests were carried out to determine whether variations in the hydraulic architecture of eight Populus deltoides×Populus nigra genotypes could be related to variations in leaf function and growth performance. Measurements were performed in a coppice plantation on 1-year-old shoots under optimal irrigation. Hydraulic architecture was characterized through estimates of hydraulic efficiency (the ratio of conducting sapwood area to leaf area, A(X):A(L); leaf- and xylem-specific hydraulic conductance of defoliated shoots, k(SL) and k(SS), respectively; apparent whole-plant leaf-specific hydraulic conductance, k(plant)) and xylem safety (water potential inducing 50% loss in hydraulic conductance). The eight genotypes spanned a significant range of k(SL) from 2.63  kg s(-1) m(-2) MPa(-1) to 4.18  kg s(-1) m(-2) MPa(-1), variations being mostly driven by k(SS) rather than A(X):A(L). There was a strong trade-off between hydraulic efficiency and xylem safety. Values of k(SL) correlated positively with k(plant), indicating that high-pressure flowmeter (HPFM) measurements of stem hydraulic efficiency accurately reflected whole-plant water transport efficiency of field-grown plants at maximum transpiration rate. No clear relationship could be found between hydraulic efficiency and either net CO(2) assimilation rates, water-use efficiency estimates (intrinsic water-use efficiency and carbon isotope discrimination against (13)C), or stomatal characteristics (stomatal density and stomatal pore area index). Estimates of hydraulic efficiency were negatively associated with relative growth rate. This unusual pattern, combined with the trade-off observed between hydraulic efficiency and xylem safety, provides the rationale for the positive link already reported between relative growth rate and xylem safety among the same eight P. deltoides×P. nigra genotypes.

  9. Diversification and Expression of the PIN, AUX/LAX, and ABCB Families of Putative Auxin Transporters in Populus

    PubMed Central

    Carraro, Nicola; Tisdale-Orr, Tracy Eizabeth; Clouse, Ronald Matthew; Knöller, Anne Sophie; Spicer, Rachel

    2012-01-01

    Intercellular transport of the plant hormone auxin is mediated by three families of membrane-bound protein carriers, with the PIN and ABCB families coding primarily for efflux proteins and the AUX/LAX family coding for influx proteins. In the last decade our understanding of gene and protein function for these transporters in Arabidopsis has expanded rapidly but very little is known about their role in woody plant development. Here we present a comprehensive account of all three families in the model woody species Populus, including chromosome distribution, protein structure, quantitative gene expression, and evolutionary relationships. The PIN and AUX/LAX gene families in Populus comprise 16 and 8 members respectively and show evidence for the retention of paralogs following a relatively recent whole genome duplication. There is also differential expression across tissues within many gene pairs. The ABCB family is previously undescribed in Populus and includes 20 members, showing a much deeper evolutionary history, including both tandem and whole genome duplication as well as probable gene loss. A striking number of these transporters are expressed in developing Populus stems and we suggest that evolutionary and structural relationships with known auxin transporters in Arabidopsis can point toward candidate genes for further study in Populus. This is especially important for the ABCBs, which is a large family and includes members in Arabidopsis that are able to transport other substrates in addition to auxin. Protein modeling, sequence alignment and expression data all point to ABCB1.1 as a likely auxin transport protein in Populus. Given that basipetal auxin flow through the cambial zone shapes the development of woody stems, it is important that we identify the full complement of genes involved in this process. This work should lay the foundation for studies targeting specific proteins for functional characterization and in situ localization. PMID:22645571

  10. Condensed tannin biosynthesis and polymerization synergistically condition carbon use, defense, sink strength and growth in Populus.

    PubMed

    Harding, Scott A; Xue, Liang-Jiao; Du, Lei; Nyamdari, Batbayar; Lindroth, Richard L; Sykes, Robert; Davis, Mark F; Tsai, Chung-Jui

    2014-11-01

    The partitioning of carbon for growth, storage and constitutive chemical defenses is widely framed in terms of a hypothetical sink-source differential that varies with nutrient supply. According to this framework, phenolics accrual is passive and occurs in source leaves when normal sink growth is not sustainable due to a nutrient limitation. In assessing this framework, we present gene and metabolite evidence that condensed tannin (CT) accrual is strongest in sink leaves and sequesters carbon in a way that impinges upon foliar sink strength and upon phenolic glycoside (PG) accrual in Populus. The work was based on two Populus fremontii × angustifolia backcross lines with contrasting rates of CT accrual and growth, and equally large foliar PG reserves. However, foliar PG accrual was developmentally delayed in the high-CT, slow-growth line (SG), and nitrogen-limitation led to increased foliar PG accrual only in the low-CT, fast-growth line (FG). Metabolite profiling of developing leaves indicated comparatively carbon-limited amino acid metabolism, depletion of several Krebs cycle intermediates and reduced organ sink strength in SG. Gene profiling indicated that CT synthesis decreased as leaves expanded and PGs increased. A most striking finding was that the nitrogenous monoamine phenylethylamine accumulated only in leaves of SG plants. The potential negative impact of CT hyper-accumulation on foliar sink strength, as well as a mechanism for phenylethylamine involvement in CT polymerization in Populus are discussed. Starch accrual in source leaves and CT accrual in sink leaves of SG may both contribute to the maintenance of a slow-growth phenotype suited to survival in nutrient-poor habitats. PMID:24336515

  11. Repeated unidirectional introgression towards Populus balsamifera in contact zones of exotic and native poplars.

    PubMed

    Thompson, Stacey Lee; Lamothe, Manuel; Meirmans, Patrick G; Périnet, Pierre; Isabel, Nathalie

    2010-01-01

    As the evolutionary significance of hybridization is largely dictated by its extent beyond the first generation, we broadly surveyed patterns of introgression across a sympatric zone of two native poplars (Populus balsamifera, Populus deltoides) in Quebec, Canada within which European exotic Populus nigra and its hybrids have been extensively planted since the 1800s. Single nucleotide polymorphisms (SNPs) that appeared fixed within each species were characterized by DNA-sequencing pools of pure individuals. Thirty-five of these diagnostic SNPs were employed in a high-throughput assay that genotyped 635 trees of different age classes, sampled from 15 sites with various degrees of anthropogenic disturbance. The degree of admixture within sampled trees was then assessed through Bayesian clustering of genotypes. Hybrids were present in seven of the populations, with 2.4% of all sampled trees showing spontaneous admixture. Sites with hybrids were significantly more disturbed than pure stands, while hybrids comprised both immature juveniles and trees of reproductive age. All three possible F1s were detected. Advanced-generation hybrids were consistently biased towards P. balsamifera regardless of whether hybridization had occurred with P. deltoides or P. nigra. Gene exchange between P. deltoides and P. nigra was not detected beyond the F1 generation; however, detection of a trihybrid demonstrates that even this apparent reproductive isolation does not necessarily result in an evolutionary dead end. Collectively, results demonstrate the natural fertility of hybrid poplars and suggest that introduced genes could potentially affect the genetic integrity of native trees, similar to that arising from introgression between natives.

  12. Association genetics and expression patterns of a CBF4 homolog in Populus under abiotic stress.

    PubMed

    Li, Ying; Xu, Baohua; Du, Qingzhang; Zhang, Deqiang

    2015-06-01

    New strategies for prevention and treatment of abiotic stress require an improved understanding of stress responses. Here, we examined response differences of a C-repeat binding factor gene (PsCBF4) between five species in the genus Populus. We also used a candidate gene-based approach to identify single nucleotide polymorphisms (SNPs) within PsCBF4 that were associated with physiological and biochemical traits in a natural population (528 unrelated individuals) of Populus simonii. We first isolated a 1,044-bp PsCBF4 cDNA encoding a polypeptide of 256 amino acids. Expression profiling revealed that CBF4 is differentially expressed under cold, heat, drought, and salt conditions among five Populus species. Cold stress is the most significant interspecific difference, and PsCBF4 transcript levels ranged from 6.5 to 379.5 times higher than in unstressed controls. A natural population of P. simonii showed high nucleotide diversity (π T = 0.00880, θ w = 0.01192) and low linkage disequilibrium (r (2) ≥ 0.1, within 700 bp) across PsCBF4. Association analysis showed that nine SNPs (false discovery rate Q < 0.10) and two haplotypes (Q < 0.10) were significantly associated with six physiological and biochemical traits, with each marker explaining 3.36-6.12 % of the phenotypic variance in the corresponding trait. Transcript analysis further detected significant differences among genotypic classes for all significant SNPs. Identification of these significant associations will help reveal the molecular bases of physiological and biochemical differences and provide a starting point for marker-assisted selection for traits involved in stress tolerance in P. simonii.

  13. Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis

    PubMed Central

    Jun, Se-Ran; Wassenaar, Trudy M.; Nookaew, Intawat; Hauser, Loren; Wanchai, Visanu; Land, Miriam; Timm, Collin M.; Lu, Tse-Yuan S.; Schadt, Christopher W.; Doktycz, Mitchel J.; Pelletier, Dale A.

    2015-01-01

    The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000 Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides (eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity. All Pseudomonas aeruginosa genomes clustered together, and these were clearly distinct from other Pseudomonas species groups on the basis of pangenome and core genome analyses. In contrast, the genomes of Pseudomonas fluorescens were organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21 Populus-associated isolates formed three distinct subgroups within the major P. fluorescens group, supported by pathway profile analysis, while two isolates were more closely related to Pseudomonas chlororaphis and Pseudomonas putida. Genes specific to Populus-associated subgroups were identified. Genes specific to subgroup 1 include several sensory systems that act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor. Genes specific to subgroup 2 contain hypothetical genes, and genes specific to subgroup 3 were annotated with hydrolase activity. This study justifies the need to sequence multiple isolates, especially from P. fluorescens, which displays the most genetic variation, in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosing Pseudomonas strains for use to promote growth and increase disease resistance in plants. PMID:26519390

  14. Condensed tannin biosynthesis and polymerization synergistically condition carbon use, defense, sink strength and growth in Populus.

    PubMed

    Harding, Scott A; Xue, Liang-Jiao; Du, Lei; Nyamdari, Batbayar; Lindroth, Richard L; Sykes, Robert; Davis, Mark F; Tsai, Chung-Jui

    2014-11-01

    The partitioning of carbon for growth, storage and constitutive chemical defenses is widely framed in terms of a hypothetical sink-source differential that varies with nutrient supply. According to this framework, phenolics accrual is passive and occurs in source leaves when normal sink growth is not sustainable due to a nutrient limitation. In assessing this framework, we present gene and metabolite evidence that condensed tannin (CT) accrual is strongest in sink leaves and sequesters carbon in a way that impinges upon foliar sink strength and upon phenolic glycoside (PG) accrual in Populus. The work was based on two Populus fremontii × angustifolia backcross lines with contrasting rates of CT accrual and growth, and equally large foliar PG reserves. However, foliar PG accrual was developmentally delayed in the high-CT, slow-growth line (SG), and nitrogen-limitation led to increased foliar PG accrual only in the low-CT, fast-growth line (FG). Metabolite profiling of developing leaves indicated comparatively carbon-limited amino acid metabolism, depletion of several Krebs cycle intermediates and reduced organ sink strength in SG. Gene profiling indicated that CT synthesis decreased as leaves expanded and PGs increased. A most striking finding was that the nitrogenous monoamine phenylethylamine accumulated only in leaves of SG plants. The potential negative impact of CT hyper-accumulation on foliar sink strength, as well as a mechanism for phenylethylamine involvement in CT polymerization in Populus are discussed. Starch accrual in source leaves and CT accrual in sink leaves of SG may both contribute to the maintenance of a slow-growth phenotype suited to survival in nutrient-poor habitats.

  15. Biosynthesis of phenolic glycosides from phenylpropanoid and benzenoid precursors in populus.

    PubMed

    Babst, Benjamin A; Harding, Scott A; Tsai, Chung-Jui

    2010-03-01

    Salicylate-containing phenolic glycosides (PGs) are abundant and often play a dominant role in plant-herbivore interactions of Populus and Salix species (family Salicaceae), but the biosynthetic pathway to PGs remains unclear. Cinnamic acid (CA) is thought to be a precursor of the salicyl moiety of PGs. However, the origin of the 6-hydroxy-2-cyclohexen-on-oyl (HCH) moiety found in certain PGs, such as salicortin, is not known. HCH is of interest because it confers toxicity and antifeedant properties against herbivores. We incubated Populus nigra leaf tissue with stable isotope-labeled CA, benzoates, and salicylates, and measured isotopic incorporation levels into both salicin, the simplest PG, and salicortin. Labeling of salicortin from [13C6]-CA provided the first evidence that HCH, like the salicyl moiety, is a phenylpropanoid derivative. Benzoic acid and benzaldehyde also labeled both salicyl and HCH, while benzyl alcohol labeled only the salicyl moiety in salicortin. Co-administration of unlabeled benzoates with [13C6]-CA confirmed their contribution to the biosynthesis of the salicyl but not the HCH moiety of salicortin. These data suggest that benzoate interconversions may modulate partitioning of phenylpropanoids to salicyl and HCH moieties, and hence toxicity of PGs. Surprisingly, labeled salicyl alcohol and salicylaldehyde were readily converted to salicin, but did not result in labeled salicortin. Co-administration of unlabeled salicylates with labeled CA suggested that salicyl alcohol and salicylaldehyde may have inhibited salicortin biosynthesis. A revised metabolic grid model of PG biosynthesis in Populus is proposed, providing a guide for functional genomic analysis of the PG biosynthetic pathway.

  16. Consolidated bioprocessing of Populus using Clostridium (Ruminiclostridium) thermocellum: a case study on the impact of lignin composition and structure

    DOE PAGESBeta

    Dumitrache, Alexandru; Akinosho, Hannah; Rodriguez, Miguel; Meng, Xianzhi; Yoo, Chang Geun; Natzke, Jace; Engle, Nancy L.; Sykes, Robert W.; Tschaplinski, Timothy J.; Muchero, Wellington; et al

    2016-02-04

    Background: Higher ratios of syringyl-to-guaiacyl (S/G) lignin components of Populus were shown to improve sugar release by enzymatic hydrolysis using commercial blends. Cellulolytic microbes are often robust biomass hydrolyzers and may offer cost advantages; however, it is unknown whether their activity can also be significantly influenced by the ratio of different monolignol types in Populus biomass. Hydrolysis and fermentation of autoclaved, but otherwise not pretreated Populus trichocarpa by Clostridium thermocellum ATCC 27405 was compared using feedstocks that had similar carbohydrate and total lignin contents but differed in S/G ratios. Results: Populus with an S/G ratio of 2.1 was converted moremore » rapidly and to a greater extent compared to similar biomass that had a ratio of 1.2. For either microbes or commercial enzymes, an approximate 50% relative difference in total solids solubilization was measured for both biomasses, which suggests that the differences and limitations in the microbial breakdown of lignocellulose may be largely from the enzymatic hydrolytic process. Unexpectedly, the reduction in glucan content per gram solid in the residual microbially processed biomass was similar (17–18%) irrespective of S/G ratio, pointing to a similar mechanism of solubilization that proceeded at different rates. Fermentation metabolome testing did not reveal the release of known biomass-derived alcohol and aldehyde inhibitors that could explain observed differences in microbial hydrolytic activity. Biomass-derived p-hydroxybenzoic acid was up to ninefold higher in low S/G ratio biomass fermentations, but was not found to be inhibitory in subsequent test fermentations. Cellulose crystallinity and degree of polymerization did not vary between Populus lines and had minor changes after fermentation. However, lignin molecular weights and cellulose accessibility determined by Simons’ staining were positively correlated to the S/G content. Conclusions: Higher

  17. Comparative genome analysis of Pseudomonas genomes including Populus-associated isolates

    SciTech Connect

    Jun, Se Ran; Wassenaar, Trudy; Nookaew, Intawat; Hauser, Loren John; Wanchai, Visanu; Land, Miriam L.; Timm, Collin M.; Lu, Tse-Yuan S.; Schadt, Christopher Warren; Doktycz, Mitchel John; Pelletier, Dale A; Ussery, David W

    2016-01-01

    The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches including the rhizosphere and endosphere of many plants influencing phylogenetic diversity and heterogeneity. In this study, comparative genome analysis was performed on over one thousand Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides. Based on average amino acid identity, genomic clusters were identified within the Pseudomonas genus, which showed agreements with clades by NCBI and cliques by IMG. The P. fluorescens group was organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. The species P. aeruginosa showed clear distinction in their genomic relatedness compared to other Pseudomonas species groups based on the pan and core genome analysis. The 19 isolates of our 21 Populus-associated isolates formed three distinct subgroups within the P. fluorescens major group, supported by pathway profiles analysis, while two isolates were more closely related to P. chlororaphis and P. putida. The specific genes to Populus-associated subgroups were identified where genes specific to subgroup 1 include several sensory systems such as proteins which act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor; specific genes to subgroup 2 contain unique hypothetical genes; and genes specific to subgroup 3 organisms have a different hydrolase activity. IMPORTANCE The comparative genome analyses of the genus Pseudomonas that included Populus-associated isolates resulted in novel insights into high diversity of Pseudomonas. Consistent and robust genomic clusters with phylogenetic homogeneity were identified, which resolved species-clades that are not clearly defined by 16S rRNA gene sequence analysis alone. The genomic clusters may be reflective of distinct ecological niches to which the organisms have adapted, but this

  18. Comparative genome analysis of Pseudomonas genomes including Populus-associated isolates

    DOE PAGESBeta

    Jun, Se Ran; Wassenaar, Trudy; Nookaew, Intawat; Hauser, Loren John; Wanchai, Visanu; Land, Miriam L.; Timm, Collin M.; Lu, Tse-Yuan S.; Schadt, Christopher Warren; Doktycz, Mitchel John; et al

    2016-01-01

    The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches including the rhizosphere and endosphere of many plants influencing phylogenetic diversity and heterogeneity. In this study, comparative genome analysis was performed on over one thousand Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides. Based on average amino acid identity, genomic clusters were identified within the Pseudomonas genus, which showed agreements with clades by NCBI and cliques by IMG. The P. fluorescens group was organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. The speciesmore » P. aeruginosa showed clear distinction in their genomic relatedness compared to other Pseudomonas species groups based on the pan and core genome analysis. The 19 isolates of our 21 Populus-associated isolates formed three distinct subgroups within the P. fluorescens major group, supported by pathway profiles analysis, while two isolates were more closely related to P. chlororaphis and P. putida. The specific genes to Populus-associated subgroups were identified where genes specific to subgroup 1 include several sensory systems such as proteins which act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor; specific genes to subgroup 2 contain unique hypothetical genes; and genes specific to subgroup 3 organisms have a different hydrolase activity. IMPORTANCE The comparative genome analyses of the genus Pseudomonas that included Populus-associated isolates resulted in novel insights into high diversity of Pseudomonas. Consistent and robust genomic clusters with phylogenetic homogeneity were identified, which resolved species-clades that are not clearly defined by 16S rRNA gene sequence analysis alone. The genomic clusters may be reflective of distinct ecological niches to which the organisms have adapted, but

  19. A Homolog of Blade-On-Petiole 1 and 2 (BOP1/2) Controls Internode Length and Homeotic Changes of the Barley Inflorescence.

    PubMed

    Jost, Matthias; Taketa, Shin; Mascher, Martin; Himmelbach, Axel; Yuo, Takahisa; Shahinnia, Fahimeh; Rutten, Twan; Druka, Arnis; Schmutzer, Thomas; Steuernagel, Burkhard; Beier, Sebastian; Taudien, Stefan; Scholz, Uwe; Morgante, Michele; Waugh, Robbie; Stein, Nils

    2016-06-01

    Inflorescence architecture in small-grain cereals has a direct effect on yield and is an important selection target in breeding for yield improvement. We analyzed the recessive mutation laxatum-a (lax-a) in barley (Hordeum vulgare), which causes pleiotropic changes in spike development, resulting in (1) extended rachis internodes conferring a more relaxed inflorescence, (2) broadened base of the lemma awns, (3) thinner grains that are largely exposed due to reduced marginal growth of the palea and lemma, and (4) and homeotic conversion of lodicules into two stamenoid structures. Map-based cloning enforced by mapping-by-sequencing of the mutant lax-a locus enabled the identification of a homolog of BLADE-ON-PETIOLE1 (BOP1) and BOP2 as the causal gene. Interestingly, the recently identified barley uniculme4 gene also is a BOP1/2 homolog and has been shown to regulate tillering and leaf sheath development. While the Arabidopsis (Arabidopsis thaliana) BOP1 and BOP2 genes act redundantly, the barley genes contribute independent effects in specifying the developmental growth of vegetative and reproductive organs, respectively. Analysis of natural genetic diversity revealed strikingly different haplotype diversity for the two paralogous barley genes, likely affected by the respective genomic environments, since no indication for an active selection process was detected. PMID:27208226

  20. A Dark Incubation Period Is Important for Agrobacterium-Mediated Transformation of Mature Internode Explants of Sweet Orange, Grapefruit, Citron, and a Citrange Rootstock

    PubMed Central

    Marutani-Hert, Mizuri; Bowman, Kim D.; McCollum, Greg T.; Mirkov, T. Erik; Evens, Terence J.; Niedz, Randall P.

    2012-01-01

    Background Citrus has an extended juvenile phase and trees can take 2–20 years to transition to the adult reproductive phase and produce fruit. For citrus variety development this substantially prolongs the time before adult traits, such as fruit yield and quality, can be evaluated. Methods to transform tissue from mature citrus trees would shorten the evaluation period via the direct production of adult phase transgenic citrus trees. Methodology/Principal Findings Factors important for promoting shoot regeneration from internode explants from adult phase citrus trees were identified and included a dark incubation period and the use of the cytokinin zeatin riboside. Transgenic trees were produced from four citrus types including sweet orange, citron, grapefruit, and a trifoliate hybrid using the identified factors and factor settings. Significance The critical importance of a dark incubation period for shoot regeneration was established. These results confirm previous reports on the feasibility of transforming mature tissue from sweet orange and are the first to document the transformation of mature tissue from grapefruit, citron, and a trifoliate hybrid. PMID:23082165

  1. A Homolog of Blade-On-Petiole 1 and 2 (BOP1/2) Controls Internode Length and Homeotic Changes of the Barley Inflorescence1[OPEN

    PubMed Central

    Taketa, Shin; Mascher, Martin; Yuo, Takahisa; Beier, Sebastian; Taudien, Stefan; Morgante, Michele

    2016-01-01

    Inflorescence architecture in small-grain cereals has a direct effect on yield and is an important selection target in breeding for yield improvement. We analyzed the recessive mutation laxatum-a (lax-a) in barley (Hordeum vulgare), which causes pleiotropic changes in spike development, resulting in (1) extended rachis internodes conferring a more relaxed inflorescence, (2) broadened base of the lemma awns, (3) thinner grains that are largely exposed due to reduced marginal growth of the palea and lemma, and (4) and homeotic conversion of lodicules into two stamenoid structures. Map-based cloning enforced by mapping-by-sequencing of the mutant lax-a locus enabled the identification of a homolog of BLADE-ON-PETIOLE1 (BOP1) and BOP2 as the causal gene. Interestingly, the recently identified barley uniculme4 gene also is a BOP1/2 homolog and has been shown to regulate tillering and leaf sheath development. While the Arabidopsis (Arabidopsis thaliana) BOP1 and BOP2 genes act redundantly, the barley genes contribute independent effects in specifying the developmental growth of vegetative and reproductive organs, respectively. Analysis of natural genetic diversity revealed strikingly different haplotype diversity for the two paralogous barley genes, likely affected by the respective genomic environments, since no indication for an active selection process was detected. PMID:27208226

  2. Expression of cell wall related genes in basal and ear internodes of silking brown-midrib-3, caffeic acid O-methyltransferase (COMT) down-regulated, and normal maize plants

    PubMed Central

    Guillaumie, Sabine; Goffner, Deborah; Barbier, Odile; Martinant, Jean-Pierre; Pichon, Magalie; Barrière, Yves

    2008-01-01

    Background Silage maize is a major forage and energy resource for cattle feeding, and several studies have shown that lignin content and structure are the determining factors in forage maize feeding value. In maize, four natural brown-midrib mutants have modified lignin content, lignin structure and cell wall digestibility. The greatest lignin reduction and the highest cell wall digestibility were observed in the brown-midrib-3 (bm3) mutant, which is disrupted in the caffeic acid O-methyltransferase (COMT) gene. Results Expression of cell wall related genes was investigated in basal and ear internodes of normal, COMT antisens (AS225), and bm3 maize plants of the INRA F2 line. A cell wall macro-array was developed with 651 gene specific tags of genes specifically involved in cell wall biogenesis. When comparing basal (older lignifying) and ear (younger lignifying) internodes of the normal line, all genes known to be involved in constitutive monolignol biosynthesis had a higher expression in younger ear internodes. The expression of the COMT gene was heavily reduced, especially in the younger lignifying tissues of the ear internode. Despite the fact that AS225 transgene expression was driven only in sclerenchyma tissues, COMT expression was also heavily reduced in AS225 ear and basal internodes. COMT disruption or down-regulation led to differential expressions of a few lignin pathway genes, which were all over-expressed, except for a phenylalanine ammonia-lyase gene. More unexpectedly, several transcription factor genes, cell signaling genes, transport and detoxification genes, genes involved in cell wall carbohydrate metabolism and genes encoding cell wall proteins, were differentially expressed, and mostly over-expressed, in COMT-deficient plants. Conclusion Differential gene expressions in COMT-deficient plants highlighted a probable disturbance in cell wall assembly. In addition, the gene expressions suggested modified chronology of the different events leading

  3. Transport and use of CO sub 2 in the xylem sap of Populus deltoides

    SciTech Connect

    Stringer, J.W.; Kimmerer, T.W. )

    1990-05-01

    Results of recent experiments indicate an internal cycling of respiratory CO{sub 2} in woody plants. The CO{sub 2} concentration of xylem sap expressed from the twigs of field grown Populus deltoides ranged from .14 to .50 mM. The pH of the xylem sap was 5.7 to 6.7, providing a significant bicarbonate concentration in many samples. Total dissolved inorganic carbon (DIC = CO{sub 2} + H{sub 2}CO{sub 3} + HCO{sub 3}{sup {minus}}) was 0.5 mM to 1.3 mM. Results from the analysis of xylem sap of 10 other species of woody plants were similar. To determine the fate of DIC delivered to the leaves of Populus deltoides, excised leaves were fed 1mM NaHCO{sub 3} (2 {mu}Ci NaH{sup 14}CO{sub 3} ml{sup {minus}1}). Less than 0.4% of the label escaped from the leaves, and {ge}93% was fixed. Of the carbon fixed 56% of the {sup 14}C was found in the petiole and midrib, and 14% was in the major veins, with the remaining 30% in the minor veins and lamina. Shading of the peptiole and midrib of leaves decreased the amount of fixed carbon in these tissues to 38% and increased the amount in the lamina to 55%.

  4. Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis

    DOE PAGESBeta

    Utturkar, Sagar M.; Cude, W. Nathan; Robeson, Jr., Michael S.; Yang, Zamin Koo; Klingeman, Dawn Marie; Land, Miriam L.; Allman, Steve L.; Lu, Tse-Yuan S.; Brown, Steven D.; Schadt, Christopher Warren; et al

    2016-07-15

    Bacterial endophytes that colonize Populus trees contribute to nutrient acquisition, prime immunity responses, and directly or indirectly increase both above- and below-ground biomasses. Endophytes are embedded within plant material, so physical separation and isolation are difficult tasks. Application of culture-independent methods, such as metagenome or bacterial transcriptome sequencing, has been limited due to the predominance of DNA from the plant biomass. In this paper, we present a modified differential and density gradient centrifugation-based protocol for the separation of endophytic bacteria from Populus roots. This protocol achieved substantial reduction in contaminating plant DNA, allowed enrichment of endophytic bacteria away from themore » plant material, and enabled single-cell genomics analysis. Four single-cell genomes were selected for whole-genome amplification based on their rarity in the microbiome (potentially uncultured taxa) as well as their inferred abilities to form associations with plants. Bioinformatics analyses, including assembly, contamination removal, and completeness estimation, were performed to obtain single-amplified genomes (SAGs) of organisms from the phyla Armatimonadetes, Verrucomicrobia, and Planctomycetes, which were unrepresented in our previous cultivation efforts. Finally, comparative genomic analysis revealed unique characteristics of each SAG that could facilitate future cultivation efforts for these bacteria.« less

  5. Water stress, photosynthesis and early growth patterns of cuttings of three Populus clones.

    PubMed

    Rhodenbaugh, E J; Pallardy, S G

    1993-10-01

    Photosynthetic attributes, leaf area and early root growth patterns were studied in three Populus clones to identify traits associated with superior growth potential on sites where water could be a limiting factor. It was found that early root growth and superior leaf area production were more closely related to growth potential than were photosynthetic capacity or carboxylation efficiency. A hybrid clone of Populus nigra var. charkowiensis (syn. P. nigra var. plantierensis) x P. nigra cv. 'Incrassata' (NE308) had more leaf area production and greater root system development in both wet and dry soil than did a P. trichocarpa clone (T6) and a P. balsamifera clone (B3). Despite greater above- and below-ground productivity, plants of clone NE308 had significantly lower photosynthetic capacity and carboxylation efficiency and a slightly higher CO(2) compensation point than plants of clones T6 and B3. Rapid early leaf and root growth appear to be key attributes associated with productivity in these clones regardless of soil water availability.

  6. Fermentation of dilute acid pretreated Populus by Clostridium thermocellum, Caldicellulosiruptor bescii, and Caldicellulosiruptor obsidiansis

    DOE PAGESBeta

    Yee, Kelsey L.; Rodriguez, Jr., Miguel; Hamilton, Choo Yieng; Hamilton-Brehm, Scott D.; Thompson, Olivia A.; Elkins, James G.; Davison, Brian H.; Mielenz, Jonathan R.

    2015-07-25

    Consolidated bioprocessing (CBP), which merges enzyme production, biomass hydrolysis, and fermentation into a single step, has the potential to become an efficient and economic strategy for the bioconversion of lignocellulosic feedstocks to transportation fuels or chemicals. In this study, we evaluated Clostridium thermocellum, Caldicellulosiruptor bescii, and Caldicellulosiruptor obsidiansis, three , thermophilic,cellulolytic, mixed-acid fermenting candidate CBP microorganisms, for their fermentation capabilities using dilute acid pretreated Populus as a model biomass feedstock. Under pH controlled, anaerobic fermentation conditions, each candidate successfully digested a minimum of 75% of the cellulose from dilute acid pretreated Populus, as indicated by an increase in planktonic cellsmore » and end-product metabolites and a concurrent decrease in glucan content. C. thermocellum, which employs a cellulosomal approach to biomass degradation, required 120 hours to achieve 75% cellulose utilization. In contrast, the non-cellulosomal, secreted hydrolytic enzyme system of the Caldicellulosiruptor sp. required 300 hours to achieve similar results. End-point fermentation conversions for C. thermocellum, C. bescii, and C. obsidiansis were determined to be 0.29, 0.34, and 0.38 grams of total metabolites per gram of loaded glucan, respectively. This data provide a starting point for future strain engineering efforts that can serve to improve the biomass fermentation capabilities of these three promising candidate CBP platforms.« less

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

    USGS Publications Warehouse

    Beauchamp, Vanessa B.; Stromberg, J.C.; Stutz, J.C.

    2006-01-01

    ??? 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. ?? New Phytologist (2006).

  8. Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correlations.

    PubMed

    Porth, Ilga; Klápště, Jaroslav; Skyba, Oleksandr; Lai, Ben S K; Geraldes, Armando; Muchero, Wellington; Tuskan, Gerald A; Douglas, Carl J; El-Kassaby, Yousry A; Mansfield, Shawn D

    2013-02-01

    The increasing ecological and economical importance of Populus species and hybrids has stimulated research into the investigation of the natural variation of the species and the estimation of the extent of genetic control over its wood quality traits for traditional forestry activities as well as the emerging bioenergy sector. A realized kinship matrix based on informative, high-density, biallelic single nucleotide polymorphism (SNP) genetic markers was constructed to estimate trait variance components, heritabilities, and genetic and phenotypic correlations. Seventeen traits related to wood chemistry and ultrastructure were examined in 334 9-yr-old Populus trichocarpa grown in a common-garden plot representing populations spanning the latitudinal range 44° to 58.6°. In these individuals, 9342 SNPs that conformed to Hardy-Weinberg expectations were employed to assess the genomic pair-wise kinship to estimate narrow-sense heritabilities and genetic correlations among traits. The range-wide phenotypic variation in all traits was substantial and several trait heritabilities were > 0.6. In total, 61 significant genetic and phenotypic correlations and a network of highly interrelated traits were identified. The high trait variation, the evidence for moderate to high heritabilities and the identification of advantageous trait combinations of industrially important characteristics should aid in providing the foundation for the enhancement of poplar tree breeding strategies for modern industrial use. PMID:23278123

  9. How to Regenerate and Protect Desert Riparian Populus euphratica Forest in Arid Areas.

    PubMed

    Ling, Hongbo; Zhang, Pei; Xu, Hailiang; Zhao, Xinfeng

    2015-01-01

    We found that the most suitable flooding disturbance model for regenerating Populus euphratica forest was two to three times per year with a duration of 15-20 days and an intensity of 25-30 m(3)/s. The flooding should take place during the seed emergence to young tree growth stages, and should be based on flooding experiments and data from vegetation quadrats and ecological water conveyance. Furthermore, we found that tree-ring width index for P. euphratica declined as the groundwater depth increased, and ascertained that the minimum groundwater depths for young trees, near-mature trees, mature trees and over-mature trees were 4.0 m, 5.0-5.4 m, 6.9 m and 7.8 m, respectively. These were derived from a quantitative relationship model between groundwater depth and tree-ring width index. The range for ecological water conveyance volume was 311-320 million m(3) in the lower reaches of the Tarim River. This study not only provides a technical basis for sustainable ecological water conveyance in the Tarim River Basin, but also offers a theoretical guide and scientific information that could be used in similar areas to regenerate and protect Populus euphratica around the world. PMID:26481290

  10. Response of photosynthesis and cellular antioxidants to ozone in Populus leaves

    SciTech Connect

    Gupta, A.S.; Alscher, R.G. ); McCune, D. )

    1991-06-01

    Atmospheric ozone causes formation of various highly reactive intermediates (e.g. peroxyl and superoxide radicals, H{sub 2}O{sub 2}, etc.) in plant tissues. A plant's productivity in environments with ozone may be related to its ability to scavenge the free radicals formed. The effects of ozone on photosynthesis and some free radical scavengers were measured in the fifth emergent leaf of poplars. Clonal poplars (Populus deltoides {times} Populus cv caudina) were fumigated with 180 parts per billion ozone for 3 hours. Photosynthesis was measured before, during, and after fumigation. During the first 90 minutes of ozone exposure, photosynthetic rates were unaffected but gluthathione levels and superoxide dismutase activity increased. After 90 minutes of ozone exposure photosynthetic rates began to decline while glutathione and superoxide dismutase continued to increase. Total glutathione (reduced plus oxidized) increased in fumigated leaves throughout the exposure period. The ratio of GSH/GSSG also decreased from 12.8 to 1.2 in ozone exposed trees. Superoxide dismutase levels increased twofold in fumigated plants. After 4 hours of ozone exposure, the photosynthetic rate was approximately half that of controls while flutathione levels and superoxide dismutase activity remained above that of the controls. The elevated antioxidant levels were maintained 21 hours after ozone exposure while photosynthetic rates recovered to about 75% of that of controls. Electron transport and NADPH levels remained unaffected by the treatment. Hence, elevated antioxidant metabolism may protect the photosynthetic apparatus during exposure to ozone.

  11. Methylation of miRNA genes in the response to temperature stress in Populus simonii.

    PubMed

    Ci, Dong; Song, Yuepeng; Tian, Min; Zhang, Deqiang

    2015-01-01

    DNA methylation and miRNAs provide crucial regulation of the transcriptional and post-transcriptional responses to abiotic stress. In this study, we used methylation-sensitive amplification polymorphisms to identify 1066 sites that were differentially methylated in response to temperature stress in Populus simonii. Among these loci, BLAST searches of miRBase identified seven miRNA genes. Expression analysis by quantitative real-time PCR suggested that the methylation pattern of these miRNA genes probably influences their expression. Annotation of these miRNA genes in the sequenced genome of Populus trichocarpa found three target genes (Potri.007G090400, Potri.014G042200, and Potri.010G176000) for the miRNAs produced from five genes (Ptc-MIR396e and g, Ptc-MIR156i and j, and Ptc-MIR390c) respectively. The products of these target genes function in lipid metabolism to deplete lipid peroxide. We also constructed a network based on the interactions between DNA methylation and miRNAs, miRNAs and target genes, and the products of target genes and the metabolic factors that they affect, including H2O2, malondialdehyde, catalase (CAT), and superoxide dismutase. Our results suggested that DNA methylation probably regulates the expression of miRNA genes, thus affecting expression of their target genes, likely through the gene-silencing function of miRNAs, to maintain cell survival under abiotic stress conditions. PMID:26579167

  12. Artificial defoliation effect on Populus growth, biomass production, and total nonstructural carbohydrate concentration

    SciTech Connect

    Reichenbacker, R.R.; Hart, E.R.; Schultz, R.C.

    1996-06-01

    The impact of artificial defoliation on Populus growth, biomass production, and total nonstructural carbohydrate concentration was examined. Four Populus clones were field planted and artificially defoliated. Assigned defoliation levels (0, 25, 50, or 75%) were applied to leaves of leaf plastochron index 0 through 8 during a 6-d period in a 3-step incremental manner to simulate cottonwood leaf beetle, Chrysomela scripta F., larval feeding patterns. Artificial defoliations were timed to coincide with the outbreaks of natural beetle populations in adjacent areas. After 2 growing seasons, trees were measured for height, diameter, and biomass accumulation. Root samples were collected from 0 and 75% defoliation treatments for each clone. Biomass was reduced an average of 33% as defoliation level increased from 0 to 75%. As defoliation level increased from 0 to 75%, a consistent allocation ratio of biomass to 2/3 above and 1/3 below ground components continued in all clones. An overcompensation response occurred in above ground biomass when a defoliation level of 25% was applied. Between 25 and 75% a strong linear trend of decreasing biomass as defoliation increased was indicated. Vitality of the tree, as indicated by total nonstructural carbohydrate content, was affected only slightly by increasing defoliation. 26 refs., 1 fig., 6 tabs.

  13. How to Regenerate and Protect Desert Riparian Populus euphratica Forest in Arid Areas

    PubMed Central

    Ling, Hongbo; Zhang, Pei; Xu, Hailiang; Zhao, Xinfeng

    2015-01-01

    We found that the most suitable flooding disturbance model for regenerating Populus euphratica forest was two to three times per year with a duration of 15–20 days and an intensity of 25–30 m3/s. The flooding should take place during the seed emergence to young tree growth stages, and should be based on flooding experiments and data from vegetation quadrats and ecological water conveyance. Furthermore, we found that tree-ring width index for P. euphratica declined as the groundwater depth increased, and ascertained that the minimum groundwater depths for young trees, near-mature trees, mature trees and over-mature trees were 4.0 m, 5.0–5.4 m, 6.9 m and 7.8 m, respectively. These were derived from a quantitative relationship model between groundwater depth and tree-ring width index. The range for ecological water conveyance volume was 311–320 million m3 in the lower reaches of the Tarim River. This study not only provides a technical basis for sustainable ecological water conveyance in the Tarim River Basin, but also offers a theoretical guide and scientific information that could be used in similar areas to regenerate and protect Populus euphratica around the world. PMID:26481290

  14. How to Regenerate and Protect Desert Riparian Populus euphratica Forest in Arid Areas.

    PubMed

    Ling, Hongbo; Zhang, Pei; Xu, Hailiang; Zhao, Xinfeng

    2015-10-20

    We found that the most suitable flooding disturbance model for regenerating Populus euphratica forest was two to three times per year with a duration of 15-20 days and an intensity of 25-30 m(3)/s. The flooding should take place during the seed emergence to young tree growth stages, and should be based on flooding experiments and data from vegetation quadrats and ecological water conveyance. Furthermore, we found that tree-ring width index for P. euphratica declined as the groundwater depth increased, and ascertained that the minimum groundwater depths for young trees, near-mature trees, mature trees and over-mature trees were 4.0 m, 5.0-5.4 m, 6.9 m and 7.8 m, respectively. These were derived from a quantitative relationship model between groundwater depth and tree-ring width index. The range for ecological water conveyance volume was 311-320 million m(3) in the lower reaches of the Tarim River. This study not only provides a technical basis for sustainable ecological water conveyance in the Tarim River Basin, but also offers a theoretical guide and scientific information that could be used in similar areas to regenerate and protect Populus euphratica around the world.

  15. How to Regenerate and Protect Desert Riparian Populus euphratica Forest in Arid Areas

    NASA Astrophysics Data System (ADS)

    Ling, Hongbo; Zhang, Pei; Xu, Hailiang; Zhao, Xinfeng

    2015-10-01

    We found that the most suitable flooding disturbance model for regenerating Populus euphratica forest was two to three times per year with a duration of 15-20 days and an intensity of 25-30 m3/s. The flooding should take place during the seed emergence to young tree growth stages, and should be based on flooding experiments and data from vegetation quadrats and ecological water conveyance. Furthermore, we found that tree-ring width index for P. euphratica declined as the groundwater depth increased, and ascertained that the minimum groundwater depths for young trees, near-mature trees, mature trees and over-mature trees were 4.0 m, 5.0-5.4 m, 6.9 m and 7.8 m, respectively. These were derived from a quantitative relationship model between groundwater depth and tree-ring width index. The range for ecological water conveyance volume was 311-320 million m3 in the lower reaches of the Tarim River. This study not only provides a technical basis for sustainable ecological water conveyance in the Tarim River Basin, but also offers a theoretical guide and scientific information that could be used in similar areas to regenerate and protect Populus euphratica around the world.

  16. The transcriptome of Populus in elevated CO2 reveals increased anthocyanin biosynthesis during delayed autumnal senescence

    SciTech Connect

    Tallis, M.J.; Rogers, A.; Lin, Y.; Zhang, J.; Street, N. R.; Miglietta, F.; Karnosky, D. F.; Angelis, P. D.; Calfapietra, C.; Taylor, G.

    2010-03-01

    The delay in autumnal senescence that has occurred in recent decades has been linked to rising temperatures. Here, we suggest that increasing atmospheric CO{sub 2} may partly account for delayed autumnal senescence and for the first time, through transcriptome analysis, identify gene expression changes associated with this delay. Using a plantation of Populus x euramericana grown in elevated [CO{sub 2}] (e[CO{sub 2}]) with free-air CO{sub 2} enrichment (FACE) technology, we investigated the molecular and biochemical basis of this response. A Populus cDNA microarray was used to identify genes representing multiple biochemical pathways influenced by e[CO{sub 2}] during senescence. Gene expression changes were confirmed through real-time quantitative PCR, and leaf biochemical assays. Pathways for secondary metabolism and glycolysis were significantly up-regulated by e[CO{sub 2}] during senescence, in particular, those related to anthocyanin biosynthesis. Expressed sequence tags (ESTs) representing the two most significantly up-regulated transcripts in e[CO{sub 2}], LDOX (leucoanthocyanidin dioxgenase) and DFR (dihydroflavonol reductase), gave (e[CO{sub 2}]/ambient CO{sub 2} (a[CO{sub 2}])) expression ratios of 39.6 and 19.3, respectively. We showed that in e[CO{sub 2}] there was increased autumnal leaf sugar accumulation and up-regulation of genes determining anthocyanin biosynthesis which, we propose, prolongs leaf longevity during natural autumnal senescence.

  17. Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica

    PubMed Central

    Qin, Yurong; Duan, Hui; Yin, Weilun; Xia, Xinli

    2011-01-01

    MicroRNAs (miRNAs) are small, non-coding RNAs that play essential roles in plant growth, development, and stress response. Populus euphratica is a typical abiotic stress-resistant woody species. This study presents an efficient method for genome-wide discovery of new drought stress responsive miRNAs in P. euphratica. High-throughput sequencing of P. euphratica leaves found 197 conserved miRNAs between P. euphratica and Populus trichocarpa. Meanwhile, 58 new miRNAs belonging to 38 families were identified, an increase in the number of P. euphratica miRNAs. Twenty-six new and 21 conserved miRNA targets were verified by degradome sequencing, and target annotation showed that these targets were involved in multiple biological processes, including transcriptional regulation and response to stimulus. Furthermore, comparison of high-throughput sequencing with miRNA microarray profiling data indicated that 104 miRNA sequences were up-regulated, whereas 27 were down-regulated under drought stress. This preliminary characterization provides a framework for future analysis of miRNA genes and their roles in key poplar traits such as stress resistance, and could be useful for plant breeding and environmental protection PMID:21511902

  18. Reproductive Characteristics of a Populus euphratica Population and Prospects for Its Restoration in China

    PubMed Central

    Cao, Dechang; Li, Jingwen; Huang, Zhenying; Baskin, Carol C.; Baskin, Jerry M.; Hao, Peng; Zhou, Weilei; Li, Junqing

    2012-01-01

    Populus euphratica is a dominant tree in riparian ecosystems in arid areas of northwest China, but it fails to regenerate in these systems. This study evaluates causes for the failure of sexual and asexual regeneration of this species in the wild. P. euphratica disperses as many as 85743 seeds/m2 during summer, and the seeds germinate to 92.0% in distilled water and to 60.8% on silt. However, very few seeds (3.6%) can germinate on unflooded soil. The seed-rain season is prolonged by temporal variability in seed dispersal among individuals, which ensures that seedling emergence can occur during favorable conditions (i.e., floods and rainfall). As a result of water shortage and river channeling due to water usage and altered river flows, there are no safe sites on river banks for seed germination, which has led to the failure of P. euphratica to regenerate from seed. Root suckers of P. euphratica were present in 86% of the forest gaps investigated. However, extensive grazing has destroyed many of them and thus has reduced this form of regeneration. This research suggests that human activities are resulting in the failure of P. euphratica to regenerate. Changes in land management such as reduced use of concrete canals in Populus forests and/or reduced sheep grazing in these areas may promote their regeneration. PMID:22848351

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

    PubMed Central

    Brosché, Mikael; Vinocur, Basia; Alatalo, Edward R; Lamminmäki, Airi; Teichmann, Thomas; Ottow, Eric A; Djilianov, Dimitar; Afif, Dany; Bogeat-Triboulot, Marie-Béatrice; Altman, Arie; Polle, Andrea; Dreyer, Erwin; Rudd, Stephen; Paulin, Lars; Auvinen, Petri; Kangasjärvi, Jaakko

    2005-01-01

    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. PMID:16356264

  20. Methylation of miRNA genes in the response to temperature stress in Populus simonii

    PubMed Central

    Ci, Dong; Song, Yuepeng; Tian, Min; Zhang, Deqiang

    2015-01-01

    DNA methylation and miRNAs provide crucial regulation of the transcriptional and post-transcriptional responses to abiotic stress. In this study, we used methylation-sensitive amplification polymorphisms to identify 1066 sites that were differentially methylated in response to temperature stress in Populus simonii. Among these loci, BLAST searches of miRBase identified seven miRNA genes. Expression analysis by quantitative real-time PCR suggested that the methylation pattern of these miRNA genes probably influences their expression. Annotation of these miRNA genes in the sequenced genome of Populus trichocarpa found three target genes (Potri.007G090400, Potri.014G042200, and Potri.010G176000) for the miRNAs produced from five genes (Ptc-MIR396e and g, Ptc-MIR156i and j, and Ptc-MIR390c) respectively. The products of these target genes function in lipid metabolism to deplete lipid peroxide. We also constructed a network based on the interactions between DNA methylation and miRNAs, miRNAs and target genes, and the products of target genes and the metabolic factors that they affect, including H2O2, malondialdehyde, catalase (CAT), and superoxide dismutase. Our results suggested that DNA methylation probably regulates the expression of miRNA genes, thus affecting expression of their target genes, likely through the gene-silencing function of miRNAs, to maintain cell survival under abiotic stress conditions. PMID:26579167

  1. Different autosomes evolved into sex chromosomes in the sister genera of Salix and Populus.

    PubMed

    Hou, Jing; Ye, Ning; Zhang, Defang; Chen, Yingnan; Fang, Lecheng; Dai, Xiaogang; Yin, Tongming

    2015-03-13

    Willows (Salix) and poplars (Populus) are dioecious plants in Salicaceae family. Sex chromosome in poplar genome was consistently reported to be associated with chromosome XIX. In contrast to poplar, this study revealed that chromosome XV was sex chromosome in willow. Previous studies revealed that both ZZ/ZW and XX/XY sex-determining systems could be present in some species of Populus. In this study, sex of S. suchowensis was found to be determined by the ZW system in which the female was the heterogametic gender. Gene syntenic and collinear comparisons revealed macrosynteny between sex chromosomes and the corresponding autosomes between these two lineages. By contrast, no syntenic segments were found to be shared between poplar's and willow's sex chromosomes. Syntenic analysis also revealed substantial chromosome rearrangements between willow's alternate sex chromatids. Since willow and poplar originate from a common ancestor, we proposed that evolution of autosomes into sex chromosomes in these two lineages occurred after their divergence. Results of this study indicate that sex chromosomes in Salicaceae are still at the early stage of evolutionary divergence. Additionally, this study provided valuable information for better understanding the genetics and evolution of sex chromosome in dioecious plants.

  2. Reproductive characteristics of a Populus euphratica population and prospects for its restoration in China.

    PubMed

    Cao, Dechang; Li, Jingwen; Huang, Zhenying; Baskin, Carol C; Baskin, Jerry M; Hao, Peng; Zhou, Weilei; Li, Junqing

    2012-01-01

    Populus euphratica is a dominant tree in riparian ecosystems in arid areas of northwest China, but it fails to regenerate in these systems. This study evaluates causes for the failure of sexual and asexual regeneration of this species in the wild. P. euphratica disperses as many as 85743 seeds/m(2) during summer, and the seeds germinate to 92.0% in distilled water and to 60.8% on silt. However, very few seeds (3.6%) can germinate on unflooded soil. The seed-rain season is prolonged by temporal variability in seed dispersal among individuals, which ensures that seedling emergence can occur during favorable conditions (i.e., floods and rainfall). As a result of water shortage and river channeling due to water usage and altered river flows, there are no safe sites on river banks for seed germination, which has led to the failure of P. euphratica to regenerate from seed. Root suckers of P. euphratica were present in 86% of the forest gaps investigated. However, extensive grazing has destroyed many of them and thus has reduced this form of regeneration. This research suggests that human activities are resulting in the failure of P. euphratica to regenerate. Changes in land management such as reduced use of concrete canals in Populus forests and/or reduced sheep grazing in these areas may promote their regeneration.

  3. Differential detection of genetic loci underlying stem and root lignin content in Populus

    SciTech Connect

    Tuskan, Gerald A; Yin, Tongming; Zhang, Xinye; Gunter, Lee E; Ranjan, Priya; Sykes, Robert; Davis, Dr. Mark F.; Wullschleger, Stan D

    2010-11-01

    For simultaneous applications directed towards improved pulp yields, enhanced bioethanol production and increased carbon sequestration, it would be desirable to reduce lignin in the harvested stem while increasing the lignin content in nonharvested roots. In this study, we established a comprehensive genetic map with a large number of progeny from a three-generation hybrid Populus intercross, and phenotyped the lignin content, S/G ratio and 28 cell wall subcomponents both in stems and roots for the mapping individuals. Phenotypic analysis revealed that lignin content and syringyl-to-guaiacyl (S/G) ratio using pyrolysis molecular beam mass spectroscopy (pyMBMS) varied among mapping individuals. Phenotypic analysis revealed that stem lignin content is significantly higher than that in root and the quantified traits can be classified into four distinct groups, with strong correlations observed among components within organs. Altogether, 179 coordinating QTLs were detected, and they were co-localized into 49 genetic loci, 27 of which appear to be pleiotropic. Many of the detected genetic loci were detected differentially in stem and root. This is the first report of separate genetic loci controlling cell wall phenotypes above and below ground. These results suggest that it may be possible to modify lignin content and composition via breed and/or engineer as a means of simultaneously improving Populus for cellulosic ethanol production and carbon sequestration.

  4. Differential Detection of Genetic Loci Underlying Stem and Root Lignin Content in Populus

    SciTech Connect

    Yin, Tongming; Zhang, Xinye; Gunter, Lee E; Ranjan, Priya; Sykes, Robert; Davis, Dr. Mark F.; Wullschleger, Stan D; Tuskan, Gerald A

    2010-01-01

    In this study, we established a comprehensive genetic map with a large number of progeny from a three-generation hybrid Populus intercross, and phenotyped the lignin content, S/G ratio and 28 cell wall subcomponents both in stems and roots for the mapping individuals. Phenotypic analysis revealed that lignin content and syringyl-to-guaiacyl (S/G) ratio using pyrolysis molecular beam mass spectroscopy (pyMBMS) varied among mapping individuals. Phenotypic analysis revealed that stem lignin content is significantly higher than that in root and the quantified traits can be classified into four distinct groups, with strong correlations observed among components within organs. Altogether, 179 coordinating QTLs were detected, and they were co-localized into 49 genetic loci, 27 of which appear to be pleiotropic. Many of the detected genetic loci were detected differentially in stem and root. This is the first report of separate genetic loci controlling cell wall phenotypes above and below ground. These results suggest that it may be possible to modify lignin content and composition via breed and/or engineer as a means of simultaneously improving Populus for cellulosic ethanol production and carbon sequestration.

  5. Hot water and dilute acid pretreatment of high and low specific gravity Populus deltoides clones.

    PubMed

    Martin, Elizabeth M; Bunnell, Kris A; Lau, Ching-Shuan; Pelkki, Matthew H; Patterson, David W; Clausen, Edgar C; Smith, James A; Carrier, Danielle Julie

    2011-02-01

    Populus sp. are hardwood feedstocks that grow in forest management areas that are logged for softwoods; however, they are also being considered as an energy-destined feedstock. The objective of this work was to determine the effect of xylose yield from dilute acid and hot water pretreatments performed in unstirred batch stainless steel reactors at temperatures ranging from 140 to 200°C. Populus deltoides clones S13C20 and S7C15 used in this study originated from Eastern Texas and were cultivated for 14 years in Pine Tree, AR. P. deltoides clones S13C20 and S7C15 had specific gravities of 0.48 and 0.40, respectively. Bark and wood were examined separately. As expected, hot water pretreatments, in the tested temperature range, resulted in very little direct xylose recovery. However, the 140°C dilute acid pretreatment of the lower specific gravity clone, S7C15, wood yielded the highest average xylose recovery of 56%. This condition also yielded the highest concentration of furfural, 9 mg/g sample, which can be inhibitory to the fermentation step. The highest xylose recovery from bark samples, 31%, was obtained with clone S7C15, using the 160°C dilute acid pretreatment for 60 min.

  6. Different autosomes evolved into sex chromosomes in the sister genera of Salix and Populus

    PubMed Central

    Hou, Jing; Ye, Ning; Zhang, Defang; Chen, Yingnan; Fang, Lecheng; Dai, Xiaogang; Yin, Tongming

    2015-01-01

    Willows (Salix) and poplars (Populus) are dioecious plants in Salicaceae family. Sex chromosome in poplar genome was consistently reported to be associated with chromosome XIX. In contrast to poplar, this study revealed that chromosome XV was sex chromosome in willow. Previous studies revealed that both ZZ/ZW and XX/XY sex-determining systems could be present in some species of Populus. In this study, sex of S. suchowensis was found to be determined by the ZW system in which the female was the heterogametic gender. Gene syntenic and collinear comparisons revealed macrosynteny between sex chromosomes and the corresponding autosomes between these two lineages. By contrast, no syntenic segments were found to be shared between poplar's and willow's sex chromosomes. Syntenic analysis also revealed substantial chromosome rearrangements between willow's alternate sex chromatids. Since willow and poplar originate from a common ancestor, we proposed that evolution of autosomes into sex chromosomes in these two lineages occurred after their divergence. Results of this study indicate that sex chromosomes in Salicaceae are still at the early stage of evolutionary divergence. Additionally, this study provided valuable information for better understanding the genetics and evolution of sex chromosome in dioecious plants. PMID:25766834

  7. Simulation of Populus euphratica root uptake of groundwater in an arid woodland of the Ejina basin, China

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Ejina Basin is an extremely arid subwatershed in Northwest China. The predominant natural tree species in the area, Populus euphratica (P. euphratica), depends on groundwater for sustenance. In recent decades, groundwater overdraft and increased water diversions from the Heihe River caused wat...

  8. Comparative physiology of allopatric Populus species: geographic clines in photosynthesis, height growth, and carbon isotope discrimination in common gardens.

    PubMed

    Soolanayakanahally, Raju Y; Guy, Robert D; Street, Nathaniel R; Robinson, Kathryn M; Silim, Salim N; Albrectsen, Benedicte R; Jansson, Stefan

    2015-01-01

    Populus species with wide geographic ranges display strong adaptation to local environments. We studied the clinal patterns in phenology and ecophysiology in allopatric Populus species adapted to similar environments on different continents under common garden settings. As a result of climatic adaptation, both Populus tremula L. and Populus balsamifera L. display latitudinal clines in photosynthetic rates (A), whereby high-latitude trees of P. tremula had higher A compared to low-latitude trees and nearly so in P. balsamifera (p = 0.06). Stomatal conductance (g s) and chlorophyll content index (CCI) follow similar latitudinal trends. However, foliar nitrogen was positively correlated with latitude in P. balsamifera and negatively correlated in P. tremula. No significant trends in carbon isotope composition of the leaf tissue (δ(13)C) were observed for both species; but, intrinsic water-use efficiency (WUEi) was negatively correlated with the latitude of origin in P. balsamifera. In spite of intrinsically higher A, high-latitude trees in both common gardens accomplished less height gain as a result of early bud set. Thus, shoot biomass was determined by height elongation duration (HED), which was well approximated by the number of days available for free growth between bud flush and bud set. We highlight the shortcoming of unreplicated outdoor common gardens for tree improvement and the crucial role of photoperiod in limiting height growth, further complicating interpretation of other secondary effects.

  9. Drought-Induced Xylem Dysfunction in Petioles, Branches, and Roots of Populus balsamifera L. and Alnus glutinosa (L.) Gaertn.

    PubMed

    Hacke, U.; Sauter, J. J.

    1996-06-01

    Variation in vulnerability to xylem cavitation was measured within individual organs of Populus balsamifera L. and Alnus glutinosa (L.) Gaertn. Cavitation was quantified by three different techniques: (a) measuring acoustic emissions, (b) measuring loss of hydraulic conductance while air-dehydrating a branch, and (c) measuring loss of hydraulic conductance as a function of positive air pressure injected into the xylem. All of these techniques gave similar results. In Populus, petioles were more resistant than branches, and branches were more resistant than roots. This corresponded to the pattern of vessel width: maximum vessel diameter in 1- to 2-year-old roots was 140 [mu]m, compared to 65 and 45 [mu]m in rapidly growing 1-year-old shoots and petioles, respectively. Cavitation in Populus petioles started at a threshold water potential of -1.1 MPa. The lowest leaf water potential observed was -0.9 MPa. In Alnus, there was no relationship between vessel diameter and the cavitation response of a plant organ. Although conduits were narrower in petioles than in branches, petioles were more vulnerable to cavitation. Cavitation in petioles was detected when water potential fell below -1.2 MPa. This value equaled midday leaf water potential in late June. As in Populus, roots were the most vulnerable organ. The significance of different cavitation thresholds in individual plant organs is discussed.

  10. Identification of candidate genes in Populus cell wall biosynthesis using text-mining, co-expression network and comparative genomics

    SciTech Connect

    Yang, Xiaohan; Ye, Chuyu; Bisaria, Anjali; Tuskan, Gerald A; Kalluri, Udaya C

    2011-01-01

    Populus is an important bioenergy crop for bioethanol production. A greater understanding of cell wall biosynthesis processes is critical in reducing biomass recalcitrance, a major hindrance in efficient generation of ethanol from lignocellulosic biomass. Here, we report the identification of candidate cell wall biosynthesis genes through the development and application of a novel bioinformatics pipeline. As a first step, via text-mining of PubMed publications, we obtained 121 Arabidopsis genes that had the experimental evidences supporting their involvement in cell wall biosynthesis or remodeling. The 121 genes were then used as bait genes to query an Arabidopsis co-expression database and additional genes were identified as neighbors of the bait genes in the network, increasing the number of genes to 548. The 548 Arabidopsis genes were then used to re-query the Arabidopsis co-expression database and re-construct a network that captured additional network neighbors, expanding to a total of 694 genes. The 694 Arabidopsis genes were computationally divided into 22 clusters. Queries of the Populus genome using the Arabidopsis genes revealed 817 Populus orthologs. Functional analysis of gene ontology and tissue-specific gene expression indicated that these Arabidopsis and Populus genes are high likelihood candidates for functional genomics in relation to cell wall biosynthesis.

  11. Comparative physiology of allopatric Populus species: geographic clines in photosynthesis, height growth, and carbon isotope discrimination in common gardens

    PubMed Central

    Soolanayakanahally, Raju Y.; Guy, Robert D.; Street, Nathaniel R.; Robinson, Kathryn M.; Silim, Salim N.; Albrectsen, Benedicte R.; Jansson, Stefan

    2015-01-01

    Populus species with wide geographic ranges display strong adaptation to local environments. We studied the clinal patterns in phenology and ecophysiology in allopatric Populus species adapted to similar environments on different continents under common garden settings. As a result of climatic adaptation, both Populus tremula L. and Populus balsamifera L. display latitudinal clines in photosynthetic rates (A), whereby high-latitude trees of P. tremula had higher A compared to low-latitude trees and nearly so in P. balsamifera (p = 0.06). Stomatal conductance (gs) and chlorophyll content index (CCI) follow similar latitudinal trends. However, foliar nitrogen was positively correlated with latitude in P. balsamifera and negatively correlated in P. tremula. No significant trends in carbon isotope composition of the leaf tissue (δ13C) were observed for both species; but, intrinsic water-use efficiency (WUEi) was negatively correlated with the latitude of origin in P. balsamifera. In spite of intrinsically higher A, high-latitude trees in both common gardens accomplished less height gain as a result of early bud set. Thus, shoot biomass was determined by height elongation duration (HED), which was well approximated by the number of days available for free growth between bud flush and bud set. We highlight the shortcoming of unreplicated outdoor common gardens for tree improvement and the crucial role of photoperiod in limiting height growth, further complicating interpretation of other secondary effects. PMID:26236324

  12. Constitutively Elevated Salicylic Acid Levels Alter Photosynthesis and Oxidative State but Not Growth in Transgenic Populus[C][W

    PubMed Central

    Xue, Liang-Jiao; Guo, Wenbing; Yuan, Yinan; Anino, Edward O.; Nyamdari, Batbayar; Wilson, Mark C.; Frost, Christopher J.; Chen, Han-Yi; Babst, Benjamin A.; Harding, Scott A.; Tsai, Chung-Jui

    2013-01-01

    Salicylic acid (SA) has long been implicated in plant responses to oxidative stress. SA overproduction in Arabidopsis thaliana leads to dwarfism, making in planta assessment of SA effects difficult in this model system. We report that transgenic Populus tremula × alba expressing a bacterial SA synthase hyperaccumulated SA and SA conjugates without negative growth consequences. In the absence of stress, endogenously elevated SA elicited widespread metabolic and transcriptional changes that resembled those of wild-type plants exposed to oxidative stress-promoting heat treatments. Potential signaling and oxidative stress markers azelaic and gluconic acids as well as antioxidant chlorogenic acids were strongly coregulated with SA, while soluble sugars and other phenylpropanoids were inversely correlated. Photosynthetic responses to heat were attenuated in SA-overproducing plants. Network analysis identified potential drivers of SA-mediated transcriptome rewiring, including receptor-like kinases and WRKY transcription factors. Orthologs of Arabidopsis SA signaling components NON-EXPRESSOR OF PATHOGENESIS-RELATED GENES1 and thioredoxins were not represented. However, all members of the expanded Populus nucleoredoxin-1 family exhibited increased expression and increased network connectivity in SA-overproducing Populus, suggesting a previously undescribed role in SA-mediated redox regulation. The SA response in Populus involved a reprogramming of carbon uptake and partitioning during stress that is compatible with constitutive chemical defense and sustained growth, contrasting with the SA response in Arabidopsis, which is transient and compromises growth if sustained. PMID:23903318

  13. Phylogeny of Populus (Salicaceae) based on nucleotide sequences of chloroplast TRNT-TRNF region and nuclear rDNA.

    PubMed

    Hamzeh, Mona; Dayanandan, Selvadurai

    2004-09-01

    The species of the genus Populus, collectively known as poplars, are widely distributed over the northern hemisphere and well known for their ecological, economical, and evolutionary importance. The extensive interspecific hybridization and high morphological diversity in this group pose difficulties in identifying taxonomic units for comparative evolutionary studies and systematics. To understand the evolutionary relationships among poplars and to provide a framework for biosystematic classification, we reconstructed a phylogeny of the genus Populus based on nucleotide sequences of three noncoding regions of the chloroplast DNA (intron of trnL and intergenic regions of trnT-trnL and trnL-trnF) and ITS1 and ITS2 of the nuclear rDNA. The resulting phylogenetic trees showed polyphyletic relationships among species in the sections Tacamahaca and Aigeiros. Based on chloroplast DNA sequence data, P. nigra had a close affinity to species of section Populus, whereas nuclear DNA sequence data suggested a close relationship between P. nigra and species of the section Aigeiros, suggesting a possible hybrid origin for P. nigra. Similarly, the chloroplast DNA sequences of P. tristis and P. szechuanica were similar to that of the species of section Aigeiros, while the nuclear sequences revealed a close affinity to species of the section Tacamahaca, suggesting a hybrid origin for these two Asiatic balsam poplars. The incongruence between phylogenetic trees based on nuclear- and chloroplast-DNA sequence data suggests a reticulate evolution in the genus Populus.

  14. Ozone fluxes and foliar injury development in the ozone-sensitive poplar clone Oxford (Populus maximowiczii x Populus berolinensis): a dose-response analysis.

    PubMed

    Marzuoli, Riccardo; Gerosa, Giacomo; Desotgiu, Rosanna; Bussotti, Filippo; Ballarin-Denti, Antonio

    2009-01-01

    Between 2004 and 2005 a combined open plot and open-top chamber (OTC) experiment was carried out at Curno (Northern Italy) with cuttings of the poplar clone Oxford (Populus maximowiczii Henry x Populus berolinensis Dippel) grown in open plots (OPs, ambient air), charcoal-filtered OTCs (CF, ozone concentration reduced to 50% of ambient) or non-filtered OTCs (NF, ozone concentration reduced to 95% of ambient). Plants in half of the chambers were kept well-watered (WET), and plants in the remaining chambers were not watered (DRY). The onset and development of visible foliar injury and the stomatal conductance to water vapor (g(w)) were assessed during each growing season. A stomatal conductance model was parameterized by the Jarvis approach, allowing the calculation of ozone stomatal fluxes of plants in each treatment. The pattern of visible symptoms was analyzed in relation to ozone exposure (AOT40, accumulated ozone over a threshold of 40 ppb) and accumulated ozone stomatal fluxes (AF(ST)). Symptoms became visible at an AOT40 between 9584 and 13,110 ppb h and an AF(ST) between 27.85 and 30.40 mmol O(3) m(-2). The development of symptoms was more widespread and faster in plants in WET plots than in DRY plots. A slightly higher dose of ozone was required to cause visible symptoms in plants in DRY plots than in WET plots. By the end of each growing season, plants in the CF OTCs had absorbed a high dose of ozone (31.60 mmol O(3) m(-2) in 2004 and 32.83 mmol O(3) m(-2) in 2005, for WET plots), without developing any visible symptoms. A reliable dose-response relationship was defined by a sigmoidal curve model. The shape of this curve expresses the change in leaf sensitivity and physiologic state over a prolonged ozone exposure. After the appearance of the first symptoms, foliar injury increased more rapidly than the increases in ozone exposure and ozone absorbed dose; however, when the injury incidence reached 75%, the plant response declined.

  15. Propagation of photoinduced signals with the cytoplasmic flow along Characean internodes: evidence from changes in chloroplast fluorescence and surface pH.

    PubMed

    Bulychev, Alexander A; Alova, Anna V; Rubin, Andrey B

    2013-06-01

    Emerging evidence suggests that cytoplasmic streaming can regulate the plasma-membrane H(+) transport and photosynthetic electron flow. Microfluorometric and surface pH measurements on Chara corallina internodes revealed the transmission of photoinduced signals by the cytoplasmic flow for a distance of few millimeters from the site of stimulus application. When a 30-s pulse of bright light was locally applied, the downstream cell regions responded with either release or enhancement of non-photochemical quenching of chlorophyll fluorescence, depending on the background irradiance of the analyzed cell area. Under dim background irradiance (<20 μmol m(-2) s(-1)), the arrival of the distant signal from the brightly illuminated 400-μm-wide zone elevated the maximal fluorescence F m (') in the analyzed downstream area, whereas at higher background irradiances it induced strong quenching of F m (') . At intermediate irradiances the increase and decrease in F m (') appeared as two successive waves. The transition between the F m (') responses of opposite polarities occurred at a narrow threshold range of irradiances. This indicates that inevitable slight variations in irradiance at the bottom chloroplast layer combined with the cyclosis-transmitted signals may contribute to the formation of a photosynthetic activity pattern. The rapid cyclosis-mediated release of non-photochemical quenching, unlike the delayed response of opposite polarity, was associated with opening of H(+) (OH(-))-conducting plasma membrane channels, as evidenced by the concurrent alkaline pH shift on the cell surface. It is proposed that the initial increase in F m (') after application of a distant photostimulus is determined, among other factors, by the wave of alkaline cytoplasmic pH.

  16. Wide-ranging effects of eight cytochalasins and latrunculin A and B on intracellular motility and actin filament reorganization in characean internodal cells.

    PubMed

    Foissner, Ilse; Wasteneys, Geoffrey O

    2007-04-01

    Numerous forms of cytochalasins have been identified and, although they share common biological activity, they may differ considerably in potency. We investigated the effects of cytochalasins A, B, C, D, E, H and J and dihydrocytochalasin B in an ideal experimental system for cell motility, the giant internodal cells of the characean alga Nitella pseudoflabellata. Cytochalasins D (60 microM) and H (30 microM) were found to be most suited for fast and reversible inhibition of actin-based motility, while cytochalasins A and E arrested streaming at lower concentrations but irreversibly. We observed no clear correlation between the ability of cytochalasins to inhibit motility and the actual disruption of the subcortical actin bundle tracks on which myosin-dependent motility occurs. Indeed, the actin bundles remained intact at the time of streaming cessation and disassembled only after one to several days' treatment. Even when applied at concentrations lower than that required to inhibit cytoplasmic streaming, all of the cytochalasins induced reorganization of the more labile cortical actin filaments into actin patches, swirling clusters or short rods. Latrunculins A and B arrested streaming only after disrupting the subcortical actin bundles, a process requiring relatively high concentrations (200 microM) and very long treatment periods of >1 d. Latrunculins, however, worked synergistically with cytochalasins. A 1 h treatment with 15 nM latrunculin A and 4 microM cytochalasin D induced reversible fragmentation of subcortical actin bundles and arrested cytoplasmic streaming. Our findings provide insights into the mechanisms by which cytochalasins and latrunculins interfere with characean actin to inhibit motility.

  17. Propagation of photoinduced signals with the cytoplasmic flow along Characean internodes: evidence from changes in chloroplast fluorescence and surface pH.

    PubMed

    Bulychev, Alexander A; Alova, Anna V; Rubin, Andrey B

    2013-06-01

    Emerging evidence suggests that cytoplasmic streaming can regulate the plasma-membrane H(+) transport and photosynthetic electron flow. Microfluorometric and surface pH measurements on Chara corallina internodes revealed the transmission of photoinduced signals by the cytoplasmic flow for a distance of few millimeters from the site of stimulus application. When a 30-s pulse of bright light was locally applied, the downstream cell regions responded with either release or enhancement of non-photochemical quenching of chlorophyll fluorescence, depending on the background irradiance of the analyzed cell area. Under dim background irradiance (<20 μmol m(-2) s(-1)), the arrival of the distant signal from the brightly illuminated 400-μm-wide zone elevated the maximal fluorescence F m (') in the analyzed downstream area, whereas at higher background irradiances it induced strong quenching of F m (') . At intermediate irradiances the increase and decrease in F m (') appeared as two successive waves. The transition between the F m (') responses of opposite polarities occurred at a narrow threshold range of irradiances. This indicates that inevitable slight variations in irradiance at the bottom chloroplast layer combined with the cyclosis-transmitted signals may contribute to the formation of a photosynthetic activity pattern. The rapid cyclosis-mediated release of non-photochemical quenching, unlike the delayed response of opposite polarity, was associated with opening of H(+) (OH(-))-conducting plasma membrane channels, as evidenced by the concurrent alkaline pH shift on the cell surface. It is proposed that the initial increase in F m (') after application of a distant photostimulus is determined, among other factors, by the wave of alkaline cytoplasmic pH. PMID:23467782

  18. The CBF1-dependent low temperature signalling pathway, regulon and increase in freeze tolerance are conserved in Populus spp.

    PubMed

    Benedict, Catherine; Skinner, Jeffrey S; Meng, Rengong; Chang, Yongjian; Bhalerao, Rishikesh; Huner, Norman P A; Finn, Chad E; Chen, Tony H H; Hurry, Vaughan

    2006-07-01

    The meristematic tissues of temperate woody perennials must acclimate to freezing temperatures to survive the winter and resume growth the following year. To determine whether the C-repeat binding factor (CBF) family of transcription factors contributing to this process in annual herbaceous species also functions in woody perennials, we investigated the changes in phenotype and transcript profile of transgenic Populus constitutively expressing CBF1 from Arabidopsis (AtCBF1). Ectopic expression of AtCBF1 was sufficient to significantly increase the freezing tolerance of non-acclimated leaves and stems relative to wild-type plants. cDNA microarray experiments identified genes up-regulated by ectopic AtCBF1 expression in Populus, demonstrated a strong conservation of the CBF regulon between Populus and Arabidopsis and identified differences between leaf and stem regulons. We studied the induction kinetics and tissue specificity of four CBF paralogues identified from the Populus balsamifera subsp. trichocarpa genome sequence (PtCBFs). All four PtCBFs are cold-inducible in leaves, but only PtCBF1 and PtCBF3 show significant induction in stems. Our results suggest that the central role played by the CBF family of transcriptional activators in cold acclimation of Arabidopsis has been maintained in Populus. However, the differential expression of the PtCBFs and differing clusters of CBF-responsive genes in annual (leaf) and perennial (stem) tissues suggest that the perennial-driven evolution of winter dormancy may have given rise to specific roles for these 'master-switches' in the different annual and perennial tissues of woody species.

  19. The SHORT-ROOT-like gene PtSHR2B is involved in Populus phellogen activity.

    PubMed

    Miguel, Andreia; Milhinhos, Ana; Novák, Ondřej; Jones, Brian; Miguel, Célia M

    2016-03-01

    SHORT-ROOT (SHR) is a GRAS transcription factor first characterized for its role in the specification of the stem cell niche and radial patterning in Arabidopsis thaliana (At) roots. Three SHR-like genes have been identified in Populus trichocarpa (Pt). PtSHR1 shares high similarity with AtSHR over the entire length of the coding sequence. The two other Populus SHR-like genes, PtSHR2A and PtSHR2B, are shorter in their 5' ends when compared with AtSHR. Unlike PtSHR1, that is expressed throughout the cambial zone of greenhouse-grown Populus trees, PtSHR2Bprom:uidA expression was detected in the phellogen. Additionally, PtSHR1 and PtSHR2B expression patterns markedly differ in the shoot apex and roots of in vitro plants. Transgenic hybrid aspen expressing PtSHR2B under the 35S constitutive promoter showed overall reduced tree growth while the proportion of bark increased relative to the wood. Reverse transcription-quantitative PCR (RT-qPCR) revealed increased transcript levels of cytokinin metabolism and response-related genes in the transgenic plants consistent with an increase of total cytokinin levels. This was confirmed by cytokinin quantification by LC-MS/MS. Our results indicate that PtSHR2B appears to function in the phellogen and therefore in the regulation of phellem and periderm formation, possibly acting through modulation of cytokinin homeostasis. Furthermore, this work points to a functional diversification of SHR after the divergence of the Populus and Arabidopsis lineages. This finding may contribute to selection and breeding strategies of cork oak in which, unlike Populus, the phellogen is active throughout the entire tree lifespan, being at the basis of a highly profitable cork industry.

  20. Xylem anatomy correlates with gas exchange, water-use efficiency and growth performance under contrasting water regimes: evidence from Populus deltoides x Populus nigra hybrids.

    PubMed

    Fichot, Régis; Laurans, Françoise; Monclus, Romain; Moreau, Alain; Pilate, Gilles; Brignolas, Franck

    2009-12-01

    Six Populus deltoides Bartr. ex Marsh. x P. nigra L. genotypes were selected to investigate whether stem xylem anatomy correlated with gas exchange rates, water-use efficiency (WUE) and growth performance. Clonal copies of the genotypes were grown in a two-plot common garden test under contrasting water regimes, with one plot maintained irrigated and the other one subjected to moderate summer water deficit. The six genotypes displayed a large range of xylem anatomy, mean vessel and fibre diameter varying from about 40 to 60 microm and from 7.5 to 10.5 microm, respectively. Decreased water availability resulted in a reduced cell size and an important rise in vessel density, but the extent of xylem plasticity was both genotype and trait dependent. Vessel diameter and theoretical xylem-specific hydraulic conductivity correlated positively with stomatal conductance, carbon isotope discrimination and growth performance-related traits and negatively with intrinsic WUE, especially under water deficit conditions. Vessel diameter and vessel density measured under water deficit conditions correlated with the relative losses in biomass production in response to water deprivation; this resulted from the fact that a more plastic xylem structure was generally accompanied by a larger loss in biomass production. PMID:19825869

  1. On the irrigation requirements of cottonwood (Populus fremontii and Populus deltoides var. wislizenii) and willow (Salix gooddingii) grown in a desert environment

    USGS Publications Warehouse

    Hartwell, S.; Morino, K.; Nagler, P.L.; Glenn, E.P.

    2010-01-01

    Native tree plots have been established in river irrigation districts in the western U.S. to provide habitat for threatened and endangered birds. Information is needed on the effective irrigation requirements of the target species. Cottonwood (Populus spp.) and willow (Salix gooddingii) trees were grown for seven years in an outdoor plot in a desert environment in Tucson, Arizona. Plants were allowed to achieve a nearly complete canopy cover over the first four years, then were subjected to three daily summer irrigation schedules of 6.20??mm??d-1; 8.26??mm??d-1 and 15.7??mm??d-1. The lowest irrigation rate was sufficient to maintain growth and high leaf area index for cottonwoods over three years, while willows suffered considerable die-back on this rate in years six and seven. These irrigation rates were applied April 15-September 15, but only 0.88??mm??d-1 was applied during the dormant period of the year. Expressed as a fraction of reference crop evapotranspiration (ETo), recommended annual water applications plus precipitation (and including some deep drainage) were 0.83 ETo for cottonwood and 1.01 ETo for willow. Current practices tend to over-irrigate restoration plots, and this study can provide guidelines for more efficient water use. ?? 2010 Elsevier Ltd.

  2. Investigating the Relationship Between Liquid Water and Leaf Area in Clonal Populus

    NASA Technical Reports Server (NTRS)

    Roberts, Dar; Brown, K.; Green, R.; Ustin, S.; Hinckley, T.

    1998-01-01

    to increase following a gradient of increasing LAI ranging from grasslands to coniferous forests. In that study, it was observed that forests, which showed little variation in NDVI, showed significant variation in liquid water. In order to test this hypothesis, we analyzed field spectra measured over Populus resprouts of known LAI and monitored changes in liquid water in young Populus stands as they aged over a 4-year time span. The study was conducted in south-central Washington, in a clonal Populus fiber farm owned and operated by Boise-Cascade near the town of Wallula.

  3. Genome-Scale Discovery of Cell Wall Biosynthesis Genes in Populus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Muchero, Wellington

    2012-03-22

    Wellington Muchero from Oak Ridge National Laboratory gives a talk titled "Discovery of Cell Wall Biosynthesis Genes in Populus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  4. Genome-Scale Discovery of Cell Wall Biosynthesis Genes in Populus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Muchero, Wellington [Oak Ridge National Laboratory

    2016-07-12

    Wellington Muchero from Oak Ridge National Laboratory gives a talk titled "Discovery of Cell Wall Biosynthesis Genes in Populus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  5. Antibacterial Balsacones J-M, Hydroxycinnamoylated Dihydrochalcones from Populus balsamifera Buds.

    PubMed

    Simard, François; Gauthier, Charles; Chiasson, Éric; Lavoie, Serge; Mshvildadze, Vakhtang; Legault, Jean; Pichette, André

    2015-05-22

    A phytochemical investigation of buds from the hardwood tree Populus balsamifera led to the isolation of six new cinnamoylated dihydrochalcones as pairs of racemates and one as a racemic mixture along with the known compound iryantherin-D (2), the absolute configuration of which was determined for the first time. The structures of balsacones J (1), K (3), L (4), and M (5) were elucidated on the basis of spectroscopic data (1D and 2D NMR, IR, and MS). Chiral HPLC separations were carried out, and the absolute configuration of the isolated enantiomers unambiguously established via X-ray diffraction analyses and electron circular dichroism spectroscopic data. Each of the purified enantiomers exhibited potent in vitro antibacterial activity against Staphylococcus aureus with IC50 values ranging from 0.61 to 6 μM.

  6. Genotypic variation in a foundation tree (Populus tremula L.) explains community structure of associated epiphytes

    PubMed Central

    Davies, Chantel; Ellis, Christopher J.; Iason, Glenn R.; Ennos, Richard A.

    2014-01-01

    Community genetics hypothesizes that within a foundation species, the genotype of an individual significantly influences the assemblage of dependent organisms. To assess whether these intra-specific genetic effects are ecologically important, it is required to compare their impact on dependent organisms with that attributable to environmental variation experienced over relevant spatial scales. We assessed bark epiphytes on 27 aspen (Populus tremula L.) genotypes grown in a randomized experimental array at two contrasting sites spanning the environmental conditions from which the aspen genotypes were collected. We found that variation in aspen genotype significantly influenced bark epiphyte community composition, and to the same degree as environmental variation between the test sites. We conclude that maintaining genotypic diversity of foundation species may be crucial for conservation of associated biodiversity. PMID:24789141

  7. Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations.

    PubMed

    Evans, Luke M; Slavov, Gancho T; Rodgers-Melnick, Eli; Martin, Joel; Ranjan, Priya; Muchero, Wellington; Brunner, Amy M; Schackwitz, Wendy; Gunter, Lee; Chen, Jin-Gui; Tuskan, Gerald A; DiFazio, Stephen P

    2014-10-01

    Forest trees are dominant components of terrestrial ecosystems that have global ecological and economic importance. Despite distributions that span wide environmental gradients, many tree populations are locally adapted, and mechanisms underlying this adaptation are poorly understood. Here we use a combination of whole-genome selection scans and association analyses of 544 Populus trichocarpa trees to reveal genomic bases of adaptive variation across a wide latitudinal range. Three hundred ninety-seven genomic regions showed evidence of recent positive and/or divergent selection and enrichment for associations with adaptive traits that also displayed patterns consistent with natural selection. These regions also provide unexpected insights into the evolutionary dynamics of duplicated genes and their roles in adaptive trait variation. PMID:25151358

  8. Combination of biological pretreatment with liquid hot water pretreatment to enhance enzymatic hydrolysis of Populus tomentosa.

    PubMed

    Wang, Wei; Yuan, Tongqi; Wang, Kun; Cui, Baokai; Dai, Yucheng

    2012-03-01

    A novel stepwise pretreatment of combination of fungal treatment with liquid hot water (LHW) treatment was conducted to enhance the enzymatic hydrolysis of Populus tomentosa. The results showed that lignin and cellulose increased with the elevating temperature, while significant amount of hemicellulose was degraded during the LHW pretreatment. A highest hemicellulose removal of 92.33% was observed by combination of Lenzites betulina C5617 with LHW treatment at 200°C, which was almost 2 times higher than that of sole LHW treatment at the same level. Saccharification of poplar co-treated with L. betulina C5617 and LHW at 200°C resulted in a 2.66-fold increase of glucose yield than that of sole LHW treatment, and an increase (2.25-fold) of glucose yield was obtained by the combination of Trametes ochracea C6888 with LHW. The combination pretreatment performed well at accelerating the enzymatic hydrolysis of poplar wood.

  9. Towards a holistic understanding of the beneficial interactions across the Populus microbiome

    SciTech Connect

    Hacquard, Stéphane; Schadt, Christopher W.

    2014-11-24

    Interactions between trees and microorganisms are extremely complex and the multispecies networks resulting from these associations have consequences for plant growth and productivity. However, a more holistic view is needed to better understand trees as ecosystems and superorganisms, where many interacting species contribute to the overall stability of the system. While much progress has been made on microbial communities associated with individual tree niches and the molecular interactions between model symbiotic partners, there is still a lack of knowledge of the multi-component interactions necessary for holistic ecosystem-level understanding. Finally, we review recent studies in Populus to emphasize the importance of such holistic efforts across the leaf, stem and rooting zones, and discuss prospects for future research in these important ecosystems.

  10. Towards a holistic understanding of the beneficial interactions across the Populus microbiome

    DOE PAGESBeta

    Hacquard, Stéphane; Schadt, Christopher W.

    2014-11-24

    Interactions between trees and microorganisms are extremely complex and the multispecies networks resulting from these associations have consequences for plant growth and productivity. However, a more holistic view is needed to better understand trees as ecosystems and superorganisms, where many interacting species contribute to the overall stability of the system. While much progress has been made on microbial communities associated with individual tree niches and the molecular interactions between model symbiotic partners, there is still a lack of knowledge of the multi-component interactions necessary for holistic ecosystem-level understanding. Finally, we review recent studies in Populus to emphasize the importance ofmore » such holistic efforts across the leaf, stem and rooting zones, and discuss prospects for future research in these important ecosystems.« less

  11. Development of polymorphic microsatellite markers based on expressed sequence tags in Populus cathayana (Salicaceae).

    PubMed

    Tian, Z Z; Zhang, F Q; Cai, Z Y; Chen, S L

    2016-01-01

    Populus cathayana occupies a large area within the northern, central, and southwestern regions of China, and is considered to be an important reforestation species in western China. In order to investigate the population genetic structure of this species, 10 polymorphic microsatellite loci were identified based on expressed sequence tags from de novo sequencing on the Illumina HiSeq 2000 platform. All microsatellite primers were tested on 48 P. cathayana individuals from four locations on the Qinghai-Tibet Plateau. The observed heterozygosity ranged from 0.000 to 1.000, and the null-allele frequency ranged from 0.000 to 0.904. These microsatellite markers may be a useful tool in genetic studies on P. cathayana and closely related species.

  12. Populus cathayana males are less affected than females by excess manganese: comparative proteomic and physiological analyses.

    PubMed

    Chen, Fugui; Zhang, Sheng; Zhu, Guoping; Korpelainen, Helena; Li, Chunyang

    2013-08-01

    The comprehension of sexually different responses in dioecious plants to excess manganese (Mn) stress requires molecular explanation. Physiological and proteomic changes in leaves of Populus cathayana males and females were analyzed after 4 wk of exposure to Mn stress. Under excess Mn conditions, shoot height and photosynthesis decreased more in females than in males. Females also showed severe browning and subcellular damage, higher Mn2+ absorption, and different antioxidant enzyme activities compared with males. There were ten differently regulated protein spots induced by excess Mn stress. They were mainly related to photosynthesis, ROS cleaning, and cell signaling associated to ROS, plant cell death, heat shock, cell defense and rescue, and gene expression and regulation. Variation in protein expression between the sexes clearly showed that males have evolved more efficient photosynthesis capacity, more stable gene expression and regulation, and better cell defense and rescue to prevent further injury under excess Mn stress. PMID:23868850

  13. Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations

    SciTech Connect

    Evans, Luke M; Slavov, Gancho; Rodgers-Melnick, Eli; Martin, Joel; Ranjan, Priya; Muchero, Wellington; Brunner, Amy M.; Schackwitz, Wendy; Gunter, Lee E; Chen, Jay; Tuskan, Gerald A; Difazio, Stephen P.

    2014-01-01

    Forest trees are dominant components of terrestrial ecosystems that have global ecological and economic importance. Despite distributions that span wide environmental gradients, many tree populations are locally adapted, and mechanisms underlying this adaptation are poorly understood. Here we use a combination of whole-genome selection scans and association analyses of 544 Populus trichocarpa trees to reveal genomic bases of adaptive variation across a wide latitudinal range. Three hundred ninety-seven genomic regions showed evidence of recent positive and/or divergent selection and enrichment for associations with adaptive traits that also displayed patterns consistent with natural selection. These regions also provide unexpected insights into the evolutionary dynamics of duplicated genes and their roles in adaptive trait variation.

  14. Stable transformation of Populus and incorporation of pest resistance by electric discharge particle acceleration.

    PubMed

    McCown, B H; McCabe, D E; Russell, D R; Robison, D J; Barton, K A; Raffa, K F

    1991-02-01

    Three different target tissues (protoplast-derived cells, nodules, and stems) and two unrelated hybrid genotypes of Populus (P. alba x P. grandidentata 'Crandon' and P. nigra 'Betulifolia' x P. trichocarpa) have been stably transformed by electric discharge particle acceleration using a 18.7 kb plasmid containing NOS-NPT, CaMV 35S-GUS, and CaMV 35S-BT. Four transformed plants of one hybrid genotype, NC5339, containing all 3 genes were recovered and analyzed. Two expressed GUS and one was highly resistant to feeding by 2 lepidopteran pests (the forest tent caterpillar, Malacosoma disstria, and the gypsy moth, Lymantria dispar.) Pretreatment of the target tissues, fine-tuning of the bombardment parameters, and the use of a selection technique employing flooding of the target tissues were important for reliable recovery of transformed plants.

  15. [Response of morphological characteristics of Populus euphratica nebkhas to groundwater in Birkum Desert, west of Taklimakan].

    PubMed

    Zhang, Zhan-he; Lai, Feng-bing; Chen, Shu-jiang

    2015-09-01

    By regarding the east of Birkum desert of the west of Taklimakan as research areas, the paper measured the basic morphological characteristics of Populus euphratica nebkhas through real-time kinematics, got the relevant data of groundwater by manual drilling, and analyzed the response of emorphological characteristics of P. euphratica nebkhas to groundwater. The results showed that the change range of morphological parameters of P. euphratica nebkhas was large. Groundwater infil- trated the research areas from west, south and southwest to northwest and the depth of groundwater ranged from 0.15 m to 83.2 m. Except for the maximums of the length and circumference, the other morphological parameters of P. euphratica nebkhas had a negative relation with the depth of groundwater. The volume of P. euphratica nebkhas was mainly in the range of 63.54-91.24 m3.

  16. Genome-wide identification of NBS resistance genes in Populus trichocarpa.

    PubMed

    Kohler, Annegret; Rinaldi, Cécile; Duplessis, Sébastien; Baucher, Marie; Geelen, Danny; Duchaussoy, Frédéric; Meyers, Blake C; Boerjan, Wout; Martin, Francis

    2008-04-01

    As the largest class of disease resistance R genes, the genes encoding nucleotide binding site and leucine-rich repeat proteins ("NBS-LRR genes") play a critical role in defending plants from a multitude of pathogens and pests. The diversity of NBS-LRR genes was examined in the Populus trichocarpa draft genome sequence. The NBS class of genes in this perennial tree is large and diverse, comprised of approximately 400 genes, at least twice the complement of Arabidopsis. The NBS family can be divided into multiple subfamilies with distinct domain organizations. It includes 119 Coiled-Coil-NBS-LRR genes, 64 TIR-NBS-LRR genes, 34 BED-finger-NBS-LRR, and both truncated and unusual NBS- and NBS-LRR-containing genes. The transcripts of only 34 NBS-LRR genes were detected in rust-infected and non-infected leaves using a whole-genome oligoarray. None showed an altered expression two days post inoculation. PMID:18247136

  17. Biodegradation of naphthalene and anthracene by chemo-tactically active rhizobacteria of populus deltoides

    PubMed Central

    Bisht, Sandeep; Pandey, Piyush; Sood, Anchal; Sharma, Shivesh; Bisht, N. S.

    2010-01-01

    Several naphthalene and anthracene degrading bacteria were isolated from rhizosphere of Populus deltoides, which were growing in non-contaminated soil. Among these, four isolates, i.e. Kurthia sp., Micrococcus varians, Deinococcus radiodurans and Bacillus circulans utilized chrysene, benzene, toluene and xylene, in addition to anthracene and naphthalene. Kurthia sp and B. circulans showed positive chemotactic response for naphthalene and anthracene. The mean growth rate constant (K) of isolates were found to increase with successive increase in substrate concentration (0.5 to 1.0 mg/50ml). B. circulans SBA12 and Kurthia SBA4 degraded 87.5% and 86.6% of anthracene while, Kurthia sp. SBA4, B. circulans SBA12, and M. varians SBA8 degraded 85.3 %, 95.8 % and 86.8 % of naphthalene respectively after 6 days of incubation as determined by HPLC analysis. PMID:24031572

  18. Development of polymorphic microsatellite markers based on expressed sequence tags in Populus cathayana (Salicaceae).

    PubMed

    Tian, Z Z; Zhang, F Q; Cai, Z Y; Chen, S L

    2016-01-01

    Populus cathayana occupies a large area within the northern, central, and southwestern regions of China, and is considered to be an important reforestation species in western China. In order to investigate the population genetic structure of this species, 10 polymorphic microsatellite loci were identified based on expressed sequence tags from de novo sequencing on the Illumina HiSeq 2000 platform. All microsatellite primers were tested on 48 P. cathayana individuals from four locations on the Qinghai-Tibet Plateau. The observed heterozygosity ranged from 0.000 to 1.000, and the null-allele frequency ranged from 0.000 to 0.904. These microsatellite markers may be a useful tool in genetic studies on P. cathayana and closely related species. PMID:27525845

  19. The essential oil of Populus balsamifera buds: its chemical composition and cytotoxic activity.

    PubMed

    Piochon-Gauthier, Marianne; Legault, Jean; Sylvestre, Muriel; Pichette, André

    2014-02-01

    The chemical composition of Populus balsamifera essential oils obtained from spring buds, fall buds, and young leaves were determined by GC and GC-MS analyses. The major constituent, (+)-alpha-bisabolol, a rare sesquiterpene, was isolated from spring oil using reverse-phase preparative HPLC. The cytotoxic activity of balsam poplar oils and isolated (+)-alpha-bisabolol was assessed in vitro against human lung carcinoma (A549) and colorectal adenocarcinoma (DLD-1) cell lines. Essential oils were cytotoxic with IC50 ranging from 35 to 50 microg/mL. (+)-alpha-Bisabolol exhibited pronounced activity (IC50 14 microg/mL) against both cancer cell lines. It also exhibited interesting cytotoxic activity (IC50 23 microg/mL) against human glioma (U251), higher than the one observed for (-)-alpha-bisabolol (IC50 34 microg/mL), which is known for its apoptosis-inducing effect against glioma cells.

  20. Restriction map and polymorphisms of nuclear ribosomal genes of Populus balsamifera.

    PubMed

    Stoehr, M U; Singh, R S

    1993-06-01

    Balsam poplar (Populus balsamifera) clones from five populations, which were collected along a transect from northern Wisconsin to the northern tree line, were evaluated for polymorphisms in nuclear ribosomal DNA. For this purpose, a restriction map was constructed using four six-cutter enzymes in single and double digests of genomic DNA. After electrophoretic separation on agarose gels and Southern transfer, blots were hybridized to non-radioactively labeled heterologous rDNA probes of soybean. Among populations, variation was detected in the length of the intergenic spacer between the tandem repeats of the coding regions and in the degree of methylation of one restriction enzyme recognition site. Based on a comparison of the derived restriction map of balsam poplar and other poplars, high homology was evident in the rDNA coding regions among species, whereas the intergenic spacer varied slightly in both length and number of restriction sites.

  1. Towards a holistic understanding of the beneficial interactions across the Populus microbiome.

    PubMed

    Hacquard, Stéphane; Schadt, Christopher W

    2015-03-01

    Interactions between trees and microorganisms are tremendously complex and the multispecies networks resulting from these associations have consequences for plant growth and productivity. However, a more holistic view is needed to better understand trees as ecosystems and superorganisms, where many interacting species contribute to the overall stability of the system. While much progress has been made on microbial communities associated with individual tree niches and the molecular interactions between model symbiotic partners, there is still a lack of knowledge of the multi-component interactions necessary for holistic ecosystem-level understanding. We review recent studies in Populus to emphasize the importance of such holistic efforts across the leaf, stem and rooting zones, and discuss prospects for future research in these important ecosystems. PMID:25422041

  2. A Putative PP2C-Encoding Gene Negatively Regulates ABA Signaling in Populus euphratica

    PubMed Central

    Chen, Jinhuan; Zhang, Dongzhi; Zhang, Chong; Xia, Xinli; Yin, Weilun; Tian, Qianqian

    2015-01-01

    A PP2C homolog gene was cloned from the drought-treated cDNA library of Populus euphratica. Multiple sequence alignment analysis suggested that the gene is a potential ortholog of HAB1. The expression of this HAB1 ortholog (PeHAB1) was markedly induced by drought and moderately induced by ABA. To characterize its function in ABA signaling, we generated transgenic Arabidopsis thaliana plants overexpressing this gene. Transgenic lines exhibited reduced responses to exogenous ABA and reduced tolerance to drought compared to wide-type lines. Yeast two-hybrid analyses indicated that PeHAB1 could interact with the ABA receptor PYL4 in an ABA-independent manner. Taken together; these results indicated that PeHAB1 is a new negative regulator of ABA responses in poplar. PMID:26431530

  3. Determination of the relative uptake of ground vs. surface water by Populus deltoides during phytoremediation

    USGS Publications Warehouse

    Clinton, B.D.; Vose, J.M.; Vroblesky, D.A.; Harvey, G.J.

    2004-01-01

    The use of plants to remediate polluted groundwater is becoming an attractive alternative to more expensive traditional techniques. In order to adequately assess the effectiveness of the phytoremediation treatment, a clear understanding of water-use habits by the selected plant species is essential. We examined the relative uptake of surface water (i.e., precipitation) vs. groundwater by mature Populus deltoides by applying irrigation water at a rate equivalent to a 5-cm rain event. We used stable isotopes of hydrogen (D) and oxygen (18O) to identify groundwater and surface water (irrigation water) in the xylem sap water. Pretreatment isotopic ratios of both deuterium and 18O, ranked from heaviest to lightest, were irrigation water > groundwater > xylem sap. The discrepancy in preirrigation isotopic signatures between groundwater and xylem sap suggests that in the absence of a surface source of water (i.e., between rain events) there is an unknown amount of water being extracted from sources other than groundwater (i.e., soil surface water). We examined changes in volumetric soil water content (%), total hourly sapflux rates, and trichloroethene (TCE) concentrations. Following the irrigation treatment, volumetric soil water increased by 86% and sapflux increased by as much as 61%. Isotopic signatures of the xylem sap became substantially heavier following irrigation, suggesting that the applied irrigation water was quickly taken up by the plants. TCE concentrations in the xylem sap were diluted by an average of 21% following irrigation; however, dilution was low relative to the increase in sapflux. Our results show that water use by Populus deltoides is variable. Hence, studies addressing phytoremediation effectiveness must account for the relative proportion of surface vs. groundwater uptake.

  4. Genome-wide transcriptional profiling reveals molecular signatures of secondary xylem differentiation in Populus tomentosa.

    PubMed

    Yang, X H; Li, X G; Li, B L; Zhang, D Q

    2014-11-11

    Wood formation occurs via cell division, primary cell wall and secondary wall formation, and programmed cell death in the vascular cambium. Transcriptional profiling of secondary xylem differentiation is essential for understanding the molecular mechanisms underlying wood formation. Differential gene expression in secondary xylem differentiation of Populus has been previously investigated using cDNA microarray analysis. However, little is known about the molecular mechanisms from a genome-wide perspective. In this study, the Affymetrix poplar genome chips containing 61,413 probes were used to investigate the changes in the transcriptome during secondary xylem differentiation in Chinese white poplar (Populus tomentosa). Two xylem tissues (newly formed and lignified) were sampled for genome-wide transcriptional profiling. In total, 6843 genes (~11%) were identified with differential expression in the two xylem tissues. Many genes involved in cell division, primary wall modification, and cellulose synthesis were preferentially expressed in the newly formed xylem. In contrast, many genes, including 4-coumarate:cinnamate-4-hydroxylase (C4H), 4-coumarate:CoA ligase (4CL), cinnamyl alcohol dehydrogenase (CAD), and caffeoyl CoA 3-O-methyltransferase (CCoAOMT), associated with lignin biosynthesis were more transcribed in the lignified xylem. The two xylem tissues also showed differential expression of genes related to various hormones; thus, the secondary xylem differentiation could be regulated by hormone signaling. Furthermore, many transcription factor genes were preferentially expressed in the lignified xylem, suggesting that wood lignification involves extensive transcription regulation. The genome-wide transcriptional profiling of secondary xylem differentiation could provide additional insights into the molecular basis of wood formation in poplar species.

  5. Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types.

    SciTech Connect

    Gottel, Neil R; Castro Gonzalez, Hector F; Kerley, Marilyn K; Yang, Zamin; Pelletier, Dale A; Podar, Mircea; Karpinets, Tatiana V; Uberbacher, Edward C; Tuskan, Gerald A; Vilgalys, Rytas; Doktycz, Mitchel John; Schadt, Christopher Warren

    2011-01-01

    The root-rhizosphere interface of Populus is the nexus of a variety of associations between bacteria, fungi, and the host plant and an ideal model for studying interactions between plants and microorganisms. However, such studies have generally been confined to greenhouse and plantation systems. Here we analyze microbial communities from the root endophytic and rhizospheric habitats of Populus deltoides in mature natural trees from both upland and bottomland sites in central Tennessee. Community profiling utilized 454 pyrosequencing with separate primers targeting the V4 region for bacterial 16S rRNA and the D1/D2 region for fungal 28S rRNA genes. Rhizosphere bacteria were dominated by Acidobacteria (31%) and Alphaproteobacteria (30%), whereas most endophytes were from the Gammaproteobacteria (54%) as well as Alphaproteobacteria (23%). A single Pseudomonas-like operational taxonomic unit (OTU) accounted for 34% of endophytic bacterial sequences. Endophytic bacterial richness was also highly variable and 10-fold lower than in rhizosphere samples originating from the same roots. Fungal rhizosphere and endophyte samples had approximately equal amounts of the Pezizomycotina (40%), while the Agaricomycotina were more abundant in the rhizosphere (34%) than endosphere (17%). Both fungal and bacterial rhizosphere samples were highly clustered compared to the more variable endophyte samples in a UniFrac principal coordinates analysis, regardless of upland or bottomland site origin. Hierarchical clustering of OTU relative abundance patterns also showed that the most abundant bacterial and fungal OTUs tended to be dominant in either the endophyte or rhizosphere samples but not both. Together, these findings demonstrate that root endophytic communities are distinct assemblages rather than opportunistic subsets of the rhizosphere.

  6. Influence of irrigation and fertilization on transpiration and hydraulic properties of Populus deltoides.

    SciTech Connect

    Samuelson, Lisa, J.; Stokes, Thomas, A.; Coleman, Mark, D.

    2007-02-01

    Summary Long-term hydraulic acclimation to resource availability was explored in 3-year-bld Populus deltoides Bartr. ex Marsh. clones by examining transpiration. leaf-specific hydraulic conductance (GL), canopy stomatal conductance (Gs) and leaf to sapwood area ratio (AL:Asi)n response to imgation (13 and 551 mm year in addition to ambient precipitation) and fertilization (0 and 120 kg N ha-' year-'). Sap flow was measured continuously over one growing season with thermal dissipation probes. Fertilization had a greater effect on growth and hydraulic properties than imgation, and fertilization effects were independent of irrigation treatment. Transpiration on a ground area basis (E) ranged between 0.3 and 1.8 mm day-', and increased 66% and 90% in response to imgation and fertilization, respectively. Increases in GL, Gs at a reference vapor pressure deficit of 1 kPa, and transpiration per unit leaf areain response to increases in resource availability were associated with reductions in AL:As and consequently a minimal change in the water potential gradient from soil to leaf. Imgation and fertilization increased leaf area index similarly, from an average 1.16 in control stands to 1.45, but sapwood area was increased from 4.0 to 6.3 m ha-' by irrigation and from 3.7 to 6.7 m2 ha-' by fertilization. The balance between leaf area and sapwood area was important in understanding long-term hydraulic acclimation to resource availability and mechanisms controlling maximum productivity in Populus deltoides.

  7. Thermospermine levels are controlled by an auxin-dependent feedback loop mechanism in Populus xylem.

    PubMed

    Milhinhos, Ana; Prestele, Jakob; Bollhöner, Benjamin; Matos, Andreia; Vera-Sirera, Francisco; Rambla, José L; Ljung, Karin; Carbonell, Juan; Blázquez, Miguel A; Tuominen, Hannele; Miguel, Célia M

    2013-08-01

    Polyamines are small polycationic amines that are widespread in living organisms. Thermospermine, synthesized by thermospermine synthase ACAULIS5 (ACL5), was recently shown to be an endogenous plant polyamine. Thermospermine is critical for proper vascular development and xylem cell specification, but it is not known how thermospermine homeostasis is controlled in the xylem. We present data in the Populus model system supporting the existence of a negative feedback control of thermospermine levels in stem xylem tissues, the main site of thermospermine biosynthesis. While over-expression of the ACL5 homologue in Populus, POPACAULIS5, resulted in strong up-regulation of ACL5 expression and thermospermine accumulation in leaves, the corresponding levels in the secondary xylem tissues of the stem were similar or lower than those in the wild-type. POPACAULIS5 over-expression had a negative effect on accumulation of indole-3-acetic acid, while exogenous auxin had a positive effect on POPACAULIS5 expression, thus promoting thermospermine accumulation. Further, over-expression of POPACAULIS5 negatively affected expression of the class III homeodomain leucine zipper (HD-Zip III) transcription factor gene PttHB8, a homologue of AtHB8, while up-regulation of PttHB8 positively affected POPACAULIS5 expression. These results indicate that excessive accumulation of thermospermine is prevented by a negative feedback control of POPACAULIS5 transcript levels through suppression of indole-3-acetic acid levels, and that PttHB8 is involved in the control of POPACAULIS5 expression. We propose that this negative feedback loop functions to maintain steady-state levels of thermospermine, which is required for proper xylem development, and that it is dependent on the presence of high concentrations of endogenous indole-3-acetic acid, such as those present in the secondary xylem tissues.

  8. Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis

    PubMed Central

    Utturkar, Sagar M.; Cude, W. Nathan; Robeson, Michael S.; Yang, Zamin K.; Klingeman, Dawn M.; Land, Miriam L.; Allman, Steve L.; Lu, Tse-Yuan S.; Brown, Steven D.; Schadt, Christopher W.; Podar, Mircea; Doktycz, Mitchel J.

    2016-01-01

    ABSTRACT Bacterial endophytes that colonize Populus trees contribute to nutrient acquisition, prime immunity responses, and directly or indirectly increase both above- and below-ground biomasses. Endophytes are embedded within plant material, so physical separation and isolation are difficult tasks. Application of culture-independent methods, such as metagenome or bacterial transcriptome sequencing, has been limited due to the predominance of DNA from the plant biomass. Here, we describe a modified differential and density gradient centrifugation-based protocol for the separation of endophytic bacteria from Populus roots. This protocol achieved substantial reduction in contaminating plant DNA, allowed enrichment of endophytic bacteria away from the plant material, and enabled single-cell genomics analysis. Four single-cell genomes were selected for whole-genome amplification based on their rarity in the microbiome (potentially uncultured taxa) as well as their inferred abilities to form associations with plants. Bioinformatics analyses, including assembly, contamination removal, and completeness estimation, were performed to obtain single-amplified genomes (SAGs) of organisms from the phyla Armatimonadetes, Verrucomicrobia, and Planctomycetes, which were unrepresented in our previous cultivation efforts. Comparative genomic analysis revealed unique characteristics of each SAG that could facilitate future cultivation efforts for these bacteria. IMPORTANCE Plant roots harbor a diverse collection of microbes that live within host tissues. To gain a comprehensive understanding of microbial adaptations to this endophytic lifestyle from strains that cannot be cultivated, it is necessary to separate bacterial cells from the predominance of plant tissue. This study provides a valuable approach for the separation and isolation of endophytic bacteria from plant root tissue. Isolated live bacteria provide material for microbiome sequencing, single-cell genomics, and analyses

  9. Developmental and Environmental Regulation of Aquaporin Gene Expression across Populus Species: Divergence or Redundancy?

    PubMed Central

    Cohen, David; Bogeat-Triboulot, Marie-Béatrice; Vialet-Chabrand, Silvère; Merret, Rémy; Courty, Pierre-Emmanuel; Moretti, Sébastien; Bizet, François; Guilliot, Agnès; Hummel, Irène

    2013-01-01

    Aquaporins (AQPs) are membrane channels belonging to the major intrinsic proteins family and are known for their ability to facilitate water movement. While in Populus trichocarpa, AQP proteins form a large family encompassing fifty-five genes, most of the experimental work focused on a few genes or subfamilies. The current work was undertaken to develop a comprehensive picture of the whole AQP gene family in Populus species by delineating gene expression domain and distinguishing responsiveness to developmental and environmental cues. Since duplication events amplified the poplar AQP family, we addressed the question of expression redundancy between gene duplicates. On these purposes, we carried a meta-analysis of all publicly available Affymetrix experiments. Our in-silico strategy controlled for previously identified biases in cross-species transcriptomics, a necessary step for any comparative transcriptomics based on multispecies design chips. Three poplar AQPs were not supported by any expression data, even in a large collection of situations (abiotic and biotic constraints, temporal oscillations and mutants). The expression of 11 AQPs was never or poorly regulated whatever the wideness of their expression domain and their expression level. Our work highlighted that PtTIP1;4 was the most responsive gene of the AQP family. A high functional divergence between gene duplicates was detected across species and in response to tested cues, except for the root-expressed PtTIP2;3/PtTIP2;4 pair exhibiting 80% convergent responses. Our meta-analysis assessed key features of aquaporin expression which had remained hidden in single experiments, such as expression wideness, response specificity and genotype and environment interactions. By consolidating expression profiles using independent experimental series, we showed that the large expansion of AQP family in poplar was accompanied with a strong divergence of gene expression, even if some cases of functional redundancy

  10. Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture

    PubMed Central

    2012-01-01

    Background High-throughput re-sequencing is rapidly becoming the method of choice for studies of neutral and adaptive processes in natural populations across taxa. As re-sequencing the genome of large numbers of samples is still cost-prohibitive in many cases, methods for genome complexity reduction have been developed in attempts to capture most ecologically-relevant genetic variation. One of these approaches is sequence capture, in which oligonucleotide baits specific to genomic regions of interest are synthesized and used to retrieve and sequence those regions. Results We used sequence capture to re-sequence most predicted exons, their upstream regulatory regions, as well as numerous random genomic intervals in a panel of 48 genotypes of the angiosperm tree Populus trichocarpa (black cottonwood, or ‘poplar’). A total of 20.76Mb (5%) of the poplar genome was targeted, corresponding to 173,040 baits. With 12 indexed samples run in each of four lanes on an Illumina HiSeq instrument (2x100 paired-end), 86.8% of the bait regions were on average sequenced at a depth ≥10X. Few off-target regions (>250bp away from any bait) were present in the data, but on average ~80bp on either side of the baits were captured and sequenced to an acceptable depth (≥10X) to call heterozygous SNPs. Nucleotide diversity estimates within and adjacent to protein-coding genes were similar to those previously reported in Populus spp., while intergenic regions had higher values consistent with a relaxation of selection. Conclusions Our results illustrate the efficiency and utility of sequence capture for re-sequencing highly heterozygous tree genomes, and suggest design considerations to optimize the use of baits in future studies. PMID:23241106

  11. Native Venturia inopina sp. nov., specific to Populus trichocarpa and its hybrids.

    PubMed

    Newcombe, George

    2003-01-01

    Venturia populina, first described on European Populus nigra, has been thought to be the only species of Venturia in Europe and North America to cause leaf and shoot blight of balsam poplars and cottonwoods in Populus sects. Tacamahaca and Aigeiros. The species of Venturia occurring on introduced P. nigra and native P. trichocarpa in the Pacific northwest were examined. Venturia populina was consistently found on P. nigra (i.e. the widespread P. nigra cv. 'italica') in the region, but V. inopina sp. nov. was present on native P. trichocarpa and its hybrids. There were neither examples of V. populina on P. trichocarpa and its hybrids nor of V. inopina on P. nigra cv. 'italica' (27 collections from 16 sites in Oregon, Washington, and Vancouver Island were made during 1995-2002). In an inoculation study, host-range separation was confirmed in that V. inopina caused sporulating leaf lesions on P. trichocarpa and its hybrids, but only non-sporulating lesions on P. nigra cv. 'italica'. These two species of Venturia can readily be distinguished by conidial septation; V. populina is primarily 2-septate, whereas V. inopina is primarily 1-septate. Growth rates on PDA at 15 degrees C, and ITS sequences (2.3% divergence) were also distinct in isolates of these congeners. Conidial shape was of more value in discriminant analysis than conidial length. Venturia inopina is homothallic, given the sexual fertility of cultures of single ascospores that were overwintered under ambient conditions. Its geographic range appears to be restricted even within the Pacific northwest, leaving open the possibility that still other undescribed, native species of Venturia occur elsewhere in North America on sects. Tacamahaca and Aigeiros.

  12. Further quantification of the role of internal unstirred layers during the measurement of transport coefficients in giant internodes of Chara by a new stop-flow technique.

    PubMed

    Kim, Yangmin; Ye, Qing; Reinhardt, Hagen; Steudle, Ernst

    2006-01-01

    A new stop-flow technique was employed to quantify the impact of internal unstirred layers on the measurement of the solute permeability coefficient (P(s)) across the plasma membrane of internodes of the giant-celled alga Chara corallina using a cell pressure probe. During permeation experiments with rapidly permeating solutes (acetone, 2-propanol, and dimethylformamide), the solute concentration inside the cell was estimated and the external medium was adjusted to stop solute transport across the membrane, after which responses in turgor were measured. This allowed estimation of the solute concentration right at the membrane. Stop-flow experiments were also simulated with a computer. Both the stop-flow experiments and simulations provided quantitative data about internal concentration gradients and the contribution of unstirred layers to overall measured values of P(meas)(s) for the three solutes. The stop-flow experimental results agreed with stop-flow simulations assuming that solutes diffused into a completely stagnant cell interior. The effects of internal unstirred layers on the underestimation of membrane P(s) declined with decreasing P(s). They were no bigger than 37% in the presence of the most rapidly permeating solute, acetone (P(meas)(s) =4.2 x 10(-6) m s(-1)), and 14% for the less rapidly permeating dimethylformamide (P(meas)(s) =1.6x10(-6) m s(-1)). It is concluded that, even in the case of rapidly permeating solutes such as isotopic water and, even when making pessimistic assumptions about the internal mixing of solutes, an upper limit for the underestimation of P(s) due to internal unstirred layers was 37%. The data are discussed in terms of recent theoretical estimates of the effect of internal unstirred layers and in terms of some recent criticism of cell pressure probe measurements of water and solute transport coefficients. The current stop-flow data are in line with earlier estimations of the role of unstirred layers in the literature on cell

  13. A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species

    SciTech Connect

    Geraldes, Armando; Hannemann, Jan; Grassa, Chris; Farzaneh, Nima; Porth, Ilga; McKown, Athena; Skyba, Oleksandr; Li, Eryang; Mike, Fujita; Friedmann, Michael; Wasteneys, Geoffrey; Guy, Robert; El-Kassaby, Yousry; Mansfield, Shawn; Cronk, Quentin; Ehlting, Juergen; Douglas, Carl; DiFazio, Stephen P; Slavov, Gancho; Ranjan, Priya; Muchero, Wellington; Gunter, Lee E; Wymore, Ann; Tuskan, Gerald A; Martin, Joel; Schackwitz, Wendy; Pennacchio, Christa; Rokhsar, Daniel

    2013-01-01

    Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. Despite the declining costs of genotyping by sequencing, for most studies, the use of large SNP genotyping arrays still offers the most cost-effective solution for large-scale targeted genotyping. Here we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species range. Due to the rapid decay of linkage disequilibrium in P. trichocarpa we adopted a candidate gene approach to the array design that resulted in the selection of 34,131 SNPs, the majority of which are located in, or within 2 kb, of 3,543 candidate genes. A subset of the SNPs (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%, indicating that high-quality data are generated with this array. We demonstrate that even among small numbers of samples (n=10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that due to ascertainment bias the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca (P. balsamifera and P. angustifolia). Finally, we provide evidence for the utility of the array for intraspecific studies of genetic differentiation and for species assignment and the detection of natural hybrids.

  14. A Populus TIR1 gene family survey reveals differential expression patterns and responses to 1-naphthaleneacetic acid and stress treatments.

    PubMed

    Shu, Wenbo; Liu, Yingli; Guo, Yinghua; Zhou, Houjun; Zhang, Jin; Zhao, Shutang; Lu, Mengzhu

    2015-01-01

    The plant hormone auxin is a central regulator of plant growth. TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFB) is a component of the E3 ubiquitin ligase complex SCF(TIR1/AFB) and acts as an auxin co-receptor for nuclear auxin signaling. The SCF(TIR1/AFB)-proteasome machinery plays a central regulatory role in development-related gene transcription. Populus trichocarpa, as a model tree, has a unique fast-growth trait to which auxin signaling may contribute. However, no systematic analyses of the genome organization, gene structure, and expression of TIR1-like genes have been undertaken in this woody model plant. In this study, we identified a total of eight TIR1 genes in the Populus genome that are phylogenetically clustered into four subgroups, PtrFBL1/PtrFBL2, PtrFBL3/PtrFBL4, PtrFBL5/PtrFBL6, and PtrFBL7/PtrFBL8, representing four paralogous pairs. In addition, the gene structure and motif composition were relatively conserved in each paralogous pair and all of the PtrFBL members were localized in the nucleus. Different sets of PtrFBLs were strongly expressed in the leaves, stems, roots, cambial zones, and immature xylem of Populus. Interestingly, PtrFBL1 and 7 were expressed mainly in vascular and cambial tissues, respectively, indicating their potential but different roles in wood formation. Furthermore, Populus FBLs responded differentially upon exposure to various stresses. Finally, over-expression studies indicated a role of FBL1 in poplar stem growth and response to drought stress. Collectively, these observations lay the foundation for further investigations into the potential roles of PtrFBL genes in tree growth and development.

  15. RNA Sequencing of Populus x canadensis Roots Identifies Key Molecular Mechanisms Underlying Physiological Adaption to Excess Zinc

    PubMed Central

    Ariani, Andrea; Di Baccio, Daniela; Romeo, Stefania; Lombardi, Lara; Andreucci, Andrea; Lux, Alexander; Horner, David Stephen; Sebastiani, Luca

    2015-01-01

    Populus x canadensis clone I-214 exhibits a general indicator phenotype in response to excess Zn, and a higher metal uptake in roots than in shoots with a reduced translocation to aerial parts under hydroponic conditions. This physiological adaptation seems mainly regulated by roots, although the molecular mechanisms that underlie these processes are still poorly understood. Here, differential expression analysis using RNA-sequencing technology was used to identify the molecular mechanisms involved in the response to excess Zn in root. In order to maximize specificity of detection of differentially expressed (DE) genes, we consider the intersection of genes identified by three distinct statistical approaches (61 up- and 19 down-regulated) and validate them by RT-qPCR, yielding an agreement of 93% between the two experimental techniques. Gene Ontology (GO) terms related to oxidation-reduction processes, transport and cellular iron ion homeostasis were enriched among DE genes, highlighting the importance of metal homeostasis in adaptation to excess Zn by P. x canadensis clone I-214. We identified the up-regulation of two Populus metal transporters (ZIP2 and NRAMP1) probably involved in metal uptake, and the down-regulation of a NAS4 gene involved in metal translocation. We identified also four Fe-homeostasis transcription factors (two bHLH38 genes, FIT and BTS) that were differentially expressed, probably for reducing Zn-induced Fe-deficiency. In particular, we suggest that the down-regulation of FIT transcription factor could be a mechanism to cope with Zn-induced Fe-deficiency in Populus. These results provide insight into the molecular mechanisms involved in adaption to excess Zn in Populus spp., but could also constitute a starting point for the identification and characterization of molecular markers or biotechnological targets for possible improvement of phytoremediation performances of poplar trees. PMID:25671786

  16. F-box gene family is expanded in herbaceous annual plants Arabidopsis and rice relative to woody perennial plant Populus

    SciTech Connect

    Yang, Xiaohan; Kalluri, Udaya C; Jawdy, Sara; Gunter, Lee E; Yin, Tongming; Tschaplinski, Timothy J; Weston, David; Ranjan, Priya; Tuskan, Gerald A

    2008-01-01

    F-box proteins are generally responsible for substrate recognition in the Skp1-Cullin-F-box complexes that are involved in protein degradation via the ubiquitin-26S proteosome pathway. In plants, F-box genes influence a variety of biological processes such as leaf senescence, branching, self-incompatibility and responses to biotic and abiotic stresses. The number of F-box genes in Populus (~320) is less than half that found in Arabidopsis (~660) or rice (~680), even though the total number of genes in Populus is equivalent to that in rice and 1.5 times that in Arabidopsis. We performed comparative genomic analysis between the woody perennial plant Populus and the herbaceous annual plants Arabidopsis and rice in order to explicate the functional implications of this large gene family. Our analyses reveal interspecific differences in genomic distribution, orthologous relationship, intron evolution, protein domain structure and gene expression. The set of F-box genes shared by these three species appear to be involved in core biological processes essential for plant growth and development; lineage-specific differences primarily occurred because of an expansion of the F-box genes via tandem duplications in Arabidopsis and rice. The present study provides insights into the relationship between the structure and composition of the F-box gene family in herbaceous and woody species and their associated developmental and physiological features.

  17. Defining the Boundaries and Characterizing the Landscape of Genome Expression in Vascular Tissues of Populus using Shotgun Proteomics

    SciTech Connect

    Abraham, Paul E; Adams, Rachel M; Giannone, Richard J; Kalluri, Udaya C; Ranjan, Priya; Erickson, Brian K; Shah, Manesh B; Tuskan, Gerald A; Hettich, Robert {Bob} L

    2012-01-01

    Current state-of-the-art experimental and computational proteomic approaches were integrated to obtain a comprehensive protein profile of Populus vascular tissue. This featured: 1) a large sample set consisting of two genotypes grown under normal and tension stress conditions, 2) bioinformatics clustering to effectively handle gene duplication, and 3) an informatics approach to track and identify single amino acid polymorphisms (SAAPs). By applying a clustering algorithm to the Populus database, the number of protein entries decreased from 64,689 proteins to a total of 43,069 protein groups, thereby reducing 7,505 identified proteins to a total of 4,226 protein groups, in which 2,016 were singletons. This reduction implies that ~50% of the measured proteins were clustered into groups that shared extensive sequence homology. Using conservative search criteria, we were able to identify 1,354 peptides containing a SAAP and 201 peptides that become tryptic due to a K or R substitution. These newly identified peptides correspond to 502 proteins, including 97 proteins that were not previously identified. In total, the integration of deep proteome measurements on an extensive sample set with protein clustering and peptide sequence variants provided an unprecedented level of proteome characterization for Populus, allowing us to spatially resolve the vascular tissue proteome.

  18. Comparative interrogation of the developing xylem transcriptomes of two wood-forming species: Populus trichocarpa and Eucalyptus grandis.

    PubMed

    Hefer, Charles A; Mizrachi, Eshchar; Myburg, Alexander A; Douglas, Carl J; Mansfield, Shawn D

    2015-06-01

    Wood formation is a complex developmental process governed by genetic and environmental stimuli. Populus and Eucalyptus are fast-growing, high-yielding tree genera that represent ecologically and economically important species suitable for generating significant lignocellulosic biomass. Comparative analysis of the developing xylem and leaf transcriptomes of Populus trichocarpa and Eucalyptus grandis together with phylogenetic analyses identified clusters of homologous genes preferentially expressed during xylem formation in both species. A conserved set of 336 single gene pairs showed highly similar xylem preferential expression patterns, as well as evidence of high functional constraint. Individual members of multi-gene orthologous clusters known to be involved in secondary cell wall biosynthesis also showed conserved xylem expression profiles. However, species-specific expression as well as opposite (xylem versus leaf) expression patterns observed for a subset of genes suggest subtle differences in the transcriptional regulation important for xylem development in each species. Using sequence similarity and gene expression status, we identified functional homologs likely to be involved in xylem developmental and biosynthetic processes in Populus and Eucalyptus. Our study suggests that, while genes involved in secondary cell wall biosynthesis show high levels of gene expression conservation, differential regulation of some xylem development genes may give rise to unique xylem properties.

  19. Suppression of PtrDUF579-3 Expression Causes Structural Changes of the Glucuronoxylan in Populus

    PubMed Central

    Song, Dongliang; Gui, Jinshan; Liu, Chenchen; Sun, Jiayan; Li, Laigeng

    2016-01-01

    DUF579 (domain unknown function 579) genes have been reported to play diverse roles in cell wall biosynthesis, such as in glucuronoxylan (GX) synthesis. As GX is a major type of hemicelluloses in hard wood species, how DUF579 genes function in wood formation remains to be demonstrated in planta. This study reports a Populus DUF579 gene, PtrDUF579-3, which is characterized for its function in wood cell wall formation. PtrDUF579-3 is localized in Golgi apparatus and catalyzes methylation of the glucuronic acid (GlcA) in GX biosynthesis. Suppression of PtrDUF579-3 expression in Populus caused a reduction in both the GlcA side chain number and GlcA side chain methylation on the GX backbone. The modified GX polymer through PtrDUF579-3 suppression was more susceptible to acid treatment and the PtrDUF579-3 suppressed plants displayed enhanced cellulose digestibility. These results suggest that PtrDUF579-3 is involved in GX biosynthesis and GX structure can be modified through PtrDUF579-3 suppression in Populus. PMID:27148318

  20. Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species: Populus trichocarpa and Prunus persica

    PubMed Central

    2013-01-01

    Background Through the diversity of cytokinin regulated processes, this phytohormone has a profound impact on plant growth and development. Cytokinin signaling is involved in the control of apical and lateral meristem activity, branching pattern of the shoot, and leaf senescence. These processes influence several traits, including the stem diameter, shoot architecture, and perennial life cycle, which define the development of woody plants. To facilitate research about the role of cytokinin in regulation of woody plant development, we have identified genes associated with cytokinin signaling and homeostasis pathways from two hardwood tree species. Results Taking advantage of the sequenced black cottonwood (Populus trichocarpa) and peach (Prunus persica) genomes, we have compiled a comprehensive list of genes involved in these pathways. We identified genes belonging to the six families of cytokinin oxidases (CKXs), isopentenyl transferases (IPTs), LONELY GUY genes (LOGs), two-component receptors, histidine containing phosphotransmitters (HPts), and response regulators (RRs). All together 85 Populus and 45 Prunus genes were identified, and compared to their Arabidopsis orthologs through phylogenetic analyses. Conclusions In general, when compared to Arabidopsis, differences in gene family structure were often seen in only one of the two tree species. However, one class of genes associated with cytokinin signal transduction, the CKI1-like family of two-component histidine kinases, was larger in both Populus and Prunus than in Arabidopsis. PMID:24341635

  1. Efficient Agrobacterium-mediated transformation of commercial hybrid poplar Populus nigra L. x P. maximowiczii A. Henry.

    PubMed

    Yevtushenko, Dmytro P; Misra, Santosh

    2010-03-01

    Many economically important species of Populus, especially those in sections Aigeiros and Tacamahaca, remain recalcitrant to genetic transformation. In this study, a simple and reliable protocol was developed for the efficient Agrobacterium-mediated transformation of a difficult-to-transform, but commercially viable, hybrid poplar Populus nigra L. x P. maximowiczii A. Henry (NM6). A plant transformation vector designed to express the beta-glucuronidase (GUS) gene was used to detect transformation events at early stages of plant regeneration and to optimize parameters affecting poplar transformation. The use of zeatin riboside in shoot-induction medium, regeneration of shoots via indirect organogenesis, and early selection pressure were the major modifications that drastically improved the efficiency of poplar transformation and minimized the number of untransformed regenerants. Transgenic shoots were routinely obtained 4-10 weeks after co-culture with A. tumefaciens, with a greater than 90% rate of plant recovery. Stable transgene integration, ranging from a single insertion to ten copies per genome, was confirmed by Southern blot analysis. The mean transformation frequency was 36.3% and about two-thirds of the lines had 1-2 transgene copies. Among the explants, petioles and leaves had a higher transformation frequency than did stem segments. Growth characteristics and the morphology of transgenic poplar plants were identical to untransformed controls. These findings will accelerate the development of P. nigra x P. maximowiczii plants with novel traits, and may also be useful to improve transformation procedures for other Populus species.

  2. Anti-adipogenic activities of Alnus incana and Populus balsamifera bark extracts, part I: sites and mechanisms of action.

    PubMed

    Martineau, Louis C; Hervé, Jessica; Muhamad, Asim; Saleem, Ammar; Harris, Cory S; Arnason, John T; Haddad, Pierre S

    2010-09-01

    Obesity is an epidemic in most developed countries and novel therapeutic approaches are needed. In the course of a screening project of medicinal plants used by the Eastern James Bay Cree of Canada and having potential for the treatment of diabetes, we have identified several products that inhibit adipogenesis, suggesting potential antiobesity activities. The inhibitory activity of two of these, the extract of the inner bark of the deciduous trees Alnus incana ssp. rugosa (Speckled Alder) and Populus balsamifera L. (Balsam Poplar), was analyzed using the 3T3-L1 cell model of adipogenesis. Intracellular triglyceride accumulation, pre-adipocyte proliferation, and PPAR- γ activity were measured. Alnus incana extracts acted early in the differentiation process but did not affect clonal expansion of pre-adipocytes nor the morphological transformation from fibroblast-like to rounded fat-laden cells. Alnus incana extracts were found to act as partial agonists toward PPAR- γ activity. In contrast, Populus balsamifera extracts completely abrogated adipogenesis, severely limited clonal expansion of pre-adipocytes and generally maintained cells in an undifferentiated fibroblast-like morphology. Populus balsamifera extracts exerted antagonistic action against PPAR- γ activity. It is concluded that, through their actions on the adipocyte, these plant products may be useful for the treatment of obesity and related metabolic diseases.

  3. Transcriptome-Wide Identification of miRNA Targets under Nitrogen Deficiency in Populus tomentosa Using Degradome Sequencing

    PubMed Central

    Chen, Min; Bao, Hai; Wu, Qiuming; Wang, Yanwei

    2015-01-01

    miRNAs are endogenous non-coding small RNAs with important regulatory roles in stress responses. Nitrogen (N) is an indispensable macronutrient required for plant growth and development. Previous studies have identified a variety of known and novel miRNAs responsive to low N stress in plants, including Populus. However, miRNAs involved in the cleavage of target genes and the corresponding regulatory networks in response to N stress in Populus remain largely unknown. Consequently, degradome sequencing was employed for global detection and validation of N-responsive miRNAs and their targets. A total of 60 unique miRNAs (39 conserved, 13 non-conserved, and eight novel) were experimentally identified to target 64 mRNA transcripts and 21 precursors. Among them, we further verified the cleavage of 11 N-responsive miRNAs identified previously and provided empirical evidence for the cleavage mode of these miRNAs on their target mRNAs. Furthermore, five miRNA stars (miRNA*s) were shown to have cleavage function. The specificity and diversity of cleavage sites on the targets and miRNA precursors in P. tomentosa were further detected. Identification and annotation of miRNA-mediated cleavage of target genes in Populus can increase our understanding of miRNA-mediated molecular mechanisms of woody plants adapted to low N environments. PMID:26096002

  4. Development and Application of Microsatellites in Candidate Genes Related to Wood Properties in the Chinese White Poplar (Populus tomentosa Carr.)

    PubMed Central

    Du, Qingzhang; Gong, Chenrui; Pan, Wei; Zhang, Deqiang

    2013-01-01

    Gene-derived simple sequence repeats (genic SSRs), also known as functional markers, are often preferred over random genomic markers because they represent variation in gene coding and/or regulatory regions. We characterized 544 genic SSR loci derived from 138 candidate genes involved in wood formation, distributed throughout the genome of Populus tomentosa, a key ecological and cultivated wood production species. Of these SSRs, three-quarters were located in the promoter or intron regions, and dinucleotide (59.7%) and trinucleotide repeat motifs (26.5%) predominated. By screening 15 wild P. tomentosa ecotypes, we identified 188 polymorphic genic SSRs with 861 alleles, 2–7 alleles for each marker. Transferability analysis of 30 random genic SSRs, testing whether these SSRs work in 26 genotypes of five genus Populus sections (outgroup, Salix matsudana), showed that 72% of the SSRs could be amplified in Turanga and 100% could be amplified in Leuce. Based on genotyping of these 26 genotypes, a neighbour-joining analysis showed the expected six phylogenetic groupings. In silico analysis of SSR variation in 220 sequences that are homologous between P. tomentosa and Populus trichocarpa suggested that genic SSR variations between relatives were predominantly affected by repeat motif variations or flanking sequence mutations. Inheritance tests and single-marker associations demonstrated the power of genic SSRs in family-based linkage mapping and candidate gene-based association studies, as well as marker-assisted selection and comparative genomic studies of P. tomentosa and related species. PMID:23213110

  5. Transcriptome sequencing of transgenic poplar (Populus × euramericana 'Guariento') expressing multiple resistance genes

    PubMed Central

    2014-01-01

    Background Transgenic poplar (Populus × euramericana 'Guariento') plants harboring five exogenous, stress-related genes exhibit increased tolerance to multiple stresses including drought, salt, waterlogging, and insect feeding, but the complex mechanisms underlying stress tolerance in these plants have not been elucidated. Here, we analyzed the differences in the transcriptomes of the transgenic poplar line D5-20 and the non-transgenic line D5-0 using high-throughput transcriptome sequencing techniques and elucidated the functions of the differentially expressed genes using various functional annotation methods. Results We generated 11.80 Gb of sequencing data containing 63, 430, 901 sequences, with an average length of 200 bp. The processed sequences were mapped to reference genome sequences of Populus trichocarpa. An average of 62.30% and 61.48% sequences could be aligned with the reference genomes for D5-20 and D5-0, respectively. We detected 11,352 (D5-20) and 11,372 expressed genes (D5-0), 7,624 (56.61%; D5-20) and 7,453 (65.54%; D5-0) of which could be functionally annotated. A total of 782 differentially expressed genes in D5-20 were identified compared with D5-0, including 628 up-regulated and 154 down-regulated genes. In addition, 196 genes with putative functions related to stress responses were also annotated. Gene Ontology (GO) analysis revealed that 346 differentially expressed genes are mainly involved in 67 biological functions, such as DNA binding and nucleus. KEGG annotation revealed that 36 genes (21 up-regulated and 15 down-regulated) were enriched in 51 biological pathways, 9 of which are linked to glucose metabolism. KOG functional classification revealed that 475 genes were enriched in 23 types of KOG functions. Conclusion These results suggest that the transferred exogenous genes altered the expression of stress (biotic and abiotic) response genes, which were distributed in different metabolic pathways and were linked to some extent. Our

  6. Extensive Transcriptome Changes During Natural Onset and Release of Vegetative Bud Dormancy in Populus

    PubMed Central

    Howe, Glenn T.; Horvath, David P.; Dharmawardhana, Palitha; Priest, Henry D.; Mockler, Todd C.; Strauss, Steven H.

    2015-01-01

    To survive winter, many perennial plants become endodormant, a state of suspended growth maintained even in favorable growing environments. To understand vegetative bud endodormancy, we collected paradormant, endodormant, and ecodormant axillary buds from Populus trees growing under natural conditions. Of 44,441 Populus gene models analyzed using NimbleGen microarrays, we found that 1,362 (3.1%) were differentially expressed among the three dormancy states, and 429 (1.0%) were differentially expressed during only one of the two dormancy transitions (FDR p-value < 0.05). Of all differentially expressed genes, 69% were down-regulated from paradormancy to endodormancy, which was expected given the lower metabolic activity associated with endodormancy. Dormancy transitions were accompanied by changes in genes associated with DNA methylation (via RNA-directed DNA methylation) and histone modifications (via Polycomb Repressive Complex 2), confirming and extending knowledge of chromatin modifications as major features of dormancy transitions. Among the chromatin-associated genes, two genes similar to SPT (SUPPRESSOR OF TY) were strongly up-regulated during endodormancy. Transcription factor genes and gene sets that were atypically up-regulated during endodormancy include a gene that seems to encode a trihelix transcription factor and genes associated with proteins involved in responses to ethylene, cold, and other abiotic stresses. These latter transcription factors include ETHYLENE INSENSITIVE 3 (EIN3), ETHYLENE-RESPONSIVE ELEMENT BINDING PROTEIN (EBP), ETHYLENE RESPONSE FACTOR (ERF), ZINC FINGER PROTEIN 10 (ZAT10), ZAT12, and WRKY DNA-binding domain proteins. Analyses of phytohormone-associated genes suggest important changes in responses to ethylene, auxin, and brassinosteroids occur during endodormancy. We found weaker evidence for changes in genes associated with salicylic acid and jasmonic acid, and little evidence for important changes in genes associated with

  7. Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus

    DOE PAGESBeta

    Ribeiro, Cintia L.; Silva, Cynthia M.; Drost, Derek R.; Novaes, Evandro; Novaes, Carolina R. D. B.; Dervinis, Christopher; Kirst, Matias

    2016-03-16

    In this study, adventitious roots (AR) develop from tissues other than the primary root, in a process physiologically regulated by phytohormones. Adventitious roots provide structural support and contribute to water and nutrient absorption, and are critical for commercial vegetative propagation of several crops. Here we quantified the number of AR, root architectural traits and root biomass in cuttings from a pseudo-backcross population of Populus deltoides and Populus trichocarpa. Quantitative trait loci (QTL) mapping and whole-transcriptome analysis of individuals with alternative QTL alleles for AR number were used to identify putative regulators of AR development. As a result, parental individuals andmore » progeny showed extensive segregation for AR developmental traits. Quantitative trait loci for number of AR mapped consistently in the same interval of linkage group (LG) II and LG XIV, explaining 7–10 % of the phenotypic variation. A time series transcriptome analysis identified 26,121 genes differentially expressed during AR development, particularly during the first 24 h after cuttings were harvested. Of those, 1929 genes were differentially regulated between individuals carrying alternative alleles for the two QTL for number of AR, in one or more time point. Eighty-one of these genes were physically located within the QTL intervals for number of AR, including putative homologs of the Arabidopsis genes SUPERROOT2 (SUR2) and TRYPTOPHAN SYNTHASE ALPHA CHAIN (TSA1), both of which are involved in the auxin indole-3-acetic acid (IAA) biosynthesis pathway. In conclusion, this study suggests the involvement of two genes of the tryptophan-dependent auxin biosynthesis pathway, SUR2 and TSA1, in the regulation of a critical trait for the clonal propagation of woody species. A possible model for this regulation is that poplar individuals that have poor AR formation synthesize auxin indole-3-acetic acid (IAA) primarily through the tryptophan (Trp) pathway. Much of

  8. Extensive Transcriptome Changes During Natural Onset and Release of Vegetative Bud Dormancy in Populus.

    PubMed

    Howe, Glenn T; Horvath, David P; Dharmawardhana, Palitha; Priest, Henry D; Mockler, Todd C; Strauss, Steven H

    2015-01-01

    To survive winter, many perennial plants become endodormant, a state of suspended growth maintained even in favorable growing environments. To understand vegetative bud endodormancy, we collected paradormant, endodormant, and ecodormant axillary buds from Populus trees growing under natural conditions. Of 44,441 Populus gene models analyzed using NimbleGen microarrays, we found that 1,362 (3.1%) were differentially expressed among the three dormancy states, and 429 (1.0%) were differentially expressed during only one of the two dormancy transitions (FDR p-value < 0.05). Of all differentially expressed genes, 69% were down-regulated from paradormancy to endodormancy, which was expected given the lower metabolic activity associated with endodormancy. Dormancy transitions were accompanied by changes in genes associated with DNA methylation (via RNA-directed DNA methylation) and histone modifications (via Polycomb Repressive Complex 2), confirming and extending knowledge of chromatin modifications as major features of dormancy transitions. Among the chromatin-associated genes, two genes similar to SPT (SUPPRESSOR OF TY) were strongly up-regulated during endodormancy. Transcription factor genes and gene sets that were atypically up-regulated during endodormancy include a gene that seems to encode a trihelix transcription factor and genes associated with proteins involved in responses to ethylene, cold, and other abiotic stresses. These latter transcription factors include ETHYLENE INSENSITIVE 3 (EIN3), ETHYLENE-RESPONSIVE ELEMENT BINDING PROTEIN (EBP), ETHYLENE RESPONSE FACTOR (ERF), ZINC FINGER PROTEIN 10 (ZAT10), ZAT12, and WRKY DNA-binding domain proteins. Analyses of phytohormone-associated genes suggest important changes in responses to ethylene, auxin, and brassinosteroids occur during endodormancy. We found weaker evidence for changes in genes associated with salicylic acid and jasmonic acid, and little evidence for important changes in genes associated with

  9. Dendroclimatic potential of plains cottonwood (Populus deltoides subsp. monilifera) from the Northern Great Plains, USA

    USGS Publications Warehouse

    Edmonson, Jesse; Friedman, Jonathan; Meko, David; Touchan, Ramzi; Scott, Julian; Edmonson, Alan

    2014-01-01

    A new 368-year tree-ring chronology (A.D. 1643–2010) has been developed in western North Dakota using plains cottonwood (Populus deltoides subsp. monilifera) growing on the relatively undisturbed floodplain of the Little Missouri River in the North Unit of Theodore Roosevelt National Park. We document many slow-growing living trees between 150–370 years old that contradict the common understanding that cottonwoods grow fast and die young. In this northern location, cottonwood produces distinct annual rings with dramatic interannual variability that strongly crossdate. The detrended tree-ring chronology is significantly positively correlated with local growing season precipitation and soil moisture conditions (r  =  0.69). This time series shows periods of prolonged low radial tree growth during the known droughts of the instrumental record (e.g. 1931–1939 and 1980–1981) and also during prehistory (e.g. 1816–1823 and 1856–1865) when other paleoclimate studies have documented droughts in this region. Tree rings of cottonwood will be a useful tool to help reconstruct climate, streamflow, and the floodplain history of the Little Missouri River and other northern river systems.

  10. Functional analysis of putative genes encoding the PIP2 water channel subfamily in Populus trichocarpa.

    PubMed

    Secchi, Francesca; MacIver, Bryce; Zeidel, Mark L; Zwieniecki, Maciej A

    2009-11-01

    We located fully sequenced putative genes of the plasma membrane intrinsic proteins (PIPs) family in the Populus trichocarpa (Torr. Gray), genome. Of 23 gene candidates, we assigned eight genes to the PIP2 subfamily. All eight putative genes were expressed in vegetative tissues (roots, leaves, bark and wood), and all of them showed water channel activity after being expressed in Xenopus oocytes. Six of eight proteins were affected by mercury ions. No proteins were affected by the presence of nickel or tungsten ions, or by lowering the pH of bathing external solution from 7.4 to 6.5. The presence of copper ions caused seven of eight PIP2 proteins to increase their water transport capacity by as much as 50%. This systematic study of the PIP2 subfamily of proteins in P. trichocarpa provides a basic overview of their activity as water channels and will be a useful reference for future physiological studies of plant water relations that use P. trichocarpa as a model system. PMID:19808706

  11. Influence of Populus genotype on gene expression by the wood decay fungus Phanerochaete chrysosporium.

    PubMed

    Gaskell, Jill; Marty, Amber; Mozuch, Michael; Kersten, Philip J; Splinter BonDurant, Sandra; Sabat, Grzegorz; Azarpira, Ali; Ralph, John; Skyba, Oleksandr; Mansfield, Shawn D; Blanchette, Robert A; Cullen, Dan

    2014-09-01

    We examined gene expression patterns in the lignin-degrading fungus Phanerochaete chrysosporium when it colonizes hybrid poplar (Populus alba × tremula) and syringyl (S)-rich transgenic derivatives. A combination of microarrays and liquid chromatography-tandem mass spectrometry (LC-MS/MS) allowed detection of a total of 9,959 transcripts and 793 proteins. Comparisons of P. chrysosporium transcript abundance in medium containing poplar or glucose as a sole carbon source showed 113 regulated genes, 11 of which were significantly higher (>2-fold, P < 0.05) in transgenic line 64 relative to the parental line. Possibly related to the very large amounts of syringyl (S) units in this transgenic tree (94 mol% S), several oxidoreductases were among the upregulated genes. Peptides corresponding to a total of 18 oxidoreductases were identified in medium consisting of biomass from line 64 or 82 (85 mol% S) but not in the parental clone (65 mol% S). These results demonstrate that P. chrysosporium gene expression patterns are substantially influenced by lignin composition.

  12. Sex-related adaptive responses to interaction of drought and salinity in Populus yunnanensis.

    PubMed

    Chen, Lianghua; Zhang, Sheng; Zhao, Hongxia; Korpelainen, Helena; Li, Chunyang

    2010-10-01

    We used Populus yunnanensis Dode., a native dioecious species in southwestern China, as a model species to study morphological, physiological, biochemical and ultrastructural responses to drought, salinity and their combination. Females exhibited more growth inhibition, gas exchange rate depression and reactive oxygen species (ROS) accumulation; higher lipid peroxide levels, lower osmotic adjustment capacity and ascorbate-glutathione cycle enzyme activities; and more damage to cell organelles than did males under drought, salinity and especially under their combination. In addition, we found sex-specific responses in total chlorophyll content (TC), carotenoid concentration and carbon isotope composition under different osmotic stresses. Our results indicated that: (1) females are more sensitive and suffer from greater negative effects than do males under drought, salinity and especially under their combination; (2) sexual differences in adaptive responses to drought, salinity and their combination are context dependent; and (3) sex-specific reactions under a combination of stresses are distinct from single-stress responses. Thus, these results provide evidence for adaptive differentiation between sexes in responses to osmotic stresses and in the sensitivity to environmental change.

  13. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment

    PubMed Central

    Timm, Collin M.; Campbell, Alisha G.; Utturkar, Sagar M.; Jun, Se-Ran; Parales, Rebecca E.; Tan, Watumesa A.; Robeson, Michael S.; Lu, Tse-Yuan S.; Jawdy, Sara; Brown, Steven D.; Ussery, David W.; Schadt, Christopher W.; Tuskan, Gerald A.; Doktycz, Mitchel J.; Weston, David J.; Pelletier, Dale A.

    2015-01-01

    The bacterial microbiota of plants is diverse, with 1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work, we used phenotypic analysis, comparative genomics, and metabolic models to investigate the differences between 19 sequenced Pseudomonas fluorescens strains. These isolates represent a single OTU and were collected from the rhizosphere and endosphere of Populus deltoides. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for plant-bacterial interactions are enriched in endosphere isolate genomes. Further, growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased toward endosphere isolates. Endosphere isolates have significantly more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways representative of plant-bacterial interactions but show metabolic bias toward chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria and are enriched among closely related isolates. PMID:26528266

  14. Water stress induces changes in polyphenol profile and antioxidant capacity in poplar plants (Populus spp.).

    PubMed

    Popović, B M; Štajner, D; Ždero-Pavlović, R; Tumbas-Šaponjac, V; Čanadanović-Brunet, J; Orlović, S

    2016-08-01

    This paper is aimed to characterize young poplar plants under the influence of water stress provoked by polyethileneglycol 6000 (PEG 6000). Three polar genotypes (M1, B229, and PE19/66) were grown in hydroponics and subjected to 100 and 200 mOsm PEG 6000 during six days. Polyphenol characterization, two enzymatic markers and antioxidant capacity in leaves and roots were investigated in stressed plants. Total phenol content, ferric reducing antioxidant capacity (FRAP) and DPPH antiradical power (DPPH ARP) were determined for estimating total antioxidant capacity. Polyphenol oxidase (PPO) and phenylalanine ammonia lyase (PAL) were determined as enzymatic markers. Polyphenol characterization of poplar samples was performed by HPLC-PDA analysis. All results were subjected to correlation analysis and principal component analysis (PCA). Inspite of the decrease of total phenol content in investigated genotypes, as well as total antioxidant capacity, some of polyphenols were affected by stress like flavonoids chrysin, myricetine, kaempferol and isoferulic acid in roots of B229 genotype (Populus deltoides). Genotype B229 also showed the increase of antioxidant capacity and PAL activity in root and leaves under stress what could be the indicator of the adaptability of poplar plants to water stress. Significant positive correlations were obtained between PAL, antioxidant capacity as well as phenolic acids among themselves. Chemometric evaluation showed close interdependence between flavonoids, FRAP, DPPH antiradical power and both investigated enzymes of polyphenol metabolism, PAL and PPO.

  15. A novel method of natural cryoprotection : intracellular glass formation in deeply frozen populus.

    PubMed

    Hirsh, A G; Williams, R J; Meryman, H T

    1985-09-01

    Correlating measurements from differential scanning calorimetry, freeze-fracture freeze-etch electron microscopy, and survival of twigs after two-step cooling experiments, we provide strong evidence that winter-hardened Populus balsamifera v. virginiana (Sarg.) resists the stresses of freezing below -28 degrees C by amorphous solidification (glass formation) of most of its intracellular contents during slow cooling (

  16. Growth and development during the establishment year of two Populus clones with contrasting morphology and phenology.

    PubMed

    Michael, D A; Isebrands, J G; Dickmann, D I; Nelson, N D

    1988-06-01

    Weekly morphological measurements of trees in permanent growth plots and periodic destructive sampling were used to monitor growth and development of two Populus clones with contrasting morphology and phenology during the establishment year in a short-rotation, intensive-culture system. Tristis (P. tristis Fisch. x P. balsamifera L.) grew rapidly for 48 days before setting bud in July. By contrast, Eugenei (P. x euramericana (Dode) Guinier) grew at a slower rate than Tristis, but maintained this rate for 75 days before setting bud in September. By early October, the total leaf area and dry weight of Eugenei exceeded that of Tristis by 39 and 11%, respectively. In addition, Eugenei had a greater harvest index than Tristis throughout most of the growing season because a larger proportion of photosynthate produced was directed to shoot growth; however, a high shoot/root ratio in Eugenei predisposed it to water stress. Differences in aboveground biomass between clones were largely attributable to clonal differences in seasonal leaf area development.

  17. Comprehensive analysis of trihelix genes and their expression under biotic and abiotic stresses in Populus trichocarpa

    PubMed Central

    Wang, Zhanchao; Liu, Quangang; Wang, Hanzeng; Zhang, Haizhen; Xu, Xuemei; Li, Chenghao; Yang, Chuanping

    2016-01-01

    Trihelix genes play important roles in plant growth and development and responses to biotic and abiotic stresses. Here, we identified 56 full-length trihelix genes in Populus trichocarpa and classified them into five groups. Most genes within a given group had similar gene structures and conserved motifs. The trihelix genes were unequally distributed across 19 different linkage groups. Fifteen paralogous pairs were identified, 14 of which have undergone segmental duplication events. Promoter cis-element analysis indicated that most trihelix genes contain stress- or phytohormone-related cis-elements. The expression profiles of the trihelix genes suggest that they are primarily expressed in leaves and roots. Quantitative real-time reverse transcription polymerase chain reaction analysis indicated that members of the trihelix gene family are significantly induced in response to osmotic, abscisic acid, salicylic acid, methyl jasmonate and pathogen infection. PtrGT10 was identified as a target gene of miR172d, which is involved in the osmotic response. Repression of PtrGT10 could increase reactive oxygen species scavenging ability and decrease cell death. This study provides novel insights into the phylogenetic relationships and functions of the P. trichocarpa trihelix genes, which will aid future functional studies investigating the divergent roles of trihelix genes belonging to other species. PMID:27782188

  18. Genetic diversity in fragmented populations of Populus talassica inferred from microsatellites: implications for conservation.

    PubMed

    Zhu, X H; Cheng, S P; Liao, T; Kang, X Y

    2016-01-01

    Populus talassica Kom. is an ecologically important species endemic to central Asia. In China, its main distribution is restricted to the Ili region in the Xinjiang Autonomous Region. An understanding of genetic diversity and population structure is crucial for the development of a feasible conservation strategy. Twenty-six high-level simple sequence repeat (SSR) markers were screened and used to genotype 220 individuals from three native populations. A high level of genetic diversity and low population differentiation were revealed. We identified 163 alleles, with a mean of 6.269 alleles per locus. The observed and expected heterozygosities ranged from 0.472 to 0.485 (with a mean of 0.477), and from 0.548 to 0.591 (mean 0.569), respectively. Analysis of molecular variance revealed 93% variation within populations and 7% among populations. A model-based population structure analysis divided P. talassica into two groups (optimal K = 2). These genetic data provide crucial insight for conservation management. PMID:27323095

  19. Genetic structure and regulation of isoprene synthase in Poplar (Populus spp.).

    PubMed

    Vickers, Claudia E; Possell, Malcolm; Nicholas Hewitt, C; Mullineaux, Philip M

    2010-07-01

    Isoprene is a volatile 5-carbon hydrocarbon derived from the chloroplastic methylerythritol 2-C-methyl-D: -erythritol 4-phosphate isoprenoid pathway. In plants, isoprene emission is controlled by the enzyme isoprene synthase; however, there is still relatively little known about the genetics and regulation of this enzyme. Isoprene synthase gene structure was analysed in three poplar species. It was found that genes encoding stromal isoprene synthase exist as a small gene family, the members of which encode virtually identical proteins and are differentially regulated. Accumulation of isoprene synthase protein is developmentally regulated, but does not differ between sun and shade leaves and does not increase when heat stress is applied. Our data suggest that, in mature leaves, isoprene emission rates are primarily determined by substrate (dimethylallyl diphosphate, DMADP) availability. In immature leaves, where isoprene synthase levels are variable, emission levels are also influenced by the amount of isoprene synthase protein. No thylakoid isoforms could be identified in Populus alba or in Salix babylonica. Together, these data show that control of isoprene emission at the genetic level is far more complicated than previously assumed.

  20. In vitro tetraploid induction from leaf explants of Populus pseudo-simonii Kitag.

    PubMed

    Cai, Xiao; Kang, Xiang-Yang

    2011-09-01

    Tetraploid plants were produced from leaf explants of diploid Populus pseudo-simonii by treating the leaves with colchicine. Leaf explants were cultured on MS basal medium containing 1.78 μM BA and 1.08 μM NAA for 0, 6 and 12 days, and then transferred to the same MS liquid medium with colchicine at concentrations of 25, 50 and 75 μM for 1, 2 and 3 days. The highest efficiency of tetraploid induction was 14.6% by treating leaf explants that were pre-cultured for 6 days and then cultured in liquid MS with 50 μM colchicine for 3 days. Flow cytometric analysis was used to screen the tetraploids out from the regenerated plants and chromosome number counting was employed to confirm the polyploidy level. Size and frequency of leaf stomata between diploid and tetraploid plants were demonstrated to have significant differences. PMID:21750904

  1. Local selection across a latitudinal gradient shapes nucleotide diversity in balsam poplar, Populus balsamifera L.

    PubMed

    Keller, Stephen R; Levsen, Nicholas; Ingvarsson, Pär K; Olson, Matthew S; Tiffin, Peter

    2011-08-01

    Molecular studies of adaptive evolution often focus on detecting selective sweeps driven by positive selection on a species-wide scale; however, much adaptation is local, particularly of ecologically important traits. Here, we look for evidence of range-wide and local adaptation at candidate genes for adaptive phenology in balsam poplar, Populus balsamifera, a widespread forest tree whose range extends across environmental gradients of photoperiod and growing season length. We examined nucleotide diversity of 27 poplar homologs of the flowering-time network-a group of genes that control plant developmental phenology through interactions with environmental cues such as photoperiod and temperature. Only one gene, ZTL2, showed evidence of reduced diversity and an excess of fixed replacement sites, consistent with a species-wide selective sweep. Two other genes, LFY and FRI, harbored high levels of nucleotide diversity and exhibited elevated differentiation between northern and southern accessions, suggesting local adaptation along a latitudinal gradient. Interestingly, FRI has also been identified as a target of local selection between northern and southern accessions of Arabidopsis thaliana, indicating that this gene may be commonly involved in ecological adaptation in distantly related species. Our findings suggest an important role for local selection shaping molecular diversity and reveal limitations of inferring molecular adaptation from analyses designed only to detect species-wide selective sweeps. PMID:21624997

  2. Boron accumulation and toxicity in hybrid poplar (Populus nigra × euramericana).

    PubMed

    Rees, Rainer; Robinson, Brett H; Menon, Manoj; Lehmann, Eberhard; Günthardt-Goerg, Madeleine S; Schulin, Rainer

    2011-12-15

    Poplars accumulate high B concentrations and are thus used for the phytomanagement of B contaminated soils. Here, we performed pot experiments in which Populus nigra × euramericana were grown on a substrate with B concentrations ranging from 13 to 280 mg kg(-1) as H(3)BO(3). Salix viminalis, Brassica juncea, and Lupinus albus were grown under some growing conditions for comparison. Poplar growth was unaffected at soil B treatment levels up to 93 mg kg(-1). Growth was progressively reduced at levels of 168 and 280 mg kg(-1). None of the other species survived at these substrate B levels. At leaf B concentrations <900 mg kg(-1) only <10% of the poplar leaf area showed signs of toxicity. Neutron radiography revealed that chlorotic leaf tissues had B concentrations of 1000-2000 mg kg(-1), while necrotic tissues had >2000 mg kg(-1). Average B concentrations of up to 3500 mg kg(-1) were found in leaves, while spots within leaves had concentrations >7000 mg kg(-1), showing that B accumulation in leaf tissue continued even after the onset of necrosis. The B accumulation ability of P. nigra × euramericana is associated with B hypertolerance in the living tissue and storage of B in dead leaf tissue. PMID:22050628

  3. Population genetics of freeze tolerance among natural populations of Populus balsamifera across the growing season.

    PubMed

    Menon, Mitra; Barnes, William J; Olson, Matthew S

    2015-08-01

    Protection against freeze damage during the growing season influences the northern range limits of plants. Freeze tolerance and freeze avoidance are the two major freeze resistance strategies. Winter survival strategies have been extensively studied in perennials, but few have addressed them and their genetic basis during the growing season. We examined intraspecific phenotypic variation in freeze resistance of Populus balsamifera across latitude and the growing season. To investigate the molecular basis of this variation, we surveyed nucleotide diversity and examined patterns of gene expression in the poplar C-repeat binding factor (CBF) gene family. Foliar freeze tolerance exhibited latitudinal and seasonal variation indicative of natural genotypic variation. CBF6 showed signatures of recent selective sweep. Of the 46 SNPs surveyed across the six CBF homologs, only CBF2_619 exhibited latitudinal differences consistent with increased freeze tolerance in the north. All six CBF genes were cold inducible, but showed varying patterns of expression across the growing season. Some Poplar CBF homologs exhibited patterns consistent with historical selection and clinal variation in freeze tolerance documented here. However, the CBF genes accounted for only a small amount of the variation, indicating that other genes in this and other molecular pathways likely play significant roles in nature.

  4. Cd, Fe, and Light Sensitivity: Interrelationships in Cd-Treated Populus

    PubMed Central

    Gáspár, László; Vági, Pál; Záray, Gyula; Fodor, Ferenc; Sárvári, Éva

    2011-01-01

    Abstract Cadmium is a toxic heavy metal causing iron deficiency in the shoot and light sensitivity of photosynthetic tissues that leads to decreased photosynthetic performance and biomass production. Light intensity had strong impact on both photosynthetic activity and metal accumulation of cadmium-treated plants. At elevated irradiation, cadmium accumulation increased due to the higher dry mass of plants, but its allocation hardly changed. A considerable amount of iron accumulated in the roots, and iron concentration was higher in leaves developed at moderate rather than low irradiation. At the same time, the higher the irradiation the lower the maximal photochemical quantum efficiency. The decreased photochemical efficiency, however, started to recover after a week of Cd treatment at moderate light without substantial change in metal concentrations but following the accumulation of green fluorescent compounds. Both cadmium treatment and higher light caused the accumulation of flavonoids in leaf mesophyll vacuoles/chloroplasts, but accumulation of flavonols, fluorescing at 510 nm, was characteristic to cadmium stress. Therefore, flavonoids, which may act by scavenging reactive radicals, chelating Cd, and shielding against excess irradiation, play an important part in Cd stress tolerance of Populus, and may have special impact on its phytoremediation capacity. PMID:22011338

  5. Flow regime effects on mature Populus fremontii (Fremont cottonwood) productivity on two contrasting dryland river floodplains

    USGS Publications Warehouse

    Andersen, Douglas C.

    2016-01-01

    I compared riparian cottonwood (Populus fremontii) productivity-discharge relationships in a relictual stand along the highly regulated Green River and in a naturally functioning stand along the unregulated Yampa River in semiarid northwest Colorado. I used multiple regression to model flow effects on annual basal area increment (BAI) from 1982 to 2011, after removing any autocorrelation present. Each BAI series was developed from 20 trees whose mean size (67 cm diameter at breast height [DBH]) was equivalent in the two stands. BAI was larger in the Yampa River stand except in 2 y when defoliating leaf beetles were present there. I found no evidence for a Yampa flood-magnitude threshold above which BAI declined. Flow variables explained ∼45% of residual BAI variability, with most explained by current-year maximum 90-d discharge (QM90) in the Yampa River stand and by a measure of the year-to-year change in QM90 in the Green River stand. The latter reflects a management-imposed ceiling on flood magnitude—Flaming Gorge Dam power plant capacity—infrequently exceeded during the study period. BAI in the relictual stand began to trend upward in 1992 when flows started to mimic a natural flow regime. Mature Fremont cottonwoods appear to be ecologically resilient. Their productivity along regulated rivers might be optimized using multiyear environmental flow designs.

  6. Quantitative Genetic Analysis of Biomass and Wood Chemistry of Populus under Different Nitrogen Levels

    SciTech Connect

    Novaes, E.; Osorio, L.; Drost, D. R.; Miles, B. L.; Boaventura-Novaes, C. R. D.; Benedict, C.; Dervinis, C.; Yu, Q.; Sykes, R.; Davis, M.; Martin, T. A.; Peter, G. F.; Kirst, M.

    2009-01-01

    The genetic control of carbon allocation and partitioning in woody perennial plants is poorly understood despite its importance for carbon sequestration, biofuels and other wood-based industries. It is also unclear how environmental cues, such as nitrogen availability, impact the genes that regulate growth, biomass allocation and wood composition in trees. We phenotyped 396 clonally replicated genotypes of an interspecific pseudo-backcross pedigree of Populus for wood composition and biomass traits in above- and below-ground organs. The loci that regulate growth, carbon allocation and partitioning under two nitrogen conditions were identified, defining the contribution of environmental cues to their genetic control. Sixty-three quantitative trait loci were identified for the 20 traits analyzed. The majority of quantitative trait loci are specific to one of the two nitrogen treatments, demonstrating significant nitrogen-dependent genetic control. A highly significant genetic correlation was observed between plant growth and lignin/cellulose composition, and quantitative trait loci co-localization identified the genomic position of potential pleiotropic regulators. Pleiotropic loci linking higher growth rates to wood with less lignin are excellent targets to engineer tree germplasm improved for pulp, paper and cellulosic ethanol production. The causative genes are being identified with a genetical genomics approach.

  7. [Simulation of soil water dynamics in triploid Populus tomentosa root zone under subsurface drip irrigation].

    PubMed

    Xi, Ben-Ye; Jia, Li-Ming; Wang, Ye; Li, Guang-De

    2011-01-01

    Based on the observed data of triploid Populus tomentosa root distribution, a one-dimensional root water uptake model was proposed. Taking the root water uptake into account, the soil water dynamics in triploid P. tomentosa root zone under subsurface drip irrigation was simulated by using HYDRUS model, and the results were validated with field experiment. Besides, the HYDRUS model was used to study the effects of various irrigation technique parameters on soil wetting patterns. The RMAE for the simulated soil water content by the end of irrigation and approximately 24 h later was 7.8% and 6.0%, and the RMSE was 0.036 and 0.026 cm3 x cm(-3), respectively, illustrating that the HYDRUS model performed well in simulating the short-term soil water dynamics in triploid P. tomentosa root zone under drip irrigation, and the root water uptake model was reasonable. Comparing with 2 and 4 L x h(-1) of drip discharge and continuous irrigation, both the 1 L x h(-1) of drip discharge and the pulsed irrigation with water applied intermittently in 30 min periods could increase the volume of wetted soil and reduce deep percolation. It was concluded that the combination of 1 L x h(-1) of drip discharge and pulsed irrigation should be the first choice when applying drip irrigation to triploid P. tomentosa root zone at the experiment site. PMID:21548283

  8. Biochemical and Physiological Studies on the Effects of Senescence Leaves of Populus deltoides on Triticum vulgare

    PubMed Central

    Khaket, Tejinder Pal; Kumar, Viney; Singh, Jasbir; Dhanda, Suman

    2014-01-01

    Triticum vulgare (Wheat) based products are the major dietary source of food in developing countries. In India, it grows in association with boundary plantations of Populus deltoids (poplar). During winter, poplar enters in dormancy which cause a heavy leaf fall at the time of wheat seed germination. Large number of poplar senescence leaves may adversely affect the wheat. Therefore, the present study was performed to examine the effect of senescence poplar leaves on wheat germ and some other biochemical parameters. Seed's germination rate was determined by measuring root and shoot lengths, percent germination, germination index, and inhibition percentage. Biochemical parameters, namely, pigment, carbohydrate, protein, and phenol content, were estimated. Activities of catalase and polyphenol oxidase which are stress marker enzymes were also measured. Results revealed that germination and other biochemical parameters of wheat were severely affected by senescence poplar leaves even at very low concentration. So, intercropping of poplar along with wheat may be chosen carefully as wheat is the major dietary staple. PMID:25610892

  9. Molecular Cloning and Characterization of Two Genes Encoding Dihydroflavonol-4-Reductase from Populus trichocarpa

    PubMed Central

    Jia, Zhichun; Yang, Li; Sun, Yimin; Xiao, Xunyan; Song, Feng; Luo, Keming

    2012-01-01

    Dihydroflavonol 4-reductase (DFR, EC 1.1.1.219) is a rate-limited enzyme in the biosynthesis of anthocyanins and condensed tannins (proanthocyanidins) that catalyzes the reduction of dihydroflavonols to leucoanthocyanins. In this study, two full-length transcripts encoding for PtrDFR1 and PtrDFR2 were isolated from Populus trichocarpa. Sequence alignment of the two PtrDFRs with other known DFRs reveals the homology of these genes. The expression profile of PtrDFRs was investigated in various tissues of P. trichocarpa. To determine their functions, two PtrDFRs were overexpressed in tobacco (Nicotiana tabacum) via Agrobacterium-mediated transformation. The associated color change in the flowers was observed in all 35S:PtrDFR1 lines, but not in 35S:PtrDFR2 lines. Compared to the wild-type control, a significantly higher accumulation of anthocyanins was detected in transgenic plants harboring the PtrDFR1. Furthermore, overexpressing PtrDFR1 in Chinese white poplar (P. tomentosa Carr.) resulted in a higher accumulation of both anthocyanins and condensed tannins, whereas constitutively expressing PtrDFR2 only improved condensed tannin accumulation, indicating the potential regulation of condensed tannins by PtrDFR2 in the biosynthetic pathway in poplars. PMID:22363429

  10. Survey of Plant Drought-Resistance Promoting Bacteria from Populus euphratica Tree Living in Arid Area.

    PubMed

    Wang, Shanshan; Ouyang, Liming; Ju, Xiangyang; Zhang, Lili; Zhang, Qin; Li, Yanbin

    2014-12-01

    Two hundred and thirty-two bacterial strains were isolated from the rhizospheric soil of Populus euphratica which is the dominant tree living in extreme arid regions in northwest China. Some strains with plant growth-promoting bacteria related metabolic characteristics were able to promote drought resistance in plants after inoculation. Ten strains with the greatest effects increased the dry weight of wheat shoots from 0.5 to 34.4 %, and the surface area of the root systems from 12.56 to 212.17 % compared to the control after drought treatment whereas no obvious promoting effect was observed in normal water conditions. These 10 strains were identified to be of the genera Pseudomonas, Bacillus, Stenotrophomonas and Serratia by 16S rRNA (rrs) gene sequence alignment. Among these strains, Serratia sp. 1-9 and Pseudomonas sp. 5-23 were the two most effective strains. Both of them produced auxin and the production increased significantly when cultured under simulated drought conditions which are inferred to be the most plausible mechanism for their plant growth-promoting effect under drought stress. PMID:25320440

  11. Adaptive mechanisms and genomic plasticity for drought tolerance identified in European black poplar (Populus nigra L.)

    PubMed Central

    Viger, Maud; Smith, Hazel K.; Cohen, David; Dewoody, Jennifer; Trewin, Harriet; Steenackers, Marijke; Bastien, Catherine; Taylor, Gail

    2016-01-01

    Summer droughts are likely to increase in frequency and intensity across Europe, yet long-lived trees may have a limited ability to tolerate drought. It is therefore critical that we improve our understanding of phenotypic plasticity to drought in natural populations for ecologically and economically important trees such as Populus nigra L. A common garden experiment was conducted using ∼500 wild P. nigra trees, collected from 11 river populations across Europe. Phenotypic variation was found across the collection, with southern genotypes from Spain and France characterized by small leaves and limited biomass production. To examine the relationship between phenotypic variation and drought tolerance, six genotypes with contrasting leaf morphologies were subjected to a water deficit experiment. ‘North eastern’ genotypes were collected at wet sites and responded to water deficit with reduced biomass growth, slow stomatal closure and reduced water use efficiency (WUE) assessed by Δ13C. In contrast, ‘southern’ genotypes originating from arid sites showed rapid stomatal closure, improved WUE and limited leaf loss. Transcriptome analyses of a genotype from Spain (Sp2, originating from an arid site) and another from northern Italy (Ita, originating from a wet site) revealed dramatic differences in gene expression response to water deficit. Transcripts controlling leaf development and stomatal patterning, including SPCH, ANT, ER, AS1, AS2, PHB, CLV1, ERL1–3 and TMM, were down-regulated in Ita but not in Sp2 in response to drought. PMID:27174702

  12. Map and Analysis of Microsatellites in Genome of Populus: the First Sequenced Perennial Plant

    SciTech Connect

    Li, Shuxian; Yin, Tongming

    2007-01-01

    We mapped and analyzed the microsatellites throughout 284295605 base pairs of the unambiguously assembled sequence scaffolds along 19 chromosomes of the haploid poplar genome. Totally, we found 150985 SSRs with repeat unit lengths between 2 and 5 bp. The established microsatellite physical map demonstrated that SSRs were distributed relatively evenly across the genome of Populus. On average, These SSRs occurred every 1883 bp within the poplar genome and the SSR densities in intergenic regions, introns, exons and UTRs were 85.4%, 10.7%, 2.7% and 1.2%, respectively. We took di-, tri-, tetra-and pentamers as the four classes of repeat units and found that the density of each class of SSRs decreased with the repeat unit lengths except for the tetranucleotide repeats. It was noteworthy that the length diversification of microsatellite sequences was negatively correlated with their repeat unit length and the SSRs with shorter repeat units gained repeats faster than the SSRs with longer repeat units. We also found that the GC content of poplar sequence significantly correlated with densities of SSRs with uneven repeat unit lengths (tri- and penta-), but had no significant correlation with densities of SSRs with even repeat unit lengths (di- and tetra-). In poplar genome, there were evidences that the occurrence of different microsatellites was under selection and the GC content in SSR sequences was found to significantly relate to the functional importance of microsatellites.

  13. Bioinformatics-Based Identification of Candidate Genes from QTLs Associated with Cell Wall Traits in Populus

    SciTech Connect

    Ranjan, Priya; Yin, Tongming; Zhang, Xinye; Kalluri, Udaya C; Yang, Xiaohan; Jawdy, Sara; Tuskan, Gerald A

    2009-11-01

    Quantitative trait locus (QTL) studies are an integral part of plant research and are used to characterize the genetic basis of phenotypic variation observed in structured populations and inform marker-assisted breeding efforts. These QTL intervals can span large physical regions on a chromosome comprising hundreds of genes, thereby hampering candidate gene identification. Genome history, evolution, and expression evidence can be used to narrow the genes in the interval to a smaller list that is manageable for detailed downstream functional genomics characterization. Our primary motivation for the present study was to address the need for a research methodology that identifies candidate genes within a broad QTL interval. Here we present a bioinformatics-based approach for subdividing candidate genes within QTL intervals into alternate groups of high probability candidates. Application of this approach in the context of studying cell wall traits, specifically lignin content and S/G ratios of stem and root in Populus plants, resulted in manageable sets of genes of both known and putative cell wall biosynthetic function. These results provide a roadmap for future experimental work leading to identification of new genes controlling cell wall recalcitrance and, ultimately, in the utility of plant biomass as an energy feedstock.

  14. Genetic variation in functional traits influences arthropod community composition in aspen (Populus tremula L.).

    PubMed

    Robinson, Kathryn M; Ingvarsson, Pär K; Jansson, Stefan; Albrectsen, Benedicte R

    2012-01-01

    We conducted a study of natural variation in functional leaf traits and herbivory in 116 clones of European aspen, Populus tremula L., the Swedish Aspen (SwAsp) collection, originating from ten degrees of latitude across Sweden and grown in a common garden. In surveys of phytophagous arthropods over two years, we found the aspen canopy supports nearly 100 morphospecies. We identified significant broad-sense heritability of plant functional traits, basic plant defence chemistry, and arthropod community traits. The majority of arthropods were specialists, those coevolved with P. tremula to tolerate and even utilize leaf defence compounds. Arthropod abundance and richness were more closely related to plant growth rates than general chemical defences and relationships were identified between the arthropod community and stem growth, leaf and petiole morphology, anthocyanins, and condensed tannins. Heritable genetic variation in plant traits in young aspen was found to structure arthropod community; however no single trait drives the preferences of arthropod folivores among young aspen genotypes. The influence of natural variation in plant traits on the arthropod community indicates the importance of maintaining genetic variation in wild trees as keystone species for biodiversity. It further suggests that aspen can be a resource for the study of mechanisms of natural resistance to herbivores.

  15. Characterization of cellulose structure of Populus plants modified in candidate cellulose biosynthesis genes

    DOE PAGESBeta

    Bali, Garima; Khunsupat, Ratayakorn; Akinosho, Hannah; Payyavula, Raja S.; Samuel, Reichel; Tuskan, Gerald A.; Kalluri, Udaya C.; Ragauskas, Arthur J.

    2016-09-10

    Here, the recalcitrant nature of lignocellulosic biomass is a combined effect of several factors such as high crystallinity and high degree of polymerization of cellulose, lignin content and structure, and the available surface area for enzymatic degradation (i.e., accessibility). Genetic improvement of feedstock cell wall properties is a path to reducing recalcitrance of lignocellulosic biomass and improving conversion to various biofuels. An advanced understanding of the cellulose biosynthesis pathway is essential to precisely modify cellulose properties of plant cell walls. Here we report on the impact of modified expression of candidate cellulose biosynthesis pathway genes on the ultra-structure of cellulose,more » a key carbohydrate polymer of Populus cell wall using advanced nuclear magnetic resonance approaches. Noteworthy changes were observed in the cell wall characteristics of downregulated KORRIGAN 1 (KOR) and KOR 2 transgenic plants in comparison to the wild-type control. It was observed that all of the transgenic lines showed variation in cellulose ultrastructure, increase in cellulose crystallinity and decrease in the cellulose degree of polymerization. Additionally, the properties of cellulose allomorph abundance and accessibility were found to be variable. Application of such cellulose characterization techniques beyond the traditional measurement of cellulose abundance to comprehensive studies of cellulose properties in larger transgenic and naturally variable populations is expected to provide deeper insights into the complex nature of lignocellulosic material, which can significantly contribute to the development of precisely tailored plants for enhanced biofuels production.« less

  16. Water stress induces changes in polyphenol profile and antioxidant capacity in poplar plants (Populus spp.).

    PubMed

    Popović, B M; Štajner, D; Ždero-Pavlović, R; Tumbas-Šaponjac, V; Čanadanović-Brunet, J; Orlović, S

    2016-08-01

    This paper is aimed to characterize young poplar plants under the influence of water stress provoked by polyethileneglycol 6000 (PEG 6000). Three polar genotypes (M1, B229, and PE19/66) were grown in hydroponics and subjected to 100 and 200 mOsm PEG 6000 during six days. Polyphenol characterization, two enzymatic markers and antioxidant capacity in leaves and roots were investigated in stressed plants. Total phenol content, ferric reducing antioxidant capacity (FRAP) and DPPH antiradical power (DPPH ARP) were determined for estimating total antioxidant capacity. Polyphenol oxidase (PPO) and phenylalanine ammonia lyase (PAL) were determined as enzymatic markers. Polyphenol characterization of poplar samples was performed by HPLC-PDA analysis. All results were subjected to correlation analysis and principal component analysis (PCA). Inspite of the decrease of total phenol content in investigated genotypes, as well as total antioxidant capacity, some of polyphenols were affected by stress like flavonoids chrysin, myricetine, kaempferol and isoferulic acid in roots of B229 genotype (Populus deltoides). Genotype B229 also showed the increase of antioxidant capacity and PAL activity in root and leaves under stress what could be the indicator of the adaptability of poplar plants to water stress. Significant positive correlations were obtained between PAL, antioxidant capacity as well as phenolic acids among themselves. Chemometric evaluation showed close interdependence between flavonoids, FRAP, DPPH antiradical power and both investigated enzymes of polyphenol metabolism, PAL and PPO. PMID:27116372

  17. Adaptive mechanisms and genomic plasticity for drought tolerance identified in European black poplar (Populus nigra L.).

    PubMed

    Viger, Maud; Smith, Hazel K; Cohen, David; Dewoody, Jennifer; Trewin, Harriet; Steenackers, Marijke; Bastien, Catherine; Taylor, Gail

    2016-07-01

    Summer droughts are likely to increase in frequency and intensity across Europe, yet long-lived trees may have a limited ability to tolerate drought. It is therefore critical that we improve our understanding of phenotypic plasticity to drought in natural populations for ecologically and economically important trees such as Populus nigra L. A common garden experiment was conducted using ∼500 wild P. nigra trees, collected from 11 river populations across Europe. Phenotypic variation was found across the collection, with southern genotypes from Spain and France characterized by small leaves and limited biomass production. To examine the relationship between phenotypic variation and drought tolerance, six genotypes with contrasting leaf morphologies were subjected to a water deficit experiment. 'North eastern' genotypes were collected at wet sites and responded to water deficit with reduced biomass growth, slow stomatal closure and reduced water use efficiency (WUE) assessed by Δ(13)C. In contrast, 'southern' genotypes originating from arid sites showed rapid stomatal closure, improved WUE and limited leaf loss. Transcriptome analyses of a genotype from Spain (Sp2, originating from an arid site) and another from northern Italy (Ita, originating from a wet site) revealed dramatic differences in gene expression response to water deficit. Transcripts controlling leaf development and stomatal patterning, including SPCH, ANT, ER, AS1, AS2, PHB, CLV1, ERL1-3 and TMM, were down-regulated in Ita but not in Sp2 in response to drought. PMID:27174702

  18. Epidermal Micromorphology and Mesophyll Structure of Populus euphratica Heteromorphic Leaves at Different Development Stages

    PubMed Central

    Liu, Yubing; Li, Xinrong; Chen, Guoxiong; Li, Mengmeng; Liu, Meiling; Liu, Dan

    2015-01-01

    Leaf epidermal micromorphology and mesophyll structure during the development of Populus euphratica heteromorphic leaves, including linear, lanceolate, ovate, dentate ovate, dentate rhombic, dentate broad-ovate and dentate fan-shaped leaves, were studied by using electron and light microscopy. During development of heteromorphic leaves, epidermal appendages (wax crystals and trichomes) and special cells (mucilage cells and crystal idioblasts) increased in all leaf types while chloroplast ultrastructure and stomatal characters show maximum photosynthetic activity in dentate ovate and rhombic leaves. Also, functional analysis by subordinate function values shows that the maximum adaptability to adverse stress was exhibited in the broad type of mature leaves. The 12 heteromorphic leaf types are classified into three major groups by hierarchical cluster analysis: young, developing and mature leaves. Mature leaves can effectively obtain the highest stress resistance by combining the protection of xerophytic anatomy from drought stress, regulation of water uptake in micro-environment by mucilage and crystal idioblasts, and assistant defense of transpiration reduction through leaf epidermal appendages, which improves photosynthetic activity under arid desert conditions. Our data confirms that the main leaf function is differentiated during the developing process of heteromorphic leaves. PMID:26356300

  19. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment

    SciTech Connect

    Timm, Collin M.; Campbell, Alicia G.; Utturkar, Sagar M.; Jun, Se Ran; Parales, Rebecca E.; Tan, Mesa; Robeson, Michael S.; Lu, Tse-Yuan S.; Jawdy, Sara; Schadt, Christopher Warren; Doktycz, Mitchel John; Weston, David; Pelletier, Dale A.

    2015-10-14

    The bacterial microbiota of plants is diverse, with ~1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work we investigate how 19 sequenced Pseudomonas fluorescens strains representing a single OTU isolated from Populus deltoides rhizosphere and endosphere differ using phenotypic analysis, comparative genomics, and metabolic models. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for bacterial-plant interactions are enriched in endosphere isolate genomes and growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased towards endosphere isolates. Endosphere isolates have more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways important for bacterial-plant interactions but show metabolic bias towards chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria that are enriched in event he most closely related isolates.

  20. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment

    DOE PAGESBeta

    Timm, Collin M.; Campbell, Alicia G.; Utturkar, Sagar M.; Jun, Se Ran; Parales, Rebecca E.; Tan, Mesa; Robeson, Michael S.; Lu, Tse-Yuan S.; Jawdy, Sara; Schadt, Christopher Warren; et al

    2015-10-14

    The bacterial microbiota of plants is diverse, with ~1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work we investigate how 19 sequenced Pseudomonas fluorescens strains representing a single OTU isolated from Populus deltoides rhizosphere and endosphere differ using phenotypic analysis, comparative genomics, and metabolic models. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for bacterial-plant interactions are enriched in endosphere isolate genomes and growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased towards endosphere isolates. Endosphere isolates have more metabolic pathwaysmore » for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways important for bacterial-plant interactions but show metabolic bias towards chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria that are enriched in event he most closely related isolates.« less

  1. Linking Populus euphratica Hydraulic Redistribution to Diversity Assembly in the Arid Desert Zone of Xinjiang, China

    PubMed Central

    Yang, Xiao-Dong; Zhang, Xue-Ni; Lv, Guang-Hui; Ali, Arshad

    2014-01-01

    The hydraulic redistribution (HR) of deep-rooted plants significantly improves the survival of shallow-rooted shrubs and herbs in arid deserts, which subsequently maintain species diversity. This study was conducted in the Ebinur desert located in the western margin of the Gurbantonggut Desert. Isotope tracing, community investigation and comparison analysis were employed to validate the HR of Populus euphratica and to explore its effects on species richness and abundance. The results showed that, P. euphratica has HR. Shrubs and herbs that grew under the P. euphratica canopy (under community: UC) showed better growth than the ones growing outside (Outside community: OC), exhibiting significantly higher species richness and abundance in UC than OC (p<0.05) along the plant growing season. Species richness and abundance were significantly logarithmically correlated with the P. euphratica crown area in UC (R2 = 0.51 and 0.84, p<0.001). In conclusion, P. euphratica HR significantly ameliorates the water conditions of the shallow soil, which then influences the diversity assembly in arid desert communities. PMID:25275494

  2. Differential transcriptome analysis between Populus and its synthesized allotriploids driven by second-division restitution.

    PubMed

    Cheng, Shiping; Huang, Zhen; Li, Yun; Liao, Ting; Suo, Yujing; Zhang, Pingdong; Wang, Jun; Kang, Xiangyang

    2015-12-01

    In this report, we compared transcriptomic differences between a synthetic Populus section Tacamahaca triploid driven by second-division restitution and its parents using a high-throughput RNA-seq method. A total of 4,080 genes were differentially expressed between the high-growth vigor allotriploids (SDR-H) and their parents, and 719 genes were non-additively expressed in SDR-H. Differences in gene expression between the allotriploid and male parent were more significant than those between the allotriploid and female parent, which may be caused by maternal effects. We observed 3,559 differentially expressed genes (DEGs) between the SDR-H and male parent. Notably, the genes were mainly involved in metabolic process, cell proliferation, DNA methylation, cell division, and meristem and developmental growth. Among the 1,056 DEGs between SDR-H and female parent, many genes were associated with metabolic process and carbon utilization. In addition, 1,789 DEGs between high- and low-growth vigor allotriploid were mainly associated with metabolic process, auxin poplar transport, and regulation of meristem growth. Our results indicated that the higher poplar ploidy level can generate extensive transcriptomic diversity compared with its parents. Overall, these results increased our understanding of the driving force for phenotypic variation and adaptation in allopolyploids driven by second-division restitution.

  3. Cytospora species from Populus and Salix in China with C. davidiana sp. nov.

    PubMed

    Wang, Yan-Li; Lu, Quan; Decock, Cony; Li, Yong-Xia; Zhang, Xing-Yao

    2015-05-01

    Poplar and willow plantations have become widespread in China, in order to meet national economic and environmental needs. The emergence of several pathogens is enhanced by climatic change and associated human factors. Species of Cytospora are well-known pathogens on poplar and willow, and cause stem cankers and diebacks. In the present study, we conducted a survey of Cytospora species occurring on Populus spp. and Salix spp. in China. We used morphological examination and phylogenetic inferences, based on the DNA sequence data from the internal transcribed spacer regions (ITS1, 5.8S rDNA, and ITS2) and partial β-tubulin gene, to identify six Cytospora species occurring on poplar and willow. Five of these species belonged to known taxa, viz. Cytospora chrysosperma (asexual state of Valsa sordida), Cytospora translucens (asexual state of Leucostoma translucens), Cytospora fugax (asexual state of Valsa salicina), Cytospora atrocirrhata, and Cytospora kantschavelii. Our study yielded a new species, Cytospora davidiana sp. nov., on poplar. The new species is characterized by typical torsellioid conidiomata. An additional Cytospora sp. 1, which formed a distinct clade in the phylogenetic inferences, remains unnamed; the paucity of available materials prevented phenotypical characterization.

  4. Degradation of exogenous caffeine by Populus alba and its effects on endogenous caffeine metabolism.

    PubMed

    Pierattini, Erika C; Francini, Alessandra; Raffaelli, Andrea; Sebastiani, Luca

    2016-04-01

    This is the first study reporting the presence of endogenous caffeine, theobromine, and theophylline in all organs of poplar plants. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was used in order to evaluate the uptake, translocation, and metabolism of caffeine-(trimethyl-(13)C) in Populus alba L. Villafranca clone grown in hydroponic conditions. We investigated the remediation of caffeine since it is one of the most widely consumed drugs and it is frequently detected in wastewater treatment plant effluents, surface water, and groundwater worldwide. Our results demonstrated that poplar can absorb and degrade exogenous caffeine without negative effects on plant health. Data showed that concentrations of all endogenous compounds varied depending on caffeine-(trimethyl-(13)C) treatments. In particular, in control conditions, endogenous caffeine, theobromine, and theophylline were mainly distributed in roots. On the other hand, once caffeine-(trimethyl-(13)C) was provided, this compound and its dimethy-(13)C metabolites are mainly localized at leaf level. In conclusion, our results support the possible use of Villafranca clone in association with other water treatment systems in order to complete the process of caffeine remediation. PMID:26681326

  5. Removal of nitrogen and phosphorus by Eucalyptus and Populus at a tertiary treated municipal wastewater sprayfield.

    PubMed

    Minogue, Patrick J; Miwa, Masato; Rockwood, Donald L; Mackowiak, Cheryl L

    2012-12-01

    Various progenies of Eucalyptus grandis and E. amplifolia, and clones of Populus deltoides, were evaluated for plant removal of nitrogen (N) and phosphorus (P) for 26 months at a municipal waste spray field in north Florida. Tertiary treated wastewater containing 2.73 mg L(-1) nitrate N and 0.30 mg L(-1) total P was applied using sprinkler irrigation (93.8 m3 ha(-1) d(-1)) to fast growing trees utilized for bioenergy. Eucalyptus amplifolia and E. grandis survived and grew very poorly as the result of severe winter injury in two successive years and were not evaluated for nutrient removal. Survival and growth of P. deltoides demonstrated suitability for phytoremediation, and selected clones were evaluated for biomass and nutrient content. Removals of total N (TN) and total P (TP) were greatest for main stem (36% and 44%, respectively) and foliage (44% and 36%, respectively). Low biomass producing clones generally had higher nutrient concentrations, but high biomass producing clones removed more TN and TP. Approximately 789 kg ha(-1) TN and 103 kg ha(-1) TP were removed by the highest biomass producing P. deltoides clone, representing 215% of N and 615% of P inputs. PMID:22908661

  6. Significant Difference in Hydrogen Isotope Composition Between Xylem and Tissue Water in Populus Euphratica.

    PubMed

    Zhao, Liangju; Wang, Lixin; Cernusak, Lucas A; Liu, Xiaohong; Xiao, Honglang; Zhou, Maoxian; Zhang, Shiqiang

    2016-08-01

    Deuterium depletions between stem water and source water have been observed in coastal halophyte plants and in multiple species under greenhouse conditions. However, the location(s) of the isotope fractionation is not clear yet and it is uncertain whether deuterium fractionation appears in other natural environments. In this study, through two extensive field campaigns utilizing a common dryland riparian tree species Populus euphratica Oliv., we showed that no significant δ(18) O differences were found between water source and various plant components, in accord with previous studies. We also found that no deuterium fractionation occurred during P. euphratica water uptake by comparing the deuterium composition (δD) of groundwater and xylem sap. However, remarkable δD differences (up to 26.4‰) between xylem sap and twig water, root water and core water provided direct evidence that deuterium fractionation occurred between xylem sap and root or stem tissue water. This study indicates that deuterium fractionation could be a common phenomenon in drylands, which has important implications in plant water source identification, palaeoclimate reconstruction based on wood cellulose and evapotranspiration partitioning using δD of stem water. PMID:27061571

  7. Stem respiration of Populus species in the third year of free-air CO2 enrichment.

    PubMed

    Gielen, Birgit; Scarascia-Mugnozza, Giuseppe; Ceulemans, Reinhart

    2003-04-01

    Carbon cycling in ecosystems, and especially in forests, is intensively studied to predict the effects of global climate change, and the role which forests may play in 'changing climate change'. One of the questions is whether the carbon balance of forests will be affected by increasing atmospheric CO2 concentrations. Regarding this question, effects of elevated [CO2] on woody-tissue respiration have frequently been neglected. Stem respiration of three Populus species (P. alba L. (Clone 2AS-11), P. nigra L. (Clone Jean Pourtet), and P. x euramericana (Clone I-214)) was measured in a managed, high-density forest plantation exposed to free-air CO2 enrichment (POPFACE). During the period of measurements, in May of the third year, stem respiration rates were not affected by the FACE treatment. Moreover, FACE did not influence the relationships between respiration rate and both stem temperature and relative growth rate. The results were supported by the reported absence of a FACE-effect on growth and stem wood density.

  8. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment.

    PubMed

    Timm, Collin M; Campbell, Alisha G; Utturkar, Sagar M; Jun, Se-Ran; Parales, Rebecca E; Tan, Watumesa A; Robeson, Michael S; Lu, Tse-Yuan S; Jawdy, Sara; Brown, Steven D; Ussery, David W; Schadt, Christopher W; Tuskan, Gerald A; Doktycz, Mitchel J; Weston, David J; Pelletier, Dale A

    2015-01-01

    The bacterial microbiota of plants is diverse, with 1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work, we used phenotypic analysis, comparative genomics, and metabolic models to investigate the differences between 19 sequenced Pseudomonas fluorescens strains. These isolates represent a single OTU and were collected from the rhizosphere and endosphere of Populus deltoides. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for plant-bacterial interactions are enriched in endosphere isolate genomes. Further, growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased toward endosphere isolates. Endosphere isolates have significantly more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways representative of plant-bacterial interactions but show metabolic bias toward chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria and are enriched among closely related isolates. PMID:26528266

  9. Survey of Plant Drought-Resistance Promoting Bacteria from Populus euphratica Tree Living in Arid Area.

    PubMed

    Wang, Shanshan; Ouyang, Liming; Ju, Xiangyang; Zhang, Lili; Zhang, Qin; Li, Yanbin

    2014-12-01

    Two hundred and thirty-two bacterial strains were isolated from the rhizospheric soil of Populus euphratica which is the dominant tree living in extreme arid regions in northwest China. Some strains with plant growth-promoting bacteria related metabolic characteristics were able to promote drought resistance in plants after inoculation. Ten strains with the greatest effects increased the dry weight of wheat shoots from 0.5 to 34.4 %, and the surface area of the root systems from 12.56 to 212.17 % compared to the control after drought treatment whereas no obvious promoting effect was observed in normal water conditions. These 10 strains were identified to be of the genera Pseudomonas, Bacillus, Stenotrophomonas and Serratia by 16S rRNA (rrs) gene sequence alignment. Among these strains, Serratia sp. 1-9 and Pseudomonas sp. 5-23 were the two most effective strains. Both of them produced auxin and the production increased significantly when cultured under simulated drought conditions which are inferred to be the most plausible mechanism for their plant growth-promoting effect under drought stress.

  10. Local selection across a latitudinal gradient shapes nucleotide diversity in balsam poplar, Populus balsamifera L.

    PubMed

    Keller, Stephen R; Levsen, Nicholas; Ingvarsson, Pär K; Olson, Matthew S; Tiffin, Peter

    2011-08-01

    Molecular studies of adaptive evolution often focus on detecting selective sweeps driven by positive selection on a species-wide scale; however, much adaptation is local, particularly of ecologically important traits. Here, we look for evidence of range-wide and local adaptation at candidate genes for adaptive phenology in balsam poplar, Populus balsamifera, a widespread forest tree whose range extends across environmental gradients of photoperiod and growing season length. We examined nucleotide diversity of 27 poplar homologs of the flowering-time network-a group of genes that control plant developmental phenology through interactions with environmental cues such as photoperiod and temperature. Only one gene, ZTL2, showed evidence of reduced diversity and an excess of fixed replacement sites, consistent with a species-wide selective sweep. Two other genes, LFY and FRI, harbored high levels of nucleotide diversity and exhibited elevated differentiation between northern and southern accessions, suggesting local adaptation along a latitudinal gradient. Interestingly, FRI has also been identified as a target of local selection between northern and southern accessions of Arabidopsis thaliana, indicating that this gene may be commonly involved in ecological adaptation in distantly related species. Our findings suggest an important role for local selection shaping molecular diversity and reveal limitations of inferring molecular adaptation from analyses designed only to detect species-wide selective sweeps.

  11. The adaptive potential of Populus balsamifera L. to phenology requirements in a warmer global climate.

    PubMed

    Olson, Matthew S; Levsen, Nicholas; Soolanayakanahally, Raju Y; Guy, Robert D; Schroeder, William R; Keller, Stephen R; Tiffin, Peter

    2013-03-01

    The manner in which organisms adapt to climate change informs a broader understanding of the evolution of biodiversity as well as conservation and mitigation plans. We apply common garden and association mapping approaches to quantify genetic variance and identify loci affecting bud flush and bud set, traits that define a tree's season for height growth, in the boreal forest tree Populus balsamifera L. (balsam poplar). Using data from 478 genotypes grown in each of two common gardens, one near the southern edge and another near the northern edge of P. balsamifera's range, we found that broad-sense heritability for bud flush and bud set was generally high (H(2) > 0.5 in most cases), suggesting that abundant genetic variation exists for phenological response to changes in the length of the growing season. To identify the molecular genetic basis of this variation, we genotyped trees for 346 candidate single nucleotide polymorphisms (SNPs) from 27 candidate genes for the CO/FT pathway in poplar. Mixed-model analyses of variance identified SNPs in 10 genes to be associated with variation in either bud flush or bud set. Multiple SNPs within FRIGIDA were associated with bud flush, whereas multiple SNPs in LEAFY and GIGANTEA 5 were associated with bud set. Although there was strong population structure in stem phenology, the geographic distribution of multilocus association SNP genotypes was widespread except at the most northern populations, indicating that geographic regions may harbour sufficient diversity in functional genes to facilitate adaption to future climatic conditions in many sites.

  12. Genomic diversity, population structure, and migration following rapid range expansion in the Balsam poplar, Populus balsamifera.

    PubMed

    Keller, Stephen R; Olson, Matthew S; Silim, Salim; Schroeder, William; Tiffin, Peter

    2010-03-01

    Rapid range expansions can cause pervasive changes in the genetic diversity and structure of populations. The postglacial history of the Balsam Poplar, Populus balsamifera, involved the colonization of most of northern North America, an area largely covered by continental ice sheets during the last glacial maximum. To characterize how this expansion shaped genomic diversity within and among populations, we developed 412 SNP markers that we assayed for a range-wide sample of 474 individuals sampled from 34 populations. We complemented the SNP data set with DNA sequence data from 11 nuclear loci from 94 individuals, and used coalescent analyses to estimate historical population size, demographic growth, and patterns of migration. Bayesian clustering identified three geographically separated demes found in the Northern, Central, and Eastern portions of the species' range. These demes varied significantly in nucleotide diversity, the abundance of private polymorphisms, and population substructure. Most measures supported the Central deme as descended from the primary refuge of diversity. Both SNPs and sequence data suggested recent population growth, and coalescent analyses of historical migration suggested a massive expansion from the Centre to the North and East. Collectively, these data demonstrate the strong influence that range expansions exert on genomic diversity, both within local populations and across the range. Our results suggest that an in-depth knowledge of nucleotide diversity following expansion requires sampling within multiple populations, and highlight the utility of combining insights from different data types in population genomic studies.

  13. Allergic contact dermatitis from salicyl alcohol and salicylaldehyde in aspen bark (Populus tremula).

    PubMed

    Aalto-Korte, Kristiina; Välimaa, Jarmo; Henriks-Eckerman, Maj-Len; Jolanki, Riitta

    2005-02-01

    Salicyl alcohol or 2-methylolphenol is a well-known allergen in phenol-formaldehyde resins and a strong sensitizer in guinea pigs. There is 1 previous report of allergic contact dermatitis from salicyl alcohol in aspen bark. We describe a second case with concomitant allergy to salicylaldehyde. An elk researcher who had handled leaves from various trees presented with eczema of the hands, face, flexures, trunk and extremities. Patch testing showed sensitivity to salicyl alcohol, salicylaldehyde, balsam of Peru (Myroxylon pereirae resin), aspen wood dust and an extract prepared from the bark of aspen (Populus tremula). Weaker reactions were observed to bark extracts of rowan (Sorbus aucuparia), tea-leaved willow (Salix phylicifolia) and goat willow (Salix caprea). We analysed salicyl alcohol and salicylaldehyde in the bark extracts and found the 2 chemicals in equal amounts, about 0.9 microg/mg in aspen bark and in lower concentrations in rowan and the willows. We did not find either of the chemicals in the test substance of balsam of Peru (Myroxylon pereirae). Besides salicyl alcohol, salicylaldehyde is also recommended to be used to screen for contact allergy to aspen. Both of these chemicals should be tested in forest workers in areas where aspen is growing.

  14. Effects of Elevated CO2 Concentration on Photosynthesis and Respiration of Populus Deltodies

    NASA Technical Reports Server (NTRS)

    Anderson, Angela M.

    1998-01-01

    To determine how increased atmospheric CO2 will affect the physiology of cottonwood trees, cuttings of the cloned Populus deltodies [cottonwood] were grown in open-top chambers containing ambient or elevated CO2 concentration. The control treatment was maintained at ambient Biosphere 2 atmospheric CO2 (c. 450 +/- 50 micro l/l), and elevated CO2 treatment was maintained at approximately double ambient Biosphere 2 atmospheric CO2 (c. 1000 +/- 50 micro l/l). The effects of elevated CO2 on leaf photosynthesis, and stomatal conductance were measured. The cottonwoods exposed to CO2 enrichment showed no significant indication of photosynthetic down-regulation. There was no significant difference in the maximum assimilation rate between the treatment and the control (P less than 0.24). The CO2 enriched treatment showed a decreased stomatal conductance of 15% (P less than 0.03). The elevated CO2 concentrated atmosphere had an effect on the respiration rates of the plants; the compensation point of the treatment was on average 13% higher than the control (P less than 0.01).

  15. Study of short-term plasticity in two contrasting genotypes of Populus nigra L.

    PubMed

    Russo, G; Sabatti, M; De Angelis, P

    2016-08-01

    Species like black poplar characterized by an indeterminate growth, can acclimate to the changing environmental conditions during the seasons through a modification of morphological and physiological features. The acclimation results fundamental for the increasing evapo-transpirative demand and water availability. In this perspective, each generation of leaf becomes an indicator of physiologic performance, determining the short-term plasticity (acclimation) of a genotype to different environmental conditions. The main objective of this work is to analyse the physiological adjustment by morphological and physiological features of leaves in two contrasting genotypes of Populus nigra L., growing in a common environment. The mesic genotype 58-861 (Northern Italy) reacts to the increasing dry conditions keeping constantly higher values of δ(13)C while the xeric genotype Poli (Southern Italy) shows lower values, despite no significant differences in the gas exchanges. Morphological and stomatal leaf traits were the main drivers of the different behaviour in the two genotypes to face the "temporal" environment, but different from the provenance. In particular the results, especially in the development phases, demonstrate how phenotypic plasticity is evident at seasonal scale, playing a role for the success of an indeterminate-growing species. They could also be generalized for similar experiments and could support further investigation about short-term plasticity. PMID:27295395

  16. Transcriptional and Hormonal Regulation of Gravitropism of Woody Stems in Populus[OPEN

    PubMed Central

    Gerttula, Suzanne; Zinkgraf, Matthew; Lewis, Daniel R.; Brumer, Harry; Hart, Foster; Filkov, Vladimir

    2015-01-01

    Angiosperm trees reorient their woody stems by asymmetrically producing a specialized xylem tissue, tension wood, which exerts a strong contractile force resulting in negative gravitropism of the stem. Here, we show, in Populus trees, that initial gravity perception and response occurs in specialized cells through sedimentation of starch-filled amyloplasts and relocalization of the auxin transport protein, PIN3. Gibberellic acid treatment stimulates the rate of tension wood formation and gravibending and enhances tissue-specific expression of an auxin-responsive reporter. Gravibending, maturation of contractile fibers, and gibberellic acid (GA) stimulation of tension wood formation are all sensitive to transcript levels of the Class I KNOX homeodomain transcription factor-encoding gene ARBORKNOX2 (ARK2). We generated genome-wide transcriptomes for trees in which gene expression was perturbed by gravistimulation, GA treatment, and modulation of ARK2 expression. These data were employed in computational analyses to model the transcriptional networks underlying wood formation, including identification and dissection of gene coexpression modules associated with wood phenotypes, GA response, and ARK2 binding to genes within modules. We propose a model for gravitropism in the woody stem in which the peripheral location of PIN3-expressing cells relative to the cambium results in auxin transport toward the cambium in the top of the stem, triggering tension wood formation, while transport away from the cambium in the bottom of the stem triggers opposite wood formation. PMID:26410302

  17. Degradation of exogenous caffeine by Populus alba and its effects on endogenous caffeine metabolism.

    PubMed

    Pierattini, Erika C; Francini, Alessandra; Raffaelli, Andrea; Sebastiani, Luca

    2016-04-01

    This is the first study reporting the presence of endogenous caffeine, theobromine, and theophylline in all organs of poplar plants. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was used in order to evaluate the uptake, translocation, and metabolism of caffeine-(trimethyl-(13)C) in Populus alba L. Villafranca clone grown in hydroponic conditions. We investigated the remediation of caffeine since it is one of the most widely consumed drugs and it is frequently detected in wastewater treatment plant effluents, surface water, and groundwater worldwide. Our results demonstrated that poplar can absorb and degrade exogenous caffeine without negative effects on plant health. Data showed that concentrations of all endogenous compounds varied depending on caffeine-(trimethyl-(13)C) treatments. In particular, in control conditions, endogenous caffeine, theobromine, and theophylline were mainly distributed in roots. On the other hand, once caffeine-(trimethyl-(13)C) was provided, this compound and its dimethy-(13)C metabolites are mainly localized at leaf level. In conclusion, our results support the possible use of Villafranca clone in association with other water treatment systems in order to complete the process of caffeine remediation.

  18. Differential transcriptome analysis between Populus and its synthesized allotriploids driven by second-division restitution.

    PubMed

    Cheng, Shiping; Huang, Zhen; Li, Yun; Liao, Ting; Suo, Yujing; Zhang, Pingdong; Wang, Jun; Kang, Xiangyang

    2015-12-01

    In this report, we compared transcriptomic differences between a synthetic Populus section Tacamahaca triploid driven by second-division restitution and its parents using a high-throughput RNA-seq method. A total of 4,080 genes were differentially expressed between the high-growth vigor allotriploids (SDR-H) and their parents, and 719 genes were non-additively expressed in SDR-H. Differences in gene expression between the allotriploid and male parent were more significant than those between the allotriploid and female parent, which may be caused by maternal effects. We observed 3,559 differentially expressed genes (DEGs) between the SDR-H and male parent. Notably, the genes were mainly involved in metabolic process, cell proliferation, DNA methylation, cell division, and meristem and developmental growth. Among the 1,056 DEGs between SDR-H and female parent, many genes were associated with metabolic process and carbon utilization. In addition, 1,789 DEGs between high- and low-growth vigor allotriploid were mainly associated with metabolic process, auxin poplar transport, and regulation of meristem growth. Our results indicated that the higher poplar ploidy level can generate extensive transcriptomic diversity compared with its parents. Overall, these results increased our understanding of the driving force for phenotypic variation and adaptation in allopolyploids driven by second-division restitution. PMID:25557321

  19. Digital Gene Expression Analysis of Populus simonii × P. nigra Pollen Germination and Tube Growth

    PubMed Central

    Zhao, Li-Juan; Yuan, Hong-Mei; Guo, Wen-Dong; Yang, Chuan-Ping

    2016-01-01

    Pollen tubes are an ideal model for the study of cell growth and morphogenesis because of their extreme elongation without cell division; however, the genetic basis of pollen germination and tube growth remains largely unknown. Using the Illumina/Solexa digital gene expression system, we identified 13,017 genes (representing 28.3% of the unigenes on the reference genes) at three stages, including mature pollen, hydrated pollen, and pollen tubes of Populus simonii × P. nigra. Comprehensive analysis of P. simonii × P. nigra pollen revealed dynamic changes in the transcriptome during pollen germination and pollen tube growth (PTG). Gene ontology analysis of differentially expressed genes showed that genes involved in functional categories such as catalytic activity, binding, transporter activity, and enzyme regulator activity were overrepresented during pollen germination and PTG. Some highly dynamic genes involved in pollen germination and PTG were detected by clustering analysis. Genes related to some key pathways such as the mitogen-activated protein kinase signaling pathway, regulation of the actin cytoskeleton, calcium signaling, and ubiquitin-mediated proteolysis were significantly changed during pollen germination and PTG. These data provide comprehensive molecular information toward further understanding molecular mechanisms underlying pollen germination and PTG. PMID:27379121

  20. Boron accumulation and toxicity in hybrid poplar (Populus nigra × euramericana).

    PubMed

    Rees, Rainer; Robinson, Brett H; Menon, Manoj; Lehmann, Eberhard; Günthardt-Goerg, Madeleine S; Schulin, Rainer

    2011-12-15

    Poplars accumulate high B concentrations and are thus used for the phytomanagement of B contaminated soils. Here, we performed pot experiments in which Populus nigra × euramericana were grown on a substrate with B concentrations ranging from 13 to 280 mg kg(-1) as H(3)BO(3). Salix viminalis, Brassica juncea, and Lupinus albus were grown under some growing conditions for comparison. Poplar growth was unaffected at soil B treatment levels up to 93 mg kg(-1). Growth was progressively reduced at levels of 168 and 280 mg kg(-1). None of the other species survived at these substrate B levels. At leaf B concentrations <900 mg kg(-1) only <10% of the poplar leaf area showed signs of toxicity. Neutron radiography revealed that chlorotic leaf tissues had B concentrations of 1000-2000 mg kg(-1), while necrotic tissues had >2000 mg kg(-1). Average B concentrations of up to 3500 mg kg(-1) were found in leaves, while spots within leaves had concentrations >7000 mg kg(-1), showing that B accumulation in leaf tissue continued even after the onset of necrosis. The B accumulation ability of P. nigra × euramericana is associated with B hypertolerance in the living tissue and storage of B in dead leaf tissue.

  1. [Coupling effects of water and fertilizer on the biomass of Populus tomentosa seedlings].

    PubMed

    Dong, Wen-yi; Zhao, Yan; Zhang, Zhi-yi; Li, Ji-yue; Nie, Li-shui

    2010-09-01

    Water and fertilizer are the two main factors promoting the fast growth and high-yielding of Populus tomentosa, and thus, to study their coupling effects on the biomass of P. tomentosa seedlings has important practical significance. Taking the P. tomentosa clone 87 seedlings as test materials, a pot experiment with rotary combination design of square regression of three factors with five levels was conducted in the nursery of Beijing Forestry University from March to October 2008 to study the coupling effects of water, fertilizer N, and fertilizer P on the biomass of the seedlings, and a related regressive mathematical model was established. The results showed that water was the main factor affecting the biomass of P. tomentosa seedlings, followed by fertilizer N, and fertilizer P. With the increasing input of the three factors, the biomass of the seedlings increased, but when the input was beyond a certain level, the biomass began to decrease. There was a significant positive interactive effect between water and fertilizer N, but a less interactive effect between fertilizer N and fertilizer P and between water and fertilizer P. In our case, the optimal combination of water and fertilizer was 73.37% of field capacity + 4.14 g x plant(-1) of N fertilization + 1.41 g x plant(-1) of P fertilization, under which, the biomass of P. tomentosa seedlings achieved 68.30 g x plant(-1).

  2. Increasing the productivity of biomass plantations of Populus species and hybrids in the Pacific Northwest. Final report, September 14, 1981--December 31, 1996

    SciTech Connect

    DeBell, D.S.; Harrington, C.A.; Clendenen, G.W.

    1997-08-01

    This final report represents the culmination of eight years of biological research devoted to increasing the productivity of short rotation plantations of Populus trichocarpa and Populus hybrids in the Pacific Northwest. Studies described herein provide an understanding of tree growth, stand development and biomass yield at various spacings, and how patterns thereof differ by Populus clone in monoclonal and polyclonal plantings. Also included is some information about factors related to wind damage in Populus plantings, use of leaf size as a predictor of growth potential, and approaches for estimating tree and stand biomass and biomass growth. The work was accomplished in three research plantations, all established cooperatively with the Washington State Department of Natural Resources (DNR) and located at the DNR Tree Improvement Center near Olympia. The first plantation was established in Spring 1986 to evaluate the highly touted {open_quotes}woodgrass{close_quotes} concept and compare it with more conventional short-rotation management regimes, using two Populus hybrid clones planted at five spacings. Besides providing scientific data to resolve the politicized {open_quotes}wood-grass{close_quotes} dispute, this plantation has furnished excellent data on stand dynamics and woody biomass yield. A second plantation was established at the same time; groups of trees therein received two levels of irrigation and different amounts of four fertilizer amendments, resulting in microsites with diverse moisture and nutrient conditions.

  3. Phylogeny Reconstruction and Hybrid Analysis of Populus (Salicaceae) Based on Nucleotide Sequences of Multiple Single-Copy Nuclear Genes and Plastid Fragments

    PubMed Central

    Dayanandan, Selvadurai; Wang, Dongsheng; Zeng, Yanfei; Zhang, Jianguo

    2014-01-01

    Populus (Salicaceae) is one of the most economically and ecologically important genera of forest trees. The complex reticulate evolution and lack of highly variable orthologous single-copy DNA markers have posed difficulties in resolving the phylogeny of this genus. Based on a large data set of nuclear and plastid DNA sequences, we reconstructed robust phylogeny of Populus using parsimony, maximum likelihood and Bayesian inference methods. The resulting phylogenetic trees showed better resolution at both inter- and intra-sectional level than previous studies. The results revealed that (1) the plastid-based phylogenetic tree resulted in two main clades, suggesting an early divergence of the maternal progenitors of Populus; (2) three advanced sections (Populus, Aigeiros and Tacamahaca) are of hybrid origin; (3) species of the section Tacamahaca could be divided into two major groups based on plastid and nuclear DNA data, suggesting a polyphyletic nature of the section; and (4) many species proved to be of hybrid origin based on the incongruence between plastid and nuclear DNA trees. Reticulate evolution may have played a significant role in the evolution history of Populus by facilitating rapid adaptive radiations into different environments. PMID:25116432

  4. A genomics investigation of partitioning into and among flavonoid-derived condensed tannins for carbon sequestration in Populus

    SciTech Connect

    Harding, Scott, A; Tsai, Chung-jui; Lindroth, Richard, L

    2013-03-24

    The project set out to use comparative (genotype and treatment) and transgenic approaches to investigate the determinants of condensed tannin (CT) accrual and chemical variability in Populus. CT type and amount are thought to effect the decomposition of plant detritus in the soil, and thereby the sequestering of carbon in the soil. The stated objectives were: 1. Genome-wide transcriptome profiling (microarrays) to analyze structural gene, transcription factor and metabolite control of CT partitioning; 2. Transcriptomic (microarray) and chemical analysis of ontogenetic effects on CT and PG partitioning; and 3. Transgenic manipulation of flavonoid biosynthetic pathway genes to modify the control of CT composition. Objective 1: A number of approaches for perturbing CT content and chemistry were tested in Objective 1, and those included nitrogen deficit, leaf wounding, drought, and salicylic acid spraying. Drought had little effect on CTs in the genotypes we used. Plants exhibited unpredictability in their response to salicylic acid spraying, leading us to abandon its use. Reduced plant nitrogen status and leaf wounding caused reproducible and magnitudinally striking increases in leaf CT content. Microarray submissions to NCBI from those experiments are the following: GSE ID 14515: Comparative transcriptomics analysis of Populus leaves under nitrogen limitation: clone 1979. Public on Jan 04, 2010; Contributor(s) Harding SA, Tsai C GSE ID 14893: Comparative transcriptomics analysis of Populus leaves under nitrogen limitation: clone 3200. Public on Feb 19, 2009; Contributor(s) Harding SA, Tsai C GSE ID 16783 Wound-induced gene expression changes in Populus: 1 week; clone RM5. Status Public on Dec 01, 2009; Contributor(s) Harding SA, Tsai C GSE ID 16785 Wound-induced gene expression changes in Populus: 90 hours; clone RM5 Status Public on Dec 01, 2009; Contributor(s) Harding SA, Tsai C Although CT amount changed in response to treatments, CT composition was essentially

  5. Method and apparatus for routing data in an inter-nodal communications lattice of a massively parallel computer system by semi-randomly varying routing policies for different packets

    DOEpatents

    Archer, Charles Jens; Musselman, Roy Glenn; Peters, Amanda; Pinnow, Kurt Walter; Swartz, Brent Allen; Wallenfelt, Brian Paul

    2010-11-23

    A massively parallel computer system contains an inter-nodal communications network of node-to-node links. Nodes vary a choice of routing policy for routing data in the network in a semi-random manner, so that similarly situated packets are not always routed along the same path. Semi-random variation of the routing policy tends to avoid certain local hot spots of network activity, which might otherwise arise using more consistent routing determinations. Preferably, the originating node chooses a routing policy for a packet, and all intermediate nodes in the path route the packet according to that policy. Policies may be rotated on a round-robin basis, selected by generating a random number, or otherwise varied.

  6. Geochemical peculiarities of black poplar leaves (Populus nigra L.) in the sites with heavy metals intensive fallouts

    NASA Astrophysics Data System (ADS)

    Yalaltdinova, Albina; Baranovskaya, Natalya; Rikhvanov, Leonid; Matveenko, Irina

    2013-04-01

    The article deals with the content of 28 chemical elements in the leaves ash of black poplar (Populus nigra L.) growing in Ust-Kamenogorsk city area. It is the major industrial center of Kazakhstan Republic on the territory where the industrial giants of non-ferrous metallurgy and nuclear energy are situated. Comparative analysis with the similar data obtained from leaves ash of Populus nigra L. in Tomsk, Ekibastuz, and Pavlodar cities has revealed that in comparison with other urban areas, leaves ash of black poplar (Populus nigra L.) from Ust-Kamenogorsk city is characterized by elevated concentration rates of Ta, U, Zn, Ag, As, Sb, Br, Sr and Na. Within the city, the sites and areas with abnormal contents of typomorphic pollutants have been revealed. In the central part of the city, in the vicinity of lead-zinc plant and Ulba metallurgical plant, the highest concentrations of Ta, U, Zn, Ag, Au, As, Sb, Cr and Fe were marked. In the northeast, where the titanium-magnesium plant is located, elevated concentrations of Br and Sr were stated. Thus, the impact of major city enterprises which are the main sources of heavy metals is reflected in the element composition. Zn, As, Sb, Ag and Au comes from lead-zinc plant and its refinery plants, while Ulba metallurgical plant can be considered source of Ta and U in the environment, producing tantalum and fuel pellets for nuclear power plants. These companies, due to the current objective circumstances, are located in the central part of the city, have a significant negative effect on the environment and form the risk factors for human health.

  7. Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing

    PubMed Central

    Tong, Chunfa; Li, Huogen; Wang, Ying; Li, Xuran; Ou, Jiajia; Wang, Deyuan; Xu, Houxi; Ma, Chao; Lang, Xianye; Liu, Guangxin; Zhang, Bo; Shi, Jisen

    2016-01-01

    Although numerous linkage maps have been constructed in the genus Populus, they are typically sparse and thus have limited applications due to low throughput of traditional molecular markers. Restriction-site associated DNA sequencing (RADSeq) technology allows us to identify a large number of single nucleotide polymorphisms (SNP) across genomes of many individuals in a fast and cost-effective way, and makes it possible to construct high-density genetic linkage maps. We performed RADSeq for 299 progeny and their two parents in an F1 hybrid population generated by crossing the female Populus deltoides ‘I-69’ and male Populus simonii ‘L3’. A total of 2,545 high quality SNP markers were obtained and two parent-specific linkage maps were constructed. The female genetic map contained 1601 SNPs and 20 linkage groups, spanning 4,249.12 cM of the genome with an average distance of 2.69 cM between adjacent markers, while the male map consisted of 940 SNPs and also 20 linkage groups with a total length of 3,816.24 cM and an average marker interval distance of 4.15 cM. Finally, our analysis revealed that synteny and collinearity are highly conserved between the parental linkage maps and the reference genome of P. trichocarpa. We demonstrated that RAD sequencing is a powerful technique capable of rapidly generating a large number of SNPs for constructing genetic maps in outbred forest trees. The high-quality linkage maps constructed here provided reliable genetic resources to facilitate locating quantitative trait loci (QTLs) that control growth and wood quality traits in the hybrid population. PMID:26964097

  8. Industrial Robustness: Understanding the Mechanism of Tolerance for the Populus Hydrolysate-Tolerant Mutant Strain of Clostridium thermocellum

    PubMed Central

    Linville, Jessica L.; Rodriguez, Miguel; Land, Miriam; Syed, Mustafa H.; Engle, Nancy L.; Tschaplinski, Timothy J.; Mielenz, Jonathan R.; Cox, Chris D.

    2013-01-01

    Background An industrially robust microorganism that can efficiently degrade and convert lignocellulosic biomass into ethanol and next-generation fuels is required to economically produce future sustainable liquid transportation fuels. The anaerobic, thermophilic, cellulolytic bacterium Clostridium thermocellum is a candidate microorganism for such conversions but it, like many bacteria, is sensitive to potential toxic inhibitors developed in the liquid hydrolysate produced during biomass processing. Microbial processes leading to tolerance of these inhibitory compounds found in the pretreated biomass hydrolysate are likely complex and involve multiple genes. Methodology/Principal Findings In this study, we developed a 17.5% v/v Populus hydrolysate tolerant mutant strain of C. thermocellum by directed evolution. The genome of the wild type strain, six intermediate population samples and seven single colony isolates were sequenced to elucidate the mechanism of tolerance. Analysis of the 224 putative mutations revealed 73 high confidence mutations. A longitudinal analysis of the intermediate population samples, a pan-genomic analysis of the isolates, and a hotspot analysis revealed 24 core genes common to all seven isolates and 8 hotspots. Genetic mutations were matched with the observed phenotype through comparison of RNA expression levels during fermentation by the wild type strain and mutant isolate 6 in various concentrations of Populus hydrolysate (0%, 10%, and 17.5% v/v). Conclusion/Significance The findings suggest that there are multiple mutations responsible for the Populus hydrolysate tolerant phenotype resulting in several simultaneous mechanisms of action, including increases in cellular repair, and altered energy metabolism. To date, this study provides the most comprehensive elucidation of the mechanism of tolerance to a pretreated biomass hydrolysate by C. thermocellum. These findings make important contributions to the development of industrially

  9. The absolute configuration of salicortin, HCH-salicortin and tremulacin from Populus trichocarpa × deltoides Beaupré.

    PubMed

    Feistel, Felix; Paetz, Christian; Lorenz, Sybille; Schneider, Bernd

    2015-01-01

    The absolute configuration of salicortin, HCH-salicortin and tremulacin, isolated from leaves of Populus trichocarpa × deltoides Beaupré, was determined by comparing spectroscopic data of these compounds with those of idescarpin, isolated from leaves of Idesia polycarpa. All compounds were characterized by nuclear magnetic resonance spectroscopy, high-resolution mass spectrometry, and circular dichroism spectroscopy. It was found that the hydroxy cyclohexenonoyl (HCH) moiety in all compounds is (S)-configured. In addition, it was shown that leaves of Idesia polycarpa contain high amounts of (-)-idescarpin (1.1%, based on dry weight). PMID:25830788

  10. Genetic variations and miRNA-target interactions contribute to natural phenotypic variations in Populus.

    PubMed

    Chen, Jinhui; Xie, Jianbo; Chen, Beibei; Quan, Mingyang; Li, Ying; Li, Bailian; Zhang, Deqiang

    2016-10-01

    Variation in regulatory factors, including microRNAs (miRNAs), contributes to variation in quantitative and complex traits. However, in plants, variants in miRNAs and their target genes that contribute to natural phenotypic variation, and the underlying regulatory networks, remain poorly characterized. We investigated the associations and interactions of single-nucleotide polymorphisms (SNPs) in miRNAs and their target genes with phenotypes in 435 individuals from a natural population of Populus. We used RNA-seq to identify 217 miRNAs differentially expressed in a tension wood system, and identified 1196 candidate target genes; degradome sequencing confirmed 60 of the target sites. In addition, 72 miRNA-target pairs showed significant co-expression. Gene ontology (GO) term analysis showed that most of the genes in the co-regulated pairs participate in biological regulation. Genome resequencing found 5383 common SNPs (frequency ≥ 0.05) in 139 miRNAs and 31 037 SNPs in 819 target genes. Single-SNP association analyses identified 232 significant associations between wood traits (P ≤ 0.05) and SNPs in 102 miRNAs and 1387 associations with 478 target genes. Among these, 102 miRNA-target pairs associated with the same traits. Multi-SNP associations found 102 epistatic pairs associated with traits. Furthermore, a reconstructed regulatory network contained 12 significantly co-expressed pairs, including eight miRNAs and nine targets associated with traits. Lastly, both expression and genetic association showed that miR156i, miR156j, miR396a and miR6445b were involved in the formation of tension wood. This study shows that variants in miRNAs and target genes contribute to natural phenotypic variation and annotated roles and interactions of miRNAs and their target genes by genetic association analysis. PMID:27265357

  11. Temperature responses of photosynthesis and respiration in Populus balsamifera L.: acclimation versus adaptation.

    PubMed

    Silim, Salim N; Ryan, Natalie; Kubien, David S

    2010-04-01

    To examine the role of acclimation versus adaptation on the temperature responses of CO(2) assimilation, we measured dark respiration (R(n)) and the CO(2) response of net photosynthesis (A) in Populus balsamifera collected from warm and cool habitats and grown at warm and cool temperatures. R(n) and the rate of photosynthetic electron transport (J) are significantly higher in plants grown at 19 versus 27 degrees C; R(n) is not affected by the native thermal habitat. By contrast, both the maximum capacity of rubisco (V(cmax)) and A are relatively insensitive to growth temperature, but both parameters are slightly higher in plants from cool habitats. A is limited by rubisco capacity from 17-37 degrees C regardless of growth temperature, and there is little evidence for an electron-transport limitation. Stomatal conductance (g(s)) is higher in warm-grown plants, but declines with increasing measurement temperature from 17 to 37 degrees C, regardless of growth temperature. The mesophyll conductance (g(m)) is relatively temperature insensitive below 25 degrees C, but g(m) declines at 37 degrees C in cool-grown plants. Plants acclimated to cool temperatures have increased R(n)/A, but this response does not differ between warm- and cool-adapted populations. Primary carbon metabolism clearly acclimates to growth temperature in P. balsamifera, but the ecotypic differences in A suggest that global warming scenarios might affect populations at the northern and southern edges of the boreal forest in different ways.

  12. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

    SciTech Connect

    Muchero, Wellington; Guo, Jianjun; Difazio, Stephen P.; Chen, Jay; Ranjan, Priya; Slavov, Gancho; Gunter, Lee E.; Jawdy, Sara; Bryan, Anthony C.; Sykes, Robert; Ziebell, Angela L.; Klapste, Jaroslav; Porth, Ilga; Skyba, Oleksandr; Unda, Faride; El-Kassaby, Yousry; Douglas, Carl; Mansfield, Shawn; Martin, Joel; Schackwitz, Wendy; Evans, Luke M.; Czarnecki, Olaf; Tuskan, Gerald A.

    2015-01-23

    We report the identification of six genetic loci and the allelic-variants associated with Populus cell wall phenotypes determined independently using pyrolysis Molecular Beam Mass Spectrometry (pyMBMS), saccharification assay and wet chemistry in two partially overlapping populations of P. trichocarpa genotypes sampled from multiple environments in the Pacific Northwest of North America. All 6 variants co-located with a quantitative trait locus (QTL) hotspot on chromosome XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6- carbon sugars identified in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree. Genomic intervals containing an amino acid transporter, a MYB transcription factor, an angustifolia CtBP transcription factor, a copper transport protein ATOX1-related, a Ca2+ transporting ATPase and a protein kinase were identified within 5 QTL regions. Each interval contained single nucleotide polymorphisms (SNPs) that were significantly associated to cell-wall phenotypes, with associations exceeding the chromosome-wise Bonferroni-adjusted p-values in at least one environment. cDNA sequencing for allelic variants of 3 of the 6 genes identified polymorphisms leading to premature stop codons in the MYB transcription factor and protein kinase. On the other hand, variants of the Angustifolia CtBP transcription factor exhibited a polyglutamine (PolyQ) length polymorphism. Results from transient protoplast assays suggested that each of the polymorphisms conferred allelic differences in activation of cellulose, hemicelluloses and lignin pathway marker genes, with truncated and short PolyQ alleles exhibiting significantly reduced marker gene activation. Genes identified in this study represent novel targets for reducing cell wall recalcitrance for lignocellulosic biofuels production using plant biomass.

  13. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

    DOE PAGESBeta

    Muchero, Wellington; Guo, Jianjun; Difazio, Stephen P.; Chen, Jay; Ranjan, Priya; Slavov, Gancho; Gunter, Lee E.; Jawdy, Sara; Bryan, Anthony C.; Sykes, Robert; et al

    2015-01-23

    We report the identification of six genetic loci and the allelic-variants associated with Populus cell wall phenotypes determined independently using pyrolysis Molecular Beam Mass Spectrometry (pyMBMS), saccharification assay and wet chemistry in two partially overlapping populations of P. trichocarpa genotypes sampled from multiple environments in the Pacific Northwest of North America. All 6 variants co-located with a quantitative trait locus (QTL) hotspot on chromosome XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6- carbon sugars identified in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree. Genomic intervals containing an amino acid transporter, a MYB transcriptionmore » factor, an angustifolia CtBP transcription factor, a copper transport protein ATOX1-related, a Ca2+ transporting ATPase and a protein kinase were identified within 5 QTL regions. Each interval contained single nucleotide polymorphisms (SNPs) that were significantly associated to cell-wall phenotypes, with associations exceeding the chromosome-wise Bonferroni-adjusted p-values in at least one environment. cDNA sequencing for allelic variants of 3 of the 6 genes identified polymorphisms leading to premature stop codons in the MYB transcription factor and protein kinase. On the other hand, variants of the Angustifolia CtBP transcription factor exhibited a polyglutamine (PolyQ) length polymorphism. Results from transient protoplast assays suggested that each of the polymorphisms conferred allelic differences in activation of cellulose, hemicelluloses and lignin pathway marker genes, with truncated and short PolyQ alleles exhibiting significantly reduced marker gene activation. Genes identified in this study represent novel targets for reducing cell wall recalcitrance for lignocellulosic biofuels production using plant biomass.« less

  14. Enzymatic characterization of two acetyl-CoA synthetase genes from Populus trichocarpa.

    PubMed

    Cao, Shan; Li, Hui; Yao, Xiaoyun; Li, Lihong; Jiang, Luyao; Zhang, Qiang; Zhang, Jiaxue; Liu, Di; Lu, Hai

    2016-01-01

    The acetyl-CoA synthetase (ACS) family is a subfamily of adenylate-forming enzymes, which has a close evolutionary relationship with the 4-coumarate:CoA ligase (4CL) family. In this study, two ACS genes were cloned from Populus trichocarpa and were named PtrACS1 and PtrACS2. Bioinformatics characterization of PtrACS1 and PtrACS2 showed that they contained the key ACS residues and a putative peroxisome targeting sequence 1 (PTS1) at the end of the C-terminal sequence. Real-time PCR results showed that PtrACS1 and PtrACS2 were expressed in the phloem, xylem, leaves, and roots of one-year-old P. trichocarpa, but were expressed primarily in the leaves. The ACS enzyme activity was higher in leaves than other tissues in P. trichocarpa. Two overexpressed recombinant proteins showed no catalytic activity toward the substrates of 4CL, but did have notable catalytic activity toward sodium acetate and substrates of ACS. The relative activities of PtrACS1 and PtrACS2 were 194.16 ± 11.23 and 422.25 ± 21.69 μM min(-1) mg(-1), respectively. The K m and V max of PtrACS1 were 0.25 mM and 698.85 μM min(-1) mg(-1), while those for PtrACS2 were 0.72 mM and 245.96 μM min(-1) mg(-1), respectively. Our results revealed that both proteins belong to the ACS family, and provide a theoretical foundation for the identification and functional analysis of members of the adenylate-forming enzyme superfamily. PMID:27390658

  15. Tubulin perturbation leads to unexpected cell wall modifications and affects stomatal behaviour in Populus.

    PubMed

    Swamy, Prashant S; Hu, Hao; Pattathil, Sivakumar; Maloney, Victoria J; Xiao, Hui; Xue, Liang-Jiao; Chung, Jeng-Der; Johnson, Virgil E; Zhu, Yingying; Peter, Gary F; Hahn, Michael G; Mansfield, Shawn D; Harding, Scott A; Tsai, Chung-Jui

    2015-10-01

    Cortical microtubules are integral to plant morphogenesis, cell wall synthesis, and stomatal behaviour, presumably by governing cellulose microfibril orientation. Genetic manipulation of tubulins often leads to abnormal plant development, making it difficult to probe additional roles of cortical microtubules in cell wall biogenesis. Here, it is shown that expressing post-translational C-terminal modification mimics of α-tubulin altered cell wall characteristics and guard cell dynamics in transgenic Populus tremula x alba that otherwise appear normal. 35S promoter-driven transgene expression was high in leaves but unusually low in xylem, suggesting high levels of tubulin transgene expression were not tolerated in wood-forming tissues during regeneration of transformants. Cellulose, hemicellulose, and lignin contents were unaffected in transgenic wood, but expression of cell wall-modifying enzymes, and extractability of lignin-bound pectin and xylan polysaccharides were increased in developing xylem. The results suggest that pectin and xylan polysaccharides deposited early during cell wall biogenesis are more sensitive to subtle tubulin perturbation than cellulose and matrix polysaccharides deposited later. Tubulin perturbation also affected guard cell behaviour, delaying drought-induced stomatal closure as well as light-induced stomatal opening in leaves. Pectins have been shown to confer cell wall flexibility critical for reversible stomatal movement, and results presented here are consistent with microtubule involvement in this process. Taken together, the data show the value of growth-compatible tubulin perturbations for discerning microtubule functions, and add to the growing body of evidence for microtubule involvement in non-cellulosic polysaccharide assembly during cell wall biogenesis.

  16. A Novel Moderate Constitutive Promoter Derived from Poplar (Populus tomentosa Carrière)

    PubMed Central

    Chen, Zhong; Wang, Jia; Ye, Mei-Xia; Li, Hao; Ji, Le-Xiang; Li, Ying; Cui, Dong-Qing; Liu, Jun-Mei; An, Xin-Min

    2013-01-01

    A novel sequence that functions as a promoter element for moderate constitutive expression of transgenes, designated as the PtMCP promoter, was isolated from the woody perennial Populus tomentosa. The PtMCP promoter was fused to the GUS reporter gene to characterize its expression pattern in different species. In stable Arabidopsis transformants, transcripts of the GUS reporter gene could be detected by RT-PCR in the root, stem, leaf, flower and silique. Further histochemical and fluorometric GUS activity assays demonstrated that the promoter could direct transgene expression in all tissues and organs, including roots, stems, rosette leaves, cauline leaves and flowers of seedlings and maturing plants. Its constitutive expression pattern was similar to that of the CaMV35S promoter, but the level of GUS activity was significantly lower than in CaMV35S promoter::GUS plants. We also characterized the promoter through transient expression in transgenic tobacco and observed similar expression patterns. Histochemical GUS staining and quantitative analysis detected GUS activity in all tissues and organs of tobacco, including roots, stems, leaves, flower buds and flowers, but GUS activity in PtMCP promoter::GUS plants was significantly lower than in CaMV35S promoter::GUS plants. Our results suggested that the PtMCP promoter from poplar is a constitutive promoter with moderate activity and that its function is presumably conserved in different species. Therefore, the PtMCP promoter may provide a practical choice to direct moderate level constitutive expression of transgenes and could be a valuable new tool in plant genetic engineering. PMID:23507754

  17. Tubulin perturbation leads to unexpected cell wall modifications and affects stomatal behaviour in Populus

    PubMed Central

    Swamy, Prashant S.; Hu, Hao; Pattathil, Sivakumar; Maloney, Victoria J.; Xiao, Hui; Xue, Liang-Jiao; Chung, Jeng-Der; Johnson, Virgil E.; Zhu, Yingying; Peter, Gary F.; Hahn, Michael G.; Mansfield, Shawn D.; Harding, Scott A.; Tsai, Chung-Jui

    2015-01-01

    Cortical microtubules are integral to plant morphogenesis, cell wall synthesis, and stomatal behaviour, presumably by governing cellulose microfibril orientation. Genetic manipulation of tubulins often leads to abnormal plant development, making it difficult to probe additional roles of cortical microtubules in cell wall biogenesis. Here, it is shown that expressing post-translational C-terminal modification mimics of α-tubulin altered cell wall characteristics and guard cell dynamics in transgenic Populus tremula x alba that otherwise appear normal. 35S promoter-driven transgene expression was high in leaves but unusually low in xylem, suggesting high levels of tubulin transgene expression were not tolerated in wood-forming tissues during regeneration of transformants. Cellulose, hemicellulose, and lignin contents were unaffected in transgenic wood, but expression of cell wall-modifying enzymes, and extractability of lignin-bound pectin and xylan polysaccharides were increased in developing xylem. The results suggest that pectin and xylan polysaccharides deposited early during cell wall biogenesis are more sensitive to subtle tubulin perturbation than cellulose and matrix polysaccharides deposited later. Tubulin perturbation also affected guard cell behaviour, delaying drought-induced stomatal closure as well as light-induced stomatal opening in leaves. Pectins have been shown to confer cell wall flexibility critical for reversible stomatal movement, and results presented here are consistent with microtubule involvement in this process. Taken together, the data show the value of growth-compatible tubulin perturbations for discerning microtubule functions, and add to the growing body of evidence for microtubule involvement in non-cellulosic polysaccharide assembly during cell wall biogenesis. PMID:26246616

  18. Genetic variations and miRNA-target interactions contribute to natural phenotypic variations in Populus.

    PubMed

    Chen, Jinhui; Xie, Jianbo; Chen, Beibei; Quan, Mingyang; Li, Ying; Li, Bailian; Zhang, Deqiang

    2016-10-01

    Variation in regulatory factors, including microRNAs (miRNAs), contributes to variation in quantitative and complex traits. However, in plants, variants in miRNAs and their target genes that contribute to natural phenotypic variation, and the underlying regulatory networks, remain poorly characterized. We investigated the associations and interactions of single-nucleotide polymorphisms (SNPs) in miRNAs and their target genes with phenotypes in 435 individuals from a natural population of Populus. We used RNA-seq to identify 217 miRNAs differentially expressed in a tension wood system, and identified 1196 candidate target genes; degradome sequencing confirmed 60 of the target sites. In addition, 72 miRNA-target pairs showed significant co-expression. Gene ontology (GO) term analysis showed that most of the genes in the co-regulated pairs participate in biological regulation. Genome resequencing found 5383 common SNPs (frequency ≥ 0.05) in 139 miRNAs and 31 037 SNPs in 819 target genes. Single-SNP association analyses identified 232 significant associations between wood traits (P ≤ 0.05) and SNPs in 102 miRNAs and 1387 associations with 478 target genes. Among these, 102 miRNA-target pairs associated with the same traits. Multi-SNP associations found 102 epistatic pairs associated with traits. Furthermore, a reconstructed regulatory network contained 12 significantly co-expressed pairs, including eight miRNAs and nine targets associated with traits. Lastly, both expression and genetic association showed that miR156i, miR156j, miR396a and miR6445b were involved in the formation of tension wood. This study shows that variants in miRNAs and target genes contribute to natural phenotypic variation and annotated roles and interactions of miRNAs and their target genes by genetic association analysis.

  19. Physiological and morphological responses of Tamarix ramosissima and Populus euphratica to altered groundwater availability.

    PubMed

    Li, J; Yu, B; Zhao, C; Nowak, Robert S; Zhao, Z; Sheng, Y; Li, J

    2013-01-01

    Riparian plants in arid areas are subject to frequent hydrological fluctuations induced through natural flow variation and water use by humans. Although many studies have focused on the success of Tamarix ramosissima Ledeb. in its invaded ranges, its major competitor in its home range, Populus euphratica Oliv., historically has dominated riparian forests where both species occur naturally. Thus, identifying ecophysiological differences between T. ramosissima and its co-evolved competitor under varying hydrological conditions may help us understand how flow regimes affect dominance in its home range and promote invasion in new ranges. We examined ecophysiological responses of T. ramosissima and P. euphratica, which are both native to the Tarim River Basin, northwest China, to experimental alterations in groundwater. Seedlings of both species were grown in lysimeters, first under well-watered conditions and then exposed to different groundwater treatments: inundation, drought, and relatively shallow, moderate and deep groundwater. Under inundation, T. ramosissima showed little growth whereas P. euphratica died after ~45 days. Droughted seedlings of both species suffered from considerable water stress evidenced by slow growth, decreased total leaf area and specific leaf area, and decreased xylem water potential (ψ), maximum photosynthetic rate and carboxylation efficiency. Both species had better ecophysiological performances under shallow and moderate groundwater conditions. When groundwater declined below rooting depth, seedlings of both species initially experienced decreased ψ, but ψ of T. ramosissima recovered late in the experiment whereas P. euphratica maintained decreased ψ. This ability of T. ramosissima to recover from water deficit might result from its rapid root elongation and subsequent ability to acquire groundwater, which in turn likely provides ecophysiological advantages over P. euphratica. Our results suggest that recent groundwater declines

  20. Streptomyces indoligenes sp. nov., isolated from rhizosphere soil of Populus euphratica.

    PubMed

    Luo, Xiaoxia; Sun, Yong; Xie, Sinan; Wan, Chuanxing; Zhang, Lili

    2016-06-01

    A novel actinobacterium, designated TRM 43006T, was isolated from the rhizosphere soil of Populus euphratica in Xinjiang Province, north-west China. Phylogenetic and phenotypic analysis demonstrated that strain TRM 43006T belongs to the genus Streptomyces. The strain was aerobic and Gram-stain-positive; the aerial mycelium branched monopodially, forming chains of arthrospores. The spores were oval to cylindrical with smooth surfaces. The whole-cell sugar pattern of strain TRM 43006T consisted of xylose, mannitol, galactose and ribose. The menaquinones were MK-9(H6), MK-9(H8) and MK-9(H10). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannosides and four unknown phospholipids. Major fatty acids were iso-C16 : 0, iso-C16 : 1, iso-C14 : 0 and anteiso-C15 : 0. The G+C content of the genomic DNA was 69.0 mol%. Comparative 16S rRNA gene sequence analysis indicated that strain TRM 43006T was phylogenetically most closely related to Streptomyces roseolilacinus NBRC 12815T (98.6 % similarity) and Streptomycessudanensis SD 504T (98.3 %); however, DNA-DNA hybridization studies between S. roseolilacinus NBRC 12815T, S. sudanensis SD 504T and TRM 43006T showed only 30.28 and 30.65  % relatedness, respectively. Based on the evidence from this polyphasic study, strain TRM 43006T represents a novel species of the genus Streptomyces, for which the name Streptomyces indoligenes sp. nov. is proposed. The type strain is TRM 43006T (=KCTC 39611T=CCTCC AA 2015010T). PMID:27031169

  1. Population genomic analysis of gibberellin-responsive long non-coding RNAs in Populus.

    PubMed

    Tian, Jiaxing; Song, Yuepeng; Du, Qingzhang; Yang, Xiaohui; Ci, Dong; Chen, Jinhui; Xie, Jianbo; Li, Bailian; Zhang, Deqiang

    2016-04-01

    Long non-coding RNAs (lncRNAs) participate in a wide range of biological processes, but lncRNAs in plants remain largely unknown; in particular, we lack a systematic identification of plant lncRNAs involved in hormone responses. Moreover, allelic variation in lncRNAs remains poorly characterized at a large scale. Here, we conducted high-throughput RNA-sequencing of leaves from control and gibberellin (GA)-treated Populus tomentosa and identified 7655 reliably expressed lncRNAs. Among the 7655 lncRNAs, the levels of 410 lncRNAs changed in response to GA. Seven GA-responsive lncRNAs were predicted to be putative targets of 18 miRNAs, and one GA-responsive lncRNA (TCONS_00264314) was predicted to be a target mimic of ptc-miR6459b. Computational analysis predicted 939 potential cis-regulated target genes and 965 potential trans-regulated target genes for GA-responsive lncRNAs. Functional annotation of these potential target genes showed that they participate in many different biological processes, including auxin signal transduction and synthesis of cellulose and pectin, indicating that GA-responsive lncRNAs may influence growth and wood properties. Finally, single nucleotide polymorphism (SNP)-based association analysis showed that 112 SNPs from 52 GA-responsive lncRNAs and 1014 SNPs from 296 potential target genes were significantly associated with growth and wood properties. Epistasis analysis also provided evidence for interactions between lncRNAs and their potential target genes. Our study provides a comprehensive view of P. tomentosa lncRNAs and offers insights into the potential functions and regulatory interactions of GA-responsive lncRNAs, thus forming the foundation for future functional analysis of GA-responsive lncRNAs in P. tomentosa.

  2. Biomass accumulation and soil nitrogen availability in an 87-year-old Populus grandidentata chronosequence

    USGS Publications Warehouse

    White, L.L.; Zak, D.R.; Barnes, B.V.

    2004-01-01

    The Upper Lake States region is marked by major disturbances of fire and logging over 100 years ago that created a landscape mosaic of early successional forests. Given the intimate link between soil N availability and forest growth in this region, it is important to understand how temporal changes in soil N constrain the rate at which forest biomass accumulates following a stand-destroying disturbance. Bigtooth aspen (Populus grandidentata Michx.) currently dominates sites where primarily old-growth pine-hemlock-oak forests once thrived, which provides an opportunity to observe nearly 100 years of succession following severe disturbance. In this study, we examine the relationship between soil N availability and biomass accrual in a series of plots undergoing secondary succession following logging and burning. Our results demonstrate that total aboveground biomass and nitrogen accrual patterns are strongly and positively related on a highly disturbed, bigtooth aspen-dominated ecosystem in northern Lower Michigan. Nitrogen mineralization and nitrification were highest immediately following disturbance, and then decreased over the next approximately 20 years of succession. Following this short-term decrease, these processes increased and attained a maximum value after 70 years of forest succession. Understory biomass accumulation showed the opposite trend of nutrient availability, with highest values during the first 20 years of succession, followed by a dramatic decrease for the next 70 years. Understory biomass began to decrease as plants grew into the overstory or died. Total aboveground biomass was correlated with N mineralization (r=0.894; P=0.041) and nitrification (r=0.782; P=0.118) and appears to be increasing steadily to some maximum that has not yet been reached. ?? 2003 Elsevier B.V. All rights reserved.

  3. Evapotranspiration in a cottonwood (Populus fremontii) restoration plantation estimated by sap flow and remote sensing methods

    USGS Publications Warehouse

    Nagler, P.; Jetton, A.; Fleming, J.; Didan, K.; Glenn, E.; Erker, J.; Morino, K.; Milliken, J.; Gloss, S.

    2007-01-01

    Native tree plantations have been proposed for the restoration of wildlife habitat in human-altered riparian corridors of western U.S. rivers. Evapotranspiration (ET) by riparian vegetation is an important, but poorly quantified, term in river water budgets. Native tree restoration plots will potentially increase ET. We used sap flow sensors and satellite imagery to estimate ET in a 8 ha, cottonwood (Populus fremontii) restoration plot on the Lower Colorado River. Biometric methods were used to scale leaf area to whole trees and stands of trees. This technique was used to validate our estimates of ET obtained by scaling from branch level to stand (or plot) level measurements of ET. Cottonwood trees used 6-10 mm day-1 of water during the peak of the growing season as determined by sap flow sensors, and annual rates scaled by time-series MODIS satellite imagery were approximately 1.2 m year-1. Although irrigation was not quantified, the field had been flood irrigated at 2 week intervals during the 3 years prior to the study, receiving approximately 2 m year-1 of water. A frequency-domain electromagnetic induction survey of soil moisture content showed that the field was saturated (26-28% gravimetric water content) at the 90-150 cm soil depth under the field. Trees were apparently rooted into the saturated soil, and considerable saving of water could potentially be achieved by modifying the irrigation regime to take into account that cottonwoods are phreatophytes. The study showed that cottonwood ET can be monitored by remote sensing methods calibrated with ground measurements with an accuracy or uncertainty of 20-30% in western riparian corridors. ?? 2007 Elsevier B.V. All rights reserved.

  4. The applications of populus fiber in removal of Cr(VI) from aqueous solution

    NASA Astrophysics Data System (ADS)

    Li, Miaomiao; Gong, Yumei; Lyu, Aichao; Liu, Yuanfa; Zhang, Hong

    2016-10-01

    The surface modification of natural materials to be applied in removal of Cr(VI) from aqueous solutions has attracted much attention. A natural sorbent for Cr(VI) based on natural populus fibers (PF) is prepared by transforming the cyano groups (AN) in polyacrylonitriles (PAN) grafted from PF into amidoxime groups (AO), which has strong ability to attract and chelate heavy metal ions. The prepared sorbent is characterized by Fourier Transform Infrared Spectra (FT-IR), thermogravimetric analysis (TGA), solid-state nuclear magnetic resonance (13C NMR) and scanning electron microscope (SEM). As potassium dichromate solution (K2Cr2O7) is used as a target solution for detecting adsorption capacity of the sorbent, the adsorption kinetics of the sorbent for chromiun is consistent with the pseudo-second-order kinetic model by analyzing the adsorption amount as a function of the sorbent dispersed duration in solution at pH = 2. The expected adsorption mechanism is that the Cr(VI) in anionic ions Cr2O72- and HCrO4- are adsorbed through electrostatic attraction but when Cr(VI) is reduced to Cr(III) by AO, the electronegative nitrogen and oxygen in AO chelate it through coordination bond. The as-prepared PF derivant with high adsorption efficiency of chromium 180.5 mg/g (3.47 mmol/g), low cost, reusability and greenly preparation process suggests that the development of natural PF as a sorbent in removal of Cr(VI) from aqueous solutions is a destined significant approach.

  5. Physiological and morphological responses of Tamarix ramosissima and Populus euphratica to altered groundwater availability.

    PubMed

    Li, J; Yu, B; Zhao, C; Nowak, Robert S; Zhao, Z; Sheng, Y; Li, J

    2013-01-01

    Riparian plants in arid areas are subject to frequent hydrological fluctuations induced through natural flow variation and water use by humans. Although many studies have focused on the success of Tamarix ramosissima Ledeb. in its invaded ranges, its major competitor in its home range, Populus euphratica Oliv., historically has dominated riparian forests where both species occur naturally. Thus, identifying ecophysiological differences between T. ramosissima and its co-evolved competitor under varying hydrological conditions may help us understand how flow regimes affect dominance in its home range and promote invasion in new ranges. We examined ecophysiological responses of T. ramosissima and P. euphratica, which are both native to the Tarim River Basin, northwest China, to experimental alterations in groundwater. Seedlings of both species were grown in lysimeters, first under well-watered conditions and then exposed to different groundwater treatments: inundation, drought, and relatively shallow, moderate and deep groundwater. Under inundation, T. ramosissima showed little growth whereas P. euphratica died after ~45 days. Droughted seedlings of both species suffered from considerable water stress evidenced by slow growth, decreased total leaf area and specific leaf area, and decreased xylem water potential (ψ), maximum photosynthetic rate and carboxylation efficiency. Both species had better ecophysiological performances under shallow and moderate groundwater conditions. When groundwater declined below rooting depth, seedlings of both species initially experienced decreased ψ, but ψ of T. ramosissima recovered late in the experiment whereas P. euphratica maintained decreased ψ. This ability of T. ramosissima to recover from water deficit might result from its rapid root elongation and subsequent ability to acquire groundwater, which in turn likely provides ecophysiological advantages over P. euphratica. Our results suggest that recent groundwater declines

  6. Streptomyces indoligenes sp. nov., isolated from rhizosphere soil of Populus euphratica.

    PubMed

    Luo, Xiaoxia; Sun, Yong; Xie, Sinan; Wan, Chuanxing; Zhang, Lili

    2016-06-01

    A novel actinobacterium, designated TRM 43006T, was isolated from the rhizosphere soil of Populus euphratica in Xinjiang Province, north-west China. Phylogenetic and phenotypic analysis demonstrated that strain TRM 43006T belongs to the genus Streptomyces. The strain was aerobic and Gram-stain-positive; the aerial mycelium branched monopodially, forming chains of arthrospores. The spores were oval to cylindrical with smooth surfaces. The whole-cell sugar pattern of strain TRM 43006T consisted of xylose, mannitol, galactose and ribose. The menaquinones were MK-9(H6), MK-9(H8) and MK-9(H10). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannosides and four unknown phospholipids. Major fatty acids were iso-C16 : 0, iso-C16 : 1, iso-C14 : 0 and anteiso-C15 : 0. The G+C content of the genomic DNA was 69.0 mol%. Comparative 16S rRNA gene sequence analysis indicated that strain TRM 43006T was phylogenetically most closely related to Streptomyces roseolilacinus NBRC 12815T (98.6 % similarity) and Streptomycessudanensis SD 504T (98.3 %); however, DNA-DNA hybridization studies between S. roseolilacinus NBRC 12815T, S. sudanensis SD 504T and TRM 43006T showed only 30.28 and 30.65  % relatedness, respectively. Based on the evidence from this polyphasic study, strain TRM 43006T represents a novel species of the genus Streptomyces, for which the name Streptomyces indoligenes sp. nov. is proposed. The type strain is TRM 43006T (=KCTC 39611T=CCTCC AA 2015010T).

  7. Genome anchored QTLs for biomass productivity in Hybrid Populus: Heterosis and detection across Contrasting Environments.

    SciTech Connect

    Muchero, Wellington; Sewell, Mitchell; Gunter, Lee E; Tschaplinski, Timothy J; Yin, Tongming; DiFazio, Steven P; Tuskan, Gerald A

    2013-01-01

    Traits related to biomass production were analyzed for the presence of quantitative trait loci (QTLs) in an interspecific F2 population derived from an outbred Populus trichocarpa P. deltoides parental cross. Three years of phenotypic data for stem growth traits (height and diameter) were collected from two parental, two F1 and 339 F2 trees in a clonal trial replicated both within and among two environmentally contrasting sites in the North American Pacific Northwest. A genetic linkage map comprised of 841 SSR, AFLP, and RAPD markers and phenotypic data from 310 progeny were used to identify genomic regions harboring QTL using the Multiple-QTL Model (MQM) package of the statistical program MapQTL 6. A total of twelve QTLs, nine putative and three suggestive, were identified with eight of these being identified at both sites in at least one experiment. Of these, three putative QTL BM-1, BM-2, BM-7, on LGs I, II, and XIV, respectively, were identified in all three years for both height and diameter. Two QTLs BM-2 and BM-7, on LG II and XIV, respectively, exhibited significant evidence of over-dominance in all three years for both traits. Conversely a QTL on BM-6 LG XIII exhibited out-breeding depression in two years for both height and diameter. The remaining nine QTLs showed difference levels of dominance and additive effects. Seven of the nine QTL were successfully anchored and QTL peak positions were estimated for each one on the P. trichocarpa genome assembly using flanking SSR markers with known physical positions positions. QTL BM-7 on LG XIV had been anchored on the genome assembly in a previous study, therefore eight QTLs identified in this study were assigned genome assembly positions. Physical distances encompassed by each QTL regions ranged from 1.3 to 8.8 Mb.

  8. Identification and characterization of nuclear genes involved in photosynthesis in Populus

    PubMed Central

    2014-01-01

    Background The gap between the real and potential photosynthetic rate under field conditions suggests that photosynthesis could potentially be improved. Nuclear genes provide possible targets for improving photosynthetic efficiency. Hence, genome-wide identification and characterization of the nuclear genes affecting photosynthetic traits in woody plants would provide key insights on genetic regulation of photosynthesis and identify candidate processes for improvement of photosynthesis. Results Using microarray and bulked segregant analysis strategies, we identified differentially expressed nuclear genes for photosynthesis traits in a segregating population of poplar. We identified 515 differentially expressed genes in this population (FC ≥ 2 or FC ≤ 0.5, P < 0.05), 163 up-regulated and 352 down-regulated. Real-time PCR expression analysis confirmed the microarray data. Singular Enrichment Analysis identified 48 significantly enriched GO terms for molecular functions (28), biological processes (18) and cell components (2). Furthermore, we selected six candidate genes for functional examination by a single-marker association approach, which demonstrated that 20 SNPs in five candidate genes significantly associated with photosynthetic traits, and the phenotypic variance explained by each SNP ranged from 2.3% to 12.6%. This revealed that regulation of photosynthesis by the nuclear genome mainly involves transport, metabolism and response to stimulus functions. Conclusions This study provides new genome-scale strategies for the discovery of potential candidate genes affecting photosynthesis in Populus, and for identification of the functions of genes involved in regulation of photosynthesis. This work also suggests that improving photosynthetic efficiency under field conditions will require the consideration of multiple factors, such as stress responses. PMID:24673936

  9. Sex-specific responses of Populus deltoides to Glomus intraradices colonization and Cd pollution.

    PubMed

    Chen, Lianghua; Zhang, Danju; Yang, Wanqin; Liu, Yang; Zhang, Li; Gao, Shun

    2016-07-01

    The positive effects of arbuscular mycorrhizal fungi (AM) on the survival, growth and physiology of plants under various stress conditions have been widely recognized. However, whether sex-dependent susceptibility to AM colonization exists, which can induce a differential tolerance between the sexes to stress conditions, is still unclear. In this study, we investigated the effects of Glomus intraradices on Cd-stressed males and females of Populus deltoides (spiked with 10 mg Cd per kg dry substrate) in terms of morphology, physiology, biochemistry, ultrastructure, and toxin storage and translocation. Exposure to Cd promoted the colonization by G. intraradices in males, but not in females. Generally, females suffered more impairments than males in response to Cd stress, reflected by leaf symptoms, the extent of lipid peroxidation, and integrity of the cellular ultrastructure, whether they were inoculated or not. Inoculation with G. intraradices alleviated the phytotoxic effects of Cd in females by stimulating antioxidant enzymes, decreasing levels of reactive oxygen species (ROS) and restricting Cd transfer to the shoots. In contrast, these beneficial effects induced by AM were not detected in mycorrhizal males compared to non-mycorrhizal males, based on thiobarbituric acid-reactive substances (TBARS) and cellular ultrastructure. Inoculation with AM promoted Cd accumulation in males but not in females, and caused the sequestration of more toxic Cd in the root systems in both sexes. Therefore, our results suggest that inoculated males of P. deltoides are suitable candidates for phytostabilization in Cd-polluted soils, due to their higher accumulation ability and greater tolerance relative to inoculated females.

  10. Populus Responses to Edaphic and Climatic Cues: Emerging Evidence from Systems Biology Research

    SciTech Connect

    Wullschleger, Stan D; Weston, David; Davis, John M

    2009-01-01

    The emergence of Populus as a model system for tree biology continues to be driven by a community of scientists dedicated to developing the resources needed to undertake genetic and functional genomic studies in this genus. As a result, understanding the molecular processes that underpin the growth and development of cottonwood, aspen, and hybrid poplar has steadily increased over the last several decades. Recently, our ability to examine the basic mechanisms whereby trees respond to a changing climate and resource limitations has benefited greatly from the sequencing of the P. trichocarpa genome. This landmark event has laid a solid foundation upon which biologists can now quantify, in breathtaking and unprecedented detail, the diversity of genes, proteins, and metabolites that govern the growth and development of some of the longest living and tallest growing organisms on Earth. Although the challenges likely to be encountered by scientists who work with trees are many, recent literature provides a few examples where a systems approach, one that focuses on integrating transcriptomic, proteomic, and metabolomic analyses, is beginning to provide insights into the molecular-scale response of poplars to their climatic and edaphic environment. In this review, our objectives are to look at evidence from studies that examine the molecular response of poplar to edaphic and climatic cues and highlight instances where two or more omic-scale measurements confirm and hopefully expand our inferences about mechanisms contributing to observed patterns of response. Based on conclusions drawn from these studies, we propose that three requirements will be essential as systems biology in poplar moves to reveal unique insights. These include use of genetically-defined individuals (e.g., pedigrees or transgenics) in studies; incorporation of modeling as a complement to transcriptomic, proteomic and metabolomic data; and inclusion of whole-tree and stand-level phenotypes to place

  11. Populus euphratica HSF binds the promoter of WRKY1 to enhance salt tolerance.

    PubMed

    Shen, Zedan; Yao, Jun; Sun, Jian; Chang, Liwei; Wang, Shaojie; Ding, Mingquan; Qian, Zeyong; Zhang, Huilong; Zhao, Nan; Sa, Gang; Hou, Peichen; Lang, Tao; Wang, Feifei; Zhao, Rui; Shen, Xin; Chen, Shaoliang

    2015-06-01

    Poplar species increase expressions of transcription factors to deal with salt environments. We assessed the salt-induced transcriptional responses of heat-shock transcription factor (HSF) and WRKY1 in Populus euphratica, and their roles in salt tolerance. High NaCl (200mM) induced PeHSF and PeWRKY1 expressions in P. euphratica, with a rapid rise in roots than in leaves. Moreover, the salt-elicited PeHSF reached its peak level 6h earlier