Mitogen‐activated protein kinase (MAPK) cascades play vital roles in regulating plant growth, development, and stress responses. MAPK‐like (MPKL) proteins are a group of kinases containing the MAPK signature TxY motif and showing sequence similarity to MAPKs. However, the functions of plant MPKL proteins are currently unknown. The maize (Zea mays) genome contains four genes encoding MPKL proteins, here named ZmMPKL1 to ZmMPKL4. In this study, we show that ZmMPKL1 possesses kinase activity and that drought‐induced ZmMPKL1 expression, ZmMPKL1 overexpression and knockout maize seedlings exhibited no visible morphological difference from wild‐type B73 seedlings when grown under normal conditions. By contrast, under drought conditions, ZmMPKL1‐overexpressing seedlings showed increased stomatal aperture, water loss, and leaf wilting and knockout seedlings showed the opposite phenotypes. Moreover, these drought‐sensitive phenotypes in ZmMPKL1‐overexpressing seedlings were restored by exogenous abscisic acid (ABA). ZmMPKL1 overexpression reduced drought‐induced ABA production in seedlings and the knockout showed enhanced ABA production. Drought‐induced transcription of ABA biosynthetic genes were suppressed and ABA catabolic genes were enhanced in ZmMPKL1‐overexpressing seedlings, while their transcription were reversely regulated in knockout seedlings. These results suggest that ZmMPKL1 positively regulates seedlings drought sensitivity by altering the transcription of ABA biosynthetic and catabolic genes, and ABA homeostasis.

The model legume Medicago truncatula possesses a single outward Shaker K+ channel, while Arabidopsis thaliana possesses two channels of this type, named AtSKOR and AtGORK, the former having been shown to play a major role in K+ secretion into the xylem sap in the root vasculature and the latter to mediate the efflux of K+ across the guard cell membrane leading to stomatal closure. Here we show that the expression pattern of the single M. truncatula outward Shaker channel, which has been named MtGORK, includes the root vasculature, guard cells and root hairs. As shown by patch‐clamp experiments on root hair protoplasts, besides the Shaker‐type slowly‐activating outwardly‐rectifying K+ conductance encoded by MtGORK, a second K+‐permeable conductance, displaying fast activation and weak rectification, can be expressed by M. truncatula. A KO mutation resulting in absence of MtGORK activity is shown to weakly reduce K+ translocation to shoots, and only in plants engaged in rhizobial symbiosis, but to strongly affect the control of stomatal aperture and transpirational water loss. In legumes, the early electrical signaling pathway triggered by Nod factor perception is known to comprise a short transient depolarization of the root hair plasma membrane. In absence of MtGORK functional expression, the rate of the membrane repolarization is found to be decreased by about 2 times. This defect was without any consequence on infection thread development and nodule production in plants grown in vitro, but a decrease in nodule production was observed in plants grown in soil.

β‐glucosidases (BG) are present in many plant tissues; among them, abscisic acid (ABA) β‐glucosidases are thought to take part in the adjustment of cellular ABA levels, yet the role of ABA BG in fruits is unclear at present. In this study, through RNA‐seq analysis of persimmon fruit, ten full‐length DkBG genes were isolated, and all were found to be expressed; in particular, DkBG1 was highly expressed in persimmon fruits with maximum expression 95 days after full bloom (DAFD). We verified that the DkBG1 protein can hydrolyze ABA glucose ester (ABA‐GE) to release free ABA in vitro. Tomato plants over‐expressing DkBG1 significantly up‐regulated the expressions of ABA receptor PYL3/7 genes, and showed typical symptoms of ABA hyper‐sensitivity in fruits compared to wild type. DkBG1‐OE accelerated fruit ripening onset by three to four days by increasing ABA levels at the pre‐breaker stage, which induced early ethylene release compared to WT fruits. DkBG1‐OE altered the expression of ripening regulator NON‐ RIPENING (NOR) and its target genes, which in turn altered fruit quality traits such as coloration. Our results demonstrate that DkBG1 plays an important role in the fruit ripening and quality by adjusting ABA levels via hydrolysis of ABA‐GE.

In this work, we review the physiological and molecular mechanisms that allow vascular plants to perform photosynthesis in extreme environments, such as deserts, polar and alpine ecosystems. Specifically, we discuss the morpho/anatomical, photochemical and metabolic adaptive processes that enable a positive carbon balance in photosynthetic tissues under extreme temperatures and/or severe water limiting conditions in C3 species. Nevertheless, only a few studies describe the in situ functioning of photoprotection in plants from extreme environments, given the intrinsic difficulties of fieldwork in remote places; however, they cover a substantial geographical and functional range, which allowed us to describe some general trends. In general, photoprotection relies on the same mechanisms as those operating in the remaining plant species, ranging from enhanced morphological photoprotection to increased scavenging of oxidative products such as reactive oxygen species. Much less information is available about the main physiological and biochemical drivers of photosynthesis: stomatal conductance (gs), mesophyll conductance (gm) and carbon fixation mostly driven by Rubisco carboxylation. Extreme environments shape adaptations in structures, such as cell wall and membrane composition, the concentration and activation state of Calvin‐Benson cycle enzymes, and Rubisco evolution, optimizing kinetic traits to ensure functionality. Altogether, these species display a combination of rearrangements, from the whole plant level to the molecular scale, to sustain a positive carbon balance in some of the most hostile environments on Earth.

Synthesis of the D1 reaction center protein of Photosystem II is dynamically regulated in response to environmental and developmental cues. In chloroplasts, much of this regulation occurs at the post‐transcriptional level, but the proteins responsible are largely unknown. To discover proteins that impact psbA expression, we identified proteins that associate with maize psbA mRNA by: (i) formaldehyde cross‐linking of leaf tissue followed by antisense oligonucleotide affinity capture of psbA mRNA; and (ii) co‐immunoprecipitation with HCF173, a psbA translational activator that is known to bind psbA mRNA. The S1 domain protein SRRP1 and two RNA Recognition Motif (RRM) domain proteins, CP33C and CP33B, were enriched with both approaches. Orthologous proteins were also among the enriched protein set in a previous study in Arabidopsis that employed a designer RNA‐binding protein as a psbA RNA affinity tag. We show here that CP33B is bound to psbA mRNA in vivo, as was shown previously for CP33C and SRRP1. Immunoblot, pulse labeling, and ribosome profiling analyses of mutants lacking CP33B and/or CP33C detected some decreases in D1 protein levels under some conditions, but no change in psbA RNA abundance or translation. However, analogous experiments showed that SRRP1 represses psbA ribosome association in the dark, represses ycf1 ribosome association, and promotes accumulation of ndhC mRNA. As SRRP1 is known to harbor RNA chaperone activity, we postulate that SRRP1 mediates these effects by modulating RNA structures. The uncharacterized proteins that emerged from our analyses provide a resource for the discovery of proteins that impact the expression of psbA and other chloroplast genes.

Cassava is an important staple crop in sub‐Saharan Africa, due to its high productivity even on nutrient poor soils. The metabolic characteristics underlying this high productivity are poorly understood including the mode of photosynthesis, reasons for the high rate of photosynthesis, the extent of source/sink limitation, the impact of environment, and the extent of variation between cultivars. Six commercial African cassava cultivars were grown in the greenhouse in Erlangen, Germany and the field in Ibadan, Nigeria. Source leaves, sink leaves, stems and storage roots were harvested during storage root bulking and analyzed for sugars, organic acids, amino acids, phosphorylated intermediates, minerals, starch, protein, activities of enzymes in central metabolism and yield traits. High ratios of Rubisco:phosphoenolpyruvate carboxylase activity support a C3 mode of photosynthesis. The high rate of photosynthesis is likely attributed to high activities of enzymes in the Calvin‐Benson cycle and pathways for sucrose and starch synthesis. Nevertheless, source limitation is indicated because root yield traits correlated with metabolic traits in leaves rather than in the stem or storage roots. This was especially so in greenhouse‐grown plants, where irradiance will have been low. In the field, plants produced more storage roots. This was associated with higher AGPase activity and lower sucrose in the roots, indicating that feedforward loops enhance sink capacity in the high light and low nitrogen environment in the field. Overall, the results indicate that carbon assimilation rate, the K battery, root starch synthesis, trehalose, and chlorogenic acid accumulation are potential target traits for genetic improvement.

Brassinosteroids (BRs) are a class of phytohormones that modulate several important agronomic traits in rice (Oryza sativa). GSK2 is one of the critical suppressors of BR signaling and targets transcription factors such as OsBZR1 and DLT to regulate BR responses. Here, we identified OFP3 (OVATE FAMILY PROTEIN 3) as an interactor of both GSK2 and DLT by yeast two‐hybrid screening and demonstrated that OFP3 plays a distinctly negative role in BR responses. While knockout of OFP3 promoted rice seedling growth, overexpression of OFP3 led to strong BR insensitivity, which resulted in reduced plant height, leaf angle, and grain size. Interestingly, both BR biosynthetic and signaling genes had decreased expression in the overexpression plants. OFP3 overexpression also enhanced the phenotypes of BR‐deficient mutants, but largely suppressed those of BR‐enhanced plants. Moreover, treatment with either BR or bikinin, a GSK3‐like kinase inhibitor, induced OFP3 depletion, whereas GSK2 or brassinazole, a BR synthesis inhibitor, promoted OFP3 accumulation. Furthermore, OFP3 exhibited transcription repressor activity and was able to interact with itself as well as additional BR‐related components, including OFP1, OSH1, OSH15, OsBZR1, and GF14c. Importantly, GSK2 can phosphorylate OFP3 and enhance these interactions. We propose that OFP3, as a suppressor of both BR synthesis and signaling but stabilized by GSK2, incorporates into a transcription factor complex to facilitate BR signaling control, which is critical for the proper development of various tissues.

Salt stress reduces crop growth and productivity globally. Here we report that a R2R3‐MYB transcription factor MYB30 participates in salt tolerance in Arabidopsis. MYB30 can be SUMOylated by SIZ1 in response to salt stress and the Lysine (K)283 of MYB30 is essential for its SUMOylation. In contrast to wild‐type MYB30, MYB30K283R mutant failed to rescue the salt‐sensitive phenotype of myb30‐2 mutant, indicating that SUMOylation of MYB30 is required for salt stress response. Through transcriptomic analysis, we identified a MYB30 target, alternative oxidase 1a (AOX1a). MYB30 binds the promoter of AOX1a and upregulates its expression in response to salt stress, however, MYB30K283R cannot bind the promoter of AOX1a. The cyanide (CN)‐resistant alternative respiration (Alt) mediated by AOX is significantly reduced in myb30‐2 mutant due to loss‐of‐function of MYB30. As a result, the redox homeostasis is disrupted in myb30‐2 mutant compared to that in wild type seedlings (WT) under salt conditions. Artificial elimination of excess ROS partially rescues the salt‐sensitive phenotype of myb30‐2 mutant, whereas exogenous application of SHAM, an inhibitor of AOXs and Alt respiration, the salt tolerance of Col‐0 and the complemented plants decreased to a level similar to that in myb30‐2. Finally, overexpression of AOX1a in myb30‐2 confers WT‐like salt tolerance compared to that of myb30‐2 mutant. Taken together, our results revealed a functional link between MYB30 and AOX1a, and that SIZ1‐mediated SUMOylation of MYB30 enhances salt tolerance by regulating Alt respiration and cellular redox homeostasis via AOX1a in Arabidopsis.

Juglans (walnuts), the most speciose genus in the walnut family (Juglandaceae), represents most of the family's commercially valuable fruit and wood‐producing trees. It includes several species used as rootstock for their resistance to various abiotic and biotic stressors. We present the full structural and functional genome annotations of six Juglans species and one outgroup within Juglandaceae (Juglans regia, J. cathayensis, J. hindsii, J. microcarpa, J. nigra, J. sigillata and Pterocarya stenoptera) produced using BRAKER2 semi‐unsupervised gene prediction pipeline and additional tools. For each annotation, gene predictors were trained using 19 tissue‐specific J. regia transcriptomes aligned to the genomes. Additional functional evidence and filters were applied to multi‐exonic and mono‐exonic putative genes to yield between 27 000 and 44 000 high‐confidence gene models per species. Comparison of gene models to the BUSCO embryophyta dataset suggested that, on average, genome annotation completeness was 85.6%. We utilized these high‐quality annotations to assess gene family evolution within Juglans, and among Juglans and selected Eurosid species. We found notable contractions in several gene families in J. hindsii, including disease resistance‐related wall‐associated kinase (WAK), Catharanthus roseus receptor‐like kinase (CrRLK1L) and others involved in abiotic stress response. Finally, we confirmed an ancient whole‐genome duplication that took place in a common ancestor of Juglandaceae using site substitution comparative analysis.

Understanding the impact of elevated CO2 (eCO2) in global agriculture is important given climate change projections. Breeding climate‐resilient crops depends on genetic variation within naturally varying populations. The effect of genetic variation in response to eCO2 is poorly understood, especially in crop species. We describe the different ways in which Solanum lycopersicum and its wild relative S. pennellii respond to eCO2, from cell anatomy, to the transcriptome, and metabolome. We further validate the importance of translational regulation as a potential mechanism for plants to adaptively respond to rising levels of atmospheric CO2.

Angiosperm reproductive development is a complex event that includes floral organ development, male and female gametophyte formation and interaction between the male and female reproductive organs for successful fertilization. Previous studies revealed the redundant function of ATP binding cassette subfamily G (ABCG) transporters ABCG1 and ABCG16 in pollen development, but whether they are involved in other reproductive processes is unknown. Here we showed that ABCG1 and ABCG16 were not only expressed in anthers and stamen filaments but also enriched in pistil tissues, including the stigma, style, transmitting tract and ovule. We further demonstrated that pistil‐expressed ABCG1 and ABCG16 promoted rapid pollen tube growth through their effects on auxin distribution and auxin flow in the pistil. Moreover, disrupted auxin homeostasis in stamen filaments was associated with defective filament elongation. Our work reveals the key functions of ABCG1 and ABCG16 in reproductive development and provides clues for identifying ABCG1 and ABCG16 substrates in Arabidopsis.

This review summarizes recent progress in understanding Crassulacean Acid Metabolism (CAM) systems and the integration of internal and external stimuli to maximize water‐use efficiency. Complex CAM traits have been reduced to a minimalist format and captured as computational models, which can now be refined using recently available data from transgenic manipulations and large‐scale omics studies. We identify three key areas in which an appropriate choice of modelling tool could help capture relevant comparative molecular data to address evolutionary drivers and plasticity of CAM. One focus is to identify the environmental and internal signals that drive inverse stomatal opening at night. Secondly, it is important to identify the regulatory processes required to orchestrate the diel pattern of carbon fluxes within mesophyll layers. Finally, the limitations imposed by contrasting succulent systems and associated hydraulic conductance components should be compared in the context of water use and evolutionary strategies. While network analysis of transcriptomic data can provide insights via co‐expression modules and hubs, alternative forms of computational modelling should be used iteratively to define the physiological significance of key components and informing targeted functional gene manipulation studies. We conclude that resultant improvements of bottom‐up, mechanistic modelling systems would enhance progress towards capturing the physiological controls for phylogenetically diverse CAM systems in the face of the recent surge of information in this omics era.

Cell wall localized heterogeneous polyesters are widespread in land plants. The composition of these polyesters, such as cutin, suberin, or more plant specific forms such as the flax seed coat lignan macromolecule, can be determined after total hydrolysis of the ester linkages. The main bottleneck in the structural characterization of these macromolecules, however, resides in the determination of the higher order monomer sequences. Partial hydrolysates of the polyesters release a complex mixture of fragments of different lengths, each present in low abundance and therefore challenging to structurally characterize. Here, a method is presented by which liquid chromatography‐mass spectrometry (LC‐MS) profiles of such partial hydrolysates are searched for pairs of related fragments. LC‐MS peaks that show a mass difference corresponding to the addition of one or more macromolecule monomers were connected in a network. Starting from the lowest molecular weight peaks in the network, the annotation of the connections as the addition of one or more polyester monomers allow the prediction of consecutive and increasingly complex adjacent peaks. MSn experiments further help to reject, corroborate, and sometimes refine the structures predicted by the network. As a proof of concept, this procedure was applied to partial hydrolysates of the flax seed coat lignan macromolecule, and allowed to characterize 120 distinct oligo‐esters, consisting of up to 6 monomers, and containing monomers and linkages of which the incorporation in the lignan macromolecule had not been described before. These results show the capacity of the approach to advance the structural elucidation of complex plant polyesters.

Telomeres, nucleoprotein structures at the ends of linear eukaryotic chromosomes, are crucial for the maintenance of genome integrity. In most plants, telomeres consist of conserved tandem repeat units comprising the TTTAGGG motif. Recently, non‐canonical telomeres were described in several plants and plant taxons, including the carnivorous plant Genlisea hispidula (TTCAGG/TTTCAGG), the genus Cestrum (Solanaceae; TTTTTTAGGG), and plants from the Asparagales order with either a vertebrate‐type telomere repeat TTAGGG or Allium genus‐specific CTCGGTTATGGG repeat. We analyzed epigenetic modifications of telomeric histones in plants with canonical and non‐canonical telomeres, and further in telomeric chromatin captured from leaves of Nicotiana benthamiana transiently transformed by telomere CRISPR‐dCas9‐eGFP, and of Arabidopsis thaliana stably transformed with TALE_telo C‐3×GFP. Two combinatorial patterns of telomeric histone modifications were identified: (i) an Arabidopsis‐like pattern (A. thaliana, G. hispidula, Genlisea nigrocaulis, Allium cepa, Narcissus pseudonarcissus, Petunia hybrida, Solanum tuberosum, Solanum lycopersicum) with telomeric histones decorated predominantly by H3K9me2; (ii) a tobacco‐like pattern (Nicotiana tabacum, N. benthamiana, C. elegans) with a strong H3K27me3 signal. Our data suggest that epigenetic modifications of plant telomere‐associated histones are related neither to the sequence of the telomere motif nor to the lengths of the telomeres. Nor the phylogenetic position of the species plays the role; representatives of the Solanaceae family are included in both groups. As both patterns of histone marks are compatible with fully functional telomeres in respective plants, we conclude that the described specific differences in histone marks are not critical for telomere functions.

Black pepper (Piper nigrum L.) is known for its high content of piperine, a cinnamoyl amide derivative regarded as largely responsible for the pungent taste of this widely used spice. Despite its long history and worldwide use, the biosynthesis of piperine and related amides has been enigmatic up to now. In this report we describe a specific piperic acid CoA ligase from immature green fruits of P. nigrum. The corresponding enzyme was cloned and functionally expressed in E. coli. The recombinant enzyme displays a high specificity for piperic acid and does not accept the structurally related feruperic acid characterized by a similar C‐2 extension of the general C6–C3 phenylpropanoid structure. The enzyme is also inactive with the standard set of hydroxycinnamic acids tested including caffeic acid, 4‐coumaric acid, ferulic acid, and sinapic acid. Substrate specificity is corroborated by in silico modelling that suggests a perfect fit for the substrate piperic acid to the active site of the piperic acid CoA ligase. The CoA ligase gene shows its highest expression levels in immature green fruits, is also expressed in leaves and flowers, but not in roots. Virus‐induced gene silencing provided some preliminary indications that the production of piperoyl‐CoA is required for the biosynthesis of piperine in black pepper fruits.

Nicotiana section Suaveolentes is an almost all‐Australian clade of allopolyploid tobacco species including the important plant model Nicotiana benthamiana. The homology relationships of this clade and its formation are not completely understood. To address this gap, we assessed phylogenies of all individual genes of N. benthamiana and the well studied N. tabacum (section Nicotiana) and their homologues in six diploid Nicotiana species. We generated sets of 44 424 and 65 457 phylogenetic trees of N. benthamiana and N. tabacum genes, respectively, each collectively called a phylome. Members of Nicotiana sections Noctiflorae and Sylvestres were represented as the species closest to N. benthamiana in most of the gene trees. Analyzing the gene trees of the phylome we: (i) dated the hybridization event giving rise to N. benthamiana to 4–5 MyA, and (ii) separated the subgenomes. We assigned 1.42 Gbp of the genome sequence to section Noctiflorae and 0.97 Gbp to section Sylvestres based on phylome analysis. In contrast, read mapping of the donor species did not succeed in separating the subgenomes of N. benthamiana. We show that the maternal progenitor of N. benthamiana was a member of section Noctiflorae, and confirm a member of section Sylvestres as paternal subgenome donor. We also demonstrate that the advanced stage of long‐term genome diploidization in N. benthamiana is reflected in its subgenome organization. Taken together, our results underscore the usefulness of phylome analysis for subgenome characterization in hybrid species.

Inorganic polyphosphates (polyPs) are linear polymers of orthophosphate units linked by phosphoanhydride bonds. Polyphosphates represent important stores of phosphate and energy, and are abundant in many pro‐ and eukaryotic organisms. In plants, the existence of polyPs has been established using microscopy and biochemical extraction methods that are now known to produce artifacts. Here we use a polyP‐specific dye and a polyP‐binding domain to detect polyPs in plant and algal cells. To develop the staining protocol, we induced polyP granules in Nicotiana benthamiana and Arabidopsis cells by heterologous expression of Escherichia coli polyphosphate kinase 1 (PPK1). Over‐expression of PPK1 but not of a catalytically impaired version of the enzyme leads to severe growth phenotypes, suggesting that ATP‐dependent synthesis and accumulation of polyPs in the plant cytosol is toxic. We next crossed stable PPK1‐expressing Arabidopsis lines with plants expressing the polyP‐binding domain of E. coli exopolyphosphatase (PPX1c), which co‐localized with PPK1‐generated polyP granules. These granules were stained by the polyP‐specific dye JC‐D7 and appeared as electron‐dense structures in transmission electron microscopy sections. Using the polyP staining protocol derived from these experiments, we screened for polyP stores in different organs and tissues of both mono‐ and dicotyledonous plants. While we could not detect polyP granules in higher plants, we could visualize the polyP‐rich acidocalcisomes in the green alga Chlamydomonas reinhardtii.

Triticum urartu (2n = 2x = 14, subgenome AuAu), a wild diploid wheat progenitor, features broad allelic diversity for a number of traits of agronomic relevance. A thorough characterization of the diversity of T. urartu natural accessions may provide wheat breeders with new alleles potentially contributing to wheat improvement. In this study, we performed an extensive genotypic and phenotypic characterization of a world collection of 299 T. urartu ex situ accessions, developing 441 327 single nucleotide polymorphisms and recording trait values for agronomic and quality traits. The collection was highly diverse, with broad variation in phenology and plant architecture traits. Seed features were also varied, and analyses of flour quality reported 18 distinct patterns of glutenins, and carotenoid concentrations and sedimentation volumes in some cases surpassing those of cultivated materials. The genome‐wide molecular markers developed on the collection were used to conduct a genome‐wide association study reporting 25 highly significant quantitative trait nucleotides for the traits under examination, only partially overlapping loci already reported in wheat. Our data show that T. urartu may be considered a valuable allele pool to support the improvement of wheat agronomy and quality.

Physcomitrella patens is a bryophyte model plant that is often used to study plant evolution and development. Its resources are of great importance for comparative genomics and evo‐devo approaches. However, expression data from Physcomitrella patens were so far generated using different gene annotation versions and three different platforms: CombiMatrix and NimbleGen expression microarrays and RNA sequencing. The currently available P. patens expression data are distributed across three tools with different visualization methods to access the data. Here, we introduce an interactive expression atlas, Physcomitrella Expression Atlas Tool (PEATmoss), that unifies publicly available expression data for P. patens and provides multiple visualization methods to query the data in a single web‐based tool. Moreover, PEATmoss includes 35 expression experiments not previously available in any other expression atlas. To facilitate gene expression queries across different gene annotation versions, and to access P. patens annotations and related resources, a lookup database and web tool linked to PEATmoss was implemented. PEATmoss can be accessed at https://peatmoss.online.uni-marburg.de

The formation of nitrogen‐fixing nodules on legume hosts is a finely tuned process involving many components of both symbiotic partners. Production of the exopolysaccharide succinoglycan by the nitrogen‐fixing bacterium Sinorhizobium meliloti 1021 is needed for an effective symbiosis with Medicago spp., and the succinyl modification to this polysaccharide is critical. However, it is not known when succinoglycan intervenes in the symbiotic process, and it is not known whether the plant lysin‐motif receptor‐like kinase MtLYK10 intervenes in recognition of succinoglycan, as might be inferred from work on the Lotus japonicus MtLYK10 ortholog, LjEPR3. We studied the symbiotic infection phenotypes of S. meliloti mutants deficient in succinoglycan production or producing modified succinoglycan, in wild‐type Medicago truncatula plants and in Mtlyk10 mutant plants. On wild‐type plants, S. meliloti strains producing no succinoglycan or only unsuccinylated succinoglycan still induced nodule primordia and epidermal infections, but further progression of the symbiotic process was blocked. These S. meliloti mutants induced a more severe infection phenotype on Mtlyk10 mutant plants. Nodulation by succinoglycan‐defective strains was achieved by in trans rescue with a Nod factor‐deficient S. meliloti mutant. While the Nod factor‐deficient strain was always more abundant inside nodules, the succinoglycan‐deficient strain was more efficient than the strain producing only unsuccinylated succinoglycan. Together, these data show that succinylated succinoglycan is essential for infection thread formation in M. truncatula, and that MtLYK10 plays an important, but different role in this symbiotic process. These data also suggest that succinoglycan is more important than Nod factors for bacterial survival inside nodules.

Due to DNA heterozygosity and repeat content, assembly of non‐model plant genomes is challenging. Herein, we report a high‐quality genome reference of one of the oldest known domesticated species, fig (Ficus carica L.), using Pacific Biosciences single‐molecule, real‐time sequencing. The fig genome is ~333 Mbp in size, of which 80% has been anchored to 13 chromosomes. Genome‐wide analysis of N6‐methyladenine and N4‐methylcytosine revealed high methylation levels in both genes and transposable elements, and a prevalence of methylated over non‐methylated genes. Furthermore, the characterization of N6‐methyladenine sites led to the identification of ANHGA, a species‐specific motif, which is prevalent for both genes and transposable elements. Finally, exploiting the contiguity of the 13 pseudomolecules, we identified 13 putative centromeric regions. The high‐quality reference genome and the characterization of methylation profiles, provides an important resource for both fig breeding and for fundamental research into the relationship between epigenetic changes and phenotype, using fig as a model species.

With the objective of studying the role of glutathione reductase (GR) in the accumulation of cysteine and methionine, we generated transgenic tobacco and Arabidopsis lines overexpressing the cytosolic AtGR1 and the plastidic AtGR2 genes. The transgenic plants had higher contents of cysteine and glutathione. To understand why cysteine levels increased in these plants, we also used gr1 and gr2 mutants. The results showed that the transgenic plants have higher levels of sulfite, cysteine, glutathione and methionine, which are downstream to adenosine 5′ phosphosulfate reductase (APR) activity. However, the mutants had lower levels of these metabolites, while the sulfate content increased. A feeding experiment using 34SO42– also showed that the levels of APR downstream metabolites increased in the transgenic lines and decreased in gr1 compared with their controls. These findings, and the results obtained from the expression levels of several genes related to the sulfur pathway, suggest that GR plays an essential role in the sulfur assimilation pathway by supporting the activity of APR, the key enzyme in this pathway. GR recycles the oxidized form of glutathione (GSSG) back to reduce glutathione (GSH), which serves as an electron donor for APR activity. The phenotypes of the transgenic plants and the mutants are not significantly altered under non‐stress and oxidative stress conditions. However, when germinating on sulfur‐deficient medium, the transgenic plants grew better, while the mutants were more sensitive than the control plants. The results give substantial evidence of the yet unreported function of GR in the sulfur assimilation pathway.

FLOWERING LOCUS T (FT) protein, physiologically florigen, has been identified as a system integrator of numerous flowering time pathways in many studies, and its homologs are found throughout the plant lineage. It is important to uncover how precisely florigenic homologs contribute to flowering initiation and how these factors interact genetically. Here we dissected the function of Brachypodium FT orthologs BdFTL1 and BdFTL2 using overexpression and gene‐editing experiments. Transgenic assays showed that both BdFTL1 and BdFTL2 could promote flowering, whereas BdFTL2 was essential for flowering initiation. Notably, BdFTL1 is subject to alternative splicing (AS), and its transcriptional level and AS are significantly affected by BdFTL2. Additionally, BdFTL2 could bind with the PHD‐containing protein BdES43, an H3K4me3 reader. Furthermore, BdES43 was antagonistic to BdFTL2 in flowering initiation in a transcription‐dependent manner and significantly affected BdFTL1 expression. BdFTL2, BdES43 and H3K4me3 also had highly similar distribution patterns within the BdFTL1 locus, indicating their interplay in regulating target genes. Taken together, florigen BdFTL2 functions as a potential epigenetic effector of BdFTL1 by interacting with a BdES43‐H3K4me3 complex. This finding provides an additional insight for the regulatory mechanism underlying the multifaceted roles of florigen.

Many plant genomes display high levels of repetitive sequences. The assembly of these complex genomes using short high‐throughput sequence reads is still a challenging task. Underestimation or disregard of repeat complexity in these datasets can easily misguide downstream analysis. Detection of repetitive regions by k‐mer counting methods has proved to be reliable. Easy‐to‐use applications utilizing k‐mer counting are in high demand, especially in the domain of plants. We present Kmasker plants, a tool that uses k‐mer count information as an assistant throughout the analytical workflow of genome data that is provided as a command‐line and web‐based solution. Beside its core competence to screen and mask repetitive sequences, we have integrated features that enable comparative studies between different cultivars or closely related species and methods that estimate target specificity of guide RNAs for application of site‐directed mutagenesis using Cas9 endonuclease. In addition, we have set up a web service for Kmasker plants that maintains pre‐computed indices for 10 of the economically most important cultivated plants. Source code for Kmasker plants has been made publically available at https://github.com/tschmutzer/kmasker. The web service is accessible at https://kmasker.ipk-gatersleben.de.

Hybridizations between closely related species commonly occur in the domestication process of many crops. Banana cultivars are derived from such hybridizations between species and subspecies of the Musa genus that have diverged in various tropical Southeast Asian regions and archipelagos. Among the diploid and triploid hybrids generated, those with seedless parthenocarpic fruits were selected by humans and thereafter dispersed through vegetative propagation. Musa acuminata subspecies contribute to most of these cultivars.

Ovule primordia formation is a complex developmental process with a strong impact on the production of seeds. In Arabidopsis this process is controlled by a gene network, including components of the signaling pathways of auxin, brassinosteroids (BRs) and cytokinins. Recently, we have shown that gibberellins (GAs) also play an important role in ovule primordia initiation, inhibiting ovule formation in both Arabidopsis and tomato. Here we reveal that BRs also participate in the control of ovule initiation in tomato, by promoting an increase on ovule primordia formation. Moreover, molecular and genetic analyses of the co‐regulation by GAs and BRs of the control of ovule initiation indicate that two different mechanisms occur in tomato and Arabidopsis. In tomato, GAs act downstream of BRs. BRs regulate ovule number through the downregulation of GA biosynthesis, which provokes a stabilization of DELLA proteins that will finally promote ovule primordia initiation. In contrast, in Arabidopsis both GAs and BRs regulate ovule number independently of the activity levels of the other hormone. Taking together, our data strongly suggest that different molecular mechanisms could operate in different plant species to regulate identical developmental processes even, as in the case of ovule primordia initiation, when the same set of hormones trigger similar responses, adding a new level of complexity.

Rapidly communicating the perception of an abiotic stress event, wounding, or pathogen infection, from its initial site of occurrence to the entire plant, i.e., rapid systemic signaling, is essential for successful plant acclimation and defense. Recent studies highlighted an important role for several rapid whole‐plant systemic signals in mediating plant acclimation and defense during different abiotic and biotic stresses. These include calcium, reactive oxygen species (ROS), hydraulic and electric waves. Although the role of some of these signals in inducing and coordinating whole‐plant systemic responses was demonstrated, many questions related to their mode of action, routes of propagation, and integration, remain unanswered. In addition, it is unclear how these signals convey specificity to the systemic response, and how are they integrated under conditions of stress combination. Here we highlight many of these questions, as well as provide a proposed model for systemic signal integration, focusing on the ROS wave.

Plants survey their environment for the presence of potentially harmful or beneficial microbes. During colonization, cell surface receptors perceive microbe‐derived or modified‐self ligands and initiate appropriate responses. The recognition of fungal chitin oligomers and the subsequent activation of plant immunity are well described. In contrast, the mechanisms underlying β‐glucan recognition and signaling activation remain largely unexplored. Here, we systematically tested immune responses towards different β‐glucan structures and show that responses vary between plant species. While leaves of the monocots Hordeum vulgare and Brachypodium distachyon can recognize longer (laminarin) and shorter (laminarihexaose) β‐1,3‐glucans with responses of varying intensity, duration and timing, leaves of the dicot Nicotiana benthamiana activate immunity in response to long β‐1,3‐glucans, whereas Arabidopsis thaliana and Capsella rubella perceive short β‐1,3‐glucans. Hydrolysis of the β‐1,6 side branches of laminarin demonstrated that not the glycosidic decoration but rather the degree of polymerization plays a pivotal role in the recognition of long‐chain β‐glucans. Moreover, in contrast to the recognition of short β‐1,3‐glucan in A. thaliana, perception of long β‐1,3‐glucan in N. benthamiana and rice is independent of CERK1, indicating that β‐glucan recognition may be mediated by multiple β‐glucan receptor systems.

Plant cells have acquired chloroplasts (plastids) with a unique genome (ptDNA), which developed during the evolution of endosymbiosis. The gene content and genome structure of ptDNAs in land plants are considerably stable, although those of algal ptDNAs are highly varied. Plant cells seem, therefore, to be intolerant of any structural or organizational changes in the ptDNA. Genome rearrangement functions as a driver of genomic evolutionary divergence. Here, we aimed to create various types of rearrangements in the ptDNA of Arabidopsis genomes using plastid‐targeted forms of restriction endonucleases (pREs). Arabidopsis plants expressing each of the three specific pREs, i.e., pTaqI, pHinP1I, and pMseI, were generated; they showed leaf variegation phenotypes associated with impaired chloroplast development. We confirmed that these pREs caused double‐strand breaks (DSBs) at their recognition sites in ptDNAs. Genome‐wide analysis of ptDNAs revealed that the transgenic lines exhibited a large number of rearrangements such as inversions and deletions/duplications, which were dominantly repaired by microhomology‐mediated recombination and microhomology‐mediated end‐joining, and less by nonhomologous end‐joining. Notably, pHinP1I, which recognized a small number of sites in ptDNA, induced drastic structural changes, including regional copy number variations throughout ptDNAs. In contrast, the transient expression of either pTaqI or pMseI, whose recognition site numbers were relatively larger, resulted in small‐scale changes at the whole genome level. These results indicate that DSB frequencies and their distribution are major determinants shaping ptDNAs.

Sessile plants have evolved distinct mechanisms to respond and adapt to adverse environmental conditions through diverse mechanisms including RNA processing. While the role of RNA processing in the stress response is well understood in Arabidopsis thaliana, limited information is available in rice (Oryza sativa). Here, we show that OsFKBP20‐1b, belonging to the immunophilin family, interacts with the splicing factor OsSR45 in both nuclear speckles and cytoplasmic foci and plays an essential role in post‐transcriptional regulation of abiotic stress response. Expression of OsFKBP20‐1b was highly upregulated under various abiotic stresses. Moreover genetic analysis revealed that OsFKBP20‐1b positively affected transcription and pre‐mRNA splicing of stress‐responsive genes under abiotic stress conditions. In osfkbp20‐1b loss‐of‐function mutants, expression of stress‐responsive genes was downregulated, while that of their splicing variants was increased. Conversely, in plants overexpressing OsFKBP20‐1b, the expression of the same stress‐responsive genes was strikingly upregulated under abiotic stress. In vivo experiments demonstrated that OsFKBP20‐1b directly maintains protein stability of OsSR45 splicing factor. Furthermore, we found that the plant‐specific OsFKBP20‐1b gene has uniquely evolved as a paralog only in some Poaceae species. Together, our findings suggest that OsFKBP20‐1b‐mediated RNA processing contributes to stress adaptation in rice.

Hyperspectral techniques are currently used to retrieve information concerning plant biophysical traits, predominantly targeting pigments, water, and nitrogen‐protein contents, structural elements, and the leaf area index. Even so, hyperspectral data could be more extensively exploited to overcome the breeding challenges being faced under global climate change by advancing high‐throughput field phenotyping. In this study, we explore the potential of field spectroscopy to predict the metabolite profiles in flag leaves and ear bracts in durum wheat. The full‐range reflectance spectra (visible (VIS)‐near‐infrared (NIR)‐short wave infrared (SWIR)) of flag leaves, ears and canopies were recorded in a collection of contrasting genotypes grown in four environments under different water regimes. GC‐MS metabolite profiles were analyzed in the flag leaves, ear bracts, glumes, and lemmas. The results from regression models exceeded 50% of the explained variation (adj‐R2 in the validation sets) for at least 15 metabolites in each plant organ, whereas their errors were considerably low. The best regressions were obtained for malate (82%), glycerate and serine (63%) in leaves; myo‐inositol (81%) in lemmas; glycolate (80%) in glumes; sucrose in leaves and glumes (68%); γ‐aminobutyric acid (GABA) in leaves and glumes (61% and 71%, respectively); proline and glucose in lemmas (74% and 71%, respectively) and glumes (72% and 69%, respectively). The selection of wavebands in the models and the performance of the models based on canopy and VIS organ spectra and yield prediction are discussed. We feel that this technique will likely to be of interest due to its broad applicability in ecophysiology research, plant breeding programmes, and the agri‐food industry.

Seeds germinating underground display a specific developmental program, termed skotomorphogenesis, to ensure survival of the emerging seedlings until they reach the light. They rapidly elongate the hypocotyl and maintain the cotyledons closed, forming a hook with the hypocotyl in order to protect apical meristematic cells from mechanical damage. Such crucial events for the fate of the seedling are tightly regulated and although some transcriptional regulators and phytohormones are known to be implicated in this regulation, we are still far from a complete understanding of these biological processes. Our work provides information on the diverse roles in skotomorphogenesis of the core components of microRNA biogenesis in Arabidopsis, HYL1, DCL1, and SE. We show that hypocotyl elongation is promoted by all these components, probably through the action of specific miRNAs. Hook development also depends on these proteins however, remarkably, HYL1 exerts its role in an opposite way to DCL1 and SE. Interestingly, we found that a specific HYL1 domain involved in protein‐protein interaction is required for this function. Genetic evidences also point to the phosphorylation status of HYL1 as important for this function. We propose that HYL1 help maintain the hook closed during early skotomorphogenesis in a microprocessor‐independent manner by repressing the activity of HY5, the transcriptional master regulator that triggers light responses. This work uncovers a previously unnoticed link between components of the miRNA biogenesis machinery, the skotomorphogenic growth and hook development in Arabidopsis.

Plant small RNAs (sRNAs) play significant roles in regulating various developmental processes and hormone signaling pathways involved in plant responses to a wide range of biotic and abiotic stresses. However, the functions of sRNAs in response to rice sheath blight remain unclear. We screened rice (Oryza sativa) sRNA expression patterns against Rhizoctonia solani and found that Tourist‐miniature inverted‐repeat transposable element (MITE)‐derived small interfering RNA (siRNA) (herein referred to as siR109944) expression was obviously suppressed upon R. solani infection. One potential target of siR109944 is the F‐Box domain and LRR‐containing protein 55 (FBL55), which encodes the transport inhibitor response 1 (TIR1)‐like protein. We found that rice had significantly enhanced susceptibility when siR109944 was overexpressed, while FBL55 OE plants showed resistance to R. solani challenge. Additionally, multiple agronomic traits of rice, including root length and flag leaf inclination, were affected by siR109944 expression. Auxin metabolism‐ and signaling pathway‐related genes were differentially expressed in the siR109944 OE and FBL55 OE plants. Importantly, pretreatment with auxin enhanced sheath blight resistance by affecting endogenous auxin homeostasis in rice. Furthermore, transgenic Arabidopsis overexpressing siR109944 exhibited early flowering, increased tiller numbers and increased susceptibility to R. solani. Our results demonstrate that siR109944 has a conserved function in interfering with plant immunity, growth and development by affecting auxin homeostasis in planta. Thus, siR109944 provides a genetic target for plant breeding in the future. Further, exogenous application of indole‐3‐acetic acid (IAA) or auxin analogues might effectively protect field crops against diseases.

Anthocyanin biosynthesis is induced by low temperatures in a number of plants. However, in peach (cv. Zhonghuashoutao), anthocyanin accumulation was observed in fruit stored at 16°C but not at or below 12°C. Fruit stored at 16°C showed elevated transcript levels of genes encoding anthocyanin biosynthetic enzymes, the transport protein GST and key transcription factors. Higher transcript levels of PpPAL1/2, PpC4H, Pp4CL4/5/8, PpF3H, PpF3’H, PpDFR1/2/3 and PpANS, as well as transcription factor gene PpbHLH3, were associated with lower methylation levels in the promoter of these genes. The DNA methylation level was further highly correlated with the expression of the DNA methyltransferase genes and DNA demethylase genes. The application of DNA methylation inhibitor 5‐azacytidine induced anthocyanin accumulation in peach flesh, further implicating a critical role of DNA demethylation in regulating anthocyanin accumulation in peach flesh. Our data reveals that temperature‐dependent DNA demethylation is a key factor to the postharvest temperature‐dependent anthocyanin accumulation in peach flesh.

Incorporating male sterility into hybrid seed production reduces its cost and ensures high varietal purity. Despite these advantages, male‐sterile lines have not been widely used to produce tomato (Solanum lycopersicum) hybrid seeds. We describe the development of a biotechnology‐based breeding platform that utilized genic male sterility to produce hybrid seeds. In this platform, we generated a novel male‐sterile tomato line by clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR‐associated protein 9 (Cas9)‐mediated mutagenesis of a stamen‐specific gene SlSTR1 and devised a transgenic maintainer by transforming male‐sterile plants with a fertility‐restoration gene linked to a seedling‐colour gene. Offspring of crosses between a hemizygous maintainer and the homozygous male‐sterile plant segregated into 50% non‐transgenic male‐sterile plants and 50% male‐fertile maintainer plants, which could be easily distinguished by seedling colour. This system has great practical potential for hybrid seed breeding and production as it overcomes the problems intrinsic to other male sterility systems and can be easily adapted for a range of tomato cultivars and diverse vegetable crops.

Gene editing techniques are currently revolutionizing biology allowing far greater precision than previous mutagenic and transgenic approaches. They are becoming applicable to a wide range of plant species and biological processes. Gene editing can rapidly improve a range of crop traits including disease resistance, abiotic stress tolerance, yield, nutritional quality and additional consumer traits. Unlike transgenic approaches, however, it is not facile to forensically detect gene‐editing events at the molecular level, as no foreign DNA exists in the elite line. These limitations in molecular detection approaches are likely to focus more attention on the products generated from the technology, than the process per se. Rapid advances in sequencing and genome assembly increasingly facilitate genome sequencing as a means of characterizing new varieties generated by gene editing techniques. Nevertheless, subtle edits such as single base changes or small deletions may be difficult to distinguish from normal variation within a genotype. Given these emerging scenarios, downstream ‘omics’ technologies reflective of edited affects, such as metabolomics, need to be utilized in a more prominent manner to fully assess compositional changes in novel foodstuffs. To achieve this goal, metabolomics or “non‐targeted metabolite analysis” needs to make significant advances to deliver greater representation across the metabolome. With the emergence of new edited crop varieties we advocate; (i) concerted efforts in the advancement of ‘omics’ technologies such as metabolomics and (ii) redress the use of the technology in the regulatory assessment for metabolically‐engineered biotech crops.

One of the main characteristics of plant cells is the presence of the cell wall located outside the plasma membrane. In particular cells, this wall can be reinforced by lignin, a polyphenolic polymer that plays a central role for vascular plants, conferring hydrophobicity to conducting tissues and mechanical support for upright growth. Lignin has been extensively studied by a range of different techniques including anatomical and morphological analyses using dyes to characterize the polymer localization in situ. With the constant improvement of imaging techniques, it is now possible to revisit old qualitative techniques and adapt them to obtain efficient, highly resolutive, quantitative, fast and safe methodologies. In this study, we revisit and exploit the potential of fluorescent microscopy coupled to safranin‐O staining to develop a quantitative approach for lignin content determination. The developed approach is based on ratiometric emission measurements and the development of an ImageJ macro. To demonstrate the interest of our methodology compared to other commonly‐used lignin reagents, we showed that safranine‐O staining was used to evaluate and compare lignin contents in previously characterized A. thaliana lignin biosynthesis mutants. In addition, the analysis of lignin content and spatial distribution in the Arabidopsis laccase mutant also provided new biological insights into the effects of laccase gene down‐regulation in different cell types. Our safranine‐O based methodology, also validated for flax, maize and poplar, significantly improves and speed‐up anatomical and developmental investigations of lignin, which we hope will contribute to new discoveries in many areas of cell wall plant research.

Nitrogen and phosphorus are two major soil nutrients required for plant growth. Because requirements of both these elements are interdependent, acquisition of one must be balanced with that of the other. However, the mechanism underlying this balanced acquisition remains unclear. Here, we show by in vivo luciferase imaging that the presence of nitrogen sources is a pre‐requisite for strong activation of phosphate starvation responses. In addition, we also show that nitrate rather than ammonium is a potent modulator of phosphate starvation‐induced gene expression. Furthermore, protoplast‐based transient expression assay and chromatin immunoprecipitation assay demonstrate that NIGT1 GARP‐type transcriptional repressors, which are encoded by nitrate‐inducible genes, directly bind to and repress the promoters of genes encoding SPX proteins. Consistent with the role of SPX proteins in the suppression of the PHR1 transcriptional activator, the master regulator for phosphate starvation responses, nitrate‐dependent enhancement of phosphate starvation responses, such as accumulation of anthocyanin and promotion of root hair growth and phosphate uptake, was less evident in the nigt1.1–nigt1.4 quadruple mutant. Consistently, NIGT1 overexpression alleviated the reduction in phosphate uptake under phosphate‐replete conditions. We further reveal the intricate feedback regulations involving PHR1, NIGT1, and SPX family proteins in the phosphate starvation signalling network. Importantly, results of mutant protoplast‐based assays and in planta analysis using NIGT1 overexpression in the spx1 spx2 double mutant indicated that the NIGT1–SPX–PHR cascade mediates nitrogen status‐responsive regulation of phosphate uptake and starvation signalling. These findings uncover the mechanism underlying the balanced acquisition of nitrogen and phosphorus.

Grain size is a major determinant of grain weight, a key component of grain yield of rice. Here, we identified the grain size gene WIDE GRAIN 7 (WG7) from a T‐DNA insertion mutant. The grain size of WG7 knockout mutants and WG7 overexpression lines indicated that WG7 is a positive regulator of grain size. WG7 encodes a cysteine‐tryptophan (CW) domain‐containing transcriptional activator. EMSAs and ChIP‐qPCR assay confirmed that WG7 directly bound to the promoter of OsMADS1, a grain size gene, and thereby significantly activated its expression. Point mutations showed that the cis‐element CATTTC motif in the promoter was the binding site of WG7. Compared with the wild‐type, deletion mutants of the cis‐element motif exhibited lower expression of OsMADS1 and produced narrower grains, implicating the requirement of this motif for WG7 function. ChIP‐qPCR assays showed that WG7 enhanced histone H3K4me3 enrichment in the promoter of OsMADS1. WG7 underwent directional selection due to the poor fertility of the non‐functional mutant. These findings demonstrated that WG7 upregulated OsMADS1 expression by directly binding to its promoter, enhanced histone H3K4me3 enrichment in the promoter and ultimately increased grain width. This study will enrich the knowledge concerning the regulatory network of grain size formation in rice.

In photosynthetic organisms many processes are light dependent and sensing of light requires light‐sensitive proteins. The supposed eyespot photoreceptor protein Babo1 (formerly Vop1) has previously been classified as an opsin due to the capacity for binding retinal. Here, we analyze Babo1 and provide evidence that it is no opsin. Due to the localization at the basal bodies, the former Vop1 and Cop1/2 proteins were renamed V.c. Babo1 and C.r. Babo1. We reveal a large family of more than 60 Babo1‐related proteins from a wide range of species. The detailed subcellular localization of fluorescence‐tagged Babo1 shows that it accumulates at the basal apparatus. More precisely, it is located predominantly at the basal bodies and to a lesser extent at the four strands of rootlet microtubules. We trace Babo1 during basal body separation and cell division. Dynamic structural rearrangements of Babo1 particularly occur right before the first cell division. In four‐celled embryos Babo1 was exclusively found at the oldest basal bodies of the embryo and on the corresponding d‐roots. The unequal distribution of Babo1 in four‐celled embryos could be an integral part of a geometrical system in early embryogenesis, which establishes the anterior–posterior polarity and influences the spatial arrangement of all embryonic structures and characteristics. Due to its retinal‐binding capacity, Babo1 could also be responsible for the unequal distribution of retinoids, knowing that such concentration gradients of retinoids can be essential for the correct patterning during embryogenesis of more complex organisms. Thus, our findings push the Babo1 research in another direction.

The biological conversion of light energy into chemical energy is performed by a flexible photosynthetic machinery located in the thylakoid membranes. Photosystems I and II (PSI and PSII) are the two complexes able to harvest light. PSI is the last complex of the electron transport chain and is composed of multiple subunits: the proteins building the catalytic core complex that are well conserved between oxygenic photosynthetic organisms, and, in green organisms, the membrane light‐harvesting complexes (Lhc) necessary to increase light absorption. In plants, four Lhca proteins (Lhca1–4) make up the antenna system of PSI, which can be further extended to optimize photosynthesis by reversible binding of LHCII, the main antenna complex of photosystem II. Here, we used biochemistry and electron microscopy in Arabidopsis to reveal a previously unknown supercomplex of PSI with LHCII that contains an additional Lhca1–a4 dimer bound on the PsaB–PsaI–PsaH side of the complex. This finding contradicts recent structural studies suggesting that the presence of an Lhca dimer at this position is an exclusive feature of algal PSI. We discuss the features of the additional Lhca dimer in the large plant PSI–LHCII supercomplex and the differences with the algal PSI. Our work provides further insights into the intricate structural plasticity of photosystems.

As a prerequisite for constant growth, plants produce vascular tissues at different sites within their postembryonic body. Interestingly, the formation of vascular tissues during longitudinal and radial expansion of shoot and root axes differs fundamentally with respect to its anatomical configuration. This raises the question to which level regulatory mechanisms of vascular tissue formation are shared throughout plant development. Here, we show that, similar to primary phloem formation during longitudinal growth, the cambium‐based formation of secondary phloem depends on the function of SUPPRESSOR OF MAX2 1‐LIKE (SMXL) genes. In particular, local SMXL5 deficiency results in the absence of secondary phloem. Moreover, the additional disruption of SMXL4 activity increases tissue production in the cambium region without that secondary phloem is formed. Using promoter reporter lines, we observe that SMXL4 and SMXL5 activities are associated with different stages of secondary phloem formation in the Arabidopsis stem. Based on genome‐wide transcriptional profiling and expression analyses of phloem‐related markers we conclude that early steps of phloem formation are impaired in smxl4;smxl5 double mutants and that the additional cambium‐derived cells fail to establish phloem‐related features. Our results show that molecular mechanisms determining primary and secondary phloem formation share important properties but differ slightly with SMXL5 playing a more dominant role in the formation of secondary phloem.

Alternative polyadenylation (APA) regulates diverse developmental and physiological processes, through its effects on gene expression, mRNA stability, translatability, and transport. Sorghum is a major cereal crop in the world and despite its importance, not much is known about the role of post‐transcriptional regulation in mediating responses to abiotic stresses in sorghum. A genome‐wide APA analysis unveiled widespread occurrence of APA in sorghum in response to drought, heat, and salt stress. Abiotic stress treatments incited changes in poly(A) site choice in a large number of genes. Interestingly, abiotic stresses led to the re‐directing of transcriptional output into non‐productive pathways defined by the class of poly(A) site utilized. This result reveals APA to be part of a larger global response of sorghum to abiotic stresses that involves the re‐direction of transcriptional output into non‐productive transcriptional and translational pathways. A large number of stress‐inducible poly(A) sites could not be linked with known, annotated genes, suggestive of the existence of numerous unidentified genes whose expression is strongly regulated by abiotic stresses. Furthermore, we uncovered a novel stress‐specific cis‐element in intronic poly(A) sites used in drought‐ and heat‐stressed plants that might play an important role in non‐canonical poly(A) site choice in response to abiotic stresses.

Photorespiratory metabolism is essential for plants to maintain functional photosynthesis in an oxygen‐containing environment. Because the oxygenation reaction of Rubisco is followed by the loss of previously fixed carbon, photorespiration is often considered a wasteful process and considerable efforts are aimed at minimizing the negative impact of photorespiration on the plant's carbon uptake. However, the photorespiratory pathway has also many positive aspects, as it is well integrated within other metabolic processes, such as nitrogen assimilation and C1 metabolism, and it is important for maintaining the redox balance of the plant. The overall effect of photorespiratory carbon loss on the net CO2 fixation of the plant is also strongly influenced by the physiology of the leaf related to CO2 diffusion. This review outlines the distinction between Rubisco oxygenation and photorespiratory CO2 release as a basis to evaluate the costs and benefits of photorespiration.

Photosynthesis measurements are traditionally taken under steady‐state conditions. However, leaves in crop fields experience frequent fluctuations in light and take time to respond. This slow response reduces the efficiency of carbon assimilation. Low to high light transitions require photosynthetic induction, including the activation of Rubisco and opening of stomata, while high to low light transitions require relaxation of dissipative energy processes collectively known as non‐photochemical quenching (NPQ). Previous attempts to assess the impact of these delays on net carbon assimilation have used simplified models of crop canopies, limiting the accuracy of predictions. Here we use ray tracing to predict the spatial and temporal dynamics of lighting of a rendered mature soybean canopy to review the relative importance of these delays on net cumulative assimilation over the course of both a sunny and a cloudy summer day. Combined limitations result in a 13 % reduction in crop carbon assimilation on both sunny and cloudy days, with induction more important on cloudy than sunny days. Genetic variation in NPQ relaxation rates and photosynthetic induction in parental lines of a soybean nested association mapping (NAM) population were assessed. Short‐term NPQ relaxation (<30 min) showed little variation across the NAM lines, but substantial variation was found in speeds of photosynthetic induction, attributable to Rubisco activation. Over the course of a sunny and an intermittently cloudy day these would translate to substantial differences in total crop carbon assimilation. These findings suggest an unexplored potential for breeding improved photosynthetic potential in our major crops.

The BASIC PENTACYSTEINE (BPC) GAGA (C‐box) binding proteins belong to a small plant transcription factor family. We previously reported that BPCs of class I bind directly to C‐boxes in the SEEDSTICK (STK) promoter and the mutagenesis of these cis‐elements affects STK expression in the flower. The MADS‐domain factor SHORT VEGETATIVE PHASE (SVP) is another key regulator of STK. Direct binding of SVP to CArG‐boxes in the STK promoter are required to repress its expression during the first stages of flower development. Here we show that BPCs of class II directly interact with SVP and that MADS‐domain binding sites in the STK promoter region are important for the correct spatial and temporal expression of this homeotic gene. Furthermore, we show that BPCs of class I and II act redundantly to repress STK expression in the flower, most likely by recruiting TERMINAL FLOWER 2/LIKE HETEROCHROMATIN PROTEIN 1 (TFL2/LHP1) and mediating the establishment and the maintenance of H3K27me3 repressive marks on the DNA. We investigate the role of LHP1 in the regulation of STK expression. Besides providing a better understanding of the role of BPC transcription factors in the regulation of STK expression, our results suggest the existence of a more general regulatory complex composed of BPCs, MADS‐domain factors and PRCs, that cooperate to regulate gene expression in reproductive tissues. We believe that our data along with the molecular model herein described could provide significant insights for a more comprehensive understanding of gene regulation in plants.

Phytohormone brassinosteroids (BRs) are essential for plant growth and development, but the mechanisms of BRs‐mediated pollen development remain largely unknown. In this study, we show that pollen viability, pollen germination and seed number decreased in BR‐deficient mutant d^im that has lesion in the BR biosynthetic gene DWARF (DWF) and bzr1 mutant which is deficient in BR signaling regulator BRASSINAZOLE RESISTANT 1 (BZR1) compared with those in wild‐type plants, while plants overexpressing DWF or BZR1 exhibited the opposite effects. Loss or gain of function in DWF or BZR1 gene altered the timing of reactive oxygen species (ROS) production and programmed cell death (PCD) in tapetal cells, resulting in a delayed or premature tapetal degeneration, respectively. Further analysis revealed that BZR1 could directly bind to the promoter of RESPIRATORY BURST OXIDASE HOMOLOG 1 (RBOH1) and that RBOH1‐mediated ROS promote pollen and seed development by triggering PCD and tapetal cell degradation. In contrast, suppression of RBOH1 compromised BR signaling‐mediated ROS production and pollen development. These findings provide strong evidence that BZR1‐dependent ROS production plays a critical role in BR‐mediated regulation of tapetal cell degeneration and pollen development in tomato (Solanum lycopersicum) plants.

Carbonic anhydrase (CA) is an abundant protein in most photosynthesizing organisms and higher plants. This review paper considers the physiological importance of the more abundant CA isoforms in photosynthesis, through their effects on CO2 diffusion and other processes in photosynthetic organisms. In plants, CA has multiple isoforms in three different families (α, β and γ) and is mainly known to catalyze the CO2 equilibrium. This reversible conversion has a clear role in photosynthesis, primarily through sustaining the CO2 concentration at the site of ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco). Despite showing the same major reaction mechanism, the three main CA families are evolutionarily distinct. For different CA isoforms, cellular localization and total gene expression as a function of developmental stage are predicted to determine the role of each family in relation to the net assimilation rate. Reaction–diffusion modeling and observational evidence support a role for CA activity in reducing resistance to CO2 diffusion inside mesophyll cells by facilitating CO2 transfer in both gas and liquid phases. In addition, physical and/or biochemical interactions between CAs and other membrane‐bound compartments, for example aquaporins, are suggested to trigger a CO2‐sensing response by stomatal movement. In response to environmental stresses, changes in the expression level of CAs and/or stimulated deactivation of CAs may correspond with lower photosynthetic capacity. We suggest that further studies should focus on the dynamics of the relationship between the activity of CAs (with different subcellular localization, abundance and gene expression) and limitations due to CO2 diffusivity through the mesophyll and supply of CO2 to photosynthetic reactions.

The photorespiratory pathway, in short photorespiration, is a metabolic repair system that enables the CO2 fixation enzyme Rubisco to sustainably operate in the presence of oxygen, that is, during oxygenic photosynthesis of plants and cyanobacteria. Photorespiration is necessary because an auto‐inhibitory metabolite, 2‐phosphoglycolate (2PG), is produced when Rubisco binds oxygen instead of CO2 as a substrate and must be removed, to avoid collapse of metabolism, and recycled as efficiently as possible. The basic principle of recycling 2PG very likely evolved several billion years ago in connection with the evolution oxyphotobacteria. It comprises the multi‐step combination of two molecules of 2PG to form 3‐phosphoglycerate. The biochemistry of this process dictates that one out of four 2PG carbons is lost as CO2, which is a long‐standing plant breeders' concern because it represents by far the largest fraction of respiratory processes that reduce gross‐photosynthesis of major crops down to about 50% and less, lowering potential yields. In addition to the ATP needed for recycling of the 2PG carbon, extra energy is needed for the refixation of liberated equal amounts of ammonia. It is thought that the energy costs of photorespiration have an additional negative impact on crop yields in at least some environments. This paper discusses recent advances concerning the origin and evolution of photorespiration and gives an overview of contemporary and envisioned strategies to engineer the biochemistry of, or even avoid, photorespiration.

Jasmonates are key regulators of the balance between defence and growth in plants. However, the molecular mechanisms by which activation of defence reduces growth are not yet fully understood. Here, we analyze the role of MYC transcription factors (TFs) and jasmonic acid (JA) in photomorphogenic growth. We found that multiple myc mutants share light‐associated phenotypes with mutants of the phytochrome B photoreceptor, such as delayed seed germination in the dark and long hypocotyl growth. Overexpression of MYC2 in a phyB background partially suppressed its long hypocotyl phenotype. Transcriptomic analysis of multiple myc mutants confirmed that MYCs are required for full expression of red (R) light‐regulated genes, including the master regulator HY5. ChIP‐seq analyses revealed that MYC2 and MYC3 bind directly to the promoter of HY5 and that HY5 gene expression and protein levels are compromised in multiple myc mutants. Altogether, our results pinpoint MYCs as photomorphogenic TFs that control phytochrome responses by activating HY5 expression. This has important implications in understanding the trade‐off between growth and defence as the same TFs that activate defence responses are photomorphogenic growth regulators.

The non‐specific lipid transfer proteins (nsLTPs) are multifunctional seed proteins engaged in several different physiological processes. The nsLTPs are stabilized by four disulfide bonds and exhibit a characteristic hydrophobic cavity, which is the primary lipid binding site. While these proteins are known to transfer lipids between membranes, the mechanism of lipid transfer has remained elusive. Four crystal structures of nsLTP from Solanum melongena, one in the apo‐state and three myristic acid bound states were determined. Among the three lipid bound states, two lipid molecules were bound on the nsLTP surface at different positions and one was inside the cavity. The lipid‐dependent conformational changes leading to opening of the cavity were revealed based on structural and spectroscopic data. The surface‐bound lipid represented a transient intermediate state and the lipid ultimately moved inside the cavity through the cavity gate as revealed by molecular dynamics simulations. Two critical residues in the loop regions played possible ‘gating’ role in the opening and closing of the cavity. Antifungal activity and membrane permeabilization effect of nsLTP against Fusarium oxysporum suggested that it could possibly involve in bleaching out the lipids. Collectively, these studies support a model of lipid transfer mechanism by nsLTP via intermediate states.

Maize exhibits marked growth and yield response to supplemental nitrogen (N). Here, we report the functional characterization of a maize NIN‐like protein ZmNLP5 as a central hub in a molecular network associated with N metabolism. Predominantly expressed and accumulated in roots and vascular tissues, ZmNLP5 was shown to rapidly respond to nitrate treatment. Under limited N supply, compared with that of wild‐type (WT) seedlings, the zmnlp5 mutant seedlings accumulated less nitrate and nitrite in the root tissues and ammonium in the shoot tissues. The zmnlp5 mutant plants accumulated less nitrogen than the WT plants in the ear leaves and seed kernels. Furthermore, the mutants carrying the transgenic ZmNLP5 cDNA fragment significantly increased the nitrate content in the root tissues compared with that of the zmnlp5 mutants. In the zmnlp5 mutant plants, loss of the ZmNLP5 function led to changes in expression for a significant number of genes involved in N signalling and metabolism. We further show that ZmNLP5 directly regulates the expression of nitrite reductase 1.1 (ZmNIR1.1) by binding to the nitrate‐responsive cis‐element at the 5′ UTR of the gene. Interestingly, a natural loss‐of‐function allele of ZmNLP5 in Mo17 conferred less N accumulation in the ear leaves and seed kernels resembling that of the zmnlp5 mutant plants. Our findings show that ZmNLP5 is involved in mediating the plant response to N in maize.

FRD3 (FERRIC REDUCTASE DEFECTIVE 3) plays a major role in iron (Fe) and zinc (Zn) homeostasis in Arabidopsis. It transports citrate, which enables metal distribution in the plant. An frd3 mutant is dwarf and chlorotic and displays a constitutive Fe‐deficiency response and strongly altered metal distribution in tissues. Here, we have examined the interaction between Fe and Zn homeostasis in an frd3 mutant exposed to varying Zn supply. Detailed phenotyping using transcriptomic, ionomic, histochemical and spectroscopic approaches revealed the full complexity of the frd3 mutant phenotype, which resulted from altered transition metal homeostasis, manganese toxicity, and oxidative and biotic stress responses. The cell wall played a key role in these processes, as a site for Fe and hydrogen peroxide accumulation, and displayed modified structure in the mutant. Finally, we showed that Zn excess interfered with these mechanisms and partially restored root growth of the mutant, without reverting the Fe‐deficiency response. In conclusion, the frd3 mutant molecular phenotype is more complex than previously described and illustrates how the response to metal imbalance depends on multiple signaling pathways.

High‐affinity ammonium uptake in roots mediate by AMT1‐type ammonium transporters, which are tightly controlled at multiple regulatory levels for adapting various nitrogen availability. For Arabidopsis AtAMT1;1 gene, besides the transcriptional and posttranslational controls, an organ‐ and N‐dependent posttranscriptional regulation was suggested as an additional regulatory step for fine‐tuning ammonium uptake, but the underlying mechanisms remain to be elucidated. Here, we showed that degradation of AtAMT1;1 transcript in roots of Pro35S:AtAMT1;1‐transformed atamt1;1‐1 Arabidopsis plants resulted from RDR6‐dependent sense transgene‐induced posttranscriptional gene silencing (S‐PTGS). The siRNAs for S‐PTGS may derive from the aberrant RNA, of which the production was codetermined by sequence feature and excessive expression of AtAMT1;1. Switching to the expression of AtAMT1;1 driven by ProAtUBQ10 or of AtAMT1;1 mutated at two siRNA‐targeted hotspots reduced AtAMT1;1‐specific siRNAs and overcame S‐PTGS in roots. In roots of these lines, however, the steady‐state transcript levels of AtAMT1;1 still significantly decreased under conditions of N‐sufficiency compared to N‐deficiency, confirming a N‐dependent posttranscriptional regulatory manner. A crucial role of 207 bp 3’‐end sequence of AtAMT1;1 was further demonstrated by N‐dependent accumulation of chimeric‐AtAMT1;1 transcript in T‐DNA insertion lines and of GFP‐tagged chimeric‐AtAMT1;1 transcript in transgenic lines. A novel non‐coding RNA (ncRNA), which was highly abundant in N‐sufficient roots, may target the above‐identified 3’‐end region for degrading AtAMT1;1 transcript. This degradation could be prevented by a mutation on AtAMT1;1 transcript at a potential cleavage site (+1458). These results suggested two distinct mechanisms of regulating AtAMT1;1 mRNA turnover by ncRNA for strictly control of ammonium uptake in roots.

Free and protein‐bound amino acids (FAAs and PBAAs) in seeds play an important role in seed desiccation, longevity, and germination. However, the effect that water stress has on these two functional pools, especially when imposed during the crucial seed setting stage is unclear. To better understand these effects, we exposed Arabidopsis plants at the seed setting stage to a range of water limitation and water deprivation conditions and then evaluated physiological, metabolic, and proteomic parameters, with special focus on FAAs and PBAAs. We found that in response to severe water limitation, seed yield decreased, while seed weight, FAA and PBAA content per seed increased. Nevertheless, the composition of FAAs and PBAAs remained unaltered. In response to severe water deprivation, however, both seed yield and weight were reduced. In addition, major alterations were observed in both FAA and proteome compositions, which indicated that both osmotic adjustment and proteomic reprogramming occurred in these naturally desiccation‐tolerant organs. However, despite the major proteomic alteration, the PBAA composition did not change, suggesting that the proteomic reprogramming was followed by a proteomic rebalancing. The proteomic rebalancing has not been observed previously in response to stress, but its occurrence under stress strongly suggests its natural function. Together, our data show that the dry seed PBAA composition plays a key role in seed fitness and therefore is rigorously maintained even under severe water stress, while the FAA composition is more plastic and adaptable to changing environments, and that both functional pools are distinctly regulated.

The wheat AP2‐like transcription factor gene Q has played a major role in domestication by conferring the free‐threshing character and pleiotropically affecting numerous other traits. However, little information is known regarding the molecular mechanisms associated with the regulation of these traits by Q, especially for the structural determination of threshability. Here, transcriptome analysis of immature spike tissues in three lines nearly isogenic for Q revealed over 3000 differentially expressed genes (DEGs) involved in a number of pathways. Using phenotypic, microscopic, transcriptomic, and tissue‐specific gene expression analyses, we demonstrated that Q governs threshability through extensive modification of wheat glumes including their structure, cell wall thickness, and chemical composition. Critical DEGs and pathways involved in secondary cell wall synthesis and regulation of the chemical composition of glumes were identified. We also showed that the mutation giving rise to the Q allele synchronized the expression of genes for micro‐sporogenesis that affected pollen fertility, and may determine the final grain number for wheat spikes. Transcriptome dissection of genes and genetic pathways regulated by Q should further our understanding of wheat domestication and improvement.

Structural Maintenance of Chromosomes 2 (SMC2) and Structural Maintenance of Chromosomes 4 (SMC4) are the core components of the condensin complexes, which are required for chromosome assembly and faithful segregation during cell division. Because of the crucial functions of both proteins in cell division, much work has been done in various vertebrates, but little information is known about their roles in plants. Here, we identified ZmSMC2 and ZmSMC4 in maize (Zea mays) and confirmed that ZmSMC2 associates with ZmSMC4 via their hinge domains. Immunostaining revealed that both proteins showed dynamic localization during mitosis. ZmSMC2 and ZmSMC4 are essential for proper chromosome segregation and for H3 phosphorylation at Serine 10 (H3S10ph) at pericentromeres during mitotic division. The loss of function of ZmSMC2 and ZmSMC4 enlarges mitotic chromosome volume and impairs sister chromatid separation to the opposite poles. Taken together, these findings confirm and extend the coordinated role of ZmSMC2 and ZmSMC4 in maintenance of normal chromosome architecture and accurate segregation during mitosis.

RuBisCO‐catalyzed CO2 fixation is the main source of organic carbon in the biosphere. This enzyme is present in all domains of life in different forms (III, II, and I) and its origin goes back to 3500 Myr, when the atmosphere was anoxygenic. However, the RuBisCO active site also catalyzes oxygenation of ribulose 1,5‐bisphosphate, therefore, the development of oxygenic photosynthesis and the subsequent oxygen‐rich atmosphere promoted the appearance of CO2 concentrating mechanisms (CCMs) and/or the evolution of a more CO2‐specific RuBisCO enzyme. The wide variability in RuBisCO kinetic traits of extant organisms reveals a history of adaptation to the prevailing CO2/O2 concentrations and the thermal environment throughout evolution. Notable differences in the kinetic parameters are found among the different forms of RuBisCO, but the differences are also associated with the presence and type of CCMs within each form, indicative of co‐evolution of RuBisCO and CCMs. Trade‐offs between RuBisCO kinetic traits vary among the RuBisCO forms and also among phylogenetic groups within the same form. These results suggest that different biochemical and structural constraints have operated on each type of RuBisCO during evolution, probably reflecting different environmental selective pressures. In a similar way, variations in carbon isotopic fractionation of the enzyme point to significant differences in its relationship to the CO2 specificity among different RuBisCO forms. A deeper knowledge of the natural variability of RuBisCO catalytic traits and the chemical mechanism of RuBisCO carboxylation and oxygenation reactions raises the possibility of finding unrevealed landscapes in RuBisCO evolution.

Thick glistening cell walls occur in sieve tubes of all major land plant taxa. Historically, these ‘nacreous walls’ have been considered a diagnostic feature of sieve elements; they represent a conundrum, though, in the context of the widely accepted pressure‐flow theory as they severely constrict sieve tubes. We employed the cucurbit Gerrardanthus macrorhizus as a model to study nacreous walls in sieve elements by standard and in situ confocal as well as electron microscopy, focusing on changes functional sieve tubes undergo when prepared for microscopic observation. Over 90% of sieve elements in tissue sections processed for microscopy by standard methods exhibited nacreous walls. Sieve elements in whole, live plants that were actively transporting as shown by phloem‐mobile tracers, lacked nacreous walls and exhibited open lumina of circular cross‐section instead, an appropriate structure for Münch‐type mass flow of the cell contents. The puncturing of transporting sieve elements with micropipettes triggered the rapid (<1 min) development of nacreous walls that occluded the cell lumen almost completely. We conclude that nacreous walls are preparational artefacts rather than structural features of transporting sieve elements. Nacreous walls in land plants resemble the reversibly swellable walls found in various algae, suggesting that they may function in turgor buffering, the amelioration of osmotic stress, wounding‐induced sieve tube occlusion, and possibly local defence responses of the phloem.

Although the interplay of covalent histone acetylation/deacetylation and ATP‐dependent chromatin remodeling is crucial for the regulation of chromatin structure and gene expression in eukaryotes, the underlying molecular mechanism in plants remains largely unclear. Here we show a direct interaction between Arabidopsis SWI3B, an essential subunit of the SWI/SNF chromatin‐remodeling complex, and the RPD3/HDA1‐type histone deacetylase HDA6 both in vitro and in vivo. Furthermore, SWI3B and HDA6 co‐repress the transcription of a subset of transposons. Both SWI3B and HDA6 maintain transposon silencing by decreasing histone H3 lysine 9 acetylation but increasing histone H3 lysine 9 di‐methylation, DNA methylation and nucleosome occupancy. Our findings reveal that SWI3B and HDA6 may act in the same co‐repressor complex to maintain transposon silencing in Arabidopsis.