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Sample records for populus tremuloides internodes

  1. 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.

  2. Gender-specific and intraspecific responses of trembling aspen (Populus tremuloides) to elevated atmospheric carbon dioxide

    NASA Astrophysics Data System (ADS)

    Wang, Xianzhong

    I studied gender-specific and intraspecific variations in the physiological responses of Populus tremuloides to elevated CO2 as affected by soil N availability. I also synthesized leaf dark respiration data from independent studies using meta-analysis. Net CO2 assimilation rate (A) of male P. tremuloides was 17.8 and 26.2 μmol m-2 s-1 at ambient and elevated CO2, significantly higher than A of females of 15.6 and 21.0 μmol m-2 s-1 . Male trembling aspen had a higher maximum rate of CO2 fixation by Rubisco and area-based leaf dark respiration (Rda). Mass-based leaf Rd (Rdm), however, was unaffected by gender and CO2 concentration, although the results of meta-analysis on 44 independent observations showed that Rdm was reduced 18.4% by elevated CO2. We found a positive correlation between Rd a and leaf starch content, which was higher at elevated CO2, but no correlation between Rda and leaf N content was observed, suggesting the importance of starch content in determining the magnitude of respiration. Total biomass accumulation of female P. tremuloides was higher than that of males in low-N soil and at ambient CO2, but not in other treatments. Elevated CO2, on the other hand, significantly increased total biomass of both male and female trees in low- and high-N soil, with the increase ranging from 22-70% for female and 58-66% for male trees. There was a significant CO2 x genotype interaction in photosynthetic responses to CO2 enrichment, wherein A was significantly enhanced by elevated CO2 for five genotypes in high-N soil and for four genotypes in low-N soil. Enhancement of A by elevated CO2 ranged from 14% to 68%. We found a correlation between the degree of A enhancement to elevated CO2 and stomatal sensitivity to CO2. Stomatal conductance and A of different genotypes also responded differentially to drought stress. Our results suggest that P. tremuloides genotypes and genders respond differentially in A and Rd to rising atmospheric CO2 , with the degree of

  3. Genotypic variation in physiological and growth responses of Populus tremuloides to elevated atmospheric CO2 concentration.

    PubMed

    Wang, X; Curtis, P S; Pregitzer, K S; Zak, D R

    2000-09-01

    Physiological and biomass responses of six genotypes of Populus tremuloides Michx., grown in ambient t (357 micromol mol(-1)) or twice ambient (707 micromol mol(-1)) CO2 concentration ([CO2]) and in low-N or high-N soils, were studied in 1995 and 1996 in northern Lower Michigan, USA. There was a significant CO2 x genotype interaction in photosynthetic responses. Net CO2 assimilation (A) was significantly enhanced by elevated [CO2] for five genotypes in high-N soil and for four genotypes in low-N soil. Enhancement of A by elevated [CO2] ranged from 14 to 68%. Genotypes also differed in their biomass responses to elevated [CO2], but biomass responses were poorly correlated with A responses. There was a correlation between magnitude of A enhancement by elevated [CO2] and stomatal sensitivity to CO2. Genotypes with low stomatal sensitivity to CO2 had a significantly higher A at elevated [CO2] than at ambient [CO2], but elevated [CO2] did not affect the ratio of intercellular [CO2] to leaf surface [CO2]. Stomatal conductance and A of different genotypes responded differentially to recovery from drought stress. Photosynthetic quantum yield and light compensation point were unaffected by elevated [CO2]. We conclude that P. tremuloides genotypes will respond differentially to rising atmospheric [CO2], with the degree of response dependent on other abiotic factors, such as soil N and water availability. The observed genotypic variation in growth could result in altered genotypic representation within natural populations and could affect the composition and structure of plant communities in a higher [CO2] environment in the future.

  4. 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

  5. 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.

  6. Inhibitor studies of leaf lamina hydraulic conductance in trembling aspen (Populus tremuloides Michx.) leaves.

    PubMed

    Voicu, Mihaela C; Zwiazek, Janusz J

    2010-02-01

    The present study investigated leaf water transport properties in trembling aspen (Populus tremuloides) leaves. Leaf lamina hydraulic conductance (K(lam)) and stomatal conductance (g(s)) were drastically suppressed by NaF (a general metabolic inhibitor). In leaves treated with 0.2 mM HgCl(2) (an aquaporin blocker), K(lam) declined by 22% when the leaves were sampled in June but the decline was not significant when the leaves were sampled in August. The leaves sampled in June that transpired 30 mM beta-mercaptoethanol following mercury application showed similar K(lam) as those in control leaves transpiring distilled water. When leaves were pressure-infiltrated with 0.1 mM HgCl(2), K(lam) significantly declined by 25%. Atrazine (a photosystem II inhibitor) drastically reduced leaf net CO(2) uptake by the leaves from seedlings and mature trees but did not have any effect on K(lam) regardless of the irradiance at the leaf level during the K(lam) measurements. When PTS(3) (trisodium 3-hydroxy-5,8,10-pyrenetrisulphonate) apoplastic tracer was pressure-infiltrated inside the leaves, its concentration in the leaf exudates did not change from ambient light to high irradiance treatment and declined in the presence of HgCl(2) in the treatment solution. Trembling aspen K(lam) appears to be linked to leaf metabolism and is uncoupled from the short-term variations in photosynthesis. Aquaporin-mediated water transport does not appear to constitute the dominant pathway for the pressure-driven water flow in the leaves of trembling aspen trees.

  7. 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

  8. 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

  9. 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

  10. Stockability, growth, and yield of the circumboreal aspens (`populus tremuloides` michx., `p. tremula` l.). Forest Service research paper

    SciTech Connect

    Perala, D.A.; Leary, R.A.; Cieszewski, C.J.

    1995-01-10

    The authors show elsewhere that quaking aspen (Populus tremuloides Michx.) and its Eurasian counterpart, P. tremula L., form a single circumpolar superspecies when viewed from the standpoint of self-thinning rates and stockability. Here the authors expand their examination to the d.b.h.-age relationships and to growth series measurements from permanent plots of aspen stands of varying densities reported in the literature. They also attempt to account for the curvilinear trend in the self-thinning relationship they detected in young stands that forced them in their first analysis to truncate their usable data set to older stands. The resulting equations satisfy the need for a framework to study variation in aspen stockability. The equations can give useful regional estimates as well, but will need refitting to local data to satisfy needs for finer resolution.

  11. 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.

  12. Elevated atmospheric CO2 concentration leads to increased whole-plant isoprene emission in hybrid aspen (Populus tremula × Populus tremuloides).

    PubMed

    Sun, Zhihong; Niinemets, Ülo; Hüve, Katja; Rasulov, Bahtijor; Noe, Steffen M

    2013-05-01

    Effects of elevated atmospheric [CO2] on plant isoprene emissions are controversial. Relying on leaf-scale measurements, most models simulating isoprene emissions in future higher [CO2] atmospheres suggest reduced emission fluxes. However, combined effects of elevated [CO2] on leaf area growth, net assimilation and isoprene emission rates have rarely been studied on the canopy scale, but stimulation of leaf area growth may largely compensate for possible [CO2] inhibition reported at the leaf scale. This study tests the hypothesis that stimulated leaf area growth leads to increased canopy isoprene emission rates. We studied the dynamics of canopy growth, and net assimilation and isoprene emission rates in hybrid aspen (Populus tremula × Populus tremuloides) grown under 380 and 780 μmol mol(-1) [CO2]. A theoretical framework based on the Chapman-Richards function to model canopy growth and numerically compare the growth dynamics among ambient and elevated atmospheric [CO2]-grown plants was developed. Plants grown under elevated [CO2] had higher C : N ratio, and greater total leaf area, and canopy net assimilation and isoprene emission rates. During ontogeny, these key canopy characteristics developed faster and stabilized earlier under elevated [CO2]. However, on a leaf area basis, foliage physiological traits remained in a transient state over the whole experiment. These results demonstrate that canopy-scale dynamics importantly complements the leaf-scale processes, and that isoprene emissions may actually increase under higher [CO2] as a result of enhanced leaf area production.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  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. Plant Signals Disrupt (regulate?) Arbuscular Mycorrhizal Fungal Growth Under Enhanced Ozone and CO2 Growing Conditions for Populus tremuloides

    NASA Astrophysics Data System (ADS)

    Miller, R. M.; Podila, G. K.

    2008-12-01

    An understanding of the genetic determinants of keystone symbiotic relationships is essential to elucidating adaptive mechanisms influencing higher-order processes, including shifts in community composition following environmental perturbations. The Aspen FACE project offers a unique opportunity to address adaptive processes with an imposed three way interaction experiment composed of the atmospheric pollutant ozone (eO3), elevated CO2 (eCO2) fumigations, five Populus tremuloides (aspen) genotypes, and both arbuscular mycorrhizal and ectomycorrhizal fungal interactions. The 10 year time span of this experiment has allowed for a realistic and mechanistic understanding of above ground responses of the aspen genotypes to eCO2, eO3 and the interaction effects of eCO2 and eO3. Even so, treatment influences to the below ground, including carbon allocation to roots and associated mycorrhizal symbionts, and rhizosphere dynamics are just beginning to be understood. We hypothesized that mycorrhizal fungal responses to eCO2, eO3, and the interaction effects of eCO2+eO3 are conditioned by the degree of response of their aspen hosts. We intend to describe the molecular mechanisms of an important critical interaction between host and fungus using microarray analysis of expression profiles, as well as metabolic profiling of aspen roots and their associated mycorrhizal partner, the arbuscular mycorrhizal fungus (AMF) Glomus intraradices, under eCO2, eO3 and eCO2+eO3. We present evidence that host-derived factors, expressed in response to eCO2+eO3, trigger responses in Glomus leading to the partitioning or metabolic shift in lipid biosynthesis that is associated with reduced extraradical hyphae growth and altered lipid metabolism. We then scale these lower-level responses to give better insight to fungal intraradical and extraradical allocation of biomass and fungal and root lipid and carbohydrate content in association with aspen genotype responses to the imposed treatments. By

  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. Impacts of greenhouse gases on epicuticular waxes of Populus tremuloides Michx.: results from an open-air exposure and a natural O3 gradient.

    PubMed

    Mankovská, B; Percy, K E; Karnosky, D F

    2005-10-01

    Epicuticular waxes of three trembling aspen (Populus tremuloides Michx.) clones differing in O3 tolerance were examined over six growing seasons (1998-2003) at three bioindicator sites in the Lake States region of the USA and at FACTS II (Aspen FACE) site in Rhinelander, WI. Differences in epicuticular wax structure were determined by scanning electron microscopy and quantified by a coefficient of occlusion. Statistically significant increases in stomatal occlusion occurred for the three O3 bioindicator sites, with the higher O3 sites having the most affected stomata for all three clones as well as for all treatments including elevated CO2, elevated O3, and elevated CO2 + O3. We recorded statistically significant differences between aspen clones and between sampling period (spring, summer, fall). We found no statistically significant differences between treatments or aspen clones in stomatal frequency.

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

    PubMed Central

    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. PMID:24155751

  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. 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

  4. 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.

  5. 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.

  6. The responses of Vitreoscilla hemoglobin-expressing hybrid aspen (Populus tremula × tremuloides) exposed to 24-h herbivory: expression of hemoglobin and stress-related genes in exposed and nonorthostichous leaves.

    PubMed

    Sutela, Suvi; Ylioja, Tiina; Jokipii-Lukkari, Soile; Anttila, Anna-Kaisa; Julkunen-Tiitto, Riitta; Niemi, Karoliina; Mölläri, Tiina; Kallio, Pauli T; Häggman, Hely

    2013-11-01

    The responses of transcriptome and phenolic compounds were determined with Populus tremula L. × Populus tremuloides Michx. expressing the hemoglobin (Hb) of Vitreoscilla (VHb) and non-transformant (wt) line. After 24-h exposure of leaves to Conistra vaccinii L., the transcript levels of endogenous non-symbiotic class 1 Hb (PttHb1) and truncated Hb (PttTrHb) genes were modestly reduced and increased, respectively, in both wt and VHb-expressing line. Besides the herbivory exposed leaves showing the most significant transcriptome changes, alterations were also detected in the transcriptome of nonorthostichous leaves positioned directly above the exposed leaves. Both wt and VHb-expressing line displayed similar herbivory-induced effects on gene expression, although the extent of responses was more pronounced in the wt than in the VHb-expressing line. The contents of phenolic compounds were not altered due to herbivory and they were alike in the wt and VHb-expressing line. In addition, we determined the relative growth rates (RGRs) of Orthosia gothica L., Ectropis crepuscularia Denis & Schiff. and Orgyia antiqua L. larvae, and found no variation in the RGRs between the lines. Thus, VHb-expressing P. tremula × tremuloides lines showed to be comparable with wt in regards to the food quality of leaves.

  7. 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

  8. Comparative leaf growth strategies in response to low-water and low-light availability: variation in leaf physiology underlies variation in leaf mass per area in Populus tremuloides.

    PubMed

    Baird, Alec S; Anderegg, Leander D L; Lacey, Melissa E; HilleRisLambers, Janneke; Van Volkenburgh, Elizabeth

    2017-04-04

    Developmental phenotypic plasticity can allow plants to buffer the effects of abiotic and biotic environmental stressors. Therefore, it is vital to improve our understanding of how phenotypic plasticity in ecological functional traits is coordinated with variation in physiological performance in plants. To identify coordinated leaf responses to low-water (LW) versus low-light (LL) availability, we measured leaf mass per area (LMA), leaf anatomical characteristics and leaf gas exchange of juvenile Populus tremuloides Michx. trees. Spongy mesophyll tissue surface area (Asmes/A) was correlated with intrinsic water-use efficiency (WUEi: photosynthesis, (Aarea)/stomatal conductance (gs)). Under LW availability, these changes occurred at the cost of greater leaf tissue density and reduced expansive growth, as leaves were denser but were only 20% the final area of control leaves, resulting in elevated LMA and elevated WUEi. Low light resulted in reduced palisade mesophyll surface area (Apmes/A) while spongy mesophyll surface area was maintained (Asmes/A), with no changes to WUEi. These leaf morphological changes may be a plastic strategy to increase laminar light capture while maintaining WUEi. With reduced density and thickness, however, leaves were 50% the area of control leaves, ultimately resulting in reduced LMA. Our results illustrate that P. tremuloides saplings partially maintain physiological function in response to water and light limitation by inducing developmental plasticity in LMA with underlying anatomical changes. We discuss additional implications of these results in the context of developmental plasticity, growth trade-offs and the ecological impacts of climate change.

  9. Influence of over-expression of the Flowering Promoting Factor 1 gene (FPF1) from Arabidopsis on wood formation in hybrid poplar (Populus tremula L. × P. tremuloides Michx.).

    PubMed

    Hoenicka, Hans; Lautner, Silke; Klingberg, Andreas; Koch, Gerald; El-Sherif, Fadia; Lehnhardt, Denise; Zhang, Bo; Burgert, Ingo; Odermatt, Jürgen; Melzer, Siegbert; Fromm, Jörg; Fladung, Matthias

    2012-02-01

    Constitutive expression of the FPF1 gene in hybrid aspen (Populus tremula L. × P. tremuloides Michx.) showed a strong effect on wood formation but no effect on flowering time. Gene expression studies showed that activity of flowering time genes PtFT1, PtCO2, and PtFUL was not increased in FPF1 transgenic plants. However, the SOC1/TM3 class gene PTM5, which has been related to wood formation and flowering time, showed a strong activity in stems of all transgenic lines studied. Wood density was lower in transgenic plants, despite significantly reduced vessel frequency which was overcompensated by thinner fibre cell walls. Chemical screening of the wood by pyrolysis GC/MS showed that FPF1 transgenics have higher fractions of cellulose and glucomannan products as well as lower lignin content. The latter observation was confirmed by UV microspectrophotometry on a cellular level. Topochemical lignin distribution revealed a slower increase of lignin incorporation in the developing xylem of the transgenics when compared with the wild-type plants. In line with the reduced wood density, micromechanical wood properties such as stiffness and ultimate stress were also significantly reduced in all transgenic lines. Thus, we provide evidence that FPF1 class genes may play a regulatory role in both wood formation and flowering in poplar.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. Internode data communications in a parallel computer

    DOEpatents

    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.

  18. Internode data communications in a parallel computer

    DOEpatents

    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.

  19. Population genetics of Chrysomela tremulae: a first step towards management of transgenic Bacillus thuringiensis poplars Populus tremula x .P. tremuloides.

    PubMed

    Génissel, A; Viard, F; Bourguet, D

    2000-01-01

    Many strategies have been proposed for delaying the development of insect resistance to Bacillus thuringiensis (Bt). The current paradigm for Bt resistance management is the high dose-refuge strategy. For this strategy to be successful: (i) heterozygotes must be killed in treated areas, (ii) resistant alleles must be rare (frequency < 10-3), and (iii) there must be a high level of gene flow between populations to ensure random mating. We studied gene flow within and between populations with a view to managing the resistance of Chrysomela tremulae (Coleoptera: Chrysomelidae) to new transgenic, highly toxic poplars expressing a synthetic Bt gene. In this study, we assessed the extent of gene flow in C. tremulae within and between 16 sites in France and Belgium, using allozyme markers. We found a high level of genetic variability in C. tremulae, with a mean of 0.206 +/- 0.16. There were no obvious limitations to gene flow between populations of C. tremulae over large geographical distances (several hundreds of kilometres). Nevertheless, a very low level of genetic differentiation was observed between a site located in the south of France and the sampled sites from the Centre region.

  20. 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

  1. Carbon Partitioning during Sucrose Accumulation in Sugarcane Internodal Tissue.

    PubMed

    Whittaker, A.; Botha, F. C.

    1997-12-01

    The temporal relationship between sucrose (Suc) accumulation and carbon partitioning was investigated in developing sugarcane internodes. Radiolabeling studies on tissue slices, which contained Suc concentrations ranging from 14 to 42% of the dry mass, indicated that maturation coincided with a redirection of carbon from water-insoluble matter, respiration, amino acids, organic acids, and phosphorylated intermediates into Suc. It is evident that a cycle of Suc synthesis and degradation exists in all of the internodes. The decreased allocation of carbon to respiration coincides with a decreased flux from the hexose pool. Both the glucose and fructose (Fru) concentrations significantly decrease during maturation. The phosphoenolpyruvate, Fru-6-phosphate (Fru-6-P), and Fru-2,6-bisphosphate (Fru-2, 6-P2) concentrations decrease between the young and older internodal tissue, whereas the inorganic phosphate concentration increases. The calculated mass-action ratios indicate that the ATP-dependent phosphofructokinase, pyruvate kinase, and Fru-1,6-bisphosphatase reactions are tightly regulated in all of the internodes, and no evidence was found that major changes in the regulation of any of these enzymes occur. The pyrophosphate-dependent phosphofructokinase reaction is in apparent equilibrium in all the internodes. Substrate availability might be one of the prime factors contributing to the observed decrease in respiration.

  2. Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.

    PubMed

    Wang, Jing; Street, Nathaniel R; Scofield, Douglas G; Ingvarsson, Pär K

    2016-03-01

    A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.

  3. Ca effect on protoplasmic streaming in Nitella internodal cell.

    PubMed

    Takamatsu, A; Aoki, T; Tsuchiya, Y

    1993-01-01

    Ca(2+) ion effect on protoplasmic streaming in an internodal cell of Nitella has been investigated for various temperatures. We have found that the protoplasmic streaming at low temperature is remarkably affected by the Ca(2+) ions in the internodal cell but larger concentrations of the Ca(2+) ions are needed to suppress the streaming velocity at higher temperatures. These streaming behaviors of the protoplasm, furthermore, have been elucidated on the basis of the reaction equations which take into account ATP hydrolysis due to actin-myosin molecules and inactivity of the molecules due to the Ca(2+) ions.

  4. 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

  5. Changes in myelin sheath thickness and internode geometry in the rabbit phrenic nerve during growth.

    PubMed Central

    Friede, R L; Brzoska, J; Hartmann, U

    1985-01-01

    The rabbit phrenic nerve was studied at seven phases of growth from the newborn to the adult to determine the length of the nerve fibres, the length of the internodes, the fibre calibre, the geometric proportions of the internodes and the thickness of the myelin sheaths. The elongation of the internodes corresponded precisely to the elongation of the nerve, indicating a constant number of approximately 140 internodes per fibre, each internode elongating commensurate with body growth. Internode elongation was accompanied by increases in fibre calibre, but these parameters did not change in precise proportion. The internodes of thick fibres were relatively short for calibre, as defined by the length/diameter quotient. This trend of foreshortening changed during growth. Sheath thickness, defined by the quotient axon diameter/fibre diameter, was determined with a computer-assisted method. Fibres of young rabbits had relatively thin sheaths for axon calibre, compared with adult rabbits. The changes in sheath thickness corresponded to the changes in internode geometry. This was consistent with previous studies showing that elongation or foreshortening of an internode of a given calibre has a slight, but definite effect on the thickness of its myelin sheath. PMID:3870716

  6. Internodal myelin volume and axon surface area. A relationship determining myelin thickness?

    PubMed

    Smith, K J; Blakemore, W F; Murray, J A; Patterson, R C

    1982-08-01

    Internodes from normal, remyelinated and regenerated nerve fibres have been isolated from rat spinal roots and sciatic nerve. The internodes have been examined quantitatively by light and electron microscopy to determine their internodal length, myelin thickness, and the circumference and cross-sectional area of both the axons and fibre. Comparison of these measurements of the axon and myelin sheath has revealed a close relationship between the volume of myelin comprising the internode and the area over which the Schwann cell and axon are in close proximity, i.e. the surface area of the axolemma beneath the internodal myelin sheath. The same relationship described not only the internodes on normal nerve fibres, where internodal length is proportional to axon diameter, but also the short and thinly myelinated internodes formed in the adult animal on remyelinated and on regenerated axons. Examination of data presented by Berthold (1978) revealed that a closely similar relationship is also present in feline nerve fibres. In view of the constancy of the relationship between such different types of internode it is suggested that the regulation of myelin volume, and thereby of myelin thickness, may be mediated via the area of the axolemma or of the Schwann cell membrane beneath the myelin sheath.

  7. Expression of lipoxygenase during organogenic nodule formation from hop internodes.

    PubMed

    Fortes, Ana Margarida; Coronado, Maria José; Testillano, Pilar S; Risueño, Maria del Carmen; Pais, Maria Salomé

    2004-02-01

    Study of lipoxygenase expression (LOX; EC 1.13.11.12) during organogenic nodule formation in hop (Humulus lupulus var. Nugget) showed that LOXs are developmentally regulated throughout the process, suggesting their involvement in the response of internodes to wounding, nodule formation, and plantlet regeneration from these nodules. LOX activity and lipid peroxides exhibited a huge increase during the first week of culture, which may indicate a role for LOX and LOX products in response to wounding in hop, as reported for other systems. Western blotting analysis showed a de novo synthesis of LOX isoenzymes in response to wounding and the detection of three different isoenzymes. Confocal analysis of LOX immunofluorescence revealed the presence of the enzyme in cortical cells of induced internodes and in prenodular cells, mostly appearing as cytoplasmic spots. Some of them were identified as lipid bodies by cytochemical and double immunofluorescence assays, suggesting the involvement of a lipid body LOX during nodule formation. Immunogold labeling detected LOX in peroxisomes, lipid bodies, and plastids of nodular cells. Quantification of the labeling density provided statistical significance for the localization of LOX (three different isoenzymes) in the three compartments, which suggested a possible involvement of LOX in metabolic functions of these organelles during organogenic nodule formation and plantlet regeneration.

  8. 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.

  9. 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...

  10. 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.

  11. 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.

  12. Action currents, internodal potentials, and extracellular records of myelinated mammalian nerve fibers derived from node potentials.

    PubMed Central

    Marks, W B; Loeb, G E

    1976-01-01

    The potential distribution within the internodal axon of mammalian nerve fibers is derived by applying known node potential waveforms to the ends of an equivalent circuit model of the internode. The complete spatial/temporal profile of action potentials synthesized from the internodal profiles is used to compute the node current waveforn, and the extracellular action potential around fibers captured within a tubular electrode. For amphibia, the results agreed with empirical values. For mammals, the amplitude of the node currents plotted against conduction velocity was fitted by a straight line. The extracellular potential waveform depended on the location of the nodes within the tube. For tubes of length from 2 to 8 internodes, extracellular wave amplitude (mammals) was about one-third of the product of peak node current and tube resistance (center to ends). The extracellular potentials developed by longitudinal and radial currents in an anisotropic medium (fiber bundle) are compared. PMID:1276389

  13. The Significance of Internode Length for Saltatory Conduction: Looking Back at the Age of 90.

    PubMed

    Friede, Reinhard L

    2017-03-14

    The development of peripheral nerve fibers involves interdependence between the timing of Schwann cell recruitment during myelination and elongation of the nerve. This adjusts the number and the length of internodes to the length of the fiber. Saltatory conduction in longer nerves involves longer saltations; this makes internode length the factor that determines conduction velocity, thereby adjusting impulse transmission in circuits of different lengths. Myelination increases conduction velocity by means of saltatory conduction but what determines the saltatory conduction is not so much the indispensable insulating adjunct of myelin as the length of the internodes that separate the excitable membrane segments. We have previously studied the development of the length and proportion of internodes in some detail. If the anatomical data are combined, the data fall in place for a revised understanding of conduction velocity and the system that adapts the conduction properties of peripheral nerves to fiber lengths and to body size.

  14. 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.

  15. Strigolactones Stimulate Internode Elongation Independently of Gibberellins1[C][W

    PubMed Central

    de Saint Germain, Alexandre; Ligerot, Yasmine; Dun, Elizabeth A.; Pillot, Jean-Paul; Ross, John J.; Beveridge, Christine A.; Rameau, Catherine

    2013-01-01

    Strigolactone (SL) mutants in diverse species show reduced stature in addition to their extensive branching. Here, we show that this dwarfism in pea (Pisum sativum) is not attributable to the strong branching of the mutants. The continuous supply of the synthetic SL GR24 via the root system using hydroponics can restore internode length of the SL-deficient rms1 mutant but not of the SL-response rms4 mutant, indicating that SLs stimulate internode elongation via RMS4. Cytological analysis of internode epidermal cells indicates that SLs control cell number but not cell length, suggesting that SL may affect stem elongation by stimulating cell division. Consequently, SLs can repress (in axillary buds) or promote (in the stem) cell division in a tissue-dependent manner. Because gibberellins (GAs) increase internode length by affecting both cell division and cell length, we tested if SLs stimulate internode elongation by affecting GA metabolism or signaling. Genetic analyses using SL-deficient and GA-deficient or DELLA-deficient double mutants, together with molecular and physiological approaches, suggest that SLs act independently from GAs to stimulate internode elongation. PMID:23943865

  16. Clone history shapes Populus drought responses

    PubMed Central

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

    2011-01-01

    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

  17. Relationship between myelin sheath diameter and internodal length in axons of the anterior medullary velum of the adult rat.

    PubMed

    Ibrahim, M; Butt, A M; Berry, M

    1995-11-01

    Relations between myelin sheath diameters and internodal lengths were measured in whole mounts of osmium stained intact anterior medullary velum (AMV) from glutaraldehyde perfused adult rats. The AMV is a sheet of CNS tissue which roofs the IVth ventricle and contains fascicles of myelinated fibres which arise mainly from the nucleus of the IVth cranial nerve. These fibers displayed a broad range of myelin sheath external diameters and internodal lengths, from < 1-12 microns and 50-750 microns, respectively. Myelin sheath external diameter was a measurement of the axonal diameter plus the thickness of its myelin sheath, while internodal length was measured as the distance between consecutive nodes. There was a broadly linear relationship between myelin sheath diameters and internodal lengths, with the smaller diameter sheaths tending to have shorter internodes than the larger. However, the correlation was weak and for any given diameter myelin sheaths displayed considerable variation in their internodal lengths. The smallest diameter myelin sheaths, < 4 microns, consistently had shorter internodes than predicted by a linear regression and, in an analysis of consecutive internodes in single fibres, the slope was flattened in fibres with a diameter > 4 microns. Our results indicated that small and large calibre fibres may have different myelin sheath diameter-internodal length interrelations.

  18. Burial depth and stolon internode length independently affect survival of small clonal fragments.

    PubMed

    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.

  19. Water relations of populus clones

    SciTech Connect

    Pallardy, S.G.; Kozlowski, T.T.

    1981-02-01

    Stomatal aperture and water balance in the field of eight Populus clones varying in growth rate were closely related to environmental factors and clonal differences were clearly expressed. Leaf water potential (psi) was influenced by solar radiation, leaf conductance, evaporative demand, and soil moisture content. The effects of soil moisture on psi were greatly modified by atmospheric conditions and stomatal conductance. Several slow-growing clones exhibited extended periods of psi below that of rapidly growing clones, despite high evaporative demand and the much greater transpiring surfaces of the fast-growing clones. Stomata of all clones responded to changes in light intensity and vapor pressure gradient (VPG). Pronounced stomatal sensitivity to VPG of two rapidly growing clones of common parentage, and the resultant capacity of these clones to moderate water deficits under high evaporative demand, were associated with drought resistance in one of the parents. Seasonal maximum leaf conductance was positively related to growth in several clones, suggesting that rapidly growing clones possess the capacity to carry on higher rates of gas exchange under favorable conditions. Analysis of changes in psi with changes in transpirational flux density (TFD) showed that for four clones, psi change per unit change in TFD decreased as TFD increased, indicating plant adaptation for prevention of damaging psi even at high TFD. More rapidly growing clones exhibited a larger initial rate of decline in psi with TFD, but reduced the rate of decline more than slow-growing clones as TFD increased. (Refs. 41).

  20. Comparative studies on hydrothermal pretreatment and enzymatic saccharification of leaves and internodes of alamo switchgrass.

    PubMed

    Hu, Zhoujian; Foston, Marcus; Ragauskas, Arthur J

    2011-07-01

    Hydrothermal pretreatment was performed on the leaves and internodes portions of Alamo switchgrass, Panicum virgatum L., to enhance the digestibility of cellulose towards cellulase. It was observed that extractives free leaves portion provided 18.1% lower pretreatment gravimetrical yield and 33.8% greater cellulose-to-glucose yield than internodes portion. The degree of polymerization (DP) and ultrastructure of cellulose were determined by gel-permeation chromatography and solid-state cross polarization/magic angle spinning (13)C NMR experiments. The results suggested that hydrothermal pretreatment hydrolyzed amorphous cellulose and yielded a product enriched in paracrystalline cellulose. Furthermore, the DP of cellulose was reduced to one third of the origin value after hydrothermal pretreatment. The resulting biomass after pretreatment for leaves and internodes has similar cellulose ultrastructure and chemical profiles. The results of the enzymatic hydrolysis studies of cellulose suggest that the reduced DP of cellulose of pretreated switchgrass was an important factor influencing the enhanced digestibility of pretreated switchgrass.

  1. Metabolomics study of Populus type propolis.

    PubMed

    Anđelković, Boban; Vujisić, Ljubodrag; Vučković, Ivan; Tešević, Vele; Vajs, Vlatka; Gođevac, Dejan

    2017-02-20

    Herein, we propose rapid and simple spectroscopic methods to determine the chemical composition of propolis derived from various Populus species using a metabolomics approach. In order to correlate variability in Populus type propolis composition with the altitude of its collection, NMR, IR, and UV spectroscopy followed by OPLS was conducted. The botanical origin of propolis was established by comparing propolis spectral data to those of buds of various Populus species. An O2PLS method was utilized to integrate two blocks of data. According to OPLS and O2PLS, the major compounds in propolis samples, collected from temperate continental climate above 500m, were phenolic glycerides originating from P. tremula buds. Flavonoids were predominant in propolis samples collected below 400m, originating from P. nigra and P. x euramericana buds. Samples collected at 400-500m were of mixed origin, with variable amounts of all detected metabolites.

  2. 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

  3. 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...

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    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.; Déjardin, A.; dePamphilis, C.; Detter, J.; Dirks, B.; Dubchak, I.; Duplessis, S.; Ehlting, 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.; Kangasjärvi, J.; Karlsson, J.; Kelleher, C.; Kirkpatrick, R.; Kirst, M.; Kohler, A.; Kalluri, U.; Larimer, F.; Leebens-Mack, J.; Leplé, J.-C.; Locascio, P.; Lou, Y.; Lucas, S.; Martin, F.; Montanini, B.; Napoli, C.; Nelson, D. R.; Nelson, C.; Nieminen, K.; Nilsson, O.; Pereda, V.; Peter, G.; Philippe, R.; Pilate, G.; Poliakov, A.; Razumovskaya, J.; Richardson, P.; Rinaldi, C.; Ritland, K.; Rouzé, P.; Ryaboy, D.; Schmutz, J.; Schrader, J.; Segerman, B.; Shin, H.; Siddiqui, A.; Sterky, F.; Terry, A.; Tsai, C.-J.; Uberbacher, E.; Unneberg, P.; Vahala, J.; Wall, K.; Wessler, S.; Yang, G.; Yin, T.; Douglas, C.; Marra, M.; Sandberg, G.; Van de 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. 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.

  6. 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

  7. Relationship of acid invertase activities to sugar content in sugarcane internodes during ripening and after harvest

    Technology Transfer Automated Retrieval System (TEKTRAN)

    It has been hypothesized that soluble acid invertase (SAI) and insoluble (cell wall) acid invertase (CWI) influence sucrose accumulation in sugarcane during ripening, and also postharvest deterioration. The activities of SAI and CWI were determined in selected immature and mature internodes during r...

  8. A mutation in the rice chalcone isomerase gene causes the golden hull and internode 1 phenotype.

    PubMed

    Hong, Lilan; Qian, Qian; Tang, Ding; Wang, Kejian; Li, Ming; Cheng, Zhukuan

    2012-07-01

    The biosynthesis of flavonoids, important secondary plant metabolites, has been investigated extensively, but few mutants of genes in this pathway have been identified in rice (Oryza sativa). The rice gold hull and internode (gh) mutants exhibit a reddish-brown pigmentation in the hull and internode and their phenotype has long been used as a morphological marker trait for breeding and genetic study. Here, we characterized that the gh1 mutant was a mutant of the rice chalcone isomerase gene (OsCHI). The result showed that gh1 had a Dasheng retrotransposon inserted in the 5′ UTR of the OsCHI gene, which resulted in the complete loss of OsCHI expression. gh1 exhibited golden pigmentation in hulls and internodes once the panicles were exposed to light. The total flavonoid content in gh1 hulls was increased threefold compared to wild type. Consistent with the gh1 phenotype, OsCHI transcripts were expressed in most tissues of rice and most abundantly in internodes. It was also expressed at high levels in panicles before heading, distributed mainly in lemmas and paleae, but its expression decreased substantially after the panicles emerged from the sheath. OsCHI encodes a protein functionally and structurally conserved to chalcone isomerases in other species. Our findings demonstrated that the OsCHI gene was indispensable for flux of the flavonoid pathway in rice.

  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. Lignification of Sheepgrass Internodes at Different Developmental Stages and Associated Alteration of Cell Wall Saccharification Efficiency

    PubMed Central

    Wang, Jianli; Ma, Lichao; Shen, Zhongbao; Sun, Dequan; Zhong, Peng; Bai, Zetao; Zhang, Hailing; Cao, Yingping; Bao, Yan; Fu, Chunxiang

    2017-01-01

    Sheepgrass (Leymus chinensis) is a high-quality cool-season forage crop used as pasture and hay for livestock feeds. The presence of lignin in cell walls, however, impairs forage digestibility of such lignocellulosic feedstock. Here, the structural characterization and cell wall composition of sheepgrass internodes were studied, and a progressive increase in cell wall lignification was observed with internode maturation. Lignin composition analysis further revealed a gradual accumulation of guaiacyl and syringyl lignin units during internode development. Consistently, the transcript abundance of lignin-related genes was upregulated in mature internodes, suggesting their potential roles in lignin biosynthesis. Furthermore, the effects of cell wall composition and lignification extent on biomass saccharification efficiency were examined in sheepgrass. The results showed that lignin content, guaiacyl and syringyl lignin unit levels inversely correlated with cell wall digestibility, indicating that lignin is a crucial obstacle for utilizing sheepgrass feedstock. The baseline information obtained in this work will facilitate establishment, grazing management, harvesting and feedstock utilization of sheepgrass in future.

  11. In vitro plant regeneration from leaves and internode sections of sweet cherry cultivars (Prunus avium L.).

    PubMed

    Matt, Andrea; Jehle, Johannes A

    2005-10-01

    Regeneration of adventitious shoots from leaves and, for the first time, from internode sections were compared and optimized for five economically important sweet cherry cultivars, i.e. "Schneiders", "Sweetheart", "Starking Hardy Giant", "Kordia" and "Regina" (Prunus avium L.). The influence of basal media, carbon source, combination and dosage of phytohormones, ethylene inhibitor such as silver thiosulfate and a 16 h:8 h light:dark photoperiod versus complete darkness were evaluated. Both, DKW/WPM (1:1) and Quoirin/Lepoivre (QL) basal media stimulated organogenesis more than QL/WPM (1:1), Chee and Pool (CP), Murashige Skoog (MS), Driver and Kuniyuki (DKW) or woody plant (WPM) media did. An induction phase in darkness resulted in lower or zero regeneration rates. The best regeneration efficiencies were generally obtained with thidiazuron in combination with indole-3-butyric-acid. The addition of silver thiosulfate resulted in a similar or reduced regeneration efficiency. Significant genotypic variability in adventitious bud formation was evident for both explant sources, leaf and internode section. Adventitious shoots were obtained from 11% of leaf explants and 50% of internode sections indicating that shoot regeneration from internodes was significantly more efficient than from leaves.

  12. 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

  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. Isolation of rice dwarf mutants with ectopic deposition of phenolic components including lignin in parenchyma cell walls of internodes.

    PubMed

    Sato, Kanna; Kawamura, Asuka; Obara, Tsukasa; Kawai, Shinya; Kajita, Shinya; Kitano, Hidemi; Katayama, Yoshihiro

    2011-12-01

    Rice internodes must have the proper shape to support high-yielding panicles. The shape of internodes is controlled by various factors involved in their formation, such as developmental patterns, cell division, cell elongation, and cell wall biosynthesis. To understand the regulation of internode development, we screened dwarf mutants to identify those with a phenotype of ectopic deposits of phenolic components in parenchyma cell walls of internodes. We named these mutants ectopic deposition of phenolic components1 (edp1). Two alleles were identified, edp1-1 and edp1-2. Furthermore, these mutants showed disordered cell files in internode parenchyma. These abnormal phenotypes were very similar to that of a previously reported dwarf50 (d50) mutant. Genetic analyses of edp1 mutants revealed that the edp1 loci are distinct from d50. Our results indicate that analyses of edp1 mutants as well as the d50 mutant will be useful for understanding the molecular mechanisms behind ectopic deposition of cell wall phenolic components in internode parenchyma cells and the regulation of internode development.

  15. 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

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

    PubMed

    Avila, Luis M; Cerrudo, Diego; Swanton, Clarence; Lukens, Lewis

    2016-03-01

    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.

  17. 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

  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. Competence for Regeneration during Tobacco Internodal Development (Involvement of Plant Age, Cell Elongation Stage, and Degree of Polysomaty).

    PubMed Central

    Gilissen, LJW.; Van Staveren, M. J.; Hakkert, J. C.; Smulders, MJM.

    1996-01-01

    This study deals with internodal development in vegetative plants of Nicotiana tabacum cv Samsun NN and its reflection in changes of the cellular competence for regeneration. During elongation of the internodes, the cells of the epidermis, subepidermis, and cortex exclusively expanded and increased their DNA content cell type specifically, generally from 2C to 4C. Cells with the 8C DNA content were found mainly among the cortex cells of mature internodes. The frequency of shoot regeneration (directly from subepidermal and epidermal cells together) on thin cell layer explants increased to an optimum along with elongation of the internodes and decreased in mature internodes along with aging. The frequencies of diploid shoots among the regenerants from elongating and mature internodes were high (88 and 75% on the average, respectively), indicating that most cells that had achieved the 4C DNA content generally retained the G2 phase of the diploid cell cycle. Shoots regenerated from explants of young plant material mainly had a vitrified appearance. The occurrence of this type of malformed growth was already determined by the physiological state of the cells in the internode and did not interfere with their acquisition of competence. Vitrification was unrelated to the degree of polysomaty of the internodal tissue. Using the occurrence of tetraploid root regenerants (from intermediate cortex-derived callus), up to a frequency of 50%, we show that the position in the plant where a majority of the 4C cortex cells switched to the G1 phase of the tetraploid cell cycle was at the transition from the elongation phase to the mature phase. PMID:12226359

  20. Investigating the molecular genetic basis of heterosis for internode expansion in maize by microRNA transcriptomic deep sequencing.

    PubMed

    Zhao, Peng; Ding, Dong; Zhang, Fangfang; Zhao, Xiaofeng; Xue, Yadong; Li, Weihua; Fu, Zhiyuan; Li, Haochuan; Tang, Jihua

    2015-05-01

    Heterosis has been used widely in the breeding of maize and other crops and plays an important role in increasing yield, improving quality, and enhancing stress resistance, but its molecular mechanism is far from clear. To determine whether microRNA (miRNA)-dependent gene regulation is responsible for heterosis of elongating internodes below the ear and ear height in maize, a deep-sequencing strategy was applied to the elite hybrid Xundan20, which is currently cultivated widely in China, and its two parents. RNA was extracted from the eighth internode because it shows clear internode length heterosis. A total of 99 conserved maize miRNAs were detected in both the hybrid and parental lines. Most of these miRNAs were expressed nonadditively in the hybrid compared with its parental lines. These results indicated that miRNAs might participate in heterosis during internode expansion in maize and exert an influence on ear and plant height via the repression of their target genes. In total, eight novel miRNAs belonging to four miRNA families were predicted in the expanding internode. Global repression of miRNAs in the hybrid, which might result in enhanced gene expression, might be one reason why the hybrid shows longer internodes and taller seedlings compared with its parental lines.

  1. Shaping the shoot: the relative contribution of cell number and cell shape to variations in internode length between parent and hybrid apple trees.

    PubMed

    Ripetti, V; Escoute, J; Verdeil, J L; Costes, E

    2008-01-01

    Genetic control of plant size and shape is a promising perspective, particularly in fruit trees, in order to select desirable genotypes. A recent study on architectural traits in an apple progeny showed that internode length was a highly heritable character. However, few studies have been devoted to internode cellular patterning in dicotyledonous stems, and the interplay between the two elementary cell processes that contribute to their length, i.e. cell division and elongation, is not fully understood. The present study aimed at unravelling their contributions in the genetic variation of internode length in a selection of F(1) and parent genotypes of apple tree, by exploring the number of cells and cell shape within mature internodes belonging to the main axes. The results highlighted that both the variables were homogeneous in samples collected either along a sagital line or along the pith width, and suggest that cell lengthening was homogeneous during internode development. They allowed the total number of cells to be estimated on the internode scale and opened up new perspectives for simplifying tissue sampling procedures for further investigations. Differences in internode length were observed between the genotypes, in particular between the parents, and partly resulted from a compensation between cell number and cell length. However, genetic variations in internode length primarily involved the number of cells, while cell length was more secondary. These results argue for an interplay between cellular and organismal control of internode shape that may involve the rib meristem.

  2. Characteristics in Sliding Motions of Small Organelles in a Nitella Internodal Cell

    NASA Astrophysics Data System (ADS)

    Uchida, Go; Nemoto, Tomomi; Tsuchiya, Yoshimi

    1995-12-01

    Steady velocities of small organelles smoothly moving on chloroplasts in a Nitella internodal cell have been investigated at various temperatures. It has been found that variance in the velocities of the organelles changes in proportion to their average velocity, which has been first elucidated from the temperature dependence of the organelle's velocity. This result suggests that the generation process of the force due to the actin-myosin is a Poisson like stochastic one. Thus, we have discussed a stochastic model for the motion of the organelle with many myosin-like molecules and estimated the force to be 4.2×10-12 N.

  3. 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.

  4. Newly identified helper bacteria stimulate ectomycorrhizal formation in Populus

    DOE PAGES

    Labbe, Jessy L.; Weston, David J.; Dunkirk, Nora; ...

    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

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

    PubMed Central

    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. PMID:26734036

  6. 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

  7. The maize d2003, a novel allele of VP8, is required for maize internode elongation.

    PubMed

    Lv, Hongkun; Zheng, Jun; Wang, Tianyu; Fu, Junjie; Huai, Junling; Min, Haowei; Zhang, Xiang; Tian, Baohua; Shi, Yunsu; Wang, Guoying

    2014-02-01

    The d2003 is a natural dwarf mutant from maize inbred line K36 and has less than one-third of K36 plant height with severely shortened internodes. In this study, we reported the cloning of d2003 gene using positional cloning. The results showed that there was a single-base insertion in the coding region of Viviparous8 (VP8) in d2003 mutant, which resulted in a premature stop codon. Further genetic allelism tests confirmed that d2003 mutation is a novel allele of VP8. VP8 is mainly expressed in the stem apex, young leaves, and developing vascular tissues, and its expression levels in nodes are significantly higher than that in internodes at 12-leaf stage. Subcellular localization demonstrated that the VP8 protein is localized to the endoplasmic reticulum and the N-terminal 26 amino acids (aa) of VP8 protein are essential to its localization in ER. Further transgenic experiments showed that lack of the 26 aa leads to loss of VP8 function in Arabidopsis amp1 phenotype rescue. These results strongly suggested that the N-terminal 26 aa is critical for VP8 protein localization, and the correct protein localization of VP8 in ER is necessary for its function.

  8. Endogenous GABA controls oligodendrocyte lineage cell number, myelination, and CNS internode length

    PubMed Central

    Clarke, Laura E.; Arancibia‐Carcamo, I. Lorena; Kougioumtzidou, Eleni; Matthey, Moritz; Káradóttir, Ragnhildur; Whiteley, Louise; Bergersen, Linda H.; Richardson, William D.; Attwell, David

    2016-01-01

    Adjusting the thickness and internodal length of the myelin sheath is a mechanism for tuning the conduction velocity of axons to match computational needs. Interactions between oligodendrocyte precursor cells (OPCs) and developing axons regulate the formation of myelin around axons. We now show, using organotypic cerebral cortex slices from mice expressing eGFP in Sox10‐positive oligodendrocytes, that endogenously released GABA, acting on GABAA receptors, greatly reduces the number of oligodendrocyte lineage cells. The decrease in oligodendrocyte number correlates with a reduction in the amount of myelination but also an increase in internode length, a parameter previously thought to be set by the axon diameter or to be a property intrinsic to oligodendrocytes. Importantly, while TTX block of neuronal activity had no effect on oligodendrocyte lineage cell number when applied alone, it was able to completely abolish the effect of blocking GABAA receptors, suggesting that control of myelination by endogenous GABA may require a permissive factor to be released from axons. In contrast, block of AMPA/KA receptors had no effect on oligodendrocyte lineage cell number or myelination. These results imply that, during development, GABA can act as a local environmental cue to control myelination and thus influence the conduction velocity of action potentials within the CNS. GLIA 2017;65:309–321 PMID:27796063

  9. Endogenous GABA controls oligodendrocyte lineage cell number, myelination, and CNS internode length.

    PubMed

    Hamilton, Nicola B; Clarke, Laura E; Arancibia-Carcamo, I Lorena; Kougioumtzidou, Eleni; Matthey, Moritz; Káradóttir, Ragnhildur; Whiteley, Louise; Bergersen, Linda H; Richardson, William D; Attwell, David

    2017-02-01

    Adjusting the thickness and internodal length of the myelin sheath is a mechanism for tuning the conduction velocity of axons to match computational needs. Interactions between oligodendrocyte precursor cells (OPCs) and developing axons regulate the formation of myelin around axons. We now show, using organotypic cerebral cortex slices from mice expressing eGFP in Sox10-positive oligodendrocytes, that endogenously released GABA, acting on GABAA receptors, greatly reduces the number of oligodendrocyte lineage cells. The decrease in oligodendrocyte number correlates with a reduction in the amount of myelination but also an increase in internode length, a parameter previously thought to be set by the axon diameter or to be a property intrinsic to oligodendrocytes. Importantly, while TTX block of neuronal activity had no effect on oligodendrocyte lineage cell number when applied alone, it was able to completely abolish the effect of blocking GABAA receptors, suggesting that control of myelination by endogenous GABA may require a permissive factor to be released from axons. In contrast, block of AMPA/KA receptors had no effect on oligodendrocyte lineage cell number or myelination. These results imply that, during development, GABA can act as a local environmental cue to control myelination and thus influence the conduction velocity of action potentials within the CNS. GLIA 2017;65:309-321.

  10. Cell walls and the developmental anatomy of the Brachypodium distachyon stem internode.

    PubMed

    Matos, Dominick A; Whitney, Ian P; Harrington, Michael J; Hazen, Samuel P

    2013-01-01

    While many aspects of plant cell wall polymer structure are known, their spatial and temporal distribution within the stem are not well understood. Here, we studied vascular system and fiber development, which has implication for both biofuel feedstock conversion efficiency and crop yield. The subject of this study, Brachypodium distachyon, has emerged as a grass model for food and energy crop research. Here, we conducted our investigation using B. distachyon by applying various histological approaches and Fourier transform infrared spectroscopy to the stem internode from three key developmental stages. While vascular bundle size and number did not change over time, the size of the interfascicular region increased dramatically, as did cell wall thickness. We also describe internal stem internode anatomy and demonstrate that lignin deposition continues after crystalline cellulose and xylan accumulation ceases. The vascular bundle anatomy of B. distachyon appears to be highly similar to domesticated grasses. While the arrangement of bundles within the stem is highly variable across grasses, B. distachyon appears to be a suitable model for the rind of large C4 grass crops. A better understanding of growth and various anatomical and cell wall features of B. distachyon will further our understanding of plant biomass accumulation processes.

  11. Kinetic analysis using low-molecular mass xyloglucan oligosaccharides defines the catalytic mechanism of a Populus xyloglucan endotransglycosylase

    PubMed Central

    Saura-Valls, Marc; Fauré, Régis; Ragàs, Sergi; Piens, Kathleen; Brumer, Harry; Teeri, Tuula T.; Cottaz, Sylvain; Driguez, Hugues; Planas, Antoni

    2005-01-01

    Plant XETs [XG (xyloglucan) endotransglycosylases] catalyse the transglycosylation from a XG donor to a XG or low-molecular-mass XG fragment as the acceptor, and are thought to be important enzymes in the formation and remodelling of the cellulose-XG three-dimensional network in the primary plant cell wall. Current methods to assay XET activity use the XG polysaccharide as the donor substrate, and present limitations for kinetic and mechanistic studies of XET action due to the polymeric and polydisperse nature of the substrate. A novel activity assay based on HPCE (high performance capillary electrophoresis), in conjunction with a defined low-molecular-mass XGO {XG oligosaccharide; (XXXGXXXG, where G=Glcβ1,4- and X=[Xylα1,6]Glcβ1,4-)} as the glycosyl donor and a heptasaccharide derivatized with ANTS [8-aminonaphthalene-1,3,6-trisulphonic acid; (XXXG-ANTS)] as the acceptor substrate was developed and validated. The recombinant enzyme PttXET16A from Populus tremula x tremuloides (hybrid aspen) was characterized using the donor/acceptor pair indicated above, for which preparative scale syntheses have been optimized. The low-molecular-mass donor underwent a single transglycosylation reaction to the acceptor substrate under initial-rate conditions, with a pH optimum at 5.0 and maximal activity between 30 and 40 °C. Kinetic data are best explained by a ping-pong bi-bi mechanism with substrate inhibition by both donor and acceptor. This is the first assay for XETs using a donor substrate other than polymeric XG, enabling quantitative kinetic analysis of different XGO donors for specificity, and subsite mapping studies of XET enzymes. PMID:16356166

  12. 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

  13. 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

  14. 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

  15. 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

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

    PubMed

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

    2009-06-15

    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.

  18. 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.

  19. 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.

  20. 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.

  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. The Aquatic Communities Inhabiting Internodes of Two Sympatric Bamboos in Argentinean Subtropical Forest

    PubMed Central

    Campos, Raúl E.

    2013-01-01

    In order to determine if phytotelmata in sympatric bamboos of the genus Guadua might be colonized by different types of arthropods and contain communities of different complexities, the following objectives were formulated: (1) to analyze the structure and species richness of the aquatic macroinvertebrate communities, (2) to comparatively analyze co-occurrences; and (3) to identify the main predators. Field studies were conducted in a subtropical forest in Argentina, where 80 water-filled bamboo internodes of Guadua chacoensis (Rojas Acosta) Londoño and Peterson (Poales: Poaceae) and G. trinii (Nees) Nees and Rupr. were sampled. Morphological measurements indicated that G. chacoensis held more fluid than G. trinii. The communities differed between Guadua species, but many macroinvertebrate species used both bamboo species. The phytotelmata were mainly colonized by Diptera of the families Culicidae and Ceratopogonidae. PMID:24224775

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. Revisiting the sequencing of the first tree genome: Populus trichocarpa.

    PubMed

    Wullschleger, Stan D; Weston, D J; DiFazio, S P; Tuskan, G A

    2013-04-01

    Ten years ago, it was announced that the Joint Genome Institute with funds provided by the Department of Energy, Office of Science, Biological and Environmental Research would sequence the black cottonwood (Populus trichocarpa Torr. & Gray) genome. This landmark decision was the culmination of work by the forest science community to develop Populus as a model system. Since its public release in late 2006, the availability of the Populus genome has spawned research in plant biology, morphology, genetics and ecology. Here we address how the tree physiologist has used this resource. More specifically, we revisit our earlier contention that the rewards of sequencing the Populus genome would depend on how quickly scientists working with woody perennials could adopt molecular approaches to investigate the mechanistic underpinnings of basic physiological processes. Several examples illustrate the integration of functional and comparative genomics into the forest sciences, especially in areas that target improved understanding of the developmental differences between woody perennials and herbaceous annuals (e.g., phase transitions). Sequencing the Populus genome and the availability of genetic and genomic resources has also been instrumental in identifying candidate genes that underlie physiological and morphological traits of interest. Genome-enabled research has advanced our understanding of how phenotype and genotype are related and provided insights into the genetic mechanisms whereby woody perennials adapt to environmental stress. In the future, we anticipate that low-cost, high-throughput sequencing will continue to facilitate research in tree physiology and enhance our understanding at scales of individual organisms and populations. A challenge remains, however, as to how genomic resources, including the Populus genome, can be used to understand ecosystem function. Although examples are limited, progress in this area is encouraging and will undoubtedly improve as

  8. 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

  9. Conservation and divergence of microRNAs in Populus

    PubMed Central

    Barakat, Abdelali; Wall, Phillip K; DiLoreto, Scott; dePamphilis, Claude W; Carlson, John E

    2007-01-01

    Background MicroRNAs (miRNAs) are small RNAs (sRNA) ~21 nucleotides in length that negatively control gene expression by cleaving or inhibiting the translation of target gene transcripts. miRNAs have been extensively analyzed in Arabidopsis and rice and partially investigated in other non-model plant species. To date, 109 and 62 miRNA families have been identified in Arabidopsis and rice respectively. However, only 33 miRNAs have been identified from the genome of the model tree species (Populus trichocarpa), of which 11 are Populus specific. The low number of miRNA families previously identified in Populus, compared with the number of families identified in Arabidopsis and rice, suggests that many miRNAs still remain to be discovered in Populus. In this study, we analyzed expressed small RNAs from leaves and vegetative buds of Populus using high throughput pyrosequencing. Results Analysis of almost eighty thousand small RNA reads allowed us to identify 123 new sequences belonging to previously identified miRNA families as well as 48 new miRNA families that could be Populus-specific. Comparison of the organization of miRNA families in Populus, Arabidopsis and rice showed that miRNA family sizes were generally expanded in Populus. The putative targets of non-conserved miRNA include both previously identified targets as well as several new putative target genes involved in development, resistance to stress, and other cellular processes. Moreover, almost half of the genes predicted to be targeted by non-conserved miRNAs appear to be Populus-specific. Comparative analyses showed that genes targeted by conserved and non-conserved miRNAs are biased mainly towards development, electron transport and signal transduction processes. Similar results were found for non-conserved miRNAs from Arabidopsis. Conclusion Our results suggest that while there is a conserved set of miRNAs among plant species, a large fraction of miRNAs vary among species. The non-conserved miRNAs may

  10. Shotgun proteome profile of Populus developing xylem.

    PubMed

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

    2009-11-01

    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 MS/MS profiling to the proteome of Populus developing xylem. Nearly 6000 different proteins were identified from the xylem proteome. To identify low-abundance DNA-regulatory proteins from the developing xylem, a selective nuclear proteome profiling method was developed. Several putative transcription factors and chromatin remodeling proteins were identified using this method, such as NAC domain, CtCP-like and CHB3-SWI/SNF-related proteins. Public databases were mined to obtain information in support of subcellular localization, transcript-level expression and functional categorization of identified proteins. In addition to finding protein-level evidence of candidate cell wall biosynthesis genes from xylem (wood) tissue such as cellulose synthase, sucrose synthase and polygalacturonase, several other potentially new candidate genes in the cell wall biosynthesis pathway were discovered. Further application of such proteomics methods will aid in plant systems biology modeling efforts by enhancing the understanding not only of cell wall biosynthesis but also of other plant developmental and physiological pathways.

  11. 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

  12. 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.

  13. Characterization of DWARF14 Genes in Populus

    SciTech Connect

    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

    2016-02-15

    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% 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.

  14. 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

  15. Characterization of DWARF14 Genes in Populus

    DOE PAGES

    Zheng, Kaijie; Wang, Xiaoping; Weighill, Deborah A.; ...

    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

  16. Defining hybrid poplar (Populus deltoides x Populus trichocarpa) tolerance to ozone: identifying key parameters.

    PubMed

    Ryan, A; Cojocariu, C; Possell, M; Davies, W J; Hewitt, C N

    2009-01-01

    This study examined whether two genotypes of hybrid poplar (Populus deltoides x Populus trichocarpa), previously classified as ozone tolerant and ozone sensitive, had differing physiological and biochemical responses when fumigated with 120 nL L(-1) ozone for 6 h per day for eight consecutive days. Isoprene emission rate, ozone uptake and a number of physiological and biochemical parameters were investigated before, during and after fumigation with ozone. Previous studies have shown that isoprene protects plants against oxidative stress. Therefore, it was hypothesized that these two genotypes would differ in either their basal isoprene emission rates or in the response of isoprene to fumigation by ozone. Our results showed that the basal emission rates of isoprene, physiological responses and ozone uptake rates were all similar. However, significant differences were found in visible damage, carotenoids, hydrogen peroxide (H(2)O(2)), thiobarbituric acid reactions (TBARS) and post-fumigation isoprene emission rates. It is shown that, although the classification of ozone tolerance or sensitivity had been previously clearly and carefully defined using one particular set of parameters, assessment of other key variables does not necessarily lead to the same conclusions. Thus, it may be necessary to reconsider the way in which plants are classified as ozone tolerant or sensitive.

  17. Molecular linkage maps of the Populus genome.

    PubMed

    Yin, Tongming; Zhang, Xinye; Huang, Minren; Wang, Minxiu; Zhuge, Qiang; Tu, Shengming; Zhu, Li-Huang; Wu, Rongling

    2002-06-01

    We report molecular genetic linkage maps for an interspecific hybrid population of Populus, a model system in forest-tree biology. The hybrids were produced by crosses between P. deltoides (mother) and P. euramericana (father), which is a natural hybrid of P. deltoides (grandmother) and P. nigra (grandfather). Linkage analysis from 93 of the 450 backcross progeny grown in the field for 15 years was performed using random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs), and inter-simple sequence repeats (ISSRs). Of a total of 839 polymorphic markers identified, 560 (67%) were testcross markers heterozygous in one parent but null in the other (segregating 1:1), 206 (25%) were intercross dominant markers heterozygous in both parents (segregating 3:1), and the remaining 73 (9%) were 19 non-parental RAPD markers (segregating 1:1) and 54 codominant AFLP markers (segregating 1:1:1:1). A mixed set of the testcross markers, non-parental RAPD markers, and codominant AFLP markers was used to construct two linkage maps, one based on the P. deltoides (D) genome and the other based on P. euramericana (E). The two maps showed nearly complete coverage of the genome, spanning 3801 and 3452 cM, respectively. The availability of non-parental RAPD and codominant AFLP markers as orthologous genes allowed for a direct comparison of the rate of meiotic recombination between the two different parental species. Generally, the rate of meiotic recombination was greater for males than females in our interspecific poplar hybrids. The confounded effect of sexes and species causes the mean recombination distance of orthologous markers to be 11% longer for the father (P. euramericana; interspecific hybrid) than for the mother (P. deltoides; pure species). The linkage maps constructed and the interspecific poplar hybrid population in which clonal replicates for individual genotypes are available present a comprehensive foundation for future genomic studies and

  18. Evolutionary Quantitative Genomics of Populus trichocarpa.

    PubMed

    Porth, Ilga; Klápště, Jaroslav; 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 climate

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. Barley morphology, genetics and hormonal regulation of internode elongation modelled by a relational growth grammar.

    PubMed

    Buck-Sorlin, Gerhard H; Kniemeyer, Ole; Kurth, Winfried

    2005-06-01

    A multiscaled ecophysiological model of barley (Hordeum vulgare) development is presented here. The model is based on the new formalism of relational growth grammars (RGG), an extension of L-systems, and implemented using the new modelling language XL. It is executable in the interactive modelling platform GroIMP. The model consists of a set of morphogenetic rules, combined with a metabolic regulatory network, which simulates the biosynthesis of gibberellic acid (GA1). GA1 and two of its metabolic precursors are transported along the developing simulated structure. Local concentrations of GA1 determine internode elongation. Furthermore, virtual barley individuals are chosen interactively from a population, based on genotype, and (sexual or asexual) reproduction is simulated. Genotype and phenotype of the population are visualized. Seven Mendelian genes have been implemented in the model so far; some of these directly influence the GA-regulation network. The model exemplifies and validates the new formalism and modelling language. RGG have the capability to represent genetic, metabolic and morphological aspects of plant development and reproduction, all within the same framework.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. Differential effect of auxin on in vivo extensibility of cortical cylinder and epidermis in pea internodes.

    PubMed

    Kutschera, U; Briggs, W R

    1987-08-01

    The effect of auxin indole-3-acetic acid (IAA) on growth and in vivo extensibility of third internode sections from red light grown pea seedlings (Pisum sativum L. cv Alaska) and the isolated tissues (cortex plus vascular tissue = cortical cylinder, and epidermis) was investigated. Living tissue was stretched at constant force (creep test) in a custom-built extensiometer. In the intact section, IAA-induced increase in total (E(tot)), elastic (E(el)), and plastic (E(pl)) extensibility is closely related to the growth rate. The extensibility of the cortical cylinder, measured immediately after peeling of intact sections incubated for 4 hours in IAA, is not increased by IAA. Epidermal strips, peeled from growing sections incubated in IAA, show a E(pl) increase, which is correlated to the growth rate of the intact segments. The isolated cortical cylinder expands in water; IAA has only a small growth-promoting effect. The extensibility of the cortical cylinder is not increased by IAA. Epidermal strips contract about 10% on isolation. When incubated in IAA, they do not elongate, but respond with an E(pl) increase. The amount of expansion of the cortical cylinder and contraction of the epidermis (tissue tension), measured immediately following excision and peeling, stays constant during IAA-induced growth of intact sections. The results support the hypothesis that IAA induces growth of the intact section by causing an E(pl) increase of the outer epidermal wall. The driving force comes from the expansion of the cortical cylinder which is under constant compression in the intact section.

  13. Overexpression of LEAFY in apple leads to a columnar phenotype with shorter internodes.

    PubMed

    Flachowsky, Henryk; Hättasch, Conny; Höfer, Monika; Peil, Andreas; Hanke, Magda-Viola

    2010-01-01

    To break the juvenile stage of apple (Malus x domestica Borkh.) we transferred the LFY gene of Arabidopsis into the genome of the apple cv. 'Pinova'. A total of five transgenic clones constitutively overexpressing the LFY gene were obtained. Approximately, 20 shoots of each clone were rooted and transferred to the glasshouse. No flowers were obtained on transgenic plants during the first 2 years of cultivation. Evaluation of the expression of possible LFY targets revealed that no transcripts could be detected for MdAP1-1 and MdAP1-2. MdTFL1 was unaffected. Based on the absence of the LFY core-binding sequence within promoter sequences of MdAP1-1 and MdAP1-2, it was concluded that LFY was not able to induce these genes. The LFY genes of apple were unaffected in transgenic plants and sequence alignments of the C-terminal amino acid sequence showed a high conservation of these proteins. A change in binding ability to DNA can therefore be excluded. Instead of early flowering, the transgenic plants showed an altered phenotype, which is similar to the columnar phenotype of the 'McIntosh Wijcik' mutant of apple. The transgenic plants showed shortened internodes and a significantly reduced length of the regrowing shoot. A negative correlation was observed between the length of the regrowing shoot and the LFY mRNA transcript level. Furthermore, the LFY transgenic apple plants showed an increased shoot diameter at node 20, which was positively correlated with the LFY mRNA transcript level. Based on our results, we assume an alternative role of LFY in apple.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. Functional Characterization and Subcellular Localization of Poplar (Populus trichocarpa × Populus deltoides) Cinnamate 4-Hydroxylase1

    PubMed Central

    Ro, Dae Kyun; Mah, Nancy; Ellis, Brian E.; Douglas, Carl J.

    2001-01-01

    Cinnamic acid 4-hydroxylase (C4H), a member of the cytochrome P450 monooxygenase superfamily, plays a central role in phenylpropanoid metabolism and lignin biosynthesis and possibly anchors a phenylpropanoid enzyme complex to the endoplasmic reticulum (ER). A full-length cDNA encoding C4H was isolated from a hybrid poplar (Populus trichocarpa × P. deltoides) young leaf cDNA library. RNA-blot analysis detected C4H transcripts in all organs tested, but the gene was most highly expressed in developing xylem. C4H expression was also strongly induced by elicitor-treatment in poplar cell cultures. To verify the catalytic activity of the putative C4H cDNA, two constructs, C4H and C4H fused to the FLAG epitope (C4H::FLAG), were expressed in yeast. Immunoblot analysis showed that C4H was present in the microsomal fraction and microsomal preparations from strains expressing both enzymes efficiently converted cinnamic acid to p-coumaric acid with high specific activities. To investigate the subcellular localization of C4H in vivo, a chimeric C4H-green fluorescent protein (GFP) gene was engineered and stably expressed in Arabidopsis. Confocal laser microscopy analysis clearly showed that in Arabidopsis the C4H::GFP chimeric enzyme was localized to the ER. When expressed in yeast, the C4H::GFP fusion enzyme was also active but displayed significantly lower specific activity than either C4H or C4H::FLAG in in vitro and in vivo enzyme assays. These data definitively show that C4H is localized to the ER in planta. PMID:11351095

  20. 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.

  1. 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

  2. Alternative splicing and gene duplication differentially shaped the regulation of isochorismate synthase in Populus and Arabidopsis

    PubMed Central

    Yuan, Yinan; Chung, Jeng-Der; Fu, Xueyan; Johnson, Virgil E.; Ranjan, Priya; Booth, Sarah L.; Harding, Scott A.; Tsai, Chung-Jui

    2009-01-01

    Isochorismate synthase (ICS) converts chorismate to isochorismate for the biosynthesis of phylloquinone, an essential cofactor for photosynthetic electron transport. ICS is also required for salicylic acid (SA) synthesis during Arabidopsis defense. In several other species, including Populus, SA is derived primarily from the phenylpropanoid pathway. We therefore sought to investigate ICS regulation in Populus to learn the extent of ICS involvement in SA synthesis and defense. Arabidopsis harbors duplicated AtICS genes that differ in their exon-intron structure, basal expression, and stress inducibility. In contrast, we found a single ICS gene in Populus and six other sequenced plant genomes, pointing to the AtICS duplication as a lineage-specific event. The Populus ICS encodes a functional plastidic enzyme, and was not responsive to stresses that stimulated phenylpropanoid accumulation. Populus ICS underwent extensive alternative splicing that was rare for the duplicated AtICSs. Sequencing of 184 RT-PCR Populus clones revealed 37 alternative splice variants, with normal transcripts representing ≈50% of the population. When expressed in Arabidopsis, Populus ICS again underwent alternative splicing, but did not produce normal transcripts to complement AtICS1 function. The splice-site sequences of Populus ICS are unusual, suggesting a causal link between junction sequence, alternative splicing, and ICS function. We propose that gene duplication and alternative splicing of ICS evolved independently in Arabidopsis and Populus in accordance with their distinct defense strategies. AtICS1 represents a divergent isoform for inducible SA synthesis during defense. Populus ICS primarily functions in phylloquinone biosynthesis, a process that can be sustained at low ICS transcript levels. PMID:19996170

  3. The complete chloroplast genome sequence of desert poplar (Populus euphratica).

    PubMed

    Zhang, Qun-jie; Gao, Li-zhi

    2016-01-01

    The complete chloroplast sequence of the desert poplar (Populus euphratica), a plant well-adapted to salt stress, was determined in this study. The genome consists of 156,766 bp containing a pair of inverted repeats (IRs) of 16,591 bp separated by a large single-copy region and a small single-copy region of 84,888 bp and 27,646 bp, respectively. The chloroplast genome contains 130 known genes, including 89 protein-coding genes, 8 ribosomal RNA genes, and 37 tRNA genes; 18 of these are located in the inverted repeat region.

  4. 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.

  5. 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.

  6. Overcoming deep roots, fast rates, and short internodes to resolve the ancient rapid radiation of eupolypod II ferns.

    PubMed

    Rothfels, Carl J; Larsson, Anders; Kuo, Li-Yaung; Korall, Petra; Chiou, Wen-Liang; Pryer, Kathleen M

    2012-05-01

    Backbone relationships within the large eupolypod II clade, which includes nearly a third of extant fern species, have resisted elucidation by both molecular and morphological data. Earlier studies suggest that much of the phylogenetic intractability of this group is due to three factors: (i) a long root that reduces apparent levels of support in the ingroup; (ii) long ingroup branches subtended by a series of very short backbone internodes (the "ancient rapid radiation" model); and (iii) significantly heterogeneous lineage-specific rates of substitution. To resolve the eupolypod II phylogeny, with a particular emphasis on the backbone internodes, we assembled a data set of five plastid loci (atpA, atpB, matK, rbcL, and trnG-R) from a sample of 81 accessions selected to capture the deepest divergences in the clade. We then evaluated our phylogenetic hypothesis against potential confounding factors, including those induced by rooting, ancient rapid radiation, rate heterogeneity, and the Bayesian star-tree paradox artifact. While the strong support we inferred for the backbone relationships proved robust to these potential problems, their investigation revealed unexpected model-mediated impacts of outgroup composition, divergent effects of methods for countering the star-tree paradox artifact, and gave no support to concerns about the applicability of the unrooted model to data sets with heterogeneous lineage-specific rates of substitution. This study is among few to investigate these factors with empirical data, and the first to compare the performance of the two primary methods for overcoming the Bayesian star-tree paradox artifact. Among the significant phylogenetic results is the near-complete support along the eupolypod II backbone, the demonstrated paraphyly of Woodsiaceae as currently circumscribed, and the well-supported placement of the enigmatic genera Homalosorus, Diplaziopsis, and Woodsia.

  7. 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.

  8. 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.

  9. Foliar pathogens of Populus angustifolia are consistent with a hypothesis of Beringian migration into North America.

    PubMed

    Busby, Posy E; Aime, M Catherine; Newcombe, George

    2012-07-01

    Populus angustifolia, the narrowleaf cottonwood, is considered one of two native species of Populus section Tacamahaca restricted to western North America. Efforts to construct a definitive phylogeny of Populus spp. are complicated by ancient hybridization, but some phylogenetic analyses suggest P. angustifolia is more closely related to Asian congeners than to Populus trichocarpa, the other species of Populus section Tacamahaca in western North America. Because hosts and their obligate symbionts can display parallel phylogeographic patterns, we evaluated the possibility of a Beringian migration into North America by an Asian ancestor of P. angustifolia by determining the distributions, host preferences, and, in some cases, closest phylogenetic relatives of fungal leaf pathogens of P. angustifolia. Phyllactinia populi, a common foliar pathogen on Populus spp. in Asia but unknown on P. trichocarpa, was found on P. angustifolia in multiple sites. Mycosphaerella angustifoliorum, also unknown on P. trichocarpa, was commonly collected on P. angustifolia. Conversely, many common foliar pathogens of P. trichocarpa in western North America were not found on P. angustifolia; only Melampsora×columbiana and Drepanopeziza populi were common to both Populus species. Phylogenetic analyses revealed that M. angustifoliorum was not part of the diversification of Mycosphaerella on Populus that includes all other Mycosphaerella species on Populus in North America: Mycosphaerella populicola, Mycosphaerella populorum, M. sp. 1, and M. sp. 2. The latter two undescribed species represent a newly discovered diversification of M. populorum in western North America. Overall, the leaf pathogen community of P. angustifolia is consistent with a Beringian migration into North America by the ancestor of P. angustifolia.

  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. The effects of gamma irradiation on growth and expression of genes encoding DNA repair-related proteins in Lombardy poplar (Populus nigra var. italica).

    PubMed

    Nishiguchi, Mitsuru; Nanjo, Tokihiko; Yoshida, Kazumasa

    2012-07-01

    In this study, to elucidate the mechanisms of adaptation and tolerance to ionizing radiation in woody plants, we investigated the various biological effects of γ-rays on the Lombardy poplar (Populus nigra L. var. italica Du Roi). We detected abnormal leaf shape and color, fusion, distorted venation, shortened internode, fasciation and increased axillary shoots in γ-irradiated poplar plants. Acute γ-irradiation with a dose of 100Gy greatly reduced the height, stem diameter and biomass of poplar plantlets. After receiving doses of 200 and 300Gy, all the plantlets stopped growing, and then most of them withered after 4-10 weeks of γ-irradiation. Comet assays showed that nuclear DNA in suspension-cultured poplar cells had been damaged by γ-rays. To determine whether DNA repair-related proteins are involved in the response to γ-rays in Lombardy poplars, we cloned the PnRAD51, PnLIG4, PnKU70, PnXRCC4, PnPCNA and PnOGG1 cDNAs and investigated their mRNA expression. The PnRAD51, PnLIG4, PnKU70, PnXRCC4 and PnPCNA mRNAs were increased by γ-rays, but the PnOGG1 mRNA was decreased. Moreover, the expression of PnLIG4, PnKU70 and PnRAD51 was also up-regulated by Zeocin known as a DNA cleavage agent. These observations suggest that the morphogenesis, growth and protective gene expression in Lombardy poplars are severely affected by the DNA damage and unknown cellular events caused by γ-irradiation.

  12. [Application of Populus Nigra preparations at experimental parodontitis].

    PubMed

    Kipiani, N V; Kuchukhidze, Dzh K; Chichua, Z Dzh; Kipiani, V A; Datunashvili, I V

    2007-09-01

    Severe oxidative stress, developed under experimental periodontitis is accompanied by disturbances in mitochondrial respiration in tissue cells of gingiva, membrane damage and release of Fe(2+) and Mn(2+), leading to the worsening of inflammation process and gingival tissue necrosis. Reduction of free nitric oxide in gingival tissue appeared to be characteristic for experimental parodontitis: decreases local immunity, antimicrobial resistance, and tissue regeneration, disturbs blood supply and tissue trophism, which forwards important role in deepening of inflammation process and wasting of gingival tissue. Application of preparations derived from black poplar (Populus Nigra) gemma standardizes mitochondrial respiration, reduces presentation of inflammation, and considerably improves EPR-spectrum of gingival tissue. Though the complete normalization is not achieved--hazard of peroxidation still remains, the applied preparations, due to their strong anti- oxidative and anti-inflammatory activities is as an effective and rehabilitative means to tackle gingivitis and peiodontitis.

  13. Highly efficient CRISPR/Cas9-mediated targeted mutagenesis of multiple genes in Populus.

    PubMed

    Tingting, Liu; Di, Fan; Lingyu, Ran; Yuanzhong, Jiang; Rui, Liu; Keming, Luo

    2015-10-01

    The typeⅡCRISPR/Cas9 system (Clustered regularly interspaced short palindromic repeats /CRISPR-associated 9) has been widely used in bacteria, yeast, animals and plants as a targeted genome editing technique. In previous work, we have successfully knocked out the endogenous phytoene dehydrogenase (PDS) gene in Populus tomentosa Carr. using this system. To study the effect of target design on the efficiency of CRISPR/Cas9-mediated gene knockout in Populus, we analyzed the efficiency of mutagenesis using different single-guide RNA (sgRNA) that target PDS DNA sequence. We found that mismatches between the sgRNA and the target DNA resulted in decreased efficiency of mutagenesis and even failed mutagenesis. Moreover, complementarity between the 3' end nucleotide of sgRNA and target DNA is especially crucial for efficient mutagenesis. Further sequencing analysis showed that two PDS homologs in Populus, PtPDS1 and PtPDS2, could be knocked out simultaneously using this system with 86.4% and 50% efficiency, respectively. These results indicated the possibility of introducing mutations in two or more endogenous genes efficiently and obtaining multi-mutant strains of Populus using this system. We have indeed generated several knockout mutants of transcription factors and structural genes in Populus, which establishes a foundation for future studies of gene function and genetic improvement of Populus.

  14. 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

  15. 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

  16. Organogenesis from internode-derived nodules of Humulus lupulus var. Nugget (Cannabinaceae): histological studies and changes in the starch content.

    PubMed

    Fortes, A M; Pais, M S

    2000-07-01

    The sequence of histological and histochemical events occurring during organogenesis from Humulus lupulus var. Nugget internode-derived nodules was studied. Sections were made and studies were carried out from the start of culture treatment until the development of shoot buds. Cell division was observed in both cambial and cortical regions during the first week of culture establishment. Cell division in cortical cells led to the formation of an incipient callus tissue. From the calluses prenodular structures of cambial origin appeared and gave rise to nodules from which shoot buds formed. Nodules kept separating into "daughter nodules" from which arose an increasing number of shoot buds. Iodide staining showed a strong starch accumulation in callus tissue and in prenodular structures. During shoot-bud primordia formation starch content decreased in nodules. Some starch was also noted in control explants (cultured on basal medium), however at a lower level than that observed in explants cultured on media with growth regulators. Shoot-bud regeneration was not observed in control explants.

  17. Differential expression and cellular localization of ERKs during organogenic nodule formation from internodes of Humulus lupulus var. Nugget.

    PubMed

    Sousa Silva, Marta; Margarida Fortes, Ana; Sanchéz Testillanob, Pilar; Risueño, Maria del Carmen; Salom'e Pais, Maria

    2004-08-01

    The expression and subcellular localization of extracellular signal-regulated kinase 1 or 2 (ERK1/2) homologues (HLERK1/2) during the process of organogenic nodule formation in Humulus lupulus var. Nugget was studied using antibodies specific for ERK1 and ERK2, and for phosphorylated mitogen-activated protein kinases (MAPKs). The increase in HLERK levels, detected by Western blotting 12 hours after wounding suggests their involvement in response to the wounding treatment applied for morphogenesis induction. In dividing cambial cells, occurring in between 4 and 7 days after morphogenesis induction, as well as in dividing prenodular cells (15 days after induction) HLERK1 and/or 2 were localized in the nucleus. However, as soon as nodular cells start proliferating to form shoot meristems, HLERK1 and 2 were detected in the cytoplasm and not in the nucleus. The data reported account for a differential expression and activation of HLERK1 and HLERK2 throughout the process of nodule formation and plantlet regeneration. HLERK1 appears to be expressed in the stages of nodule formation and plantlet regeneration, playing a possible role in controlling cell proliferation and differentiation. HLERK2 may be induced as a response to reactive oxygen species (ROS) generated by wounding of internodes as its expression is reduced in liquid medium with less oxygen availability compared to solid medium. However, addition of a ROS inhibitor to the liquid medium does not result in a further decrease in the HLERK2 level.

  18. Diurnal regulation of plastid genes in Populus deltoides.

    PubMed

    Reddy, M S; Naithani, S; Tuli, R; Sane, P V

    2000-12-01

    Light regulates leaf and chloroplast development, together with overall chloroplast gene expression at various levels. Plants respond to diurnal and seasonal changes in light by changing expression of photosynthesis genes and metabolism. In Populus deltoides, a deciduous tree species, leaf development begins in the month of March and leaf maturation is attained by summer, which is subsequently followed by autumnal senescence and fall. In the present study, diurnal changes in the steady state transcript levels of plastid genes were examined in the fully developed leaves during summer season. Our results show that steady state level of the psaA/B, psbA, psbEFLJ and petA transcripts showed differential accumulation during diurnal cycle in summer. However, there was no significant change in the pigment composition during the day/night cycle. Our studies suggest that the diurnal regulation of steady state mRNA accumulation may play a crucial role during daily adjustments in plants life with rapidly changing light irradiance and temperature.

  19. 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

  20. Rhizobacteria of Populus euphratica Promoting Plant Growth Against Heavy Metals.

    PubMed

    Zhu, Donglin; Ouyang, Liming; Xu, Zhaohui; Zhang, Lili

    2015-01-01

    The heavy metal-resistant bacteria from rhizospheric soils of wild Populus euphratica forest growing in arid and saline area of northwestern China were investigated by cultivation-dependent methods. After screening on medium sparked with zinc, copper, nickel and lead, 146 bacteria strains with different morphology were isolated and most of them were found to be resistant to at least two kinds of heavy metals. Significant increase in fresh weight and leaf surface area of Arabidopsis thaliana seedlings under metal stress were noticed after inoculated with strains especially those having multiple-resistance to heavy metals such as Phyllobacterium sp. strain C65. Investigation on relationship between auxin production and exogenous zinc concentration revealed that Phyllobacterium sp. strain C65 produced auxin, and production decreased as the concentration of zinc in medium increased. For wheat seedlings treated with zinc of 2 mM, zinc contents in roots of inoculated plants decreased by 27% (P < 0.05) compared to the uninoculated control. Meanwhile, zinc accumulation in the above-ground tissues increased by 22% (P < 0.05). The translocation of zinc from root to above-ground tissues induced by Phyllobacterium sp. strain C65 helped host plants extract zinc from contaminated environments more efficiently thus alleviated the growth inhibition caused by heavy metals.

  1. Chemical responses to modified lignin composition in tension wood of hybrid poplar (Populus tremula x Populus alba).

    PubMed

    Al-Haddad, Jameel M; Kang, Kyu-Young; Mansfield, Shawn D; Telewski, Frank W

    2013-04-01

    The effect of altering the expression level of the F5H gene was investigated in three wood tissues (normal, opposite and tension wood) in 1-year-old hybrid poplar clone 717 (Populus tremula × Populus alba L.), containing the F5H gene under the control of the C4H promoter. Elevated expression of the F5H gene in poplar has been previously reported to increase the percent syringyl content of lignin. The wild-type and three transgenic lines were inclined 45° for 3 months to induce tension wood formation. Tension and opposite wood from inclined trees, along with normal wood from control trees, were analyzed separately for carbohydrates, lignin, cellulose crystallinity and microfibril angle (MFA). In the wild-type poplar, the lignin in tension wood contained a significantly higher percentage of syringyl than normal wood or opposite wood. However, there was no significant difference in the percent syringyl content of the three wood types within each of the transgenic lines. Increasing the F5H gene expression caused an increase in the percent syringyl content and a slight decrease in the total lignin in normal wood. In tension wood, the addition of a gelatinous layer in the fiber walls resulted in a consistently lower percentage of total lignin in the tissue. Acid-soluble lignin was observed to increase by up to 2.3-fold in the transgenic lines. Compared with normal wood and opposite wood, cell wall crystallinity in tension wood was higher and the MFA was smaller, as expected, with no evidence of an effect from modifying the syringyl monomer ratio. Tension wood in all the lines contained consistently higher total sugar and glucose percentages when compared with normal wood within the respective lines. However, both sugar and glucose percentages were lower in the tension wood of transgenic lines when compared with the tension wood of wild-type trees. Evaluating the response of trees with altered syringyl content to gravity will improve our understanding of the changes

  2. A survey of Populus PIN-FORMED family genes reveals their diversified expression patterns.

    PubMed

    Liu, Bobin; Zhang, Jin; Wang, Lin; Li, Jianbo; Zheng, Huanquan; Chen, Jun; Lu, Mengzhu

    2014-06-01

    The plant hormone auxin is a key regulator of plant development, and its uneven distribution maintained by polar intercellular auxin transport in plant tissues can trigger a wide range of developmental processes. Although the roles of PIN-FORMED (PIN) proteins in intercellular auxin flow have been extensively characterized in Arabidopsis, their roles in woody plants remain unclear. Here, a comprehensive analysis of PIN proteins in Populus is presented. Fifteen PINs are encoded in the genome of Populus, including four PIN1s, one PIN2, two PIN3s, three PIN5s, three PIN6s, and two PIN8s. Similar to Arabidopsis AtPIN proteins, PtPINs share conserved topology and transmembrane domains, and are either plasma membrane- or endoplasmic reticulum-localized. The more diversified expansion of the PIN family in Populus, comparing to that in Arabidopsis, indicates that some auxin-regulated developmental processes, such as secondary growth, may exhibit unique features in trees. More importantly, different sets of PtoPINs have been found to be strongly expressed in the roots, leaves, and cambium in Populus; the dynamic expression patterns of selected PtoPINs were further examined during the regeneration of shoots and roots. This genome-wide analysis of the Populus PIN family provides important cues for their potential roles in tree growth and development.

  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. Adaptive evolution and functional innovation of Populus-specific recently evolved microRNAs.

    PubMed

    Xie, Jianbo; Yang, Xiaohui; Song, Yuepeng; Du, Qingzhang; Li, Ying; Chen, Jinhui; Zhang, Deqiang

    2017-01-01

    Lineage-specific microRNAs (miRNAs) undergo rapid turnover during evolution; however, their origin and functional importance have remained controversial. Here, we examine the origin, evolution, and potential roles in local adaptation of Populus-specific miRNAs, which originated after the recent salicoid-specific, whole-genome duplication. RNA sequencing was used to generate extensive, comparable miRNA and gene expression data for six tissues. A natural population of Populus trichocarpa and closely related species were used to study the divergence rates, evolution, and adaptive variation of miRNAs. MiRNAs that originated in 5' untranslated regions had higher expression levels and their expression showed high correlation with their host genes. Compared with conserved miRNAs, a significantly higher proportion of Populus-specific miRNAs appear to target genes that were duplicated in salicoids. Examination of single nucleotide polymorphisms in Populus-specific miRNA precursors showed high amounts of population differentiation. We also characterized the newly emerged MIR6445 family, which could trigger the production of phased small interfering RNAs from NAC mRNAs, which encode a transcription factor with primary roles in a variety of plant developmental processes. Together, these observations provide evolutionary insights into the birth and potential roles of Populus-specific miRNAs in genome maintenance, local adaptation, and functional innovation.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. Soil plant interactions of Populus alba in contrasting environments.

    PubMed

    Ciadamidaro, Lisa; Madejón, Engracia; Robinson, Brett; Madejón, Paula

    2014-01-01

    The effects of the Populus alba tree on different biochemical soil properties, growing in a contaminated area, were studied for two years under field conditions. Two types of trace element contaminated soils were studied: a neutral contaminated soil (NC) and an acid contaminated soil (AC). One neutral non-contaminated area was studied as control. Soil samples were collected at depths of 0-20 cm and 20-40 cm. Leaves and litter samples were analysed. The addition of organic matter, through root exudates and litter, contributed to an increase in soil pH, especially in acid soil. Microbial Biomass Carbon (MBC) was significantly increased by the presence of the trees in all studied areas, especially in the upper soil layer. Similar results were also observed for protease activity. Both MBC and Protease activity were more sensitive to contamination than β-glucosidase activity. These changes resulted in a decrease of available trace element concentrations in soil and in an improvement of soil quality after a 2-year study. The total concentration of Cd and Zn in soil did not increase over time due to litter deposition. Analysis of P. alba leaves did not show a significant nutritional imbalance and trace element concentrations were normal for plants, except for Cd and Zn. These results indicate that P. alba is suitable for the improvement of soil quality in riparian contaminated areas. However, due to the high Cd and Zn concentrations in leaves, further monitoring of this area is required.

  11. Stress-responsive microRNAs in Populus.

    PubMed

    Lu, Shanfa; Sun, Ying-Hsuan; Chiang, Vincent L

    2008-07-01

    MicroRNAs (miRNAs), a group of small non-coding RNAs, have recently become the subject of intense study. They are a class of post-transcriptional negative regulators playing vital roles in plant development and growth. However, little is known about their regulatory roles in the responses of trees to the stressful environments incurred over their long-term growth. Here, we report the cloning of small RNAs from abiotic stressed tissues of Populus trichocarpa (Ptc) and the identification of 68 putative miRNA sequences that can be classified into 27 families based on sequence homology. Among them, nine families are novel, increasing the number of the known Ptc-miRNA families from 33 to 42. A total of 346 targets was predicted for the cloned Ptc-miRNAs using penalty scores of

  12. 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.

  13. 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.

  14. 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.

  15. Response to drought and salt stress in leaves of poplar (Populus alba × Populus glandulosa): expression profiling by oligonucleotide microarray analysis.

    PubMed

    Yoon, Seo-Kyung; Park, Eung-Jun; Choi, Young-Im; Bae, Eun-Kyung; Kim, Joon-Hyeok; Park, So-Young; Kang, Kyu-Suk; Lee, Hyoshin

    2014-11-01

    Drought and salt stresses are major environmental constraints on forest productivity. To identify genes responsible for stress tolerance, we conducted a genome-wide analysis in poplar (Populus alba × Populus glandulosa) leaves exposed to drought and salt (NaCl) stresses. We investigated gene expression at the mRNA level using oligonucleotide microarrays containing 44,718 genes from Populus trichocarpa. A total of 1604 and 1042 genes were up-regulated (≥2-fold; P value < 0.05) by drought and salt stresses, respectively, and 765 genes were up-regulated by both stresses. In addition, 2742 and 1685 genes were down-regulated by drought and salt stresses, respectively, and 1564 genes were down-regulated by both stresses. The large number of genes regulated by both stresses suggests that crosstalk occurs between the drought and salt stress responses. Most up-regulated genes were involved in functions such as subcellular localization, signal transduction, metabolism, and transcription. Among the up-regulated genes, we identified 47 signaling proteins, 65 transcription factors, and 43 abiotic stress-related genes. Several genes were modulated by only one of the two stresses. About 25% of the genes significantly regulated by these stresses are of unknown function, suggesting that poplar may provide an opportunity to discover novel stress-related genes.

  16. Dense genetic linkage maps of three Populus species (Populus deltoides, P. nigra and P. trichocarpa) based on AFLP and microsatellite markers.

    PubMed Central

    Cervera, M T; Storme, V; Ivens, B; Gusmão, J; Liu, B H; Hostyn, V; Van Slycken, J; Van Montagu, M; Boerjan, W

    2001-01-01

    Populus deltoides, P. nigra, and P. trichocarpa are the most important species for poplar breeding programs worldwide. In addition, Populus has become a model for fundamental research on trees. Linkage maps were constructed for these three species by analyzing progeny of two controlled crosses sharing the same female parent, Populus deltoides cv. S9-2 x P. nigra cv. Ghoy and P. deltoides cv. S9-2 x P. trichocarpa cv. V24. The two-way pseudotestcross mapping strategy was used to construct the maps. Amplified fragment length polymorphism (AFLP) markers that segregated 1:1 were used to form the four parental maps. Microsatellites and sequence-tagged sites were used to align homoeologous groups between the maps and to merge linkage groups within the individual maps. Linkage analysis and alignment of the homoeologous groups resulted in 566 markers distributed over 19 groups for P. deltoides covering 86% of the genome, 339 markers distributed over 19 groups for P. trichocarpa covering 73%, and 369 markers distributed over 28 groups for P. nigra covering 61%. Several tests for randomness showed that the AFLP markers were randomly distributed over the genome. PMID:11404342

  17. 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.

  18. Seedling competition between native Populus deltoides (Salicaceae) and exotic Tamarix ramosissima (Tamaricaceae) across water regimes and substrate types.

    PubMed

    Sher, Anna A; Marshall, Diane L

    2003-03-01

    Populus deltoides subsp. wislizinii (Salicaceae), a cottonwood native to the Middle Rio Grande of New Mexico, must potentially compete against exotic Tamarix ramosissima (Tamaricaceae) during establishment after flooding. We investigated competitive interactions between seedlings of Tamarix and Populus in two substrates representing field textures and declining (i.e., draw-down) or stagnant water tables. The experiment was performed using a full-additive series design and interpreted with response surface models for each species. As reflected in both aboveground mass and height, Populus suppressed aboveground growth of Tamarix across all treatments, whereas competitive effects of Tamarix against Populus could only be seen at low Populus densities. Clay substrates with draw-down stimulated the greatest growth and created the most intense competitive environment for both species. Tamarix was competitively suppressed in every substrate tested, with the weakest response in sand with no draw-down, where growth of Populus was poorest. These results suggest that stream flow management that promotes Populus establishment could also aid in controlling Tamarix invasion across a range of substrates.

  19. Identification of genes involved in cell wall biogenesis in grasses by differential gene expression profiling of elongating and non-elongating maize internodes

    PubMed Central

    Bosch, Maurice; Mayer, Claus-Dieter; Cookson, Alan; Donnison, Iain S.

    2011-01-01

    Despite the economic importance of grasses as food, feed, and energy crops, little is known about the genes that control their cell wall synthesis, assembly, and remodelling. Here a detailed transcriptome analysis that allowed the identification of genes involved in grass cell wall biogenesis is provided. Differential gene expression profiling, using maize oligonucleotide arrays, was used to identify genes differentially expressed between an elongating internode, containing cells exhibiting primary cell wall synthesis, and an internode that had just ceased elongation and in which many cells were depositing secondary cell wall material. This is one of only a few studies specifically aimed at the identification of cell wall-related genes in grasses. Analysis identified new candidate genes for a role in primary and secondary cell wall biogenesis in grasses. The results suggest that many proteins involved in cell wall processes during normal development are also recruited during defence-related cell wall remodelling events. This work provides a platform for studies in which candidate genes will be functionally tested for involvement in cell wall-related processes, increasing our knowledge of cell wall biogenesis and its regulation in grasses. Since several grasses are currently being developed as lignocellulosic feedstocks for biofuel production, this improved understanding of grass cell wall biogenesis is timely, as it will facilitate the manipulation of traits favourable for sustainable food and biofuel production. PMID:21402660

  20. Identification of a 98-kb DNA segment containing the rice Eui gene controlling uppermost internode elongation, and construction of a TAC transgene sublibrary.

    PubMed

    Xu, Y-H; Zhu, Y-Y; Zhou, H-C; Li, Q; Sun, Z-X; Liu, Y-G; Lin, H-X; He, Z-H

    2004-09-01

    The recessive 'tall rice' phenotype associated with the mutation eui (elongated upper-most internode) is an important agronomic trait that has been introduced into hybrid rice to eliminate panicle enclosure in all types of male-sterile lines and produce good-quality seeds in high yield and at low cost. Based on our previous Eui mapping data, we conducted fine-structure mapping and positional cloning of the gene using an F2 population comprising more than 5000 individuals derived from a cross of the near-isogenic lines 307T (eui/eui) with the recurrent parent Zhenshan 97 (Eui/Eui). In total 45 CAPS (cleaved amplified polymorphic sequences) markers located within an interval of 14.5 cM were analyzed in the subpopulation of 1298 homozygous recessive plants. The resulting high-resolution map defined a 98-kb interval containing the Eui locus flanked by the markers M0387 and M01, and three markers were found to co-segregate with Eui. In order to facilitate the identification of the Eui gene, we used a transformation-competent artificial chromosome (TAC) vector to construct a set of contiguous TAC clones from the Nipponbare BACs (obtained from the Clemson University Genome Institute; CUGI) spanning this region. These clones can be used to streamline complementation testing. The markers tightly linked to the Eui locus can also be used in breeding male-sterile lines with the elongated uppermost internode.

  1. 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.

  2. 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

  3. Regeneration capacity of small clonal fragments of the invasive Mikania micrantha H.B.K.: effects of burial depth and stolon internode length.

    PubMed

    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.

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

    DOE PAGES

    Klingeman, Dawn M.; Utturkar, Sagar; Lu, Tse -Yuan S.; ...

    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. 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.

  6. 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.

  7. Populus seed fibers as a natural source for production of oil super absorbents.

    PubMed

    Likon, Marko; Remškar, Maja; Ducman, Vilma; Švegl, Franc

    2013-01-15

    The genus Populus, which includes poplars, cottonwoods and aspen trees, represents a huge natural source of fibers with exceptional physical properties. In this study, the oil absorption properties of poplar seed hair fibers obtained from Populus nigra italica when tested with high-density motor oil and diesel fuel are reported. Poplar seed hair fibers are hollow hydrophobic microtubes with an external diameter between 3 and 12 μm, an average length of 4±1 mm and average tube wall thickness of 400±100 nm. The solid skeleton of the hollow fibers consists of lignocellulosic material coated by a hydrophobic waxy coating. The exceptional chemical, physical and microstructural properties of poplar seed hair fibers enable super-absorbent behavior with high absorption capacity for heavy motor oil and diesel fuel. The absorption values of 182-211 g heavy oil/g fiber and 55-60 g heavy oil/g fiber for packing densities of 0.005 g/cm(3) and 0.02 g/cm(3), respectively, surpass all known natural absorbents. Thus, poplar seed hair fibers obtained from Populus nigra italica and other trees of the genus Populus are an extremely promising natural source for the production of oil super absorbents.

  8. 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.

  9. Draft Genome Sequence of the Growth-Promoting Endophyte Paenibacillus sp. P22, Isolated from Populus

    PubMed Central

    Hanak, Anne M.; Nagler, Matthias; Weinmaier, Thomas; Sun, Xiaoliang; Fragner, Lena; Schwab, Clarissa; Rattei, Thomas; Ulrich, Kristina; Ewald, Dietrich; Engel, Marion; Schloter, Michael; Bittner, Romana; Schleper, Christa

    2014-01-01

    Paenibacillus sp. P22 is a Gram-negative facultative anaerobic endospore-forming bacterium isolated from poplar hybrid 741 (♀[Populus alba × (P. davidiana + P. simonii) × P. tomentosa]). This bacterium shows strong similarities to Paenibacillus humicus, and important growth-promoting effects on in vitro grown explants of poplar hybrid 741 have been described. PMID:24723717

  10. Characterization of Dof Transcription Factors and Their Responses to Osmotic Stress in Poplar (Populus trichocarpa).

    PubMed

    Wang, Han; Zhao, Shicheng; Gao, Yuchi; Yang, Jingli

    2017-01-01

    The DNA-binding One Zinc Finger (Dof) genes are ubiquitous in many plant species and are especial transcription regulators that participate in plant growth, development and various procedures, including biotic and abiotic stress reactions. In this study, we identified 41 PtrDof members from Populus trichocarpa genomes and classified them into four groups. The conserved motifs and gene structures of some PtrDof genes belonging to the same subgroup were almost the same. The 41 PtrDof genes were dispersed on 18 of the 19 Populus chromosomes. Many key stress- or phytohormone-related cis-elements were discovered in the PtrDof gene promoter regions. Consequently, we undertook expression profiling of the PtrDof genes in leaves and roots in response to osmotic stress and abscisic acid. A total of seven genes (PtrDof14, 16, 25, 27, 28, 37 and 39) in the Populus Dof gene family were consistently upregulated at point in all time in the leaves and roots under osmotic and abscisic acid (ABA) stress. We observed that 12 PtrDof genes could be targeted by 15 miRNAs. Moreover, we mapped the cleavage site in PtrDof30 using the 5'RLM-RACE. The results showed that PtrDofs may have a role in resistance to abiotic stress in Populus trichocarpa.

  11. Characterization of Dof Transcription Factors and Their Responses to Osmotic Stress in Poplar (Populus trichocarpa)

    PubMed Central

    Wang, Han; Zhao, Shicheng; Gao, Yuchi; Yang, Jingli

    2017-01-01

    The DNA-binding One Zinc Finger (Dof) genes are ubiquitous in many plant species and are especial transcription regulators that participate in plant growth, development and various procedures, including biotic and abiotic stress reactions. In this study, we identified 41 PtrDof members from Populus trichocarpa genomes and classified them into four groups. The conserved motifs and gene structures of some PtrDof genes belonging to the same subgroup were almost the same. The 41 PtrDof genes were dispersed on 18 of the 19 Populus chromosomes. Many key stress- or phytohormone-related cis-elements were discovered in the PtrDof gene promoter regions. Consequently, we undertook expression profiling of the PtrDof genes in leaves and roots in response to osmotic stress and abscisic acid. A total of seven genes (PtrDof14, 16, 25, 27, 28, 37 and 39) in the Populus Dof gene family were consistently upregulated at point in all time in the leaves and roots under osmotic and abscisic acid (ABA) stress. We observed that 12 PtrDof genes could be targeted by 15 miRNAs. Moreover, we mapped the cleavage site in PtrDof30 using the 5’RLM-RACE. The results showed that PtrDofs may have a role in resistance to abiotic stress in Populus trichocarpa. PMID:28095469

  12. 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/

  13. 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.

  14. The response of Populus spp. to cadmium stress: chemical, morphological and proteomics study.

    PubMed

    Marmiroli, Marta; Imperiale, Davide; Maestri, Elena; Marmiroli, Nelson

    2013-10-01

    Poplar (Populus) species are seen as candidates for removing heavy metal contamination from polluted soil. A bottom-up multidisciplinary approach was utilized to compare the performances of clones 58-861 and Poli (Populus nigra) and A4A, a Populus nigra × Populus deltoides hybrid to Cd toxicity. Qualitative and quantitative differences in their tolerance to Cd exposure and the uptake, accumulation and translocation of Cd were noted following the hydroponic exposure of rooted cuttings to 20 μM CdSO₄ for either 48 h or 14 d. Cadmium was less toxic for the hybrid clone A4A as compared to Poli and 58-861. Cd uptake and root to shoot translocation were determined by AAS, and its compartmentation was analyzed using SEM/EDX. A comparative proteomic approach was utilized to identify changes in proteins expression according to dose and time of exposure. Toxicity to Cd mainly influenced proteins related to general defense, stress response and carbohydrate metabolism.

  15. 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...

  16. 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

  17. 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.

  18. 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.

  19. Genome-wide association implicates numerous genes and pleiotropy underlying ecological trait variation in natural populations of Populus trichocarpa

    SciTech Connect

    McKown, Athena; Klapste, Jaroslav; Guy, Robert; Geraldes, Armando; Porth, Ilga; Hannemann, Jan; Friedmann, Michael; Muchero, Wellington; Tuskan, Gerald A; Ehlting, Juergen; Cronk, Quentin; El-Kassaby, Yousry; Mansfield, Shawn; Douglas, Carl

    2014-01-01

    To uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa Torr. & Gray) from natural populations throughout western North America. Extensive information from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34K Populus SNP array) of all accessions were used for gene discovery in a genome-wide association study (GWAS).

  20. 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.

  1. Productivity, water-use efficiency and tolerance to moderate water deficit correlate in 33 poplar genotypes from a Populus deltoides x Populus trichocarpa F1 progeny.

    PubMed

    Monclus, R; Villar, M; Barbaroux, C; Bastien, C; Fichot, R; Delmotte, F M; Delay, D; Petit, J-M; Bréchet, C; Dreyer, E; Brignolas, F

    2009-11-01

    Genotypic variability for productivity, water-use efficiency and leaf traits in 33 genotypes selected from an F1 progeny of Populus deltoides Bartr. ex Marsh x Populus trichocarpa L. was explored under optimal and moderate water-deficit conditions. Saplings of the 33 genotypes were grown in a two-plot open field at INRA Orléans (France) and coppiced every year. A moderate water deficit was induced during two successive years on one plot by withholding irrigation, while the second one remained irrigated (control). Stem biomass and leaf structure (e.g., specific leaf area and leaf area) were measured in 2004 and 2005 and functional leaf traits (e.g., carbon isotope discrimination, Delta) were measured only in 2004. Tolerance to water deficit was estimated at genotype level as the ability to limit losses in biomass production in water deficit versus control trees. Stem biomass, leaf structure and Delta displayed a significant genotypic variability whatever the irrigation regime. For all traits, genotype ranks remained stable across years for similar irrigation conditions. Carbon isotope discrimination scaled negatively with productivity and leaf nitrogen content in controls. The most productive genotypes were the least tolerant to moderate water deficit. No relationship was evidenced between Delta and the level of tolerance to water deficit. The relationships between traits evidenced in this collection of P. deltoides x P. trichocarpa F1 genotypes contrast with the ones that were previously detected in a collection of P. deltoides x Populus nigra L. cultivars tested in the same field trial.

  2. Microautoradiographic localization of phosphate and carbohydrates in mycorrhizal roots of Populus tremula x Populus alba and the implications for transfer processes in ectomycorrhizal associations.

    PubMed

    Bücking, H; Heyser, W

    2001-02-01

    Microautoradiographic studies were carried out to examine the distribution and exchange of phosphate and labeled carbohydrates in mycorrhizal roots of Populus tremula x Populus alba L. following application of 33P-orthophosphate (Pi) and 14CO2. Labeled Pi was not homogeneously distributed along the mycorrhizal longitudinal axis. The fungal sheath and the Hartig net contained more 33Pi in the median parts of the root than in the apical or basal root zones, indicating that uptake and transfer of Pi to the host plant was localized mainly in this area. The Pi was translocated by the Hartig net and the interfacial apoplast to the host plant. It was distributed by way of the stele within the plant. Young leaves and meristematic tissue in the shoot tip were the main sinks for Pi. In plants that were left in the dark for 5 days before 33Pi application, the reduced carbohydrate supply caused a decrease in Pi absorption by mycorrhizal roots. Microautoradiography of mycorrhizal roots after assimilation of 14CO2 revealed that: (1) the fungal partner had a high capacity to attract photosynthates; (2) the main transfer of carbohydrates was localized in the median zone of a mycorrhizal root; (3) carbohydrates that were absorbed by the mycorrhizal fungus were translocated to the fungal sheath and were homogeneously distributed; and (4) in the main exchange zone, cortical cell nuclei showed a high sink capacity, indicating increased metabolic activity in these cells. We postulate that (1) the phosphate demand of the host plant regulates absorption of Pi by the fungus, and (2) a bidirectional transfer of carbohydrates and Pi occurs across the same interface structure in ectomycorrhizal roots of Populus.

  3. Leaf-Induced Gibberellin Signaling Is Essential for Internode Elongation, Cambial Activity, and Fiber Differentiation in Tobacco Stems[C][W

    PubMed Central

    Dayan, Jonathan; Voronin, Nickolay; Gong, Fan; Sun, Tai-ping; Hedden, Peter; Fromm, Hillel; Aloni, Roni

    2012-01-01

    The gibberellins (GAs) are a group of endogenous compounds that promote the growth of most plant organs, including stem internodes. We show that in tobacco (Nicotiana tabacum) the presence of leaves is essential for the accumulation of bioactive GAs and their immediate precursors in the stem and consequently for normal stem elongation, cambial proliferation, and xylem fiber differentiation. These processes do not occur in the absence of maturing leaves but can be restored by application of C19-GAs, identifying the presence of leaves as a requirement for GA signaling in stems and revealing the fundamental role of GAs in secondary growth regulation. The use of reporter genes for GA activity and GA-directed DELLA protein degradation in Arabidopsis thaliana confirms the presence of a mobile signal from leaves to the stem that induces GA signaling. PMID:22253226

  4. Expression of a putative dioxygenase gene adjacent to an insertion mutation is involved in the short internodes of columnar apples (Malus × domestica).

    PubMed

    Okada, Kazuma; Wada, Masato; Moriya, Shigeki; Katayose, Yuichi; Fujisawa, Hiroko; Wu, Jianzhong; Kanamori, Hiroyuki; Kurita, Kanako; Sasaki, Harumi; Fujii, Hiroshi; Terakami, Shingo; Iwanami, Hiroshi; Yamamoto, Toshiya; Abe, Kazuyuki

    2016-11-01

    Determining the molecular mechanism of fruit tree architecture is important for tree management and fruit production. An apple mutant 'McIntosh Wijcik', which was discovered as a bud mutation from 'McIntosh', exhibits a columnar growth phenotype that is controlled by a single dominant gene, Co. In this study, the mutation and the Co gene were analyzed. Fine mapping narrowed the Co region to a 101 kb region. Sequence analysis of the Co region and the original wild-type co region identified an insertion mutation of an 8202 bp long terminal repeat (LTR) retroposon in the Co region. Segregation analysis using a DNA marker based on the insertion polymorphism showed that the LTR retroposon was closely associated with the columnar growth phenotype. RNA-seq and RT-PCR analysis identified a promising Co candidate gene (91071-gene) within the Co region that is specifically expressed in 'McIntosh Wijcik' but not in 'McIntosh'. The 91071-gene was located approximately 16 kb downstream of the insertion mutation and is predicted to encode a 2-oxoglutarate-dependent dioxygenase involved in an unknown reaction. Overexpression of the 91071-gene in transgenic tobaccos and apples resulted in phenotypes with short internodes, like columnar apples. These data suggested that the 8202 bp retroposon insertion in 'McIntosh Wijcik' is associated with the short internodes of the columnar growth phenotype via upregulated expression of the adjacent 91071-gene. Furthermore, the DNA marker based on the insertion polymorphism could be useful for the marker-assisted selection of columnar apples.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Cytogenetic analysis of Populus trichocarpa--ribosomal DNA, telomere repeat sequence, and marker-selected BACs.

    PubMed

    Islam-Faridi, M N; Nelson, C D; DiFazio, S P; Gunter, L E; Tuskan, G A

    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.

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

    SciTech Connect

    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 from 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.

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

    DOE PAGES

    Bonito, Gregory; Hameed, Khalid; Ventura, Rafael; ...

    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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

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

    DOE PAGES

    Payyavula, Raja S.; Tschaplinski, Timothy J.; Jawdy, Sara; ...

    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

  17. 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.

  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. [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.

  20. Rapid Activation of Phenylpropanoid Metabolism in Elicitor-Treated Hybrid Poplar (Populus trichocarpa Torr. & Gray × Populus deltoides Marsh) Suspension-Cultured Cells 1

    PubMed Central

    de Sá, Mário Moniz; Subramaniam, Rajgopal; Williams, Frank E.; Douglas, Carl J.

    1992-01-01

    Elicitor induction of phenylpropanoid metabolism was investigated in suspension-cultured cells of the fast-growing poplar hybrid (Populus trichocarpa Torr. & Gray × Populus deltoides Marsh) H11-11. Treatment of cells with polygalacturonic acid lyase or two fungal elicitors resulted in rapid and transient increases in extractable l-phenylalanine ammonia lyase and 4-coumarate:coenzyme A ligase enzyme activities. The substrate specificity of the inducible 4-coumarate:coenzyme A ligase enzyme activity appeared to differ from substrate specificity of 4-coumarate:coenzyme A ligase enzyme activity in untreated control cells. Large and transient increases in the accumulation of l-phenylalanine ammonia-lyase and 4-coumarate:coenzyme A ligase mRNAs preceded the increases in enzyme activities and were detectable by 30 minutes after the start of elicitor treatment. Chalcone synthase, cinnamyl alcohol dehydrogenase, and coniferin β-glucosidase enzyme activities were unaffected by the elicitors, but a large and transient increase in β-glucosidase activity capable of hydrolyzing 4-nitrophenyl-β-glucoside was observed. Subsequent to increases in l-phenylalanine ammonialyase and 4-coumarate:coenzyme A ligase enzyme activities, cell wall-bound thioglycolic acid-extractable compounds accumulated in elicitor-treated cultures, and these cells exhibited strong staining with phloroglucinol, suggesting the accumulation of wall-bound phenolic compounds. ImagesFigure 7Figure 9 PMID:16668702

  1. 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

  2. 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.

  3. Differentiation of Populus species using chloroplast single nucleotide polymorphism (SNP) markers--essential for comprehensible and reliable poplar breeding.

    PubMed

    Schroeder, H; Hoeltken, A M; Fladung, M

    2012-03-01

    Within the genus Populus several species belonging to different sections are cross-compatible. Hence, high numbers of interspecies hybrids occur naturally and, additionally, have been artificially produced in huge breeding programmes during the last 100 years. Therefore, determination of a single poplar species, used for the production of 'multi-species hybrids' is often difficult, and represents a great challenge for the use of molecular markers in species identification. Within this study, over 20 chloroplast regions, both intergenic spacers and coding regions, have been tested for their ability to differentiate different poplar species using 23 already published barcoding primer combinations and 17 newly designed primer combinations. About half of the published barcoding primers yielded amplification products, whereas the new primers designed on the basis of the total sequenced cpDNA genome of Populus trichocarpa Torr. & Gray yielded much higher amplification success. Intergenic spacers were found to be more variable than coding regions within the genus Populus. The highest discrimination power of Populus species was found in the combination of two intergenic spacers (trnG-psbK, psbK-psbl) and the coding region rpoC. In barcoding projects, the coding regions matK and rbcL are often recommended, but within the genus Populus they only show moderate variability and are not efficient in species discrimination.

  4. 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.

  5. 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

  6. Interaction of nitrogen nutrition and salinity in Grey poplar (Populus tremula x alba).

    PubMed

    Ehlting, B; Dluzniewska, P; Dietrich, H; Selle, A; Teuber, M; Hänsch, R; Nehls, U; Polle, A; Schnitzler, J-P; Rennenberg, H; Gessler, A

    2007-07-01

    Salinity represents an increasing environmental problem in managed ecosystems. Populus spp. is widely used for wood production by short-rotation forestry in fertilized plantations and can be grown on saline soil. Because N fertilization plays an important role in salt tolerance, we analysed Grey poplar (Populus tremula x alba, syn. Populus canescens) grown with either 1 mM nitrate or ammonium subjected to moderate 75 mM NaCl. The impact of N nutrition on amelioration of salt tolerance was analysed on different levels of N metabolism such as N uptake, assimilation and N (total N, proteins and amino compounds) accumulation. Na concentration increased in all tissues over time of salt exposure. The N nutrition-dependent effects of salt exposure were more intensive in roots than in leaves. Application of salt reduced root increment as well as stem height increase and, at the same time, increased the concentration of total amino compounds more intensively in roots of ammonium-fed plants. In leaves, salt treatment increased concentrations of total N more intensively in nitrate-fed plants and concentrations of amino compounds independently of N nutrition. The major changes in N metabolism of Grey poplar exposed to moderate salt concentrations were detected in the significant increase of amino acid concentrations. The present results indicate that N metabolism of Grey poplar exposed to salt performed better when the plants were fed with nitrate instead of ammonium as sole N source. Therefore, nitrate fertilization of poplar plantations grown on saline soil should be preferred.

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

    PubMed

    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; Ussery, David W

    2015-10-30

    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.

  8. 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

  9. 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

  10. Studies on callose and cutin during the expression of competence and determination for organogenic nodule formation from internodes of Humulus lupulus var. Nugget.

    PubMed

    Fortes, Ana M; Testillano, Pilar S; Del Carmen Risueño, Maria; Pais, Maria S

    2002-09-01

    Callose and cutin deposition were followed by staining with Aniline Blue and Nile Red and by immunolocalization using antibodies raised against callose. Along with morphogenesis induction from internodes of Humulus lupulus var. Nugget, a temporal and spatial differential deposition of callose and cutin was observed. A cutin layer showing bright yellow autofluorescence appears, surrounding cells or groups of cells committed to express morphogenic competence. This cutin layer that evolves to a randomly organized network appeared underneath a callose layer and may create a specific cellular environment with altered permeability and altered receptors providing conditions for entering the cell cycle. The incipient callose accumulation in control explants cultured on basal medium suggests the involvement of callose in the initiation of the morphogenic programme leading to nodule formation. A scanning electron microscopic study during the organogenic process showed that before shoot bud regeneration, the cutin layer increases in thickness and acquires a smooth texture. This cutin layer is specific to nodular organogenic regions and disappeared with plantlet regeneration. This layer may control permeability to water and solute transfer throughout plantlet regeneration.

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

    DOE PAGES

    Jun, Se Ran; Wassenaar, Trudy; Nookaew, Intawat; ...

    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

  12. 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

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

    SciTech Connect

    Dumitrache, Alexandru; Akinosho, Hannah; Rodriguez, Miguel; Meng, Xianzhi; Yoo, Chang Geun; Natzke, Jace; Engle, Nancy L.; Sykes, Robert W.; Tschaplinski, Timothy J.; Muchero, Wellington; Ragauskas, Arthur J.; Davison, Brian H.; Brown, Steven D.

    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 more 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 S

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

    DOE PAGES

    Dumitrache, Alexandru; Akinosho, Hannah; Rodriguez, Miguel; ...

    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

  15. Extensive allelic variation in gene expression in populus F1 hybrids.

    PubMed

    Zhuang, Yan; Adams, Keith L

    2007-12-01

    Hybridization between plant species can induce speciation as well as phenotypic novelty and heterosis. Hybrids also can show genome rearrangements and gene expression changes compared with their parents. Here we determined the allelic variation in gene expression in Populus trichocarpa x Populus deltoides F(1) hybrids. Among 30 genes analyzed in four independently formed hybrids, 17 showed >1.5-fold expression biases for one of the two alleles, and there was monoallelic expression of one gene. Expression ratios of the alleles differed between leaves and stems for 10 genes. The results suggest differential regulation of the two parental alleles in the hybrids. To determine if the allelic expression biases were caused by hybridization we compared the ratios of species-specific transcripts between an F(1) hybrid and its parents. Thirteen of 19 genes showed allelic expression ratios in the hybrid that were significantly different from the ratios of the parental species. The P. deltoides allele of one gene was silenced in the hybrid. Modes of gene regulation were inferred from the hybrid-parent comparisons. Cis-regulation was inferred for 6 genes, trans-regulation for 1 gene, and combined cis- and trans-regulation for 9 genes. The results from this study indicate that hybridization between plant species can have extensive effects on allelic expression patterns, some of which might lead to phenotypic changes.

  16. 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%.

  17. 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.

  18. 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.

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

    SciTech Connect

    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; Podar, Mircea; Doktycz, Mitchel J.; Pelletier, Dale A.

    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 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. Finally, comparative genomic analysis revealed unique characteristics of each SAG that could facilitate future cultivation efforts for these bacteria.

  20. 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.

  1. 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).

  2. 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.

  3. 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.

  4. Isolation and expression analysis of low temperature-induced genes in white poplar (Populus alba).

    PubMed

    Maestrini, Pierluigi; Cavallini, Andrea; Rizzo, Milena; Giordani, Tommaso; Bernardi, Rodolfo; Durante, Mauro; Natali, Lucia

    2009-09-15

    Poplar is an important crop and a model system to understand molecular processes of growth, development and responses to environmental stimuli in trees. In this study, we analyzed gene expression in white poplar (Populus alba) plants subjected to chilling. Two forward suppression-subtractive-hybridization libraries were constructed from P. alba plants exposed to low non-freezing temperature for 6 or 48h. Hundred and sixty-two cDNAs, 54 from the 6-h library and 108 from the 48-h library, were obtained. Isolated genes belonged to six categories of genes, specifically those that: (i) encode stress and defense proteins; (ii) are involved in signal transduction; (iii) are related to regulation of gene expression; (iv) encode proteins involved in cell cycle and DNA processing; (v) encode proteins involved in metabolism and energetic processes; and (vi) are involved in protein fate. Different expression patterns at 3, 6, 12, 24, 48h at 4 degrees C and after a recovery of 24h at 20 degrees C were observed for isolated genes, as expected according to the class in which the gene putatively belongs. Forty-four of 162 genes contained DRE/LTRE cis-elements in the 5' proximal promoter of their orthologs in Populus trichocarpa, suggesting that they putatively belong to the CBF regulon. The results contribute new data to the list of possible candidate genes involved in cold response in poplar.

  5. Enzymatic digestibility and pretreatment degradation products of AFEX-treated hardwoods (Populus nigra).

    PubMed

    Balan, Venkatesh; Sousa, Leonardo da Costa; Chundawat, Shishir P S; Marshall, Derek; Sharma, Lekh N; Chambliss, C Kevin; Dale, Bruce E

    2009-01-01

    There is a growing need to find alternatives to crude oil as the primary feed stock for the chemicals and fuel industry and ethanol has been demonstrated to be a viable alternative. Among the various feed stocks for producing ethanol, poplar (Populus nigra x Populus maximowiczii) is considered to have great potential as a biorefinery feedstock in the United States, due to their widespread availability and good productivity in several parts of the country. We have optimized AFEX pretreatment conditions (180 degrees C, 2:1 ammonia to biomass loading, 233% moisture, 30 minutes residence time) and by using various combinations of enzymes (commercical celluloses and xylanases) to achieve high glucan and xylan conversion (93 and 65%, respectively). We have also identified and quantified several important degradation products formed during AFEX using liquid chromatography followed by mass spectrometry (LC-MS/MS). As a part of degradation product analysis, we have also quantified oligosaccharides in the AFEX water wash extracts by acid hydrolysis. It is interesting to note that corn stover (C4 grass) can be pretreated effectively using mild AFEX pretreatment conditions, while on the other hand hardwood poplar requires much harsher AFEX conditions to obtain equivalent sugar yields upon enzymatic hydrolysis. Comparing corn stover and poplar, we conclude that pretreatment severity and enzymatic hydrolysis efficiency are dictated to a large extent by lignin carbohydrate complexes and arabinoxylan cross-linkages for AFEX.

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

    DOE PAGES

    Utturkar, Sagar M.; Cude, W. Nathan; Robeson, Jr., Michael S.; ...

    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

  7. 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

  8. Salt stress induces the formation of a novel type of 'pressure wood' in two Populus species.

    PubMed

    Janz, Dennis; Lautner, Silke; Wildhagen, Henning; Behnke, Katja; Schnitzler, Jörg-Peter; Rennenberg, Heinz; Fromm, Jörg; Polle, Andrea

    2012-04-01

    • Salinity causes osmotic stress and limits biomass production of plants. The goal of this study was to investigate mechanisms underlying hydraulic adaptation to salinity. • Anatomical, ecophysiological and transcriptional responses to salinity were investigated in the xylem of a salt-sensitive (Populus × canescens) and a salt-tolerant species (Populus euphratica). • Moderate salt stress, which suppressed but did not abolish photosynthesis and radial growth in P. × canescens, resulted in hydraulic adaptation by increased vessel frequencies and decreased vessel lumina. Transcript abundances of a suite of genes (FLA, COB-like, BAM, XET, etc.) previously shown to be activated during tension wood formation, were collectively suppressed in developing xylem, whereas those for stress and defense-related genes increased. A subset of cell wall-related genes was also suppressed in salt-exposed P. euphratica, although this species largely excluded sodium and showed no anatomical alterations. Salt exposure influenced cell wall composition involving increases in the lignin : carbohydrate ratio in both species. • In conclusion, hydraulic stress adaptation involves cell wall modifications reciprocal to tension wood formation that result in the formation of a novel type of reaction wood in upright stems named 'pressure wood'. Our data suggest that transcriptional co-regulation of a core set of genes determines reaction wood composition.

  9. 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.

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

    DOE PAGES

    Yee, Kelsey L.; Rodriguez, Jr., Miguel; Hamilton, Choo Yieng; ...

    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

  11. Fractionation of alkali-solubilized hemicelluloses from delignified Populus gansuensis: structure and properties.

    PubMed

    Peng, Feng; Ren, Jun-Li; Xu, Feng; Bian, Jing; Peng, Pai; Sun, Run-Cang

    2010-05-12

    The dewaxed cell walls of Populus gansuensis were delignified with NaClO(2) and then sequentially extracted with 0.25, 0.5, and 1.0 M KOH under a solid to liquid ratio of 1: 25 (g mL(-1)) at 25 degrees C for 10 h. The successive treatments together resulted in the dissolution of 83.7% of original hemicelluloses. The solubilized hemicellulosic fractions were further fractionated into six hemicellulosic subfractions by an iodine-complex precipitation technique. Their chemical and physical characteristics were determined by HPAEC, GPC, FT-IR, and (1)H and (13)C NMR spectroscopy. Neutral sugar composition and molecular weight analysis showed that, for each extract, the hemicellulosic subfractions that precipitated with aqueous potassium iodide-iodine had lower overall uronic acid/xylose (Uro/Xyl) ratios and higher molecular weights (M(w)) than those remaining in the solution. FT-IR, (1)H, and (13)C NMR spectroscopy analysis indicated that the alkali-soluble hemicelluloses of Populus gansuensis had a structure composed of the (1 --> 4)-linked beta-D-xylopyranosyl backbone with 4-O-methyl-alpha-D-glucuronic acid attached to O-2 of the xylose residues.

  12. 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

  13. Drought-Induced Xylem Dysfunction in Petioles, Branches, and Roots of Populus balsamifera L. and Alnus glutinosa (L.) Gaertn.

    PubMed Central

    Hacke, U.; Sauter, J. J.

    1996-01-01

    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. PMID:12226296

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species.

    PubMed

    Geraldes, A; Difazio, S P; Slavov, G T; Ranjan, P; Muchero, W; Hannemann, J; Gunter, L E; Wymore, A M; Grassa, C J; Farzaneh, N; Porth, I; McKown, A D; Skyba, O; Li, E; Fujita, M; Klápště, J; Martin, J; Schackwitz, W; Pennacchio, C; Rokhsar, D; Friedmann, M C; Wasteneys, G O; Guy, R D; El-Kassaby, Y A; Mansfield, S D; Cronk, Q C B; Ehlting, J; Douglas, C J; Tuskan, G A

    2013-03-01

    Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein 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 latitudinal range. 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, 3543 candidate genes. A subset of the SNPs on the array (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%. 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 the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids.

  19. 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.

  20. High rates of virus-induced gene silencing by tobacco rattle virus in Populus.

    PubMed

    Shen, Zedan; Sun, Jian; Yao, Jun; Wang, Shaojie; Ding, Mingquan; Zhang, Huilong; Qian, Zeyong; Zhao, Nan; Sa, Gang; Zhao, Rui; Shen, Xin; Polle, Andrea; Chen, Shaoliang

    2015-09-01

    Virus-induced gene silencing (VIGS) has been shown to be an effective tool for investigating gene functions in herbaceous plant species, but has rarely been tested in trees. The establishment of a fast and reliable transformation system is especially important for woody plants, many of which are recalcitrant to transformation. In this study, we established a tobacco rattle virus (TRV)-based VIGS system for two Populus species, Populus euphratica and P. × canescens. Here, TRV constructs carrying a 266 bp or a 558 bp fragment of the phytoene desaturase (PDS) gene were Agrobacterium-infiltrated into leaves of the two poplar species. Agrobacterium-mediated delivery of the shorter insert, TRV2-PePDS266, into the host poplars resulted in expected photobleaching in both tree species, but not the longer insert, PePDS558. The efficiency of VIGS was temperature-dependent, increasing by raising the temperature from 18 to 28 °C. The optimized TRV-VIGS system at 28 °C resulted in a high silencing frequency and efficiency up to 65-73 and 83-94%, respectively, in the two tested poplars. Moreover, syringe inoculation of Agrobacterium in 100 mM acetosyringone induced a more efficient silencing in the two poplar species, compared with other agroinfiltration methods, e.g., direct injection, misting and agrodrench. There were plant species-related differences in the response to VIGS because the photobleaching symptoms were more severe in P. × canescens than in P. euphratica. Furthermore, VIGS-treated P. euphratica exhibited a higher recovery rate (50%) after several weeks of the virus infection, compared with TRV-infected P. × canescens plants (20%). Expression stability of reference genes was screened to assess the relative abundance of PePDS mRNA in VIGS-treated P. euphratica and P. × canescens. PeACT7 was stably expressed in P. euphratica and UBQ-L was selected as the most suitable reference gene for P. × canescens using three different

  1. 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.

  2. 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.

  3. Expression of chloroplastic genes during autumnal senescence in a deciduous tree Populus deltiodes.

    PubMed

    Reddy, M S; Trivedi, P K; Tuli, R; Sane, P V

    1997-10-01

    In Populus deltoides, a deciduous tree, the development on new leaves starts in the month of March, the leaves reach maturity by October and fall by December. Changes in the composition and function of the photosynthetic apparatus were analysed during autumnal senescence. With the progress of senescence, there was an initial increase followed by a decrease in the steady state levels of psbA, psbD/C and psaA/B gene transcripts. Decrease in the steady state level of D1 protein was faster than that of Cytochrome f. The decline in LHCP level was seen only during late senescence. Although the leaves continue to look green and healthy till late November, the electron transport driven by individual photosystems started declining by October end suggesting the onset of senescence.

  4. 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.

  5. Biochemical and physiological studies on the effects of senescence leaves of Populus deltoides on Triticum vulgare.

    PubMed

    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.

  6. Towards a holistic understanding of the beneficial interactions across the Populus microbiome

    DOE PAGES

    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

  7. Within tree variability of lignin composition in Populus

    SciTech Connect

    Sykes, Robert; Kodrzycki, Bob; Tuskan, Gerald A; Foutz, Kirk; Davis, M F

    2008-01-01

    Clonal variability among trees has been studied and found to have profound effects on nearly all measured phenotypes. However, when estimating wood properties it is important to consider variability within the tree. The position in which a tree is sampled could have a large influence on biomass characterization. We looked at variability in lignin content as height increases and as the number of rings from the pith increase in Populus species. Seven trees were destructively sampled; subsamples were obtained along a 2.4 m length of each stem and across increment rings. All samples were analyzed by pyrolysis molecular beam mass spectroscopy to map the variability across sampling heights and/or ring positions inlignin content. The results of this study indicate that when sampling a tree, there is more variability from ring to ring than at different heights going up the stem.

  8. 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

  9. Climate, migration, and the local food security context: Introducing Terra Populus

    PubMed Central

    Schlak, Allison M.; Kugler, Tracy A.

    2016-01-01

    Studies investigating the connection between environmental factors and migration are difficult to execute because they require the integration of microdata and spatial information. In this article, we introduce the novel, publically available data extraction system Terra Populus (TerraPop), which was designed to facilitate population-environment studies. We showcase the use of TerraPop by exploring variations in the climate-migration association in Burkina Faso and Senegal based on differences in the local food security context. Food security was approximated using anthropometric indicators of child stunting and wasting derived from Demographic and Health Surveys (DHS) and linked to the TerraPop extract of climate and migration information. We find that an increase in heat waves was associated with a decrease in international migration from Burkina Faso, while excessive precipitation increased international moves from Senegal. Significant interactions reveal that the adverse effects of heat waves and droughts are strongly amplified in highly food insecure Senegalese departments. PMID:27974863

  10. A Putative PP2C-Encoding Gene Negatively Regulates ABA Signaling in Populus euphratica.

    PubMed

    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.

  11. Genotypic variation in a foundation tree (Populus tremula L.) explains community structure of associated epiphytes.

    PubMed

    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.

  12. In-situ reduced silver nanoparticles on populus fiber and the catalytic application

    NASA Astrophysics Data System (ADS)

    Li, Miaomiao; Gong, Yumei; Wang, Wenheng; Xu, Guangpeng; Liu, Yuanfa; Guo, Jing

    2017-02-01

    One kind of composites involved in silver nanoparticles (AgNPs) loading in-situ on natural populus fiber (PF) matrix was prepared by polyamidoxime (PAO) functionalized the cellulose fiber. In which PAO worked as trapping and stabilizing agents chelating silver ions and made it reduced in-situ to obtain AgNPs by borohydride at room temperature. The synthesized composites were characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA) and scanning electron microscopy (SEM). Moreover, the composites showed significant catalytic activity 1.87 s-1 g-1 and repeated usability more than 7 cycles in reducing 4-nitrophenol (4-NP) into 4-aminophenol (4-AP) detected by UV-vis spectrophotometer in aqueous solution due to the surface-enhanced immobility and large amount of AgNPs. The natural cellulose fiber provides a green platform to react and support other noble metals for wide catalytic reactions.

  13. Climate, migration, and the local food security context: Introducing Terra Populus.

    PubMed

    Nawrotzki, Raphael J; Schlak, Allison M; Kugler, Tracy A

    2016-12-01

    Studies investigating the connection between environmental factors and migration are difficult to execute because they require the integration of microdata and spatial information. In this article, we introduce the novel, publically available data extraction system Terra Populus (TerraPop), which was designed to facilitate population-environment studies. We showcase the use of TerraPop by exploring variations in the climate-migration association in Burkina Faso and Senegal based on differences in the local food security context. Food security was approximated using anthropometric indicators of child stunting and wasting derived from Demographic and Health Surveys (DHS) and linked to the TerraPop extract of climate and migration information. We find that an increase in heat waves was associated with a decrease in international migration from Burkina Faso, while excessive precipitation increased international moves from Senegal. Significant interactions reveal that the adverse effects of heat waves and droughts are strongly amplified in highly food insecure Senegalese departments.

  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. 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.

  16. Stem injection of Populus nigra with EDU to study ozone effects under field conditions.

    PubMed

    Bortier, K; Dekelver, G; De Temmerman, L; Ceulemans, R

    2001-01-01

    EDU or ethylenediurea (N-[2-(2-oxo-1-imidazolidinyl)ethyl]-N'-phenylurea) has been used in experiments to assess ozone effects on vegetation under field conditions because it provides protection against oxidative damage. Tests have mainly been conducted on crop plants, but for woody species only few reports have provided evidence that it can be used in long-term experiments. In this study we tested the technique of stem injection of EDU to study the effects of ozone exposure on Populus nigra cv. Wolterson over one growing season. Cuttings of Populus nigra were grown in pots in the field and between mid-July and early September plants were repeatedly injected with EDU solution (5 mg/plant) or with water at 14-day intervals. Significant differences were found between EDU- and water-injected plants: water-treated plants had more foliar injury, more chlorotic leaves, and shedding of leaves started earlier, suggesting EDU was effective in preventing visible ozone injury and acceleration of senescence. Photosynthetic rates, measured for one leaf age, showed no differences but were mostly higher for the EDU-treated plants. At the end of the growing season diameter increment was 16% higher and there was a non-significant trend for above-ground biomass to be increased by 9% for the EDU-treated plants. This experiment has provided evidence that for this clone serious ozone damage occurs at relatively low concentrations and that EDU can provide protection against visible injury, as well as against longer term growth reductions.

  17. 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.

  18. Molecular Population Genetics of Elicitor-Induced Resistance Genes in European Aspen (Populus tremula L., Salicaceae)

    PubMed Central

    Bernhardsson, Carolina; Ingvarsson, Pär K.

    2011-01-01

    Owing to their long life span and ecological dominance in many communities, forest trees are subject to attack from a diverse array of herbivores throughout their range, and have therefore developed a large number of both constitutive and inducible defenses. We used molecular population genetics methods to examine the evolution of eight genes in European aspen, Populus tremula, that are all associated with defensive responses against pests and/or pathogens, and have earlier been shown to become strongly up-regulated in poplars as a response to wounding and insect herbivory. Our results show that the majority of these defense genes show patterns of intraspecific polymorphism and site-frequency spectra that are consistent with a neutral model of evolution. However, two of the genes, both belonging to a small gene family of polyphenol oxidases, show multiple deviations from the neutral model. The gene PPO1 has a 600 bp region with a highly elevated KA/KS ratio and reduced synonymous diversity. PPO1 also shows a skew toward intermediate frequency variants in the SFS, and a pronounced fixation of non-synonymous mutations, all pointing to the fact that PPO1 has been subjected to recurrent selective sweeps. The gene PPO2 shows a marked excess of high frequency, derived variants and shows many of the same trends as PPO1 does, even though the pattern is less pronounced, suggesting that PPO2 might have been the target of a recent selective sweep. Our results supports data from both Populus and other species which have found that the the majority of defense-associated genes show few signs of selection but that a number of genes involved in mediating defense against herbivores show signs of adaptive evolution. PMID:21949772

  19. Influence of irrigation and fertilization on transpiration and hydraulic properties of Populus deltoides.

    PubMed

    Samuelson, Lisa J; Stokes, Thomas A; Coleman, Mark D

    2007-05-01

    Long-term hydraulic acclimation to resource availability was explored in 3-year-old Populus deltoides Bartr. ex Marsh. clones by examining transpiration, leaf-specific hydraulic conductance (G(L)), canopy stomatal conductance (G(S)) and leaf to sapwood area ratio (A(L):A(S)) in response to irrigation (13 and 551 mm year(-1) in addition to ambient precipitation) and fertilization (0 and 120 kg N ha(-1) year(-1)). Sap flow was measured continuously over one growing season with thermal dissipation probes. Fertilization had a greater effect on growth and hydraulic properties than irrigation, and fertilization effects were independent of irrigation treatment. Transpiration on a ground area basis (E) ranged between 0.3 and 1.8 mm day(-1), and increased 66% and 90% in response to irrigation and fertilization, respectively. Increases in G(L), G(S) at a reference vapor pressure deficit of 1 kPa, and transpiration per unit leaf area in response to increases in resource availability were associated with reductions in A(L):A(S) and consequently a minimal change in the water potential gradient from soil to leaf. Irrigation 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(2) ha(-1) by irrigation and from 3.7 to 6.7 m(2) ha(-1) 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. Elevated CO2 differentially affects photosynthetic induction response in two Populus species with different stomatal behavior.

    PubMed

    Tomimatsu, Hajime; Tang, Yanhong

    2012-08-01

    To understand dynamic photosynthetic characteristics in response to fluctuating light under a high CO(2) environment, we examined photosynthetic induction in two poplar genotypes from two species, Populus koreana 9 trichocarpa cv. Peace and Populus euramericana cv. I-55, respectively. Stomata of cv. Peace barely respond to changes in photosynthetic photon flux density (PFD), whereas those of cv. I-55 show a normal response to variations in PFD at ambient CO(2). The plants were grown under three CO2 regimes (380, 700, and 1,020 μmol CO(2) mol(-1) in air) for approximately 2 months. CO2 gas exchange was measured in situ in the three CO2 regimes under a sudden PFD increase from 20 to 800 μmol m(-2) s(-1). In both genotypes, plants grown under higher CO(2) conditions had a higher photosynthetic induction state, shorter induction time, and reduced induction limitation to photosynthetic carbon gain. Plants of cv. I-55 showed a much larger increase in induction state and decrease in induction time under high CO(2) regimes than did plants of cv. Peace. These showed that, throughout the whole induction process, genotype cv. I-55 had a much smaller reduction of leaf carbon gain under the two high CO(2) regimes than under the ambient CO(2) regime, while the high CO(2) effect was smaller in genotype cv. Peace. The results suggest that a high CO(2) environment can reduce both biochemical and stomatal limitations of leaf carbon gain during the photosynthetic induction process, and that a rapid stomatal response can further enhance the high CO(2) effect.

  5. 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.

  6. Characterization of the orf31-petG gene cluster from the plastid genome of Populus deltoides.

    PubMed

    Naithani, S; Trivedi, P K; Sane, P V

    1997-10-01

    The orf31-petG gene cluster is located approximately 1.2 kb away from the psbEFLJ operon in the chloroplast genome of Populus deltoides. The orf31 (ycf7) encodes an unidentified polypeptide while the petG gene encodes subunit V of an important component, cytochrome b6/f complex, involved in photosynthetic electron transport. We have determined the nucleotide sequence of the orf31-petG gene cluster from the plastid genome of a tree, Populus deltoides. Our sequence analysis suggests that these genes possess high homology with the published sequences of these genes from other plants. Northern analysis suggests development dependent transcription of the orf31-petG cluster in leaves.

  7. Sodium and chloride accumulation in leaf, woody, and root tissue of Populus after irrigation with landfill leachate.

    PubMed

    Zalesny, Jill A; Zalesny, Ronald S; Wiese, Adam H; Sexton, Bart; Hall, Richard B

    2008-09-01

    The response of Populus to irrigation sources containing elevated levels of sodium (Na(+)) and chloride (Cl(-)) is poorly understood. We irrigated eight Populus clones with fertilized well water (control) (N, P, K) or municipal solid waste landfill leachate weekly during 2005 and 2006 in Rhinelander, Wisconsin, USA (45.6 degrees N, 89.4 degrees W). During August 2006, we tested for differences in total Na(+) and Cl(-) concentration in preplanting and harvest soils, and in leaf, woody (stems+branches), and root tissue. The leachate-irrigated soils at harvest had the greatest Na(+) and Cl(-) levels. Genotypes exhibited elevated total tree Cl(-) concentration and increased biomass (clones NC14104, NM2, NM6), elevated Cl(-) and decreased biomass (NC14018, NC14106, DM115), or mid levels of Cl(-) and biomass (NC13460, DN5). Leachate tissue concentrations were 17 (Na(+)) and four (Cl(-)) times greater than water. Sodium and Cl(-) levels were greatest in roots and leaves, respectively.

  8. A Populus TIR1 gene family survey reveals differential expression patterns and responses to 1-naphthaleneacetic acid and stress treatments

    PubMed Central

    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 SCFTIR1/AFB and acts as an auxin co-receptor for nuclear auxin signaling. The SCFTIR1/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. PMID:26442033

  9. First Record of the Genus Zygina from a Neotropical Region on Populus spp.: Taxonomic and Biological Characteristics

    PubMed Central

    Catalano, M.I.; Brentassi, M.E.; Paradell, S. L.; Remes de Lenicov, A.M.M.

    2011-01-01

    The typhlocybine, Zygina nivea Mulsant & Rey 1855, was found in urban areas of Argentina colonizing trees of poplar (Populus alba L. and P. nigra L.). This is the first mention of the genus Zygina Fieber from the Neotropical region. In this paper redescription of the male, description of the female, distributional and host plant data, and behavioural observations of this species are given. PMID:21870983

  10. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map

    SciTech Connect

    Kelleher, Colin; CHIU, Dr. R.; Shin, Dr. H.; Krywinski, Martin; Fjell, Chris; Wilkin, Jennifer; Yin, Tongming; Difazio, Stephen P.

    2007-01-01

    As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 {+-} 10 Mb in size. BAC ends were sequenced to assist long-range assembly of whole-genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa, version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.

  11. RNA sequencing of Populus x canadensis roots identifies key molecular mechanisms underlying physiological adaption to excess zinc.

    PubMed

    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.

  12. [Morphological analysis of transgenic tobacco plants expressing the PnEXPA3 gene of black poplar (Populus nigra)].

    PubMed

    Kuluev, B R; Safiullina, M G; Kniazev, A V; Chemeris, A V

    2013-01-01

    Transgenic tobacco plants overexpressing the PnEXPA3 gene of black poplar (Populus nigra), which encodes alpha-expansin, were obtained. The transgenic plants were characterized by increased size of epidermic and mesophyll cells of leaves. However, the size of leaves remained normal. Overexpression of the PnEXPA3 gene provided stimulatory effect only on the stem length. Other morphological traits of the transgenic plants remained unchanged.

  13. 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

  14. Effects of fragment traits, burial orientation and nutrient supply on survival and growth in Populus deltoides × P. simonii.

    PubMed

    Zhang, Ping; Su, Zhi-Qin; Xu, Lie; Shi, Xue-Ping; Du, Ke-Bing; Zheng, Bo; Wang, Yong-Jian

    2016-02-15

    Clonal propagations of shoot or root fragments play pivotal roles in adaptation of clonal trees to environmental heterogeneity, i.e. soil nutrient heterogeneity and burials after disturbance. However, little is known about whether burial orientation and nutrient supply can alter the effects of fragment traits in Populus. Shoot and root fragments of Populus deltoides × P. simonii were subjected to burials in two different fragment diameters (0.5 and 2.0 cm), two fragment lengths (5 and 15 cm) and three burial orientations (horizontal, upward and downward). For the shoot fragments, survival and growth were significantly higher in the larger pieces (either in length or diameter) and the horizontal/upward burial position. On the contrary, the effect of burial position was reversed for the root fragments. Shoot/root fragments of 15 cm in length in horizontal burial position were then subjected to two different fragment diameters (0.5 and 2.0 cm) and four types of nutrient supplies (without nutrient, low frequency, high frequency and patchy). Growth of shoot fragments of 2.0 cm in diameter significantly increased in high frequency and patchy nutrient supplies than that of without nutrient treatment. These results suggest that burial orientation and nutrient supply could be employed in clonal propagations of cuttings, afforestation or regeneration in Populus.

  15. Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of Populus using shotgun proteomics.

    PubMed

    Abraham, Paul; Adams, Rachel; Giannone, Richard J; Kalluri, Udaya; Ranjan, Priya; Erickson, Brian; Shah, Manesh; Tuskan, Gerald A; Hettich, Robert 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 7505 identified proteins to a total of 4226 protein groups, in which 2016 were singletons. This reduction implies that ∼50% of the measured proteins shared extensive sequence homology. Using conservative search criteria, we were able to identify 1354 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 previously unidentified proteins. In total, the integration of deep proteome measurements on an extensive sample set with protein clustering and peptide sequence variants provided an exceptional level of proteome characterization for Populus, allowing us to spatially resolve the vascular tissue proteome.

  16. 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.

  17. 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

  18. Changes in sulphur metabolism of grey poplar (Populus x canescens) leaves during salt stress: a metabolic link to photorespiration.

    PubMed

    Herschbach, Cornelia; Teuber, Markus; Eiblmeier, Monika; Ehlting, Barbara; Ache, Peter; Polle, Andrea; Schnitzler, Jörg-Peter; Rennenberg, Heinz

    2010-09-01

    The poplar hybrid Populus x canescens (syn. Populus tremula x Populus alba) was subjected to salt stress by applying 75 mM NaCl for 2 weeks in hydroponic cultures. Decreasing maximum quantum yield (Fv/Fm) indicated damage of photosystem II (PS II), which was more pronounced under nitrate compared with ammonium nutrition. In vivo staining with diaminobenzidine showed no accumulation of H(2)O(2) in the leaf lamina; moreover, staining intensity even decreased. But at the leaf margins, development of necrotic tissue was associated with a strong accumulation of H(2)O(2). Glutathione (GSH) contents increased in response to NaCl stress in leaves but not in roots, the primary site of salt exposure. The increasing leaf GSH concentrations correlated with stress-induced decreases in transpiration and net CO(2) assimilation rates at light saturation. Enhanced rates of photorespiration could also be involved in preventing reactive oxygen species formation in chloroplasts and, thus, in protecting PS II from damage. Accumulation of Gly and Ser in leaves indeed indicates increasing rates of photorespiration. Since Ser and Gly are both immediate precursors of GSH that can limit GSH synthesis, it is concluded that the salt-induced accumulation of leaf GSH results from enhanced photorespiration and is thus probably restricted to the cytosol.

  19. Development and application of microsatellites in candidate genes related to wood properties in the Chinese white poplar (Populus tomentosa Carr.).

    PubMed

    Du, Qingzhang; Gong, Chenrui; Pan, Wei; Zhang, Deqiang

    2013-02-01

    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.

  20. Expression of glutathione S-transferases in poplar trees (Populus trichocarpa) exposed to 2,4,6-trinitrotoluene (TNT).

    PubMed

    Brentner, Laura B; Mukherji, Sachiyo T; Merchie, Kate M; Yoon, Jong Moon; Schnoor, Jerald L; Van Aken, Benoit

    2008-10-01

    Twelve Populus genes were identified from Arabidopsis thaliana sequences previously shown to be induced by exposure to 2,4,6-trinitrotoluene (TNT). Using the resources of the Poplar Genome Project and National Center for Biotechnology Information databases, Populus conserved domains were identified and used to design gene specific primers. RNA extracted from root tissues of TNT-exposed hydroponic poplar plants was used to quantify the expression of genes by reverse-transcriptase real-time polymerase chain reaction. Cyclophilin and 18S ribosomal DNA genes were used as internal standards. Exposure to TNT resulted in a significant increase of gene expression of two glutathione S-transferases (GST), peaking at levels of 25.0 +/- 13.1 and 10 +/- 0.7 fold the expression level of non-exposed plants after 24 h for each of the GST genes, respectively. This paper demonstrates the use of functional genomics information from the model plant species, Arabidopsis, to identify genes which may be important in detoxification of TNT in the model phytoremediation species, Populus trichocarpa.

  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. 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.

  3. 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.

  4. Phylogenetic and Taxonomic Status Analyses of the Abaso Section from Multiple Nuclear Genes and Plastid Fragments Reveal New Insights into the North America Origin of Populus (Salicaceae)

    PubMed Central

    Liu, Xia; Wang, Zhaoshan; Shao, Wenhao; Ye, Zhanyang; Zhang, Jianguo

    2017-01-01

    Although, the Abaso section is widely accepted as an independent section, the taxonomic status of Populus mexicana (section Abaso) has not yet been resolved due to the limited availability markers and/or the lack of P. mexicana specimens in previous studies. Thirty-one poplar species that represent six sections of the Populus genus were sampled, and 23 single-copy nuclear DNA and 34 chloroplast fragments were sequenced. The present study obtained two updated phylogenies of Populus. We found that monophyly of the genus Populus is strongly supported by nuclear and plastid gene, which is consistent with previous studies. P. mexicana, diverged first in the nuclear DNA tree, which occupied the basal position, implying that the section Abaso may be the most ancestral lineage in extant populous species. Given that the short branches and low statistical support for the divergence of sections Abaso and Turanga, this observation probably indicated that a rapid radiation evolution following the early split of the genus Populus. In the plastid tree, P. mexicana clustered with modern-day species of section Tacamahaca in the plastid tree. Based on cytoplasmic and single-copy nuclear marker sequences, we hypothesized that chloroplast capture resulted in the inconsistent position of P. mexicana between the phylogenetic trees. Given the first unequivocal records of poplar fossils from the Eocene with similar leaf morphology to the extant P. mexicana and the phylogenetic positions of P. mexicana in our study, we support the hypothesis that the Populus genus originated in North America, which will provide new insights to the development of the origin of Populus species. PMID:28101098

  5. Comparative expression analysis of resistant and susceptible Populus clones inoculated with Septoria musiva.

    PubMed

    Liang, Haiying; Staton, Margaret; Xu, Yi; Xu, Tao; Leboldus, Jared

    2014-06-01

    Septoria musiva is a major pathogen of Populus and can cause leaf spots and stem cankers in susceptible clones. In order to investigate defense mechanisms of Populus in response to S. musiva, differential gene expression in leaf tissues of two resistant (DN34, P. deltoides×nigra; NM6, P. nigra×maximowiczii) and two susceptible clones (DN164, P. deltoides×nigra; NC11505, P. maximowiczii×trichocarpa) was analyzed by RNA-Seq. Of the 511 million reads obtained, 78% and 0.01% were successfully aligned to the genomes of P. trichocarpa and S. musiva, respectively. Functional annotation of differentially expressed genes based on comparisons between resistant and susceptible clones revealed that there were significant differences in the expression of genes involved in disease/stress resistance and oxidation-reduction in mock-inoculated leaves. Four days post inoculation with S. musiva, 36 differentially expressed genes were found to be regulated in the same direction in both resistant clones. The 22 up-regulated loci in resistant clones included genes involved in protein fate, cell wall structure, and responsiveness to various biotic and abiotic stresses. In particular, Potri.008G187100 locus encodes a putative multi antimicrobial extrusion protein and Potri.006G272600 encodes a family1 glycosyltransferase required for pathogen resistance. The differentially expressed loci with increased expression in the susceptible clones corresponded to NB-ARC domain-containing disease resistance protein, phospholipase A 2A, MutT/nudix family protein, and an elicitor-activated gene 3-1 product. The results from this study indicate that strong defense mechanisms involved in oxidation-reduction, protein fate, secondary metabolism, and accumulation of defense-related gene products may contribute to Septoria resistance in DN34 and NM6, while increased expression of hypersensitive response-loci, particularly those encoding NB-ARC domain-containing disease resistance proteins, may

  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 PAGES

    Ribeiro, Cintia L.; Silva, Cynthia M.; Drost, Derek R.; ...

    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. Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus

    SciTech Connect

    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 and 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 the Trp

  9. Shifting dominance of riparian Populus and Tamarix along gradients of flow alteration in western North American rivers.

    PubMed

    Merritt, David M; Poff, N LeRoy

    2010-01-01

    Tamarix ramosissima is a naturalized, nonnative plant species which has become widespread along riparian corridors throughout the western United States. We test the hypothesis that the distribution and success of Tamarix result from human modification of river-flow regimes. We conducted a natural experiment in eight ecoregions in arid and semiarid portions of the western United States, measuring Tamarix and native Populus recruitment and abundance at 64 sites along 13 perennial rivers spanning a range of altered flow regimes. We quantified biologically relevant attributes of flow alteration as an integrated measure (the index of flow modification, IFM), which was then used to explain between-site variation in abundance and recruitment of native and nonnative riparian plant species. We found the likelihood of successful recruitment of Tamarix to be highest along unregulated river reaches and to remain high across a gradient of regulated flows. Recruitment probability for Populus, in contrast, was highest under free-flowing conditions and declined abruptly under even slight flow modification (IFM > 0.1). Adult Tamarix was most abundant at intermediate levels of IFM. Populus abundance declined sharply with modest flow regulation (IFM > 0.2) and was not present at the most flow-regulated sites. Dominance of Tamarix was highest along rivers with the most altered flow regimes. At the 16 least regulated sites, Tamarix and Populus were equally abundant. Given observed patterns of Tamarix recruitment and abundance, we infer that Tamarix would likely have naturalized, spread, and established widely in riparian communities in the absence of dam construction, diversions, and flow regulation in western North America. However, Tamarix dominance over native species would likely be less extensive in the absence of human alteration of river-flow regimes. Restoration that combines active mechanical removal of established stands of Tamarix with a program of flow releases conducive to

  10. Organization and post-transcriptional processing of the psb B operon from chloroplasts of Populus deltoides.

    PubMed

    Dixit, R; Trivedi, P K; Nath, P; Sane, P V

    1999-09-01

    Chloroplast genes are typically organized into polycistronic transcription units that give rise to complex sets of mono- and oligo-cistronic overlapping RNAs through a series of processing steps. The psbB operon contains genes for the PSII (psbB, psbT, psbH) and cytochrome b(6)f (petB and petD) complexes which are needed in different amounts during chloroplast biogenesis. The functional significance of gene organization in this polycistronic unit, containing information for two different complexes, is not known and is of interest. To determine the organization and expression of these complexes, studies have been carried out on crop plants by different groups, but not much information is known about trees. We present the nucleotide sequences of PSII genes and RNA profiles of the genes located in the psbB operon from Populus deltoides, a tree species. Although the gene organization of this operon in P. deltoides is similar to that in other species, a few variations have been observed in the processing scheme.

  11. Physiological and biochemical responses to high Mn concentrations in two contrasting Populus cathayana populations.

    PubMed

    Lei, Yanbao; Korpelainen, Helena; Li, Chunyang

    2007-06-01

    We exposed the cuttings of Populus cathayana to Hoagland's solution containing four different manganese (Mn) concentrations (0, 0.1, 0.5 and 1mM) in a greenhouse to characterize the physiological and biochemical basis of Mn resistance in woody plants. Two contrasting populations of P. cathayana were used in our study, which were from the wet and dry climate regions in western China, respectively. The results showed that Mn treatments significantly decreased chlorophyll content and growth characteristics, including shoot height, basal diameter, biomass accumulation and total leaf area in the two populations. Mn treatments also significantly increased the levels of abscisic acid (ABA), polyamines and free amino acids especially proline (Pro), histidine (His) and phenylalanine (Phe) available for cellular signaling and heavy metal chelation. In addition, high Mn concentrations also caused oxidative stress indicated as the accumulation of hydrogen peroxide (H(2)O(2)) and malondialdehyde (MDA) contents. On the other hand, there were different responses to Mn stress between the two contrasting populations. Compared with the dry climate population, the wet climate population accumulated more Mn in plant tissues especially in leaves; it showed lower tolerance index and more pronounced decrease in growth and chlorophyll contents. The wet climate population not only accumulated less ABA, putrescine and free amino acids, but also exhibited lower activities of superoxide dismutase (SOD) and ascorbate peroxidase (APX), thus suffering from more serious oxidative damage. Therefore, our results showed that the wet climate population was more susceptible to Mn stress than the dry climate population.

  12. 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.

  13. 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.

  14. Characterization of cellulose structure of Populus plants modified in candidate cellulose biosynthesis genes

    DOE PAGES

    Bali, Garima; Khunsupat, Ratayakorn; Akinosho, Hannah; ...

    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

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. [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.

  3. White poplar (Populus alba) as a biomonitor of trace elements in contaminated riparian forests.

    PubMed

    Madejón, Paula; Marañón, Teodoro; Murillo, José M; Robinson, Brett

    2004-11-01

    Trees can be used to monitor the level of pollution of trace elements in the soil and atmosphere. In this paper, we surveyed the content of eight trace elements (As, Cd, Cu, Fe, Mn, Ni, Pb and Zn) in leaves and stems of white poplar (Populus alba) trees. We selected 25 trees in the riparian forest of the Guadiamar River (S. Spain), one year after this area was contaminated by a mine spill, and 10 trees in non-affected sites. The spill-affected soils had significantly higher levels of available cadmium (mean of 1.25 mg kg(-1)), zinc (117 mg kg(-1)), lead (63.3 mg kg(-1)), copper (58.0 mg kg(-1)) and arsenic (1.70 mg kg(-1)), than non-affected sites. The concentration of trace element in poplar leaves was positively and significantly correlated with the soil availability for cadmium and zinc, and to a lesser extent for arsenic (log-log relationship). Thus, poplar leaves could be used as biomonitors for soil pollution of Cd and Zn, and moderately for As.

  4. 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

  5. Comparative “Golgi” Proteome Study of Lolium multiflorum and Populus trichocarpa

    PubMed Central

    Ford, Kristina L.; Chin, Tony; Srivastava, Vaibhav; Zeng, Wei; Doblin, Monika S.; Bulone, Vincent; Bacic, Antony

    2016-01-01

    The Golgi apparatus (GA) is a crucial organelle in the biosynthesis of non-cellulosic polysaccharides, glycoproteins and proteoglycans that are primarily destined for secretion to the cell surface (plasma membrane, cell wall and apoplast). Only a small proportion of the proteins involved in these processes have been identified in plants, with the majority of their functions still unknown. The availability of a GA proteome would greatly assist plant biochemists, cell and molecular biologists in determining the precise function of the cell wall-related proteins. There has been some progress towards defining the GA proteome in the model plant system Arabidopsis thaliana, yet in commercially important species, such as either the cereals or woody species there has been relatively less progress. In this study, we applied discontinuous sucrose gradient centrifugation to partially enrich GA from suspension cell cultures (SCCs) and combined this with stable isotope labelling (iTRAQ) to determine protein sub-cellular locations. Results from a representative grass species, Italian ryegrass (Lolium multiflorum) and a dicot species, black cottonwood (Populus trichocarpa) are compared. The results confirm that membrane fractionation approaches that provide effective GA-enriched fractions for proteomic analyses in Arabidopsis are much less effective in the species examined here and highlight the complexity of the GA, both within and between species. PMID:28248233

  6. The effects of exogenous putrescine on sex-specific responses of Populus cathayana to copper stress.

    PubMed

    Chen, Lianghua; Wang, Ling; Chen, Fugui; Korpelainen, Helena; Li, Chunyang

    2013-11-01

    We used the dioecious tree, Populus cathayana, as a model species to study plants' physiological and biochemical responses to copper (Cu) stress, exogenous putrescine (Put) treatment and their interaction. Although males accumulated higher Cu concentrations in leaves than did females under Cu stress, they did not suffer more damage than females, as reflected by changes in gas exchange, pigment contents, membrane lipid peroxidation (thiobarbituric acid reactive substances, TBARS) and protein oxidation (carbonyl). Higher Cu tolerance of males was correlated with a higher H2O2 scavenging ability and proline responses, and a better maintenance of non-protein thiols (NP-SHs) and spermine (Spm) contents. We also discovered that mitigation effects of exogenous Put on Cu stress occurred, as visible as a recovery of the total chlorophyll content, and lower TBARS and carbonyl under interaction treatment when compared to Cu stress alone. Exogenous Put decreased the Cu concentration in leaves of both sexes, but to different degrees. Such effects of exogenous Put suggested that Put may play important roles in the stabilization of membrane integrity and protein structures, and it may modulate the uptake and transportation of Cu. Our results indicated that (1) males are more tolerant to Cu stress than females; (2) Put could mitigate Cu toxicity in P. cathayana, but to a different degree in males and females; (3) males are better candidates than females for Cu extraction and phytoremediation.

  7. 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.

  8. Sexually different physiological responses of Populus cathayana to nitrogen and phosphorus deficiencies.

    PubMed

    Zhang, Sheng; Jiang, Hao; Zhao, Hongxia; Korpelainen, Helena; Li, Chunyang

    2014-04-01

    Previous studies have shown that there are significant sexual differences in the morphological and physiological responses of Populus cathayana Rehder under stressful conditions. However, little is known about sex-specific differences in responses to nutrient deficiencies. In this study, the effects of nitrogen (N) and phosphorus (P) deficiencies on the morphological, physiological and chloroplast ultrastructural traits of P. cathayana males and females were investigated. The results showed that N and P deficiencies significantly decreased plant growth, foliar N and P contents, chlorophyll content, photosynthesis, and instantaneous photosynthetic N- and P-use efficiencies (PNUE and PPUE) in both sexes. Males had higher photosynthesis, higher PNUE and PPUE rates, and a lower accumulation of plastoglobules in chloroplasts than did females when exposed to N- and P-deficiency conditions. Nitrogen-deficient males had higher glutamate dehydrogenase and peroxidase activities, and a more intact chloroplast ultrastructure, but less starch accumulation than did N-deficient females. Phosphorus-deficient males had higher nitrate reductase, glutamine synthetase and acid phosphatase activities, but a lower foliar N : P ratio and less PSII damage than did P-deficient females. These results suggest that N and P deficiencies cause greater negative effects on females than on males, and that the different sexes of P. cathayana may employ different strategies to cope with N and P deficiencies.

  9. 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.

  10. Latitudinal variation in cold hardiness in introduced Tamarix and native Populus

    PubMed Central

    Friedman, Jonathan M; Roelle, James E; Gaskin, John F; Pepper, Alan E; Manhart, James R

    2008-01-01

    To investigate the evolution of clinal variation in an invasive plant, we compared cold hardiness in the introduced saltcedar (Tamarix ramosissima, Tamarix chinensis, and hybrids) and the native plains cottonwood (Populus deltoides subsp. monilifera). In a shadehouse in Colorado (41°N), we grew plants collected along a latitudinal gradient in the central United States (29–48°N). On 17 occasions between September 2005 and June 2006, we determined killing temperatures using freeze-induced electrolyte leakage and direct observation. In midwinter, cottonwood survived cooling to −70°C, while saltcedar was killed at −33 to −47°C. Frost sensitivity, therefore, may limit northward expansion of saltcedar in North America. Both species demonstrated inherited latitudinal variation in cold hardiness. For example, from September through January killing temperatures for saltcedar from 29.18°N were 5–21°C higher than those for saltcedar from 47.60°N, and on September 26 and October 11, killing temperatures for cottonwood from 33.06°N were >43°C higher than those for cottonwood from 47.60°N. Analysis of nine microsatellite loci showed that southern saltcedars are more closely related to T. chinensis while northern plants are more closely related to T. ramosissima. Hybridization may have introduced the genetic variability necessary for rapid evolution of the cline in saltcedar cold hardiness. PMID:25567800

  11. 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.

  12. Dynamic changes in the transcriptome of Populus hopeiensis in response to abscisic acid

    PubMed Central

    Chen, Zhong; Ji, Lexiang; Wang, Jia; Jin, Jinpu; Yang, Xiaoyu; Rao, Pian; Gao, Kai; Liao, Weihua; Ye, Meixia; An, Xinmin

    2017-01-01

    Abscisic acid (ABA) plays a fundamental role in plant response and adaptation to abiotic stresses, such as drought, high salinity and low temperature. Populus hopeiensis exhibits exceptional tolerance to water-deficit environments and is therefore an excellent choice for studying drought tolerance in trees. This study provides a global view of transcriptome dynamics in P. hopeiensis in response to exogenous ABA using Illumina RNA-sequencing. Endogenous ABA content increased and reached a peak at 8 h after ABA treatment and then significantly decreased at latter time points. Differential expression analysis and Gene ontology enrichment revealed that the number of transcripts exhibited significant increase during the first 8 hours after ABA treatment, which then significantly decreased at 12 and 24 h. Transcription factors (TFs) analysis showed that six different patterns were observed based on the expression of the six TFs families (AP2/ERF, NAC, MYB, MYB-related, bZIP and WRKY) and the majority of differentially expressed TFs increased rapidly after ABA treatment. This study provides a robust resource for investigating the functions of genes induced by ABA and will help to develop a better understanding of the molecular regulatory mechanism in response to drought in poplar. PMID:28198429

  13. 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.

  14. 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

  15. Latitudinal variation in cold hardiness in introduced Tamarix and native Populus

    USGS Publications Warehouse

    Friedman, Jonathan M.; Roelle, James E.; Gaskin, John F.; Pepper, Alan E.; Manhart, James R.

    2008-01-01

    To investigate the evolution of clinal variation in an invasive plant, we compared cold hardiness in the introduced saltcedar (Tamarix ramosissima, Tamarix chinensis, and hybrids) and the native plains cottonwood (Populus deltoidessubsp. monilifera). In a shadehouse in Colorado (41°N), we grew plants collected along a latitudinal gradient in the central United States (29–48°N). On 17 occasions between September 2005 and June 2006, we determined killing temperatures using freeze-induced electrolyte leakage and direct observation. In midwinter, cottonwood survived cooling to −70°C, while saltcedar was killed at −33 to −47°C. Frost sensitivity, therefore, may limit northward expansion of saltcedar in North America. Both species demonstrated inherited latitudinal variation in cold hardiness. For example, from September through January killing temperatures for saltcedar from 29.18°N were 5–21°C higher than those for saltcedar from 47.60°N, and on September 26 and October 11, killing temperatures for cottonwood from 33.06°N were >43°C higher than those for cottonwood from 47.60°N. Analysis of nine microsatellite loci showed that southern saltcedars are more closely related to T. chinensis while northern plants are more closely related to T. ramosissima. Hybridization may have introduced the genetic variability necessary for rapid evolution of the cline in saltcedar cold hardiness.

  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. 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).

  18. Comparative physiological and proteomic analyses of poplar (Populus yunnanensis) plantlets exposed to high temperature and drought.

    PubMed

    Li, Xiong; Yang, Yunqiang; Sun, Xudong; Lin, Huaming; Chen, Jinhui; Ren, Jian; Hu, Xiangyang; Yang, Yongping

    2014-01-01

    Plantlets of Populus yunnanensis Dode were examined in a greenhouse for 48 h to analyze their physiological and proteomic responses to sustained heat, drought, and combined heat and drought. Compared with the application of a single stress, simultaneous treatment with both stresses damaged the plantlets more heavily. The plantlets experienced two apparent response stages under sustained heat and drought. During the first stage, malondialdehyde and reactive oxygen species (ROS) contents were induced by heat, but many protective substances, including antioxidant enzymes, proline, abscisic acid (ABA), dehydrin, and small heat shock proteins (sHSPs), were also stimulated. The plants thus actively defended themselves against stress and exhibited few pathological morphological features, most likely because a new cellular homeostasis was established through the collaborative operation of physiological and proteomic responses. During the second stage, ROS homeostasis was overwhelmed by substantial ROS production and a sharp decline in antioxidant enzyme activities, while the synthesis of some protective elements, such as proline and ABA, was suppressed. As a result, photosynthetic levels in P. yunnanensis decreased sharply and buds began to die, despite continued accumulation of sHSPs and dehydrin. This study supplies important information about the effects of extreme abiotic environments on woody plants.

  19. 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.

  20. Genome-scale transcriptome analysis of the desert poplar, Populus euphratica.

    PubMed

    Qiu, Qiang; Ma, Tao; Hu, Quanjun; Liu, Bingbing; Wu, Yuxia; Zhou, Haihong; Wang, Qian; Wang, Juan; Liu, Jianquan

    2011-04-01

    Populus euphratica is well-adapted to extreme desert environments and is an important model species for studying the effects of abiotic stresses on trees. Here we present the first deep transcriptomic analysis of this species. To maximize representation of conditional transcripts, mRNA was obtained from living tissues of desert-grown trees and two types of callus (salt-stressed and unstressed). De novo assembly generated 86,777 Unigenes using Solexa sequence data. These sequences covered 92% of previously reported P. euphratica expressed sequence tags (ESTs) and 90% of the TIGR poplar ESTs, and a total of 58,499 high-quality unique sequences were annotated by BLAST similarity searches against public databases. We found that 27% of the total Unigenes were differentially expressed (up- or down-regulated) in response to salt stress in P. euphratica callus. These differentially expressed genes are mainly involved in transport, transcription, cellular communication and metabolism. In addition, we found that numerous putative genes involved in ABA regulation and biosynthesis were also differentially regulated. This study represents the deepest transcriptomic and gene-annotation analysis of P. euphratica to date. The genetic knowledge acquired should be very useful for future studies of the molecular adaptation of this tree species to abiotic stress and facilitate genetic manipulation of other poplar species.

  1. Molecular Responses to Climate and Resource Availability: Emerging Evidence from Systems Biology Research in Populus.

    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 benefitted greatly from the sequencing of the P. trichocarpa genome. This landmark event has laid a solid foundation upon which tree biologists can now explore the genome-wide effects of temperature, water and nutrient limitations on processes 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 number of examples whereby a systems approach, one that focuses on transcriptomic, proteomic, and metabolomic analyses is beginning to provide insights into the molecular-scale response of poplars to their climatic and edaphic environment.

  2. Two highly validated SSR multiplexes (8-plex) for Euphrates' poplar, Populus euphratica (Salicaceae).

    PubMed

    Xu, Fang; Feng, Sisi; Wu, Rongling; Du, Fang K

    2013-01-01

    Multiplex PCR amplification of microsatellites has significantly increased the throughput and decreased the costs of genotyping. We have developed two highly polymorphic microsatellite multiplexes for Populus euphratica, the only tree species found in desert regions of Western China and adjacent Central Asian countries. The first of these multiplex kits comprises an eight-Plex of genomic SSRs (gSSRs) obtained from published databases. The second comprises an eight-plex of newly designed EST-SSRs (eSSRs) based on expressed sequence tags for P. euphratica. Both kits were tested on a sample of 170 individuals from four populations. The gSSRs exhibited slightly more polymorphism than the eSSRs. The new multiplex protocols yielded consistent results in the hands of multiple researchers, demonstrating their robustness. The 16 loci used in the kits exhibited a high transferability rate (82.0%) in eight other poplar species belonging to five different sections of the genus. Both kits should therefore be useful for further investigations of population genetics in P. euphratica and related species. Our results indicate that it is essential to follow recently established recommendations when developing microsatellite markers, including verifying the amplification efficiency, detecting null alleles and carefully measuring error rates.

  3. 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.

  4. In silico identification and characterization of N-Terminal acetyltransferase genes of poplar (Populus trichocarpa).

    PubMed

    Zhu, Hang-Yong; Li, Chun-Ming; Wang, Li-Feng; Bai, Hui; Li, Yan-Ping; Yu, Wen-Xi; Xia, De-An; Liu, Chang-Cai

    2014-01-27

    N-terminal acetyltransferase (Nats) complex is responsible for protein N-terminal acetylation (Nα-acetylation), which is one of the most common covalent modifications of eukaryotic proteins. Although genome-wide investigation and characterization of Nat catalytic subunits (CS) and auxiliary subunits (AS) have been conducted in yeast and humans they remain unexplored in plants. Here we report on the identification of eleven genes encoding eleven putative Nat CS polypeptides, and five genes encoding five putative Nat AS polypeptides in Populus. We document that the expansion of Nat CS genes occurs as duplicated blocks distributed across 10 of the 19 poplar chromosomes, likely only as a result of segmental duplication events. Based on phylogenetic analysis, poplar Nat CS were assigned to six subgroups, which corresponded well to the Nat CS types (CS of Nat A-F), being consistent with previous reports in humans and yeast. In silico analysis of microarray data showed that in the process of normal development of the poplar, their Nat CS and AS genes are commonly expressed at one relatively low level but share distinct tissue-specific expression patterns. This exhaustive survey of Nat genes in poplar provides important information to assist future studies on their functional role in poplar.

  5. 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.

  6. Genetic diversity and population structure of Chinese White poplar (Populus tomentosa) revealed by SSR markers.

    PubMed

    Du, Qingzhang; Wang, Bowen; Wei, Zunzheng; Zhang, Deqiang; Li, Bailian

    2012-01-01

    An understanding of allelic diversity and population structure is important in developing association studies and constructing core collections for tree breeding. We examined population genetic differentiation in the native Populus tomentosa by genotyping 460 unrelated individuals using 20 species-specific microsatellite markers. We identified 99 alleles with a mean of 4.95 observed alleles per locus, indicating a moderate level of polymorphism across all individuals. A model-based population structure analysis divided P. tomentosa into 11 subpopulations (K = 11). The pattern of individual assignments into the subsets (K = 3) provided reasonable evidence for treating climatic zones as genetic regions for population genetics. The highest level of genetic variation was found in the southern region (i.e., N = 93, N (P) = 11, H (E) = 0.445, F = -0.102), followed by the northeastern and northwestern regions. Thus, the southern region is probably the center of the current species distribution. No correlation was found between population genetic distance and geographic distance (r = 0.0855, P = 0.3140), indicating that geographical distance was not the principal factor influencing genetic differentiation in P. tomentosa. These data provide a starting point for conserving valuable natural resources and optimizing breeding programs.

  7. Association genetics of chemical wood properties in black poplar (Populus nigra).

    PubMed

    Guerra, Fernando P; Wegrzyn, Jill L; Sykes, Robert; Davis, Mark F; Stanton, Brian J; Neale, David B

    2013-01-01

    Black poplar (Populus nigra) is a potential feedstock for cellulosic ethanol production, although breeding for this specific end use is required. Our goal was to identify associations between single nucleotide polymorphism (SNP) markers within candidate genes encoding cellulose and lignin biosynthetic enzymes, with chemical wood property phenotypic traits, toward the aim of developing genomics-based breeding technologies for bioethanol production. Pyrolysis molecular beam mass spectrometry was used to determine contents of five- and six-carbon sugars, lignin, and syringyl : guaiacyl ratio. The association population included 599 clones from 17 half-sib families, which were successfully genotyped using 433 SNPs from 39 candidate genes. Statistical analyses were performed to estimate genetic parameters, linkage disequilibrium (LD), and single marker and haplotype-based associations. A moderate to high heritability was observed for all traits. The LD, across all candidate genes, showed a rapid decay with physical distance. Analysis of single marker-phenotype associations identified six significant marker-trait pairs, whereas nearly 280 haplotypes were associated with phenotypic traits, in both an individual and multiple trait-specific manner. The rapid decay of LD within candidate genes in this population and the genetic associations identified suggest a close relationship between the associated SNPs and the causative polymorphisms underlying the genetic variation of lignocellulosic traits in black poplar.

  8. 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.

  9. 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.

  10. Different Proteome Profiles between Male and Female Populus cathayana Exposed to UV-B Radiation

    PubMed Central

    Zhang, Yunxiang; Feng, Lihua; Jiang, Hao; Zhang, Yuanbin; Zhang, Sheng

    2017-01-01

    With increasing altitude, solar UV-B radiation is enhanced. Based on the phenomenon of male-biased sex ratio of Populus cathayana Rehder in high altitude alpine area, we hypothesized that males have a faster and more sophisticated responsive mechanism to high UV-B radiation than that of females. Our previous studies have shown sexually different responses to high UV-B radiation were existed in P. cathayana at the morphological, physiological, and transcriptomic levels. However, the responses at the proteomic level remain unclear. In this study, an isobaric tag for relative and absolute quantification (iTRAQ)-based quantitative proteome analysis was performed in P. cathayana females and males. A total of 2,405 proteins were identified, with 331 proteins defined as differentially expressed proteins (DEPs). Among of these, 79 and 138 DEPs were decreased and 47 and 107 DEPs were increased under high solar UV-B radiation in females and males, respectively. A bioinformatics analysis categorized the common responsive proteins in the sexes as related to carbohydrate and energy metabolism, translation/transcription/post-transcriptional modification, photosynthesis, and redox reactions. The responsive proteins that showed differences in sex were mainly those involved in amino acid metabolism, stress response, and translation/transcription/post-transcriptional modification. This study provides proteomic profiles that poplars responding to solar UV-B radiation, and it also provides new insights into differentially sex-related responses to UV-B radiation. PMID:28326097

  11. 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.

  12. Characterization of cellulose structure of Populus plants modified in candidate cellulose biosynthesis genes

    SciTech Connect

    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, 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.

  13. Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides

    DOE PAGES

    Fahrenkrog, Annette M.; Neves, Leandro G.; Resende, Jr., Marcio F. R.; ...

    2016-09-06

    Genome-wide association studies (GWAS) have been used extensively to dissect the genetic regulation of complex traits in plants. These studies have focused largely on the analysis of common genetic variants despite the abundance of rare polymorphisms in several species, and their potential role in trait variation. Here, we conducted the first GWAS in Populus deltoides, a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits, and common and low-frequency single-nucleotide polymorphisms detected by targeted resequencing of 18 153 genesmore » in a population of 391 unrelated individuals. To increase power to detect associations with low-frequency variants, multiple-marker association tests were used in combination with single-marker association tests. Significant associations were discovered for all phenotypes and are indicative that low-frequency polymorphisms contribute to phenotypic variance of several bioenergy traits. Our results suggest that both common and low-frequency variants need to be considered for a comprehensive understanding of the genetic regulation of complex traits, particularly in species that carry large numbers of rare polymorphisms. Lastly, these polymorphisms may be critical for the development of specialized plant feedstocks for bioenergy.« less

  14. Phyllotactic transitions in the vascular system of Populus deltoides bartr. as determined by (14)C labeling.

    PubMed

    Larson, P R

    1977-01-01

    Populus deltoides seedlings progress through 2/5, 3/8, and 5/13 orders of phyllotaxis in attaining Plastochron Index 16 (PI 16). The manner in which the vascular system was reoriented during these phyllotactic transitions was determined by anatomical analysis of serial microsections, whereas the positions of the transitions were determined by (14)C labeling. The midvein at the tip of leaves representing plants of different PI and leaves of different Leaf Plastochron Index (LPI) was fed (14)CO2 photosynthetically, and primordia LPI 0 through LPI-9 were dissected from the buds and analyzed for (14)C. By combining the labeling data with the anatomical observations it was possible to reconstruct the vascular system of a plant of PI 16 and to locate the phyllotactic transitions. Both the anatomical and the labeling data showed a high degree of reproducibility among plants suggesting that the phyllotactic pattern to which the vascular system conforms may be programmed in the plant and transmitted acropetally through the developing leaves and procambial strands. The origin of new primordia and the concepts of orthostichy, ontogenetic helix, and Fibonacci sequence are discussed as they apply to the vascular system of P. deltoides.

  15. 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.

  16. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment

    DOE PAGES

    Timm, Collin M.; Campbell, Alicia G.; Utturkar, Sagar M.; ...

    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

  17. Description of Acinetobacter populi sp. nov. isolated from symptomatic bark of Populus x euramericana canker.

    PubMed

    Li, Yong; Chang, Jupu; Guo, Li-min; Wang, Hai-Ming; Xie, Shou-jiang; Piao, Chun-gen; He, Wei

    2015-12-01

    Five Gram-negative, non-motile, rod-shaped bacterial strains were isolated from cankers of Populus x euramericana collected from different locations in Puyang city, Henan Province, China. The five strains were characterized by nutritional and physiological testing and DNA sequence analysis. Haemolysis was not observed on agar media supplemented with sheep erythrocytes. The strains could be distinguished from members of most species of the genus Acinetobacter by their inability to assimilate L-arginine and benzoate. The five strains formed a single branch in phylogenetic trees based on 16S rRNA, gyrB and rpoB individual gene sequence analysis,indicating that they all belonged to a single taxon within the genus Acinetobacter. DNA-DNA hybridization results indicated that the five isolates represented to a single species that was separate from Acinetobacter puyangensis. On the basis of the phenotypic, genotypic and phylogenetic characteristics, the five strains are considered to represent a novel species of the genus Acinetobacter, for which the name Acinetobacter populi sp. nov. is proposed. The typestrain of A. populi sp. nov. is PBJ7T (CFCC 11170T=KCTC 42272T).

  18. Expression Pattern of ERF Gene Family under Multiple Abiotic Stresses in Populus simonii × P. nigra.

    PubMed

    Yao, Wenjing; Zhang, Xuemei; Zhou, Boru; Zhao, Kai; Li, Renhua; Jiang, Tingbo

    2017-01-01

    Identification of gene expression patterns of key genes across multiple abiotic stresses is critical for mechanistic understanding of stress resistance in plant. In the present study, we identified differentially expressed genes (DEGs) in di-haploid Populus simonii × P. nigra under respective stresses of NaCl, KCl, CdCl2, and PEG. On the basis of RNA-Seq, we detected 247 DEGs that are shared by the four stresses in wild type poplar, and mRNA abundance of the DEGs were validated in transgenic poplar overexpressing ERF76 gene by RNA-Seq and RT-qPCR. Results from gene ontology analysis indicated that these genes are enriched in significant pathways, such as phenylpropanoid biosynthesis, phenylalanine metabolism, starch and sucrose metabolism, and plant hormone signal transduction. Ethylene response factor (ERF) gene family plays significant role in plant abiotic stress responses. We also investigated expression pattern of ERF gene family under the four stresses. The ERFs and DEGs share similar expression pattern across the four stresses. The transgenic poplar is superior to WT in morphologic, physiological and biochemical traits, which demonstrated the ERF76 gene plays a significant role in stress resistance. These studies will give a rise in understanding the stress response mechanisms in poplar.

  19. 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

  20. Expression Pattern of ERF Gene Family under Multiple Abiotic Stresses in Populus simonii × P. nigra

    PubMed Central

    Yao, Wenjing; Zhang, Xuemei; Zhou, Boru; Zhao, Kai; Li, Renhua; Jiang, Tingbo

    2017-01-01

    Identification of gene expression patterns of key genes across multiple abiotic stresses is critical for mechanistic understanding of stress resistance in plant. In the present study, we identified differentially expressed genes (DEGs) in di-haploid Populus simonii × P. nigra under respective stresses of NaCl, KCl, CdCl2, and PEG. On the basis of RNA-Seq, we detected 247 DEGs that are shared by the four stresses in wild type poplar, and mRNA abundance of the DEGs were validated in transgenic poplar overexpressing ERF76 gene by RNA-Seq and RT-qPCR. Results from gene ontology analysis indicated that these genes are enriched in significant pathways, such as phenylpropanoid biosynthesis, phenylalanine metabolism, starch and sucrose metabolism, and plant hormone signal transduction. Ethylene response factor (ERF) gene family plays significant role in plant abiotic stress responses. We also investigated expression pattern of ERF gene family under the four stresses. The ERFs and DEGs share similar expression pattern across the four stresses. The transgenic poplar is superior to WT in morphologic, physiological and biochemical traits, which demonstrated the ERF76 gene plays a significant role in stress resistance. These studies will give a rise in understanding the stress response mechanisms in poplar. PMID:28265277

  1. Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides.

    PubMed

    Fahrenkrog, Annette M; Neves, Leandro G; Resende, Márcio F R; Vazquez, Ana I; de Los Campos, Gustavo; Dervinis, Christopher; Sykes, Robert; Davis, Mark; Davenport, Ruth; Barbazuk, William B; Kirst, Matias

    2017-01-01

    Genome-wide association studies (GWAS) have been used extensively to dissect the genetic regulation of complex traits in plants. These studies have focused largely on the analysis of common genetic variants despite the abundance of rare polymorphisms in several species, and their potential role in trait variation. Here, we conducted the first GWAS in Populus deltoides, a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits, and common and low-frequency single-nucleotide polymorphisms detected by targeted resequencing of 18 153 genes in a population of 391 unrelated individuals. To increase power to detect associations with low-frequency variants, multiple-marker association tests were used in combination with single-marker association tests. Significant associations were discovered for all phenotypes and are indicative that low-frequency polymorphisms contribute to phenotypic variance of several bioenergy traits. Our results suggest that both common and low-frequency variants need to be considered for a comprehensive understanding of the genetic regulation of complex traits, particularly in species that carry large numbers of rare polymorphisms. These polymorphisms may be critical for the development of specialized plant feedstocks for bioenergy.

  2. Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula.

    PubMed

    Ingvarsson, Pär K

    2007-03-01

    Codon bias is generally thought to be determined by a balance between mutation, genetic drift, and natural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes. In this paper, I study associations between codon usage, gene expression, and molecular evolution at synonymous and nonsynonymous sites in the long-lived, woody perennial plant Populus tremula (Salicaceae). Using expression data for 558 genes derived from expressed sequence tags (EST) libraries from 19 different tissues and developmental stages, I study how gene expression levels within single tissues as well as across tissues affect codon usage and rates sequence evolution at synonymous and nonsynonymous sites. I show that gene expression have direct effects on both codon usage and the level of selective constraint of proteins in P. tremula, although in different ways. Codon usage genes is primarily determined by how highly expressed a genes is, whereas rates of sequence evolution are primarily determined by how widely expressed genes are. In addition to the effects of gene expression, protein length appear to be an important factor influencing virtually all aspects of molecular evolution in P. tremula.

  3. Media formulation influences in vitro ectomycorrhizal synthesis on the European aspen Populus tremula L.

    PubMed

    Langer, Ingrid; Krpata, Doris; Peintner, Ursula; Wenzel, Walter W; Schweiger, Peter

    2008-09-01

    The effect of various media formulations on in vitro ectomycorrhizal synthesis of identified fungal strains with European aspen (Populus tremula L.) was tested in Petri dishes. Pre-grown seedlings were transferred to various nutrient media and inoculated with Paxillus involutus isolates using modified sandwich techniques. Mycorrhiza formation was evaluated macroscopically and further confirmed by microscopic examination of semi-thin sections for anatomical features of the mantle and the Hartig net. Standard media formulations did not support successful ectomycorrhiza formation because of either very poor plant survival (below 20%) or impaired fungal growth. The inclusion of micronutrients and vitamins in a Melin Norkrans (MMN)-based medium increased plant survival rate to above 60% and supported successful mycorrhizal synthesis. P. involutus isolates formed mycorrhizas with a characteristic Hartig net restricted to the epidermis. Mantle density and thickness varied depending on the isolate. In a follow-up experiment, the adapted medium supported successful ectomycorrhiza formation by various Laccaria and Hebeloma isolates. Our results show that an exogenous supply of vitamins and micronutrients in the medium was a prerequisite for successful mycorrhization of P. tremula in vitro in Petri dishes.

  4. 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

  5. Seasonal variation of leaf respiration and the alternative pathway in field-grown Populus × canadensis.

    PubMed

    Searle, Stephanie Y; Turnbull, Matthew H

    2011-04-01

    The temperature response of plant respiration varies between species and can acclimate to changing temperatures. Mitochondrial respiration in plants has two terminal oxidases: the cytochrome c oxidase (COX) and the cyanide-resistant alternative oxidase (AOX). In Populus × canadensis var. italica, a deciduous tree species, we investigated the temperature response of leaf respiration via the alternative and cytochrome pathways, as well as seasonal changes in these pathways, using the oxygen isotope fractionation technique. The electron partitioning through the alternative pathway (τ(a) ) increased from 0 to 30-40% with measurement temperatures from 6 to 30°C at all times measured throughout the growing season. τ(a) at the growth temperature (the average temperature during 3 days prior to sampling) increased from 12 to 29% from spring until late summer and decreased thereafter. Total respiration declined throughout the growing season by 50%, concomitantly with decreases in both AOX (64%) and COX (32%) protein abundances. Our results provide new insight into the natural variability of AOX protein abundances and alternative respiration electron partitioning over immediate and seasonal timescales.

  6. 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

  7. Evolutionary transfers of mitochondrial genes to the nucleus in the Populus lineage and coexpression of nuclear and mitochondrial Sdh4 genes.

    PubMed

    Choi, Catherine; Liu, Zhenlan; Adams, Keith L

    2006-01-01

    The transfer of mitochondrial genes to the nucleus is an ongoing evolutionary process in flowering plants. Evolutionarily recent gene transfers provide insights into the evolutionary dynamics of the process and the way in which transferred genes become functional in the nucleus. Genes that are present in the mitochondrion of some angiosperms but have been transferred to the nucleus in the Populus lineage were identified by searches of Populus sequence databases. Sequence analyses and expression experiments were used to characterize the transferred genes. Two succinate dehydrogenase genes and six mitochondrial ribosomal protein genes have been transferred to the nucleus in the Populus lineage and have become expressed. Three transferred genes have gained an N-terminal mitochondrial targeting presequence from other pre-existing genes and two of the transferred genes do not contain an N-terminal targeting presequence. Intact copies of the succinate dehydrogenase gene Sdh4 are present in both the mitochondrion and the nucleus. Both copies of Sdh4 are expressed in multiple organs of two Populus species and RNA editing occurs in the mitochondrial copy. These results provide a genome-wide perspective on mitochondrial genes that were transferred to the nucleus and became expressed, functional genes during the evolutionary history of Populus.

  8. Molecular evolution and expression divergence of the Populus polygalacturonase supergene family shed light on the evolution of increasingly complex organs in plants.

    PubMed

    Yang, Zhi-Ling; Liu, Hai-Jing; Wang, Xiao-Ru; Zeng, Qing-Yin

    2013-03-01

    Plant polygalacturonases (PGs) are involved in cell separation processes during many stages of plant development. Investigation into the diversification of this large gene family in land plants could shed light on the evolution of structural development. We conducted whole-genome annotation, molecular evolution and gene expression analyses of PG genes in five species of land plant: Populus, Arabidopsis, rice, Selaginella and Physcomitrella. We identified 75, 44, 16 and 11 PG genes from Populus, rice, Selaginella and Physcomitrella genomes, respectively, which were divided into three classes. We inferred rapid expansion of class I PG genes in Populus, Arabidopsis and rice, while copy numbers of classes II and III PG genes were relatively conserved in all five species. Populus, Arabidopsis and rice class I PG genes were under more relaxed selection constraints than class II PG genes, while this selective pressure divergence was not observed in Selaginella and Physcomitrella PG families. In addition, class I PG genes underwent marked expression divergence in Populus, rice and Selaginella. Our results suggest that PG gene expansion occurred after the divergence of the lycophytes and euphyllophytes, and this expansion was likely paralleled by the evolution of increasingly complex organs in land plants.

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. 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

  14. Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing.

    PubMed

    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.

  15. Identification and analysis of safener-inducible expressed sequence tags in Populus using a cDNA microarray.

    PubMed

    Rishi, A S; Munir, Shirin; Kapur, Vivek; Nelson, Neil D; Goyal, Arun

    2004-12-01

    Safeners are the chemicals used to protect plants from detrimental effects of herbicides, but their mode of action at the molecular level is not well understood. As an initial step towards understanding the molecular mechanism of safener action in trees, homologous genes in hybrid poplar (Populus nigra x Populus maximowiczii) that were induced by a safener were identified. We here describe the identification of differentially expressed genes in Populus that are induced by Concep-III, a herbicide safener. Expressed sequence tags (ESTs) enriched for transcriptionally induced genes were isolated by suppressive subtractive hybridization (SSH). The SSH library cDNA inserts were used to construct a cDNA microarray for high-throughput validation of the up-regulated expression of safener-induced genes. Single-pass and partial sequences of 1,344 safener-induced ESTs were assembled into 418 singletons and 328 clusters, but the putative functions of almost 53% of the ESTs are not known. Genes encoding proteins involved in all three different phases of safener action, viz., oxidation, conjugation, and sequestration, were found in the SSH library. Almost 75% of genes that showed greater than 2-fold expression upon safener treatment were redundant in the SSH library. The expression pattern for selected genes was validated by reverse transcription-polymerase chain reaction. A few safener-induced genes that were not previously reported to be induced by safeners, but which may have a role in herbicide metabolism, were identified. The newly identified genes could have potential for application in genetic engineering of plants for herbicide detoxification and tolerance.

  16. Genome-wide identification, characterization and expression analysis of populus leucine-rich repeat receptor-like protein kinase genes

    PubMed Central

    2013-01-01

    Background Leucine-rich repeat receptor-like kinases (LRR-RLKs) comprise the largest group within the receptor-like kinase (RLK) superfamily in plants. This gene family plays critical and diverse roles in plant growth, development and stress response. Although the LRR-RLK families in Arabidopsis and rice have been previously analyzed, no comprehensive studies have been performed on this gene family in tree species. Results In this work, 379 LRR-RLK genes were retrieved from the Populus trichocarpa genome and further grouped into 14 subfamilies based on their structural and sequence similarities. Approximately 82% (312 out of 379) of the PtLRR-RLK genes are located in segmental duplication blocks indicating the role of duplication process in the expansion of this gene family. The conservation and variation in motif composition and intron/exon arrangement among PtLRR-RLK subfamilies were analyzed to provide additional support for their phylogenetic relationship and more importantly to indicate the potential divergence in their functions. Expression profiling of PtLRR-RLKs showed that they were differentially expressed in different organs and tissues and some PtLRR-RLKs were specifically expressed in meristem tissues, which indicated their potential involvement in tissue development and differentiation. For most AtLRR-RLKs with defined functions, Populus homologues exhibiting similar expression patterns could be identified, which might indicate the functional conservation during evolution. Among 12 types of environmental cues analyzed by the genome-wide microarray data, PtLRR-RLKs showed specific responses to shoot organogenesis, wounding, low ammonium feeding, hypoxia and seasonal dormancy, but not to drought, re-watering after drought, flooding, AlCl3 treatment and bacteria or fungi treatments. Conclusions This study provides the first comprehensive genomic analysis of the Populus LRR-RLK gene family. Segmental duplication contributes significantly to the expansion

  17. Nitrate and Ammonium Contribute to the Distinct Nitrogen Metabolism of Populus simonii during Moderate Salt Stress

    PubMed Central

    Meng, Sen; Su, Li; Li, Yiming; Wang, Yinjuan; Zhang, Chunxia; Zhao, Zhong

    2016-01-01

    Soil salinity is a major abiotic stressor affecting plant growth. Salinity affects nitrification and ammonification in the soil, however, limited information is available on the influence of different N sources on N metabolism during salt stress. To understand the N metabolism changes in response to different N sources during moderate salt stress, we investigated N uptake, assimilation and the transcript abundance of associated genes in Populus simonii seedlings treated with moderate salt stress (75mM NaCl) under hydroponic culture conditions with nitrate (NO3-) or ammonium (NH4+). Salt stress negatively affected plant growth in both NH4+-fed and NO3--fed plants. Both NH4+ uptake and the total N concentration were significantly increased in the roots of the NH4+-fed plants during salt stress. However, the NO3- uptake and nitrate reductase (NR) and nitrite reductase (NiR) activity primarily depended on the NO3- supply and was not influenced by salt stress. Salt stress decreased glutamine synthetase (GS) and glutamate synthase (GOGAT) activity in the roots and leaves. Most genes associated with NO3-uptake, reduction and N metabolism were down-regulated or remained unchanged; while two NH4+ transporter genes closely associated with NH4+ uptake (AMT1;2 and AMT1;6) were up-regulated in response to salt stress in the NH4+-fed plants. The accumulation of different amino acid compounds was observed in the NH4+- and NO3-- fed plants during salt treatment. The results suggested that N metabolism in P. simonii plants exposed to salt enhanced salt resistance in the plants that were fed with NO3- instead of NH4+ as the sole N source. PMID:26950941

  18. 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.

  19. Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus.

    PubMed

    Drost, Derek R; Benedict, Catherine I; Berg, Arthur; Novaes, Evandro; Novaes, Carolina R D B; Yu, Qibin; Dervinis, Christopher; Maia, Jessica M; Yap, John; Miles, Brianna; Kirst, Matias

    2010-05-04

    A fundamental goal of systems biology is to identify genetic elements that contribute to complex phenotypes and to understand how they interact in networks predictive of system response to genetic variation. Few studies in plants have developed such networks, and none have examined their conservation among functionally specialized organs. Here we used genetical genomics in an interspecific hybrid population of the model hardwood plant Populus to uncover transcriptional networks in xylem, leaves, and roots. Pleiotropic eQTL hotspots were detected and used to construct coexpression networks a posteriori, for which regulators were predicted based on cis-acting expression regulation. Networks were shown to be enriched for groups of genes that function in biologically coherent processes and for cis-acting promoter motifs with known roles in regulating common groups of genes. When contrasted among xylem, leaves, and roots, transcriptional networks were frequently conserved in composition, but almost invariably regulated by different loci. Similarly, the genetic architecture of gene expression regulation is highly diversified among plant organs, with less than one-third of genes with eQTL detected in two organs being regulated by the same locus. However, colocalization in eQTL position increases to 50% when they are detected in all three organs, suggesting conservation in the genetic regulation is a function of ubiquitous expression. Genes conserved in their genetic regulation among all organs are primarily cis regulated (approximately 92%), whereas genes with eQTL in only one organ are largely trans regulated. Trans-acting regulation may therefore be the primary driver of differentiation in function between plant organs.

  20. Transcript identification and profiling during salt stress and recovery of Populus euphratica.

    PubMed

    Gu, Ruisheng; Fonseca, Sandra; Puskás, László G; Hackler, László; Zvara, Agnes; Dudits, Dénes; Pais, Maria S

    2004-03-01

    Populus euphratica Oli. is a salt-tolerant species that can cope with up to 450 mM NaCl under hydroponic conditions and can tolerate high accumulations of Na+ and Cl- in roots and leaves when grown in 300 mM NaCl. Transcript responses to salt stress and recovery were monitored by microarray hybridization of 315 cDNAs preselected by suppression subtractive hybridization. Transcripts of a heat-shock protein and a hydroxyproline-rich glycoprotein accumulated 1.5 and 3 h, respectively, after adding 300 mM NaCl to the culture medium. Transcripts significantly up-regulated by salt stress included ionic and osmotic homeostasis elements such as magnesium transporter-like protein, syntaxin-like protein, seed imbibition protein and plasma membrane intrinsic protein; metabolism regulators like cytochrome P450, zinc finger protein, cleavage factor and aminotransferase; and the photosynthesis-activating enzyme Rubisco activase and photorespiration-related glycolate oxidase. Several photosynthesis-related transcripts were down-regulated in response to 72 h of salt stress but were up-regulated after long-term recovery (48 h). Sucrose synthase, ABC transporter, calmodulin, Pop3 peptide and aquaporin appeared to be actively involved in the process of plant recovery from salt stress. Several transcripts encoding proteins of unknown function were regulated by salt stress. Selected transcripts exhibiting altered transcript profiles in response to salt stress were also analyzed by real-time quantitative PCR. Transcript analysis during salt stress and recovery of this woody species revealed several genes and corresponding proteins deserving special attention in future studies of salt tolerance in woody species.

  1. 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 than PeWRKY1 in leaves. PeWRKY1 was down-regulated in salinized P. euphratica when PeHSF was silenced by tobacco rattle virus-based gene silencing. Subcellular assays in onion epidermal cells and Arabidopsis protoplasts revealed that PeHSF and PeWRKY1 were restricted to the nucleus. Transgenic tobacco plants overexpressing PeWRKY1 showed improved salt tolerance in terms of survival rate, root growth, photosynthesis, and ion fluxes. We further isolated an 1182-bp promoter fragment upstream of the translational start of PeWRKY1 from P. euphratica. Promoter sequence analysis revealed that PeWRKY1 harbours four tandem repeats of heat shock element (HSE) in the upstream regulatory region. Yeast one-hybrid assay showed that PeHSF directly binds the cis-acting HSE. To determine whether the HSE cluster was important for salt-induced PeWRKY1 expression, the promoter-reporter construct PeWRKY1-pro::GUS was transferred to tobacco plants. β-glucuronidase activities increased in root, leaf, and stem tissues under salt stress. Therefore, we conclude that salinity increased PeHSF transcription in P. euphratica, and that PeHSF binds the cis-acting HSE of the PeWRKY1 promoter, thus activating PeWRKY1 expression.

  2. 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.

  3. 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

  4. 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.

  5. Molecular and biochemical characterization of the jasmonic acid methyltransferase gene from black cottonwood (Populus trichocarpa)

    SciTech Connect

    Zhao, Nan; Yao, Jianzhuang; Chaiprasongsuk, Minta; Li, Guanglin; Guan, Ju; Tschaplinski, Timothy J; Guo, Hong; Chen, Feng

    2013-01-01

    Methyl jasmonate is a metabolite known to be produced by many plants and has roles in diverse biological processes. It is biosynthesized by the action of S-adenosyl-L-methionine:jasmonic acid carboxyl methyltransferase (JMT), which belongs to the SABATH family of methyltransferases. Herein is reported the isolation and biochemical characterization of a JMT gene from black cottonwood (Populus trichocarpa). The genome of P. trichocarpa contains 28 SABATH genes (PtSABATH1 to PtSABATH28). Recombinant PtSABATH3 expressed in Escherichia coli showed the highest level of activity with jasmonic acid (JA) among carboxylic acids tested. It was therefore renamed PtJMT1. PtJMT1 also displayed activity with benzoic acid (BA), with which the activity was about 22% of that with JA. PtSABATH2 and PtSABATH4 were most similar to PtJMT1 among all PtSABATHs. However, neither of them had activity with JA. The apparent Km values of PtJMT1 using JA and BA as substrate were 175 lM and 341 lM, respectively. Mutation of Ser-153 and Asn-361, two residues in the active site of PtJMT1, to Tyr and Ser respectively, led to higher specific activity with BA than with JA. Homology-based structural modeling indicated that substrate alignment, in which Asn-361 is involved, plays a role in determining the substrate specificity of PtJMT1. In the leaves of young seedlings of black cottonwood, the expression of PtJMT1 was induced by plant defense signal molecules methyl jasmonate and salicylic acid and a fungal elicitor alamethicin, suggesting that PtJMT1 may have a role in plant defense against biotic stresses. Phylogenetic analysis suggests that PtJMT1 shares a common ancestor with the Arabidopsis JMT, and functional divergence of these two apparent JMT orthologs has occurred since the split of poplar and Arabidopsis lineages.

  6. Tubulin perturbation leads to unexpected cell wall modifications and affects stomatal behaviour in Populus

    DOE PAGES

    Swamy, Prashant S.; Hu, Hao; Pattathil, Sivakumar; ...

    2015-08-05

    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 duringmore » 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. In conclusion, 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.« less

  7. Overexpression of Populus trichocarpa CYP85A3 promotes growth and biomass production in transgenic trees.

    PubMed

    Jin, Yan-Li; Tang, Ren-Jie; Wang, Hai-Hai; Jiang, Chun-Mei; Bao, Yan; Yang, Yang; Liang, Mei-Xia; Kong, Fanjing; Li, Bei; Zhang, Hong-Xia

    2017-03-04

    Brassinosteroids (BRs) are essential hormones that play crucial roles in plant growth, reproduction and response to abiotic and biotic stress. In Arabidopsis, AtCYP85A2 works as a bifunctional cytochrome P450 monooxygenase to catalyze the conversion of castasterone (CS) to brassinolide (BL), a final rate-limiting step in the BR biosynthetic pathway. Here, we report the functional characterizations of PtCYP85A3, one of the three AtCYP85A2 homologous genes from Populus trichocarpa. PtCYP85A3 shares the highest similarity with AtCYP85A2 and can rescue the retarded-growth phenotype of the Arabidopsis cyp85a2-2 and tomato d(x) mutants. Constitutive expression of PtCYP85A3, driven by the cauliflower mosaic virus 35S promoter, increased the endogenous BR levels and significantly promoted the growth and biomass production in both transgenic tomato and poplar. Compared to the wild type (WT), plant height, shoot fresh weight and fruit yield increased 50%, 56% and 43%, respectively, in transgenic tomato plants. Similarly, plant height and stem diameter increased 15% and 25%, respectively, in transgenic poplar plants. Further study revealed that overexpression of PtCYP85A3 enhanced xylem formation without affecting the composition of cellulose and lignin, as well as the cell wall thickness in transgenic poplar. Our finding suggest that PtCYP85A3 could be used as a potential candidate gene for engineering fast growing trees with improved wood production. This article is protected by copyright. All rights reserved.

  8. 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.

  9. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

    DOE PAGES

    Muchero, Wellington; Guo, Jianjun; Difazio, Stephen P.; ...

    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

  10. Modelling the growth of Populus species using Ecosystem Demography (ED) model

    NASA Astrophysics Data System (ADS)

    Wang, D.; Lebauer, D. S.; Feng, X.; Dietze, M. C.

    2010-12-01

    Hybrid poplar plantations are an important source being evaluated for biomass production. Effective management of such plantations requires adequate growth and yield models. The Ecosystem Demography model (ED) makes predictions about the large scales of interest in above- and belowground ecosystem structure and the fluxes of carbon and water from a description of the fine-scale physiological processes. In this study, we used a workflow management tool, the Predictive Ecophysiological Carbon flux Analyzer (PECAn), to integrate literature data, field measurement and the ED model to provide predictions of ecosystem functioning. Parameters for the ED ensemble runs were sampled from the posterior distribution of ecophysiological traits of Populus species compiled from the literature using a Bayesian meta-analysis approach. Sensitivity analysis was performed to identify the parameters which contribute the most to the uncertainties of the ED model output. Model emulation techniques were used to update parameter posterior distributions using field-observed data in northern Wisconsin hybrid poplar plantations. Model results were evaluated with 5-year field-observed data in a hybrid poplar plantation at New Franklin, MO. ED was then used to predict the spatial variability of poplar yield in the coterminous United States (United States minus Alaska and Hawaii). Sensitivity analysis showed that root respiration, dark respiration, growth respiration, stomatal slope and specific leaf area contribute the most to the uncertainty, which suggests that our field measurements and data collection should focus on these parameters. The ED model successfully captured the inter-annual and spatial variability of the yield of poplar. Analyses in progress with the ED model focus on evaluating the ecosystem services of short-rotation woody plantations, such as impacts on soil carbon storage, water use, and nutrient retention.

  11. Elevation of night-time temperature increases terpenoid emissions from Betula pendula and Populus tremula

    PubMed Central

    Ibrahim, Mohamed A.; Mäenpää, Maarit; Hassinen, Viivi; Kontunen-Soppela, Sari; Malec, Lukáš; Rousi, Matti; Pietikäinen, Liisa; Tervahauta, Arja; Kärenlampi, Sirpa; Holopainen, Jarmo K.; Oksanen, Elina J.

    2010-01-01

    Volatile organic compounds (VOCs) are expected to have an important role in plant adaptation to high temperatures. The impacts of increasing night-time temperature on daytime terpenoid emissions and related gene expression in silver birch (Betula pendula) and European aspen (Populus tremula) clones were studied. The plants were grown under five different night-time temperatures (6, 10, 14, 18, and 22 °C) while daytime temperature was kept at a constant 22 °C. VOC emissions were collected during the daytime and analysed by gas chromatography–mass spectrometry (GC-MS). In birch, emissions per leaf area of the C11 homoterpene 4,8-dimethy1-nona-1,3,7-triene (DMNT) and several sesquiterpenes were consistently increased with increasing night-time temperature. Total sesquiterpene (SQT) emissions showed an increase at higher temperatures. In aspen, emissions of DMNT and β-ocimene increased from 6 °C to 14 °C, while several other monoterpenes and the SQTs (Z,E)-α-farnesene and (E,E)-α-farnesene increased up to 18 °C. Total monoterpene and sesquiterpene emission peaked at 18 °C, whereas isoprene emissions decreased at 22 °C. Leaf area increased across the temperature range of 6–22 °C by 32% in birch and by 59% in aspen. Specific leaf area (SLA) was also increased in both species. The genetic regulation of VOC emissions seems to be very complex, as indicated by several inverse relationships between emission profiles and expression of several regulatory genes (DXR, DXS, and IPP). The study indicates that increasing night temperature may strongly affect the quantity and quality of daytime VOC emissions of northern deciduous trees. PMID:20181662

  12. Growth of Populus alba and its influence on soil trace element availability.

    PubMed

    Ciadamidaro, L; Madejón, E; Puschenreiter, M; Madejón, P

    2013-06-01

    The use of fast growing trees is a common practice for phytoremediation of contaminated soils. Plant roots can change trace element bioavailability in soils. We studied the effect of Populus alba on trace element bioavailability on two contaminated soils (one with neutral pH and other with acid pH) comparing two methods (0.01 M CaCl2-extractable in soil and concentration in soil pore water SPW), trace element accumulation in leaves and plant development over 36 months. Results were compared to those obtained with a non-contaminated soil. The experiment was carried out in containers (95 L of volume and 1m height). Half of the containers for each soil were planted with P. alba saplings and the others remained without plant. In neutral soils plant growth did not influence soil pH; the greatest effect due to plant growth was found in acid soil. Values of pH obtained by SPW showed a similar trend compared to those obtained after soil KCl extraction. Bioavailability of trace elements determined by both methods followed the same behavior in the three studied soils. Both methods for determining trace element bioavailability in soil were accurate to predict plant uptake. In non-contaminated soil, plants tended to increase micronutrients (Cu, Mn and Zn) availability. However, in case of contaminated soil, the growth of P. alba did not increase trace element availability. Moreover, results on height and diameter of the trunk of the trees, during 36 months, demonstrated that the presence of total trace elements in soil did not affect plant development.

  13. Males exhibit competitive advantages over females of Populus deltoides under salinity stress.

    PubMed

    Li, Yan; Duan, Baoli; Chen, Juan; Korpelainen, Helena; Niinemets, Ülo; Li, Chunyang

    2016-12-01

    Sexual competition among dioecious plants affects sex ratios and the spatial distribution of the sexes in different environments. At present, little is known about sexual dimorphisms induced by different competition patterns under salinity stress. We employed Populus deltoides as a model to investigate sex-related growth as well as physiological and biochemical responses to salinity stress under conditions of intrasexual and intersexual competition. Potted seedlings (two seedlings per pot; two females, two males, or one female and one male) were exposed to two salt levels (0 and 50 mM NaCl) and salinity- and competition-driven differences in growth, assimilation rate, water use, contents of leaf pigments and osmotica, hydrogen peroxide (H2O2), and antioxidant enzyme and nitrate reductase activity were examined. In the absence of salinity, no significant differences in competitive ability between males and females subjected to intrasexual competition were observed, although the growth of females was moderately greater under intersexual competition. The salinity treatment significantly increased the sex differences in competitive ability, especially under intersexual competition. Under salinity stress, males showed decreased height, but displayed greater capacity for osmotic adjustment, enhancement of long-term water-use efficiency and increase in antioxidant enzyme activities. The absolute values of these traits were greater in salt-stressed males than in females under intersexual competition. In addition, salt-stressed males accumulated less Cl(-) and had lower H2O2 contents than females. These data collectively demonstrate that the competitive advantage of females in non-stressed conditions is lost under salinity. Greater salinity resistance of males growing intermixed with females under salt stress can importantly affect the sex ratio of P. deltoides populations.

  14. Sexual dimorphism floral microRNA profiling and target gene expression in andromonoecious poplar (Populus tomentosa).

    PubMed

    Song, Yuepeng; Ma, Kaifeng; Ci, Dong; Zhang, Zhiyi; Zhang, Deqiang

    2013-01-01

    Although the molecular basis of poplar sex-specific flower development remains largely unknown, increasing evidence indicates an essential role for microRNAs (miRNAs). The specific miRNA types and precise miRNA expression patterns in dioecious plant flower development remain unclear. Here, we used andromonoecious poplar, an exceptional model system, to eliminate the confounding effects of genetic background of dioecious plants. This system, combined with high-throughput sequencing and computational analysis, allowed us to characterize sex-specific miRNAomes from female and male flowers. Comparative miRNAome analysis combined with quantitative real-time PCR revealed the expression patterns of 27 miRNAs in poplar flower and showed that the targets of these miRNAs are involved in flower organogenesis, Ca(2+) transport, phytohormone synthesis and metabolism, and DNA methylation. This paper describes a complex regulatory network consisting of these miRNAs expressed in sex-specific flower development in a dioecious plant. The conserved and novel miRNA locations were annotated in the Populus trichocarpa genome. Among these, miRNA Pto-F70 and 4 targets are located in the sex-determination regions of chromosome XIX. Furthermore, two novel miRNAs, Pto-F47 and Pto-F68, were shown for the first time to be regulatory factors in phytohormone interactions. To our knowledge, this report is the first systematic investigation of sex-specific flower-related miRNAs and their targets in poplar, and it deepens our understanding of the important regulatory functions of miRNAs in female and male flower development in this dioecious plant.

  15. Local adaptation in the flowering-time gene network of balsam poplar, Populus balsamifera L.

    PubMed

    Keller, Stephen R; Levsen, Nicholas; Olson, Matthew S; Tiffin, Peter

    2012-10-01

    Identifying the signature and targets of local adaptation is an increasingly important goal in empirical population genetics. Using data from 443 balsam poplar Populus balsamifera trees sampled from 31 populations, we tested for evidence of geographically variable selection shaping diversity at 27 homologues of the Arabidopsis flowering-time network. These genes are implicated in the control of seasonal phenology, an important determinant of fitness. Using 335 candidate and 412 reference single nucleotide polymorphisms (SNPs), we tested for evidence of local adaptation by searching for elevated population differentiation using F(ST)-based outlier analyses implemented in BayeScan or a Hierarchical Model in Arelquin and by testing for significant associations between allele frequency and environmental variables using BAYENV. A total of 46 SNPs from 14 candidate genes had signatures of local adaptation-either significantly greater population differentiation or significant covariance with one or more environmental variable relative to reference SNP distributions. Only 11 SNPs from two genes exhibited both elevated population differentiation and covariance with one or more environmental variables. Several genes including the abscisic acid gene ABI1B and the circadian clock genes ELF3 and GI5 harbored a large number of SNPs with signatures of local adaptation-with SNPs in GI5 strongly covarying with both latitude and precipitation and SNPs in ABI1B strongly covarying with temperature. In contrast to several other systems, we find little evidence that photoreceptors, including phytochromes, play an important role in local adaptation. Our results additionally show that detecting local adaptation is sensitive to the analytical approaches used and that model-based significance thresholds should be viewed with caution.

  16. 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

  17. Flavitalea populi gen. nov., sp. nov., isolated from soil of a Euphrates poplar (Populus euphratica) forest.

    PubMed

    Wang, Yang; Cai, Feng; Tang, Yali; Dai, Jun; Qi, Huan; Rahman, Erkin; Peng, Fang; Fang, Chengxiang

    2011-07-01

    A novel strain, designated HY-50R(T), isolated from soil of a Euphrates poplar (Populus euphratica) forest in Xinjiang, China, was characterized using a polyphasic taxonomic approach. Cells of the isolate were gram-reaction-negative, strictly aerobic, rod-shaped, non-motile, oxidase-negative and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate was a member of the phylum Bacteroidetes, its closest relatives being Niastella populi THYL-44(T) (93.6 % similarity), Flavisolibacter ginsengisoli Gsoil 643(T) (93.5 %), Terrimonas ferruginea IAM 15098(T) (93.3 %) and Flavisolibacter ginsengiterrae Gsoil 492(T) (93.2 %). The major fatty acids were iso-C(15 : 1) G (11.7 %), iso-C(15 : 0) (19.6 %) and iso-C(17 : 0) 3-OH (19.3 %). The predominant menaquinone of strain HY-50R(T) was MK-7 and the genomic DNA G+C content was 46.8 mol%. Flexirubin-type pigments were not produced. Based on phylogenetic evidence and the results of phenotypic, genotypic and chemotaxonomic analysis, strain HY-50R(T) represents a novel species of a novel genus, for which the name Flavitalea populi gen. nov., sp. nov. is proposed. The type strain is HY-50R(T) ( = CCTCC AB 208255(T)  = NRRL B-59222(T)).

  18. 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.

  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. Different growth sensitivity to enhanced UV-B radiation between male and female Populus cathayana.

    PubMed

    Xu, Xiao; Zhao, Hongxia; Zhang, Xiaolu; Hänninen, Heikki; Korpelainen, Helena; Li, Chunyang

    2010-12-01

    We investigated sex-related morphological and physiological responses to enhanced UV-B radiation in the dioecious species Populus cathayana Rehd. Cuttings were subjected to two UV-B radiation regimes: ambient (4.5 kJ m⁻² day⁻¹) and enhanced (12.5 kJ m⁻² day⁻¹) biologically effective UV-B radiation for one growing season. Enhanced UV-B radiation was found to significantly decrease the shoot height and basal diameter and to reduce the leaf area, dry matter accumulation, net photosynthesis rate (P(n)), chlorophyll a/b ratio (Chl a/b) and anthocyanin content. Enhanced UV-B radiation also increased chlorophyll pigment, leaf nitrogen, malondialdehyde and abscisic acid (ABA) content, superoxide dismutase and peroxidase activities and UV-B-absorbing compounds. No significant effects of enhanced UV-B radiation were found on biomass allocation, gas exchange (except for P(n)), photochemical efficiency of photosystem II or water use efficiency. Moreover, different sensitivity to enhanced UV-B radiation between males and females was detected. Under enhanced UV-B radiation, males exhibited significantly higher basal diameter and leaf nitrogen, and lower Chl a/b, ABA content, UV-B-absorbing compounds, as well as less decrement of leaf area and dry matter accumulation than did females. However, no significant sexual differences in these traits were found under ambient UV-B radiation. Our results suggest that males may possess a greater UV-B resistance than do females, with males having a more efficient antioxidant system and higher anthocyanin content to alleviate UV-B penetration stress than females.

  1. Elevation of night-time temperature increases terpenoid emissions from Betula pendula and Populus tremula.

    PubMed

    Ibrahim, Mohamed A; Mäenpää, Maarit; Hassinen, Viivi; Kontunen-Soppela, Sari; Malec, Lukás; Rousi, Matti; Pietikäinen, Liisa; Tervahauta, Arja; Kärenlampi, Sirpa; Holopainen, Jarmo K; Oksanen, Elina J

    2010-06-01

    Volatile organic compounds (VOCs) are expected to have an important role in plant adaptation to high temperatures. The impacts of increasing night-time temperature on daytime terpenoid emissions and related gene expression in silver birch (Betula pendula) and European aspen (Populus tremula) clones were studied. The plants were grown under five different night-time temperatures (6, 10, 14, 18, and 22 degrees C) while daytime temperature was kept at a constant 22 degrees C. VOC emissions were collected during the daytime and analysed by gas chromatography-mass spectrometry (GC-MS). In birch, emissions per leaf area of the C11 homoterpene 4,8-dimethy1-nona-1,3,7-triene (DMNT) and several sesquiterpenes were consistently increased with increasing night-time temperature. Total sesquiterpene (SQT) emissions showed an increase at higher temperatures. In aspen, emissions of DMNT and beta-ocimene increased from 6 degrees C to 14 degrees C, while several other monoterpenes and the SQTs (Z,E)-alpha-farnesene and (E,E)-alpha-farnesene increased up to 18 degrees C. Total monoterpene and sesquiterpene emission peaked at 18 degrees C, whereas isoprene emissions decreased at 22 degrees C. Leaf area increased across the temperature range of 6-22 degrees C by 32% in birch and by 59% in aspen. Specific leaf area (SLA) was also increased in both species. The genetic regulation of VOC emissions seems to be very complex, as indicated by several inverse relationships between emission profiles and expression of several regulatory genes (DXR, DXS, and IPP). The study indicates that increasing night temperature may strongly affect the quantity and quality of daytime VOC emissions of northern deciduous trees.

  2. Effect of sprayer settings on spray drift during pesticide application in poplar plantations (Populus spp.).

    PubMed

    Grella, Marco; Marucco, Paolo; Manzone, Marco; Gallart, Montserrat; Balsari, Paolo

    2017-02-01

    This study assessed spray drift generated by sprayer settings commonly used for pesticide application in poplar plantations (Populus spp.). Tests were conducted per the ISO 22866 methodology using a mounted air-assisted sprayer (Tifone VRP600) equipped with a swivel-cannon air conveyor (model Cannone 50S). Trials evaluated sprayer settings, combinations of nozzle types, airflow rates, and air direction in both adult and young poplar plantations. Overall, spray drift amounts registered downwind of poplar plantations were less than those obtained to derive reference drift curves during the EU Plant Protection Product registration process that used late-growth-stage fruit crops. In the adult poplar plantation, Venturi nozzles (TVI 8004 red) yielded the highest drift reductions compared to reference sprayer setting, especially at distances farthest from the sprayed area (86% between 40 and 47m). Highest total drift reductions were achieved when conventional nozzles (1.81mm ceramic disc-core) were combined with their spray direction modified for an inclined cannon spray unit. Alternatively, the young poplar plantation showed no drift reduction for distances farthest from the sprayed area, regardless of sprayer settings, which likely resulted from lower foliage density and widely-spaced rows. Yet, both Venturi nozzles combined with high fan flow rates and conventional nozzles combined with reduced fan flow rate showed total spray drift reductions of over 70% within the downwind sampling area. These experimental results represent the first set of data on spray drift amounts in poplar plantations, which is key for defining the reference curves and best practices to reduce spray drift in tall tree plantations.

  3. PtaRHE1, a Populus tremula × Populus alba RING-H2 protein of the ATL family, has a regulatory role in secondary phloem fibre development.

    PubMed

    Baldacci-Cresp, Fabien; Moussawi, Jihad; Leplé, Jean-Charles; Van Acker, Rebecca; Kohler, Annegret; Candiracci, Julie; Twyffels, Laure; Spokevicius, Antanas V; Bossinger, Gerd; Laurans, Françoise; Brunel, Nicole; Vermeersch, Marjorie; Boerjan, Wout; El Jaziri, Mondher; Baucher, Marie

    2015-06-01

    REALLY INTERESTING NEW GENE (RING) proteins play important roles in the regulation of many processes by recognizing target proteins for ubiquitination. Previously, we have shown that the expression of PtaRHE1, encoding a Populus tremula × Populus alba RING-H2 protein with E3 ubiquitin ligase activity, is associated with tissues undergoing secondary growth. To further elucidate the role of PtaRHE1 in vascular tissues, we have undertaken a reverse genetic analysis in poplar. Within stem secondary vascular tissues, PtaRHE1 and its corresponding protein are expressed predominantly in the phloem. The downregulation of PtaRHE1 in poplar by artificial miRNA triggers alterations in phloem fibre patterning, characterized by an increased portion of secondary phloem fibres that have a reduced cell wall thickness and a change in lignin composition, with lower levels of syringyl units as compared with wild-type plants. Following an RNA-seq analysis, a biological network involving hormone stress signalling, as well as developmental processes, could be delineated. Several candidate genes possibly associated with the altered phloem fibre phenotype observed in amiRPtaRHE1 poplar were identified. Altogether, our data suggest a regulatory role for PtaRHE1 in secondary phloem fibre development.

  4. Microarray and suppression subtractive hybridization analyses of gene expression in hybrid poplar (Populus alba × Populus tremula var. glandulosa) cell suspension cultures after exposure to NaCl.

    PubMed

    Bae, Eun-Kyung; Lee, Hyoshin; Lee, Jae-Soon; Noh, Eun-Woon; Choi, Young-Im; Lee, Byung-Hyun; Choi, Dong-Woog

    2012-09-01

    The gene expression profiles of hybrid poplar (Populus alba × Populus tremula var. glandulosa) cells in suspension culture after exposure to salinity (NaCl) induced stress were examined by constructing two suppression subtractive hybridization (SSH) libraries. cDNA from non-treated cells was used as a driver and cDNA samples from cell suspension cultures exposed to 150 mM NaCl for 2 or 10 h were used as testers. Randomly selected clones from each SSH library were sequenced and 727 high-quality expressed sequence tags (ESTs) were obtained and analyzed. Four novel ESTs were identified. Between the two libraries, 542 unique SSH clones were selected for placement on a cDNA microarray. In total, 18 differentially expressed genes were identified with 4 and 12 genes being significantly differentially expressed 2 and 10 h after the treatment, respectively. Genes related to metabolism and protein synthesis and several genes whose protein products are implicated in salt or other abiotic stress-related responses were expressed in the salt-stressed cells.

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

    PubMed

    Gilchrist, Erin J; Haughn, George W; Ying, Cheng C; Otto, Sarah P; Zhuang, Jun; Cheung, Dorothy; Hamberger, Björn; Aboutorabi, Fariba; Kalynyak, Tatyana; Johnson, Lee; Bohlmann, Joerg; Ellis, Brian E; Douglas, Carl J; Cronk, Quentin C B

    2006-04-01

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

  6. Moderate drought did not affect the effectiveness of ethylenediurea (EDU) in protecting Populus cathayana from ambient ozone.

    PubMed

    Xin, Yue; Yuan, Xiangyang; Shang, Bo; Manning, William J; Yang, Aizhen; Wang, Younian; Feng, Zhaozhong

    2016-11-01

    A field study was conducted to evaluate the effects of ambient ozone (O3) on an O3-sensitive poplar (Populus cathayana) by using ethylenediurea (EDU) as a chemical protectant under two soil water treatments (well-watered (WW) and moderate drought (MD, 50-60% of WW in volumetric soil water content). EDU was applied as foliar spray at 0, 300, 450, and 600ppm. Photosynthetic parameters, pigment contents, leaf nitrogen, antioxidant capacity, growth, and biomass were measured. The 8h (9:00-17:00) average ambient O3 concentration was 71.7ppb, and AOT40 was 29.2ppmh during the experimental period (9 June to 21 September), which was high enough to cause plant injury. MD had significantly negative effects on P. cathayana, as indicated by reduced photosynthesis, growth, and biomass, and higher MDA contents. On the other hand, EDU significantly increased photosynthesis rate, chlorophyll a fluorescence, Vcmax and Jmax, photosynthetic pigments, total antioxidant capacity, tree growth and biomass accumulation, and reduced lipid peroxidation, but there was no significant interaction between EDU and drought for most parameters, indicating that EDU can efficiently protect Populus cathayana against ambient O3 and the protection was not affected by soil water contents when soil water reached moderate drought level. Among all doses, EDU at 450ppm provided maximum protection. Comparison of EDU-treated and non-treated P. cathayana could be used as a biomarker system in risk assessment of the effects of ambient O3 on forest health.

  7. Comparative analysis of GT14/GT14-like family genes in Arabidopsis, Oryza, Populus, Sorghum and Vitis

    SciTech Connect

    Ye, Chuyu; Li, Ting; Tuskan, Gerald A; Tschaplinski, Timothy J; Yang, Xiaohan

    2011-01-01

    Glycosyltransferase family14 (GT14) belongs to the glycosyltransferase (GT) superfamily that plays important roles in the biosynthesis of cell walls, the most abundant source of cellulosic biomass for bioethanol production. It has been hypothesized that DUF266 proteins are a new class of GTs related to GT14. In this study, we identified 62 GT14 and 106 DUF266 genes (named GT14-like herein) in Arabidopsis, Oryza, Populus, Sorghum and Vitis. Our phylogenetic analysis separated GT14 and GT14-like genes into two distinct clades, which were further divided into eight and five groups, respectively. Similarities in protein domain, 3D structure and gene expression were uncovered between the two phylogenetic clades, supporting the hypothesis that GT14 and GT14-like genes belong to one family. Therefore, we proposed a new family name, GT14/GT14-like family that combines both subfamilies. Variation in gene expression and protein subcellular localization within the GT14-like subfamily were greater than those within the GT14 subfamily. One-half of the Arabidopsis and Populus GT14/GT14-like genes were found to be preferentially expressed in stem/xylem, indicating that they are likely involved in cell wall biosynthesis. This study provided new insights into the evolution and functional diversification of the GT14/GT14-like family genes.

  8. Tubulin C-terminal Post-translational Modifications Do Not Occur in Wood Forming Tissue of Populus

    PubMed Central

    Hu, Hao; Gu, Xi; Xue, Liang-Jiao; Swamy, Prashant S.; Harding, Scott A.; Tsai, Chung-Jui

    2016-01-01

    Cortical microtubules (MTs) are evolutionarily conserved cytoskeletal components with specialized roles in plants, including regulation of cell wall biogenesis. MT functions and dynamics are dictated by the composition of their monomeric subunits, α- (TUA) and β-tubulins (TUB), which in animals and protists are subject to both transcriptional regulation and post-translational modifications (PTM). While spatiotemporal regulation of tubulin gene expression has been reported in plants, whether and to what extent tubulin PTMs occur in these species remain poorly understood. We chose the woody perennial Populus for investigation of tubulin PTMs in this study, with a particular focus on developing xylem where high tubulin transcript levels support MT-dependent secondary cell wall deposition. Mass spectrometry and immunodetection concurred that detyrosination, non-tyrosination and glutamylation were essentially absent in tubulins isolated from wood-forming tissues of P. deltoides and P. tremula ×alba. Label-free quantification of tubulin isotypes and RNA-Seq estimation of tubulin transcript abundance were largely consistent with transcriptional regulation. However, two TUB isotypes were detected at noticeably lower levels than expected based on RNA-Seq transcript abundance in both Populus species. These findings led us to conclude that MT composition during wood formation depends exclusively on transcriptional and, to a lesser extent, translational regulation of tubulin isotypes. PMID:27790223

  9. Expression Patterns of ERF Genes Underlying Abiotic Stresses in Di-Haploid Populus simonii × P. nigra

    PubMed Central

    Yao, Wenjing; Jiang, Tingbo; Zhou, Boru

    2014-01-01

    176 ERF genes from Populus were identified by bioinformatics analysis, 13 of these in di-haploid Populus simonii × P. nigra were investigate by real-time RT-PCR, the results demonstrated that 13 ERF genes were highly responsive to salt stress, drought stress and ABA treatment, and all were expressed in root, stem, and leaf tissues, whereas their expression levels were markedly different in the various tissues. In roots, PthERF99, 110, 119, and 168 were primarily downregulated under drought and ABA treatment but were specifically upregulated under high salt condition. Interestingly, in poplar stems, all ERF genes showed the similar trends in expression in response to NaCl stress, drought stress, and ABA treatment, indicating that they may not play either specific or unique roles in stems in abiotic stress responses. In poplar leaves, PthERF168 was highly induced by ABA treatment, but was suppressed by high salinity and drought stresses, implying that PthERF168 participated in the ABA signaling pathway. The results of this study indicated that ERF genes could play essential but distinct roles in various plant tissues in response to different environment cues and hormonal treatment. PMID:24737991

  10. Genome-Wide Analysis and Heavy Metal-Induced Expression Profiling of the HMA Gene Family in Populus trichocarpa

    PubMed Central

    Li, Dandan; Xu, Xuemei; Hu, Xiaoqing; Liu, Quangang; Wang, Zhanchao; Zhang, Haizhen; Wang, Han; Wei, Ming; Wang, Hanzeng; Liu, Haimei; Li, Chenghao

    2015-01-01

    The heavy metal ATPase (HMA) family plays an important role in transition metal transport in plants. However, this gene family has not been extensively studied in Populus trichocarpa. We identified 17 HMA genes in P. trichocarpa (PtHMAs), of which PtHMA1–PtHMA4 belonged to the zinc (Zn)/cobalt (Co)/cadmium (Cd)/lead (Pb) subgroup, and PtHMA5–PtHMA8 were members of the copper (Cu)/silver (Ag) subgroup. Most of the genes were localized to chromosomes I and III. Gene structure, gene chromosomal location, and synteny analyses of PtHMAs indicated that tandem and segmental duplications likely contributed to the expansion and evolution of the PtHMAs. Most of the HMA genes contained abiotic stress-related cis-elements. Tissue-specific expression of PtHMA genes showed that PtHMA1 and PtHMA4 had relatively high expression levels in the leaves, whereas Cu/Ag subgroup (PtHMA5.1- PtHMA8) genes were upregulated in the roots. High concentrations of Cu, Ag, Zn, Cd, Co, Pb, and Mn differentially regulated the expression of PtHMAs in various tissues. The preliminary results of the present study generated basic information on the HMA family of Populus that may serve as foundation for future functional studies. PMID:26779188

  11. Morpho-physiological response of Populus alba to erythromycin: A timeline of the health status of the plant.

    PubMed

    Pierattini, Erika Carla; Francini, Alessandra; Raffaelli, Andrea; Sebastiani, Luca

    2016-11-01

    Populus alba Villafranca clone was chosen for a proof of concept study to determine the potential uptake and accumulation of antibiotics by trees. Plants were grown hydroponically and irrigated with a recirculating Hoagland's nutrient solution (control) and Hoagland's nutrient solution fortified with erythromycin at 0.01, 0.1 and 1mgL(-1). After 3 and 28days of treatment, poplar plants were separated into roots, stem, and leaves. Plants showed good health all over the period of treatment, and no differences in poplar growth for all the concentrations of erythromycin tested were observed. Quantification of erythromycin was performed using liquid chromatography electrospray ionization tandem mass spectrometry (LC-MS/MS) in positive ion mode using multiple reaction ion monitoring. Erythromycin was detected in all organs analyzed. Roots showed an erythromycin concentration tenfold higher than leaves. The photochemical efficiency of photosystem II did not show a dose-dependant trend. From the quenching analysis of chlorophyll fluorescence, low nonphotochemical quenching (NPQ) and high photochemical quenching (qP) for the first week of erythromycin exposure was observed, depending on leaves position along the stem. Results suggest a short term adaptation of the photosynthetic apparatus of Populus alba in response to environmental realistic erythromycin concentrations.

  12. Genetic Map Construction and Detection of Genetic Loci Underlying Segregation Distortion in an Intraspecific Cross of Populus deltoides.

    PubMed

    Zhou, Wencai; Tang, Zaixiang; Hou, Jing; Hu, Nan; Yin, Tongming

    2015-01-01

    Based on a two-way pseudo-testcross strategy, high density and complete coverage linkage maps were constructed for the maternal and paternal parents of an intraspecific F2 pedigree of Populus deltoides. A total of 1,107 testcross markers were obtained, and the mapping population consisted of 376 progeny. Among these markers, 597 were from the mother, and were assigned into 19 linkage groups, spanning a total genetic distance of 1,940.3 cM. The remaining 519 markers were from the father, and were also were mapped into 19 linkage groups, covering 2,496.3 cM. The genome coverage of both maps was estimated as greater than 99.9% at 20 cM per marker, and the numbers of linkage groups of both maps were in accordance with the 19 haploid chromosomes in Populus. Marker segregation distortion was observed in large contiguous blocks on some of the linkage groups. Subsequently, we mapped the segregation distortion loci in this mapping pedigree. Altogether, eight segregation distortion loci with significant logarithm of odds supports were detected. Segregation distortion indicated the uneven transmission of the alternate alleles from the mapping parents. The corresponding genome regions might contain deleterious genes or be associated with hybridization incompatibility. In addition to the detection of segregation distortion loci, the established genetic maps will serve as a basic resource for mapping genetic loci controlling traits of interest in future studies.

  13. Genetic Map Construction and Detection of Genetic Loci Underlying Segregation Distortion in an Intraspecific Cross of Populus deltoides

    PubMed Central

    Hou, Jing; Hu, Nan; Yin, Tongming

    2015-01-01

    Based on a two-way pseudo-testcross strategy, high density and complete coverage linkage maps were constructed for the maternal and paternal parents of an intraspecific F2 pedigree of Populus deltoides. A total of 1,107 testcross markers were obtained, and the mapping population consisted of 376 progeny. Among these markers, 597 were from the mother, and were assigned into 19 linkage groups, spanning a total genetic distance of 1,940.3 cM. The remaining 519 markers were from the father, and were also were mapped into 19 linkage groups, covering 2,496.3 cM. The genome coverage of both maps was estimated as greater than 99.9% at 20 cM per marker, and the numbers of linkage groups of both maps were in accordance with the 19 haploid chromosomes in Populus. Marker segregation distortion was observed in large contiguous blocks on some of the linkage groups. Subsequently, we mapped the segregation distortion loci in this mapping pedigree. Altogether, eight segregation distortion loci with significant logarithm of odds supports were detected. Segregation distortion indicated the uneven transmission of the alternate alleles from the mapping parents. The corresponding genome regions might contain deleterious genes or be associated with hybridization incompatibility. In addition to the detection of segregation distortion loci, the established genetic maps will serve as a basic resource for mapping genetic loci controlling traits of interest in future studies. PMID:25942445

  14. A systems biology, whole-genome association analysis of the molecular regulation of biomass growth and composition in Populus deltoides

    SciTech Connect

    Kirst, Matias

    2015-04-15

    Poplars trees are well suited for biofuel production due to their fast growing habit, favorable wood composition and adaptation to a broad range of environments. The availability of a reference genome sequence, ease of vegetative propagation and availability of transformation methods also make poplar an ideal model for the study of wood formation and biomass growth in woody, perennial plants. The objective of this project was to conduct a genome-wide association genetics study to identify genes that regulate bioenergy traits in Populus deltoides (eastern cottonwood). Populus deltoides is a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits and common and low-frequency single-nucleotide polymorphisms (SNPs) detected by targeted resequencing of 18,153 genes in a population of 391 unrelated individuals. To increase power to detect associations with low-frequency variants, multiple-marker association tests were used in combination with single-marker association tests. Significant associations were discovered for all phenotypes and are indicative that low-frequency polymorphisms contribute to phenotypic variance of several bioenergy traits. These polymorphism are critical tools for the development of specialized plant feedstocks for bioenergy.

  15. Comparative proteomics analysis of salt response reveals sex-related photosynthetic inhibition by salinity in Populus cathayana cuttings.

    PubMed

    Chen, Fugui; Zhang, Sheng; Jiang, Hao; Ma, Wujun; Korpelainen, Helena; Li, Chunyang

    2011-09-02

    Male and female poplar ( Populus cathayana Rehd.) cuttings respond differently to salinity stress. To understand these differences better, comparative morphological, physiological, and proteomics analyses were performed. Treatments with different concentrations of NaCl applied to male and female poplar cuttings for 4 weeks showed that females reacted more negatively at the morphological and physiological levels than did males, visible as shriveled leaves, decreased growth, lowered photosynthetic capacities, and greater Na(+) accumulation. The proteome analysis identified 73 proteins from 82 sexually related salt-responsive spots. They were involved in photosynthesis, protein folding and assembly, synthesis and degradation, carbon, energy and steroid metabolism, plant stress and defense, redox homeostasis, signal transduction, and so forth. The sex-related changes of these proteins were consistent with the different morphological and physiological responses in males and females. In conclusion, the higher salt resistance of male P. cathayana cuttings is related to higher expression and lower degradation of proteins in the photosynthetic apparatus, more effective metabolic mechanism and protective system, and greater capacity of hydrogen peroxide scavenging. This research allows us to further understand the possible different management strategies of cellular activities in male and female Populus when confronted by salt stress.

  16. Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa.

    PubMed

    McKown, Athena D; Klápště, Jaroslav; Guy, Robert D; Geraldes, Armando; Porth, Ilga; Hannemann, Jan; Friedmann, Michael; Muchero, Wellington; Tuskan, Gerald A; Ehlting, Jürgen; Cronk, Quentin C B; El-Kassaby, Yousry A; Mansfield, Shawn D; Douglas, Carl J

    2014-07-01

    In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa) from much of its range in western North America. Extensive data from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34 K Populus single nucleotide polymorphism (SNP) array) of all accessions were used for gene discovery in a genome-wide association study (GWAS). We performed GWAS with 40 biomass, ecophysiology and phenology traits and 29,355 filtered SNPs representing 3518 genes. The association analyses were carried out using a Unified Mixed Model accounting for population structure effects among accessions. We uncovered 410 significant SNPs using a Bonferroni-corrected threshold (P<1.7×10(-6)). Markers were found across 19 chromosomes, explained 1-13% of trait variation, and implicated 275 unique genes in trait associations. Phenology had the largest number of associated genes (240 genes), followed by biomass (53 genes) and ecophysiology traits (25 genes). The GWAS results propose numerous loci for further investigation. Many traits had significant associations with multiple genes, underscoring their genetic complexity. Genes were also identified with multiple trait associations within and/or across trait categories. In some cases, traits were genetically correlated while in others they were not.

  17. Nucleotide Polymorphism and Linkage Disequilibrium Within and Among Natural Populations of European Aspen (Populus tremula L., Salicaceae)

    PubMed Central

    Ingvarsson, Pär K.

    2005-01-01

    Populus is an important model organism in forest biology, but levels of nucleotide polymorphisms and linkage disequilibrium have never been investigated in natural populations. Here I present a study on levels of nucleotide polymorphism, haplotype structure, and population subdivision in five nuclear genes in the European aspen Populus tremula. Results show substantial levels of genetic variation. Levels of silent site polymorphisms, πs, averaged 0.016 across the five genes. Linkage disequilibrium was generally low, extending only a few hundred base pairs, suggesting that rates of recombination are high in this obligate outcrossing species. Significant genetic differentiation was found at all five genes, with an average estimate of FST = 0.116. Levels of polymorphism in P. tremula are 2- to 10-fold higher than those in other woody, long-lived perennial plants, such as Pinus and Cryptomeria. The high levels of nucleotide polymorphism and low linkage disequilibrium suggest that it may be possible to map functional variation to very fine scales in P. tremula using association-mapping approaches. PMID:15489521

  18. Genetic architecture of growth traits in Populus revealed by integrated quantitative trait locus (QTL) analysis and association studies.

    PubMed

    Du, Qingzhang; Gong, Chenrui; Wang, Qingshi; Zhou, Daling; Yang, Haijiao; Pan, Wei; Li, Bailian; Zhang, Deqiang

    2016-02-01

    Deciphering the genetic architecture underlying polygenic traits in perennial species can inform molecular marker-assisted breeding. Recent advances in high-throughput sequencing have enabled strategies that integrate linkage-linkage disequilibrium (LD) mapping in Populus. We used an integrated method of quantitative trait locus (QTL) dissection with a high-resolution linkage map and multi-gene association mapping to decipher the nature of genetic architecture (additive, dominant, and epistatic effects) of potential QTLs for growth traits in a Populus linkage population (1200 progeny) and a natural population (435 individuals). Seventeen QTLs for tree height, diameter at breast height, and stem volume mapped to 11 linkage groups (logarithm of odds (LOD) ≥ 2.5), and explained 2.7-18.5% of the phenotypic variance. After comparative mapping and transcriptome analysis, 187 expressed genes (10 046 common single nucleotide polymorphisms (SNPs)) were selected from the segmental homology regions (SHRs) of 13 QTLs. Using multi-gene association models, we observed 202 significant SNPs in 63 promising genes from 10 QTLs (P ≤ 0.0001; FDR ≤ 0.10) that exhibited reproducible associations with additive/dominant effects, and further determined 11 top-ranked genes tightly linked to the QTLs. Epistasis analysis uncovered a uniquely interconnected gene-gene network for each trait. This study opens up opportunities to uncover the causal networks of interacting genes in plants using an integrated linkage-LD mapping approach.

  19. A systems biology, whole-genome association analysis of the molecular regulation of biomass growth and composition in Populus deltoides

    SciTech Connect

    Kirst, Matias

    2014-04-14

    Poplars trees are well suited for biofuel production due to their fast growing habit, favorable wood composition and adaptation to a broad range of environments. The availability of a reference genome sequence, ease of vegetative propagation and availability of transformation methods also make poplar an ideal model for the study of wood formation and biomass growth in woody, perennial plants. The objective of this project was to conduct a genome-wide association genetics study to identify genes that regulate bioenergy traits in Populus deltoides (eastern cottonwood). Populus deltoides is a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits and common and low-frequency single-nucleotide polymorphisms (SNPs) detected by targeted resequencing of 18,153 genes in a population of 391 unrelated individuals. To increase power to detect associations with low-frequency variants, multiple-marker association tests were used in combination with single-marker association tests. Significant associations were discovered for all phenotypes and are indicative that low-frequency polymorphisms contribute to phenotypic variance of several bioenergy traits. These polymorphism are critical tools for the development of specialized plant feedstocks for bioenergy.

  20. Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics.

    PubMed

    Yang, Xiaohan; Ye, Chu-Yu; Bisaria, Anjali; Tuskan, Gerald A; Kalluri, Udaya C

    2011-12-01

    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 biofuels 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 evidence 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 characterization in relation to cell wall biosynthesis.

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

    SciTech Connect

    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.

  2. Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae).

    PubMed

    Huang, Daisie I; Hefer, Charles A; Kolosova, Natalia; Douglas, Carl J; Cronk, Quentin C B

    2014-11-01

    As molecular phylogenetic analyses incorporate ever-greater numbers of loci, cases of cytonuclear discordance - the phenomenon in which nuclear gene trees deviate significantly from organellar gene trees - are being reported more frequently. Plant examples of topological discordance, caused by recent hybridization between extant species, are well known. However, examples of branch-length discordance are less reported in plants relative to animals. We use a combination of de novo assembly and reference-based mapping using short-read shotgun sequences to construct a robust phylogeny of the plastome for multiple individuals of all the common Populus species in North America. We demonstrate a case of strikingly high plastome divergence, in contrast to little nuclear genome divergence, in two closely related balsam poplars, Populus balsamifera and Populus trichocarpa (Populus balsamifera ssp. trichocarpa). Previous studies with nuclear loci indicate that the two species (or subspecies) diverged since the late Pleistocene, whereas their plastomes indicate deep divergence, dating to at least the Pliocene (6-7 Myr ago). Our finding is in marked contrast to the estimated Pleistocene divergence of the nuclear genomes, previously calculated at 75 000 yr ago, suggesting plastid capture from a 'ghost lineage' of a now-extinct North American poplar.

  3. [Radial variation and time lag of sap flow of Populus gansuensis in Minqin Oasis, Northwest].

    PubMed

    Dang, Hong-Zhong; Yang, Wen-Bin; Li, Wei; Zhang, You-Yan; Li, Chang-Long

    2014-09-01

    Sap flow of tree trunk is very important to reflect the dynamics of physiological activities, as well as to estimate the water consumption of individual plant. In the present study, we used the thermal dissipation technique to monitor the sap flow velocity (J) at four depth loci (i. e. 2 cm, 3 cm, 5 cm, 8 cm) of three Populus gansuensis trees (30 year-old) in Minqin Oasis for two consecutive growing seasons. The results showed that there were significant differences among J values at four depth loci under tree trunk cambium. J value at the 3 cm depth locus (J3) of the tree trunk was the highest, and then in sequences, were 2 cm, 5 cm and 8 cm depth loci (J2, J5 and J8). J value (J3) on typical sunny days in June with the highest atmospheric potential evapotranspiration (ET0) was up to 28.53 g · cm(-2) · h(-1), which was 1.42, 2.74 and 4.4 times of J2, J5 and J8, respectively. In the process of diurnal variation of sap flow velocity, the peak value time of J at the four depth loci of the tree trunk was different, but the differences among them were within 20 min. Furthermore, the peak value time of sap flow velocity was very different to that of solar radiation (Rs) and air vapour pressure deficit (VPD). The time lag between J and Rs was from 55 to 88 min on typical sunny days during the main growing seasons (from June to August), and, positively related to the depth of the locus under tree trunk cambium, while the time lag between J and VPD reached 60-96 min, and was negatively related to the depth of the locus. The seasonal variation patterns of J were consistent with ET0. With the increase of tree physiological activities, there was a trend that the major water transportation layer extended to the interior sapwood. The most important meteorological factor was the solar radiation, which primarily drove sap flow at different depths of tree trunk. However, the secondary factor changed along with the depth, and VPD became increasingly important with increasing the

  4. Rhizobium populi sp. nov., an endophytic bacterium isolated from Populus euphratica.

    PubMed

    Rozahon, Manziram; Ismayil, Nurimangul; Hamood, Buayshem; Erkin, Raziya; Abdurahman, Mehfuzem; Mamtimin, Hormathan; Abdukerim, Muhtar; Lal, Rup; Rahman, Erkin

    2014-09-01

    An endophytic bacterium, designated K-38(T), was isolated from the storage liquid in the stems of Populus euphratica trees at the ancient Ugan River in Xinjiang, PR China. Strain K-38(T) was found to be rod-shaped, Gram-stain-negative, aerobic, non-motile and non-spore-forming. Strain K-38(T) grew at temperatures of 25-37 °C (optimum, 28 °C), at pH 6.0-9.0 (optimum, pH 7.5) and in the presence of 0-3 % (w/v) NaCl with 1 % as the optimum concentration for growth. According to phylogenetic analysis based on 16S rRNA gene sequences, strain K-38(T) was assigned to the genus Rhizobium with highest 16S rRNA gene sequence similarity of 97.2 % to Rhizobium rosettiformans W3(T), followed by Rhizobium nepotum 39/7(T) (96.5 %) and Rhizobium borbori DN316(T) (96.2 %). Phylogenetic analysis of strain K-38(T) based on the protein coding genes recA, atpD and nifH confirmed (similarities were less than 90 %) it to be a representative of a distinctly delineated species of the genus Rhizobium. The DNA G+C content was determined to be 63.5 mol%. DNA-DNA relatedness between K-38(T) and R. rosettiformans W3(T) was 48.4 %, indicating genetic separation of strain K-38(T) from the latter strain. The major components of the cellular fatty acids in strain K-38(T) were revealed to be summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c; 57.2 %), C16 : 0 (13.6 %) and summed feature 2 (comprising C12 : 0 aldehyde, C14 : 0 3-OH/iso-C16 : 1 I and/or unknown ECL 10.928; 11.0 %). Polar lipids of strain K-38(T) include phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids and two unidentified phospholipids. Q-10 was the major quinone in strain K-38(T). Based on phenotypic, chemotaxonomic and phylogenetic properties, strain K-38(T) represents a novel species of the genus Rhizobium, for which the name Rhizobium populi sp. nov. is proposed

  5. Involvement of hydrogen peroxide and nitric oxide in salt resistance in the calluses from Populus euphratica.

    PubMed

    Zhang, Feng; Wang, Yuping; Yang, Yingli; Wu, Hao; Wang, Di; Liu, Jianquan

    2007-07-01

    Nitric oxide (NO) and hydrogen peroxide (H2O2) function as signalling molecules in plants under abiotic and biotic stresses. Calluses from Populus euphratica, which show salt tolerance, were used to study the interaction of NO and H2O2 in plant adaptation to salt resistance. The nitric oxide synthase (NOS) activity was identified in the calluses, and this activity was induced under 150 mM NaCl treatment. Under 150 mM NaCl treatment, the sodium (Na) percentage decreased, but the potassium (K) percentage and the K/Na ratio increased in P. euphratica calluses. Application of glucose/glucose oxidase (G/GO, a H2O2 donor) and sodium nitroprusside (SNP, a NO donor) revealed that both H2O2 and NO resulted in increased K/Na ratio in a concentration-dependent manner. Diphenylene iodonium (DPI, an NADPH oxidase inhibitor) counteracted H2O2 and NO effect by increasing the Na percentage, decreasing the K percentage and K/Na ratio. NG-monomethyl-L-Arg monoacetate (NMMA, an NO synthase inhibitor) and 2-phenyl-4,4,5,5-tetramethyl-imidazoline-1-oxyl-3-oxyde (PTIO, a specific NO scavenger) only reversed NO effect, but did not block H2O2 effect. The increased activity of plasma membrane (PM) H+ -ATPase caused by salt stress was reversed by treatment with DPI and NMMA. Exogenous H2O2 increased the activity of PM H+ -ATPase, but the effect could not be diminished by NMMA and PTIO. The NO-induced increase of PM H+ -ATPase can be reversed by NMMA and PTIO, but not by DPI. Western blot analysis demonstrated that NO and H2O2 stimulated the expression of PM H+ -ATPase in P. euphratica calluses. These results indicate that NO and H2O2 served as intermediate molecules in inducing salt resistance in the calluses from P. euphratica under slat stress by increasing the K/Na ratio, which was dependent on the increased PM H+ -ATPase activity.

  6. Expression and molecular evolution of two DREB1 genes in black poplar (Populus nigra).

    PubMed

    Chu, Yanguang; Huang, Qinjun; Zhang, Bingyu; Ding, Changjun; Su, Xiaohua

    2014-01-01

    Environmental stresses such as low temperature, drought, and high salinity significantly affect plant growth and yield. As selective forces, these adverse factors play essential roles in shaping phenotypic variation in plant populations. Black poplar (Populus nigra) is an economically and ecologically important forest tree species with widely distributed populations and is thus suitable for experiments detecting evolutionary footprints left by stress. Here, we performed expression and evolutionary analysis of two duplicated DREB A1-subgroup (DREB1) genes, PnDREB68 and PnDREB69, encoding transcription factors that are involved in stress responses. The two genes showed partially overlapping but distinct expression patterns in response to stresses. These genes were strongly and rapidly induced by cold stress in leaves, stems, and roots. In leaf tissue, dehydration stress induced the expression of PnDREB68 but not PnDREB69. PnDREB69 displayed more rapid responses and longer expression durations than PnDREB68 under salt and ABA stress, respectively. Based on single nucleotide polymorphism (SNP) analysis, we found significant population genetic differentiation, with a greater FST value (0.09189) for PnDREB69 than for PnDREB68 (0.07743). Nucleotide diversity analysis revealed a two-fold higher πT for PnDREB68 than for PnDREB69 (0.00563 vs. 0.00243), reflecting strong purifying selection acting on the former. The results suggest that positive selection acted on PnDREB69, as evidenced by neutral testing using Tajima's D statistic. The distinct selective forces to which each of the genes was subjected may be associated with expression divergence. Linkage disequilibrium (LD) was low for the sequenced region, with a higher level for PnDREB68 than for PnDREB69. Additionally, analysis of the relationship among carbon isotope ratios, SNP classes and gene expression, together with motif and domain analysis, suggested that 14 polymorphisms within the two genes may be candidates

  7. Shoot structure and growth along a vertical profile within a Populus-Tilia canopy.

    PubMed

    Kull, Olevi; Tulva, Ingmar

    2002-11-01

    We investigated shoot growth patterns and their relationship to the canopy radiation environment and the distribution of leaf photosynthetic production in a 27-m-tall stand of light-demanding Populus tremula L. and shade-tolerant Tilia cordata Mill. The species formed two distinct layers in the leaf canopy and showed different responses in branch architecture to the canopy light gradient. In P. tremula, shoot bifurcation decreased rapidly with decreasing light, and leaf display allowed capture of multidirectional light. In contrast, leaf display in T. cordata was limited to efficient interception of unidirectional light, and shoot growth and branching pattern facilitated relatively rapid expansion into potentially unoccupied space even in the low light of the lower canopy. At the canopy level, T. cordata had higher photosynthetic light-use efficiency than P. tremula, whereas P. tremula had higher nitrogen-use efficiency than T. cordata. However, at the individual leaf level, both species had similar efficiencies under comparable light conditions. Production of new leaf area in the canopy followed the pattern of photosynthetic production. However, the species differed substantially in extension growth and space-filling strategy. Light-demanding P. tremula expanded into new space with a few long shoots, with shoot length strongly dependent on photosynthetic photon flux density (PPFD). Production of new leaf area and extension growth were largely uncoupled in this species because short shoots, which do not contribute to extension growth, produced many new leaves. Thus, in P. tremula, the growth pattern was strongly directed toward the top of the canopy. In contrast, in shade-tolerant T. cordata, shoot growth was weakly related to PPFD and more was invested in long shoot growth on a leaf area basis compared with P. tremula. However, this extension growth was not directed and may serve as a passive means of avoiding self-shading. This study supports the hypothesis that

  8. Spatial distribution of leaf morphological and physiological characteristics in relation to local radiation regime within the canopies of 3-year-old Populus clones in coppice culture.

    PubMed

    Casella, E; Ceulemans, R

    2002-12-01

    Spatial distributions of leaf characteristics relevant to photosynthesis were compared within high-density coppice canopies of Populus spp. of contrasting genetic origin. We studied three clones representative of the range in growth potential, leaf morphology, coppice and canopy structure: Clone Hoogvorst (Hoo) (Populus trichocarpa Torr. & Gray x Populus deltoides Bartr. & Marsh), Clone Fritzi Pauley (Fri) (Populus trichocarpa Torr. & Gray) and Clone Wolterson (Wol) (Populus nigra L.). Leaf area index ranged from 2.7 (Fri and Wol) to 3.8 (Hoo). The clones exhibited large vertical variation in leaf area density (0.02-1.42 m2 m-3). Leaf dry mass per unit leaf area (DM(A)) increased with increasing light in Clones Hoo and Fri, from about 56 g m-2 at the bottom of the canopy to 162 g m-2 at the top. In Clone Wol, DM(A) varied only from 65 to 100 g m-2, with no consistent relationship with respect to light. Conversely, nitrogen concentration on a mass basis was nearly constant (around 1.3-2.1%) within the canopies of Clones Hoo and Fri, but increased strongly with light in Clone Wol, from 1.4% at the bottom of the canopy to 4.1% at the top. As a result, nitrogen per unit leaf area (N(A)) increased with light in the canopies of all clones, from 0.9 g m-2 at the bottom to 2.9 g m-2 at the top. Although a single linear relationship described the dependence of maximum carboxylation rate (17-93 micromol CO2 m-2 s-1) or electron transport capacity (45-186 micromol electrons m-2 s-1) on N(A), for all clones, Clone Wol differed from Clones Hoo and Fri by exhibiting a higher dark respiration rate at low N(A) (1.8 versus 0.8 micromol CO2 m-2 s-1).

  9. Identification of quantitative trait loci affecting ectomycorrhizal symbiosis in an interspecific F1 poplar cross and differential expression of genes in ectomycorrhizas of the two parents: Populus deltoides and Populus trichocarpa

    SciTech Connect

    Labbe, Jessy L; Jorge, Veronique; Vion, Patrice; Marcais, Benoit; Bastien, Catherine; Tuskan, Gerald A; Martin, Francis; Le Tacon, F

    2011-01-01

    A Populus deltoides Populus trichocarpa F1 pedigree was analyzed for quantitative trait loci (QTLs) affecting ectomycorrhizal development and for microarray characterization of gene networks involved in this symbiosis. A 300 genotype progeny set was evaluated for its ability to form ectomycorrhiza with the basidiomycete Laccaria bicolor. The percentage of mycorrhizal root tips was determined on the root systems of all 300 progeny and their two parents. QTL analysis identified four significant QTLs, one on the P. deltoides and three on the P. trichocarpa genetic maps. These QTLs were aligned to the P. trichocarpa genome and each contained several megabases and encompass numerous genes. NimbleGen whole-genome microarray, using cDNA from RNA extracts of ectomycorrhizal root tips from the parental genotypes P. trichocarpa and P. deltoides, was used to narrow the candidate gene list. Among the 1,543 differentially expressed genes (p value 0.05; 5.0-fold change in transcript level) having different transcript levels in mycorrhiza of the two parents, 41 transcripts were located in the QTL intervals: 20 in Myc_d1, 14 in Myc_t1, and seven in Myc_t2, while no significant differences among transcripts were found in Myc_t3. Among these 41 transcripts, 25 were overrepresented in P. deltoides relative to P. trichocarpa; 16 were overrepresented in P. trichocarpa. The transcript showing the highest overrepresentation in P. trichocarpa mycorrhiza libraries compared to P. deltoides mycorrhiza codes for an ethylene-sensitive EREBP-4 protein which may repress defense mechanisms in P. trichocarpa while the highest overrepresented transcripts in P. deltoides code for proteins/genes typically associated with pathogen resistance.

  10. Effects of in vitro ozone treatment on proteolysis of purified rubisco from two hybrid poplar clones. [Populus maximowizii x trichocarpa

    SciTech Connect

    Landry, L.G.; Pell, E.J. )

    1989-04-01

    Plants exposed to ozone (O{sub 3}) exhibited symptoms of premature senescence, including early decline in quantity of rubisco. O{sub 3}-induced oxidation may cause changes in protein conformation of rubisco, resulting in enhanced proteolysis. To test this hypothesis, rubisco was purified from two hybrid clones of Populus maximowizii x trichocarpa, clones 388 and 245, and treated in vitro with O{sub 3} or air. Rubisco was then challenged with bromelain, papain, chymotrypsin, carboxypeptidase A, or endoproteinase Glu-C and percent degradation measured by SDS-PAGE and densitometric scanning of the gels. Degree of rubisco sensitivity to oxidation may be related to available sulfhydryl (SH) groups on the protein. The number of SH groups in native and denatured rubisco was measured for purified rubisco of both clones by DTNB titration method. The relationship between sensitivity to proteolysis and number and availability of SH groups is discussed.

  11. Determining the syringyl/guaiacyl lignin ratio in the vessel and fiber cell walls of transgenic Populus plants

    DOE PAGES

    Tolbert, Allison K.; Ma, Tao; Kalluri, Udaya C.; ...

    2016-06-20

    Observation of the spatial lignin distribution throughout the plant cell wall provides insight into the physicochemical characteristics of lignocellulosic biomass. The distribution of syringyl (S) and guaiacyl (G) lignin in cell walls of a genetically modified Populus deltoides and its corresponding empty vector control were analyzed with time-of-flight secondary ion mass spectrometry (ToF-SIMS) and then mapped to determine the S/G lignin ratio of the sample surface and specific regions of interest (ROIs). The surface characterizations of transgenic cross-sections within 1 cm vertical distance of each other on the stem possess similar S/G lignin ratios. Furthermore, the analysis of the ROIsmore » determined that there was a 50% decrease in the S/G lignin ratio of the transgenic xylem fiber cell walls.« less

  12. A ThCAP gene from Tamarix hispida confers cold tolerance in transgenic Populus (P. davidiana x P. bolleana).

    PubMed

    Guo, Xiao-Hong; Jiang, Jing; Lin, Shi-Jie; Wang, Bai-Chen; Wang, Yu-Cheng; Liu, Gui-Feng; Yang, Chuan-Ping

    2009-07-01

    The ThCAP gene, which encodes a cold acclimation protein, was isolated from a Tamarix hispida NaCl-stress root cDNA library; its expression patterns were then assayed by qRT-PCR in different T. hispida tissues treated with low temperature (4 degrees C), salt (400 mM NaCl), drought (20% PEG6000) and exogenous abscisic acid (100 microM). Induction of ThCAP gene was not only responsive to different stress conditions but was also organ specific. When transgenic Populus (P. davidiana x P. bolleana) plants were generated, expressing ThCAP under regulation of the cauliflower mosaic virus CaMV 35S promoter, they had a greater resistance to low temperature than non-transgenic seedlings, suggesting that ThCAP might play an important role in cold tolerance.

  13. Improvement of enzymatic saccharification of Populus and switchgrass by combined pretreatment with steam and wet disk milling

    DOE PAGES

    Kumagai, Akio; Wu, Long; Iwamoto, Shinichiro; ...

    2014-12-15

    In this study, to reduce the recalcitrance of lignocellulosic biomass for subsequent biological processing, we pretreated energy crop feedstocks with mild steam treatment (ST; 130 and 150 °C for 60 min) and wet disk milling (WDM). We tested two phylogenetically different, but typical energy crop feedstocks: Populus trichocarpa and switchgrass (Panicum virgatum). WDM after ST facilitated the fibrillation of both types of biomass, resulting in an increase of specific surface area, improved enzymatic saccharification yield, and decrease in cellulose crystallinity. Lastly, after steam treatment at 150 °C followed by 17 cycles of WDM, enzymatic hydrolysis resulted in almost complete glucanmore » to glucose conversion in both feedstocks.« less

  14. Pretreatment of Populus tomentosa with Trametes velutina supplemented with inorganic salts enhances enzymatic hydrolysis for ethanol production.

    PubMed

    Wang, Wei; Yuan, Tongqi; Cui, Baokai; Dai, Yucheng

    2012-12-01

    Different nutrients were added into the solid fermentation of woody biomass, Populus tomentosa, to improve pretreatment by a white rot fungus, Trametes velutina. Fungal pretreatment supplemented with trace elements resulted in large amount of lignin loss but low degradation of carbohydrate. Only 12.6 % of Klason lignin was left in the residues pretreated by T. velutina for 8 weeks supplemented with 1 % trace elements (TE group). When fungal-pretreated residues were subjected to enzymatic hydrolysis for 96 h, a maximum reducing sugar yield of 44 % was obtained from the TE group at the 8th week, 2.3 times higher than that of untreated samples. In addition, the highest ethanol yield of 22 % was observed by the fermentation of 8-week pretreated residues from the basic medium plus trace element group, which was five times more than that of untreated samples.

  15. Somatic embryogenesis and plant regeneration from cell suspension and tissue cultures of mature himalayan poplar (Populus ciliata).

    PubMed

    Cheema, G S

    1989-02-01

    Somatic embryogenesis and plantlet formation were obtained from callus and cell suspension cultures of 40-year- old Himalayan Poplar (Populus ciliata Wall ex Royle). Callus and cell suspensions were obtained by transfer of inoculum of semiorganized leaf cultures, which were maintained on Murashige and Skoog (MS) medium supplemented with benzylaminopurine (BAP), to MS with 2,4-dichlorophenoxyacetic acid (2,4-D). Reduction of 2,4-D concentration during subsequent subculture of cell suspensions resulted in the formation of embryoids. These embryoids developed further only after being transferred to agar-based MS medium supplemented with BAP and naphthalene acetic acid. Loss of embryogenic potential was observed in cell suspensions after 6 subcultures. However, callus cultures retained the embryogenic potential even after repeated subcultures for more than a year. Plantlets could be successfully hardened and grown in natural outdoor conditions.

  16. Improvement of enzymatic saccharification of Populus and switchgrass by combined pretreatment with steam and wet disk milling

    SciTech Connect

    Kumagai, Akio; Wu, Long; Iwamoto, Shinichiro; Lee, Seung-Hwan; Endo, Takashi; Rodriguez, Miguel; Mielenz, Jonathan R.

    2014-12-15

    In this study, to reduce the recalcitrance of lignocellulosic biomass for subsequent biological processing, we pretreated energy crop feedstocks with mild steam treatment (ST; 130 and 150 °C for 60 min) and wet disk milling (WDM). We tested two phylogenetically different, but typical energy crop feedstocks: Populus trichocarpa and switchgrass (Panicum virgatum). WDM after ST facilitated the fibrillation of both types of biomass, resulting in an increase of specific surface area, improved enzymatic saccharification yield, and decrease in cellulose crystallinity. Lastly, after steam treatment at 150 °C followed by 17 cycles of WDM, enzymatic hydrolysis resulted in almost complete glucan to glucose conversion in both feedstocks.

  17. Towards a map of the Populus biomass protein-protein interaction network

    SciTech Connect

    Beers, Eric; Brunner, Amy; Helm, Richard; Dickerman, Allan

    2015-07-31

    Biofuels can be produced from a variety of plant feedstocks. The value of a particular feedstock for biofuels production depends in part on the degree of difficulty associated with the extraction of fermentable sugars from the plant biomass. The wood of trees is potentially a rich source fermentable sugars. However, the sugars in wood exist in a tightly cross-linked matrix of cellulose, hemicellulose, and lignin, making them largely recalcitrant to release and fermentation for biofuels production. Before breeders and genetic engineers can effectively develop plants with reduced recalcitrance to fermentation, it is necessary to gain a better understanding of the fundamental biology of the mechanisms responsible for wood formation. Regulatory, structural, and enzymatic proteins are required for the complicated process of wood formation. To function properly, proteins must interact with other proteins. Yet, very few of the protein-protein interactions necessary for wood formation are known. The main objectives of this project were to 1) identify new protein-protein interactions relevant to wood formation, and 2) perform in-depth characterizations of selected protein-protein interactions. To identify relevant protein-protein interactions, we cloned a set of approximately 400 genes that were highly expressed in the wood-forming tissue (known as secondary xylem) of poplar (Populus trichocarpa). We tested whether the proteins encoded by these biomass genes interacted with each other in a binary matrix design using the yeast two-hybrid (Y2H) method for protein-protein interaction discovery. We also tested a subset of the 400 biomass proteins for interactions with all proteins present in wood-forming tissue of poplar in a biomass library screen design using Y2H. Together, these two Y2H screens yielded over 270 interactions involving over 75 biomass proteins. For the second main objective we selected several interacting pairs or groups of interacting proteins for in

  18. Underground riparian wood: Buried stem and coarse root structures of Black Poplar (Populus nigra L.)

    NASA Astrophysics Data System (ADS)

    Holloway, James V.; Rillig, Matthias C.; Gurnell, Angela M.

    2017-02-01

    Despite the potential importance of tree species in influencing the processes of wood recruitment, transport, retention, and decay that control river wood budgets, focus has been relatively limited on this theme within fluvial wood research. Furthermore, one of the least investigated topics is the belowground living wood component of riparian trees. This paper presents observations of the morphology and age of buried stem and coarse root structures of eight Populus nigra individuals located in the riparian woodland of two sites on the middle to lower Tagliamento River, Italy. This species was selected because of its wide distribution along European rivers and its frequent dominance of riparian woodland. Each tree was excavated by hand to expose a minimum of half of the root system with complete exposure of the main axis. Smaller roots were then removed and larger protruding roots cut back to permit access to the main axis. The excavated structures were photographed from multiple angles for photogrammetric modelling; the structure and character of the exposed sediments around the tree's main axis were recorded; and wood samples were taken from the main aboveground stem(s), sections of the main buried axis, and major roots for dendrochronological analysis. Results from these field observations and laboratory dating of the wood samples were combined to describe the belowground morphology of each tree and to draw inferences concerning the impact of fluvial disturbances. Common features of these excavated structures included: (i) rooting depths to below the bar surface where the original tree established, with many young roots also existing at depth; (ii) translocation of the main buried axis in a downstream direction; (iii) a main buried axis comprised mainly of stems that have become buried and then generated new shoots, including multistem patches, and adventitious roots; (iv) the presence of steps and bends in the main buried axis associated with the generation of

  19. Association genetics, geography and ecophysiology link stomatal patterning in Populus trichocarpa with carbon gain and disease resistance trade-offs.

    PubMed

    McKown, Athena D; Guy, Robert D; Quamme, Linda; Klápště, Jaroslav; La Mantia, Jonathan; Constabel, C P; El-Kassaby, Yousry A; Hamelin, Richard C; Zifkin, Michael; Azam, M S

    2014-12-01

    Stomata are essential for diffusive entry of gases to support photosynthesis, but may also expose internal leaf tissues to pathogens. To uncover trade-offs in range-wide adaptation relating to stomata, we investigated the underlying genetics of stomatal traits and linked variability in these traits with geoclimate, ecophysiology, condensed foliar tannins and pathogen susceptibility in black cottonwood (Populus trichocarpa). Upper (adaxial) and lower (abaxial) leaf stomatal traits were measured from 454 accessions collected throughout much of the species range. We calculated broad-sense heritability (H(2) ) of stomatal traits and, using SNP data from a 34K Populus SNP array, performed a genome-wide association studies (GWAS) to uncover genes underlying stomatal trait variation. H(2) values for stomatal traits were moderate (average H(2) = 0.33). GWAS identified genes associated primarily with adaxial stomata, including polarity genes (PHABULOSA), stomatal development genes (BRASSINOSTEROID-INSENSITIVE 2) and disease/wound-response genes (GLUTAMATE-CYSTEINE LIGASE). Stomatal traits correlated with latitude, gas exchange, condensed tannins and leaf rust (Melampsora) infection. Latitudinal trends of greater adaxial stomata numbers and guard cell pore size corresponded with higher stomatal conductance (gs ) and photosynthesis (Amax ), faster shoot elongation, lower foliar tannins and greater Melampsora susceptibility. This suggests an evolutionary trade-off related to differing selection pressures across the species range. In northern environments, more adaxial stomata and larger pore sizes reflect selection for rapid carbon gain and growth. By contrast, southern genotypes have fewer adaxial stomata, smaller pore sizes and higher levels of condensed tannins, possibly linked to greater pressure from natural leaf pathogens, which are less significant in northern ecosystems.

  20. A comparative analysis of phenylpropanoid metabolism, N utilization, and carbon partitioning in fast- and slow-growing Populus hybrid clones

    PubMed Central

    Harding, Scott A.; Jarvie, Michelle M.; Lindroth, Richard L.; Tsai, Chung-Jui

    2009-01-01

    The biosynthetic costs of phenylpropanoid-derived condensed tannins (CTs) and phenolic glycosides (PGs) are substantial. However, despite reports of negative correlations between leaf phenolic content and growth of Populus, it remains unclear whether or how foliar biosynthesis of CT/PG interferes with tree growth. A comparison was made of carbon partitioning and N content in developmentally staged leaves, stems, and roots of two closely related Populus hybrid genotypes. The genotypes were selected as two of the most phytochemically divergent from a series of seven previously analysed clones that exhibit a range of height growth rates and foliar amino acid, CT, and PG concentrations. The objective was to analyse the relationship between leaf phenolic content and plant growth, using whole-plant carbon partitioning and N distribution data from the two divergent clones. Total N as a percentage of tissue dry mass was comparatively low, and CT and PG accrual comparatively high in leaves of the slow-growing clone. Phenylpropanoid accrual and N content were comparatively high in stems of the slow-growing clone. Carbon partitioning within phenylpropanoid and carbohydrate networks in developing stems differed sharply between clones. The results did not support the idea that foliar production of phenylpropanoid defence chemicals was the primary cause of reduced plant growth in the slow-growing clone. The findings are discussed in the context of metabolic mechanism(s) which may contribute to reduced N delivery from roots to leaves, thereby compromising tree growth and promoting leaf phenolic accrual in the slow-growing clone. PMID:19516073

  1. Chemical, ultrastructural and supramolecular analysis of tension wood in Populus tremula x alba as a model substrate for reduced recalcitrance

    SciTech Connect

    Foston, Marcus B; Hubbell, Christopher A; Samuel, Reichel; Jung, Seung-Yong; Ding, Shi-You; Zeng, Yining; Jawdy, Sara; Sykes, Virginia R; Tuskan, Gerald A; Kalluri, Udaya C; Ragauskas, Arthur J

    2011-01-01

    Biomass is one of the most abundant potential sustainable sources for fuel and material production, however to fully realize this potential an improved understanding of lignocellulosic recalcitrance must be developed. In an effort to appreciate the underlying phenotypic, biochemical and morphological properties associated with the reduced recalcitrance observed in tension stress-induced reaction wood, we report the increased enzymatic sugar yield and corresponding chemical and ultrastructural properties of Populus tension wood. Populus tremula x alba (PTA) was grown under tension and stem segments containing three different wood types: normal wood (NW), tension wood (TW) from the elongated stem side and opposite wood (OW) from the compressed stem side were collected. A variety of analytical techniques were used to describe changes occurring as a result of the tension stress-induced formation of a gelatinous cell wall layer (G-layer). For example, gel permeation chromatography (GPC) and 13C solid-state nuclear magnetic resonance (NMR) revealed that the molecular weight and crystallinity of cellulose in TW is greater than that of cellulose acquired from NW. Whole cell ionic liquid and other solid-state NMR analysis detailed the structure of lignin and hemicellulose in the samples, detecting the presence of variations in lignin and hemicellulose sub-units, linkages and semi-quantitatively estimating the relative amounts of syringyl (S), guaiacyl (G) and p-hydroxybenzoate (PB) monolignol units. It was confirmed that TW displayed an increase in PB or H-like lignin and S to G ratio from 1.25 to 1.50 when compared to the NW sample. Scanning electron microscopy (SEM) and coherent anti-Stokes Raman scattering (CARS) were also used to evaluate the morphology and corresponding spatial distribution of the major lignocellulosic components. We found changes in a combination of cell wall properties appear to influence recalcitrance more than any single factor alone.

  2. Genome-Wide Analysis of MicroRNA Responses to the Phytohormone Abscisic Acid in Populus euphratica

    PubMed Central

    Duan, Hui; Lu, Xin; Lian, Conglong; An, Yi; Xia, Xinli; Yin, Weilun

    2016-01-01

    MicroRNA (miRNA) is a type of non-coding small RNA with a regulatory function at the posttranscriptional level in plant growth development and in response to abiotic stress. Previous studies have not reported on miRNAs responses to the phytohormone abscisic acid (ABA) at a genome-wide level in Populus euphratica, a model tree for studying abiotic stress responses in woody plants. Here we analyzed the miRNA response to ABA at a genome-wide level in P. euphratica utilizing high-throughput sequencing. To systematically perform a genome-wide analysis of ABA-responsive miRNAs in P. euphratica, nine sRNA libraries derived from three groups (control, treated with ABA for 1 day and treated with ABA for 4 days) were constructed. Each group included three libraries from three individual plantlets as biological replicate. In total, 151 unique mature sequences belonging to 75 conserved miRNA families were identified, and 94 unique sequences were determined to be novel miRNAs, including 56 miRNAs with miRNA* sequences. In all, 31 conserved miRNAs and 31 novel miRNAs response to ABA significantly differed among the groups. In addition, 4132 target genes were predicted for the conserved and novel miRNAs. Confirmed by real-time qPCR, expression changes of miRNAs were inversely correlated with the expression profiles of their putative targets. The Populus special or novel miRNA-target interactions were predicted might be involved in some biological process related stress tolerance. Our analysis provides a comprehensive view of how P. euphratica miRNA respond to ABA, and moreover, different temporal dynamics were observed in different ABA-treated libraries. PMID:27582743

  3. In vitro adventitious shoot regeneration via indirect organogenesis from inflorescence explants and peroxidase involvement in morphogenesis of Populus euphratica Olivier.

    PubMed

    Zhou, Yan; Gao, Ziyang; Gao, Shumin; Sun, Fangfang; Cheng, Pengjun; Li, Fenglan

    2012-12-01

    The inflorescences as explants for rapid propagation in vitro remained unknown in Populus euphratica Olivier. Here, we reported that multiple shoots were initiation from calli of both male and female inflorescences. The optimum medium for shoot induction from male inflorescences was lactose sulfite medium containing 1.0 mg L(-1) 6-benzylaminopurine (BA) and 0.5 mg L(-1) α-naphthalene acetic acid (NAA) or Murashige and Skoog (MS) medium containing 0.5 mg L(-1) BA and 0.2 mg L(-1) NAA. The optimum medium of shoot induction from female inflorescence calli was the MS medium containing 0.5 mg L(-1) BA and 0.2 mg L(-1) NAA. Rooting of regenerated shoots was obtained on 1/2 MS medium supplemented with 0.5∼1.0 mg L(-1) indole-3-butyric acid (IBA) and the highest frequency rooting was on medium containing 0.5 mg L(-1) IBA. No shoots were obtained on medium without BA and NAA. Peroxidase (POD) activity was measured by polyacrylamide gel electrophoresis during shoot induction and differentiation stages. The results showed that two bands of POD (2a and 2b) activity appeared lowest during the early 8 days at the dedifferentiation phase of leaves inducing calli, whereas POD 2a, 2b activity appeared to be increasing at the homeochronous dedifferentiation phase of inflorescence. Five most intensive bands, POD 1a, 1b, 1c, 2a, and ab, appeared in 8th and 28th days at the redifferentiation phase during shoot morphogenesis. These results demonstrated that the POD was involved in shoot morphogenesis from both leaf and inflorescence explants of Populus euphratica.

  4. Allelic variation in PtoPsbW associated with photosynthesis, growth, and wood properties in Populus tomentosa.

    PubMed

    Wang, Longxin; Wang, Bowen; Du, Qingzhang; Chen, Jinhui; Tian, Jiaxing; Yang, Xiaohui; Zhang, Deqiang

    2017-02-01

    Photosynthesis is one of the most important reactions on earth. PsbW, a nuclear-encoded subunit of photosystem II (PSII), stabilizes PSII structure and plays an important role in photosynthesis. Here, we used candidate gene-based linkage disequilibrium (LD) mapping to detect significant associations between allelic variations of PtoPsbW and traits related to photosynthesis, growth, and wood properties in Populus tomentosa. PtoPsbW showed the highest expression in leaves and it increased during the development of these leaves, suggesting that PtoPsbW may play an important role in plant growth and development. Analysis of nucleotide diversity and LD revealed that PtoPsbW has low single-nucleotide polymorphism (SNP) diversity (π tot = 0.0048 and θ w = 0.0050) and relatively low average value of LD (0.1500), indicating that PtoPsbW is conserved due to its indispensable function. Using single-SNP associations in an association population of 435 individuals, we identified five significant associations at the threshold of P ≤ 0.05, explaining 3.28-15.98 % of the phenotypic variation. Haplotype-based association analyses indicated that 13 haplotypes (P ≤ 0.05) from six blocks were associated with photosynthesis, growth, and wood properties. Our work shows that identifying allelic variation and LD can help to decipher the genetic basis of photosynthesis and could potentially be applied for molecular marker-assisted selection in Populus.

  5. Effect of environmental stress factors on ecophysiological traits and susceptibility to pathogens of five Populus clones throughout the growing season.

    PubMed

    Fernàndez-Martínez, Jordi; Zacchini, Massimo; Elena, Georgina; Fernández-Marín, Beatriz; Fleck, Isabel

    2013-06-01

    The variability of ecophysiological traits associated with productivity (e.g., water relations, leaf structure, photosynthesis and nitrogen (N) content) and susceptibility to fungal and insect infection were investigated in five poplar clones (Populus deltoides Batr.-Lux clone; Populus nigra L.-58-861 clone and Populus × canadensis Mönch.-Luisa Avanzo, I-214 and Adige clones) during their growing season. The objective of the study was to determine their physiological responses under summer constraints (characteristic of the Mediterranean climate) and to propose clone candidates for environmental restoration activities such as phytoremediation. Relative water content, the radiometric water index and (13)C isotope discrimination (Δ(13)C) results reflected improved water relations in Adige and Lux during summer drought. Leaf structural parameters such as leaf area, leaf mass per area, density (D) and thickness (T) indicated poorer structural adaptations to summer drought in clone 58-861. Nitrogen content and Δ(13)C results pointed to a stomatal component as the main limitant of photosynthesis in all clones. Adige and Lux showed enhanced photoprotection as indicated by the size and the de-epoxidation index of the xanthophyll-cycle pool, and also improved antioxidant defence displayed by higher ascorbate, reduced glutathione, total phenolics and α-tocopherol levels. Photoprotective and antioxidative responses allowed all clones to maintain a high maximum quantum yield of PSII (Fv/Fm) with the exception of Luisa Avanzo and 58-861 which experienced slight photoinhibition in late spring. The study of susceptibility to rust (Melampsora sp.) and lace bug (Monosteira unicostata Muls. and Rey) infections showed Adige and Lux to be the most tolerant. Overall, these two clones presented high adaptability to summer conditions and improved resistance to abiotic and biotic stress, thereby making them highly commendable clones for use in environmental remediation programmes.

  6. Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types ▿†

    PubMed Central

    Gottel, Neil R.; Castro, Hector F.; Kerley, Marilyn; Yang, Zamin; Pelletier, Dale A.; Podar, Mircea; Karpinets, Tatiana; Uberbacher, Ed; Tuskan, Gerald A.; Vilgalys, Rytas; Doktycz, Mitchel J.; Schadt, Christopher W.

    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. PMID:21764952

  7. Putting the Pieces Together: High-performance LC-MS/MS Provides Network-, Pathway-, and Protein-level Perspectives in Populus

    SciTech Connect

    Abraham, Paul E; Giannone, Richard J; Adams, Rachel M; Kalluri, Udaya C; Tuskan, Gerald A; Hettich, Robert {Bob} L

    2013-01-01

    High-performance mass spectrometry (MS)-based proteomics enabled the construction of a detailed proteome atlas for Populus, a woody perennial plant model organism. Optimization of experimental procedures and implementation of current state-of-the-art instrumentation afforded the most detailed look into the predicted proteome space of Populus, offering varying proteome perspectives: 1) network-wide, 2) pathway-specific, and 3) protein-level viewpoints. Together, enhanced protein retrieval through a detergent-based lysis approach and maximized peptide sampling via the dual-pressure linear ion trap mass spectrometer (LTQ Velos), have resulted in the identification of 63,056 tryptic peptides. The technological advancements, specifically spectral- acquisition and sequencing speed, afforded the deepest look into the Populus proteome, with peptide abundances spanning 6 orders of magnitude and mapping to~25% of the predicted proteome space. In total, tryptic peptides mapped to 13,574 protein assignments across four organ-types: mature (fully expanded, leaf plastichronic index (LPI) 10-12) leaf, young (juvenile, LPI 4-6) leaf, root, and stem. To resolve protein ambiguity, identified proteins were grouped by sequence similarity ( 90%), thereby reducing the protein assignments into 7,538 protein groups. In addition, this large-scale data set features the first systems-wide survey of protein expression across different Populus organs. As a demonstration of the precision and comprehensiveness of the semi-quantitative analysis, we were able to contrast two stages of leaf development, mature versus young leaf. Statistical comparison through ANOVA analysis revealed 1,432 protein groups that exhibited statistically significant (p 0.01) differences in protein abundance. Experimental validation of the metabolic circuitry expected in mature leaf (characterized by photosynthesis and carbon fixation) compared to young leaf (characterized by rapid growth and moderate photosynthetic

  8. Putting the Pieces Together: High-performance LC-MS/MS Provides Network-, Pathway-, and Protein-level Perspectives in Populus*

    PubMed Central

    Abraham, Paul; Giannone, Richard J.; Adams, Rachel M.; Kalluri, Udaya; Tuskan, Gerald A.; Hettich, Robert L.

    2013-01-01

    High-performance mass spectrometry (MS)-based proteomics enabled the construction of a detailed proteome atlas for Populus, a woody perennial plant model organism. Optimization of experimental procedures and implementation of current state-of-the-art instrumentation afforded the most detailed look into the predicted proteome space of Populus, offering varying proteome perspectives: (1) network-wide, (2) pathway-specific, and (3) protein-level viewpoints. Together, enhanced protein retrieval through a detergent-based lysis approach and maximized peptide sampling via the dual-pressure linear ion trap mass spectrometer (LTQ Velos), have resulted in the identification of 63,056 tryptic peptides. The technological advancements, specifically spectral-acquisition and sequencing speed, afforded the deepest look into the Populus proteome, with peptide abundances spanning 6 orders of magnitude and mapping to ∼25% of the predicted proteome space. In total, tryptic peptides mapped to 11,689 protein assignments across four organ-types: mature (fully expanded, leaf plastichronic index (LPI) 10–12) leaf, young (juvenile, LPI 4–6) leaf, root, and stem. To resolve protein ambiguity, identified proteins were grouped by sequence similarity (≥ 90%), thereby reducing the protein assignments into 7538 protein groups. In addition, this large-scale data set features the first systems-wide survey of protein expression across different Populus organs. As a demonstration of the precision and comprehensiveness of the semiquantitative analysis, we were able to contrast two stages of leaf development, mature versus young leaf. Statistical comparison through ANOVA analysis revealed 1432 protein groups that exhibited statistically significant (p ≤ 0.01) differences in protein abundance. Experimental validation of the metabolic circuitry expected in mature leaf (characterized by photosynthesis and carbon fixation) compared with young leaf (characterized by rapid growth and moderate

  9. Alternative Splicing Studies of the Reactive Oxygen Species Gene Network in Populus Reveal Two Isoforms of High-Isoelectric-Point Superoxide Dismutase1[C][W

    PubMed Central

    Srivastava, Vaibhav; Srivastava, Manoj Kumar; Chibani, Kamel; Nilsson, Robert; Rouhier, Nicolas; Melzer, Michael; Wingsle, Gunnar

    2009-01-01

    Recent evidence has shown that alternative splicing (AS) is widely involved in the regulation of gene expression, substantially extending the diversity of numerous proteins. In this study, a subset of expressed sequence tags representing members of the reactive oxygen species gene network was selected from the PopulusDB database to investigate AS mechanisms in Populus. Examples of all known types of AS were detected, but intron retention was the most common. Interestingly, the closest Arabidopsis (Arabidopsis thaliana) homologs of half of the AS genes identified in Populus are not reportedly alternatively spliced. Two genes encoding the protein of most interest in our study (high-isoelectric-point superoxide dismutase [hipI-SOD]) have been found in black cottonwood (Populus trichocarpa), designated PthipI-SODC1 and PthipI-SODC2. Analysis of the expressed sequence tag libraries has indicated the presence of two transcripts of PthipI-SODC1 (hipI-SODC1b and hipI-SODC1s). Alignment of these sequences with the PthipI-SODC1 gene showed that hipI-SODC1b was 69 bp longer than hipI-SODC1s due to an AS event involving the use of an alternative donor splice site in the sixth intron. Transcript analysis showed that the splice variant hipI-SODC1b was differentially expressed, being clearly expressed in cambial and xylem, but not phloem, regions. In addition, immunolocalization and mass spectrometric data confirmed the presence of hipI-SOD proteins in vascular tissue. The functionalities of the spliced gene products were assessed by expressing recombinant hipI-SOD proteins and in vitro SOD activity assays. PMID:19176719

  10. Moving Away from the Reference Genome: Evaluating a Peptide Sequencing Tagging Approach for Single Amino Acid Polymorphism Identifications in the Genus Populus

    SciTech Connect

    Abraham, Paul E; Adams, Rachel M; Tuskan, Gerald A; Hettich, Robert {Bob} L

    2013-01-01

    The genetic diversity across natural populations of the model organism, Populus, is extensive, containing a single nucleotide polymorphism roughly every 200 base pairs. When deviations from the reference genome occur in coding regions, they can impact protein sequences. Rather than relying on a static reference database to profile protein expression, we employed a peptide sequence tagging (PST) approach capable of decoding the plasticity of the Populus proteome. Using shotgun proteomics data from two genotypes of P. trichocarpa, a tag-based approach enabled the detection of 6,653 unexpected sequence variants. Through manual validation, our study investigated how the most abundant chemical modification (methionine oxidation) could masquerade as a sequence variant (AlaSer) when few site-determining ions existed. In fact, precise localization of an oxidation site for peptides with more than one potential placement was indeterminate for 70% of the MS/MS spectra. We demonstrate that additional fragment ions made available by high energy collisional dissociation enhances the robustness of the peptide sequence tagging approach (81% of oxidation events could be exclusively localized to a methionine). We are confident that augmenting fragmentation processes for a PST approach will further improve the identification of single amino acid polymorphism in Populus and potentially other species as well.

  11. PtrCel9A6, an endo-1,4-β-glucanase, is required for cell wall formation during xylem differentiation in populus.

    PubMed

    Yu, Liangliang; Sun, Jiayan; Li, Laigeng

    2013-11-01

    Endo-1,4-β-glucanases (EGases) are involved in many aspects of plant growth. Our previous study found that an EGase, PtrCel9A6, is specifically expressed in differentiating xylem cells during Populus secondary growth. In this study, the xylem-specific PtrCel9A6 was characterized for its role in xylem differentiation. The EGase is localized on the plasma membrane with catalytic domain toward the outside cell wall, hydrolyzing amorphous cellulose. Suppression of PtrCel9A6 expression caused secondary cell wall defects in xylem cells and significant cellulose reduction in Populus. Heterologous expression of PtrCel9A6 in Arabidopsis enhanced plant growth as well as increased fiber cell length. In addition, introduction of PtrCel9A6 into Arabidopsis resulted in male sterility due to defects in anther dehiscence. Together, these results demonstrate that PtrCel9A6 plays a critical role in remodeling the 1,4-β-glucan chains in the wall matrix and is required for cell wall thickening during Populus xylem differentiation.

  12. Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass

    SciTech Connect

    Wilson, Charlotte M; Rodriguez Jr, Miguel; Johnson, Courtney M; Martin, S L.; Chu, Tzu Ming; Wolfinger, Russ; Hauser, Loren John; Land, Miriam L; Klingeman, Dawn Marie; Tschaplinski, Timothy J; Mielenz, Jonathan R; Brown, Steven D

    2013-01-01

    Background The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. The aim of this study was to investigate C. thermocellum genes required to ferment biomass substrates and to conduct a robust comparison of DNA microarray and RNA sequencing (RNA-seq) analytical platforms. Results C. thermocellum ATCC 27405 fermentations were conducted with a 5 g/L solid substrate loading of either pretreated switchgrass or Populus. Quantitative saccharification and inductively coupled plasma emission spectroscopy (ICP-ES) for elemental analysis revealed composition differences between biomass substrates, which may have influenced growth and transcriptomic profiles. High quality RNA was prepared for C. thermocellum grown on solid substrates and transcriptome profiles were obtained for two time points during active growth (12 hours and 37 hours postinoculation). A comparison of two transcriptomic analytical techniques, microarray and RNA-seq, was performed and the data analyzed for statistical significance. Large expression differences for cellulosomal genes were not observed. We updated gene predictions for the strain and a small novel gene, Cthe_3383, with a putative AgrD peptide quorum sensing function was among the most highly expressed genes. RNAseq data also supported different small regulatory RNA predictions over others. The DNA microarray gave a greater number (2,351) of significant genes relative to RNA-seq (280 genes when normalized by the kernel density mean of M component (KDMM) method) in an analysis of variance (ANOVA) testing method with a 5 %