Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress

Plant stress studies are more and more based on gene expression. The analysis of gene expression requires sensitive, precise, and reproducible measurements for specific mRNA sequences. Real-time RT-PCR is at present the most sensitive method for the detection of low abundance mRNA. To avoid bias, real-time RT-PCR is referred to one or several internal control genes, which should not fluctuate during treatments. Here, the non-regulation of seven housekeeping genes (beta-tubulin, cyclophilin, actin, elongation factor 1-alpha (ef1alpha), 18S rRNA, adenine phosphoribosyl transferase (aprt), and cytoplasmic ribosomal protein L2) during biotic (late blight) and abiotic stresses (cold and salt stress) was tested on potato plants using geNorm software. Results from the three experimental conditions indicated that ef1alpha was the most stable among the seven tested. The expression of the other housekeeping genes tested varied upon stress. In parallel, a study of the variability of expression of hsp20.2, shown to be implicated in late blight stress, was realized. The relative quantification of the hsp20.2 gene varied according to the internal control and the number of internal controls used, thus highlighting the importance of the choice of internal controls in such experiments.     

Early detection of Biscogniauxia nummularia in symptomless European beech (Fagus sylvatica L.) by TaqMan quantitative real-time PCR

AIMS: To develop a quantitative real-time PCR (Rt PCR) assay for the early detection of Biscogniauxia nummularia, a xylariaceous fungus that causes strip-canker and wood decay on European beech (Fagus sylvatica L.). METHODS AND RESULTS: The molecular assay was based on TaqMan chemistry using species-specific primers and a fluorogenic probe designed on the ITS1 sequence of rRNA gene clusters. The specificity of the oligonucleotides and the probe were tested using the DNA of B. nummularia isolates from different geographic areas, of phylogenetically related species, and of some fungi commonly colonizing European beech bark and wood. A total of 31 symptomless and symptomatic shoots of European beech were collected from three forest sites in the Apennine Mountains of Italy. The percentage of positive detections of B. nummularia with the TaqMan assay was 78.6%, compared with only 14.3% of positive isolations on growth media for two sites. CONCLUSIONS: In shoots, the quantitative Rt PCR assay detected down to 8.0-fg fungal DNA per microgram of total DNA extracted. SIGNIFICANCE AND IMPACT OF THE STUDY: The assay developed in quantitative Rt PCR, by using TaqMan chemistry, revealed a rapid and sensitive method useful for the early detection of B. nummularia in symptomless European beech twigs.     

Potential risks for European beech (Fagus sylvatica L.) in a changing climate

Over large areas of Europe, coniferous monocultures are being transformed into mixed forests by the re-introduction of broadleaf tree species belonging to the potential natural vegetation. One important species of interest in this changing forest policy is European beech (Fagus sylvatica). However, at present, this forest management directive has ignored potential adverse effects of global climate change on wide-spread re-introduction of beech to these areas. Average global surface temperatures have risen by approx. 0.8°C in the period between 1861 and 2005 and are expected to continue to increase until the end of this century by 1.5–5.8°C above the 1990 value. To estimate the climate change in the southern part of central Europe in future, we reviewed calculations from regional climate models. Temperature increase for the southern part of central Europe is projected to be up to 2°C within the next 40 years. In contrast, the annual precipitation will most likely remain constant over the same time period, but will experience significant changes in seasonal patterns. Rising intensities of individual precipitation events may result in increasing number and intensities of flooding events and reduced precipitation during the growing season in a higher frequency of summer droughts. Growth and competitive ability of European beech will not, necessarily, respond to increasing CO₂ concentrations but may be strongly impacted by intensive drought that occurs during the growing season. Seedlings as well as adult trees may suffer from xylem embolism, restricted nutrient uptake capacity and reduced growth under limited water availability. However, it remains uncertain to what extent other environmental factors (e.g. soil properties, competitive interactions) may modify the drought response of beech, thus either enhancing susceptibility or increasing drought tolerance and resilience potential. Water-logged soils, predicted during the spring for several regions due to higher than average precipitation, could negatively impact nutrient uptake and growth of beech. Whereas other dominant species as, e.g. oak are well adapted to that environmental stress, beech is known to be sensitive to water-logging and flooding. Thus, the competitive capacity of beech might—depending on the other environmental conditions—be reduced under the expected future climate conditions. Silvicultural practices must be aware today of the potential risks which a changing climate may impose on sustainable forest development.     

Developmental and seasonal changes of stress responsiveness in beech leaves (Fagus sylvatica L.)

The development of beech leaves (Fagus sylvatica L.) was characterized by determination of the pigment and electrolyte concentrations as well as the accumulation of dry mass and specific leaf mass from bud break to senescence. To test the hypothesis that stress tolerance and responsiveness of defences show developmental and/or seasonal changes, leaf discs were either incubated in the absence (control) or presence of paraquat to induce oxidative stress. Controls displayed developmental changes in stress susceptibility ranging from less than 15% of maximum electrolyte leakage in mature leaves to more than 20% leakage in senescent and 36–46% in immature leaves. Paraquat concentrations were chosen to result in about 95% of maximum electrolyte conductivity within 24 h in all developmental stages. Paraquat accumulation was about two‐fold lower in senescent as compared with immature leaves, whereas stress susceptibility, as characterized by the kinetics of the increase in relative leakage, was similar in these developmental stages with 50% of maximum electrolyte conductivity (EC₅₀) = 6·5 h in immature and 7·5 h in senescent leaves. In mature leaves with intermediate paraquat accumulation rates, two classes of stress‐sensitivity were distinguished, namely stress‐resistant and stress‐susceptible leaves with EC₅₀= 9·5 and 5·2 h, respectively. Stress‐resistance of mature leaves was accompanied by a rapid, approximately two‐fold induction of superoxide dismutase activity. Stress‐sensitive mature leaves initially contained high superoxide dismutase activities but showed a rapid, more than six‐ fold loss in activity in 24 h. Correlation of meteorological data with leakage rates suggested that high air temperatures and low precipitation might have been predisposing for loss of resistance against oxidative stress in beech leaves.     

Photoprotection mechanisms in European beech (Fagus sylvatica L.) seedlings from diverse climatic origins

This study shows that beech leaves adapt to their light environment by inducing dramatic changes to antioxidant systems and pigment composition. Thus, ascorbate, tocopherol, glutathione, β-carotene and xanthophyll cycle pigments are much more concentrated in sun leaves, while α-carotene is much less concentrated than in shade leaves. These characteristics were used to identify the inherent potential of beech cotyledons from three contrasting climatic origins to tolerate light stress. The antioxidant content was initially different in the three provenances tested, but these initial differences tended to reduce with leaf ageing. The higher antioxidant and de-epoxidized xanthophyll content found in developing cotyledons indicated a superior potential for tolerance to photo-oxidative damage in those plants collected from the stressful climate of the Pyrenees. Nevertheless under an experimental high irradiation treatment no differences in light stress tolerance were observed between provenances. Received: 31 May 1999 / Accepted: 16 November 1999     

Gene Flow in European Beech (Fagus sylvatica L.)

Three relatively isolated stands were used to study gene flow in European beech (Fagus sylvatica L.) in Northern Germany. Nine allozyme loci (Got-B, Idh-A, Lap-A, Mdh-B, Mdh-C, Mnr-A, 6-pgdh-A, Pgi-B and Pgm-A) were utilized for multilocus-genotyping adult trees and seeds. Expected heterozygosity (He) ranged from 0.325 to 0.351 for the three stands. F(ST) revealed that there was small differentiation among stands (mean F(ST) = 0.013). The indirect estimates of gene flow (Nm) based on the mean F(ST) were high and the average Nm was 19.14. External gene flow by pollen ranged from 0.7 to 1.2% inferred from new alleles in seed samples. Moreover, paternity analysis was used to assess effective pollen dispersal by inferring paternity of offspring. The weighted mean distances of pollen dispersal for these three stands were 36.8 and 37.1 m based on simple exclusion procedure and most-likely method, respectively. Two of the trees in one stand had rare allozyme alleles (Lap-A1 and Idh-A4, respectively), which were used to directly measure pollen movement away from those trees. The frequency of the rare Lap and Idh alleles in seeds declines as the distance from the source tree increases. The weighted mean distance of pollen dispersal with rare allele Lap-A1 or Idh-A4 was 26.3 m.     

Comparison of pollen gene flow among four European beech (Fagus sylvatica L.) populations characterized by different management regimes

The study of the dispersal capability of a species can provide essential information for the management and conservation of its genetic variability. Comparison of gene flow rates among populations characterized by different management and evolutionary histories allows one to decipher the role of factors such as isolation and tree density on gene movements. We used two paternity analysis approaches and different strategies to handle the possible presence of genotyping errors to obtain robust estimates of pollen flow in four European beech (Fagus sylvatica L.) populations from Austria and France. In each country one of the two plots is located in an unmanaged forest; the other plots are managed with a shelterwood system and inside a colonization area (in Austria and France, respectively). The two paternity analysis approaches provided almost identical estimates of gene flow. In general, we found high pollen immigration (~75% of pollen from outside), with the exception of the plot from a highly isolated forest remnant (~50%). In the two unmanaged plots, the average within-population pollen dispersal distances (from 80 to 184 m) were higher than previously estimated for beech. From the comparison between the Austrian managed and unmanaged plots, that are only 500 m apart, we found no evidence that either gene flow or reproductive success distributions were significantly altered by forest management. The investigated phenotypic traits (crown area, height, diameter and flowering phenology) were not significantly related with male reproductive success. Shelterwood seems to have an effect on the distribution of within-population pollen dispersal distances. In the managed plot, pollen dispersal distances were shorter, possibly because adult tree density is three-fold (163 versus 57 trees per hectare) with respect to the unmanaged one.     

Factors toxic to beech (Fagus sylvatica L.) seedlings in acid soils

The effects of highly and moderately acid soils on total biomass, biomass partitioning, fine root characteristics and nutritional status of beech seedlings (Fagus sylvatica L.) were studied in a growth chamber experiment. In Haplic Arenosols seedlings grew slowly but equally well without damage symptoms in a highly acid and a moderately acid soil horizon. The moderately acid A_h+B_w-horizon of a Eutric Cambisol was favourable to seedling growth. The fine root development was reduced in the highly acid A+B_w-horizon of a Dystric Cambisol and in the A_h+E-horizon of a Haplic Podzol, the latter of which also caused increased mortality. Seedling growth in the B₂-horizon of the Haplic Podzol was vigorous, in spite of a higher level of extractable Al and lower base saturation as compared with the A_h+E-horizon. These results are interpreted in relation to soil acidity, soil Al and nutritional status of the seedlings. We conclude that neither Al-toxicity nor nutrient deficiency cause the damage symptoms observed in the A_h+E-horizon of a Haplic Podzol and the fine root reduction in the A+B_w-horizon of a Dystric Cambisol. The damage symptoms of the PZh_A treatment seems to be more the result of H-toxicity or H-related factors other than nutrient shortage or Al-toxicity. Other pH-related toxic factors are discussed.     

Climate-tree-growth relationships of European beech (Fagus sylvatica L.) in the French Permanent Plot Network (RENECOFOR)

The influence of climate on the radial growth of Fagus sylvatica was investigated using 15 chronologies developed from mature stands of the French Permanent Plot Network (RENECOFOR) growing under different climatic and soil conditions. The relationships between climate and ring widths were analyzed using extreme growth years, simple correlations and response functions analysis. Monthly climatic regressors were derived by a physiological water balance model that used daily climatic data and stand parameters to estimate soil water deficits. The three most frequent negative pointer years (1959, 1989, 1976) result from a particularly intense and durable drought, whereas positive years (1977, 1958) coincide with wet conditions. The total ring chronology variance attributable to climate averages 34.1% (15.8% –57%). Current early-summer soil water deficit enters in 10 models and the deficit in June explains alone a large part of the radial growth variability (mean value: 26.6%). Temperature or soil water deficit for the other months and weather conditions during the previous season were of little consistency across stands. The response pattern of earlywood is very similar and the percentage of variance explained is higher (16.2% –57.8%). Latewood widths present a different response pattern. High minimum temperature in August and/or September often favour wide latewood widths and monthly water deficits play a secondary role. The percentage of variance explained ranges from 8.8% to 67.4%. Soil water capacity strongly modulates ring characteristics and climate-growth relationships. Mean sensitivity, expressed population signal, signal-to-noise ratio and the strength of growth-climate correlations increase with decreasing soil water capacity.     

Effects of drought on photoprotective mechanisms in European beech (Fagus sylvatica L.) seedlings from different provenances

The effects of drought on photoprotection mechanisms of three beech provenances from three contrasting climatic origins have been studied. Morphology differed among provenances, with a lower leaf area/fine roots ratio in the xeric populations (Moncayo). This characteristic allowed this provenance to respond later than the others to a drought-stress treatment. However, in desiccating leaves the stability of PSII was higher in the plants from the stressful climate of the Pyrenees (Belagoa). Drought resulted in a reduction in pigment content (except in Belagoa) with simultaneous increases in antheraxanthin, zeaxanthin and tocopherol pools. These molecules play an important photoprotective role and reached similar values in stressed leaves from the three provenances. These antioxidants also protected the leaves from paraquat-induced oxidation. It is concluded that drought tolerance in the studied xeric ecotype is based to a greater extent on morphological characteristics than on a better photoprotective system.     

Stem hydraulic conductance of European beech (Fagus sylvatica L.) and pedunculate oak (Quercus robur L.) grown in elevated CO2

Over two seasons in c. 600 ppm CO₂, oak had lower stomatal conductancein CO₂-enriched compared to amblent air. Beech showed no responseto CO₂ concentration on sunny days. Mirroring this pattern,exposure to elevated CO₂ reduced whole-shoot hydraulic conductanceper unit leaf area in oak, but not in beech. Key words: Climate change, Fagaceae, gas exchange, trees, water relations     

High chloroplast haplotype diversity in Greek populations of beech (Fagus sylvatica L.)

The distribution of chloroplast DNA (cpDNA) variations in Greek beech ( Fagus sylvatica L.) populations was studied using chloroplast microsatellite markers. Thirteen haplotypes were identified from 40 populations by combining three different primers. Most of the cpDNA variation was distributed among populations, but a considerable variation was also observed within populations. The total diversity was very high for all regions. The N_st/G_st comparison was significant, indicating phylogenetic subdivision, but no strong spatial structure was detected, suggesting complex post-glacial migration patterns. Possible scenarios explaining this diversity pattern include the existence of several separated refugia in the region, the recolonisation of mountains by different beech lineages and the formation of an introgression zone between two different beech subspecies in the eastern part of the country.     

The induction of sun and shade leaves of the European beech (Fagus sylvatica L.): anatomical studies

Summary Primordia from buds of sun and shade twigs of European beech (Fagus sylvatica L.) were collected six times a year for anatomical investigations. Differentiation into sun-leaf and shade-leaf primordia was first observed in early August. Sun-leaf primordia had five, and shade-leaf primordia four layers of mesophyll meristem cells. With potted graft unions of beeches possible structural changes of leaf primordia were investigated. Trees adapted to shade develop sun-leaf primordia when put into full daylight, provided the transfer happened before July. Trees adapted to full daylight developed leaf primordia which remained structurally sun-leaf primordia when the plant was kept under shade conditions. Shadeleaf branches of young beech trees cut in February in order to expose the shade buds to full daylight developed either shade leaves or intermediate shade/sun leaves. These experiments show that the subtending leaf may provide the developing axillary bud with photoassimilates, but its character, whether sun or shade leaf, has no influence on the character of the developing leaf primordia.     

Growth and nutrient dynamics of beech (Fagus sylvatica L.) seedlings in acid soils

The relative uptake rates of N, P, K, S, Ca, Mg, Fe, Mn, Zn, Cu, and Al were estimated in beech seedlings pot cultured in the field in six acid soils (treatments). The relative uptake rates were compared with the relative growth rates. The relative uptake rates of N, K and Ca agreed well with the growth rates of the seedlings irrespective of widely differing soil conditions (acid sand-clayey till, pH 4–6). The relative uptake rates of P, Fe, and Al differed from that predicted by the growth rate. The uptake rates of Fe and Al were highest at the lowest growth rates, and the P uptake rate was lower than the growth rate in these treatments. Thus the P availability probably limited growth in an eluvial (E) horizon of a podzol, and possibly in the illuvial (B) horizon of a podzol and in an acid clayey till (Dystric Cambisol). Low P uptake was associated with a tendency towards higher relative root growth rates. In terms of the concept of steady state nutrition the high relative root growth rate in some treatments may be interpreted as an acclimation to low P supply. The P limitation seemed to be related to interactions among Fe, Al and organic compounds of the soil solution.FAX no: +4646104423