According to the survey, wild purslane (Portulaca oleracea L.) has two different ecotypes, one with the red stem living in an arid environment and one with the green stem living in a humid environment. In order to explore the physiological response strategies of plants to environmental changes, these two ecotypes of purslane were selected as experimental materials. Physiological indices were determined and transcriptome analysis was carried out to screen the differentially expressed genes (DEGs) from two ecotypes of purslane. The results showed that the content of soluble sugars, proline, anthocyanins, and chlorophylls was significantly different, and most DEGs belonged to the WRKY and NAC families. Finally, the results of transcriptome analysis were verified by real-time qPCR. Therefore, it can be inferred that the transcription factor (TF) families may play an important role in physiological response strategies by regulating the changes of anthocyanins and osmotic regulators (soluble sugars, proline, etc.) through the abscisic acid signalling pathway. This will accelerate the study of purslane at the molecular level, provide corresponding theoretical support for its artificial domestication, and drought breeding.

Agarwood, the resin part of Aquilaria spp., is valued in medicine, perfumes, and incense. The most important components of agarwood are sesquiterpenes, which are produced only when a healthy tree is wounded. Agarwood sesquiterpene synthase 1 (ASS1) is one of key enzymes responsible for the biosynthesis of sesquiterpenes in Aquilaria sinensis (Lour.) Gilg, and it is a typical wound-inducible synthase. To elucidate its regulatory mechanism at the transcriptional level, a 978-bp sequence upstream of the translation initiation codon ATG of the promoter for ASS1 was cloned. Computational analysis revealed that this promoter contained many known cis-elements including several defense related transcriptional factor-binding boxes. To functionally validate the promoter, a 5' truncated fragment fused with the β-glucuronidase (GUS) reporter gene was used for generating stable transgenic Arabidopsis plants. The spatial and temporal expression patterns of GUS in transgenic Arabidopsis showed that the promoter of ASS1 was induced by mechanical wound and mainly expressed in vascular bundles. Subcellular localization showed that ASS1 localized in the nucleus and plasma membrane. Here, identification of the ASS1 promoter not only lays a foundation for studying its transcriptional regulation, but also provides clues for studying the synthesis mechanism of agarwood sesquiterpenes.

Tamarix ramosissima is a deciduous shrub that resides in arid and semi-arid regions. Although of ecological and medicinal values, some Tamarix species are considered invasive as they have dominated the riparian zones of dryland in some parts of the world. Here, the complete chloroplast (cp) genome of T. ramosissima was sequenced and analyzed, showing a size of 156 150 bp and a GC content of 36.5 %. The plastome displayed a typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions of 26 554 bp, separated by a large single copy (LSC) region of 84 795 bp, and a small single copy (SSC) region of 18 247 bp. The cp genome encoded 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. A total of 32 repeat sequences and 64 simple sequence repeat (SSR) were identified in the plastome, and an obvious A/T bias was observed in the majority of the SSRs detected. By comparing the T. ramosissima cp genome with those of the other four Tamaricaceae species, a number of divergence hotspots were identified among these plastomes. Together with SSRs and long repeats identified, these divergence hotspots could be developed as potential molecular markers facilitating species discrimination and evolutionary studies. Using plastome sequences, we re-investigated the phylogenetic relationship among 19 species, and T. ramosissima was found to be a sister of Tamarix chinensis. Taken together, our study provides valuable genomic resources to deepen the understanding of plant photosynthetic mechanism and phylogenomics.

The trihelix genes encode plant-specific transcription factors, which play a vital role in plant morphological and developmental processes. However, information about the presence of trihelix genes in sunflower (Helianthus annuus L.) is scarce. Sunflower belongs to composite family and possesses strong drought and salt-alkali tolerance. In this study based on H. annuus genome data, we have identified and analyzed the trihelix genes with a complete description of their physical and chemical properties, phylogenetic relationships, motif composition, chromosome distribution, exon-intron structure, cis-acting elements, and chromosome collinearity. In H. annuus, 31 full-length trihelix genes were identified and categorized into six subgroups (SIP, GT1, SH4, Gδ, GT-γ, and GT2). Multiple Em for motif elicitation (MEME), used for conservative motif analysis, identified 10 distinct motifs unevenly distributed on 31 trihelix genes. In addition to that, chromosome localization analysis showed the number and distribution of these trihelix genes on 17 chromosomes of H. annuus. Transcriptional structure analysis revealed the structure of introns and exons of different gene members. Furthermore, cis-element analysis identified 19 different types of cis-elements mainly related to abiotic stress, hormones, and growth and development of plant. Results of this study manifested novel insights into phylogenetic relationships and possible functions of H. annuus trihelix genes. Moreover, these findings can assist in future studies regarding specific physiological effects of H. annuus trihelix transcription factors.

Nucleotides are the basic elements of the genetic material, participate in bio-energetic processes, are cofactors and components of secondary metabolites, etc. Nucleotide hydrolases (nucleotidases) are phosphatases that remove the 5'-phosphate group from the nucleotides and play a crucial role in nucleotide metabolism. In this study, genes encoding putative nucleotidases in Phaseolus vulgaris have been identified, and the effect of methyl jasmonate (MeJA) on both nucleotidase activity and gene expression has been addressed. The predicted nucleotidase peptides include the conserved domains characteristic of the haloacid dehalogenase-like hydrolase superfamily. The analysis of the expression of the 11 identified genes in radicles of common bean seedlings elicited with MeJA showed that 3 of them are highly induced by this phytohormone in a dose-dependent manner. Nucleotidase activity in radicles from MeJA treated plants was higher than in not elicited seedlings, and this induction was observed with all the nucleotides assayed (mono-, di- or triphosphate) and with purine or pyrimidine nucleotides. MeJA is involved in biotic and abiotic stress, and the induction of nucleotide metabolism in response to this treatment suggests a relevant role for nucleotides in the seedlings response to unfavourable conditions.

Finger millet (Eleusine coracana) is one of important crops, and its grains contain an exceptionally high content of calcium. In order to investigate the molecular mechanism by which it orchestrate the accumulation of Ca²⁺ during grain filling, some candidate genes encoding calcium transporters [calcium exchangers (CAX1, CAX3)] and sensors [calcineurin-B like (CBL4 and 10)], a CBL-interacting protein kinase (CIPK24), and calmodulin (CaM) were identified using transcriptomics and differential expression analysis in two genotypes of finger millet differing in grain calcium content. These transporters and sensors are highly expressed in leaves and developing spikes of the genotype with a high grain Ca²⁺ indicating their potential role in Ca²⁺ accumulation. Calcium transporters, mainly CAXs, pump Ca²⁺ inside the cell through plasmalemma and tonoplast, and their activities are regulated by CaM dependent and independent Ca²⁺ sensor proteins of CaM and CBL-CIPK networks. Abundance of CaM in a high grain Ca²⁺ genotype is suggestive that CaM might also contribute for grain calcium accumulation by interaction with Ca²⁺ATPase. The upregulation of CAX1 in vegetative tissues and developing spikes and CAX3 only in developing spikes provides the most plausible clue for calcium transport and accumulation regulated by tripartite interaction in finger millet.

Medicinal plants are a rich source of secondary metabolites, extensively used in traditional health care systems. High altitude biodiversity encompasses the diversified and valuable medicinal plant species. The extreme environmental conditions of high altitude region viz. fluctuating temperatures, high UV radiation, salinity, low oxygen concentration, and high wind velocity limits the plant growth and distribution. Yet, how medicinal plants respond to these extreme conditions is not sufficiently understood. Therefore, addressing plant acclimation to different stresses presents an opportunity to unravel adaptive mechanism of medicinal plants along altitude gradient. This article reviews the recently published research that highlights the major role of proteins in plant adaptation to extreme environmental conditions. In the last few decades, climate change has made a profound impact on high altitude plants. Stress conditions alter cellular homeostasis of plants. With the advent of proteomics, it has become evident that stresses induce changes in proteome by synthesis/expression of novel stress responsive proteins. These proteins constitute a highly organized, complex network that leads to changes in the molecular, biochemical, physiological, and morphological responses of plants. Herein, we comprehensively discuss the proteomics of medicinal plants and its role in adaptation along altitude gradient. This review aims to provide impetus to current research in medicinal plants ranging from developmental to stress biology and to generate basis for genetic engineers and plant breeders to produce next-generation medicinal plants.

A large-scale expression profiling study was performed to investigate candidate genes associated with the two quantitative trait loci (QTLs) for aluminum (Al) tolerance (Alt1 and Alt2). They have been identified in rye and localized on chromosomes 6R and 3R, respectively. Materials employed were hexaploid wheat (cv. Chinese Spring), and two wheat-rye addition lines (3R-AL and 6R-AL). Seedlings were treated with and without Al for 24 h to examine genes up-regulated or down-regulated by Al. Measurements of root growth at different Al concentrations showed the Al tolerance was higher in 3R-AL than in 6R-AL and wheat. Initial transcriptomic results revealed that more genes changed expression (>10 fold) in the wheat and in the 6R-AL line (moderately tolerant) than in the 3R-AL line (highly tolerant). A method was developed to determine whether candidate genes are involved in Al tolerance or in responses to Al toxicity. Real-time qPCRs were carried out in a subset of six genes with known function in near isogenic rye lines 389 (Al-sensitive) and 390 (Al tolerant). All six genes were up-regulated by Al in line 389 but not in line 390, indicating that they were involved in Al stress response but not in Al tolerance mechanisms. Subsequent analysis of Arabidopsis lines with knockout mutations in homologues of these six genes showed an Al sensitivity similar to the wild-type, providing more evidence towards their participation in the response to stress rather than to Al tolerance. Once the stress response genes were ruled out, the focus was turned to the identification of tolerance genes by studying transcripts up-regulated and down-regulated in the tolerant 3R line with respect to wheat and 6R line. Finally, a list of candidate genes that could be conferring increased tolerance was obtained.

Hemp (Cannabis sativa L.) seeds have been recognized as a nutritional protein source for humans and animals. In this study, gene families encoding precursor polypeptides of three storage protein classes, including six 11S edestin, two 2S albumin and one 7S vicilin-like genes were identified and characterized from an inbred line of hemp. All edestins showed typical 11S globulin features but based on the amino acid composition, they were grouped in three edestin types (type1, -2 and -3). Genes encoding edestin type1 and -3, were very close to each other in a DNA fragment of 16 071 bp, whereas the two isoforms of edestin type2 were linked on a different DNA fragment of 8 232 bp and arranged in a tailto- tail fashion. All edestin types were very rich in arginine and glutamic acid, but edestin type3 was the richest in cysteine and methionine. Regarding the 2S albumin (Cs2S) two genes were identified in a fragment of 13 738 bp in a tail-to-head array. Finally, only one 7S-vicilin like gene (Cs7S) that exhibited typical 7S vicilin features such as the presence of two cupin domains and several N-glycosylation sites was isolated. Southern blot hybridization is in agreement with the number of genes isolated, and real-time qPCR analysis revealed that all genes are expressed in the seed. The highest expression was observed for edestin type1 (CsEde1) and Cs2S, whereas the lowest expression was detected for Cs7S. The results of this study provide a complete overview of the genes encoding hemp storage proteins and significantly advance our knowledge on the organization of these gene families.

Low temperature can affect the growth and development of lily, limiting the application of commercial cultivars in outdoor. Lilium lancifolium is an important cold-resistant wild lily, but little is known about how L. lancifolium tolerates cold stress at the molecular level. In this study, we identified and characterized genes and transcription factors associated with cold stress in control plants and plants treated by 4° C for 1 - 24 h. The construction of a highest reciprocal rank-based gene co-expression network along with its partition into defined functional modules using Markov cluster algorithm resulted in identification of 30 gene modules and some of them were significantly enriched with various kinds of stress response under 4° C. These gene modules were associated with metabolic processes, cellular processes, regulation of biological processes, establishment of localization, and responses to stimuli. Moreover, three transcription factors that may regulate the downstream genes involved in response to stimuli were also found. We further studied the expression pattern and tissue specificity of these transcription factors. The functional evaluation of the various interesting genes in this study will probably provide novel discovery of pathway members and regulators associated with cold resistance in lily.

Virus-induced gene silencing (VIGS) is a post-transcriptional gene silencing method used for unraveling gene functions. As an attractive alternative to mutant collections or stable transgenic plants, it has been widely used in reverse-genetics studies owing to its ease use and quick turnaround time. Turnip yellow mosaic virus (TYMV) has the ability to induce VIGS in Arabidopsis thaliana. However, the conventional vector construction is difficult and the efficiencies of the infection methods are low. Here, we improved the vector construction and viral infection methods, inserted an inverted-repeat fragment of the phytoene desaturase gene into a TYMV-derived vector by homologous recombination and transformed Brassica rapa with plasmid DNA harboring a cDNA copy of the TYMV genome through particle bombardment. An apparent photobleaching phenotype was detected and efficient VIGS was induced. An 80-bp fragment was sufficient to produce VIGS in leaves, stems, roots, flowers, siliques, and stalks of B. rapa. Because TYMV has a wide host range in Brassica, the VIGS system described here will contribute to the improvement of high-throughput technology and efficient functional research in B. rapa and other Brassicaceae crops.

Cannabis sativa, an annual herbaceous plant, produce wide variety of secondary metabolites among which delta-9-tetrahydrocannabinol (THC) is the most important one. The dissection of biosynthetic pathway(s) of this compound and its regulation by transcription factors (TFs) is an important prerequisite for efficient biotechnological manipulation of its secondary metabolome. A polyketide synthase (PKS) of C. sativa catalyzes the first step of cannabinoid biosynthesis, leading to the biosynthesis of olivetolic acid. Cloning and analysis of PKS promoter based on online PLACE, PlantCARE, and Genomatix Matinspector professional databases, indicated that PKS promoter consisted of cis-elements such as TATA-box, CAAT-box, W-box, Myb-box, E-box, and P-box. Plant expression vector PKS::GUS was constructed in such a way that the ATG of the PKS gene was in the frame with the β-glucuronidase (GUS) coding region. Using a combinatorial transient GUS expression system in Nicotiana benthamania leaves, it was shown that heterologous TFs such as HlWRKY1, HlMYB3, HlWDR1 and HlbZIP1 from Humulus lupulus significantly activated PKS promoter. Moreover, Tombusvirus p19 core protein, which is known for silencing suppressor functions, acted in our combinatorial transient expression system as an enhancer of PKS promoter activity along with hop TFs. Our analyses suggested the involvement of the hop derived TFs (HlWRKY1, HlMYB3, HlWDR1 and HlbZIP1A) and p19 in the activation of PKS gene promoter, which could be used for the genetic manipulation of C. sativa to enhance the cannabinoid production.

The GRAS transcription factors encoding proteins ranging from 400 to 700 residues are recognized by their conserved C terminus. Here, a set of 23 CmGRAS genes was identified from a scan of the chrysanthemum (Chrysanthemum morifolium) transcriptome. A phylogenetic analysis implied that nine of these genes could be assigned orthologs to the GRAS gene family, and that four of them formed two pairs of paralogs. A phylogenetic analysis of the GRAS protein family based on the chrysanthemum and recent study of eight representative species of angiosperms showed that most of the CmGRAS genes belonged to a recognized sub-group. CmGRAS4 and CmGRAS10 were strongly transcribed in flowers and roots, respectively. The DELLA subfamily transcript abundance of the CmGRAS19 and CmGRAS20 was high in the reproductive tissues and they were responsive to phytohormones and stresses. Establishment of the orthology relationships between the known representative GRAS genes and CmGRAS, and transcriptional profiles of CmGRASs after phytohormone treatments or stresses will facilitate subsequent functional analyses in the GRAS gene family.

The gene NCED1 encodes 9-cis-epoxycarotenoid dioxygenase, which catalyzes oxidative cleavage of 9-cis-epoxycarotenoids neoxanthin and violaxanthin to xanthoxin, a key step in the biosynthesis of abscisic acid in higher plants. In the present study, the complete NCED1 of 1 917 bp was cloned and characterized from rice (Oryza sativa L. cv. N22) as no earlier reports were available for its characterization from indica cultivar. The NCED1 had no intron and encoded a protein of 639 amino acids with a predicted molecular mass of 68.62 kD and pI of 6.07. The aliphatic index and grand average of hydropathicity were found to be 77.04 and -0.148, respectively. Multiple alignment analysis revealed that the sequence shared a high identity with the Oryza sativa japonica group (100 %) followed by Triticum aestivum (90 %), Hordeum vulgare (90 %), and Zea mays (89 %). The enzyme had a RPE65 domain of 476 amino acid residues. The RPE65 domain requires Fe(II) as a cofactor coordinated with 4 histidine residues and 3 glutamic acid residues. The phylogenic tree shows that NCED1 of japonica rice and NCED1 of indica rice were in the same group. They might have been evolved from a common ancestor. Analysis with a PSORT III tool shows that NCED is a chloroplastic protein. The real-time quantitative PCR and RNA-sequencing studies show that the expression of NCED1 was progressively reduced with increasing water stress, and a negative correlation between expression of OsNCED1 and severity of stress was established. Further, NCED1 expression negatively correlated with abscisic acid (ABA) accumulation under water stress whereas in some other species its expression increased along with ABA accumulation. This might be due to feedback inhibition of the ABA biosynthesis in rice.

Strawberry is an economically important fruit crop worldwide. Circadian clock genes are endogenous timers that regulate a wide range of metabolic processes and consequently plant development. However, little is known about the circadian clock genes in strawberry. In the present work, we identified 12 primary circadian clock genes from the diploid woodland strawberry (Fragaria vesca L.) genome. Phylogenetic, conserved motif, and gene structure analyses revealed the evolutionary relationships of strawberry circadian clock genes with homologous genes from other species. Promoter analysis revealed different regulatory elements responding to abiotic and biotic stresses and phytohormones. We characterized the transcript patterns of strawberry circadian clock genes over a 48-h period. The expression patterns of seven circadian clock genes displayed circadian rhythms. We also examined the expression patterns of these genes in response to low-temperature stress and six of them showed an upregulated expression. Interestingly, most of these upregulated genes were highly expressed during the day. Our study reveals the characteristics of primary circadian clock components in diploid woodland strawberry and their responses to low-temperature stress and lays a foundation for future functional studies of these circadian clock genes during the growth and development of diploid woodland strawberry.

Elymus nutans is an important alpine perennial forage of the Pooideae subfamily, that can survive subzero temperatures. To understand the molecular mechanisms underlying cold tolerance in E. nutans, we performed the transcriptional analysis by RNA-Seq in two genotypes, the tolerant Damxung (DX) and the sensitive Gannan (GN), under cold stress. The new E. nutans transcriptomes comprised 200 520/200 836 and 181 331/211 973 transcripts in leaves/crowns of DX and GN, respectively. More cold-stress-related genes were identified in leaves than in crowns of both genotypes throughout the whole cold stress. The most prominent functional category in leaves of both genotypes at 3 h of stress was transcriptional regulation. Brassinosteroid and jasmonic acid mediated signalling pathways play central roles in regulating downstream protective responses in DX after 24 h of cold stress. Prolonged cold stress caused more severe transcriptome responses in crowns and leaves of DX compared to GN. The most significant transcriptomic changes in both genotypes were associated with the response to abiotic stresses and the oxidation-reduction processes, implying reprogramming of the cellular metabolism as an adaptation to cold stress. This study reveals mechanisms of genotype- and organ-specific cold stress response in E. nutans and thus provides a basis for future breeding strategies aimed at improving the tolerance of cold-sensitive plants.

Leek is an economically important vegetable. In model plants, the CONSTANS (CO) and CONSTANS-like (COL) genes play central roles in plant flowering modulation. However, none of leek CO homolog has been identified, because of limited gene resources obtained in this crop. Here, we reported the transcriptome analysis of leek, along with the identification of putative leek CONSTANS-like (COL) (ApCOL) genes. A total of 189 713 non-redundant transcripts were de novo assembled by using about 128.9 million clean sequence reads, of which, 48 621 were achieved for functional annotation. Thereafter, the search for putative ApCOL genes against the assembled transcripts was performed, and 17 genes were identified. The 17 putative ApCOL proteins, together with 16 function-known COL proteins published for other species, were subjected to phylogenetic analysis and divided into four groups. Some putative ApCOL members showed high sequence similarity with published COL proteins involved in flowering regulation. Expression analysis revealed that, among the 17 putative ApCOL genes, eight, two, and three genes showed higher expression in leaves, cauloids, and roots, respectively. The discovery of putative ApCOL genes and the characterization of their expression patterns will provide a basis for future clarification of their functions in leek growth and development.

Root hairs play important roles in plant nutrient and water acquisition. To better understand the genetic mechanism controlling root hair development in rice (Oryza sativa L.), a rice mutant with root hair defects was isolated and characterized. Cryo-scanning electron microscope (SEM) showed that the density and length of root hairs in the mutant were significantly reduced compared to wild type (WT). Map-based cloning and complementation test revealed that the mutation occurred in a NADPH oxidase gene OsNOX3 (LOC_Os01g61880). The OsNOX3 displays high sequence similarity with the previously characterized NOX genes RTH5 in maize and RHD2 in Arabidopsis, which play critical roles in root hair development. Expression pattern analysis indicated that OsNOX3 is expressed in various tissues throughout the plant with high expression in roots and root hairs. Subcellular localization analysis confirmed that OsNOX3 is located on the plasma membrane. Staining assays showed that the content of superoxide and hydrogen peroxide are significantly reduced in root hair tips of Osnox3 when compared to WT. Our results showed critical roles of OsNOX3 in regulating both root hair initiation and elongation in rice, which is similar to RTH5 but different from RHD2, confirming the difference of genetic mechanisms regulating root hair morphogenesis in monocot and dicot plants.

The MYB transcription factor superfamily is a large gene family that plays central roles in developmental processes and defence responses in plants. Unlike in Arabidopsis, only few members of the R2R3-MYB gene family have been functionally well characterized in maize, especially in abiotic stress-response pathways. Subgroup-specific conserved motifs outside the MYB domain may reflect functional conservation. A comparative genomics study using Arabidopsis abiotic stress-responsive MYB protein sequences identified 46 ZmMYB genes that may be involve in abiotic stress responses of Zea mays. An expression pattern analysis of the 46 ZmMYB genes under abiotic stress treatments was used to identify 22 MYB genes that were induced by one or more of the stress treatments. ZmMYB30 was highly upregulated under the four stress treatments. The ectopic expression of ZmMYB30 in transgenic Arabidopsis plants promoted salt-stress tolerance and also increased the expression of a number of abiotic stress-related genes, allowing the plants to overcome adverse conditions.

Three genes encoding novel D-hordeins, Ns 1.3, Ns 2.6, and Ns 2.9 were isolated from Psathyrostachys juncea. The Ns 1.3 differed from Ns 2.6 and Ns 2.9 by having a shorter open reading frame (< 1.5 kb versus > 2.5 kb), and was probably not expressed as a normal protein, while the activities for Ns 2.6 and Ns 2.9 were verified by bacterial expression. Though highly similar primary structure to wheat high molecular mass glutenin subunits (HMM-GSs) and barley D-hordeins, Ns 2.6 and Ns 2.9 had more cysteine residues (nine in total) and a larger molecular mass than HMMGSs, and a longer N-terminal length than D-hordeins. Phylogenetic analysis revealed that the Ps. juncea D-hordeins were divided into Ns 1.3 type and Ns 2.6/Ns 2.9 type. Divergence times indicated that Ns 1.3 diverged the earliest from the orthologous Triticeae locus, while Ns 2.6 and Ns 2.9 and the D-hordeins from two Hordeum species diverged nearly at the same time from those loci, and the divergence between the D-hordeins of H. chilense and Ns 2.6/Ns 2.9 was more recent than between the two Hordeum species. The novel Ps. juncea D-hordeins have the potential to be very important for improving the end-use quality of wheat flours because of the presence of extra cysteine residues and longer repetitive domain, in addition they can contribute to the understanding of the evolution of Triticeae prolamins.

Glucosinolates are a branch of amino acid-derived metabolites, which are specifically found in Brassicales. In Arabidopsis, tryptophan derived indolic glucosinolates are required for plant defense against a wide range of pathogens and herbivores due to their strong antimicrobial activity and potential signaling function. An important enzyme in indolic glucosinolate biosynthesis pathway is CYP83B1, which oxidizes indole-3-acetaldoxime, a precursor of indole-3-acetic acid (IAA). In this study, we reported isolation and expression characterization of a CYP83B1 gene from Brassica oleracea L. var. italica Plenck, which we termed BoCYP83B1. Overexpression of BoCYP83B1 in Arabidopsis resulted in an altered glucosinolate profile and early flowering phenotype. By expressing the reporter gene β-glucuronidase under the control of the BoCYP83B1 promoter in Arabidopsis, we analyzed the spatial expression pattern of BoCYP83B1 under normal growth conditions as well as in response to several hormones and stresses. The BoCYP83B1 was primarily expressed in vascular tissue through the almost whole plant. It was strongly induced by methyl jasmonate, 1-amino-1-cyclopropanecarboxylic acid, salicylic acid (SA), gibberellin, and IAA, suggesting its involvement in complex signaling pathways. Mannitol, NaCl, UV, and Flagelin 22 significantly up-regulated BoCYP83B1 expression, indicating its possible role in stress response. Interestingly, the response of BoCYP83B1 to SA and NaCl showed tissue specificity. Thus, BoCYP83B1 might have different functions in different tissues.

Small RNAs (sRNAs) are essential components of gene-regulatory networks, which guide plant development and tune it to environmental challenges. Though the past years have witnessed evidences on sRNA importance for stress response, there is scarce data on their involvement in resurrection plant survival under severe drought. Haberlea rhodopensis (hrh) is an angiosperm resurrection species, whose vegetative tissues can tolerate desiccation and recover upon rehydration. In this study, high-throughput sequencing sRNAs indicated a higher complexity of the sRNA population, especially of a 24 nt sRNA category, in the desiccated vegetative tissue of H. rhodopensis compared to unstressed tissues. The cross-species discovery was performed to predict 77 mature microRNAs (miRNAs), most of which were assigned to 23 high-confidence conserved miRNA families in the leaf tissue. Several members of the miR156/157, miR166, and miR399 families were found to be desiccation-responsive. The miR156/157 family members were found up-regulated upon dehydration and down-regulated upon rehydration, while the miR166 and miR399 family members followed an opposite trend of expression. A probable miR156/157 target, orthologous to the SQUAMOSA promoter binding protein-like, was reconstructed in H. rhodopensis based on genomic data available for this species and the closely related Boea hygrometrica. Reverse transcription quantittative PCR analysis confirmed the expression profile of hrh-miR156a-5p and hrh-miR157-5p established by sRNA sequencing and revealed an inverse expression pattern between these miRNAs and their targets in the desiccated tissue. Our study suggests that the miR156/157 and miR399 families are essential for plant survival under severe drought due to their ability to control plant development and growth by modulating transcription factor expression.

Heat stress is one of the most crucial factors affecting crop growth and productivity worldwide. So, searching for a potent eco-friendly heat stress alleviator is the main issue nowadays. The current study was conducted to assess the ameliorative effects of 1.5 mM potassium silicate (K₂SiO₃, further only Si) or 1.66 mM silicon dioxide nanoparticles (SiNPs) on wheat (Triticum aestivum L.) seedlings exposed to heat stress (45 °C, 4 h). The observations show that Si or SiNPs treatments significantly restored the heat stress-provoked ultrastructural distortions of cellular organelles, particularly chloroplasts and the nucleus. Further, both Si and SiNPs enhanced the photosynthetic capacity as revealed by increments in the photochemical efficiency of photosystem II and the performance index as well as the content of photosynthetic pigments. A reduction in malondialdehyde accumulation in Si and SiNPs treated plants was positively related to their membrane stability index. The reverse transcription PCR analysis showed that Si treatment but not SiNP treatment stimulated the overexpressions of both Triticum aestivum plasma membrane intrinsic protein (TaPIP1) and Triticum aestivum nodulin 26-like intrinsic protein (TaNIP2) aquaporin genes parallelly with an improvement in the relative water content. This investigation reveals that Si was more effective than SiNPs in restoring the heat stress injuries. To the best of our knowledge, this is the first investigation exploring the effects of Si and SiNPs in improving thermotolerance of wheat seedlings.

Real time quantitative PCR (qPCR) is a powerful tool for studying the expression of specific genes. The accuracy and reliability of qPCR analysis data require the selection of reference genes with stable expression. However, the reference genes that can be used for qPCR of Rehmannia chingii and R. henryi have not yet been identified. In this study, based on the transcriptome data of R. chingii and R. henryi, we initially selected genes with relatively stable expression in different samples. We screened six candidate reference genes in R. chingii and R. henryi and calculated their expression abundance by real time qPCR. Their expression stability was evaluated by three algorithms geNorm, NormFinder, and BestKeeper. Although the results obtained by different algorithms were not completely consistent, R. chingii type 2A phosphatase activator TIP41 and R. chingii 18S ribosomal RNA had the highest expression stability in six different samples of R. chingii, and R. henryi 18S ribosomal RNA and R. henryi actin showed the most stable expression in different samples of R. henryi. In addition, based on transcriptome data, four genes were screened in R. chingii and R. henryi, and the expression stability of the selected reference genes was further verified. This study laid the foundation for further analysis and verification of the functions of important genes in R. chingii and R. henryi.

Interspecific and intergeneric hybridization within the Festuca-Lolium complex is frequently used in forage plant breeding. However, little is known about the natural occurrence and competitiveness of such hybrids. We collected naturally formed hybrids between Festuca apennina, Festuca pratensis, and Lolium perenne in different habitats of Switzerland and the British Isles and studied their origin, the ease of their spontaneous formation, and their competitiveness with parental species. A special attention was paid to the largely sterile triploid forms and their rare sexual progeny. The triploid hybrid F. apennina × F. pratensis proved to be widespread and often highly competitive in Swiss permanent pastures. The majority of these hybrids originated from F. apennina as the seed parent although little or no F. apennina grew nearby. In an experimental setting with ample F. pratensis pollen provided by neighbouring plants, up to 20 % of seeds from open pollinated F. apennina plants were interspecific hybrids; among seeds collected in natural habitats, only 0.35 % were hybrids. At an experimental site at 1 000 m altitude, these triploid hybrids grew much more vigorously than corresponding tetraploid pure F. apennina, confirming their great competitiveness at such altitudes in permanent grasslands. The triploid hybrids were only marginally fertile suggesting that vegetative propagation by rhizomes is the cause of their competitive success in grassland. Moreover, triploid progeny retained the chromosome constitution of their mother plants indicating the possibility of apomixis. Natural triploid F. pratensis × L. perenne hybrids were partially female fertile (a seed set of 0.1 % or less) whereas diploid hybrids did not produce any viable seeds. Progenies of these triploids showed considerable chromosome alterations, such as loss of a genome or recombination due to homoeologous pairing, and only rarely the chromosome constitution of the triploid mother plant was retained. It was concluded that natural triploid interspecific hybrids could expand the range of their progenitor species and might function as bridges transferring genes between them.

Plasmodiophora brassicae is a biotrophic pathogen causing clubroots of cruciferous crops. The Brassica rapa accession T1-145 has an ability to produce small spheroid galls (SSGs), which represent neither a fully compatible interaction nor a complete resistance. To explore the defense response in SSGs induced by P. brassicae infection, global transcriptome profiling SSGs was performed at different time points. By comparing gene expression patterns, we identified many defense related genes. The first group included genes encoding receptor-like protein/kinases, such as cysteine-rich receptor-like protein kinases, receptor-like proteins, phloem intercalated with xylem/tracheary element differentiation inhibitory factor receptor (PXY/TDR), PXY-correlated 1, wall-associated kinases, nuclear shuttle protein-interacting kinase, lectin receptor-like kinases, and flagelin-sensitive 2, which might activate a basal defense. The second group involved robust effector-triggered immunity response genes such as resistance to leptosphaeria maculans 1B, constitutive shade-avoidance 1, target of avirulence B operation 1, ribosomal protein of the small subunit 6, resistance to Pseudomonas maculicola 1-interacting protein 4, enhanced disease resistance 2L, and recognition of Peronospora parasitica 13-like protein 4. The third group included genes encoding secondary cell wall formation related protein/s, a nodulin-like protein, a germin-like protein, a jacalin-related lectin, a defensin-like protein, tumor inhibitors, and sugars will eventually be exported transporter, which might contribute to quantitative resistance against P. brassicae. The gene expressions were the highest at the late stage of infection. To our knowledge, it is the first report on exploring defense response genes during SSG occurrence by a transcriptome analysis. Our data would provide useful information to further explore molecular mechanisms of the incomplete resistance.

Grasslands play a significant role in livestock fodder production and thus, contribute to food security worldwide while providing numerous additional ecosystem services. However, how agroclimatic conditions and adverse weather events relevant for grasslands will change across the European grassland areas has not been examined to date. Using a single reference setup for soil and management over 476 European sites defined by climate stations, we show the probability of eight selected adverse weather events with the potential to significantly affect grassland productivity under climate change and how these events vary regionally across Europe. Changes in these eight key agroclimatic indicators create markedly specific spatial patterns. We found that by 2050, the exposure of the south and west European grasslands to heat and drought may double in comparison with today and that the area with frequent occurrences of heat and drought will expand northwards. However, across Ukraine, Belarus, and the Baltic countries to southern Finland and Sweden, the likelihood of these events is likely to decrease. While changing cultivars and management strategies are unavoidable, shifting grassland production to other regions to reduce the risk may not be possible as the risk of adverse events beyond the key grassland-growing areas increases even further. Moreover, we found marked changes in the overall thermal and water regimes across European regions. The effect of adverse weather events in the future could be different in other regions of the world compared to regions in Europe, emphasizing the importance of conducting similar analyses for other major grassland producing regions. To mitigate the impact of climate change, new ways of maintaining grassland productivity need to be developed. These methods include more efficient selection of species mixtures for specific regions, including increased use of legumes and forbs; incorporation of new genetic resources, including the development of hybrid cultivars, such as Festulolium hybrids; and incorporation of state-of-the-art technologies in breeding programs and new grazing management.

Bupleurum chinense DC., a source of the traditional Chinese medicine Bupleuri Radix, is rich in triterpenoid saikosaponins with high pharmacological activities. The enzyme β-amyrin synthase (BAS), which converts the precursor 2,3-oxidosqualene to produce the triterpene skeleton, is crucial for the biosynthesis of triterpenoid saponins. In this study, we cloned the full-length sequence of the BAS gene from B. chinense, conducted a bioinformatics analysis, and expressed it in Saccharomyces cerevisiae to investigate its function. The cDNA of β-amyrin synthase (BcBAS, GenBank accession number: MN186093) cloned from aseptic seedlings of B. chinense was 2 307 bp with a 2 286 bp open reading frame coding for 761 amino acids. Phylogenetic analysis suggests that the BcBAS protein was closely related to the BAS proteins from Panax ginseng and Betula platyphylla. as chromatography mass spectrometry analysis showed that the enzymatic product was indeed β-amyrin, the precursor of oleanane type triterpenes. Overall, our findings lay the foundation for in-depth analysis of the biosynthesis pathway of saikosaponins.

Ferredoxin-thioredoxin reductase (FTR) is an iron-sulfur protein that supplies electrons from photochemically reduced ferredoxin (Fd) to thioredoxin (Trx) in the ferredoxin/thioredoxin system in chloroplasts. The FTR is a heterodimer with a variable subunit (FTRv) and a catalytic subunit (FTRc). The function of FTRv is not well known. In petunia (Petunia hybrida), FTRv is a single-copy gene, which is named PhFTRv. In this study, the spatio-temporal expression of PhFTRv in petunia was analyzed, and PhFTRv transcription was found to be high in leaves and stems. A tobacco rattle virus gene silencing was used in this study. Virus induced gene silencing-mediated PhFTRv silencing resulted in large yellow-green leaves, delayed flowering, and reduced cold tolerance in petunia plants.

Columnar apple is a valuable resource for genetic improvement of cultivated apples due to its special tree architecture. Strigolactones (SLs) are a novel class of plant hormones controlling shoot branching. The content of SLs is higher in columnar apple than in standard apples. In this study, the members of major gene families involved in SLs biosynthesis and signaling were identified from apple genomic sequences and their expression profiles were characterized in columnar and standard apples using reverse transcription quantitative polymerase chain reactions. In comparison with standard apple, the higher expressions of MORE AXILLARY GROWTH genes MdMAX3-1 and MdMAX4-4 were detected in both buds and shoots of columnar apple but the expression of DWARF gene MdD53-4 showed a lower expression in columnar apple. Overexpression of Columnar gene MdCo31 in tobacco increased SLs content and weakened the inhibition of SLs signal transduction by increasing expression of MAX3 and down-regulating the transcription of D53. Thus MdCo31 could be a strong candidate gene for the control of columnar habit.