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Small RNAs (sRNAs) control a wide range of development and physiological pathways in plants. To address the response of sRNA biogenesis to drought stress, we identified sRNA biogenesis genes, including 11 encoding argonautes (AGO), 8 encoding Dicer-like proteins (DCL), and 9 encoding RNA-dependent RNA polymerases (RDR) in the peach genome. Notably, the largest numbers of sRNA biogenesis genes are located to chromosome 1. The PAZ, PIWI, and MID domains were identified in PpAGOs, while the ribonuclease IIIa and IIIb domains were characterized in PpDCLs. The RDRP domain was recognized in PpRDRs. Orthologous similarity and collinearity analyses between Arabidopsis and peach revealed 5, 1, and 2 collinear blocks in AGOs, DCLs, and RDRs, respectively. Moreover, 41, 40, and 42 cis-acting elements were located in the promoters of PpAGOs, PpDCLs, and PpRDRs, respectively, with the majority related to drought stress response. Analysis of RNA sequencing (RNA-seq) data revealed that sRNA biogenesis genes were involved in drought stress response in different tissues. Furthermore, the expression of candidate genes was verified in two peach cultivars, Beijing 2-7 (BJ2-7) and Sinai (SN), which are tested as drought-tolerant and sensitive cultivars, respectively, based on the physiological and biochemical analyses, which revealed that the Chinese peach cultivar ‘BJ2-7’ exhibits greater drought resistance compared to the Egyptian peach cultivar ‘SN’. Interestingly, the expression of PpAGO2b, PpDCL2b, PpDCL4, and PpRDR4 genes was induced in ‘BJ2-7’ but inhibited in ‘SN’ under drought stress. Overall, this study provides insight into the roles of sRNA biogenesis genes in response to drought stress in peach.

Tomato is one of the major economically domesticated crops, and it is extensively used in different ways and purposes worldwide. Cell metabolism is the central core of all the biological processes to sustain life including cell growth, differentiation, maintenance, and response to environmental stress. To evaluate how genetic engineering can improve tomato fruit metabolome, the transcriptomic and metabolomic datasets of two transgenic tomatoes (SlMX1 overexpression and RNAi lines) have been compared with wild-type. The combined results demonstrated that the constitutive expression of SlMX1 not only increased trichome formation, carotenoids, and terpenoids as has been stated in several studies, but has also up- and down-regulated the expression of multiple genes related to cell growth (cell wall turnover), primary (carbohydrates, vitamins, and phytohormones), and secondary (phenylpropanoids, carotenoids, and terpenoids) metabolism, cell signaling, and stress responses. These changes in gene expression due to the constitutive expression of SlMX1 promote the most important agroeconomic traits such as fruit yield and quality, biosynthesis of health-promoting phytochemicals (including phenolic acids, flavonoids, and anthocyanins), and finally, activate resistance to Botrytis cinerea and repress the expression of over-ripening-related genes, thus extending the fruit shelf-life. In conclusion, the traits improvement achieved by SlMX1 overexpression can be harnessed in molecular breeding programs to engineer fruit size and yield, induce health-promoting secondary metabolites, promote fungal resistance, and finally extend the fruit shelf-life.

Abstract Selenium nanoparticles (SeNPs) have attracted considerable attention globally due to their significant potential for alleviating abiotic stresses in plants. Accordingly, further research has been conducted to develop nanoparticles using chemical ways. However, our knowledge about the potential benefit or phytotoxicity of bioSeNPs in rapeseed is still unclear. Herein, we investigated the effect of bioSeNPs on growth and physiochemical attributes, and selenium detoxification pathways compared to sodium selenite (Se (IV)) during the early seedling stage under normal and salt stress conditions. Our findings showed that the range between optimal and toxic levels of bioSeNPs was wider than Se (IV), which increased the plant’s ability to reduce salinity-induced oxidative stress. BioSeNPs improved the phenotypic characteristics of rapeseed seedlings without the sign of toxicity, markedly elevated germination, growth, photosynthetic efficiency and osmolyte accumulation versus Se (IV) under normal and salt stress conditions. In addition to modulation of Na+ and K+ uptake, bioSeNPs minimized the ROS level and MDA content by activating the antioxidant enzymes engaged in ROS detoxification by regulating these enzyme-related genes expression patterns. Importantly, the main effect of bioSeNPs and Se (IV) on plant growth appeared to be correlated with the change in the expression levels of Se-related genes. Our qRT-PCR results revealed that the genes involved in Se detoxification in root tissue were upregulated upon Se (IV) treated seedlings compared to NPs, indicating that bioSeNPs have a slightly toxic effect under higher concentrations. Furthermore, bioSeNPs might improve lateral root production by increasing the expression level of LBD16. Taken together, transamination and selenation were more functional methods of Se detoxification and proposed different degradation pathways that synthesized malformed or deformed selenoproteins, which provided essential mechanisms to increase Se tolerance at higher concentrations in rapeseed seedlings. Current findings could add more knowledge regarding the mechanisms underlying bioSeNPs induced plant growth. Graphical Abstract

Soluble sugars are an important determinant of fruit taste, but their accumulation mechanisms remain elusive. In this study, we report two vacuolar invertase inhibitor genes involved in sugar accumulation in peach, PpINHa and PpINH3. Transient overexpression of PpINH3 in peach fruits resulted in an increase in sugar content, while the opposite trend was detected for PpINHa. Unexpectedly, PpINH3 and PpINHa both had no physical interaction with vacuolar invertase (VIN). Moreover, the PpVIN genes had no or extremely low expression in fruits at the ripening stage. These results suggested that the regulatory role of PpINHa and PpINH3 in sugar accumulation is unlikely due to their interaction with PpVINs. Additionally, overexpression of PpINHa and PpINH3 had an impact on transcription of genes related to fruit sugar metabolism and transport, which is likely responsible for their regulatory role in fruit sugar accumulation. Altogether, these results indicated an important role of PpINHs in fruit accumulation in peach. Our study provides new insights into molecular mechanisms underlying sugar accumulation, which could be useful for genetic improvement of fruit taste in breeding programs of peach and other fruit crops.

Abstract Background Elevated ultraviolet-B (UV-B) radiation is potentially deleterious to many organisms specifically crop plants and has become a global challenge. Rice is an exceptionally important staple food which is grown worldwide, and many efforts have been done recently to improve rice varieties against UV-B stress. This current study aims to investigate the effects of exogenous application of β-sitosterol (βSito) on growth improvement and tolerance level of rice plants against prolonged UV-B stress. The physiological and metabolic responses were evaluated in rice plants not supplemented with βSito (Nβ) and those supplemented with βSito (Sβ). Results The Nβ and Sβ plants were grown under non-stress (ns) and under prolonged UV-B stress (uvs) conditions and termed as Nβns, Sβns and Nβuvs, Sβuvs, respectively. The application of βSito contributes positively under non-stress and specifically to UV-B stress in terms of improving numerous physiological parameters associated with growth and development such as shoot and root length, RWC, whole plant biomass, chlorophyll pigments, and photosynthetic-related parameters (Pn, Gs, Tr, WUEi, Fv/Fm, and NPQ) in Sβ compared with Nβ plants. Moreover, enhanced oxidative stress tolerance of Sβuvs vs. Nβuvs plants under stress was attributed to low levels of ROS and substantial trigger in activities of antioxidant enzymes (SOD, POD, CAT, and APX). Metabolic analysis was performed using GC-TOFMS, which revealed higher accumulation of several key metabolites including organic acids, sugars, amino acids, and others in Sβuvs vs. Nβuvs plants, which were mainly reduced in Nβ plants under stress vs. non-stress conditions. Conclusion These results provide useful data regarding the important role of βSito on growth maintenance and modulation of several metabolites associated with osmotic and redox adjustments during UV-B stress tolerance in rice plants. Importantly, βSito-regulated plasticity could further be explored specifically in relation to different environmental stresses in other economically useful crop plants.

Abstract Background Releasing the draft genome of sweet orange provides useful information on genetic structure and molecular marker association with heritable breeding traits in citrus species and their structures. Last decades, microsatellite and retrotransposons are well known as a significant diverse component of the structural evolution. They represented the most potent elements for assessing sustainable utilization of the complicated classification in citrus breeding. Our study was performed to verify the structure analysis and the parentage genetic diversity among the Egyptian citrus rootstocks and the related species. Results Here, the performance of 26 SSR and 14 LTR-IRAP in addition to 20 LTR-REMAP markers have been used to conduct the discriminating power and the status of the genetic structure analysis among twenty specimens of citrus genotypes. As a result, the three markers approach exhibited a remarkable variation among the tested genotypes. Overall, the three markers have different discrimination power; the co-dominant SSR markers can differentiate within the group level only in addition to the species level of sour orange, while the dominant markers LTR-IRAP had the ability to discriminate among the group level in addition to species level and the origin of acids. Similarly, LTR-REMAP is suitable for classifying the group level and species level for mandarins as well the origin of Egyptian acids; probably due to it is integration of SSR and LTR-IRAP techniques. Structure and PCoA results of LTR-REMAP marker in strong support for the group structure of citrus species have been divided into four sets: acids, grapefruit/pummelo, mandarin/orange, and sour orange. Conclusion Our findings of the genetic structure analysis support the monophyletic nature of the citrus species; are able to provide unambiguous identification and disposition of true species and related hybrids like lemon, lime, citron, sour orange, grapefruit, mandarin, sweet orange, pummelo, and fortunella; and resulted in their placement in individual or overlap groups. The outcomes of these results will offer helpful and potential information for breeding programs and conservation approaches as a key stage toward identifying the interspecific admixture and the inferred structure origins of Egyptian citrus rootstock and acid cultivars.

Salt stress hinders plant growth and disrupts many physio-biochemical and molecular processes. The present study evaluated the potential role of foliar applied 24-epibrassinolide (EBR) for mitigating the adverse effects of salinity in rice plants. Our findings showed that salt stress reduced several growth and physiological parameters, and substantially increased oxidative stress in rice seedlings. The foliar application of EBR replenished the negative effects of salt stress by improving plant growth and physiological attributes in rice plants. Moreover, application of EBR substantially reduced oxidative injuries by enhancing antioxidant enzymes and phenolic compounds in rice plants during salt stress. Interestingly, the endogenous ABA levels were declined in stressed plants by EBR treatment, also validated by expression analysis of ABA-related genes. In addition, application of EBR upregulated carotenoids and flavonoids pathway genes, thus showing its function to activate secondary metabolism in rice plants during salt stress. The principal component analysis (PCA) indicated that, under salt stress, the response of EBR-treated rice plants was strongly correlated with the accumulation of phenolic compounds and flavonoids. Collectively, this study presents useful insight into the distinct role of EBR by activating underlying enzymatic and non-enzymatic defense mechanisms to mitigate salinity in rice plants.

Abstract Background Phytochromes are plant photoreceptors that have long been associated with photomorphogenesis in plants; however, more recently, their crucial role in the regulation of variety of abiotic stresses has been explored. Chilling stress is one of the abiotic factors that severely affect growth, development, and productivity of crops. In the present work, we have analyzed and compared physiological, biochemical, and molecular responses in two contrasting phytochrome mutants of tomato, namely aurea (aur) and high pigment1 (hp1), along with wild-type cultivar Micro-Tom (MT) under chilling stress. In tomato, aur is phytochrome-deficient mutant while hp1 is a phytochrome-sensitive mutant. The genotype-specific physiological, biochemical, and molecular responses under chilling stress in tomato mutants strongly validated phytochrome-mediated regulation of abiotic stress. Results Here, we demonstrate that phytochrome-sensitive mutant hp1 show improved performance compared to phytochrome-deficient mutant aur and wild-type MT plants under chilling stress. Interestingly, we noticed significant increase in several photosynthetic-related parameters in hp1 under chilling stress that include photosynthetic rate, stomatal conductance, stomatal aperture, transpiration rate, chlorophyll a and carotenoids. Whereas most parameters were negatively affected in aur and MT except a slight increase in carotenoids in MT plants under chilling stress. Further, we found that PSII quantum efficiency (Fv/Fm), PSII operating efficiency (Fq′/Fm′), and non-photochemical quenching (NPQ) were all positively regulated in hp1, which demonstrate enhanced photosynthetic performance of hp1 under stress. On the other hand, Fv/Fm and Fq′/Fm′ were decreased significantly in aur and wild-type plants. In addition, NPQ was not affected in MT but declined in aur mutant after chilling stress. Noticeably, the transcript analysis show that PHY genes which were previously reported to act as molecular switches in response to several abiotic stresses were mainly induced in hp1 and repressed in aur and MT in response to stress. As expected, we also found reduced levels of malondialdehyde (MDA), enhanced activities of antioxidant enzymes, and higher accumulation of protecting osmolytes (soluble sugars, proline, glycine betaine) which further elaborate the underlying tolerance mechanism of hp1 genotype under chilling stress. Conclusion Our findings clearly demonstrate that phytochrome-sensitive and phytochrome-deficient tomato mutants respond differently under chilling stress thereby regulating physiological, biochemical, and molecular responses and thus establish a strong link between phytochromes and their role in stress tolerance.

Salvia officinalis is one of the most important medicinal and aromatic plants in terms of nutritional and medicinal value because it contains a variety of vital active ingredients. Terpenoid compounds, particularly monoterpenes (C10) and sesquiterpenes, are the most important and abundant among these active substances (C15). Terpenes play a variety of roles and have beneficial biological properties in plants. With these considerations, the current study sought to clone theNAD+-dependent farnesol dehydrogenase (SoFLDH, EC: 1.1.1.354) gene from S. officinalis. Functional analysis revealed that, SoFLDH has an open reading frame of 2,580 base pairs that encodes 860 amino acids.SoFLDH has two conserved domains and four types of highly conserved motifs: YxxxK, RXR, RR (X8) W, TGxxGhaG. However, SoFLDH was cloned from Salvia officinalis leaves and functionally overexpressed in Arabidopsis thaliana to investigate its role in sesquiterpenoid synthases. In comparison to the transgenic plants, the wild-type plants showed a slight delay in growth and flowering formation. To this end, a gas chromatography-mass spectrometry analysis revealed that SoFLDH transgenic plants were responsible for numerous forms of terpene synthesis, particularly sesquiterpene. These results provide a base for further investigation on SoFLDH gene role and elucidating the regulatory mechanisms for sesquiterpene synthesis in S. offcinalis. And our study paves the way for the future metabolic engineering of the biosynthesis of useful terpene compounds in S. offcinalis.

The advent of the nanotechnology era offers a unique opportunity for sustainable agriculture, and the contribution of nanoparticles (NPs) to ameliorate abiotic stresses became the new area of interest for researchers due to their special physiochemical characteristics in the biological system. Salinity is a key devastating abiotic factor that hinders the development and yield of rapeseed. On the flip side, the impact of nanoparticles on plant hormones upon salt stress during seed imbibition and germination has been poorly understood. Hence, we aimed to study the influence of nanopriming on plant hormones and germination processes using selenium and zinc oxide nanoparticles (SeNPs and ZnONPs) during seed imbibition and the early seedling stage upon salinity stress. Nanopriming showed a positive effect on final germination percentage, germination rate, seed microstructure, and antioxidant enzyme activity of two rapeseed cultivars under salt stress. Moreover, nano-treatment decreased the expression of abscisic acid related genes BnCYP707A1, 3, and 4 during the priming time and after sowing, where the levels of BnCYP707A1, and 3 genes showed a slightly significant difference between the nanopriming and hydropriming, which gave an evidence that the nanopriming influenced the ABA levels then elevated the seed germination with SeNPs and ZnONPs. Likewise, nanoparticles significantly elevated the expression levels of BnGA20ox, BnGA3ox and BnCPS genes during the germination stage, especially at 24 h after being sown in salt stress. That confirms the positive role of SeNPs and ZnONPs in regulating gibberellic acid level, which increases the germination in primed seeds as compared to unprimed seeds and hydroprimed seeds. Additionally, our results demonstrated that nanopriming regulated the expression level of BnCAM and BnPER during priming time and after sowing, along with the various levels of expression remarkably in BnEXP4 and BnRAB28, especially at 24 h of being sown under salt stress, which promoted seed germination and early seedling growth. Overall, this work provides new insights into mechanisms underlying the interactions of SeNPs and ZnONPs with plant hormones during the seed imbibition and early seedling stage, consequently enhanced plant growth and development. Additionally, these findings portrayed that the application of SeNPs and ZnONPs could be a new strategy and useful approach to enhance tolerance against salinity in rapeseed plants.

Solenostemma argel (Delile) Hayne is a desert plant that survives harsh environmental conditions with several vital medicinal properties. Salt stress is a major constraint limiting agricultural production around the globe. However, response mechanisms behind the adaptation of S. argel plants to salt stress are still poorly understood. In the current study, we applied an omics approach to explore how this plant adapts to salt stress by integrating transcriptomic and metabolomic changes in the roots and leaves of S. argel plants under salt stress. De novo assembly of transcriptome produced 57,796 unigenes represented by 165,147 transcripts/isoforms. A total of 730 differentially expressed genes (DEGs) were identified in the roots (396 and 334 were up- and down-regulated, respectively). In the leaves, 927 DEGs were identified (601 and 326 were up- and down-regulated, respectively). Gene ontology and Kyoto Encyclopedia of Genes And Genomes pathway enrichment analyses revealed that several defense-related biological processes, such as response to osmotic and oxidative stress, hormonal signal transduction, mitogen-activated protein kinase signaling, and phenylpropanoid biosynthesis pathways are the potential mechanisms involved in the tolerance of S. argel plants to salt stress. Furthermore, liquid chromatography-tandem mass spectrometry was used to detect the metabolic variations of the leaves and roots of S. argel under control and salt stress. 45 and 56 critical metabolites showed changes in their levels in the stressed roots and leaves, respectively; there were 20 metabolites in common between the roots and leaves. Differentially accumulated metabolites included amino acids, polyamines, hydroxycinnamic acids, monolignols, flavonoids, and saccharides that improve antioxidant ability and osmotic adjustment of S. argel plants under salt stress. The results present insights into potential salt response mechanisms in S. argel desert plants and increase the knowledge in order to generate more tolerant crops to salt stress.

In contrast to flavonols, the functions of plant flavones are largely unknown. Here, the authors report the two differentially evolved glucosyltranferases (flavone 7-O-glucosyltransferase and flavone 5-O-glucosyltransferase) determine natural variation of rice flavone accumulation and UV-tolerance.