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Sample records for populus tremuloides cell

  1. Glycosylation-mediated phenylpropanoid partitioning in Populus tremuloides cell cultures

    PubMed Central

    2009-01-01

    Background Phenylpropanoid-derived phenolic glycosides (PGs) and condensed tannins (CTs) comprise large, multi-purpose non-structural carbon sinks in Populus. A negative correlation between PG and CT concentrations has been observed in several studies. However, the molecular mechanism underlying the relationship is not known. Results Populus cell cultures produce CTs but not PGs under normal conditions. Feeding salicyl alcohol resulted in accumulation of salicins, the simplest PG, in the cells, but not higher-order PGs. Salicin accrual reflected the stimulation of a glycosylation response which altered a number of metabolic activities. We utilized this suspension cell feeding system as a model for analyzing the possible role of glycosylation in regulating the metabolic competition between PG formation, CT synthesis and growth. Cells accumulated salicins in a dose-dependent manner following salicyl alcohol feeding. Higher feeding levels led to a decrease in cellular CT concentrations (at 5 or 10 mM), and a negative effect on cell growth (at 10 mM). The competition between salicin and CT formation was reciprocal, and depended on the metabolic status of the cells. We analyzed gene expression changes between controls and cells fed with 5 mM salicyl alcohol for 48 hr, a time point when salicin accumulation was near maximum and CT synthesis was reduced, with no effect on growth. Several stress-responsive genes were up-regulated, suggestive of a general stress response in the fed cells. Salicyl alcohol feeding also induced expression of genes associated with sucrose catabolism, glycolysis and the Krebs cycle. Transcript levels of phenylalanine ammonia lyase and most of the flavonoid pathway genes were reduced, consistent with down-regulated CT synthesis. Conclusions Exogenous salicyl alcohol was readily glycosylated in Populus cell cultures, a process that altered sugar utilization and phenolic partitioning in the cells. Using this system, we identified candidate genes

  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. PMID:24943986

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

    PubMed Central

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

    2012-01-01

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

  4. Changes in Spectral Properties, Chlorophyll Content and Internal Mesophyll Structure of Senescing Populus balsamifera and Populus tremuloides Leaves

    PubMed Central

    Castro, Karen L.; Sanchez-Azofeifa, G. Arturo

    2008-01-01

    In this paper we compare leaf traits and spectral reflectance for sunlit and shafded leaves of Populus tremuloides and Populus balsamifera during autumn senescence using information derived from an Analytical Spectral Devise (ASD) Full Range spectrometer. The modified simple ratio (mSR705) and modified normalized difference index (mND705) were effective in describing changes in chlorophyll content over this period. Highly significant (P<0.01) correlation coefficients were found between the chlorophyll indices (mSR705, mND705)) and chlorophyll a, b, total chlorophyll and chlorophyll a/b. Changes in mesophyll structure were better described by the plant senescence reflectance index (PSRI) than by near-infrared wavebands. Overall, P. balsamifera exhibited lower total chlorophyll and earlier senescence than P. tremuloides. Leaves of P. balsamifera were also thicker, had a higher proportion of intercellular space in the spongy mesophyll, and higher reflectance at 800 nm. Further research, using larger sample sizes over a broader range of sites will extend our understanding of the spectral and temporal dynamics of senescence in P. tremuloides and P. balsamifera and will be particularly useful if species differences are detectable at the crown level using remotely sensed imagery.

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

    PubMed

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

    2016-05-01

    Quaking aspens (Populus tremuloides Michx.) are found in diverse habitats throughout North America. While the biogeography of aspens' distribution has been documented, the drivers of the phenotypic diversity of aspen are still being explored. In our study, we examined differences in climate between northern and southwestern populations of aspen, finding large-scale differences between the populations. Our results suggest that northern and southwestern populations live in distinct climates and support the inclusion of genetic and phenotypic data with species distribution modeling for predicting aspens' distribution. PMID:27217950

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

    PubMed Central

    Foote, Knowlton C.; Schaedle, Michail

    1976-01-01

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

  7. 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.

  8. 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

  9. Molecular and dendrochronological analysis of natural root grafting in Populus tremuloides (Salicaceae).

    PubMed

    Jelínková, Hana; Tremblay, Francine; Desrochers, Annie

    2009-08-01

    Trembling aspen (Populus tremuloides) is a clonal tree species, which regenerates mostly through root suckering. In spite of vegetative propagation, aspen maintains high levels of clonal diversity. We hypothesized that the maintenance of clonal diversity in this species can be facilitated by integrating different clones through natural root grafts into aspen's communal root system. To verify this hypothesis, we analyzed root systems of three pure aspen stands where clones had been delineated with the help of molecular markers. Grafting between roots was frequent regardless of their genotypes. Root system excavations revealed that many roots were still living below trees that had been dead for several years. Some of these roots had no root connections other than grafts to living ramets of different clones. The uncovered root systems did not include any unique genotypes that would not occur among stems. Nevertheless, acquiring roots of dead trees helps to maintain extensive root systems, which increases the chances of clone survival. Substantial interconnectivity within clones as well as between clones via interclonal grafts results in formation of large genetically diverse physiological units. Such a clonal structure can significantly affect interpretations of diverse ecophysiological processes in forests of trembling aspen. PMID:21628295

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

    PubMed

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

    2016-07-01

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

  11. Extrafloral Nectaries in Aspen (Populus tremuloides): Heritable Genetic Variation and Herbivore-induced Expression

    PubMed Central

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

    2007-01-01

    Background and Aims A wide variety of plants produce extrafloral nectaries (EFNs) that are visited by predatory arthropods. But very few studies have investigated the relationship between plant genetic variation and EFNs. The presence of foliar EFNs is highly variable among different aspen (Populus tremuloides) genotypes and the EFNs are visited by parasitic wasps and predatory flies. The aim here was to determine the heritability of EFNs among aspen genotypes and age classes, possible trade-offs between direct and indirect defences, EFN induction following herbivory, and the relationship between EFNs and predatory insects. Methods EFN density was quantified among aspen genotypes in Wisconsin on trees of different ages and broad-sense heritability from common garden trees was calculated. EFNs were also quantified in natural aspen stands in Utah. From the common garden trees foliar defensive chemical levels were quantified to evaluate their relationship with EFN density. A defoliation experiment was performed to determine if EFNs can be induced in response to herbivory. Finally, predatory arthropod abundance among aspen trees was quantified to determine the relationship between arthropod abundance and EFNs. Key Results Broad-sense heritability for expression (0·74–0·82) and induction (0·85) of EFNs was high. One-year-old trees had 20% greater EFN density than 4-year-old trees and more than 50% greater EFN density than ≥10-year-old trees. No trade-offs were found between foliar chemical concentrations and EFN density. Predatory fly abundance varied among aspen genotypes, but predatory arthropod abundance and average EFN density were not related. Conclusions Aspen extrafloral nectaries are strongly genetically determined and have the potential to respond rapidly to evolutionary forces. The pattern of EFN expression among different age classes of trees appears to follow predictions of optimal defence theory. The relationship between EFNs and predators likely

  12. Molecular cloning and biochemical characterization of carbonic anhydrase from Populus tremula x tremuloides.

    PubMed

    Larsson, S; Björkbacka, H; Forsman, C; Samuelsson, G; Olsson, O

    1997-07-01

    A leaf cDNA library from hybrid aspen, Populus tremula x tremuloides, was constructed. From this two different cDNA clones, denoted CA1a and CA1b, encoding a chloroplastic carbonic anhydrase (CA) were isolated and DNA sequenced. Analysis of the deduced amino acid sequences showed that the isolated CAs belong to the beta-CA family, and have identities around 70% to other dicotyledonous plant CAs. The two hybrid aspen cDNA clones display a high nucleotide sequence identity, only 12 nucleotides differ. Since only one gene copy of this soluble chloroplastic CA is present in the nuclear genome, we postulate that the two isolated cDNA clones are alleles. Northern blot hybridization revealed a CA transcript of ca. 1300 bases, 140 bases shorter than in pea. Western and northern blot hybridizations on crude protein extracts and on total RNA, respectively, isolated from stem and leaves, showed that hybrid aspen CA is expressed specifically in the leaf under the growth conditions used. Based on the deduced amino acid sequence, the mature hybrid aspen CA enzyme subunit has a molecular mass of 24.8 kDa. The enzyme was over-expressed in Escherichia coli, and purified by affinity chromatography. Biochemical characterization showed that the protein structure and the CO2-hydration activity are similar to the pea enzyme. Molecular characterization of a CA from a perennial plant has not previously been performed, and it demonstrates that both the structure and activity of hybrid aspen CA resembles CAs from annual plants. PMID:9247540

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

    PubMed Central

    Foote, Knowlton C.; Schaedle, Michail

    1976-01-01

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

  14. 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

  15. 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

  16. 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.

  17. 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

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

    PubMed

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

    2015-07-01

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

  19. 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. PMID:11473716

  20. 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. PMID:12472686

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

    PubMed

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

    2013-11-01

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

  2. 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

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

    PubMed

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

    2011-05-01

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

  4. Genotypic variation in growth and physiological responses of Finnish hybrid aspen (Populus tremuloides x P. tremula) to elevated tropospheric ozone concentration.

    PubMed

    Oksanen, E; Amores, G; Kokko, H; Amores, J M; Kärenlampi, L

    2001-10-01

    Saplings of six Finnish hybrid aspen (Populus tremuloides Michx. x P. tremula L.) clones were exposed to 0, 50, 100 and 150 ppb ozone (O3) for 32 days in a chamber experiment to determine differences in O3 sensitivity among genotypes. Based on the chamber experiment, three clones with intermediate sensitivity to O3 were selected for a free-air O3 enrichment experiment in which plants were exposed for 2 months to either ambient air (control) or air containing 1.3 x the ambient O3 concentration. We measured stem height and radial growth, number of leaves, dry mass and relative growth rate of leaves, stem and roots, visible leaf injuries, net photosynthesis and stomatal conductance of the clones. There was high clonal variation in susceptibility to O3 in the chamber experiment, indicated by foliar injuries and differential reductions in growth and net photosynthesis. In the free-air O3 enrichment experiment, ozone caused a shift in resource allocation toward stem height growth, thereby altering the shoot to root balance. In both experiments, low O3 concentrations tended to stimulate growth of most clones, whereas 100 and 150 ppb O3 in the chamber experiment impaired growth of most clones. However, growth of the most O3-tolerant clone was not significantly affected by any O3 treatment. PMID:11600339

  5. 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

  6. 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. PMID:21909761

  7. 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.

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

    PubMed

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

    2014-07-01

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

  9. 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.

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

    DOE PAGESBeta

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

    2016-07-15

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

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

    SciTech Connect

    Yang, Xiaohan; Ye, Chuyu; Bisaria, Anjali; Tuskan, Gerald A; Kalluri, Udaya C

    2011-01-01

    Populus is an important bioenergy crop for bioethanol production. A greater understanding of cell wall biosynthesis processes is critical in reducing biomass recalcitrance, a major hindrance in efficient generation of ethanol from lignocellulosic biomass. Here, we report the identification of candidate cell wall biosynthesis genes through the development and application of a novel bioinformatics pipeline. As a first step, via text-mining of PubMed publications, we obtained 121 Arabidopsis genes that had the experimental evidences supporting their involvement in cell wall biosynthesis or remodeling. The 121 genes were then used as bait genes to query an Arabidopsis co-expression database and additional genes were identified as neighbors of the bait genes in the network, increasing the number of genes to 548. The 548 Arabidopsis genes were then used to re-query the Arabidopsis co-expression database and re-construct a network that captured additional network neighbors, expanding to a total of 694 genes. The 694 Arabidopsis genes were computationally divided into 22 clusters. Queries of the Populus genome using the Arabidopsis genes revealed 817 Populus orthologs. Functional analysis of gene ontology and tissue-specific gene expression indicated that these Arabidopsis and Populus genes are high likelihood candidates for functional genomics in relation to cell wall biosynthesis.

  12. 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

  13. 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

    2013-01-22

    Wellington Muchero from Oak Ridge National Laboratory gives a talk titled "Discovery of Cell Wall Biosynthesis Genes in Populus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  14. Genome-Scale Discovery of Cell Wall Biosynthesis Genes in Populus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Muchero, Wellington

    2012-03-22

    Wellington Muchero from Oak Ridge National Laboratory gives a talk titled "Discovery of Cell Wall Biosynthesis Genes in Populus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  15. 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

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

    PubMed

    Swamy, Prashant S; Hu, Hao; Pattathil, Sivakumar; Maloney, Victoria J; Xiao, Hui; Xue, Liang-Jiao; Chung, Jeng-Der; Johnson, Virgil E; Zhu, Yingying; Peter, Gary F; Hahn, Michael G; Mansfield, Shawn D; Harding, Scott A; Tsai, Chung-Jui

    2015-10-01

    Cortical microtubules are integral to plant morphogenesis, cell wall synthesis, and stomatal behaviour, presumably by governing cellulose microfibril orientation. Genetic manipulation of tubulins often leads to abnormal plant development, making it difficult to probe additional roles of cortical microtubules in cell wall biogenesis. Here, it is shown that expressing post-translational C-terminal modification mimics of α-tubulin altered cell wall characteristics and guard cell dynamics in transgenic Populus tremula x alba that otherwise appear normal. 35S promoter-driven transgene expression was high in leaves but unusually low in xylem, suggesting high levels of tubulin transgene expression were not tolerated in wood-forming tissues during regeneration of transformants. Cellulose, hemicellulose, and lignin contents were unaffected in transgenic wood, but expression of cell wall-modifying enzymes, and extractability of lignin-bound pectin and xylan polysaccharides were increased in developing xylem. The results suggest that pectin and xylan polysaccharides deposited early during cell wall biogenesis are more sensitive to subtle tubulin perturbation than cellulose and matrix polysaccharides deposited later. Tubulin perturbation also affected guard cell behaviour, delaying drought-induced stomatal closure as well as light-induced stomatal opening in leaves. Pectins have been shown to confer cell wall flexibility critical for reversible stomatal movement, and results presented here are consistent with microtubule involvement in this process. Taken together, the data show the value of growth-compatible tubulin perturbations for discerning microtubule functions, and add to the growing body of evidence for microtubule involvement in non-cellulosic polysaccharide assembly during cell wall biogenesis. PMID:26246616

  17. 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.

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

    DOE PAGESBeta

    Muchero, Wellington; Guo, Jianjun; Difazio, Stephen P.; Chen, Jay; Ranjan, Priya; Slavov, Gancho; Gunter, Lee E.; Jawdy, Sara; Bryan, Anthony C.; Sykes, Robert; et al

    2015-01-23

    We report the identification of six genetic loci and the allelic-variants associated with Populus cell wall phenotypes determined independently using pyrolysis Molecular Beam Mass Spectrometry (pyMBMS), saccharification assay and wet chemistry in two partially overlapping populations of P. trichocarpa genotypes sampled from multiple environments in the Pacific Northwest of North America. All 6 variants co-located with a quantitative trait locus (QTL) hotspot on chromosome XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6- carbon sugars identified in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree. Genomic intervals containing an amino acid transporter, a MYB transcriptionmore » factor, an angustifolia CtBP transcription factor, a copper transport protein ATOX1-related, a Ca2+ transporting ATPase and a protein kinase were identified within 5 QTL regions. Each interval contained single nucleotide polymorphisms (SNPs) that were significantly associated to cell-wall phenotypes, with associations exceeding the chromosome-wise Bonferroni-adjusted p-values in at least one environment. cDNA sequencing for allelic variants of 3 of the 6 genes identified polymorphisms leading to premature stop codons in the MYB transcription factor and protein kinase. On the other hand, variants of the Angustifolia CtBP transcription factor exhibited a polyglutamine (PolyQ) length polymorphism. Results from transient protoplast assays suggested that each of the polymorphisms conferred allelic differences in activation of cellulose, hemicelluloses and lignin pathway marker genes, with truncated and short PolyQ alleles exhibiting significantly reduced marker gene activation. Genes identified in this study represent novel targets for reducing cell wall recalcitrance for lignocellulosic biofuels production using plant biomass.« less

  19. 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.

  20. 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.

  1. 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.

  2. Multilocus analysis of nucleotide variation and speciation in three closely related Populus (Salicaceae) species.

    PubMed

    Du, Shuhui; Wang, Zhaoshan; Ingvarsson, Pär K; Wang, Dongsheng; Wang, Junhui; Wu, Zhiqiang; Tembrock, Luke R; Zhang, Jianguo

    2015-10-01

    Historical tectonism and climate oscillations can isolate and contract the geographical distributions of many plant species, and they are even known to trigger species divergence and ultimately speciation. Here, we estimated the nucleotide variation and speciation in three closely related Populus species, Populus tremuloides, P. tremula and P. davidiana, distributed in North America and Eurasia. We analysed the sequence variation in six single-copy nuclear loci and three chloroplast (cpDNA) fragments in 497 individuals sampled from 33 populations of these three species across their geographic distributions. These three Populus species harboured relatively high levels of nucleotide diversity and showed high levels of nucleotide differentiation. Phylogenetic analysis revealed that P. tremuloides diverged earlier than the other two species. The cpDNA haplotype network result clearly illustrated the dispersal route from North America to eastern Asia and then into Europe. Molecular dating results confirmed that the divergence of these three species coincided with the sundering of the Bering land bridge in the late Miocene and a rapid uplift of the Qinghai-Tibetan Plateau around the Miocene/Pliocene boundary. Vicariance-driven successful allopatric speciation resulting from historical tectonism and climate oscillations most likely played roles in the formation of the disjunct distributions and divergence of these three Populus species. PMID:26334549

  3. 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. PMID:24372544

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

    SciTech Connect

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

    2006-01-01

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

  5. 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.

  6. 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. PMID:11338433

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed Central

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

    2016-01-01

    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. PMID:26721855

  9. Near-ambient ozone concentrations reduce the vigor of Betula and Populus species in Finland.

    PubMed

    Oksanen, Elina; Manninen, Sirkku; Vapaavuori, Elina; Holopainen, Toini

    2009-12-01

    In this review the main growth responses of Finnish birch (Betula pendula, B. pubescens) and aspen species (Populus tremula and P. tremuloides x P. tremula) are correlated with ozone exposure, indicated as the AOT40 value. Data are derived from 23 different laboratory, open-top chamber, and free-air fumigation experiments. Our results indicate that these tree species are sensitive to increasing ozone concentrations, though high intraspecific variation exists. The roots are the most vulnerable targets in both genera. These growth reductions, determined from trees grown under optimal nutrient and water supply, were generally accompanied by increased visible foliar injuries, carbon allocation toward defensive compounds, reduced carbohydrate contents of leaves, impaired photosynthesis processes, disturbances in stomatal function, and earlier autumn senescence. Because both genera have shown complex ozone defense and response mechanisms, which are modified by variable environmental conditions, a mechanistically based approach is necessary for accurate ozone risk assessment. PMID:20175439

  10. Sense-, antisense- and RNAi-4CL1 regulate soluble phenolic acids, cell wall components and growth in transgenic Populus tomentosa Carr.

    PubMed

    Tian, Xiaoming; Xie, Jin; Zhao, Yanling; Lu, Hai; Liu, Shichang; Qu, Long; Li, Jianmei; Gai, Ying; Jiang, Xiangning

    2013-04-01

    Regulation of lignin biosynthesis affects plant growth and wood properties. Transgenic downregulation of 4-coumarate:coenzyme A ligase (4CL, EC 6.2.1.12) may reduce lignin content in cell walls, which could improve the qualities of pulp in papermaking and increase the efficiency of bioenergy applications. To determine the effects of Ptc4CL1 on lignin biosynthesis and plant growth, Populus tomentosa Carr. was transformed using sense-, antisense-, and RNAi-4CL1 genes. The growth properties, gene expression, enzyme activity, lignin content and composition and content of soluble phenolic acids were investigated in 1-year-old field-grown transgenic poplar trees. Transgenic up- and down-regulation of 4CL1 altered lignin content and composition in transgenic poplars, but there were no negative effects on the growth of transgenic plants. In addition, the severe changes in auxin observed in transgenic lines led to significantly enhanced growth performance. Furthermore, lignin content was tightly correlated with the alteration of 4CL1 enzymatic activity, which was correlated with 4CL1 gene expression. A significant increase in S units in lignin with a slight increase in sinapic acid was observed in 4CL1 down-regulated transgenic poplars. These results suggest that 4CL1 is a traffic control gene in monolignol biosynthesis and confirm that 4CL1 activity has been implicated with sinapoyl activation. Finally, our data demonstrate that there is cross-correlation among 4CL1 gene expression, 4CL1 enzyme activity, soluble phenolic acid, lignin monomer biosynthesis, and lignin content. PMID:23434928

  11. Tissue- and Cell-Specific Cytokinin Activity in Populus × canescens Monitored by ARR5::GUS Reporter Lines in Summer and Winter

    PubMed Central

    Paul, Shanty; Wildhagen, Henning; Janz, Dennis; Teichmann, Thomas; Hänsch, Robert; Polle, Andrea

    2016-01-01

    Cytokinins play an important role in vascular development. But knowledge on the cellular localization of this growth hormone in the stem and other organs of woody plants is lacking. The main focus of this study was to investigate the occurrence and cellular localization of active cytokinins in leaves, roots, and along the stem of Populus × canescens and to find out how the pattern is changed between summer and winter. An ARR5::GUS reporter construct was used to monitor distribution of active cytokinins in different tissues of transgenic poplar lines. Three transgenic lines tested under outdoor conditions showed no influence of ARR5::GUS reporter construct on the growth performance compared with the wild-type, but one line lost the reporter activity. ARR5::GUS activity indicated changes in the tissue- and cell type-specific pattern of cytokinin activity during dormancy compared with the growth phase. ARR5::GUS activity, which was present in the root tips in the growing season, disappeared in winter. In the stem apex ground tissue, ARR5::GUS activity was higher in winter than in summer. Immature leaves from tissue-culture grown plants showed inducible ARR5::GUS activity. Leaf primordia in summer showed ARR5::GUS activity, but not the expanded leaves of outdoor plants or leaf primordia in winter. In stem cross sections, the most prominent ARR5::GUS activity was detected in the cortex region and in the rays of bark in summer and in winter. In the cambial zone the ARR5::GUS activity was more pronounced in the dormant than in growth phase. The pith and the ray cells adjacent to the vessels also displayed ARR5::GUS activity. In silico analyses of the tissue-specific expression patterns of the whole PtRR type-A family of poplar showed that PtRR10, the closest ortholog to the Arabidopsis ARR5 gene, was usually the most highly expressed gene in all tissues. In conclusion, gene expression and tissue-localization indicate high activity of cytokinins not only in summer, but

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

    SciTech Connect

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

    2012-01-01

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

  13. 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.

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

    PubMed

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

    2009-02-01

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

  15. Using Populus as a lignocellulosic feedstock for bioethanol.

    PubMed

    Porth, Ilga; El-Kassaby, Yousry A

    2015-04-01

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

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

    SciTech Connect

    Potkar, Rewati; Recla, Jill; Busov, Victor

    2013-02-15

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

  17. 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.

  18. H2O2 and cytosolic Ca2+ signals triggered by the PM H-coupled transport system mediate K+/Na+ homeostasis in NaCl-stressed Populus euphratica cells.

    PubMed

    Sun, Jian; Wang, Mei-Juan; Ding, Ming-Quan; Deng, Shu-Rong; Liu, Mei-Qin; Lu, Cun-Fu; Zhou, Xiao-Yang; Shen, Xin; Zheng, Xiao-Jiang; Zhang, Zeng-Kai; Song, Jin; Hu, Zan-Min; Xu, Yue; Chen, Shao-Liang

    2010-06-01

    Using confocal microscopy, X-ray microanalysis and the scanning ion-selective electrode technique, we investigated the signalling of H(2)O(2), cytosolic Ca(2+) ([Ca(2+)](cyt)) and the PM H(+)-coupled transport system in K(+)/Na(+) homeostasis control in NaCl-stressed calluses of Populus euphratica. An obvious Na(+)/H(+) antiport was seen in salinized cells; however, NaCl stress caused a net K(+) efflux, because of the salt-induced membrane depolarization. H(2)O(2) levels, regulated upwards by salinity, contributed to ionic homeostasis, because H(2)O(2) restrictions by DPI or DMTU caused enhanced K(+) efflux and decreased Na(+)/H(+) antiport activity. NaCl induced a net Ca(2+) influx and a subsequent rise of [Ca(2+)](cyt), which is involved in H(2)O(2)-mediated K(+)/Na(+) homeostasis in salinized P. euphratica cells. When callus cells were pretreated with inhibitors of the Na(+)/H(+) antiport system, the NaCl-induced elevation of H(2)O(2) and [Ca(2+)](cyt) was correspondingly restricted, leading to a greater K(+) efflux and a more pronounced reduction in Na(+)/H(+) antiport activity. Results suggest that the PM H(+)-coupled transport system mediates H(+) translocation and triggers the stress signalling of H(2)O(2) and Ca(2+), which results in a K(+)/Na(+) homeostasis via mediations of K(+) channels and the Na(+)/H(+) antiport system in the PM of NaCl-stressed cells. Accordingly, a salt stress signalling pathway of P. euphratica cells is proposed. PMID:20082667

  19. Clone history shapes Populus drought responses.

    PubMed

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

    2011-07-26

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

  20. The CLE gene family in Populus trichocarpa.

    PubMed

    Liu, Zhijun; Yang, Nan; Lv, Yanting; Pan, Lixia; Lv, Shuo; Han, Huibin; Wang, Guodong

    2016-06-01

    The CLE (CLAVATA3/Embryo Surrounding Region-related) peptides are small secreted signaling peptides that are primarily involved in the regulation of stem cell homeostasis in different plant meristems. Particularly, the characterization of the CLE41-PXY/TDR signaling pathway has greatly advanced our understanding on the potential roles of CLE peptides in vascular development and wood formation. Nevertheless, our knowledge on this gene family in a tree species is limited. In a recent study, we reported on a systematically investigation of the CLE gene family in Populus trichocarpa. The potential roles of PtCLE genes were studied by comparative analysis and transcriptional profiling. Among fifty PtCLE members, many PtCLE proteins share identical CLE motifs or contain the same CLE motif as that of AtCLEs, while PtCLE genes exhibited either comparable or distinct expression patterns comparing to their Arabidopsis counterparts. These findings indicate the existence of both functional conservation and functional divergence between PtCLEs and their AtCLE orthologues. Our results provide valuable resources for future functional investigations of these critical signaling molecules in woody plants. PMID:27232947

  1. 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

  2. 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.

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

    SciTech Connect

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

    2006-01-01

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

  4. 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.

  5. 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

  6. 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

  7. Gas exchange characteristics of Populus trichocarpa, Populus deltoides and Populus trichocarpa x P. deltoides clones.

    PubMed

    Bassman, J H; Zwier, J C

    1991-03-01

    Responses of net photosynthesis, dark respiration, photorespiration, transpiration, and stomatal conductance to irradiance, temperature, leaf-to-air vapor density difference (VDD), and plant water stress were examined in two Populus trichocarpa clones (one from a moist, coastal climate in western Washington and one from a dry, continental climate in eastern Washington), one P. deltoides clone, and two P. trichocarpa x P. deltoides clones. Light saturation of photosynthesis in greenhouse-grown trees occurred at about 800 micromol m(-2) s(-1) for P. deltoides, P. trichocarpa x P. deltoides, and the eastern Washington ecotype of P. trichocarpa, but at about 600 micromol m(-2) s(-1) for the western Washington ecotype of P. trichocarpa. Average net photosynthesis (at saturating irradiance and the optimum temperature of 25 degrees C) was 20.7, 18.8, 18.2 and 13.4 micromol CO(2) m(-2) s(-1) for P. deltoides, P. trichocarpa x P. deltoides, and the eastern and western Washington clones of P. trichocarpa, respectively. In all clones, net photosynthesis decreased about 14% as VDD increased from 3 to 18 g H(2)O m(-3). Stomatal conductance decreased sharply with decreasing xylem pressure potential (XPP) in all clones except the western Washington clone of P. trichocarpa. Stomata in this clone were insensitive to changes in XPP and did not control water loss. Complete stomatal closure (stomatal conductance < 0.05 cm s(-1)) occurred at about -2.0 MPa in the eastern Washington clone of P. trichocarpa and around -1.25 MPa in the P. deltoides and P. trichocarpa x P. deltoides clones. Transpiration rates were highest in the P. trichocarpa x P. deltoides clone and lowest in the western Washington clone of P. trichocarpa. The P. deltoides clone and eastern Washington clone of P. trichocarpa had the highest water use efficiency (WUE) and the western Washington clone of P. trichocarpa had the lowest WUE. The hybrids were intermediate. It was concluded that: (1) gas exchange

  8. Populus species from diverse habitats maintain high night-time conductance under drought.

    PubMed

    Cirelli, Damián; Equiza, María Alejandra; Lieffers, Victor James; Tyree, Melvin Thomas

    2016-02-01

    We investigated the interspecific variability in nocturnal whole-plant stomatal conductance under well-watered and drought conditions in seedlings of four species of Populus from habitats characterized by abundant water supply (mesic and riparian) or from drier upland sites. The study was carried out to determine whether (i) nocturnal conductance varies across different species of Populus according to their natural habitat, (ii) nocturnal conductance is affected by water stress similarly to daytime conductance based on species habitat and (iii) differences in conductance among species could be explained partly by differences in stomatal traits. We measured whole-plant transpiration and conductance (G) of greenhouse-grown seedlings using an automated high-resolution gravimetric technique. No relationship was found between habitat preference and daytime G (GD), but night-time G (GN) was on average 1.5 times higher in riparian and mesic species (P. deltoides Bartr. ex Marsh. and P. trichocarpa Torr. & Gray) than in those from drier environments (P. tremuloides Michx. and P. × petrowskyana Schr.). GN was not significantly reduced under drought in riparian species. Upland species restricted GN significantly in response to drought, but it was still at least one order of magnitude greater that the cuticular conductance until leaf death was imminent. Under both well-watered and drought conditions, GN declined with increasing vapour pressure deficit (D). Also, a small increase in GN towards the end of the night period was observed in P. deltoides and P. × petrowskyana, suggesting the involvement of endogenous regulation. The anatomical analyses indicated a positive correlation between G and variable stomatal pore index among species and revealed that stomata are not likely to be leaky but instead seem capable of complete occlusion, which raises the question of the possible physiological role of the significant GN observed under drought. Further comparisons among

  9. 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

  10. Differential Expression of Two Distinct Phenylalanine Ammonia-Lyase Genes in Condensed Tannin-Accumulating and Lignifying Cells of Quaking Aspen

    PubMed Central

    Kao, Yu-Ying; Harding, Scott A.; Tsai, Chung-Jui

    2002-01-01

    Lignins, along with condensed tannins (CTs) and salicylate-derived phenolic glycosides, constitute potentially large phenylpropanoid carbon sinks in tissues of quaking aspen (Populus tremuloides Michx.). Metabolic commitment to each of these sinks varies during development and adaptation, and depends on l-phenylalanine ammonia-lyase (PAL), an enzyme catalyzing the deamination of l-phenylalanine to initiate phenylpropanoid metabolism. In Populus spp., PAL is encoded by multiple genes whose expression has been associated with lignification in primary and secondary tissues. We now report cloning two differentially expressed PAL cDNAs that exhibit distinct spatial associations with CT and lignin biosynthesis in developing shoot and root tissues of aspen. PtPAL1 was expressed in certain CT-accumulating, non-lignifying cells of stems, leaves, and roots, and the pattern of PtPAL1 expression varied coordinately with that of CT accumulation along the primary to secondary growth transition in stems. PtPAL2 was expressed in heavily lignified structural cells of shoots, but was also expressed in non-lignifying cells of root tips. Evidence of a role for Pt4CL2, encoding 4-coumarate:coenzyme A ligase, in determining CT sink strength was gained from cellular co-expression analysis with PAL1 and CTs, and from experiments in which leaf wounding increased PAL1 and 4CL2 expression as well as the relative allocation of carbon to CT with respect to phenolic glycoside, the dominant phenolic sink in aspen leaves. Leaf wounding also increased PAL2 and lignin pathway gene expression, but to a smaller extent. The absence of PAL2 in most CT-accumulating cells provides in situ support for the idea that PAL isoforms function in specific metabolic milieus. PMID:12376645

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

    SciTech Connect

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

    2011-01-01

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

  12. 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

  13. 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

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

    DOE PAGESBeta

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

    2014-10-07

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

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

    PubMed

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

    2015-01-01

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

  17. 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.

  18. Newly identified helper bacteria stimulate ectomycorrhizal formation in Populus

    DOE PAGESBeta

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

    2014-10-24

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

  19. 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

  20. Enzymatic Properties of Populus α- and β-NAD-ME Recombinant Proteins

    PubMed Central

    Liu, Jinwen; Yu, Qiguo; Elsheery, Nabil I.; Cheng, Yuxiang

    2013-01-01

    Plant mitochondrial NAD-malic enzyme (NAD-ME), which is composed of α- and β-subunits in many species, participates in many plant biosynthetic pathways and in plant respiratory metabolism. However, little is known about the properties of woody plant NAD-MEs. In this study, we analyzed four NAD-ME genes (PtNAD-ME1 through PtNAD-ME4) in the genome of Populus trichocarpa. PtNAD-ME1 and -2 encode putative α-subunits, while PtNAD-ME3 and -4 encode putative β-subunits. The Populus NAD-MEs were expressed in Escherichia coli cells as GST-tagged fusion proteins. Each recombinant GST-PtNAD-ME protein was purified to near homogeneity by glutathione-Sepharose 4B affinity chromatography. Milligram quantities of each native protein were obtained from 1 L bacterial cultures after cleavage of the GST tag. Analysis of the enzymatic properties of these proteins in vitro indicated that α-NAD-MEs are more active than β-NAD-MEs and that α- and β-NAD-MEs presented different kinetic properties (Vmax, kcat and kcat/Km). The effect of different amounts of metabolites on the activities of Populus α- and β-NAD-MEs was assessed in vitro. While none of the metabolites evaluated in our assays activated Populus NAD-ME, oxalacetate and citrate inhibited all α- and β-NAD-MEs and glucose-6-P and fructose inhibited only the α-NAD-MEs. PMID:23797660

  1. Identification and Biochemical Characterization of Four Wood-Associated Glucuronoxylan Methyltransferases in Populus

    PubMed Central

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

    2014-01-01

    Wood is one of the promising bioenergy feedstocks for lignocellulosic biofuel production. Understanding how wood components are synthesized will help us design strategies for better utilization of wood for biofuel production. One of the major wood components is xylan, in which about 10% of xylosyl residues are substituted with glucuronic acid (GlcA) side chains. All the GlcA side chains of xylan in wood of Populus trichocarpa are methylated, which is different from Arabidopsis xylan in which about 60% of GlcA side chains are methylated. Genes responsible for methylation of GlcA side chains in Populus xylan have not been identified. Here, we report genetic and biochemical analyses of four DUF579 domain-containing proteins, PtrGXM1, PtrGXM2, PtrGXM3 and PtrGXM4, from Populus trichocarpa and their roles in GlcA methylation in xylan. The PtrGXM genes were found to be highly expressed in wood-forming cells and their encoded proteins were shown to be localized in the Golgi. When overexpressed in the Arabidopsis gxm1/2/3 triple mutant, PtrGXMs were able to partially complement the mutant phenotypes including defects in glucuronoxylan methyltransferase activity and GlcA methylation in xylan, indicating that PtrGXMs most likely function as glucuronoxylan methyltransferases. Direct evidence was provided by enzymatic analysis of recombinant PtrGXM proteins showing that they possessed a methyltransferase activity capable of transferring the methyl group onto GlcA-substituted xylooligomers. Kinetic analysis showed that PtrGXMs exhibited differential affinities toward the GlcA-substituted xylooligomer acceptor with PtrGXM3 and PtrGXM4 having 10 times higher Km values than PtrGXM1 and PtrGXM2. Together, these findings indicate that PtrGXMs are methyltransferases mediating GlcA methylation in Populus xylan during wood formation. PMID:24523868

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

    PubMed

    Taylor, Gail

    2002-12-01

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

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

    SciTech Connect

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

    1980-01-01

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

  4. 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

  5. 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. PMID:26709311

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

    PubMed Central

    Guo, Jianjun; Morrell-Falvey, Jennifer L.; Labbé, Jessy L.; Muchero, Wellington; Kalluri, Udaya C.; Tuskan, Gerald A.; Chen, Jin-Gui

    2012-01-01

    Background Populus is a model woody plant and a promising feedstock for lignocellulosic biofuel production. However, its lengthy life cycle impedes rapid characterization of gene function. Methodology/Principal Findings We optimized a Populus leaf mesophyll protoplast isolation protocol and established a Populus protoplast transient expression system. We demonstrated that Populus protoplasts are able to respond to hormonal stimuli and that a series of organelle markers are correctly localized in the Populus protoplasts. Furthermore, we showed that the Populus protoplast transient expression system is suitable for studying protein-protein interaction, gene activation, and cellular signaling events. Conclusions/Significance This study established a method for efficient isolation of protoplasts from Populus leaf and demonstrated the efficacy of using Populus protoplast transient expression assays as an in vivo system to characterize genes and pathways. PMID:23028673

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

    SciTech Connect

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

    2012-01-01

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

  8. Characterization and ectopic expression of a populus hydroxyacid hydroxycinnamoyltransferase.

    PubMed

    Cheng, Ai-Xia; Gou, Jin-Ying; Yu, Xiao-Hong; Yang, Huijun; Fang, Xin; Chen, Xiao-Ya; Liu, Chang-Jun

    2013-11-01

    Cutinized and suberized cell walls in plants constitute physiologically important environment interfaces. They act as barriers limiting the loss of water and nutrients and protecting against radiation and invasion of pathogens. The roles of cutin- and suberin polyesters are often attributed to their dominant aliphatic components, but the contribution of aromatic composition to their physiological function remains unclear. By functionally screening a subset of Populus trichocarpa BAHD/HXXXD acyltransferases, we identified a hydroxycinnamoyltransferase that shows specific transacylation activity on ω-hydroxyacids using both feruloyl- and p-coumaroyl- CoA as the acyl donors. We named this enzyme P. trichocarpa hydroxyacid/fatty alcohol hydroxycinnamoyltransferase 1 (PtFHT1). The ectopic expression of the PtFHT1 gene in Arabidopsis increased the incorporation of ferulate in root and seed suberins and in leaf cutin, but not that of p-coumarate, while the aliphatic load in both suberin and cutin polyesters essentially remained unaffected. The overaccumulation of ferulate in lipophilic polyester significantly increased the tolerance of transgenic plants to salt stress treatment; under sub-lethal conditions of salt stress, the ratios of their seed germination and seedling establishment were 50% higher than those of wild-type plants. Our study suggests that, although aromatics are the minor component of polyesters, they play important role in the sealing function of lipidic polymers in planta. PMID:23709341

  9. Pleistocene Speciation in the Genus Populus (Salicaceae)

    PubMed Central

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

    2012-01-01

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

  10. 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

  11. Comparative analysis of the transcriptomes of Populus

    SciTech Connect

    Tuskan, Gerald A; Davis, John M

    2008-01-01

    Sequencing of the Populus trichocarpa genome creates an opportunity to describe the transcriptome of a woody perennial species and establish an atlas of gene expression. A comparison with the transcriptomes of other species can also define genes that are conserved or diverging in plant species. Here, the transcriptome in vegetative organs of the P. trichocarpa reference genotype Nisqually-1 was characterized. A comparison with Arabidopsis thaliana orthologs was used to distinguish gene functional categories that may be evolving differently in a woody perennial and an annual herbaceous species. A core set of genes expressed in common among vegetative organs was detected, as well as organ-specific genes. Statistical tests identified chromatin domains, where adjacent genes were expressed more frequently than expected by chance. Extensive divergence was detected in the expression patterns of A. thaliana and P. trichocarpa orthologs, but transcription of a small number of genes appeared to have remained conserved in the two species. Despite separation of lineages for over 100 million yr, these results suggest that selection has limited transcriptional divergence of genes associated with some essential functions in A. thaliana and P. trichocarpa. However, extensive remodeling of transcriptional networks indicates that expression regulation may be a key determinant of plant diversity.

  12. Characterization of DWARF14 Genes in Populus

    DOE PAGESBeta

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

    2016-02-15

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

  13. 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

  14. Variable Nitrogen Fixation in Wild Populus.

    PubMed

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

    2016-01-01

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

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

    PubMed

    Maheshwari, Priti; Kovalchuk, Igor

    2016-01-01

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

  16. 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

  17. 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

  18. Lignin content in natural Populus variants affects sugar release

    PubMed Central

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

    2011-01-01

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

  19. Anti-adipogenic activities of Alnus incana and Populus balsamifera bark extracts, part I: sites and mechanisms of action.

    PubMed

    Martineau, Louis C; Hervé, Jessica; Muhamad, Asim; Saleem, Ammar; Harris, Cory S; Arnason, John T; Haddad, Pierre S

    2010-09-01

    Obesity is an epidemic in most developed countries and novel therapeutic approaches are needed. In the course of a screening project of medicinal plants used by the Eastern James Bay Cree of Canada and having potential for the treatment of diabetes, we have identified several products that inhibit adipogenesis, suggesting potential antiobesity activities. The inhibitory activity of two of these, the extract of the inner bark of the deciduous trees Alnus incana ssp. rugosa (Speckled Alder) and Populus balsamifera L. (Balsam Poplar), was analyzed using the 3T3-L1 cell model of adipogenesis. Intracellular triglyceride accumulation, pre-adipocyte proliferation, and PPAR- γ activity were measured. Alnus incana extracts acted early in the differentiation process but did not affect clonal expansion of pre-adipocytes nor the morphological transformation from fibroblast-like to rounded fat-laden cells. Alnus incana extracts were found to act as partial agonists toward PPAR- γ activity. In contrast, Populus balsamifera extracts completely abrogated adipogenesis, severely limited clonal expansion of pre-adipocytes and generally maintained cells in an undifferentiated fibroblast-like morphology. Populus balsamifera extracts exerted antagonistic action against PPAR- γ activity. It is concluded that, through their actions on the adipocyte, these plant products may be useful for the treatment of obesity and related metabolic diseases. PMID:20301057

  20. 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.

  1. Suppression of PtrDUF579-3 Expression Causes Structural Changes of the Glucuronoxylan in Populus.

    PubMed

    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

  2. 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

  3. Differential detection of genetic loci underlying stem and root lignin content in Populus

    SciTech Connect

    Tuskan, Gerald A; Yin, Tongming; Zhang, Xinye; Gunter, Lee E; Ranjan, Priya; Sykes, Robert; Davis, Dr. Mark F.; Wullschleger, Stan D

    2010-11-01

    For simultaneous applications directed towards improved pulp yields, enhanced bioethanol production and increased carbon sequestration, it would be desirable to reduce lignin in the harvested stem while increasing the lignin content in nonharvested roots. In this study, we established a comprehensive genetic map with a large number of progeny from a three-generation hybrid Populus intercross, and phenotyped the lignin content, S/G ratio and 28 cell wall subcomponents both in stems and roots for the mapping individuals. Phenotypic analysis revealed that lignin content and syringyl-to-guaiacyl (S/G) ratio using pyrolysis molecular beam mass spectroscopy (pyMBMS) varied among mapping individuals. Phenotypic analysis revealed that stem lignin content is significantly higher than that in root and the quantified traits can be classified into four distinct groups, with strong correlations observed among components within organs. Altogether, 179 coordinating QTLs were detected, and they were co-localized into 49 genetic loci, 27 of which appear to be pleiotropic. Many of the detected genetic loci were detected differentially in stem and root. This is the first report of separate genetic loci controlling cell wall phenotypes above and below ground. These results suggest that it may be possible to modify lignin content and composition via breed and/or engineer as a means of simultaneously improving Populus for cellulosic ethanol production and carbon sequestration.

  4. Differential Detection of Genetic Loci Underlying Stem and Root Lignin Content in Populus

    PubMed Central

    Yin, Tongming; Zhang, Xinye; Gunter, Lee; Priya, Ranjan; Sykes, Robert; Davis, Mark; 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. PMID:21151641

  5. 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.

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

    PubMed Central

    Campbell, Malcolm M

    2012-01-01

    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. PMID:22760471

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

    SciTech Connect

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

    2010-01-01

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

  8. GENETICAL METABOLOMICS OF FLAVONOID BIOSYNTHESIS IN POPULUS: A CASE STUDY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetical metabolomics (metabolite profiling combined with quantitative trait locus [QTL] analysis) is proposed as a new tool to identify loci that control metabolite abundances. This concept was evaluated in a case study with the model tree Populus. By using HPLC, the peak abundances were analyzed ...

  9. Methylation of miRNA genes in the response to temperature stress in Populus simonii.

    PubMed

    Ci, Dong; Song, Yuepeng; Tian, Min; Zhang, Deqiang

    2015-01-01

    DNA methylation and miRNAs provide crucial regulation of the transcriptional and post-transcriptional responses to abiotic stress. In this study, we used methylation-sensitive amplification polymorphisms to identify 1066 sites that were differentially methylated in response to temperature stress in Populus simonii. Among these loci, BLAST searches of miRBase identified seven miRNA genes. Expression analysis by quantitative real-time PCR suggested that the methylation pattern of these miRNA genes probably influences their expression. Annotation of these miRNA genes in the sequenced genome of Populus trichocarpa found three target genes (Potri.007G090400, Potri.014G042200, and Potri.010G176000) for the miRNAs produced from five genes (Ptc-MIR396e and g, Ptc-MIR156i and j, and Ptc-MIR390c) respectively. The products of these target genes function in lipid metabolism to deplete lipid peroxide. We also constructed a network based on the interactions between DNA methylation and miRNAs, miRNAs and target genes, and the products of target genes and the metabolic factors that they affect, including H2O2, malondialdehyde, catalase (CAT), and superoxide dismutase. Our results suggested that DNA methylation probably regulates the expression of miRNA genes, thus affecting expression of their target genes, likely through the gene-silencing function of miRNAs, to maintain cell survival under abiotic stress conditions. PMID:26579167

  10. Phylogenetic, Expression, and Bioinformatic Analysis of the ABC1 Gene Family in Populus trichocarpa

    PubMed Central

    Zhang, Haizhen; Chen, Yunlin; Xu, Xuemei; Mao, Xuliang; Li, Chenghao

    2013-01-01

    We studied 17 ABC1 genes in Populus trichocarpa, all of which contained an ABC1 domain consisting of about 120 amino acid residues. Most of the ABC1 gene products were located in the mitochondria or chloroplasts. All had a conserved VAVK-like motif and a DFG motif. Phylogenetic analysis grouped the genes into three subgroups. In addition, the chromosomal locations of the genes on the 19 Populus chromosomes were determined. Gene structure was studied through exon/intron organization and the MEME motif finder, while heatmap was used to study the expression diversity using EST libraries. According to the heatmap, PtrABC1P14 was highlighted because of the high expression in tension wood which related to secondary cell wall formation and cellulose synthesis, thus making a contribution to follow-up experiment in wood formation. Promoter cis-element analysis indicated that almost all of the ABC1 genes contained one or two cis-elements related to ABA signal transduction pathway and drought stress. Quantitative real-time PCR was carried out to evaluate the expression of all of the genes under abiotic stress conditions (ABA, CdCl2, high temperature, high salinity, and drought); the results showed that some of the genes were affected by these stresses and confirmed the results of promoter cis-element analysis. PMID:24163630

  11. 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

  12. 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.

  13. 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. PMID:24220719

  14. Antisense expression of the fasciclin-like arabinogalactan protein FLA6 gene in Populus inhibits expression of its homologous genes and alters stem biomechanics and cell wall composition in transgenic trees

    PubMed Central

    Wang, Haihai; Jiang, Chunmei; Wang, Cuiting; Yang, Yang; Yang, Lei; Gao, Xiaoyan; Zhang, Hongxia

    2015-01-01

    Fasciclin-like arabinogalactan proteins (FLAs) play important roles in the growth and development of roots, stems, and seeds in Arabidopsis. However, their biological functions in woody plants are largely unknown. In this work, we investigated the possible function of PtFLA6 in poplar. Quantitative real-time PCR, PtFLA6–yellow fluorescent protein (YFP) fusion protein subcellular localization, Western blotting, and immunohistochemical analyses demonstrated that the PtFLA6 gene was expressed specifically in the xylem of mature stem, and PtFLA6 protein was distributed ubiquitous in plant cells and accumulated predominantly in stem xylem fibres. Antisense expression of PtFLA6 in the aspen hybrid clone Poplar davidiana×Poplar bolleana reduced the transcripts of PtFLA6 and its homologous genes. Transgenic plants that showed a significant reduction in the transcripts of PtFLAs accumulated fewer PtFLA6 and arabinogalactan proteins than did the non-transgenic plants, leading to reduced stem flexural strength and stiffness. Further studies revealed that the altered stem biomechanics of transgenic plants could be attributed to the decreased cellulose and lignin composition in the xylem. In addition expression of some xylem-specific genes involved in cell wall biosynthesis was downregulated in these transgenic plants. All these results suggest that engineering the expression of PtFLA6 and its homologues could modulate stem mechanical properties by affecting cell wall composition in trees. PMID:25428999

  15. Overexpression of PeRHD3 alters the root architecture in Populus.

    PubMed

    Xu, Meng; Xie, Wenfan; Huang, Minren

    2012-07-27

    Adventitious rooting is essential for the vegetative propagation of economically important woody species. A better understanding of the genetic and physiological mechanisms that promote or hinder rooting will enhance the potential for successful commercial deployment of trees. ROOT HAIR DEFECTIVE 3 (RHD3), a large GTP-binding protein, is ubiquitously expressed in plants. Our previous microarray study identified differential expression patterns of genes belonging to the RHD3 family during adventitious root development from hardwood cuttings, and indicated that the RHD3 genes were involved in adventitious rooting in Populus. In this study, we cloned and characterized cDNAs of the two Populus RHD3 genes, designated as PeRHD3a and PeRHD3b. Transcripts encoded by the two genes were detected in roots, stems, leaves and petioles. To characterize the cellular functions of the genes, Agrobacterium tumifaciens was used to transform poplar with a vector that places expression of the target gene under the control of the strong constitutive promoter, Cauliflower Mosaic Virus 35S (Pro35S) promoter. Both PeRHD3a transgenic lines and PeRHD3b transgenic lines showed very similar phenotypic characteristics. Overexpression of PeRHD3a or PeRHD3b in poplar plants resulted in the formation of only a single prominent adventitious root with well-developed lateral roots, characteristic abnormalities in the root tip, and longer and more plentiful root hairs. These results imply that RHD3 may control adventitious and lateral root formation, as well as root hair development by regulating anisotropic cell expansion. PMID:22732403

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

    PubMed

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

    2014-09-01

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

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

    PubMed

    Ye, Chu-Yu; Li, Ting; Tuskan, Gerald A; Tschaplinski, Timothy J; Yang, Xiaohan

    2011-12-01

    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. PMID:21958711

  18. 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.

  19. Downregulation of GAUT12 in Populus deltoides by RNA silencing results in reduced recalcitrance, increased growth and reduced xylan and pectin in a woody biofuel feedstock

    DOE PAGESBeta

    Biswal, Ajaya K.; Hao, Zhangying; Pattathil, Sivakumar; Yang, Xiaohan; Winkeler, Kim; Collins, Cassandra; Mohanty, Sushree S.; Richardson, Elizabeth A.; Gelineo-Albersheim, Ivana; Hunt, Kimberly; et al

    2015-03-12

    The inherent recalcitrance of woody bioenergy feedstocks is a major challenge for their use as a source of second-generation biofuel. Secondary cell walls that constitute the majority of hardwood biomass are rich in cellulose, xylan, and lignin. The interactions among these polymers prevent facile accessibility and deconstruction by enzymes and chemicals. Plant biomass that can with minimal pretreatment be degraded into sugars is required to produce renewable biofuels in a cost-effective manner. The following are the results: GAUT12/IRX8 is a putative glycosyltransferase proposed to be involved in secondary cell wall glucuronoxylan and/or pectin biosynthesis based on concomitant reductions of bothmore » xylan and the pectin homogalacturonan (HG) in Arabidopsis irx8 mutants. Two GAUT12 homologs exist in Populus trichocarpa, PtGAUT12.1 and PtGAUT12.2. Knockdown expression of both genes simultaneously has been shown to reduce xylan content in Populus wood. We tested the proposition that RNA interference (RNAi) downregulation of GAUT12.1 alone would lead to increased sugar release in Populus wood, that is, reduced recalcitrance, based on the hypothesis that GAUT12 synthesizes a wall structure required for deposition of xylan and that cell walls with less xylan and/or modified cell wall architecture would have reduced recalcitrance. Using an RNAi approach, we generated 11 Populus deltoides transgenic lines with 50 to 67% reduced PdGAUT12.1 transcript expression compared to wild type (WT) and vector controls. Ten of the eleven RNAi lines yielded 4 to 8% greater glucose release upon enzymatic saccharification than the controls. The PdGAUT12.1 knockdown (PdGAUT12.1-KD) lines also displayed 12 to 52% and 12 to 44% increased plant height and radial stem diameter, respectively, compared to the controls. Knockdown of PdGAUT12.1 resulted in a 25 to 47% reduction in galacturonic acid and 17 to 30% reduction in xylose without affecting total lignin content, revealing that in

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

    PubMed Central

    2012-01-01

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

  1. 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.

  2. Involvement of an Extracellular Glucan Sheath during Degradation of Populus Wood by Phanerochaete chrysosporium

    PubMed Central

    Ruel, Katia; Joseleau, Jean-Paul

    1991-01-01

    Observations by transmission electron microscopy of wood samples of Populus tremula inoculated with the white rot fungus Phanerochaete chrysosporium showed that, at certain stages of their growth cycle, hyphae were encapsulated by a sheath which seems to play an active role in the wood cell wall degradation. Chemical and immunochemical techniques and 13C nuclear magnetic resonance spectroscopy were applied to demonstrate the β-1,3-1,6-d-glucan nature of the sheath. Double-staining methods revealed the interaction between the extracellular peroxidases involved in lignin degradation and the glucan mucilage. The glucan was also shown to establish a material junction between the fungus and the wood cell wall. It was concluded that, by means of these interactions, the sheath provides a transient junction between the hyphae and the wood, thus establishing a point of attachment to the site of the degradation. The association of peroxidases to the glucan matrix is in favor of the role of the sheath as a supporting structure. Furthermore, that the sheath was hydrolyzed during the attack demonstrated its active role both in providing the H2O2 necessary to the action of peroxidases and in providing a mode of transport of the fungal enzymes to their substrates at the surface of the wood cell wall. Images PMID:16348406

  3. Endogenous overexpression of Populus MYB186 increases trichome density, improves insect pest resistance, and impacts plant growth.

    PubMed

    Plett, Jonathan M; Wilkins, Olivia; Campbell, Malcolm M; Ralph, Steven G; Regan, Sharon

    2010-11-01

    Trichomes are specialized epidermal cells that generally play a role in reducing transpiration and act as a deterrent to herbivory. In a screen of activation-tagged Populus tremula × Populus alba 717-1B4 trees, we identified a mutant line, fuzzy, with increased foliar trichome density. This mutant also had a 35% increase in growth rate and a 200% increase in the rate of photosynthesis as compared with wild-type poplar. The fuzzy mutant had significant resistance to feeding by larvae of the white-spotted tussock moth (Orgyia leucostigma), a generalist insect pest of poplar trees. The fuzzy trichome phenotype is attributable to activation tagging and increased expression of the gene encoding PtaMYB186, which is related to Arabidopsis thaliana MYB106, a known regulator of trichome initiation. The fuzzy phenotype can be recapitulated by overexpressing PtaMYB186 in poplar. PtaMYB186 overexpression results in reconfiguration of the poplar transcriptome, with changes in the transcript abundance of suites of genes that are related to trichome differentiation. It is notable that a plant with misexpression of a gene responsible for trichome development also had altered traits related to growth rate and pest resistance, suggesting that non-intuitive facets of plant development might be useful targets for plant improvement. PMID:20807210

  4. Genome-wide profiling of Populus small RNAs

    PubMed Central

    2009-01-01

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

  5. Stress-responsive hydroxycinnamate glycosyltransferase modulates phenylpropanoid metabolism in Populus

    PubMed Central

    Babst, Benjamin A.; Chen, Han-Yi; Wang, Hong-Qiang; Payyavula, Raja S.; Thomas, Tina P.; Harding, Scott A.; Tsai, Chung-Jui

    2014-01-01

    The diversity of phenylpropanoids offers a rich inventory of bioactive chemicals that can be exploited for plant improvement and human health. Recent evidence suggests that glycosylation may play a role in the partitioning of phenylpropanoid precursors for a variety of downstream uses. This work reports the functional characterization of a stress-responsive glycosyltransferase, GT1-316 in Populus. GT1-316 belongs to the UGT84A subfamily of plant glycosyltransferase family 1 and is designated UGT84A17. Recombinant protein analysis showed that UGT84A17 is a hydroxycinnamate glycosyltransferase and able to accept a range of unsubstituted and substituted cinnamic and benzoic acids as substrates in vitro. Overexpression of GT1-316 in transgenic Populus led to plant-wide increases of hydroxycinnamoyl-glucose esters, which were further elevated under N-limiting conditions. Levels of the two most abundant flavonoid glycosides, rutin and kaempferol-3-O-rutinoside, decreased, while levels of other less abundant flavonoid and phenylpropanoid conjugates increased in leaves of the GT1-316-overexpressing plants. Transcript levels of representative phenylpropanoid pathway genes were unchanged in transgenic plants, supporting a glycosylation-mediated redirection of phenylpropanoid carbon flow as opposed to enhanced phenylpropanoid pathway flux. The metabolic response of N-replete transgenic plants overlapped with that of N-stressed wild types, as the majority of phenylpropanoid derivatives significantly affected by GT1-316 overexpression were also significantly changed by N stress in the wild types. These results suggest that UGT84A17 plays an important role in phenylpropanoid metabolism by modulating biosynthesis of hydroxycinnamoyl-glucose esters and their derivatives in response to developmental and environmental cues. PMID:24803501

  6. 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. PMID:26496757

  7. 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

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

    ScienceCinema

    Tuskan, Gerry

    2011-06-03

    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

  9. 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

  10. 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

  11. 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

  12. Differential transcriptome analysis between Populus and its synthesized allotriploids driven by second-division restitution.

    PubMed

    Cheng, Shiping; Huang, Zhen; Li, Yun; Liao, Ting; Suo, Yujing; Zhang, Pingdong; Wang, Jun; Kang, Xiangyang

    2015-12-01

    In this report, we compared transcriptomic differences between a synthetic Populus section Tacamahaca triploid driven by second-division restitution and its parents using a high-throughput RNA-seq method. A total of 4,080 genes were differentially expressed between the high-growth vigor allotriploids (SDR-H) and their parents, and 719 genes were non-additively expressed in SDR-H. Differences in gene expression between the allotriploid and male parent were more significant than those between the allotriploid and female parent, which may be caused by maternal effects. We observed 3,559 differentially expressed genes (DEGs) between the SDR-H and male parent. Notably, the genes were mainly involved in metabolic process, cell proliferation, DNA methylation, cell division, and meristem and developmental growth. Among the 1,056 DEGs between SDR-H and female parent, many genes were associated with metabolic process and carbon utilization. In addition, 1,789 DEGs between high- and low-growth vigor allotriploid were mainly associated with metabolic process, auxin poplar transport, and regulation of meristem growth. Our results indicated that the higher poplar ploidy level can generate extensive transcriptomic diversity compared with its parents. Overall, these results increased our understanding of the driving force for phenotypic variation and adaptation in allopolyploids driven by second-division restitution. PMID:25557321

  13. Leaf hydraulic conductance in relation to anatomical and functional traits during Populus tremula leaf ontogeny.

    PubMed

    Aasamaa, Krõõt; Niinemets, Ulo; Sõber, Anu

    2005-11-01

    Leaf hydraulic conductance (K(leaf)) and several characteristics of hydraulic architecture and physiology were measured during the first 10 weeks of leaf ontogeny in Populus tremula L. saplings growing under control, mild water deficit or elevated temperature conditions. During the initial 3 weeks of leaf ontogeny, most measured characteristics rapidly increased. Thereafter, a gradual decrease in K(leaf) was correlated with a decrease in leaf osmotic potential under all conditions, and with increases in leaf dry mass per area and bulk modulus of elasticity under mild water deficit and control conditions. From about Week 3 onward, K(leaf) was 33% lower in trees subjected to mild water deficit and 33% higher in trees held at an elevated temperature relative to control trees. Mild water deficit and elevated temperature treatment had significant and opposite effects on most of the other characteristics measured. The ontogenetic maximum in K(leaf) was correlated positively with the width of xylem conduits in the midrib, but negatively with the overall width of the midrib xylem, number of lateral ribs, leaf dry mass per area and bulk modulus of elasticity. The ontogenetic maximum in K(leaf) was also correlated positively with the proportion of intercellular spaces and leaf osmotic potential, but negatively with leaf thickness, volume of mesophyll cells and epidermis and number of cells per total mesophyll cell volume, the closest relationships being between leaf osmotic potential and number of cells per total mesophyll cell volume. It was concluded that differences in protoplast traits are more important than differences in xylem or parenchymal cell wall traits in determining the variability in K(leaf) among leaves growing under different environmental conditions. PMID:16105808

  14. 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.

  15. Season-associated modifications in symplasmic organization of the cambium in Populus nigra

    PubMed Central

    Fuchs, Maike; van Bel, Aart J. E.; Ehlers, Katrin

    2010-01-01

    Background and Aims Alterations of plasmodesma (PD) connectivity are likely to be very important for plant development. Here, the repetitive division pattern of cambial initials in Populus nigra ‘italica’ was studied to follow the development of the PD network during maturation. Furthermore, seasonal changes were investigated in order to trace indications for developmental and functional adaptations. Methods Cambium samples of P. nigra twigs, collected in summer, autumn and spring, were chemically fixed for transmission electron microscopy. The parameters, PD density (number of PDs per square micrometre cell-wall area) and PD frequency (total number of PDs per average cell-wall area), were determined for radial and tangential cell interfaces deposited in chronological order. Key Results Data sets, presented in plasmodesmograms, show a strong variability in the PD network throughout the year. In summer, high PD numbers occur at the division wall which, after PD doubling by longitudinal fission, decline with further development both at the xylem and the phloem side. In autumn, the number of PDs at the division wall is low as they are in subsequent tangential interfaces. In spring, the first cell division coincides with a massive increase in PD numbers, in particular at the division wall. Only the radial walls between initials maintain their PD equipment throughout the year. This feature can be exploited for identification of the initial layer. Conclusions PD networks in the cambium go through a strict developmental programme depending on the season, which is associated with changing functional requirements. For instance, PD numbers correlate with proliferative activity and potential pathways for intercellular signalling. Increases in PD numbers are ascribed to longitudinal fission as a major mechanism, whereas the decline in older derivatives is ascribed to PD degradation. PMID:20045870

  16. Spatiotemporal distribution of essential elements through Populus leaf ontogeny.

    PubMed

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

    2016-04-01

    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

  17. The genetics and genomics of the drought response in Populus.

    PubMed

    Street, Nathaniel Robert; Skogström, Oskar; Sjödin, Andreas; Tucker, James; Rodríguez-Acosta, Maricela; Nilsson, Peter; Jansson, Stefan; Taylor, Gail

    2006-11-01

    The genetic nature of tree adaptation to drought stress was examined by utilizing variation in the drought response of a full-sib second generation (F(2)) mapping population from a cross between Populus trichocarpa (93-968) and P. deltoides Bart (ILL-129) and known to be highly divergent for a vast range of phenotypic traits. We combined phenotyping, quantitative trait loci (QTL) analysis and microarray experiments to demonstrate that 'genetical genomics' can be used to provide information on adaptation at the species level. The grandparents and F(2) population were subjected to soil drying, and contrasting responses to drought across genotypes, including leaf coloration, expansion and abscission, were observed, and QTL for these traits mapped. A subset of extreme genotypes exhibiting extreme sensitivity and insensitivity to drought on the basis of leaf abscission were defined, and microarray experiments conducted on these genotypes and the grandparent species. The extreme genotype groups induced a different set of genes: 215 and 125 genes differed in their expression response between groups in control and drought, respectively, suggesting species adaptation at the gene expression level. Co-location of differentially expressed genes with drought-specific and drought-responsive QTLs was examined, and these may represent candidate genes contributing to the variation in drought response. PMID:17005011

  18. 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

  19. Association of Allelic Variation in PtoXET16A with Growth and Wood Properties in Populus tomentosa

    PubMed Central

    Wang, Bowen; Zhang, Deqiang

    2014-01-01

    Xyloglucan endo-transglycosylases (XETs) modify the xyloglucan-cellulose framework of plant cell walls and, thus, affect cell wall expansion and strength. Dissecting the mechanism by which natural variation in XETs affects wood properties can inform breeding efforts to improve wood quality and yield traits. To this end, we isolated a full-length PtoXET16A cDNA clone from Populus tomentosa. Real-time PCR analysis showed that PtoXET16A was maximally expressed in the root, followed by phloem, cambium, and developing xylem, suggesting that PtoXET16A plays important roles in the development of vascular tissues. Nucleotide diversity and linkage disequilibrium analysis revealed that PtoXET16A has high single nucleotide polymorphism (SNP) diversity (π = 0.01266 and θw = 0.01392) and low linkage disequilibrium (r2 ≥ 0.1, within 900 bp). SNP- and haplotype-based association analyses of 426 individuals from a natural population indicated that nine SNPs (including two non-synonymous markers and one splicing variant) (p ≤ 0.05, false discovery rate Q ≤ 0.01), and nine haplotypes (p ≤ 0.05) were significantly associated with growth and wood properties, each explaining from 3.40%–10.95% of phenotypic variance. This work shows that examination of allelic variation and linkage disequilibrium by a candidate-gene-based approach can help to decipher the genetic basis of wood formation. Moreover, the SNP markers identified in this study can potentially be applied for marker-assisted selection to improve growth and wood-property traits in Populus. PMID:25250912

  20. SEXUAL DEMOGRAPHICS OF RIPARIAN POPULATIONS OF POPULUS DELTOIDES: CAN MORTALITY BE PREDICTED FROM A CHANGE IN REPRODUCTIVE STATUS?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Populus deltoides forests along the Rio Grande river drainage are predicted to disappear within this century. We evaluated stand health over three years by examining the sex ratio, size, and spatial distribution of male, female, and non-reproductive trees in six even-aged stands of Populus deltoide...

  1. Solution-state 2D NMR of ball-milled plant cell wall gels in DMSO-d6/pyridine-d5†

    PubMed Central

    Ralph, John

    2014-01-01

    NMR fingerprinting of the components of finely divided plant cell walls swelled in DMSO has been recently described. Cell wall gels, produced directly in the NMR tube with perdeutero-dimethylsulfoxide, allowed the acquisition of well resolved/dispersed 2D 13C–1H correlated solution-state NMR spectra of the entire array of wall polymers, without the need for component fractionation. That is, without actual solubilization, and without apparent structural modification beyond that inflicted by the ball milling and ultrasonication steps, satisfactorily interpretable spectra can be acquired that reveal compositional and structural details regarding the polysaccharide and lignin components in the wall. Here, the profiling method has been improved by using a mixture of perdeuterated DMSO and pyridine (4:1, v/v). Adding pyridine provided not only easier sample handling because of the better mobility compared to the DMSO-d6-only system but also considerably elevated intensities and improved resolution of the NMR spectra due to the enhanced swelling of the cell walls. This modification therefore provides a more rapid method for comparative structural evaluation of plant cell walls than is currently available. We examined loblolly pine (Pinus taeda, a gymnosperm), aspen (Populus tremuloides, an angiosperm), kenaf (Hibiscus cannabinus, an herbaceous plant), and corn (Zea mays L., a grass, i.e., from the Poaceae family). In principle, lignin composition (notably, the syringyl : guaiacyl : p-hydroxyphenyl ratio) can be quantified without the need for lignin isolation. Correlations for p-coumarate units in the corn sample are readily seen, and a variety of the ferulate correlations are also well resolved; ferulates are important components responsible for cell wall cross-linking in grasses. Polysaccharide anomeric correlations were tentatively assigned for each plant sample based on standard samples and various literature data. With the new potential for chemometric analysis

  2. 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.

  3. 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.

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

    PubMed

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

    2014-07-01

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

  5. Transcriptome Profiles of Populus euphratica upon Heat Shock stress

    PubMed Central

    Chen, Jinhuan; Yin, Weilun; Xia, Xinli

    2014-01-01

    Heat stress, which strongly affects plant performance and often results in reduced vegetative growth and yields depression, has become an increasingly serious global problem. Populus euphratica Oliv. which has been considered as a tree model for the study of plant response to abiotic stresses, could be resistant to an extremely wide environmental temperature range (–40 °C to 45 °C). Previous study is mainly focused on its gene regulation upon drought and salt stress. However, little is known about gene regulation at the global transcriptome level upon heat stress. To understand the gene network controlling heat stress in P. euphratica, a transcriptome sequencing using Illumina Hiseq 2000 was performed to generate a 10 gigabases depth for each sample in the tissue of leaf. 119,573 unigeneswere generated with an average length of 474 bp. Approximately 49,605 (41.49%) unigenes exhibited significantly different expressions between two libraries. Among these unigenes, 11,165 (9.34%) were upregulated and 38,440 (32.15%) were down regulated. Heat shock proteins classified as molecular chaperones showed a significant percentage (1.13%) in the up regulated group. Heat responsive genes, such as polyubiquitins, were over expressed in heat treated sample. GO enrichment analysis revealed that the Go terms for differentially expressed unigenes were significantly enriched in hormone-mediated signal, biological process regulation and metabolic process regulation. Our data revealed a global transcriptome picture of P. euphratica in response to heat shock. The identified potential heat stress-related transcripts can be used to infer the gene regulation networks underlying the molecular mechanisms of heat response in P. euphratica. PMID:25435796

  6. Paenibacillus populi sp. nov., a novel bacterium isolated from the rhizosphere of Populus alba.

    PubMed

    Han, Tong-Yan; Tong, Xiao-Mei; Wang, Yan-Wei; Wang, Hui-Min; Chen, Xiao-Rong; Kong, De-Long; Guo, Xiang; Ruan, Zhi-Yong

    2015-09-01

    A novel aerobic bacterium, designated strain LAM0705(T), was isolated from the rhizosphere of Populus alba in the Peking University Third Hospital. Cells of strain LAM0705(T) were observed to be Gram-stain positive, motile, spore-forming and rod-shaped. The optimal temperature and pH for growth were found to be 30 °C and pH 7.5, respectively. Strain LAM0705(T) was found to be able to grow in the presence 0-5 % NaCl (w/v) (optimum 1.0 %). The major fatty acids of strain LAM0705(T) were identified as anteiso-C15:0, C16:0 and iso-C16:0. The dominant polar lipids were found to consist of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The cell wall peptidoglycan of strain LAM0705(T) was found to contain meso-diaminopimelic acid. The predominant menaquinone was identified as MK-7. The G+C content of genomic DNA was found to be 48 mol% when determined by the T m method. The 16S rRNA gene sequence similarity analysis indicated that strain LAM0705(T) is closely related to Paenibacillus agaridevorans DSM 1355(T) and Paenibacillus thailandensis KCTC 13043(T) with 97.8 and 96.1 % sequence similarity, respectively. The DNA-DNA hybridization value between strain LAM0705(T) and P. agaridevorans DSM 1355(T) was 47 ± 0.8 %. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM0705(T) is concluded to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus populi sp. nov. is proposed. The type strain is LAM0705(T) (=ACCC 06427(T) = JCM 19843(T)). PMID:26133115

  7. 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

  8. 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.

  9. 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. PMID:25900569

  10. Identification and characterization of nuclear genes involved in photosynthesis in Populus

    PubMed Central

    2014-01-01

    Background The gap between the real and potential photosynthetic rate under field conditions suggests that photosynthesis could potentially be improved. Nuclear genes provide possible targets for improving photosynthetic efficiency. Hence, genome-wide identification and characterization of the nuclear genes affecting photosynthetic traits in woody plants would provide key insights on genetic regulation of photosynthesis and identify candidate processes for improvement of photosynthesis. Results Using microarray and bulked segregant analysis strategies, we identified differentially expressed nuclear genes for photosynthesis traits in a segregating population of poplar. We identified 515 differentially expressed genes in this population (FC ≥ 2 or FC ≤ 0.5, P < 0.05), 163 up-regulated and 352 down-regulated. Real-time PCR expression analysis confirmed the microarray data. Singular Enrichment Analysis identified 48 significantly enriched GO terms for molecular functions (28), biological processes (18) and cell components (2). Furthermore, we selected six candidate genes for functional examination by a single-marker association approach, which demonstrated that 20 SNPs in five candidate genes significantly associated with photosynthetic traits, and the phenotypic variance explained by each SNP ranged from 2.3% to 12.6%. This revealed that regulation of photosynthesis by the nuclear genome mainly involves transport, metabolism and response to stimulus functions. Conclusions This study provides new genome-scale strategies for the discovery of potential candidate genes affecting photosynthesis in Populus, and for identification of the functions of genes involved in regulation of photosynthesis. This work also suggests that improving photosynthetic efficiency under field conditions will require the consideration of multiple factors, such as stress responses. PMID:24673936

  11. Streptomyces indoligenes sp. nov., isolated from rhizosphere soil of Populus euphratica.

    PubMed

    Luo, Xiaoxia; Sun, Yong; Xie, Sinan; Wan, Chuanxing; Zhang, Lili

    2016-06-01

    A novel actinobacterium, designated TRM 43006T, was isolated from the rhizosphere soil of Populus euphratica in Xinjiang Province, north-west China. Phylogenetic and phenotypic analysis demonstrated that strain TRM 43006T belongs to the genus Streptomyces. The strain was aerobic and Gram-stain-positive; the aerial mycelium branched monopodially, forming chains of arthrospores. The spores were oval to cylindrical with smooth surfaces. The whole-cell sugar pattern of strain TRM 43006T consisted of xylose, mannitol, galactose and ribose. The menaquinones were MK-9(H6), MK-9(H8) and MK-9(H10). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannosides and four unknown phospholipids. Major fatty acids were iso-C16 : 0, iso-C16 : 1, iso-C14 : 0 and anteiso-C15 : 0. The G+C content of the genomic DNA was 69.0 mol%. Comparative 16S rRNA gene sequence analysis indicated that strain TRM 43006T was phylogenetically most closely related to Streptomyces roseolilacinus NBRC 12815T (98.6 % similarity) and Streptomycessudanensis SD 504T (98.3 %); however, DNA-DNA hybridization studies between S. roseolilacinus NBRC 12815T, S. sudanensis SD 504T and TRM 43006T showed only 30.28 and 30.65  % relatedness, respectively. Based on the evidence from this polyphasic study, strain TRM 43006T represents a novel species of the genus Streptomyces, for which the name Streptomyces indoligenes sp. nov. is proposed. The type strain is TRM 43006T (=KCTC 39611T=CCTCC AA 2015010T). PMID:27031169

  12. 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.

  13. 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...

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

    PubMed Central

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

    2015-01-01

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

  15. 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

  16. 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.

  17. 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/

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

    PubMed Central

    Yin, Tongming; DiFazio, Stephen P.; Gunter, Lee E.; Zhang, Xinye; Sewell, Michell M.; Woolbright, Scott A.; Allan, Gery J.; Kelleher, Collin T.; Douglas, Carl J.; Wang, 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. PMID:18256239

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

    DOE PAGESBeta

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

    2015-11-12

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

  20. 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.

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

    PubMed

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

    2003-09-01

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

  2. Downregulation of GAUT12 in Populus deltoides by RNA silencing results in reduced recalcitrance, increased growth and reduced xylan and pectin in a woody biofuel feedstock

    SciTech Connect

    Biswal, Ajaya K.; Hao, Zhangying; Pattathil, Sivakumar; Yang, Xiaohan; Winkeler, Kim; Collins, Cassandra; Mohanty, Sushree S.; Richardson, Elizabeth A.; Gelineo-Albersheim, Ivana; Hunt, Kimberly; Ryno, David; Sykes, Robert W.; Turner, Geoffrey B.; Ziebell, Angela; Gjersing, Erica; Lukowitz, Wolfgang; Davis, Mark F.; Decker, Stephen R.; Hahn, Michael G.; Mohnen, Debra

    2015-03-12

    The inherent recalcitrance of woody bioenergy feedstocks is a major challenge for their use as a source of second-generation biofuel. Secondary cell walls that constitute the majority of hardwood biomass are rich in cellulose, xylan, and lignin. The interactions among these polymers prevent facile accessibility and deconstruction by enzymes and chemicals. Plant biomass that can with minimal pretreatment be degraded into sugars is required to produce renewable biofuels in a cost-effective manner. The following are the results: GAUT12/IRX8 is a putative glycosyltransferase proposed to be involved in secondary cell wall glucuronoxylan and/or pectin biosynthesis based on concomitant reductions of both xylan and the pectin homogalacturonan (HG) in Arabidopsis irx8 mutants. Two GAUT12 homologs exist in Populus trichocarpa, PtGAUT12.1 and PtGAUT12.2. Knockdown expression of both genes simultaneously has been shown to reduce xylan content in Populus wood. We tested the proposition that RNA interference (RNAi) downregulation of GAUT12.1 alone would lead to increased sugar release in Populus wood, that is, reduced recalcitrance, based on the hypothesis that GAUT12 synthesizes a wall structure required for deposition of xylan and that cell walls with less xylan and/or modified cell wall architecture would have reduced recalcitrance. Using an RNAi approach, we generated 11 Populus deltoides transgenic lines with 50 to 67% reduced PdGAUT12.1 transcript expression compared to wild type (WT) and vector controls. Ten of the eleven RNAi lines yielded 4 to 8% greater glucose release upon enzymatic saccharification than the controls. The PdGAUT12.1 knockdown (PdGAUT12.1-KD) lines also displayed 12 to 52% and 12 to 44% increased plant height and radial stem diameter, respectively, compared to the controls. Knockdown of PdGAUT12.1 resulted in a 25 to 47% reduction in galacturonic acid and 17 to 30% reduction in xylose without affecting total lignin content, revealing that in Populus

  3. Genome-Wide Analysis of the Fasciclin-Like Arabinogalactan Protein Gene Family Reveals Differential Expression Patterns, Localization, and Salt Stress Response in Populus

    PubMed Central

    Zang, Lina; Zheng, Tangchun; Chu, Yanguang; Ding, Changjun; Zhang, Weixi; Huang, Qinjun; Su, Xiaohua

    2015-01-01

    Fasciclin-like arabinogalactan proteins (FLAs) are a subclass of arabinogalactan proteins (AGPs) involved in plant growth, development and response to abiotic stress. Although many studies have been performed to identify molecular functions of individual family members, little information is available on genome-wide identification and characterization of FLAs in the genus Populus. Based on genome-wide analysis, we have identified 35 Populus FLAs which were distributed on 16 chromosomes and phylogenetically clustered into four major groups. Gene structure and motif composition were relatively conserved in each group. All the members contained N-terminal signal peptide, 23 of which included predicted glycosylphosphatidylinositol (GPI) modification sites and were anchored to plasma membranes. Subcellular localization analysis showed that PtrFLA2/20/26 were localized in cell membrane and cytoplasm of protoplasts from Populus stem-differentiating xylem. The Ka/Ks ratios showed that purifying selection has played a leading role in the long-term evolutionary period which greatly maintained the function of this family. The expression profiles showed that 32 PtrFLAs were differentially expressed in four tissues at four seasons based on publicly available microarray data. 18 FLAs were further verified with qRT-PCR in different tissues, which indicated that PtrFLA1/2/3/7/11/12/20/21/22/24/26/30 were significantly expressed in male and female flowers, suggesting close correlations with the reproductive development. In addition, PtrFLA1/9/10/11/17/21/23/24/26/28 were highly expressed in the stems and differentiating xylem, which may be involved in stem development. To determine salt response of FLAs, qRT-PCR was performed to analyze the expression of 18 genes under salinity stress across two time points. Results demonstrated that all the 18 FLAs were expressed in root tissues; especially, PtrFLA2/12/20/21/24/30 were significantly induced at different time points. In summary

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

    PubMed Central

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

    2015-01-01

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

  5. 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.

  6. 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.

  7. 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. PMID:19773340

  8. WUSCHEL-related Homeobox genes in Populus tomentosa: diversified expression patterns and a functional similarity in adventitious root formation

    PubMed Central

    2014-01-01

    Background WUSCHEL (WUS)-related homeobox (WOX) protein family members play important roles in the maintenance and proliferation of the stem cell niche in the shoot apical meristem (SAM), root apical meristem (RAM), and cambium (CAM). Although the roles of some WOXs in meristematic cell regulation have been well studied in annual plants such as Arabidopsis and rice, the expression and function of WOX members in woody plant poplars has not been systematically investigated. Here, we present the identification and comprehensive analysis of the expression and function of WOXs in Populus tomentosa. Results A genome-wide survey identified 18 WOX encoding sequences in the sequenced genome of Populus trichocarpa (PtrWOXs). Phylogenetic and gene structure analysis revealed that these 18 PtrWOXs fall into modern/WUS, intermediate, and ancient clades, but that the WOX genes in P. trichocarpa may have expanded differently from the WOX genes in Arabidopsis. In the P. trichocarpa genome, no WOX members could be closely classified as AtWOX3, AtWOX6, AtWOX7, AtWOX10, and AtWOX14, but there were two copies of WOX genes that could be classified as PtrWUS, PtrWOX2, PtrWOX4, PtrWOX5, PtrWOX8/9, and PtrWOX11/12, and three copies of WOX genes that could be classified as PtrWOX1 and PtrWOX13. The use of primers specific for each PtrWOX gene allowed the identification and cloning of 18 WOX genes from P. tomentosa (PtoWOXs), a poplar species physiologically close to P. trichocarpa. It was found that PtoWOXs and PtrWOXs shared very high amino acid sequence identity, and that PtoWOXs could be classified identically to PtrWOXs. We revealed that the expression patterns of some PtoWOXs were different to their Arabidopsis counterparts. When PtoWOX5a and PtoWOX11/12a, as well as PtoWUSa and PtoWOX4a were ectopically expressed in transgenic hybrid poplars, the regeneration of adventitious root (AR) was promoted, indicating a functional similarity of these four WOXs in AR regeneration. Conclusions

  9. Auxin is a long-range signal that acts independently of ethylene signaling on leaf abscission in Populus

    PubMed Central

    Jin, Xu; Zimmermann, Jorma; Polle, Andrea; Fischer, Urs

    2015-01-01

    Timing of leaf abscission is an important trait for biomass production and seasonal acclimation in deciduous trees. The signaling leading to organ separation, from the external cue (decreasing photoperiod) to ethylene-regulated hydrolysis of the middle lamellae in the abscission zone, is only poorly understood. Data from annual species indicate that the formation of an auxin gradient spanning the abscission zone regulates the timing of abscission. We established an experimental system in Populus to induce leaf shedding synchronously under controlled greenhouse conditions in order to test the function of auxin in leaf abscission. Here, we show that exogenous auxin delayed abscission of dark-induced leaves over short and long distances and that a new auxin response maximum preceded the formation of an abscission zone. Several auxin transporters were down-regulated during abscission and inhibition of polar auxin transport delayed leaf shedding. Ethylene signaling was not involved in the regulation of these auxin transporters and in the formation of an abscission zone, but was required for the expression of hydrolytic enzymes associated with cell separation. Since exogenous auxin delayed abscission in absence of ethylene signaling auxin likely acts independently of ethylene signaling on cell separation. PMID:26322071

  10. Subcellular Relocalization and Positive Selection Play Key Roles in the Retention of Duplicate Genes of Populus Class III Peroxidase Family.

    PubMed

    Ren, Lin-Ling; Liu, Yan-Jing; Liu, Hai-Jing; Qian, Ting-Ting; Qi, Li-Wang; Wang, Xiao-Ru; Zeng, Qing-Yin

    2014-06-16

    Gene duplication is the primary source of new genes and novel functions. Over the course of evolution, many duplicate genes lose their function and are eventually removed by deletion. However, some duplicates have persisted and evolved diverse functions. A particular challenge is to understand how this diversity arises and whether positive selection plays a role. In this study, we reconstructed the evolutionary history of the class III peroxidase (PRX) genes from the Populus trichocarpa genome. PRXs are plant-specific enzymes that play important roles in cell wall metabolism and in response to biotic and abiotic stresses. We found that two large tandem-arrayed clusters of PRXs evolved from an ancestral cell wall type PRX to vacuole type, followed by tandem duplications and subsequent functional specification. Substitution models identified seven positively selected sites in the vacuole PRXs. These positively selected sites showed significant effects on the biochemical functions of the enzymes. We also found that positive selection acts more frequently on residues adjacent to, rather than directly at, a critical active site of the enzyme, and on flexible regions rather than on rigid structural elements of the protein. Our study provides new insights into the adaptive molecular evolution of plant enzyme families. PMID:24934172

  11. 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.

  12. Selecting and utilizing Populus and Salix for landfill covers: implications for leachate irrigation.

    PubMed

    Zalesny, Ronald S; Bauer, Edmund O

    2007-01-01

    The success of using Populus and Salix for phytoremediation has prompted further use of leachate as a combination of irrigation and fertilization for the trees. A common protocol for such efforts has been to utilize a limited number of readily-available genotypes with decades of deployment in other applications, such as fiber or windbreaks. However, it may be possible to increase phytoremediation success with proper genotypic screening and selection, followed by the field establishment of clones that exhibited favorable potential for cleanup of specific contaminants. There is an overwhelming need for testing and subsequent deployment of diverse Populus and Salix genotypes, given current availability of clonal material and the inherent genetic variation among and within these genera. Therefore, we detail phyto-recurrent selection, a method that consists of revising and combining crop and tree improvement protocols to meet the objective of utilizing superior Populus and Salix clones for remediation applications. Although such information is lacking for environmental clean-up technologies, centuries of plant selection success in agronomy, horticulture, and forestry validate the need for similar approaches in phytoremediation. We bridge the gap between these disciplines by describing project development, clone selection, tree establishment, and evaluation of success metrics in the context of their importance to utilizing trees for phytoremediation. PMID:18246776

  13. 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.

  14. 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.

  15. 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. PMID:15309534

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

    PubMed Central

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

    2013-01-01

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

  17. Comparative Physiological and Proteomic Analysis Reveals the Leaf Response to Cadmium-Induced Stress in Poplar (Populus yunnanensis)

    PubMed Central

    Yang, Shihai; Zhou, Yanli; Dong, Chao; Ren, Jian; Sun, Xudong; Yang, Yongping

    2015-01-01

    Excess amounts of heavy metals are important environmental pollutants with significant ecological and nutritional effects. Cdmium (Cd) is of particular concern because of its widespread occurrence and high toxicity. We conducted physiological and proteomic analyses to improve our understanding of the responses of Populus yunnanensis to Cd stress. The plantlets experienced two apparent stages in their response to Cd stress. During the first stage, transiently induced defense-response molecules, photosynthesis- and energy-associated proteins, antioxidant enzymes and heat shock proteins (HSPs) accumulated to enhance protein stability and establish a new cellular homeostasis. This activity explains why plant photosynthetic capability during this period barely changed. During the second stage, a decline of ribulose-1, 5-bisphosphate carboxylase (RuBisCO) and HSP levels led to imbalance of the plant photosynthetic system. Additionally, the expression of Mitogen-activated protein kinase 3 (MPK3), Mitogen-activated protein kinase 6 (MPK6) and a homeobox-leucine zipper protein was higher in the second stage. Higher expression of caffeoyl-CoA O-methyltransferase (CCoAOMT) may regulate plant cell wall synthesis for greater Cd storage. These genes may be candidates for further research and use in genetic manipulation of poplar tolerance to Cd stress. PMID:26349064

  18. Ethylene and jasmonic acid act as negative modulators during mutualistic symbiosis between Laccaria bicolor and Populus roots.

    PubMed

    Plett, Jonathan M; Khachane, Amit; Ouassou, Malika; Sundberg, Björn; Kohler, Annegret; Martin, Francis

    2014-04-01

    The plant hormones ethylene, jasmonic acid and salicylic acid have interconnecting roles during the response of plant tissues to mutualistic and pathogenic symbionts. We used morphological studies of transgenic- or hormone-treated Populus roots as well as whole-genome oligoarrays to examine how these hormones affect root colonization by the mutualistic ectomycorrhizal fungus Laccaria bicolor S238N. We found that genes regulated by ethylene, jasmonic acid and salicylic acid were regulated in the late stages of the interaction between L. bicolor and poplar. Both ethylene and jasmonic acid treatments were found to impede fungal colonization of roots, and this effect was correlated to an increase in the expression of certain transcription factors (e.g. ETHYLENE RESPONSE FACTOR1) and a decrease in the expression of genes associated with microbial perception and cell wall modification. Further, we found that ethylene and jasmonic acid showed extensive transcriptional cross-talk, cross-talk that was opposed by salicylic acid signaling. We conclude that ethylene and jasmonic acid pathways are induced late in the colonization of root tissues in order to limit fungal growth within roots. This induction is probably an adaptive response by the plant such that its growth and vigor are not compromised by the fungus. PMID:24383411

  19. A Transcriptomic Network Underlies Microstructural and Physiological Responses to Cadmium in Populus × canescens1[C][W

    PubMed Central

    He, Jiali; Li, Hong; Luo, Jie; Ma, Chaofeng; Li, Shaojun; Qu, Long; Gai, Ying; Jiang, Xiangning; Janz, Dennis; Polle, Andrea; Tyree, Melvin; Luo, Zhi-Bin

    2013-01-01

    Bark tissue of Populus × canescens can hyperaccumulate cadmium, but microstructural, transcriptomic, and physiological response mechanisms are poorly understood. Histochemical assays, transmission electron microscopic observations, energy-dispersive x-ray microanalysis, and transcriptomic and physiological analyses have been performed to enhance our understanding of cadmium accumulation and detoxification in P. × canescens. Cadmium was allocated to the phloem of the bark, and subcellular cadmium compartmentalization occurred mainly in vacuoles of phloem cells. Transcripts involved in microstructural alteration, changes in nutrition and primary metabolism, and stimulation of stress responses showed significantly differential expression in the bark of P. × canescens exposed to cadmium. About 48% of the differentially regulated transcripts formed a coregulation network in which 43 hub genes played a central role both in cross talk among distinct biological processes and in coordinating the transcriptomic regulation in the bark of P. × canescens in response to cadmium. The cadmium transcriptome in the bark of P. × canescens was mirrored by physiological readouts. Cadmium accumulation led to decreased total nitrogen, phosphorus, and calcium and increased sulfur in the bark. Cadmium inhibited photosynthesis, resulting in decreased carbohydrate levels. Cadmium induced oxidative stress and antioxidants, including free proline, soluble phenolics, ascorbate, and thiol compounds. These results suggest that orchestrated microstructural, transcriptomic, and physiological regulation may sustain cadmium hyperaccumulation in P. × canescens bark and provide new insights into engineering woody plants for phytoremediation. PMID:23530184

  20. Identification of microRNAs Involved in Regeneration of the Secondary Vascular System in Populus tomentosa Carr

    PubMed Central

    Tang, Fang; Wei, Hairong; Zhao, Shutang; Wang, Lijuan; Zheng, Huanquan; Lu, Mengzhu

    2016-01-01

    Wood formation is a complex developmental process primarily controlled by a regulatory transcription network. MicroRNAs (miRNAs) can modulate the expression of target genes involved in plant growth and development by inducing mRNA degradation and translational repression. In this study, we used a model of secondary vascular system regeneration established in Populus tomentosa to harvest differentiating xylem tissues over time for high-throughput sequencing of small RNAs. Analysis of the sequencing data identified 209 known and 187 novel miRNAs during this regeneration process. Degradome sequencing analysis was then performed, revealing 157 and 75 genes targeted by 21 known and 30 novel miRNA families, respectively. Gene ontology enrichment of these target genes revealed that the targets of 15 miRNAs were enriched in the auxin signaling pathway, cell differentiation, meristem development, and pattern specification process. The major biological events during regeneration of the secondary vascular system included the sequential stages of vascular cambium initiation, formation, and differentiation stages in sequence. This study provides the basis for further analysis of these miRNAs to gain greater insight into their regulatory roles in wood development in trees. PMID:27303419

  1. Populus × canescens grown on Cr-rich tannery waste: Comparison of leaf and root biochemical and proteomic responses.

    PubMed

    Zemleduch-Barylska, Agata; Lorenc-Plucińska, Gabriela

    2015-05-01

    Treatment of tannery effluents generates large amounts of sediments containing concentrated doses of metals (mainly chromium). Such waste is most commonly disposed of by landfilling, which is hazardous to the ecosystem due to Cr leaching. Afforestation of disposal sites with fast growing trees could stabilize contaminants in the soil and prevent them from spreading. The aim of this study was to examine the adaptation of Populus × canescens Sm. to tannery waste using biochemical and proteomic methods. We analyzed changes in the leaves and fine roots of poplar planted in soil or tannery waste. We found no obvious symptoms of metal stress, such as: elevated hydrogen peroxide levels or lipid peroxidation, but we observed activation of many elements of antioxidative system. Comparison of 2-DE protein profiles of leaves and fine roots from poplar grown on soil or tannery waste revealed increased expression of glycolytic enzymes and proteins involved in the synthesis of cell wall components, changes in the levels of proteins associated with photosynthesis, stress-related proteins, proteasome subunits and methionine biosynthesis enzymes. This experiment demonstrated that proteomic analysis has the potential to link the effects of Cr-rich tannery waste with biological consequences. PMID:25749730

  2. New insights into pioneer root xylem development: evidence obtained from Populus trichocarpa plants grown under field conditions

    PubMed Central

    Bagniewska-Zadworna, Agnieszka; Arasimowicz-Jelonek, Magdalena; Smoliński, Dariusz J.; Stelmasik, Agnieszka

    2014-01-01

    Background and Aims Effective programmed xylogenesis is critical to the structural framework of the plant root system and its central role in the acquisition and long-distance transport of water and nutrients. The process of xylem differentiation in pioneer roots under field conditions is poorly understood. In this study it is hypothesized that xylogenesis, an example of developmental programmed cell death (PCD), in the roots of woody plants demonstrates a clearly defined sequence of events resulting in cell death. A comprehensive analysis was therefore undertaken to identify the stages of xylogenesis in pioneer roots from procambial cells to fully functional vessels with lignified cell walls and secondary cell wall thickenings. Methods Xylem differentiation was monitored in the pioneer roots of Populus trichocarpa at the cytological level using rhizotrons under field conditions. Detection and localization of the signalling molecule nitric oxide (NO) and hydrogen peroxide (H2O2) was undertaken and a detailed examination of nuclear changes during xylogenesis was conducted. In addition, analyses of the expression of genes involved in secondary cell wall synthesis were performed in situ. Key Results The primary event in initially differentiating tracheary elements (TEs) was a burst of NO in thin-walled cells, followed by H2O2 synthesis and the appearance of TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick end labelling)-positive nuclei. The first changes in nuclear structure were observed in the early stages of xylogenesis of pioneer roots, prior to lignification; however, the nucleus was detectable under transmission electron microscopy in differentiating cells until the stage at which vacuole integrity was maintained, indicating that their degradation was slow and prolonged. The subsequent sequence of events involved secondary cell wall formation and autophagy. Potential gene markers from the cinnamyl alcohol dehydrogenase (CAD) gene family that were

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

    PubMed Central

    2013-01-01

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

  4. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 first maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2,...

  5. 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.

  6. Allelic variation within the S-adenosyl-L-homocysteine hydrolase gene family is associated with wood properties in Chinese white poplar (Populus tomentosa)

    PubMed Central

    2014-01-01

    Background S-adenosyl-l-homocysteine hydrolase (SAHH) is the only eukaryotic enzyme capable of S-adenosyl-l-homocysteine (SAH) catabolism for the maintenance of cellular transmethylation potential. Recently, biochemical and genetic studies in herbaceous species have obtained important discoveries in the function of SAHH, and an extensive characterization of SAHH family in even one tree species is essential, but currently lacking. Results Here, we first identified the SAHH family from Populus tomentosa using molecular cloning method. Phylogenetic analyses of 28 SAHH proteins from dicotyledons, monocotyledons, and lower plants revealed that the sequences formed two monophyletic groups: the PtrSAHHA with PtoSAHHA and PtrSAHHB with PtoSAHHB. Examination of tissue-specific expression profiles of the PtoSAHH family revealed similar expression patterns; high levels of expression in xylem were found. Nucleotide diversity and linkage disequilibrium (LD) in the PtoSAHH family, sampled from P. tomentosa natural distribution, revealed that PtoSAHH harbors high single-nucleotide polymorphism (SNP) diversity (π=0.01059±0.00122 and 0.00930±0.00079,respectively) and low LD (r2 > 0.1, within 800 bp and 2,200 bp, respectively). Using an LD-linkage analysis approach, two noncoding SNPs (PtoSAHHB_1065 and PtoSAHHA_2203) and the corresponding haplotypes were found to significantly associate with α-cellulose content, and a nonsynonymous SNP (PtoSAHHB_410) within the SAHH signature motifs showed significant association with fiber length, with an average of 3.14% of the phenotypic variance explained. Conclusions The present study demonstrates that PtoSAHHs were split off prior to the divergence of interspecies in Populus, and SAHHs may play a key role promoting transmethylation reactions in the secondary cell walls biosynthesis in trees. Hence, our findings provide insights into SAHH function and evolution in woody species and also offer a theoretical basis for marker

  7. Compositional characterization and imaging of "Wall-bound" acylesters of Populus trichocarpa Reveal Differential Accumulation of acyl Molecules in Normal and Reactive Woods

    SciTech Connect

    Guo, J.; Park, S; Yu, X; Liu, C

    2008-01-01

    Acylesterification is one of the common modifications of cell wall non-cellulosic polysaccharides and/or lignin primarily in monocot plants. We analyzed the cell-wall acylesters of black cottonwood (Populus trichocarpa Torr. & Gray) with liquid chromatography-mass spectrometry (LC-MS), Fourier transform-infrared (FT-IR) microspectroscopy, and synchrotron infrared (IR) imaging facility. The results revealed that the cell wall of dicotyledonous poplar, as the walls of many monocot grasses, contains a considerable amount of acylesters, primarily acetyl and p-hydroxycinnamoyl molecules. The 'wall-bound' acetate and phenolics display a distinct tissue specific-, bending stress responsible- and developmental-accumulation pattern. The 'wall-bound' p-coumarate predominantly accumulated in young leaves and decreased in mature leaves, whereas acetate and ferulate mostly amassed in the cell wall of stems. Along the development of stem, the level of the 'wall-bound' ferulate gradually increased, while the basal level of p-coumarate further decreased. Induction of tension wood decreased the accumulation of the 'wall-bound' phenolics while the level of acetate remained constant. Synchrotron IR-mediated chemical compositional imaging revealed a close spatial distribution of acylesters with cell wall polysaccharides in poplar stem. These results indicate that different 'wall-bound' acylesters play distinct roles in poplar cell wall structural construction and/or metabolism of cell wall matrix components.

  8. 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

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

    PubMed

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

    2014-11-01

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

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

    PubMed

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

    2010-03-01

    Salicylate-containing phenolic glycosides (PGs) are abundant and often play a dominant role in plant-herbivore interactions of Populus and Salix species (family Salicaceae), but the biosynthetic pathway to PGs remains unclear. Cinnamic acid (CA) is thought to be a precursor of the salicyl moiety of PGs. However, the origin of the 6-hydroxy-2-cyclohexen-on-oyl (HCH) moiety found in certain PGs, such as salicortin, is not known. HCH is of interest because it confers toxicity and antifeedant properties against herbivores. We incubated Populus nigra leaf tissue with stable isotope-labeled CA, benzoates, and salicylates, and measured isotopic incorporation levels into both salicin, the simplest PG, and salicortin. Labeling of salicortin from [13C6]-CA provided the first evidence that HCH, like the salicyl moiety, is a phenylpropanoid derivative. Benzoic acid and benzaldehyde also labeled both salicyl and HCH, while benzyl alcohol labeled only the salicyl moiety in salicortin. Co-administration of unlabeled benzoates with [13C6]-CA confirmed their contribution to the biosynthesis of the salicyl but not the HCH moiety of salicortin. These data suggest that benzoate interconversions may modulate partitioning of phenylpropanoids to salicyl and HCH moieties, and hence toxicity of PGs. Surprisingly, labeled salicyl alcohol and salicylaldehyde were readily converted to salicin, but did not result in labeled salicortin. Co-administration of unlabeled salicylates with labeled CA suggested that salicyl alcohol and salicylaldehyde may have inhibited salicortin biosynthesis. A revised metabolic grid model of PG biosynthesis in Populus is proposed, providing a guide for functional genomic analysis of the PG biosynthetic pathway. PMID:20177744

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

    DOE PAGESBeta

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

    2016-02-04

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

  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. Characterization of the NADP-malic enzymes in the woody plant Populus trichocarpa.

    PubMed

    Yu, Qiguo; Liu, Jinwen; Wang, Zhifeng; Nai, Jiefei; Lü, Mengyan; Zhou, Xiying; Cheng, Yuxiang

    2013-02-01

    Plant NADP-malic enzyme (NADP-ME, EC 1.1.1.40) participates in a large number of metabolic pathways, but little is known about the NADP-ME family in woody plants or trees. Here, we characterized the tree Populus trichocarpa NADP-ME (PtNADP-ME) family and the properties of the family members. Five NADP-ME genes (PtNADP-ME1-PtNADP-ME5) were found in the genome of Populus. Semi-quantitative RT-PCR analysis show that the transcription levels of PtNADP-ME1 in lignified stems and roots are clearly higher than in other tissues, and PtNADP-ME2, PtNADP-ME3, PtNADP-ME4 and PtNADP-ME5 are broadly expressed in various tissues. PtNADP-ME gene expression was found to respond to salt and osmotic stresses, and NaCl salts upregulated the transcripts of putative plastidic ones (PtNADP-ME4 and PtNADP-ME5) significantly. Further, the NADP-ME activities of Populus seedlings increased at least two-fold under NaCl, mannitol and PEG treatments. Also, the expression of PtNADP-ME2 and PtNADP-ME3 increased during the course of leaf wounding. Each recombinant PtNADP-ME proteins were expressed and purified from Escherichia coli, respectively. Coomassie brilliant blue and NADP-ME activity staining on native polyacrylamide gels showed different oligomeric states of the recombinant PtNADP-MEs in vitro. Noticeably, the cytosolic PtNADP-ME2 aggregates as octamers and hexadecamers while the plastidic PtNADP-ME4 resembles hexamers and octamers. The four PtNADP-ME proteins except for PtNADP-ME1 have high activities on native polyacrylamide gels including different forms for PtNADP-ME2 (octamers and hexadecamers) or for PtNADP-ME4 (hexamers and octamers). High concentrations of NADP substrate decreased the activities of all PtNADP-MEs slightly, while the malate had no effect on them. The kinetic parameters (V (max), K (m), K (cat), and K (cat)/K (m)) of each isoforms were summarized. Our data show the different effects of metabolites (influx into tricarboxylic acid cycle or Calvin cycle) on the

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

    DOE PAGESBeta

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

    2016-01-01

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

  15. Populus euphratica APYRASE2 Enhances Cold Tolerance by Modulating Vesicular Trafficking and Extracellular ATP in Arabidopsis Plants1[OPEN

    PubMed Central

    Deng, Shurong; Sun, Jian; Zhao, Rui; Ding, Mingquan; Zhang, Yinan; Sun, Yuanling; Wang, Wei; Tan, Yeqing; Liu, Dandan; Ma, Xujun; Hou, Peichen; Wang, Meijuan; Lu, Cunfu; Shen, Xin; Chen, Shaoliang

    2015-01-01

    Apyrase and extracellular ATP play crucial roles in mediating plant growth and defense responses. In the cold-tolerant poplar, Populus euphratica, low temperatures up-regulate APYRASE2 (PeAPY2) expression in callus cells. We investigated the biochemical characteristics of PeAPY2 and its role in cold tolerance. We found that PeAPY2 predominantly localized to the plasma membrane, but punctate signals also appeared in the endoplasmic reticulum and Golgi apparatus. PeAPY2 exhibited broad substrate specificity, but it most efficiently hydrolyzed purine nucleotides, particularly ATP. PeAPY2 preferred Mg2+ as a cofactor, and it was insensitive to various, specific ATPase inhibitors. When PeAPY2 was ectopically expressed in Arabidopsis (Arabidopsis thaliana), cold tolerance was enhanced, based on root growth measurements and survival rates. Moreover, under cold stress, PeAPY2-transgenic plants maintained plasma membrane integrity and showed reduced cold-elicited electrolyte leakage compared with wild-type plants. These responses probably resulted from efficient plasma membrane repair via vesicular trafficking. Indeed, transgenic plants showed accelerated endocytosis and exocytosis during cold stress and recovery. We found that low doses of extracellular ATP accelerated vesicular trafficking, but high extracellular ATP inhibited trafficking and reduced cell viability. Cold stress caused significant increases in root medium extracellular ATP. However, under these conditions, PeAPY2-transgenic lines showed greater control of extracellular ATP levels than wild-type plants. We conclude that Arabidopsis plants that overexpressed PeAPY2 could increase membrane repair by accelerating vesicular trafficking and hydrolyzing extracellular ATP to avoid excessive, cold-elicited ATP accumulation in the root medium and, thus, reduced ATP-induced inhibition of vesicular trafficking. PMID:26224801

  16. Populus euphratica APYRASE2 Enhances Cold Tolerance by Modulating Vesicular Trafficking and Extracellular ATP in Arabidopsis Plants.

    PubMed

    Deng, Shurong; Sun, Jian; Zhao, Rui; Ding, Mingquan; Zhang, Yinan; Sun, Yuanling; Wang, Wei; Tan, Yeqing; Liu, Dandan; Ma, Xujun; Hou, Peichen; Wang, Meijuan; Lu, Cunfu; Shen, Xin; Chen, Shaoliang

    2015-09-01

    Apyrase and extracellular ATP play crucial roles in mediating plant growth and defense responses. In the cold-tolerant poplar, Populus euphratica, low temperatures up-regulate APYRASE2 (PeAPY2) expression in callus cells. We investigated the biochemical characteristics of PeAPY2 and its role in cold tolerance. We found that PeAPY2 predominantly localized to the plasma membrane, but punctate signals also appeared in the endoplasmic reticulum and Golgi apparatus. PeAPY2 exhibited broad substrate specificity, but it most efficiently hydrolyzed purine nucleotides, particularly ATP. PeAPY2 preferred Mg(2+) as a cofactor, and it was insensitive to various, specific ATPase inhibitors. When PeAPY2 was ectopically expressed in Arabidopsis (Arabidopsis thaliana), cold tolerance was enhanced, based on root growth measurements and survival rates. Moreover, under cold stress, PeAPY2-transgenic plants maintained plasma membrane integrity and showed reduced cold-elicited electrolyte leakage compared with wild-type plants. These responses probably resulted from efficient plasma membrane repair via vesicular trafficking. Indeed, transgenic plants showed accelerated endocytosis and exocytosis during cold stress and recovery. We found that low doses of extracellular ATP accelerated vesicular trafficking, but high extracellular ATP inhibited trafficking and reduced cell viability. Cold stress caused significant increases in root medium extracellular ATP. However, under these conditions, PeAPY2-transgenic lines showed greater control of extracellular ATP levels than wild-type plants. We conclude that Arabidopsis plants that overexpressed PeAPY2 could increase membrane repair by accelerating vesicular trafficking and hydrolyzing extracellular ATP to avoid excessive, cold-elicited ATP accumulation in the root medium and, thus, reduced ATP-induced inhibition of vesicular trafficking. PMID:26224801

  17. Prevalence of LuxR- and LuxI-type quorum sensing circuits in members of the Populus deltoides microbiome

    SciTech Connect

    Schaefer, Amy L; Lappala, Colin; Morlen, Ryan; Pelletier, Dale A; Lu, Tse-Yuan; Lankford, Patricia K; Harwood, Caroline S; Greenberg, E. Peter

    2013-01-01

    We are interested in the root microbiome of the fast-growing Eastern cottonwood tree, Populus 25 deltoides. There is a large bank of bacterial isolates from P. deltoides and there are 44 draft 26 genomes of bacterial endophyte and rhizosphere isolates. As a first step in efforts to understand 27 the roles of bacterial communication and plant-bacterial signaling in P. deltoides we focused on 28 the prevalence of acyl-homoserine lactone (AHL) quorum sensing signal production and 29 reception in members of the P. deltoides microbiome. We screened 129 bacterial isolates for 30 AHL production using a broad-spectrum bioassay that responds to many but not all AHLs, and 31 we queried the available genome sequences of microbiome isolates for homologs of AHL 32 synthase and receptor genes. AHL signal production was detected in 40% of 129 strains tested. 33 Positive isolates included -, - and -Proteobacteria. Members of the luxI family of AHL 34 synthases were identified in 18 of 39 Proteobacteria genomes including genomes of some 35 isolates that tested negative in the bioassay. Members of the luxR family of transcription factors, 36 that include AHL-responsive factors, were more abundant than luxI homologs. There were 72 in 37 the 39 Proteobacteria genomes. Some of the luxR homologs appear to be members of a 38 subfamily of LuxRs that respond to as yet unknown plant signals rather than bacterial AHLs. 39 Apparently, there is a substantial capacity for AHL cell-to-cell communication in Proteobacteria 40 of the P. deltoides microbiota and there are also Proteobacteria with LuxR homologs of the type 41 hypothesized to respond to plant signals or cues.

  18. Monolignol Pathway 4-Coumaric Acid:Coenzyme A Ligases in Populus. trichocarpa: Novel Specificity, Metabolic Regulation, and Simulation of Coenzyme A Ligation Fluxes1[W

    PubMed Central

    Chen, Hsi-Chuan; Song, Jina; Williams, Cranos M.; Shuford, Christopher M.; Liu, Jie; Wang, Jack P.; Li, Quanzi; Shi, Rui; Gokce, Emine; Ducoste, Joel; Muddiman, David C.; Sederoff, Ronald R.; Chiang, Vincent L.

    2013-01-01

    4-Coumaric acid:coenzyme A ligase (4CL) is involved in monolignol biosynthesis for lignification in plant cell walls. It ligates coenzyme A (CoA) with hydroxycinnamic acids, such as 4-coumaric and caffeic acids, into hydroxycinnamoyl-CoA thioesters. The ligation ensures the activated state of the acid for reduction into monolignols. In Populus spp., it has long been thought that one monolignol-specific 4CL is involved. Here, we present evidence of two monolignol 4CLs, Ptr4CL3 and Ptr4CL5, in Populus trichocarpa. Ptr4CL3 is the ortholog of the monolignol 4CL reported for many other species. Ptr4CL5 is novel. The two Ptr4CLs exhibited distinct Michaelis-Menten kinetic properties. Inhibition kinetics demonstrated that hydroxycinnamic acid substrates are also inhibitors of 4CL and suggested that Ptr4CL5 is an allosteric enzyme. Experimentally validated flux simulation, incorporating reaction/inhibition kinetics, suggested two CoA ligation paths in vivo: one through 4-coumaric acid and the other through caffeic acid. We previously showed that a membrane protein complex mediated the 3-hydroxylation of 4-coumaric acid to caffeic acid. The demonstration here of two ligation paths requiring these acids supports this 3-hydroxylation function. Ptr4CL3 regulates both CoA ligation paths with similar efficiencies, whereas Ptr4CL5 regulates primarily the caffeic acid path. Both paths can be inhibited by caffeic acid. The Ptr4CL5-catalyzed caffeic acid metabolism, therefore, may also act to mitigate the inhibition by caffeic acid to maintain a proper ligation flux. A high level of caffeic acid was detected in stem-differentiating xylem of P. trichocarpa. Our results suggest that Ptr4CL5 and caffeic acid coordinately modulate the CoA ligation flux for monolignol biosynthesis. PMID:23344904

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

    PubMed Central

    Brosché, Mikael; Vinocur, Basia; Alatalo, Edward R; Lamminmäki, Airi; Teichmann, Thomas; Ottow, Eric A; Djilianov, Dimitar; Afif, Dany; Bogeat-Triboulot, Marie-Béatrice; Altman, Arie; Polle, Andrea; Dreyer, Erwin; Rudd, Stephen; Paulin, Lars; Auvinen, Petri; Kangasjärvi, Jaakko

    2005-01-01

    Background Plants growing in their natural habitat represent a valuable resource for elucidating mechanisms of acclimation to environmental constraints. Populus euphratica is a salt-tolerant tree species growing in saline semi-arid areas. To identify genes involved in abiotic stress responses under natural conditions we constructed several normalized and subtracted cDNA libraries from control, stress-exposed and desert-grown P. euphratica trees. In addition, we identified several metabolites in desert-grown P. euphratica trees. Results About 14,000 expressed sequence tag (EST) sequences were obtained with a good representation of genes putatively involved in resistance and tolerance to salt and other abiotic stresses. A P. euphratica DNA microarray with a uni-gene set of ESTs representing approximately 6,340 different genes was constructed. The microarray was used to study gene expression in adult P. euphratica trees growing in the desert canyon of Ein Avdat in Israel. In parallel, 22 selected metabolites were profiled in the same trees. Conclusion Of the obtained ESTs, 98% were found in the sequenced P. trichocarpa genome and 74% in other Populus EST collections. This implies that the P. euphratica genome does not contain different genes per se, but that regulation of gene expression might be different and that P. euphratica expresses a different set of genes that contribute to adaptation to saline growth conditions. Also, all of the five measured amino acids show increased levels in trees growing in the more saline soil. PMID:16356264

  20. 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.

  1. Effect of rotation, site, and clone on the chemical composition of Populus hybrids

    SciTech Connect

    Blanckenhorn, P.R.; Bowersox, T.W.; Kuklewski, K.M.; Stimely, S.L.

    1985-01-01

    Chemical content values were determined for three Populus clones grown on two dissimilar sites by component (wood, bark, and wood/bark specimens), tissue age (1-, 2- and 4-year-old), and rotation. The chemical content values obtained included extractives, holocellulose, ..alpha..-cellulose, and lignin. In general, analysis of the data for the wood, bark, and wood/bark specimens indicated that: 1) wood was high in holocellulose and ..alpha..-cellulose content compared to bark, 2) bark was high in lignin and extractive content values compared to wood, and 3) wood/bark chemical content values were between the values for the wood and bark specimens. The chemical content data were analyzed to identify: 1) significant differences between rotations by component (wood, bark and wood/bark) for a given age, clone, and site, and 2) significant differences between sites for four-year-old wood, bark and wood/bark specimens of a given rotation, and clone. Statistical analyses indicated that significant differences existed among clones, sites, ages, and rotations. Within the wood, bark and wood/bark specimens, tissue age, rotation, and site influenced the chemical content values more than the parentage. Potential chemical yields derived from the three Populus hybrid clones investigated will depend on component, age, rotation, and site with limited parentage effects.

  2. Comparison of selected fuel and chemical content values for seven Populus hybrid clones

    SciTech Connect

    Blankenhorn, P.R.; Bowersox, T.W.; Kuklewski, K.M.; Stimely, G.L.; Murphey, W.K.

    1985-04-01

    Fuel and chemical content values were determined for seven Populus clones by component (wood, bark, and wood/bark specimens) and tissue age (1 to 8 years old). The fuel and chemical content values obtained included: gross heat of combustion, extractives, holocellulose, alpha-cellulose, lignin and ash. In general, analysis of the data for the wood, bark, and wood/bark specimens indicated that: 1) wood was higher in holocellulose and alpha-cellulose content than bark; 2) bark was higher in gross heat of combustion, lignin, extractive, and ash content values than wood; and 3) combined wood/bark fuel and chemical content values were usually between the individual values for the wood and bark. Statistical analyses indicated that significant differences existed within and among clones. Within the wood, bark, and wood/bark specimens, tissue age influenced the chemical content values more than the parentage. Potential chemical yields derived from the seven Populus hybrid clones investigated will depend on component and age with limited parentage effects. 15 references.

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

    SciTech Connect

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

    1990-05-01

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

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

    DOE PAGESBeta

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

    2015-07-25

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

  5. 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.

  6. 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).

  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. How to Regenerate and Protect Desert Riparian Populus euphratica Forest in Arid Areas

    NASA Astrophysics Data System (ADS)

    Ling, Hongbo; Zhang, Pei; Xu, Hailiang; Zhao, Xinfeng

    2015-10-01

    We found that the most suitable flooding disturbance model for regenerating Populus euphratica forest was two to three times per year with a duration of 15-20 days and an intensity of 25-30 m3/s. The flooding should take place during the seed emergence to young tree growth stages, and should be based on flooding experiments and data from vegetation quadrats and ecological water conveyance. Furthermore, we found that tree-ring width index for P. euphratica declined as the groundwater depth increased, and ascertained that the minimum groundwater depths for young trees, near-mature trees, mature trees and over-mature trees were 4.0 m, 5.0-5.4 m, 6.9 m and 7.8 m, respectively. These were derived from a quantitative relationship model between groundwater depth and tree-ring width index. The range for ecological water conveyance volume was 311-320 million m3 in the lower reaches of the Tarim River. This study not only provides a technical basis for sustainable ecological water conveyance in the Tarim River Basin, but also offers a theoretical guide and scientific information that could be used in similar areas to regenerate and protect Populus euphratica around the world.

  9. How to Regenerate and Protect Desert Riparian Populus euphratica Forest in Arid Areas.

    PubMed

    Ling, Hongbo; Zhang, Pei; Xu, Hailiang; Zhao, Xinfeng

    2015-01-01

    We found that the most suitable flooding disturbance model for regenerating Populus euphratica forest was two to three times per year with a duration of 15-20 days and an intensity of 25-30 m(3)/s. The flooding should take place during the seed emergence to young tree growth stages, and should be based on flooding experiments and data from vegetation quadrats and ecological water conveyance. Furthermore, we found that tree-ring width index for P. euphratica declined as the groundwater depth increased, and ascertained that the minimum groundwater depths for young trees, near-mature trees, mature trees and over-mature trees were 4.0 m, 5.0-5.4 m, 6.9 m and 7.8 m, respectively. These were derived from a quantitative relationship model between groundwater depth and tree-ring width index. The range for ecological water conveyance volume was 311-320 million m(3) in the lower reaches of the Tarim River. This study not only provides a technical basis for sustainable ecological water conveyance in the Tarim River Basin, but also offers a theoretical guide and scientific information that could be used in similar areas to regenerate and protect Populus euphratica around the world. PMID:26481290

  10. Uptake, translocation, and transformation of quantum dots with cationic versus anionic coatings by Populus deltoides × nigra cuttings.

    PubMed

    Wang, Jing; Yang, Yu; Zhu, Huiguang; Braam, Janet; Schnoor, Jerald L; Alvarez, Pedro J J

    2014-06-17

    Manipulation of the organic coatings of nanoparticles such as quantum dots (QDs) to enhance specific applications may also affect their interaction and uptake by different organisms. In this study, poplar trees (Populus deltoides × nigra) were exposed hydroponically to 50-nM CdSe/CdZnS QDs coated with cationic polyethylenimine (PEI) (35.3 ± 6.6 nm) or poly(ethylene glycol) of anionic poly(acrylic acid) (PAA-EG) (19.5 ± 7.2 nm) to discern how coating charge affects nanoparticle uptake, translocation, and transformation within woody plants. Uptake of cationic PEI-QDs was 10 times faster despite their larger hydrodynamic size and higher extent of aggregation (17 times larger than PAA-EG-QDs after 11-day incubation in the hydroponic medium), possibly due to electrostatic attraction to the negatively charged root cell wall. QDs cores aggregated upon root uptake, and their translocation to poplar shoots (negligible for PAA-EG-QDs and 0.7 ng Cd/mg stem for PEI-QDs) was likely limited by the endodermis. After 2-day exposure, PEI and PAA-EG coatings were likely degraded from the internalized QDs inside the plant, leading to the aggregation of the metallic cores and a "red-shift" of fluorescence. The fluorescence of PEI-QD aggregates was stable inside the roots through the 11-day exposure period. In contrast, the PAA-EG-QD aggregates lost fluorescence inside the plant after 11 days probably due to destabilization of the coating, even though these QDs were stable in the hydroponic solution. Overall, these results highlight the importance of coating properties in the rate and extent to which nanoparticles are assimilated by plants and potentially introduced into food webs. PMID:24870363

  11. Isolation and Functional Characterization of a Novel Gene Encoding a Dehydration Responsive Element Binding Transcription Factor from Populus euphratica.

    PubMed

    Wei, Li; Ma, Jiangtao; Wang, Suomin; Wu, Yanmin

    2016-01-01

    Dehydration responsive element binding (DREB) transcription factors (TFs) play a key role in regulating abiotic stress related genes. A new gene (PeDREB2b) encoding an unidentified DRE-binding protein was isolated from 20% PEG6000 treated Populus euphratica Oliv. seedlings by RT-PCR and RACE. Full length of PeDREB2b cDNA was 1110 bp, and an ORF of 870 bp, which encoded 289-amino-acids polypeptide, were included. The deduced amino acid sequence analysis revealed that this protein was a putative AP2/EREBP transcription factor with a conserved AP2/EREBP domain of 64 amino acids and a potential nuclear localization signal (NLS). Based on phylogenetic characterization, PeDREB2b was classified as a member of A-5 group belonged to the DREB family. The PeDREB2b gene is induced by salinization, low temperature, drought and phytohormones GA3, NAA and 6BA, but not by ABA treatment. The fact that the product of PeDREB2b as a DREB transcription factor was verified in our further experiment: the nuclear localization of the gene when it was expressed transiently as a GFP fusion in onion epidermal cells. In addition, PeDREB2b was capable of activating reporter gene expression. To study the salt and drought stress responses for PeDREB2b transgenic Arabidopsis thaliana in detail, integrated physiological, biochemical and genetic approach methods were used. Results indicated that the PeDREB2b gene was over-expressed under stress-inducible rd29A promotor in transgenic plants alleviates the adverse effects of environmental stresses. PMID:27001404

  12. Simulation of Populus euphratica root uptake of groundwater in an arid woodland of the Ejina basin, China

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Ejina Basin is an extremely arid subwatershed in Northwest China. The predominant natural tree species in the area, Populus euphratica (P. euphratica), depends on groundwater for sustenance. In recent decades, groundwater overdraft and increased water diversions from the Heihe River caused wat...

  13. 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

  14. 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

  15. 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. PMID:26236324

  16. PtrWRKY19, a novel WRKY transcription factor, contributes to the regulation of pith secondary wall formation in Populus trichocarpa

    PubMed Central

    Yang, Li; Zhao, Xin; Yang, Fan; Fan, Di; Jiang, Yuanzhong; Luo, Keming

    2016-01-01

    WRKY proteins are one of the largest transcription factor families in higher plants and play diverse roles in various biological processes. Previous studies have shown that some WRKY members act as negative regulators of secondary cell wall formation in pith parenchyma cells. However, the regulatory mechanism of pith secondary wall formation in tree species remains largely unknown. In this study, PtrWRKY19 encoding a homolog of Arabidopsis WRKY12 was isolated from Populus trichocarpa. PtrWRKY19 was expressed in all tissues tested, with highest expression in stems, especially in pith. PtrWRKY19 was located in the nucleus and functioned as a transcriptional repressor. Ectopic expression of PtrWRKY19 in an atwrky12 mutant successfully rescued the phenotype in pith cell walls caused by the defect of AtWRKY12, suggesting that PtrWRKY19 had conserved functions for homologous AtWRKY12. Overexpression of PtrWRKY19 in poplar plants led to a significant increase in the number of pith parenchyma cells. qRT-PCR analysis showed that lignin biosynthesis-related genes were repressed in transgenic plants. In transcient reporter assays, PtrWRKY19 was identified to repress transcription from the PtoC4H2 promoter containing the conserved W-box elements. These results indicated that PtrWRKY19 may function as a negative regulator of pith secondary wall formation in poplar. PMID:26819184

  17. The CBF1-dependent low temperature signalling pathway, regulon and increase in freeze tolerance are conserved in Populus spp.

    PubMed

    Benedict, Catherine; Skinner, Jeffrey S; Meng, Rengong; Chang, Yongjian; Bhalerao, Rishikesh; Huner, Norman P A; Finn, Chad E; Chen, Tony H H; Hurry, Vaughan

    2006-07-01

    The meristematic tissues of temperate woody perennials must acclimate to freezing temperatures to survive the winter and resume growth the following year. To determine whether the C-repeat binding factor (CBF) family of transcription factors contributing to this process in annual herbaceous species also functions in woody perennials, we investigated the changes in phenotype and transcript profile of transgenic Populus constitutively expressing CBF1 from Arabidopsis (AtCBF1). Ectopic expression of AtCBF1 was sufficient to significantly increase the freezing tolerance of non-acclimated leaves and stems relative to wild-type plants. cDNA microarray experiments identified genes up-regulated by ectopic AtCBF1 expression in Populus, demonstrated a strong conservation of the CBF regulon between Populus and Arabidopsis and identified differences between leaf and stem regulons. We studied the induction kinetics and tissue specificity of four CBF paralogues identified from the Populus balsamifera subsp. trichocarpa genome sequence (PtCBFs). All four PtCBFs are cold-inducible in leaves, but only PtCBF1 and PtCBF3 show significant induction in stems. Our results suggest that the central role played by the CBF family of transcriptional activators in cold acclimation of Arabidopsis has been maintained in Populus. However, the differential expression of the PtCBFs and differing clusters of CBF-responsive genes in annual (leaf) and perennial (stem) tissues suggest that the perennial-driven evolution of winter dormancy may have given rise to specific roles for these 'master-switches' in the different annual and perennial tissues of woody species. PMID:17080948

  18. 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.

  19. 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.

  20. Genome-wide identification and characterization of novel lncRNAs in Populus under nitrogen deficiency.

    PubMed

    Chen, Min; Wang, Chenlu; Bao, Hai; Chen, Hui; Wang, Yanwei

    2016-08-01

    Long non-coding RNAs (lncRNAs) have been identified as important regulatory factors of gene expression in eukaryotic species, such as Homo sapiens, Arabidopsis thaliana, and Oryza sativa. However, the systematic identification of potential lncRNAs in trees is comparatively rare. In particular, the characteristics, expression, and regulatory roles of lncRNAs in trees under nutrient stress remain largely unknown. A genome-wide strategy was used in this investigation to identify and characterize novel and low-nitrogen (N)-responsive lncRNAs in Populus tomentosa; 388 unique lncRNA candidates belonging to 380 gene loci were detected and only seven lncRNAs were found to belong to seven conserved non-coding RNA families indicating the majority of P. tomentosa lncRNAs are species-specific. In total, 126 lncRNAs were significantly altered under low-N stress; 8 were repressed, and 118 were induced. Furthermore, 9 and 5 lncRNAs were detected as precursors of 11 known and 14 novel Populus miRNAs, respectively, whereas 4 lncRNAs were targeted by 29 miRNAs belonging to 5 families, including 22 conserved and 7 non-conserved miRNAs. In addition, 15 antisense lncRNAs were identified to be generated from opposite strands of 14 corresponding protein-coding genes. In total, 111 protein-coding genes with regions complementary to 38 lncRNAs were also predicted with some lncRNAs corresponding to multiple genes and vice versa, and their functions were annotated, which further demonstrated the complex regulatory relationship between lncRNAs and protein-coding genes in plants. Moreover, an interaction network among lncRNAs, miRNAs, and mRNAs was investigated. These findings enrich our understanding of lncRNAs in Populus, expand the methods of miRNA identification. Our results present the first global characterization of lncRNAs and their potential target genes in response to nitrogen stress in trees, which provides more information on low-nutrition adaptation mechanisms in woody plants

  1. 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.

  2. 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. PMID:26431530

  3. Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations.

    PubMed

    Evans, Luke M; Slavov, Gancho T; Rodgers-Melnick, Eli; Martin, Joel; Ranjan, Priya; Muchero, Wellington; Brunner, Amy M; Schackwitz, Wendy; Gunter, Lee; Chen, Jin-Gui; Tuskan, Gerald A; DiFazio, Stephen P

    2014-10-01

    Forest trees are dominant components of terrestrial ecosystems that have global ecological and economic importance. Despite distributions that span wide environmental gradients, many tree populations are locally adapted, and mechanisms underlying this adaptation are poorly understood. Here we use a combination of whole-genome selection scans and association analyses of 544 Populus trichocarpa trees to reveal genomic bases of adaptive variation across a wide latitudinal range. Three hundred ninety-seven genomic regions showed evidence of recent positive and/or divergent selection and enrichment for associations with adaptive traits that also displayed patterns consistent with natural selection. These regions also provide unexpected insights into the evolutionary dynamics of duplicated genes and their roles in adaptive trait variation. PMID:25151358

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

    PubMed Central

    Davies, Chantel; Ellis, Christopher J.; Iason, Glenn R.; Ennos, Richard A.

    2014-01-01

    Community genetics hypothesizes that within a foundation species, the genotype of an individual significantly influences the assemblage of dependent organisms. To assess whether these intra-specific genetic effects are ecologically important, it is required to compare their impact on dependent organisms with that attributable to environmental variation experienced over relevant spatial scales. We assessed bark epiphytes on 27 aspen (Populus tremula L.) genotypes grown in a randomized experimental array at two contrasting sites spanning the environmental conditions from which the aspen genotypes were collected. We found that variation in aspen genotype significantly influenced bark epiphyte community composition, and to the same degree as environmental variation between the test sites. We conclude that maintaining genotypic diversity of foundation species may be crucial for conservation of associated biodiversity. PMID:24789141

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

    DOE PAGESBeta

    Hacquard, Stéphane; Schadt, Christopher W.

    2014-11-24

    Interactions between trees and microorganisms are extremely complex and the multispecies networks resulting from these associations have consequences for plant growth and productivity. However, a more holistic view is needed to better understand trees as ecosystems and superorganisms, where many interacting species contribute to the overall stability of the system. While much progress has been made on microbial communities associated with individual tree niches and the molecular interactions between model symbiotic partners, there is still a lack of knowledge of the multi-component interactions necessary for holistic ecosystem-level understanding. Finally, we review recent studies in Populus to emphasize the importance ofmore » such holistic efforts across the leaf, stem and rooting zones, and discuss prospects for future research in these important ecosystems.« less

  6. 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.

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

    PubMed Central

    Chen, Jinhuan; Zhang, Dongzhi; Zhang, Chong; Xia, Xinli; Yin, Weilun; Tian, Qianqian

    2015-01-01

    A PP2C homolog gene was cloned from the drought-treated cDNA library of Populus euphratica. Multiple sequence alignment analysis suggested that the gene is a potential ortholog of HAB1. The expression of this HAB1 ortholog (PeHAB1) was markedly induced by drought and moderately induced by ABA. To characterize its function in ABA signaling, we generated transgenic Arabidopsis thaliana plants overexpressing this gene. Transgenic lines exhibited reduced responses to exogenous ABA and reduced tolerance to drought compared to wide-type lines. Yeast two-hybrid analyses indicated that PeHAB1 could interact with the ABA receptor PYL4 in an ABA-independent manner. Taken together; these results indicated that PeHAB1 is a new negative regulator of ABA responses in poplar. PMID:26431530

  8. Development of polymorphic microsatellite markers based on expressed sequence tags in Populus cathayana (Salicaceae).

    PubMed

    Tian, Z Z; Zhang, F Q; Cai, Z Y; Chen, S L

    2016-01-01

    Populus cathayana occupies a large area within the northern, central, and southwestern regions of China, and is considered to be an important reforestation species in western China. In order to investigate the population genetic structure of this species, 10 polymorphic microsatellite loci were identified based on expressed sequence tags from de novo sequencing on the Illumina HiSeq 2000 platform. All microsatellite primers were tested on 48 P. cathayana individuals from four locations on the Qinghai-Tibet Plateau. The observed heterozygosity ranged from 0.000 to 1.000, and the null-allele frequency ranged from 0.000 to 0.904. These microsatellite markers may be a useful tool in genetic studies on P. cathayana and closely related species. PMID:27525845

  9. Proteomic analysis and candidate allergenic proteins in Populus deltoides CL. "2KEN8" mature pollen.

    PubMed

    Zhang, Jin; Wu, Li-Shuan; Fan, Wei; Zhang, Xiao-Ling; Jia, Hui-Xia; Li, Yu; Yin, Ya-Fang; Hu, Jian-Jun; Lu, Meng-Zhu

    2015-01-01

    Proteomic analysis was used to generate a map of Populus deltoides CL. "2KEN8" mature pollen proteins. By applying 2-D electrophoresis, we resolved 403 protein spots from mature pollen. Using the matrix-assisted laser desorption/ionization time time-of-flight/time-of-flight tandem mass spectrometry method, we identified 178 distinct proteins from 218 protein spots expressed in mature pollen. Moreover, out of these, 28 proteins were identified as putative allergens. The expression patterns of these putative allergen genes indicate that several of these genes are highly expressed in pollen. In addition, the members of profilin allergen family were analyzed and their expression patterns were compared with their homologous genes in Arabidopsis and rice. Knowledge of these identified allergens has the potential to improve specific diagnosis and allergen immunotherapy treatment for patients with poplar pollen allergy. PMID:26284084

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

    PubMed

    Hacquard, Stéphane; Schadt, Christopher W

    2015-03-01

    Interactions between trees and microorganisms are tremendously complex and the multispecies networks resulting from these associations have consequences for plant growth and productivity. However, a more holistic view is needed to better understand trees as ecosystems and superorganisms, where many interacting species contribute to the overall stability of the system. While much progress has been made on microbial communities associated with individual tree niches and the molecular interactions between model symbiotic partners, there is still a lack of knowledge of the multi-component interactions necessary for holistic ecosystem-level understanding. We review recent studies in Populus to emphasize the importance of such holistic efforts across the leaf, stem and rooting zones, and discuss prospects for future research in these important ecosystems. PMID:25422041

  11. 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. PMID:17267367

  12. 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.

  13. Developmental and Environmental Regulation of Aquaporin Gene Expression across Populus Species: Divergence or Redundancy?

    PubMed Central

    Cohen, David; Bogeat-Triboulot, Marie-Béatrice; Vialet-Chabrand, Silvère; Merret, Rémy; Courty, Pierre-Emmanuel; Moretti, Sébastien; Bizet, François; Guilliot, Agnès; Hummel, Irène

    2013-01-01

    Aquaporins (AQPs) are membrane channels belonging to the major intrinsic proteins family and are known for their ability to facilitate water movement. While in Populus trichocarpa, AQP proteins form a large family encompassing fifty-five genes, most of the experimental work focused on a few genes or subfamilies. The current work was undertaken to develop a comprehensive picture of the whole AQP gene family in Populus species by delineating gene expression domain and distinguishing responsiveness to developmental and environmental cues. Since duplication events amplified the poplar AQP family, we addressed the question of expression redundancy between gene duplicates. On these purposes, we carried a meta-analysis of all publicly available Affymetrix experiments. Our in-silico strategy controlled for previously identified biases in cross-species transcriptomics, a necessary step for any comparative transcriptomics based on multispecies design chips. Three poplar AQPs were not supported by any expression data, even in a large collection of situations (abiotic and biotic constraints, temporal oscillations and mutants). The expression of 11 AQPs was never or poorly regulated whatever the wideness of their expression domain and their expression level. Our work highlighted that PtTIP1;4 was the most responsive gene of the AQP family. A high functional divergence between gene duplicates was detected across species and in response to tested cues, except for the root-expressed PtTIP2;3/PtTIP2;4 pair exhibiting 80% convergent responses. Our meta-analysis assessed key features of aquaporin expression which had remained hidden in single experiments, such as expression wideness, response specificity and genotype and environment interactions. By consolidating expression profiles using independent experimental series, we showed that the large expansion of AQP family in poplar was accompanied with a strong divergence of gene expression, even if some cases of functional redundancy

  14. 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.

  15. 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.

  16. 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.

  17. Enhancing a Pathway-Genome Database (PGDB) to Capture Subcellular Localization of Metabolites and Enzymes: The Nucleotide-Sugar Biosynthetic Pathways of Populus trichocarpa

    SciTech Connect

    Nag, A.; Karpinets, T. V.; Chang, C. H.; Bar-Peled, M.

    2012-01-01

    Understanding how cellular metabolism works and is regulated requires that the underlying biochemical pathways be adequately represented and integrated with large metabolomic data sets to establish a robust network model. Genetically engineering energy crops to be less recalcitrant to saccharification requires detailed knowledge of plant polysaccharide structures and a thorough understanding of the metabolic pathways involved in forming and regulating cell-wall synthesis. Nucleotide-sugars are building blocks for synthesis of cell wall polysaccharides. The biosynthesis of nucleotide-sugars is catalyzed by a multitude of enzymes that reside in different subcellular organelles, and precise representation of these pathways requires accurate capture of this biological compartmentalization. The lack of simple localization cues in genomic sequence data and annotations however leads to missing compartmentalization information for eukaryotes in automatically generated databases, such as the Pathway-Genome Databases (PGDBs) of the SRI Pathway Tools software that drives much biochemical knowledge representation on the internet. In this report, we provide an informal mechanism using the existing Pathway Tools framework to integrate protein and metabolite sub-cellular localization data with the existing representation of the nucleotide-sugar metabolic pathways in a prototype PGDB for Populus trichocarpa. The enhanced pathway representations have been successfully used to map SNP abundance data to individual nucleotide-sugar biosynthetic genes in the PGDB. The manually curated pathway representations are more conducive to the construction of a computational platform that will allow the simulation of natural and engineered nucleotide-sugar precursor fluxes into specific recalcitrant polysaccharide(s).

  18. Subcellular Relocalization and Positive Selection Play Key Roles in the Retention of Duplicate Genes of Populus Class III Peroxidase Family[W][OPEN

    PubMed Central

    Ren, Lin-Ling; Liu, Yan-Jing; Liu, Hai-Jing; Qian, Ting-Ting; Qi, Li-Wang; Wang, Xiao-Ru; Zeng, Qing-Yin

    2014-01-01

    Gene duplication is the primary source of new genes and novel functions. Over the course of evolution, many duplicate genes lose their function and are eventually removed by deletion. However, some duplicates have persisted and evolved diverse functions. A particular challenge is to understand how this diversity arises and whether positive selection plays a role. In this study, we reconstructed the evolutionary history of the class III peroxidase (PRX) genes from the Populus trichocarpa genome. PRXs are plant-specific enzymes that play important roles in cell wall metabolism and in response to biotic and abiotic stresses. We found that two large tandem-arrayed clusters of PRXs evolved from an ancestral cell wall type PRX to vacuole type, followed by tandem duplications and subsequent functional specification. Substitution models identified seven positively selected sites in the vacuole PRXs. These positively selected sites showed significant effects on the biochemical functions of the enzymes. We also found that positive selection acts more frequently on residues adjacent to, rather than directly at, a critical active site of the enzyme, and on flexible regions rather than on rigid structural elements of the protein. Our study provides new insights into the adaptive molecular evolution of plant enzyme families. PMID:24934172

  19. Populus euphratica Displays Apoplastic Sodium Accumulation, Osmotic Adjustment by Decreases in Calcium and Soluble Carbohydrates, and Develops Leaf Succulence under Salt Stress1[W

    PubMed Central

    Ottow, Eric A.; Brinker, Monika; Teichmann, Thomas; Fritz, Eberhard; Kaiser, Werner; Brosché, Mikael; Kangasjärvi, Jaakko; Jiang, Xiangning; Polle, Andrea

    2005-01-01

    Populus euphratica Olivier is known to exist in saline and arid environments. In this study we investigated the physiological mechanisms enabling this species to cope with stress caused by salinity. Acclimation to increasing Na+ concentrations required adjustments of the osmotic pressure of leaves, which were achieved by accumulation of Na+ and compensatory decreases in calcium and soluble carbohydrates. The counterbalance of Na+/Ca2+ was also observed in mature leaves from field-grown P. euphratica trees exposed to an environmental gradient of increasing salinity. X-ray microanalysis showed that a primary strategy to protect the cytosol against sodium toxicity was apoplastic but not vacuolar salt accumulation. The ability to cope with salinity also included maintenance of cytosolic potassium concentrations and development of leaf succulence due to an increase in cell number and cell volume leading to sodium dilution. Decreases in apoplastic and vacuolar Ca2+ combined with suppression of calcineurin B-like protein transcripts suggest that Na+ adaptation required suppression of calcium-related signaling pathways. Significant increases in galactinol synthase and alternative oxidase after salt shock and salt adaptation point to shifts in carbohydrate metabolism and suppression of reactive oxygen species in mitochondria under salt stress. PMID:16299175

  20. RNA Sequencing of Populus x canadensis Roots Identifies Key Molecular Mechanisms Underlying Physiological Adaption to Excess Zinc

    PubMed Central

    Ariani, Andrea; Di Baccio, Daniela; Romeo, Stefania; Lombardi, Lara; Andreucci, Andrea; Lux, Alexander; Horner, David Stephen; Sebastiani, Luca

    2015-01-01

    Populus x canadensis clone I-214 exhibits a general indicator phenotype in response to excess Zn, and a higher metal uptake in roots than in shoots with a reduced translocation to aerial parts under hydroponic conditions. This physiological adaptation seems mainly regulated by roots, although the molecular mechanisms that underlie these processes are still poorly understood. Here, differential expression analysis using RNA-sequencing technology was used to identify the molecular mechanisms involved in the response to excess Zn in root. In order to maximize specificity of detection of differentially expressed (DE) genes, we consider the intersection of genes identified by three distinct statistical approaches (61 up- and 19 down-regulated) and validate them by RT-qPCR, yielding an agreement of 93% between the two experimental techniques. Gene Ontology (GO) terms related to oxidation-reduction processes, transport and cellular iron ion homeostasis were enriched among DE genes, highlighting the importance of metal homeostasis in adaptation to excess Zn by P. x canadensis clone I-214. We identified the up-regulation of two Populus metal transporters (ZIP2 and NRAMP1) probably involved in metal uptake, and the down-regulation of a NAS4 gene involved in metal translocation. We identified also four Fe-homeostasis transcription factors (two bHLH38 genes, FIT and BTS) that were differentially expressed, probably for reducing Zn-induced Fe-deficiency. In particular, we suggest that the down-regulation of FIT transcription factor could be a mechanism to cope with Zn-induced Fe-deficiency in Populus. These results provide insight into the molecular mechanisms involved in adaption to excess Zn in Populus spp., but could also constitute a starting point for the identification and characterization of molecular markers or biotechnological targets for possible improvement of phytoremediation performances of poplar trees. PMID:25671786

  1. 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.

  2. 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. PMID:20516486

  3. 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.

  4. 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

  5. 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.

  6. Transcriptome-Wide Identification of miRNA Targets under Nitrogen Deficiency in Populus tomentosa Using Degradome Sequencing

    PubMed Central

    Chen, Min; Bao, Hai; Wu, Qiuming; Wang, Yanwei

    2015-01-01

    miRNAs are endogenous non-coding small RNAs with important regulatory roles in stress responses. Nitrogen (N) is an indispensable macronutrient required for plant growth and development. Previous studies have identified a variety of known and novel miRNAs responsive to low N stress in plants, including Populus. However, miRNAs involved in the cleavage of target genes and the corresponding regulatory networks in response to N stress in Populus remain largely unknown. Consequently, degradome sequencing was employed for global detection and validation of N-responsive miRNAs and their targets. A total of 60 unique miRNAs (39 conserved, 13 non-conserved, and eight novel) were experimentally identified to target 64 mRNA transcripts and 21 precursors. Among them, we further verified the cleavage of 11 N-responsive miRNAs identified previously and provided empirical evidence for the cleavage mode of these miRNAs on their target mRNAs. Furthermore, five miRNA stars (miRNA*s) were shown to have cleavage function. The specificity and diversity of cleavage sites on the targets and miRNA precursors in P. tomentosa were further detected. Identification and annotation of miRNA-mediated cleavage of target genes in Populus can increase our understanding of miRNA-mediated molecular mechanisms of woody plants adapted to low N environments. PMID:26096002

  7. Leaf responsiveness of Populus tremula and Salix viminalis to soil contaminated with heavy metals and acidic rainwater.

    PubMed

    Hermle, Sandra; Vollenweider, Pierre; Günthardt-Goerg, Madeleine S; McQuattie, Carolyn J; Matyssek, Rainer

    2007-11-01

    Fast-growing trees such as Salix viminalis L. and Populus tremula L. are well suited to phytoremediate heavy metal contaminated soils. However, information on tree performance, particularly leaf function, under conditions of heavy metal contamination is scarce. We used yearly coppiced saplings of S. viminalis and P. tremula growing in model ecosytems to test four hypotheses: (1) heavy metal contamination impairs photosynthesis by injuring leaf structure; (2) the effects of heavy metal contamination are enhanced by acidified rainwater and low soil pH; (3) heavy metal contamination increases dark respiration and, thus, repair processes; and (4) heavy metal contamination is tolerated and remediated better by S. viminalis than by P. tremula. We investigated heavy metal accumulation, tissue injury and gas exchange in leaves of plants subjected to controlled soil contamination with heavy metal dust. Additional treatments included acidic and calcareous natural forest subsoils in combination with irrigation with rainwater at pH 5.5 or 3.5. In both provenances of P. tremula that were studied, but not in S. viminalis, heavy metal treatment reduced photosynthesis and transpiration by varying amounts, except in the hot and dry summer of 2003, but had no effect on dark respiration. At light saturation, net CO(2) uptake and water-use efficiency were reduced by heavy metal contamination, whereas the CO(2) concentration in the leaf intercellular air space was increased. Rainwater pH and subsoil pH only slightly modified the effects of the heavy metal treatment on P. tremula. Gas exchange responses of P. tremula to heavy metals were attributed to leaf structural and ultrastructural changes resulting from hypersensitive-response-like processes and accelerated mesophyll cell senescence and necroses in the lower epidermis, especially along the transport pathways of heavy metals in the leaf lamina. Overall, the effects of heavy metals on P. tremula corroborated Hypothesis 1, but

  8. 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

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

    PubMed

    Qin, Juan; Shangguan, Zhouping

    2006-06-01

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

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

    DOE PAGESBeta

    Ribeiro, Cintia L.; Silva, Cynthia M.; Drost, Derek R.; Novaes, Evandro; Novaes, Carolina R. D. B.; Dervinis, Christopher; Kirst, Matias

    2016-03-16

    In this study, adventitious roots (AR) develop from tissues other than the primary root, in a process physiologically regulated by phytohormones. Adventitious roots provide structural support and contribute to water and nutrient absorption, and are critical for commercial vegetative propagation of several crops. Here we quantified the number of AR, root architectural traits and root biomass in cuttings from a pseudo-backcross population of Populus deltoides and Populus trichocarpa. Quantitative trait loci (QTL) mapping and whole-transcriptome analysis of individuals with alternative QTL alleles for AR number were used to identify putative regulators of AR development. As a result, parental individuals andmore » progeny showed extensive segregation for AR developmental traits. Quantitative trait loci for number of AR mapped consistently in the same interval of linkage group (LG) II and LG XIV, explaining 7–10 % of the phenotypic variation. A time series transcriptome analysis identified 26,121 genes differentially expressed during AR development, particularly during the first 24 h after cuttings were harvested. Of those, 1929 genes were differentially regulated between individuals carrying alternative alleles for the two QTL for number of AR, in one or more time point. Eighty-one of these genes were physically located within the QTL intervals for number of AR, including putative homologs of the Arabidopsis genes SUPERROOT2 (SUR2) and TRYPTOPHAN SYNTHASE ALPHA CHAIN (TSA1), both of which are involved in the auxin indole-3-acetic acid (IAA) biosynthesis pathway. In conclusion, this study suggests the involvement of two genes of the tryptophan-dependent auxin biosynthesis pathway, SUR2 and TSA1, in the regulation of a critical trait for the clonal propagation of woody species. A possible model for this regulation is that poplar individuals that have poor AR formation synthesize auxin indole-3-acetic acid (IAA) primarily through the tryptophan (Trp) pathway. Much of