Roses use a non‐canonical pathway involving a Nudix hydrolase, RhNUDX1 , to synthesize their monoterpenes, especially geraniol. Here we report the characterization of another expressed NUDX1 gene from the rose cultivar Rosa x wichurana , RwNUDX1‐2 . In order to study the function of the RwNUDX1‐2 protein, we analysed the volatile profiles of an F1‐progeny generated by crossing R. chinensis cv. ‘Old

Chloroplast perturbations activate retrograde signalling pathways causing dynamic changes of gene expression. Besides transcriptional control of gene expression different classes of small non‐coding RNAs (sRNAs) act in gene expression control, but comprehensive analyses regarding their role in retrograde signalling is lacking. We performed sRNA profiling in response to norflurazon (NF) that provokes

Leaf senescence represents the final stage of leaf growth and development, and its onset and progression are strictly regulated. However, the underlying regulatory mechanisms remain largely unknown. In this study we found that WRKY42 was highly induced during leaf senescence. Loss‐of‐function wrky42 mutants showed delayed leaf senescence while overexpression of WRKY42 accelerated senescence. Transcriptome

Jasmonates (JAs) are important for pathogen resistance in many plants, but the role of these phytohormones in fungal pathogen resistance in rose is unclear. Here, we determined that exogenous application of methyl jasmonate increased resistance to the important fungal pathogen Botrytis cinerea in Rosa chinensis ‘Old blush’, whereas silencing the JA biosynthetic pathway gene Allene Oxide Synthase (AOS

Fertilization Independent Endosperm (FIE) is an essential member of Polycomb Repressive Complex 2 (PRC2) that plays important roles in the developmental regulation of plants. OsFIE1 and OsFIE2 are two FIE homologs in the rice genome. Here, we showed that OsFIE1 probably duplicated from OsFIE2 after the origin of the tribe Oryzeae, but has a specific expression pattern and methylation landscape. During

Metabolites are the intermediate and final products of metabolism, which play essential roles in plant growth, evolution and adaptation to changing climates. However, it is unclear how evolution contributes to metabolic variation in plants. Here, we investigated the metabolomics data from leaf and seed tissues in maize and rice. Using principal components analysis based on leaf metabolites but not

Potato (Solanum tuberosum L.) is one of the world's most important crops, but it is facing major challenges due to climatic changes. To investigate the effects of intermittent drought on the natural variability of plant morphology and tuber metabolism in a novel potato association panel comprising 258 varieties we performed an augmented block design field study under normal irrigation and under water‐deficit

The existence and formation of covalent lignin‐carbohydrate (LC) linkages in plant cell walls has long been a matter of debate in terms of their roles in cell wall development and biomass utilization. Of the various putative LC linkages proposed to date, evidence of the native existence and formation mechanism of phenyl‐glycoside (PG)‐type LC linkages in planta is particularly scarce. The present study

Interactions between plant‐parasitic nematodes and their hosts are mediated by effectors; secreted proteins that manipulate the plant to the benefit of the pathogen. To understand the role of effectors in host adaptation in nematodes we analysed the transcriptome of Heterodera sacchari, a cyst nematode parasite of rice and sugarcane. A multi‐gene phylogenetic analysis showed that H. sacchari and the

Because carotenoids act as accessory pigments in photosynthesis, play a key photoprotective role, and are of major nutritional importance, carotenogenesis has been a target for crop improvement. Although carotenoids are important precursors of phytohormones, previous genetic manipulations reported little if any effects on biomass production and plant development, but resulted in specific modifications

Nucleolar dominance (ND) consists of the reversible silencing of 35S/45S rDNA loci inherited from one of the ancestors of an allopolyploid. The molecular mechanisms by which one ancestral rDNA set is selected for silencing remain unclear. We applied a combination of molecular (Southern blot hybridization and reverse‐transcription cleaved amplified polymorphic sequence analysis), genomic (analysis of

In flowering plants, pollen development is under a dynamic and well‐orchestrated transcriptional control, characterized by an early phase with high transcript diversity and a late post‐mitotic phase skewed to a cell‐type‐specific transcriptome. Such transcriptional changes require a balance between synthesis and degradation of mRNA transcripts, the latter being initiated by deadenylation. The CCR4‐NOT

Proton gradient regulation 5‐like photosynthetic phenotype 1 (PGRL1)‐dependent cyclic electron transport around photosystem I (PSI) plays important roles in the response to different stresses, including high light. Although the function of PGRL1 in higher plants and green algae has been thoroughly investigated, little information is available on the molecular mechanism of PGRL1 in diatoms. We created

Hydroxyproline‐rich glycoproteins (HRGPs) constitute a major group of proteins of the extracellular matrix (ECM). The multicellular green alga Volvox carteri is a suitable model organism to study the evolutionary transition to multicellularity including basic principles and characteristics of an ECM. In Volvox , the ECM is dominated by a single HRGP family: the pherophorins. Our inventory amounts in

Trichomes are universal specific structures originating from nearly all terrestrial plants. Although quantities of long non‐coding RNAs (lncRNAs) have been identified in many plant species, the role of lncRNAs in trichome formation still remains unknown. Here, we identified a total of 1303 lncRNAs in the young stems of woolly mutant LA3560 (Wo ) and its non‐woolly segregants (WT). Out of these lncRNAs

Primary cell wall cellulose is synthesized by the cellulose synthase complex (CSC) containing CELLULOSE SYNTHASE1 (CESA1), CESA3 and one of four CESA6‐like proteins in Arabidopsis. It has been proposed that the CESA6‐like proteins occupy the same position in the CSC, but their underlying selection mechanism remains unclear. We produced a chimeric CESA5 by replacing its N‐terminal zinc finger with its

Meiotic recombination is initiated by formation of DNA double strand breaks (DSBs). This involves a protein complex that includes in plants the two similar proteins, SPO11‐1 and SPO11‐2. We analysed the sequences of SPO11‐2 in hexaploid bread wheat (Triticum aestivum ) as well as in its diploid and tetraploid progenitors. We investigated its role during meiosis using single, double and triple mutants

Ferredoxins (Fd) play a crucial role in photosynthesis by regulating the distribution of electrons to downstream enzymes. Multiple Fd genes have been annotated in the rice (Oryza sativa L.) genome; however, their specific functions are not well understood. Here, we report the functional characterization of rice Fd1 . Sequence alignment, phylogenetic analysis of seven rice Fd proteins, and RT‐qPCR analysis

Transgenes have become essential to modern biology, being an important tool in functional genomic studies and also in the development of biotechnological products. One of the major challenges in the generation of transgenic lines concerns the expression of transgenes, which, compared to endogenes, are particularly susceptible to silencing mediated by small RNAs (sRNAs). Several reasons have been put

Arabidopsis encodes 10 ARGONAUTE (AGO) effectors of RNA silencing, canonically loaded with either 21–22 nucleotide (nt) long small RNAs (sRNAs) to mediate post‐transcriptional gene silencing (PTGS) or 24 nt sRNAs to promote RNA‐directed DNA methylation. Using full‐locus constructs, we characterized the expression, biochemical properties and possible modes of action of AGO3. Although AGO3 arose from

Nitrogen (N) is a macronutrient that is essential for plant growth and development, which is required for the synthesis of a myriad of important biomolecules, including amino acids, proteins, nucleic acids and hormones such as auxin and cytokinin (Yang et al. , 2015). Consequently, plant productivity depends heavily on N fertilization and N is a major limiting factor for agriculture. This is particularly

Nitrogen (N) is a major factor for plant development and productivity. However, the application of nitrogenous fertilizers generates environmental and economic problems. To cope with the increasing global food demand, the development of rice varieties with high nitrogen use efficiency (NUE) is indispensable for reducing environmental issues and achieving sustainable agriculture. Here, we report that

In the article “Biosynthesis of the psychotropic plant diterpene salvinorin A: Discovery and characterization of the Salvia divinorum clerodienyl diphosphate synthase” by Pelot et al . (2017), the name of the fourth author has been corrected to Lynne M. Hagelthorn in the online version.

It has been argued that the application of metabolomics to gene‐edited crops would present value in three areas: 1) detection of gene‐edited crops, 2) characterization of unexpected changes that might affect safety, and 3) building on the track record of rigorous government regulation in supporting consumer acceptance of GMOs. Here, we offer a different perspective relative to each of these areas.

Advancements in ‐omics techniques provide powerful tools to assess potential effects in composition of a plant at the RNA, protein and metabolite levels. These technologies can thus be deployed to assess whether genetic engineering causes changes in plants that go beyond the changes introduced by conventionally plant breeding. Here, we compare the extent of transcriptome and metabolome modification

Potato tuber formation is a secondary developmental program by which cells in the subapical stolon region divide and radially expand, to further differentiate into starch accumulating parenchyma. Whilst some details of the molecular pathway that signals tuberization are known, important gaps in our knowledge persist. Here the role of a member of the TERMINAL FLOWER 1/ CENTRORADIALIS gene family (termed

Cold acclimation (CA) is a well‐known strategy employed by plants to enhance freezing tolerance in winter. Global warming could disturb CA and increase the potential for winter freeze‐injury. Thus, developing robust freezing tolerance through complete CA is essential. To explore the molecular mechanisms of CA in woody perennials, we compared field and artificial CAs. Transcriptomic data showed that

Rubisco activase (Rca) facilitates the release of sugar‐phosphate inhibitors from the active sites of Rubisco and thereby plays a central role in initiating and sustaining Rubisco activation. In Arabidopsis, alternative splicing of a single Rca gene results in two Rca isoforms, Rca‐α and Rca‐β. Redox modulation of Rca‐α regulates the function of Rca‐α and Rca‐β acting together to control Rubisco activation

We designed a dicistronic plastid marker system that relies on the plastid's ability to translate polycistronic mRNAs. The identification of transplastomic clones is based on selection for antibiotic resistance encoded in the first open reading frame (ORF) and accumulation of the reporter gene product in tobacco chloroplasts encoded in the second ORF. The antibiotic resistance gene may encode spectinomycin

Cassava (Manihot esculenta Crantz) is one of the important staple foods in Sub‐Saharan Africa. It produces starchy storage roots that provide food and income for several hundred million people, mainly in tropical agriculture zones. Increasing cassava storage root and starch yield is one of the major breeding targets with respect to securing the future food supply for the growing population of Sub‐Saharan

Long non‐coding RNAs (lncRNAs) are involved in the resistance of plants to infection by pathogens via interactions with microRNAs (miRNAs). Long non‐coding RNAs are cleaved by miRNAs to produce phased small interfering RNAs (phasiRNAs), which, as competing endogenous RNAs (ceRNAs), function as decoys for mature miRNAs, thus inhibiting their expression, and contain pre‐miRNA sequences to produce mature

Small interfering RNAs (siRNAs) are responsible for establishing and maintaining DNA methylation through the RNA‐directed DNA methylation (RdDM) pathway in plants. Although siRNA biogenesis is well known, it is relatively unclear about how the process is regulated. By a forward genetic screen in Arabidopsis thaliana , we identified a mutant defective in NOT1 and demonstrated that NOT1 is required for

Pathogens and other adverse environmental conditions can trigger endoplasmic reticulum (ER) stress. ER stress signaling increases the expression of cytoprotective ER‐chaperones. The inositol‐requiring enzyme (IRE1) is one ER stress sensor that is activated to splice the bZIP60 mRNA that produces a truncated transcription factor that activates gene expression in the nucleus. The IRE1/bZIP60 pathway

We previously developed a large‐scale genome restructuring technology called the TAQing system. It can induce genome rearrangements by introducing transient and conditional formation of DNA double strand breaks (DSBs) via heat activation of a restriction enzyme TaqI, which can cleave DNA at 5'‐TCGA‐3' sequences in the genome at higher temperature (37–42°C). Such heat treatment sometimes confers lethal

Some plant miRNA families contain multiple members generating identical or highly similar mature miRNA variants. Mechanisms underlying expansion of miRNA families remain elusive, although tandem and/or segmental duplications have been proposed. In this study in two tetraploid cottons Gossypium hirsutum and G. barbadense , and their extant diploid progenitors G. arboreum and G. raimondii , we investigated

Plant responses to coincident nutrient deficiencies cannot be predicted from the responses to individual deficiencies. Although copper (Cu) and iron (Fe) are essential micronutrients for plant growth that are often and concurrently limited in soils, the combinatorial response to Cu‐Fe deficiency remains elusive. In this work, we characterised the responses of Arabidopsis thaliana plants deprived of

Reliable identification of individual chromosomes in eukaryotic species is the foundation for comparative chromosome synteny and evolutionary studies. Chromosome identification, unfortunately, has been a major challenge for plants with small chromosomes, such as the Citrus species. We developed oligonucleotide (oligo)‐based chromosome painting probes for all nine chromosomes in Citrus maxima (Pummelo)

Members of the fungal genus Trichoderma stimulate growth and reinforce plant immunity. Nevertheless, how fungal signaling elements mediate the establishment of a successful Trichoderma ‐plant interaction is largely unknown. In this work, we analyzed growth, root architecture, and defense in an Arabidopsis ‐Trichoderma co‐cultivation system, including the WT strain of the fungus and mutants affected

Brachypodium distachyon is an annual C3 grass used as a monocot model system in functional genomics research. Insertional mutagenesis is a powerful tool for both forward and reverse genetics studies. In this study, we explored the possibility of using the tobacco retrotransposon Tnt1 to create a transposon‐based insertion mutant population in B. distachyon . We developed transgenic B. distachyon plants

Arabidopsis thaliana AKR2A plays an important role in plant responses to cold stress. However, its exact function in plant resistance to cold stress remains unclear. In the present study, we found that the contents of very long‐chain fatty acids (VLCFAs) in akr2a mutants were decreased, and the expression level of KCS1 was also reduced. Overexpression of KCS1 in the akr2a mutants could enhance VLCFAs

Heat shock protein 70 (Hsp70) chaperones are highly conserved and essential proteins with diverse cellular functions including plant abiotic stress tolerance. Hsp70 proteins have been linked with basal heat tolerance in plants. Hsp101 likewise is an important chaperone protein which plays critical role in heat tolerance in plants. We observed that Arabidopsis hsc70‐1 mutant seedlings show elevated

Anther development and pollen tube elongation are key steps for pollination and fertilization. The timing and spatial distribution of reactive oxygen species (ROS) and programmed cell death (PCD) are central to these processes, but the regulatory mechanism of ROS production is not well understood. Inflorescence deficient in abscission (IDA) is implicated in many plant development and responses to environmental

For decades, genetic engineering approaches to produce unusual fatty acids (UFAs) in crops has reached a bottleneck, including reduced seed oil production and seed vigor. Currently, plant models in the field of research are primarily used to investigate defects in oil production and seedling development, while the role of UFAs in embryonic developmental defects remains unknown. In this study, we developed

Increased photosynthetic activity is closely linked to heterosis in plants, but the underlying molecular mechanisms remain elusive. Pak choi (Brassica rapa ssp. chinensis ) is a widely grown vegetable in Asia, and the most commercial cultivars are F1 hybrids. Here, the inbred pak choi lines WTC and 2Q, and their reciprocal F1 hybrids WQ and QW were used to characterize the increased photosynthetic

The firmness of fleshy fruit crops has a significant effect on their quality, consumer preference, shelf‐life and transportability. In a combined quantitative trait locus (QTL) and genome‐wide association studies (GWAS) study of apple fruit texture, we identified a mutation （C‐G） in the ethylene response factor‐associated amphiphilic repression (EAR) motif in the coding region of the apple ETHYLENE

The manipulation of meiotic recombination in crops is essential to rapidly develop new plant varieties, producing more in a sustainable manner. One option is to control the formation and repair of the meiosis‐specific DNA double strand breaks (DSBs) that initiate recombination between the homologous chromosomes and ultimately lead to crossovers. These DSBs are introduced by the evolutionarily conserved

The self‐splicing of group II introns during RNA processing depends on their catalytic structure and is influenced by numerous factors that promote the formation of that structure through direct binding. Here we report that C‐to‐U editing at a specific position in two nad7 introns is essential to splicing, which also implies that the catalytic activity of nonfunctional group II introns could be restored

Vernalization accelerates flowering after prolonged winter cold. Transcriptional and epigenetic changes are known to be involved in the regulation of the vernalization response. Despite intensive applications of next‐generation sequencing in diverse aspects of plant research, genome‐wide transcriptome and epigenome profiling during the vernalization response has not been conducted. In this work, to

Arabidopsis thaliana ABSCISIC ACID INSENSITIVE3 (ABI3) is a transcription factor in the B3 domain family. ABI3, along with B3 domain transcription factors LEAFY COTYLEDON2 (LEC2) and FUSCA3 (FUS3), and LEC1, a subunit of the CCAAT box‐binding complex, form the so‐called LAFL network to control various aspects of seed development and maturation. ABI3 also contributes to the abscisic acid (ABA) response

Soybean nodulation is a highly controlled process that involves complex gene regulation at both transcriptional and post‐transcriptional levels. In the present study, we profiled gene expression changes, alternative splicing events, and DNA methylation patterns during nodule formation, development, and senescence. The transcriptome data uncovered key transcription patterns of nodule development that

The establishment of the nitrogen‐fixing symbiosis between soybean and Bradyrhizobium japonicum is a complex process. To document the changes in plant metabolism as a result of symbiosis, we utilized laser ablation electrospray ionization‐mass spectrometry (LAESI‐MS) for in situ metabolic profiling of wild‐type nodules, nodules infected with a B. japonicum nifH mutant unable to fix nitrogen, nodules

Tomato (Solanum lycopersicum L.) has become a popular model for genetic studies of fruit flavor in the last two decades. In this article we present a study of tomato fruit flavor, including an analysis of the genetic, metabolic and sensorial variation of a collection of contemporary commercial glasshouse tomato cultivars, followed by a validation of the associations found by quantitative trait locus

Traditional genetic studies focus on identifying genetic variants associated with the mean difference in a quantitative trait. Because genetic variants also influence phenotypic variation via heterogeneity, we conducted a variance‐heterogeneity genome‐wide association study to examine the contribution of variance heterogeneity to oil‐related quantitative traits. We identified 79 unique variance‐controlling

Sweet cherry (Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geographic areas with important questions arising on their historical relationships. Little is known about the effects of the domestication process on the evolution of the sweet