Profiling microRNAs in Eucalyptus grandis reveals no mutual relationship between alterations in miR156 and miR172 expression and adventitious root induction during development

Background

The change from juvenile to mature phase in woody plants is often accompanied by a gradual loss of rooting ability, as well as by reduced microRNA (miR) 156 and increased miR172 expression.

Results

We characterized the population of miRNAs of Eucalyptus grandis and compared the gradual reduction in miR156 and increase in miR172 expression during development to the loss of rooting ability. Forty known and eight novel miRNAs were discovered and their predicted targets are listed. The expression pattern of nine miRNAs was determined during adventitious root formation in juvenile and mature cuttings. While the expression levels of miR156 and miR172 were inverse in juvenile and mature tissues, no mutual relationship was found between high miR156 expression and rooting ability, or high miR172 expression and loss of rooting ability. This is shown both in E. grandis and in E. brachyphylla, in which explants that underwent rejuvenation in tissue culture conditions were also examined.

Conclusions

It is suggested that in these Eucalyptus species, there is no correlation between the switch of miR156 with miR172 expression in the stems and the loss of rooting ability.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-524) contains supplementary material, which is available to authorized users.     

农杆菌介导巨桉Eg5高效遗传转化

以巨桉(Eucalyptus grandis)无性系Eg5叶片为外植体, 探讨了农杆菌(Agrobacterium tumefaciens)侵染时间、共培养pH值和共培养时间对瞬时转化效率的影响, 分析了不同筛选策略对遗传转化植株筛选效果的影响。结果表明, 外植体侵染45分钟, 共培养pH值为5.8, 共培养3天所得到的瞬时转化效率最高; 逐步提高卡那霉素(Km)浓度筛选转基因植株有效, 筛选率达到15%, 转化率达到0.26%。经过GUS染色分析和PCR检测, 证实为转基因植株。     

一个年龄序列巨桉人工林植物和土壤生物多样性

为了全面、系统研究和评价退耕后桉树人工林生物多样性,采用立地条件控制及空间代替时间法,对四川丹棱县退耕营造的巨桉(Eucalyptus grands)人工林(1-10a)植物和土壤生物多样性进行了同步研究.结果显示,植物和土壤动物的物种数、密度和多样性指数及土壤微生物数量呈相似变化趋势,即轮伐期前同步(4a左右)降低,此后随林龄显著增加.CCA分析显示,植物生活型随林龄由藤本植物、地面芽和1年生植物向多年生草本高位芽和高位芽植物过渡.土壤微生物以细菌占据数量优势;土壤动物以腐食性功能团占据优势,杂食性次之.腐食性功能团1-7a降低而后升高,杂食性呈S型升高趋势;植食性和捕食性功能团百分比较低随林龄显著降低.土壤动物优势类群中线虫纲个体百分比随林龄显著降低,蜱螨目百分比和A/C值(蜱螨目/弹尾目数量比)呈S型上升趋势.各林龄巨桉林地植物多样性均显著高于对照农耕地;除1,2a及4-7a样地植物多样性显著低于对照马尾松林,其余均与其无显著差异.土壤生物多样性,轮伐期前巨桉林地与对照农耕地差异不显著,此后则显著高于农耕地;各林龄样地土壤生物多样性均显著低于对照马尾松林.植物和土壤生物多样性指标显著相关,且相关系数随土壤层次加深而降低.     

A strigolactone signal is required for adventitious root formation in rice

Background and Aims Strigolactones (SLs) and their derivatives are plant hormones that have recently been identified as regulating root development. This study examines whether SLs play a role in mediating production of adventious roots (ARs) in rice (Oryza sativa), and also investigates possible interactions between SLs and auxin.Methods Wild-type (WT), SL-deficient (d10) and SL-insensitive (d3) rice mutants were used to investigate AR development in an auxin-distribution experiment that considered DR5::GUS activity, [³H] indole-3-acetic acid (IAA) transport, and associated expression of auxin transporter genes. The effects of exogenous application of GR24 (a synthetic SL analogue), NAA (α-naphthylacetic acid, exogenous auxin) and NPA (N-1-naphthylphalamic acid, a polar auxin transport inhibitor) on rice AR development in seedlings were investigated.Key Results The rice d mutants with impaired SL biosynthesis and signalling exhibited reduced AR production compared with the WT. Application of GR24 increased the number of ARs and average AR number per tiller in d10, but not in d3. These results indicate that rice AR production is positively regulated by SLs. Higher endogenous IAA concentration, stronger expression of DR5::GUS and higher [³H] IAA activity were found in the d mutants. Exogenous GR24 application decreased the expression of DR5::GUS, probably indicating that SLs modulate AR formation by inhibiting polar auxin transport. The WT and the d10 and d3 mutants had similar expression of DR5::GUS regardless of exogenous application of NAA or NPA; however, AR number was greater in the WT than in the d mutants.Conclusions The results suggest that AR formation is positively regulated by SLs via the D3 response pathway. The positive effect of NAA application and the opposite effect of NPA application on AR number of WT plants also suggests the importance of auxin for AR formation, but the interaction between auxin and SLs is complex.     

Stimulation of adventitious root formation in non-woody stem cuttings by uridine

Uridine strongly stimulated adventitious root formation in stem cuttings of sunflower (Helianthus annuus L.), mung bean (Vigna radiata L.) and common bean (Phaseolus vulgaris L.). A dose response curve of uridine induced rooting showed that the optimum concentration of uridine was 0.1 µM. At all concentrations employed, uridine had no significant effect on root elongation. The rooting response of stem cuttings to the optimal concentration of indole-3-butyric acid (10 µM) in combination with 0.1 µM uridine did not significantly differ from their response to either of these compounds when applied alone. However, the rooting response of the cuttings to sub-optimal IBA (0.01 µM) was significantly stimulated by uridine. These findings suggested that uridine may have stimulated rooting by increasing the sensitivity of the rooting tissue to auxin.     

Spatial distributions of foliar nitrogen and phosphorus in crowns of Eucalyptus grandis

Summary Eucalyptus grandis trees were grown in plantations with and without added fertiliser to examine the effects of plant nutrition on photosynthesis and growth. Leaves were sampled from known locations within canopies of selected trees and leaf N and P concentrations were measured. Contour maps of N and P distributions were then produced for crowns of trees aged between 6 and 16 months. Gas exchange measurements on sample leaves were used to estimate parameters of a model of C₃ photosynthesis as a function of leaf N and P contentrations. Linear relationships were obtained between model parameters and leaf N concentration, but P appeared to be present in excess, since no correlation was found with P contentration. Photosynthetic light response curves were calculated for model leaves with differing N concentrations. The curves show that optimal concentrations of N in leaves depend on mean levels of irradiance during growth.     

Auxin and cytokinin control formation of the quiescent centre in the adventitious root apex of arabidopsis

Background and Aims

Adventitious roots (ARs) are part of the root system in numerous plants, and are required for successful micropropagation. In the Arabidopsis thaliana primary root (PR) and lateral roots (LRs), the quiescent centre (QC) in the stem cell niche of the meristem controls apical growth with the involvement of auxin and cytokinin. In arabidopsis, ARs emerge in planta from the hypocotyl pericycle, and from different tissues in in vitro cultured explants, e.g. from the stem endodermis in thin cell layer (TCL) explants. The aim of this study was to investigate the establishment and maintenance of the QC in arabidopsis ARs, in planta and in TCL explants, because information about this process is still lacking, and it has potential use for biotechnological applications.

Methods

Expression of PR/LR QC markers and auxin influx (LAX3)/efflux (PIN1) genes was investigated in the presence/absence of exogenous auxin and cytokinin. Auxin was monitored by the DR5::GUS system and cytokinin by immunolocalization. The expression of the auxin-biosynthetic YUCCA6 gene was also investigated by in situ hybridization in planta and in AR-forming TCLs from the indole acetic acid (IAA)-overproducing superroot2-1 mutant and its wild type.

Key Results

The accumulation of auxin and the expression of the QC marker WOX5 characterized the early derivatives of the AR founder cells, in planta and in in vitro cultured TCLs. By determination of PIN1 auxin efflux carrier and LAX3 auxin influx carrier activities, an auxin maximum was determined to occur at the AR tip, to which WOX5 expression was restricted, establishing the positioning of the QC. Cytokinin caused a restriction of LAX3 and PIN1 expression domains, and concomitantly the auxin biosynthesis YUCCA6 gene was expressed in the apex.

Conclusions

In ARs formed in planta and TCLs, the QC is established in a similar way, and auxin transport and biosynthesis are involved through cytokinin tuning.     

Chemical induction of adventitious root formation in Taxus baccata cuttings

The effect of some auxins (IBA and NAA), phenolic compounds (phloroglucinol, gentisic acid and coumarin), a combination of auxins and phenolics, and a systemic fungicide (Bavistin) have been examined for stimulatory effects on adventitious root formation in stem cuttings (current season's growth) of Taxus baccata L. In general lower concentration (0.25 mM) of both IBA and NAA was more effective in inducing rooting of cuttings taken from both male and female trees. The combined treatment of IBA+NAA (0.25 mM each) showed some success in cuttings from male trees only (55%, compared to 15% rooting in cuttings from female trees). Generally, the callus formation was quite high (70%) in all auxin treatments (alone or in combination). Among the phenolics, 40% rooting success was achieved with phloroglucinol only, while coumarin and gentisic acid were ineffective. The combined treatment of auxins and phenolics also failed to promote rooting. On the other hand, Bavistin was extremely effective for callusing (90%) as well as rooting (80%). The effectiveness of various compounds tested for rooting of young stem cuttings declined in the order: 0.25 mM IBA>0.05% Bavistin>0.25 mM NAA>1.25 mM IBA>15 mM phloroglucinol>IBA+NAA (0.25 mM each). In addition to the auxins, IBA and NAA that are widely used for commercial propagation, the auxin-like properties of the fungicide Bavistin could be exploited for adventitious rooting in T. baccata, and in other plant species.     

Gene expression profiling of candidate virulence factors in the laminated root rot pathogen Phellinus sulphurascens

Background

Phellinus sulphurascens is a fungal pathogen that causes laminar root rot in conifers, one of the most damaging root diseases in western North America. Despite its importance as a forest pathogen, this fungus is still poorly studied at the genomic level. An understanding of the molecular events involved in establishment of the disease should help to develop new methods for control of this disease.

Results

We generated over 4600 expressed sequence tags from two cDNA libraries constructed using either mycelia grown on cellophane sheets and exposed to Douglas-fir roots or tissues from P. sulphurascens-infected Douglas-fir roots. A total of 890 unique genes were identified from the two libraries, and functional classification of 636 of these genes was possible using the Functional Catalogue (FunCat) annotation scheme. cDNAs were identified that encoded 79 potential virulence factors, including numerous genes implicated in virulence in a variety of phytopathogenic fungi. Many of these putative virulence factors were also among 82 genes identified as encoding putatively secreted proteins. The expression patterns of 86 selected fungal genes over 7 days of infection of Douglas-fir were examined using real-time PCR, and those significantly up-regulated included rhamnogalacturonan acetylesterase, 1,4-benzoquinone reductase, a cyclophilin, a glucoamylase, 3 hydrophobins, a lipase, a serine carboxypeptidase, a putative Ran-binding protein, and two unknown putatively secreted proteins called 1 J04 and 2 J12. Significantly down-regulated genes included a manganese-superoxide dismutase, two metalloproteases, and an unknown putatively secreted protein called Ps0058.

Conclusions

This first collection of Phellinus sulphurascens EST sequences and its annotation provide an important resource for future research aimed at understanding key virulence factors of this forest pathogen. We examined the expression patterns of numerous fungal genes with potential roles in virulence, and found a collection of functionally diverse genes that are significantly up- or down-regulated during infection of Douglas-fir seedling roots by P. sulphurascens.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-603) contains supplementary material, which is available to authorized users.     

Chloroplast DNA variation and population structure in the widespread forest tree, Eucalyptus grandis

Recognition of genetic structure of populations and the ability to identify vulnerable populations is useful for the formation of conservation management strategies for plants. Eucalyptus grandis is a tall forest tree that has a major area of occurrence in subtropical eastern Australia, with smaller populations located in the east coast tropics. Many widespread forest species exhibit population differentiation that corresponds to geographic regions. However, Eucalyptus grandis appears to be an exception based on isozyme and morphological data. This is intriguing given a large discontinuity between northern populations and those in the southern part of the species range. In this study, the distribution of a maternally inherited chloroplast locus was examined because it was more likely to reveal genetic structure due to the slower evolution of the chloroplast genome and limited dispersal of seed in eucalypts. As expected, the G _ST for chloroplast DNA was higher than that for nuclear DNA but indicated low population differentiation for a forest tree species. Phylogeographic analysis indicated that the 15 populations grouped into three broad geographical regions; however, overall population structure was weak suggesting that the large geographical disjunction in the distribution of E. grandis may be relatively recent. A paradigm for conservation management of E. grandis based on chloroplast DNA haplotype distribution would take into account the low differentiation among populations.     

Model simulations of spatial distributions and daily totals of photosynthesis in Eucalyptus grandis canopies

Summary A simulation model for radiation absorption and photosynthesis was used to test the hypothesis that observed nonuniform distributions of nitrogen concentrations in young Eucalyptus grandis trees result in greater amounts of daily assimilation than in hypothetical trees with uniform N distributions. Simulations were performed for trees aged 6, 9, 12 and 16 months which had been grown in plantations under a factorial combination of two levels of fertilization and irrigation. Observed leaf N distribution patterns yielded daily assimilation rates which were only marginally greater (<5%) than for hypothetical trees with uniform distributions. Patterns of assimilation distribution in individual tree crowns closely resembled those for absorbed radiation, rather than for N. These conclusions were unaffected by three choices of alternative leaf area density distributions. The simulation model was also used to calculate hourly and daily rates of canopy assimilation to investigate the relative importance of radiation absorption and total canopy nitrogen on assimilation. Simulated hourly rates of carbon assimilation were often lightsaturated, whereas daily carbon gain was directly proportional to radiation absorbed by the tree crown and to total mass of N in the leaves. Leaf nitrogen concentrations determined photosynthetic capacity, whereas total leaf area determined the amount of radiation absorbed and thus the degree to which capacity was realized. Observed total leaf area and total crown N were closely correlated. The model predicted that nitrogen use efficiences (NUE, mol CO₂ mol^–1 N) were 60% higher for unfertilized than for fertilized trees at low levels of absorbed photosynthetically active radiation (PAR). Nitrogen use efficiency was dependent on fertilizer treatment and on the amount of absorbed PAR; NUE declined with increasing absorbed PAR, but decreased more rapidly for unfertilized than for fertilized trees. Annual primary productivity was linearly related to both radiation absorbed and to mass of N in the canopy.     

Fluctuations of cambial activity in relation to precipitation result in annual rings and intra-annual growth zones of xylem and phloem in teak (Tectona grandis) in Ivory Coast

Background and Aims Teak forms xylem rings that potentially carry records of carbon sequestration and climate in the tropics. These records are only useful when the structural variations of tree rings and their periodicity of formation are known. Methods The seasonality of ring formation in mature teak trees was examined via correlative analysis of cambial activity, xylem and phloem formation, and climate throughout 1·5 years. Xylem and phloem differentiation were visualized by light microscopy and scanning electron microscopy. Key Results A 3 month dry season resulted in semi-deciduousness, cambial dormancy and formation of annual xylem growth rings (AXGRs). Intra-annual xylem and phloem growth was characterized by variable intensity. Morphometric features of cambium such as cambium thickness and differentiating xylem layers were positively correlated. Cambium thickness was strongly correlated with monthly rainfall (R(2) = 0·7535). In all sampled trees, xylem growth zones (XGZs) were formed within the AXGRs during the seasonal development of new foliage. When trees achieved full leaf, the xylem in the new XGZs appeared completely differentiated and functional for water transport. Two phloem growth rings were formed in one growing season. Conclusions The seasonal formation pattern and microstructure of teak xylem suggest that AXGRs and XGZs can be used as proxies for analyses of the tree history and climate at annual and intra-annual resolution.     

Increased root initiation in cuttings of Eucalyptus nitens by delayed auxin application.

Root initiation in cuttings of Eucalyptus nitens(Deane & Maiden) Maiden. was stimulated by application of auxin dips in theform of 20 mg/l solution administered for 48 h. Thegreatest stimulation of rooting was obtained when auxin was applied to thecuttings at least four weeks after the cuttings were first collected and set ona mist-bed.