Elucidating the role of genetic drift and natural selection in cork oak differentiation regarding drought tolerance

Drought is the main selection agent in Mediterranean ecosystems and it has been suggested as an important evolutionary force responsible for population diversification in these types of environments. However, population divergence in quantitative traits can be driven by either natural selection, genetic drift or both. To investigate the roles of these forces on among-population divergence in ecophysiological traits related to drought tolerance (carbon isotope discrimination, specific leaf area, leaf size and leaf nitrogen content), we compared molecular and quantitative genetic differentiation in a common garden experiment including thirteen cork oak ( Quercus suber L.) populations across a gradient of rainfall and temperature. Population differentiation for height, specific leaf area, leaf size and nitrogen leaf content measured during a dry year far exceeded the molecular differentiation measured by six nuclear microsatellites. Populations from dry-cool sites showed the lowest nitrogen leaf content and the smallest and thickest leaves contrasting with those from humid-warm sites. These results suggest (i) these traits are subjected to divergence selection and (ii) the genetic differences among populations are partly due to climate adaptation. By contrast, the low among-population divergence found in basal diameter, annual growth and carbon isotopic discrimination (a surrogate for water use efficiency) suggests low or no divergence selection for these traits. Among-population differentiation for neutral markers was not a good predictor for differentiation regarding the quantitative traits studied here, except for leaf size. The correlation observed between the genetic differentiation for leaf size and that for molecular markers was exclusively due to the association between leaf size and the microsatellite Qp ZAG46, which suggests a possible linkage between Qp ZAG46 and genes encoding for leaf size.     

Population variation and natural selection on leaf traits in cork oak throughout its distribution range

A central issue in evolutionary biology is the exploration of functional trait variation among populations and the extent to which this variation has adaptive value. It was recently proposed that specific leaf area (SLA), leaf nitrogen concentration per mass (N_mass) and water use efficiency in cork oak play an important role in adaptation to water availability in the environment. In order to investigate this hypothesis, we explored, first, whether there was population-level variation in cork oak (Quercus suber) for these functional traits throughout its distribution range; if this were the case, it would be consistent with the hypothesis that different rainfall patterns have led to ecotypic differentiation in this species. Second, we studied whether the population-level variation matched short-term selection on these traits under different water availability conditions using two fitness components: survival and growth. We found high population-level differentiation in SLA and N_mass, with populations from dry places exhibiting the lowest values for SLA and N_mass. Likewise, reduced SLA had fitness benefits in terms of growth for plants under dry conditions. However, contrary to our expectations, we did not find any pattern of association between functional traits and survival in nine-year-old saplings despite considerable drought during one year of the study period. These results together with findings from the literature suggest that early stages of development are the most critical period for this species. Most importantly, these findings suggest that cork oak saplings have a considerable potential to cope with dry conditions. This capacity to withstand aridity has important implications for conservation of cork oak woodlands under the ongoing climate change.     

Identifying signatures of natural selection in cork oak (Quercus suber L.) genes through SNP analysis

Cork oak (Quercus suber L.) is an evergreen tree species endemic to the western Mediterranean Basin with a major economical, social and ecological relevance, associated with cork extraction and exploitation. In the last years, cork oak stands have been facing a significant decline, which may be aggravated by the climate changes that are predicted to occur within cork oak distribution range during this century. Under this scenario, the assessment of adaptive genetic variation is essential to understand how cork oak may cope with these threats and to delineate strategies for the management of its genetic resources. In this study, six candidate genes possibly significant for environmental adaptation were analysed in cork oak populations from its entire distribution range. Signatures of natural selection were investigated using population genetic statistics and environmental association tests under alternative scenarios of population genetic structure. Signals of balancing selection were detected in the putative non-expressor of pathogenesis-related gene 1 (NPR1), involved in plant defence response against pathogens, in auxin response factor 16 (ARF16), a gene implicated in root development, in RAN3, also involved in developmental processes, and in glutamine synthetase nodule isozyme (GS), involved in nitrogen fixation. Furthermore, for ARF16, a class I heat shock protein (sHSP) and GS, associations were found between SNP allele and haplotype frequencies and several spatial and climatic variables, suggesting that these genes may have a role on cork oak local adaptation. In this study, the first steps were taken into gathering information on cork oak adaptation to environmental conditions.     

Allozyme variation in cork oak (Quercus suber L.): the role of phylogeography and genetic introgression by other Mediterranean oak species and human activities

 Genetic variation in the cork oak (Quercus suber L.) was investigated using 11 loci from seven enzyme systems in 40 populations sampled over the entire distribution of this species in the western Mediterranean Basin. Mean heterozygosity values over the polymorphic loci (Ho=0.283), the percentage of polymorphic populations (M=0.76), and the total genetic diversity (Ht=0.31) from which 11% was accounted for among-population variation, are among the highest recorded in oak species. In contrast to previous results in holm oak (Q. ilex L.), another evergreen species in the same area, cork oak possessed a smaller allele pool and a lower average number of alleles per locus and per population (A=2.0). More particularly, very few low-frequency alleles were observed in cork oak except for eight populations in which allozyme polymorphism at locus Pgi 1, diagnostic between both species, indicates that these low-frequency alleles are introgressed from holm oak. On the basis of the genetic distance estimated from allozyme frequencies, 32 of the 40 cork oak populations studied were classified into two very distinct sets which also corresponded to distinct geographic areas. One set gathered together the 18 populations from the Iberian peninsula and two adjacent areas in France, i.e. the centre of origin of cork oak, according to paleobotanical data. This set was characterized by a larger allele pool, a higher within-population genetic diversity and a lower differentiation between populations than was observed in the other set, which comprised the populations from North Africa, Sicily, Sardinia, Corsica, continental Italy and the region of Provence (southeastern France). In these more southern and eastern disjunct areas, cork oak migration from Iberia may have occurred at different periods since the end of the Tertiary. The possible effect of human activity on cork oak genetic structure, i.e. the selection of good-quality cork, acorn over-use for animal food, and even human nutrition, is discussed. Received: 3 March 1998 / Accepted: 19 March 1998     

Factors affecting cork oak growth under dry conditions: local adaptation and contrasting additive genetic variance within populations

Increased drought severity is expected in the Mediterranean Basin over the twenty-first century, but our understanding of the potential of most forest tree species to cope with it remains uncertain. In this study, (1) we examined the potential effects of long-term selection and the capacity to respond to future changes in selective pressures in three populations of cork oak (Quercus suber L.). For this purpose, we evaluated the response to dry conditions of 45 open-pollinated trees originating from populations in Morocco, Portugal, and Spain. Growth, leaf size, specific leaf area (SLA), carbon isotope discrimination (Δ¹³C), leaf nitrogen content (N_mass), and total chlorophyll content (Chl_mass) were measured in 9-year-old plants. (2) We also investigated the relationships between functional traits and aboveground growth by regression models. Plants presenting larger and more sclerophyllous leaves (low SLA and high leaf thickness) exhibited higher growths, with results suggesting that these traits are subjected to divergent selection in this species. Heritability estimates were moderately high for Δ¹³C (0.43 ± 0.25–0.83 ± 0.31) and stem diameter (0.40 ± 0.15–0.71 ± 0.28) for the tree populations. For the rest of the traits (except for annual growth), heritability values varied among populations, particularly for height, leaf size, leaf thickness, and N_mass. Our results suggest that natural selection has led to local adaptations and has also affected the genetic variance intrapopulation in these cork oak populations, although studies with a higher number of populations should be carried out across different years. Additionally, the absence of significant genetic correlations and the fact that correlated traits did not undergo opposing selection provided little evidence for constraints on evolution caused by genetic correlations.     

Evolutionary dynamics of the leaf phenological cycle in an oak metapopulation along an elevation gradient

It has been predicted that environmental changes will radically alter the selective pressures on phenological traits. Long‐lived species, such as trees, will be particularly affected, as they may need to undergo major adaptive change over only one or a few generations. The traits describing the annual life cycle of trees are generally highly evolvable, but nothing is known about the strength of their genetic correlations. Tight correlations can impose strong evolutionary constraints, potentially hampering the adaptation of multivariate phenological phenotypes. In this study, we investigated the evolutionary, genetic and environmental components of the timing of leaf unfolding and senescence within an oak metapopulation along an elevation gradient. Population divergence, estimated from in situ and common‐garden data, was compared to expectations under neutral evolution, based on microsatellite markers. This approach made it possible (1) to evaluate the influence of genetic correlation on multivariate local adaptation to elevation and (2) to identify traits probably exposed to past selective pressures due to the colder climate at high elevation. The genetic correlation was positive but very weak, indicating that genetic constraints did not shape the local adaptation pattern for leaf phenology. Both spring and fall (leaf unfolding and senescence, respectively) phenology timings were involved in local adaptation, but leaf unfolding was probably the trait most exposed to climate change‐induced selection. Our data indicated that genetic variation makes a much smaller contribution to adaptation than the considerable plastic variation displayed by a tree during its lifetime. The evolutionary potential of leaf phenology is, therefore, probably not the most critical aspect for short‐term population survival in a changing climate.     

Climate response of cork growth in the Mediterranean oak (Quercus suber L.) woodlands of southwestern Portugal

In the Mediterranean climate regions, drought events are expected to affect the growth of forests ecosystems by changing trees growth rates and eventually inducing shifts in their growth patterns. Cork oak (Quercus suber L.) is a strictly western Mediterranean tree species periodically harvested for its bark, the cork. So far, cork oak has received limited attention for dendroclimatological studies due to its typical faint and erratic tree wood rings. Moreover, its distinct cork rings chronologies have been completely neglected. In this study we introduce an approach using cork ring chronologies dated back 9–10 years for climate response. Despite enhancing interannual variability and increasing statistical response to short-term climatic variability, still poorly understood, this study will possibly allow infer long-term climate response. We analyzed the cork ring chronologies of 55 cork samples collected in mature (under exploitation) trees in three distinct locations in southwestern Portugal. Cork growth recorded a high climate signal, with highly significant and coherent responses to the yearly climate-related sources of variation. We successfully assessed trends of cork growth via correlation analysis including selected climate variables among mean monthly temperature, monthly precipitation and, on an annual basis, eight precipitation indices. The high mean sensitivities and inter-series correlations found for cork ring chronologies combined with the significant variance explained by climate variables suggest that climate is likely one dominant signal that affects cork growth, but local environmental stresses can decisively affect this (climate) signal. Assuming cork growth as a proxy for cork oak growth, it seems conceivable that despite the trees being highly resistant to drought stress, cork oak woodlands in southwestern Portugal would have to face lesser growth in a global warming scenario.     

Natural selection and neutral evolutionary processes contribute to genetic divergence in leaf traits across a precipitation gradient in the tropical oak Quercus oleoides

The impacts of drought are expanding worldwide as a consequence of climate change. However, there is still little knowledge of how species respond to long‐term selection in seasonally dry ecosystems. In this study, we used Q_ST‐F_ST comparisons to investigate (i) the role of natural selection on population genetic differentiation for a set of functional traits related to drought resistance in the seasonally dry tropical oak Quercus oleoides and (ii) the influence of water availability at the site of population origin and in experimental treatments on patterns of trait divergence. We conducted a thorough phenotypic characterization of 1912 seedlings from ten populations growing in field and greenhouse common gardens under replicated watering treatments. We also genotyped 218 individuals from the same set of populations using eleven nuclear microsatellites. Q_ST distributions for leaf lamina area, specific leaf area, leaf thickness and stomatal pore index were higher than F_ST distribution. Results were consistent across growth environments. Genetic differentiation among populations for these functional traits was associated with the index of moisture at the origin of the populations. Together, our results suggest that drought is an important selective agent for Q. oleoides and that differences in length and severity of the dry season have driven the evolution of genetic differences in functional traits.     

Antimitotic agents increase the production of doubled-haploid embryos from cork oak anther culture

The objective of this study is to induce the nuclear DNA duplication of anther-derived embryos of cork oak (Quercus suber L.) to obtain doubled-haploid plants. Anther culture of this species produces a low percentage (7.78%) of spontaneous diploids, as assessed by flow cytometry. Therefore, three antimitotic agents, colchicine, oryzalin and amiprophos-methyl (APM), were applied in vitro to anther-derived cork oak haploid embryos from six genotypes at different concentrations and for different treatment durations. Antimitotic toxicity was determined by embryo survival. Efficiency in inducing chromosome doubling of haploid embryos was evaluated by flow cytometry measurements and differences were observed between treatments. Nuclear DNA duplication and embryo survival of cork oak haploid embryos was most efficiently induced with oryzalin 0.01 mM for 48 h. Around 50% diploid embryos were obtained. The rate of chromosome duplication induced by APM 0.01 mM was also acceptable but lower than that induced by oryzalin, regardless of the duration of the treatment. Colchicine 1.3 or 8.8 mM was the least efficient, with the induction of necrosis and only a small rate of nuclear DNA duplication.     

miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

The differentiation of cork (phellem) cells from the phellogen (cork cambium) is a secondary growth process observed in the cork oak tree conferring a unique ability to produce a thick layer of cork. At present, the molecular regulators of phellem differentiation are unknown. The previously documented involvement of microRNAs (miRNAs) in the regulation of developmental processes, including secondary growth, motivated the search for these regulators in cork oak tissues. We performed deep sequencing of the small RNA fraction obtained from cork oak leaves and differentiating phellem. RNA sequences with lengths of 19–25 nt derived from the two libraries were analysed, leading to the identification of 41 families of conserved miRNAs, of which the most abundant were miR167, miR165/166, miR396 and miR159. Thirty novel miRNA candidates were also unveiled, 11 of which were unique to leaves and 13 to phellem. Northern blot detection of a set of conserved and novel miRNAs confirmed their differential expression profile. Prediction and analysis of putative miRNA target genes provided clues regarding processes taking place in leaf and phellem tissues, but further experimental work will be needed for functional characterization. In conclusion, we here provide a first characterization of the miRNA population in a Fagacea species, and the comparative analysis of miRNA expression in leaf and phellem libraries represents an important step to uncovering specific regulatory networks controlling phellem differentiation.     

New insights into adaptation and population structure of cork oak using genotyping by sequencing

Species respond to global climatic changes in a local context. Understanding this process, including its speed and intensity, is paramount due to the pace at which such changes are currently occurring. Tree species are particularly interesting to study in this regard due to their long generation times, sedentarism, and ecological and economic importance. Quercus suber L. is an evergreen forest tree species of the Fagaceae family with an essentially Western Mediterranean distribution. Despite frequent assessments of the species’ evolutionary history, large‐scale genetic studies have mostly relied on plastidial markers, whereas nuclear markers have been used on studies with locally focused sampling strategies. In this work, “Genotyping by sequencing” is used to derive 1,996 single nucleotide polymorphism markers to assess the species’ evolutionary history from a nuclear DNA perspective, gain insights into how local adaptation is shaping the species’ genetic background, and to forecast how Q. suber may respond to global climatic changes from a genetic perspective. Results reveal (a) an essentially unstructured species, where (b) a balance between gene flow and local adaptation keeps the species’ gene pool somewhat homogeneous across its distribution, but still allowing (c) variation clines for the individuals to cope with local conditions. “Risk of Non‐Adaptedness” (RONA) analyses suggest that for the considered variables and most sampled locations, (d) the cork oak should not require large shifts in allele frequencies to survive the predicted climatic changes. Future directions include integrating these results with ecological niche modeling perspectives, improving the RONA methodology, and expanding its use to other species. With the implementation presented in this work, the RONA can now also be easily assessed for other organisms.     

Seasonal and spatial patterns of foliar nutrients in cork oak (Quercus suber L.) growing on siliceous soils in Provence (France)

Cork oak forests in Mediterranean, southeastern France represent animportant ecosystem in terms of both ecological and economical values, but aredeclining due to conservation problems. While management protocols are now inplace for the long-term conservation of this ecotype, we require a betterunderstanding of cork oak nutrition to assist with management. Here we usefoliar nutrient analyses for two objectives: firstly, to assess to what extentvariations in nutrient content are explained by seasonal and spatialvariability, and second, to document the nutrient dynamics of cork oak trees innatural conditions during one biological cycle (16 months) in the Maures massif(western part of the siliceous Provence). Main results showed that time was theprimary factor influencing cork oak nutrition and was mainly expressed by leafageing process. Spatial variability was a 'secondary determinant' of nutrient variations, but was more important at the very early stages of leafgrowth according to leafing and nutrient flushing, and reduced with leaf age.Nutritional responses of cork oak trees fitted general trends observed in theliterature, with some regional differences. The properties of siliceous soilalso influenced the uptake of some nutrients.     

Role of carbohydrates in micropropagation of cork oak

The influences of carbon sources, fructose, glucose, sorbitol and sucrose on shoot proliferation and in vitro rooting of cork oak (Quercus suber L.) were compared at a wide range of concentrations (1–6%, w/v). The highest number of shoots occurred on glucose-containing medium. Nevertheless, we have chosen 3% sucrose which induced a similar rate of proliferation but favoured shoot elongation, permitting an effectively higher number of shoots during transfers. Sorbitol and autoclaved fructose did not stimulate shoot proliferation. Adventitious root formation was strongly dependent on carbohydrate supply. Sorbitol and autoclaved fructose were completely ineffectively on rooting induction. Glucose was the most effective carbon source on rooting promotion followed by sucrose and filter-sterilized fructose. The rooting response induced by fructose was dependent on the sterilizing procedure. The number of adventitious roots produced per shoot increased with increasing glucose and sucrose concentration. The content of reducing sugars in leaves of proliferation cultures and in leaves and roots of rooted plantlets was more dependent on carbon concentration than on glucose or sucrose supplement. The results presented here show that carbohydrate requirements during cork oak micropropagation depend upon the phase of culture. Sucrose (3%) and glucose (4%) were the best carbon sources respectively during proliferation and rooting phases.     

Patterns and ecological consequences of abiotic heterogeneity in managed cork oak forests of Southern Spain

Spatial heterogeneity of abiotic factors influences the structure and function of forests and must be taken into account for their conservation and sustainable management. In this study, we evaluate the heterogeneity of abiotic environmental variables in managed cork oak (Quercus suber L.) forests in southern Spain at patch, site and regional scales. The extent of spatial heterogeneity depended on the environmental variable examined and the scale considered. For example, soil Mn and P and light availability in the understorey were very heterogeneous at the regional scale, while soil N had low regional heterogeneity, but high spatial variability, at patch scale, attributed to open overstorey and grazing disturbance. There was a general trend of increasing heterogeneity with spatial scale. We also study the effects of a silvicultural practice—shrub clearing on the forest environment and its consequence for spatial heterogeneity. Shrub clearing increased understorey light and decreased its spatial heterogeneity with idiosyncratic effects on soil properties and their spatial heterogeneity at each site. Finally, we compare the heterogeneity (estimated by the coefficient of variation) obtained in these cork oak forests with a database compiled from published studies on other forest environments. The comparison revealed a remarkable extent of abiotic heterogeneity in the cork oak forests studied, suggesting that a sustainable management of these forests should combine intrinsic and human induced abiotic heterogeneity to preserve crucial ecological processes and to maintain high levels of biodiversity.     

The role of habitat patches on mammalian diversity in cork oak agroforestry systems

Habitat patches, depending on the degree of differentiation from the matrix, can add few or many elements to the species pool of a particular landscape. Their importance to biodiversity is particularly relevant in areas with complex landscapes, where natural, naturalized, or managed habitats are interspersed by small patches of habitat types with very different biophysical characteristics; e.g., fruit orchards and riparian areas. This is the case of the montado landscape, a cork oak agroforestry system that largely covers south-western Portugal. We evaluated whether the high mammalian biodiversity found in this system is, in part, the cumulative result of the species found in the non-matrix habitats. Our results indicate that in areas where there are inclusions of orchards/olive yards and riparian vegetation in the cork oak woodland, a significantly higher number of mammalian species are present. We further detected a positive effect of low human disturbance on mammal diversity. Ultimately, our results can be used by managers to augment their management options, since we show that the inclusion and maintenance of non-matrix habitat patches in cork oak agro-silvo-forestry systems can help to maximize mammal biodiversity without compromising services associated with agriculture and forestry.     

Biscogniauxia mediterranea associated with cork oak (Quercus suber) in Tunisia: Relationships between phenotypic variation,genetic diversity and ecological factors

Biscogniauxia mediterranea is a xylariaceous ascomycete responsible for ‘charcoal disease’, the most frequent disease of cork oak in the Mediterranean basin. However, little is known regarding this fungus in North Africa. This is the first report on the morphological and genetic diversity of B. mediterranea populations in Tunisia.A total of forty-eight isolates from cork oak trees, corresponding to three different sites and three tree parts, were identified as B. mediterranea based on morphological and molecular diagnosis. Variability among the isolates was evaluated using morphological traits and microsatellite-primed PCR (MSP-PCR). B. mediterranea isolates showed high variability in culture, specifically in colony color. A high level of genetic diversity within populations and within tree parts was detected (H = 0.417, I = 0.605, and H = 0.415, I = 0.601 respectively). Significant genetic differentiation among populations (G_ST = 0.116 and Φ_ST = 0.137; p < 0.001) was determined. However, a low genetic differentiation among tree parts (G_ST = 0.066 and Φ_ST = 0.018; p = 0.07) was observed. Principal coordinate analysis showed that genetic divergence was partially related to the geographical origin. Cluster analysis based on morphological traits showed that the grouping of the isolates occurs independently of the geographic location and the tree part. The effective number of alleles (Ne), the Nei's gene diversity index (H), the Shannon's information index (I), the colony color and the presence of exudates were significantly correlated with the altitude and the rainfall. The number of alleles (Na), the percentage of polymorphic loci (PPL), the texture and the density of the mycelium were significantly correlated with the temperature. These results provide a deeper understanding of population genetics of B. mediterranea and its adaptation to environmental conditions which could help to develop control strategies against charcoal canker disease.     

Synthetic seed production from encapsulated somatic embryos of cork oak (Quercus suber L.) and automated growth monitoring

Cork oak (Quercus suber) somatic embryos were coated with alginate for the production of synthetic seeds and their storability for commercialization was investigated. Also, the automatic monitoring of somatic embryo growth with a digital system of image capture was tested. A power regression model was fitted between size and fresh weight (Adjusted R-squared = 0.96). This method permitted growth assessment without contamination risk and opens the possibility of an automated control of culture growth for the future up scaling of plant production. Conversion rate of synthetic seeds was higher on medium supplemented with mineral nutrients than on medium without nutrients. Also, when the somatic embryos were coated without mineral nutrients added to the capsule, conversion rate was significantly lower. The addition of sucrose to the capsule had no significant effect on the conversion rate. No differences were recorded between 50 and 100 mM CaCl₂ for capsule complexation. Synthetic seeds were cold stored at 4°C for two months without significant loss of conversion capacity. The present study reports the first attempts to determine optimal storage time and conditions for conversion of encapsulated somatic embryos of cork oak.     

The roles of genetic drift and natural selection in quantitative trait divergence along an altitudinal gradient in Arabidopsis thaliana

Understanding how natural selection and genetic drift shape biological variation is a central topic in biology, yet our understanding of the agents of natural selection and their target traits is limited. We investigated to what extent selection along an altitudinal gradient or genetic drift contributed to variation in ecologically relevant traits in Arabidopsis thaliana. We collected seeds from 8 to 14 individuals from each of 14 A. thaliana populations originating from sites between 800 and 2700 m above sea level in the Swiss Alps. Seed families were grown with and without vernalization, corresponding to winter-annual and summer-annual life histories, respectively. We analyzed putatively neutral genetic divergence between these populations using 24 simple sequence repeat markers. We measured seven traits related to growth, phenology and leaf morphology that are rarely reported in A. thaliana and performed analyses of altitudinal clines, as well as overall Q_ST-F_ST comparisons and correlation analyses among pair-wise Q_ST, F_ST and altitude of origin differences. Multivariate analyses suggested adaptive differentiation along altitude in the entire suite of traits, particularly when expressed in the summer-annual life history. Of the individual traits, a decrease in rosette leaf number in the vegetative state and an increase in leaf succulence with increasing altitude could be attributed to adaptive divergence. Interestingly, these patterns relate well to common within- and between-species trends of smaller plant size and thicker leaves at high altitude. Our results thus offer exciting possibilities to unravel the underlying mechanisms for these conspicuous trends using the model species A. thaliana.     

Involvement of free and conjugated polyamines and free amino acids in the adventitious rooting of micropropagated cork oak and grapevine shoots

The recent advances in biotechnology have boosted interest in the differentiation processes, including adventitious rooting. Differentiation processes depend on endogenous factors, among which auxins and polyamines are believed to play a major role. A positive correlation between polyamine accumulation and the induction of adventitious rooting by auxin has been observed in numerous woody species, suggesting that polyamines could be used as markers of the rooting process. The aim of the present work is to investigate whether primary and secondary nitrogen metabolism is involved in adventitious root induction by auxin treatments in cork oak (Quercus suber L.) and grapevine (Vitis vinifera L.) shoots cultured in vitro. For this purpose, we followed the profile of free and conjugated polyamines, free amino acid pools and ¹⁵N-labelling profiles during root induction and expression. We have also observed the effects of cyclohexylamine (CHA), an inhibitor of spermidine synthase. Taking the results together, it is possible to conclude that: (a) glutamine is the most abundant free amino acid in grapevine, while in cork oak, asparagine and arginine are the major amino acids; (b) in grapevine, auxin did not significantly affect the glutamine levels, but changed the ¹⁵N-enrichment and labelling pattern of arginine; (c) auxin affected asparagine levels and ¹⁵N-labelling pattern of glutamine in cork oak; (d) in both cork oak and grapevine, free putrescine (Put) can be considered as a marker of in vitro root induction; (e) in both species, the presence of CHA resulted in the accumulation of free Put; (f) no Put catabolism was detected in the form of ¹⁵N-NMR products, namely ¹⁵N-γ-aminobutyric acid; (g) the CHA-induced accumulation of Put only increased grapevine rooting rate.