Prunus Knotted-like Genes: Genome-Wide Analysis, Transcriptional Response to Cytokinin in Micropropagation, and Rootstock Transformation.

Knotted1-like homeobox (KNOX) transcription factors are involved in plant development, playing complex roles in aerial organs. As Prunus species include important fruit tree crops of Italy, an exhaustive investigation of KNOX genes was performed using genomic and RNA-seq meta-analyses. Micropropagation is an essential technology for rootstock multiplication; hence, we investigated KNOX transcriptional behavior upon increasing 6-benzylaminopurine (BA) doses and the effects on GF677 propagules. Moreover, gene function in Prunus spp. was assessed by Gisela 6 rootstock transformation using fluorescence and peach KNOX transgenes. Based on ten Prunus spp., KNOX proteins fit into I-II-M classes named after Arabidopsis. Gene number, class member distribution, and chromosome positions were maintained, and exceptions supported the diversification of Prunus from Cerasus subgenera, and that of Armeniaca from the other sections within Prunus. Cytokinin (CK) cis-elements occurred in peach and almond KNOX promoters, suggesting a BA regulatory role in GF677 shoot multiplication as confirmed by KNOX expression variation dependent on dose, time, and interaction. The tripled BA concentration exacerbated stress, altered CK perception genes, and modified KNOX transcriptions, which are proposed to concur in in vitro anomalies. Finally, Gisela 6 transformation efficiency varied (2.6-0.6%) with the genetic construct, with 35S:GFP being more stable than 35S:KNOPE1 lines, which showed leaf modification typical of KNOX overexpression.

The Role of Italy in the Use of Advanced Plant Genomic Techniques on Fruit Trees: State of the Art and Future Perspectives.

Climate change is deeply impacting the food chain production, lowering quality and yield. In this context, the international scientific community has dedicated many efforts to enhancing resilience and sustainability in agriculture. Italy is among the main European producers of several fruit trees; therefore, national research centers and universities undertook several initiatives to maintain the specificity of the 'Made in Italy' label. Despite their importance, fruit crops are suffering from difficulties associated with the conventional breeding approaches, especially in terms of financial commitment, land resources availability, and long generation times. The 'new genomic techniques' (NGTs), renamed in Italy as 'technologies for assisted evolution' (TEAs), reduce the time required to obtain genetically improved cultivars while precisely targeting specific DNA sequences. This review aims to illustrate the role of the Italian scientific community in the use of NGTs, with a specific focus on Citrus, grapevine, apple, pear, chestnut, strawberry, peach, and kiwifruit. For each crop, the key genes and traits on which the scientific community is working, as well as the technological improvements and advancements on the regeneration of local varieties, are presented. Lastly, a focus is placed on the legal aspects in the European and in Italian contexts.

Effect of Bacillus subtilis on antioxidant enzyme activities in tomato grafting.

Grafting generally means stress to a plant and this triggers antioxidant defense systems. An imbalance in reactive oxygen species may negatively affect the grafting success. Several research projects have studied the association with plant growth-promoting rhizobacteria (PGPR) and it has been documented that they enhance nutrient acquisition, regulate hormone levels, and influence the antioxidant response in crops. However, little is known about the strategy of inoculating grafted herbaceous plants with PGPR and its effect on the antioxidant response. The effects of inoculating a strain of Bacillus subtilis on the antioxidant metabolism of grafted tomato were evaluated. In this study, two different rootstocks were used for tomato (Solanum lycopersicum L. var. Rio Grande (RG)): [S. lycopersicum L. var. cerasiforme (Ch)] and eggplant [(Solanum melanogena L. (Ber)] to establish a compatible graft (RGCh) and a semicompatible graft (RGBer). Enzyme activities involved in the antioxidant defense system: superoxide dismutase (SOD), catalase (CAT), phenylalanine ammonia lyase (PAL), polyphenol oxidase (PPO), peroxidase (POD), and total phenols were measured during 4 weeks after grafting. The results show that for RGCh, during the first two weeks after grafting, the tendency was a decrease of the enzyme activity for SOD, CAT, PAL when inoculated with B. subtilis; while in the semicompatible graft RGBer, PPO and PAL decreased their activity after inoculation. For both combinations, the quantity of total phenols varied depending on the day. In both graft combinations, applications of B. subtilis resulted in 86 and 80% callusing compared with the uninoculated control where the percentages were 74 and 70% for RGCh and RGBer, respectively. The highest significant graft success (95%) was recorded 28 days after grafting for inoculated RGBer. These findings imply that B. subtilis induced antioxidant mechanisms in grafted plants and suggest that inoculation with this growth-promoting bacterium can represent a biotechnological approach to improve success in tomato grafting.

Extracts from Cell Suspension Cultures of Strawberry (Fragaria x ananassa Duch): Cytotoxic Effects on Human Cancer Cells.

Natural compounds are emerging as agents for the treatment of malignant diseases. We previously showed that extracts from in vitro cell suspension cultures of strawberry reduced murine melanoma cell proliferation, as shown for fruit extracts. In this work, chromatographic, mass spectrometric, and spectrophotometric analyses were carried out to identify the bioactive compound exerting the detected cytotoxic activity. Moreover, aiming to confirm the anti-proliferative activity of the extracts against both paediatric and adult human tumors, cytotoxic experiments were performed on neuroblastoma, colon, and cervix carcinoma cell lines. Extracts from in vitro cell suspension cultures of strawberry induced a statistically significant reduction of cell growth in all the tumor cell lines tested. Interestingly, human fibroblasts from healthy donors were not subjected to this cytotoxic effect, highlighting the importance of further preclinical investigations. The accurate mass measurement, fragmentation patterns, and characteristic mass spectra and mass losses, together with the differences in chromatographic retention times and absorbance spectra, led us to hypothesize that the compound acting as an anti-proliferative agent could be a novel acetal dihydrofurofuran derivative (C8H10O3, molecular mass 154.0630 amu).

Anthocyanic pigments from elicited in vitro grown shoot cultures of Vaccinium corymbosum L., cv. Brigitta Blue, as photosensitizer in natural dye-sensitized solar cells (NDSSC).

We investigated the effect on anthocyanins and total phenols content and antioxidant capacity of in vitro shoot cultures of Vaccinium corymbosum L., cv. Brigitta Blue, grown on an eliciting medium supplied with 10 µM naphthalene acetic acid, in combination with reduced content of salts and organics in respect to the basal medium. After 45 days, higher content of total phenols and anthocyanins was obtained from extracts of shoots grown on the elicitation medium. Anthocyanin molecules, absent in control shoots, were identified by HPLC-MS as delphinidine-glycoside, cyanidine-glycoside, delphinidine-arabinoside, cyanidine- arabinoside and cyanidine-acetylglycoside. Chlorogenic acid, present in control shoots, was nearly absent in elicited shoots. We exploited the anthocyanin - based raw extracts of "Brigitta Blue" shoots grown on the elicitation medium as a source of natural dye photosensitizers for Dye Sensitized Solar Cells, taking into account that such raw extracts showed antioxidant properties and photostability features. A purified dye was also prepared and the comparison of the latter with the raw one has been analysed by spectrophotometric, chromatographic and power conversion efficiency determination. The power conversion efficiencies from the raw and the purified dye were not different and they were comparable to the data obtained by other authors with anthocyanin-based dyes from in vivo grown plants.

EpiHRMAssay, in tube and in silico combined approach for the scanning and epityping of heterogeneous DNA methylation.

Reliable and cost-effective assays with adequate sensitivity are required to detect the DNA methylation profile in plants for scientific and industrial purposes. The proposed novel assay, named EpiHRMAssay, allows to quantify the overall methylation status at target loci and to enable high-throughput analyses. It combines in tube High Resolution Melting Analysis on bisulphite-treated templates with the in silico prediction of the melting profile of virtual epialleles using uMELTSM software. The predicted melting temperatures (T m-s) of a set of epialleles characterized by different numbers of methylated cytosines (#mC) or different mC configurations were obtained and used to build calibration models, enabling the quantification of methylation in unknown samples using only the in tube observed melting temperature (T m-o). EpiHRMAssay was validated by analysing the promoter region of CMT3, DDM1, and ROS1 genes involved in the regulation of methylation/demethylation processes and chromatin remodelling within a population of peach plants. Results demonstrate that EpiHRMAssay is a sensitive and reliable tool for locus-specific large-scale research and diagnostic contexts of the regulative regions of genes, in a broad range of organisms, including mammals. EpiHRMAssay also provides complementary information for the assessment of heterogeneous methylation and can address an array of biological questions on epigenetic regulation for diversity studies and for large-scale functional genomics.

Ecophysiological and phytochemical response to ozone of wine grape cultivars of Vitis vinifera L.

Vitis vinifera sensitivity to tropospheric ozone (O3) has been evidenced in several studies. In this work, physiological and metabolic effects of O3 on two wine cultivars of V. vinifera (i.e. Maturano and San Giuseppe) have been studied. Moreover, chlorogenic acid (CGA) production, in consideration of its importance in the biosynthetic pathway of polyphenols and as antioxidant, has been investigated. Maturano cultivar resulted more sensitive to O3, as evidenced by the gas exchange reduction at the early stage of treatment, and by the increase in Ci/Ca and the decoupling of net photosynthesis and the stomatal conductance at the end of the treatment. Unexpectedly, O3 did not activate stilbene production. Ozone induced an early CGA decrease, significantly more consistent in cv. Maturano, and an increase after 8 days, more consistent in cv. S. Giuseppe. These results suggest that CGA could be considered a biochemical marker of O3-induced stress in V. vinifera.

The KNOTTED-like genes of peach (Prunus persica L. Batsch) are differentially expressed during drupe growth and the class 1 KNOPE1 contributes to mesocarp development.

The Knotted-like transcription factors (KNOX) contribute to plant organ development. The expression patterns of peach KNOX genes showed that the class 1 members act precociously (S1-S2 stages) and differentially during drupe growth. Specifically, the transcription of KNOPE1 and 6 decreased from early (cell division) to late (cell expansion) S1 sub-stages, whilst that of STMlike1, 2, KNOPE2, 2.1 ceased at early S1. The KNOPE1 role in mesocarp was further addressed by studying the mRNA localization in the pulp cells and vascular net at early and late S1. The message signal was first diffuse in parenchymatous cells and then confined to hypodermal cell layers, showing that the gene down-tuning accompanied cell expansion. As for bundles, the mRNA mainly featured in the procambium/phloem of collateral open types and subsequently in the phloem side of complex structures (converging bundles, ducts). The KNOPE1 overexpression in Arabidopsis caused fruit shortening, decrease of mesocarp cell size, diminution of vascular lignification together with the repression of the major gibberellin synthesis genes AtGA20ox1 and AtGA3ox1. Negative correlation between the expression of KNOPE1 and PpGA3ox1 was observed in four cultivars at S1, suggesting that the KNOPE1 repression of PpGA3ox1 may regulate mesocarp differentiation by acting on gibberellin homeostasis.

The peach (Prunus persica L. Batsch) genome harbours 10 KNOX genes, which are differentially expressed in stem development, and the class 1 KNOPE1 regulates elongation and lignification during primary growth.

The KNOTTED-like (KNOX) genes encode homeodomain transcription factors and regulate several processes of plant organ development. The peach (Prunus persica L. Batsch) genome was found to contain 10 KNOX members (KNOPE genes); six of them were experimentally located on the Prunus reference map and the class 1 KNOPE1 was found to link to a quantitative trait locus (QTL) for the internode length in the peach×Ferganensis population. All the KNOPE genes were differentially transcribed in the internodes of growing shoots; the KNOPE1 mRNA abundance decreased progressively from primary (elongation) to secondary growth (radial expansion). During primary growth, the KNOPE1 mRNA was localized in the cortex and in the procambium/metaphloem zones, whereas it was undetected in incipient phloem and xylem fibres. KNOPE1 overexpression in the Arabidopsis bp4 loss-of-function background (35S:KNOPE1/bp genotype) restored the rachis length, suggesting, together with the QTL association, a role for KNOPE1 in peach shoot elongation. Several lignin biosynthesis genes were up-regulated in the bp4 internodes but repressed in the 35S:KNOPE1/bp lines similarly to the wild type. Moreover, the lignin deposition pattern of the 35S:KNOPE1/bp and the wild-type internodes were the same. The KNOPE1 protein was found to recognize in vitro one of the typical KNOX DNA-binding sites that recurred in peach and Arabidopsis lignin genes. KNOPE1 expression was inversely correlated with that of lignin genes and lignin deposition along the peach shoot stems and was down-regulated in lignifying vascular tissues. These data strongly support that KNOPE1 prevents cell lignification by repressing lignin genes during peach stem primary growth.

The peach (Prunus persica [L.] Batsch) homeobox gene KNOPE3, which encodes a class 2 knotted-like transcription factor, is regulated during leaf development and triggered by sugars.

Class 1 KNOTTED1-like transcription factors (KNOX) are known to regulate plant development, whereas information on class 2 KNOX has been limited. The peach KNOPE3 gene was cloned, belonged to a family of few class 2 members and was located at 66 cM in the Prunus spp. G1 linkage-group. The mRNA localization was diversified in leaf, stem, flower and drupe, but recurred in all organ sieves, suggesting a role in sap nutrient transport. During leaf development, the mRNA earliest localized to primordia sieves and subsequently to mesophyll cells of growing leaves. Consistently, its abundance augmented with leaf expansion. The transcription was monitored in leaves responding to darkening, supply and transport block of sugars. It peaked at 4 h after darkness and dropped under prolonged obscurity, showing a similar kinetic to that of sucrose content variation. Feeding leaflets via the transpiration stream caused KNOPE3 up-regulation at 3 h after fructose, glucose and sucrose absorption and at 12 h after sorbitol. In girdling experiments, leaf KNOPE3 was triggered from 6 h onwards along with sucrose and sorbitol raise. Both the phloem-associated expression and sugar-specific gene modulation suggest that KNOPE3 may play a role in sugar translocation during the development of agro-relevant organs such as drupe.

In vitro regeneration of wild pear (Pyrus pyraster Burgsd) clones tolerant to Fe-chlorosis and somaclonal variation analysis by RAPD markers.

An in vitro adventitious regeneration system under selective pressure was established in Pyrus pyraster Burgsd to obtain somaclones with higher adaptability to calcareous soils. P. pyraster is important species, both for its relative closeness to cultivated pear and for reforestation of marginal farmland and for the production of timber. Shoot regeneration was induced from leaves and vegetative apices of in vitro-grown shoots on a modified LP medium supplemented with naphtaleneacetic acid (1.07 microM) and benziladenine (BA, 8.9 microM). After 30 days, explants were transferred to an expression medium consisting of the same basal medium with only BA present. Selective treatments utilized MS medium with Fe-EDTA replaced by equimolar amount of FeSO4 with either KHCO(3) or NaHCO(3). Through the selection process 11 putatively tolerant lines were obtained from vegetative shoot apices. RAPD analysis was performed on these lines to allow comparison to the mother clone. A total of seven 10-mer primers were used to amplify all the genotypes and 74 scorable fragments were produced. These were analysed using the Dice similarity index, showing genetic variability among the 11 regenerated clones and between them and the mother clone.