Transcriptional, metabolic and DNA methylation changes underpinning the response of Arundo donax ecotypes to NaCl excess

Modulation of class III peroxidase pathways and phenylpropanoids in Arundo donax under salt and phosphorus stress

Arundo donax L. is an invasive species that has been recently employed for biomass production due to its well-known ability to colonize harsh environment. Based on previous observations, the present study investigated the potential role of phenylpropanoids and class III peroxidases to confer adaptation through biochemical and transcriptomic analysis in A. donax after Na⁺ and P excess supply, both in single stress and in combination, and after growth at low P level. The levels of hydrogen peroxide, flavonoids (i.e., quercetin, apigenin and kaempferol derivatives) and the activity of class III peroxidases, as well as the expression of several genes encoding for their enzymes involved in their biosynthesis, increased when Na⁺ was supplied in combination with P. These results suggest that those biomolecules are involved in the response of A. donax, to the presence of +Na and P in the soil. Moreover, even though at the sampling time no significant accumulation of lignin has been determined, the trend of accumulation of such metabolite and most of all the increase of several transcripts involved in its synthesis was found. This work for the first time indicates the need for further investigation devoted to elucidating whether the strengthening of cell walls via lignin synthesis is one of the mechanisms used by A. donax to adapt to harsh environments.

Identification of Known and Novel Arundo donax L. MicroRNAs and Their Targets Using High-Throughput Sequencing and Degradome Analysis

MicroRNAs (miRNAs) are a class of non-coding molecules involved in the regulation of a variety of biological processes. They have been identified and characterized in several plant species, but only limited data are available for Arundo donax L., one of the most promising bioenergy crops. Here we identified, for the first time, A. donax conserved and novel miRNAs together with their targets, through a combined analysis of high-throughput sequencing of small RNAs, transcriptome and degradome data. A total of 134 conserved miRNAs, belonging to 45 families, and 27 novel miRNA candidates were identified, along with the corresponding primary and precursor miRNA sequences. A total of 96 targets, 69 for known miRNAs and 27 for novel miRNA candidates, were also identified by degradome analysis and selected slice sites were validated by 5′-RACE. The identified set of conserved and novel candidate miRNAs, together with their targets, extends our knowledge about miRNAs in monocots and pave the way to further investigations on miRNAs-mediated regulatory processes in A. donax, Poaceae and other bioenergy crops.

Genetic Improvement of Arundo donax L.: Opportunities and Challenges

Arundo donax L., the giant reed-being a long-duration, low-cost, non-food energy crop able to grow in marginal lands-has emerged as a potential alternative to produce biomass for both energy production, with low carbon emissions, and industrial bioproducts. In recent years, pioneering efforts have been made to genetically improve this very promising energy crop. This review analyses the recent advances and challenges encountered in using clonal selection, mutagenesis/somaclonal variation and transgenesis/genome editing. Attempts to improve crop yield, in vitro propagation efficiency, salt and heavy metal tolerance by clonal selection were carried out, although limited by the species' low genetic diversity and availability of mutants. Mutagenesis and somaclonal variation have also been attempted on this species; however, since Arundo donax is polyploid, it is very difficult to induce and select promising mutations. In more recent years, genomics and transcriptomics data are becoming available in Arundo, closing the gap to make possible the genetic manipulation of this energy crop in the near future. The challenge will regard the functional characterization of the genes/sequences generated by genomic sequencing and transcriptomic analysis in a complex polyploid genome.

Genetic and epigenetic dynamics affecting anthocyanin biosynthesis in potato cell culture

Anthocyanins are antioxidant pigments widely used in drugs and food preparations. Flesh-coloured tubers of the cultivated potato Solanum tuberosum are important sources of different anthocyanins. Due to the high degree of decoration achieved by acylation, anthocyanins from potato are very stable and suitable for the food processing industry. The use of cell culture allows to extract anthocyanins on-demand, avoiding seasonality and consequences associated with land-based-tuber production. However, a well-known limit of cell culture is the metabolic instability and loss of anthocyanin production during successive subcultures. To get a general picture of mechanisms responsible for this instability, we explored both genetic and epigenetic regulation that may affect anthocyanin production in cell culture. We selected two clonally related populations of anthocyanin-producing (purple) and non-producing (white) potato cells. Through targeted molecular investigations, we identified and functionally characterized an R3-MYB, here named StMYBATV. This transcription factor can interact with bHLHs belonging to the MBW (R2R3-MYB, bHLH and WD40) anthocyanin activator complex and, potentially, may interfere with its formation. Genome methylation analysis revealed that, for several genomic loci, anthocyanin-producing cells were more methylated than clonally related white cells. In particular, we localized some methylation events in ribosomal protein-coding genes. Overall, our study explores novel molecular aspects associated with loss of anthocyanins in cell culture systems.

Physiological, Biochemical, and Metabolic Responses to Short and Prolonged Saline Stress in Two Cultivated Cardoon Genotypes

Cultivated cardoon is a multipurpose crop with adaptability to limiting environments. Two genotypes ("Bianco Avorio" and "Spagnolo") were comparatively characterized in response to short and prolonged 100 mM NaCl stress in hydroponics. Salt induced no growth variations between genotypes or symptoms of NaCl toxicity, but boosted ABA accumulation in roots and leaves. Both genotypes had high constitutive phenol content, whose major components were depleted upon 2 days of stress only in "Bianco Avorio". Prolonged stress stimulated accumulation of proline, phenylpropanoids, and related transcripts, and non-enzymatic antioxidant activity. Decreased antioxidant enzymes activities upon short stress did not occur for APX in "Spagnolo", indicating a stronger impairment of enzymatic defenses in "Bianco Avorio". Nonetheless, H2O2 and lipid peroxidation did not increase under short and prolonged stress in both genotypes. Overall, the two genotypes appear to share similar defense mechanisms but, in the short term, "Bianco Avorio" depends mainly on non-enzymatic antioxidant phenylpropanoids for ROS scavenging, while "Spagnolo" maintains a larger arsenal of defenses. Upon prolonged stress, proline could have contributed to protection of metabolic functions in both genotypes. Our results provide cues that can be exploited for cardoon genetic improvement and highlight genotypic differences for breeding salinity tolerant varieties.