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Additional file 6: Figure S5. Three-dimension PCA for RNAseq correlation. Principal Component coordinates were calculated using sample read counts. Figure S6 - Hierarchical clustering map for differential expression genes.

Additional file 3: Figure S3. Flowchart of sequencing and de novo assembly of A.donax leaf and root transcriptome under cadmium treatment.

Additional file 4: Figure S4. Length distribution of transcripts and unigenes.

Additional file 2: Figure S2. Effect of cadmium treatment on morpho-biometric and physiological parameters of A. donax G10 ecotype. A) Main stem height per pot. B) Biomass dry weight. C) Net photosynthesis efficiency.

Uncertainty in predictions of long-term yields of perennial grasses makes business plans untenable in the short run. Long-term data across varied environments, including marginal lands, will help in preventing uncertainty while providing farmers and entrepreneurs with sound information to estimate reliable and affordable strategies on what, where, and how long to grow perennial grasses. In the present study, the long-term yields (11 to 22years) of switchgrass (Panicum virgatum L.), miscanthus (Miscanthus × giganteus Greef et Deuter), and giant reed (Arundo donax L.) grown in northern and southern Mediterranean environments are reported. Switchgrass was grown in Greece and northern Italy, giant reed in southern and northern Italy, and miscanthus in southern Italy. Furthermore, lowland and upland switchgrass ecotypes were compared in Greece. Despite similar biomass productions (9.8 and 10.0Mg DM ha−1 for uplands and lowlands, respectively), the upland ecotypes showed a significantly higher yield stability (CV of 24 and 32% for uplands and lowlands, respectively) over a 17-year period. Biomass yield varied considerably across years and locations; giant reed outperformed switchgrass under northern Italy environment (21.2 and 13.6Mg DM ha−1 for giant reed and switchgrass, respectively). Annual yield of switchgrass was 30% higher in the north than south Mediterranean; miscanthus showed intermediate production compared to giant reed and switchgrass (average of 22years) and a CV similar to switchgrass. In summary, these results evidence that multi-location, long-term trials are strongly needed to reduce uncertainties on crop yield variability and provide more accurate data from which optimized socio-economic and environmental predictions can be achieved.

Figure S6. Phylogenetic relationship among A. donax salt responsive clusters and orthologues belonging to different plant sources. a cluster 14,027–155,903 homolog of Phramites australis Na+/H+ antiporter (NHX1). b cluster 14,027–181,583 homolog of Arabidopsis thaliana Na+/H+ exchanger 2 (NHX2). c cluster 14,027–182,899 homolog of Oryza sativa CBL-interacting protein kinase 1 (CIPK1-SOS2-like). d cluster 14,027–182,899 homolog of Oryza sativa CBL-interacting protein kinase 24 (SOS2). e cluster 14,027–54,233 homolog of Setaria italica cation transporter (HKT9). f cluster 14,027–231,386 homolog of Arabidopsis thaliana persulfide dioxygenase (ETHE1). (DOCX 171 kb)

Figure S1. Effect of salt stress upon G2, G18 and G20 ecotype morpho-biometric and physiological parameters. . a Leaf number per pot. b Stem number per pot. c Main stem height. d SPAD. e Net photosynthesis. f Dry biomass (PDF 97 kb)

Table S2. Distribution of KEGG pathways for DEGs in the three sample sets. (DOCX 15 kb)

Research is needed to look for plants or lines that can thrive on soils affected by water deficit or other constraints. The present work investigated the potentiality of Saccharum spontaneum L. spp. aegyptiacum (Willd.) Hack., a lignocellulosic, perennial, rhizomatous, no-food crop in semi-arid Mediterranean area. A 3-year field trial was carried out with the aim to evaluate its physiology, biomass yield, water use efficiency, and biomass quality under different soil water availability. During 2011/2012, 2012/2013, and 2013/2014 growing seasons (hereinafter referred as 2011, 2012, and 2013, respectively), three levels of maximum evapotranspiration restitution (ETm) were compared: I 100 (100% ETm restitution), I 50 (50% ETm restitution), and I 0 (rainfed condition). Net photosynthesis, stomatal conductance, and transpiration rate were strictly related to the available soil water content (ASWC), with maximum gas exchange at field capacity. However, gas exchange between plants and atmosphere was also measured when ASWC was close to wilting point. Biomass dry matter (DM) yield and main morpho-biometric traits (e.g., stem height and basal stem diameter) were significantly affected by ASWC. A non-linear model showed that maximum DM yield, 37.86 Mg ha −1 , can be achieved when 1150 mm of water were used by the crop. Water use efficiency (WUE) was always highest in rainfed condition ( I 0 ), however, only in 2013 I 0 was significantly higher than I 50 and I 100 (5.89 g L −1 vs 4.26 and 3.33 g L −1 ). Within the variables employed, a linear model showed that WUE was negatively related to crop water use (CWU). The fiber content was not affected by the irrigation treatments. In the average, hemicellulose, cellulose, and lignin accounted for 23.9 (% w/w), 35.0 (% w/w), and 19.9 (% w/w), respectively. On the other hand, moisture and ash content, bulk density, low heating value, and ash melting point resulted significantly affected by the treatment. Present results suggested that S. spontaneum spp. aegyptiacum possesses a range of agronomically desirable traits of biomass crop: C4 plant, high biomass yield, active assimilation rates during drought–stress periods, able to use water efficiently, and satisfactory biomass quality.

This chapter describes the physiology of kenaf from seed germination and root development till the effects of water and nutrients stress on grown plants. Review on kenaf agro-physiology of experiments carried out worldwide are presented and discussed mainly at the canopy and whole-plant level with the aim to help producers to make decisions and planning of production. However, few literature reports experimental results on the physiology of this multipurpose crop especially in terms of assimilation rate and its relation with environmental and agronomic factors. Knowledge on gas exchange rate and stomatal conductance may be a key support in understanding the physiology of Kenaf in terms of water requirements, its ability of light conversion into carbonaceous molecules influencing crop production potential and, indirectly, the carbon sequestration activity. In kenaf seedling development takes place when temperatures are higher than 10 °C, supporting the idea that kenaf is a macrothermal plant and optimal sowing has to be carried out during spring-summer, depending on the area of cultivation. Kenaf is very sensitive to reduced soil water availability, however, under moderate water stress conditions the crop maintains root development while reducing final biomass yield. Recent studies from Greece and Italy showed that even though kenaf uses CO2, solar radiation, water, and nitrogen less efficiently than C4 crops its assimilation rates can reach 50–58 kg of CO2 ha−1 h−1. However, great differences in terms of net photosynthesis have been reported by various authors, which may be related to the different environmental variables and agronomic managements during field and controlled experimental environments, such as air temperature, light intensity, water supply, nutrients availability, relative humidity, wind, cultivar, plant density, and soil type. Similar results were reported in the literature regarding stomatal conductance and transpiration rates. In experiments carried out during the night, stomatal conductance and transpiration rate determined water looses probably affecting the water requirement of the crop. Kenaf could be described as opportunistic in relation to water availability, with a high rate of stomatal conductance and transpiration when soil water is available but with markedly reduced leaf conductance and transpiration rate when water is limited. Extinction coefficient for light (K L ) and nitrogen (K N ), under water limited conditions, were found to be always smaller than under irrigated conditions, as a result of irregular adjustment of leaf orientation to incident radiation particularly during midday. Vertical Specific Leaf Nitrogen (SLN) distributions were found in canopies when leaf area index (LAI) was >1.5. It was observed a strong association between SLN and PAR distributions in irrigated kenaf canopies. Due to its tropical origin, kenaf behaves as a short-day plant remaining vegetative until daylength falls below 12.9 or 12.45 h. Flowering of late-maturity cultivars is under photoperiodic control; conversely, photoperiod does not influence the flowering of early maturity cultivars. Radiation use efficiency (RUE) in kenaf is positively associated with specific leaf nitrogen. RUE decreased under water deficit and nitrogen supply. Water use efficiency (WUE) decreased as the level of irrigation increased. It was higher than other C3 crops, but lower as compared to C4 crops tested in the same environments. Information on nutrient use efficiency (NUE) for kenaf is scarce and not well quantified to date. Higher NUE values were reported for micronutrients than for macronutrients. This last characteristic needs further investigation, since improvement of NUE is an essential and challenging prerequisite for the expansion of bioenergy crop productions into less fertile soils and marginal lands.

The European Union (EU) has set quite an ambitious goal for biofuels contribution to the makeup of the renewable energy mix in the next decades. While substantial efforts have been made to develop the technologies for the transformation of biomass into biofuels, it is still uncertain to what extent the EU will be able to generate the biomass needed to meet its targets without compromising domestic food security. Using a bottom-up approach, this review addresses one of the key elements: the potential availability of land for non-food crops in the EU. The assess-ment is based on a land allocation model, which calculates surplus land that would be available for non-food crops after satisfying food and feed demands. Projections of future agriculture productivity and changes in population are the most important parameters of the modeling applied for two future scenarios established for the years 2020 and 2030. The total area potentially available for non-food crops in the EU-27 (excluding Cyprus and Malta) is estimated to be 13.2 million ha in the current situation, with fallow land the largest contributor. In scenarios 2020 and 2030, addi-tional land would be released from food and fodder crops, resulting in total land potential of 20.5 million ha in 2020 and 26.2 million ha in 2030. Results presented on a regional basis indicate potential locations for biomass transforma-tion plants in terms of feedstock production. A set of non-food crops can be recommended for the diverse climate and agronomic conditions of the entire EU area. © 2010 Society of Chemical Industry and John Wiley & Sons, LtdKeywords: land assessment; land use; energy crops; non-food crops; bioenergy; biofuels