The Plant Journal

SUMMARY Controlled plant growth in laboratories can be achieved by cultivating plants under sterile or axenic conditions on predefined synthetic growth media, typically supplemented with sugar. In nature, plants do not receive exogenous sugar supplies, form symbiosis with microbes, and plant growth is influenced by soil edaphic factors. Thus, physiological and multi‐omic analyses of plants grown …

SUMMARY Seed germination directly influences seedling establishment and ultimately crop yield. While hormonal and transcriptional regulations of germination are well characterized, the role of post‐translational modifications (PTMs) remains largely unexplored. In this resource article, we developed a phosphate‐affinity tag‐switch (PAT‐switch) proteomics workflow enabling simultaneous, site‐specif…

Sprouting of overwintering buds is an important biological process in tea plants (Camellia sinensis) that determines spring shoot yield and economic benefits. Epigenetic modifications, such as DNA methylation and histone marks, regulate plant growth and development; however, their precise mechanisms in tea dormancy release remain unclear. This study aimed to highlight how epigenetic auxin (IAA) c…

Neoblechnum brasiliense, a leptosporangiate fern of the family Blechnaceae, is known to have a rich phenolic metabolism. Rosmarinic acid and blechnic acid B have been detected beside chlorogenic acid. As BAHD acyltransferases often are responsible for the formation of this kind of esters, for example, rosmarinic acid synthases or 4-coumaroyl-CoA:shikimic or quinic acid hydroxycinnamoyltransferase…

While sex determination has been extensively studied in animals, the origin and early evolution of sex chromosomes in plants remain poorly understood. Magnolia kwangsiensis, an early-diverging dioecious flowering plant, provides a unique opportunity to investigate sex chromosome evolution at early stages. Here we generated phased chromosome-level genome assemblies for male and female M. kwangsien…

Symbiotic nitrogen fixation (SNF), a unique nitrogen acquisition mechanism formed through the interaction between leguminous plants and rhizobia, plays a critical role in reducing dependence on chemical fertilizers. However, in alfalfa (Medicago sativa L.), the mechanisms underlying nitrate-responsive SNF remain poorly understood. In this study, we elucidate a nitrate-responsive regulatory networ…

Developing climate-resilient crops requires a detailed understanding of stress-induced gene expression dynamics, as maladaptive responses can compromise their productivity and survival. Sorghum, a globally important cereal with exceptional tolerance to multiple abiotic stresses, provides a powerful system for investigating these dynamics. However, how stress type, tissue specificity, and temporal…

Salinity stress is a major abiotic stress that impairs growth and lowers yield in tomato (Solanum lycopersicum L.). Enhancing tolerance to salinity stress through breeding requires a comprehensive understanding of the molecular mechanisms underpinning tomato responses to salinity stress. In this study, we characterized the role of the C2H2 zinc-finger protein WIP domain protein 2 (SlWIP2) as a po…

Since the introduction of various structural prediction programs, the emerging transformative power of these technologies in plant science is apparent. Not only programs like AlphaFold but also RoseTTAFold, Chai-1 and Boltz suddenly enable plant scientists to predict structures with high confidence. This ability has facilitated the discovery of novel protein functions inspired by structural homol…

Steroidal glycoalkaloids (SGAs) are a class of important secondary metabolites in tomato fruit development and ripening, which enhance fruit disease resistance but also act as antinutritional factors for human health. Although previous studies have reported that SGAs metabolism is influenced by light, the specific regulatory mechanisms remain insufficiently explored. This study demonstrates that …

CRISPR/Cas9 is a cornerstone of plant genome editing, yet the determinants of editing efficiency for a given single-guide RNAs (sgRNAs) and DNA double-strand break (DSB) repair outcomes remain poorly understood, particularly in plants. Here, we generated a large experimental dataset comprising 420 sgRNAs targeting promoters, exons, and introns of 137 genes in tomato protoplasts, and quantified ed…

Romy Petroll is a PhD student in the Borg group at the Max Planck Institute for Biology in Tübingen, Germany, where she studies genome evolution in red algae. Raised in Wiesbaden alongside her twin sister, she traces her early interest in biology to a high school teacher whose own background in plant research offered a first glimpse into academic science. Petroll later studied biology at the Univ…

Meiosis is a key process in sexual reproduction, orchestrated by numerous proteins that differ in their spatiotemporal expression level and dynamics. Employing meiotic gene promoters typically leads to varying levels of transgene expression within meiotic and non-meiotic cells in plants. Hence, their application for protein expression during meiosis is limited. Here, we present a tool for meiosis…

Apomixis, the asexual formation of seeds, holds revolutionary potential for fixing hybrid vigor in crops. For decades, research in this field has been dominated by a gene-centric view that focuses on identifying key regulators of apomeiosis and parthenogenesis. Although this strategy has achieved notable success in rice (Oryza sativa), it fails to explain several fundamental aspects of apomixis s…

Seed oil accumulation is orchestrated by complicated multi-level networks, with transcriptional regulation playing pivotal roles in this process. However, the mechanism underlying how transcription factors (TFs) and their regulatory network regulate oil accumulation in seeds is not completely understood to date. In this study, we identified two TFs, basic helix-loop-helix112 (bHLH112) and ARABIDO…

The epidermis plays essential physiological roles in plants, yet its underlying gene regulatory programs remain poorly defined. To address this gap, we integrated 11 public single-cell RNA-seq datasets of Arabidopsis shoots and leaves, extracted 30 247 epidermal cells, and constructed a single-cell gene co-expression network, AtEpidermisGGM, using the SingleCellGGM algorithm. From this network, w…

Light is a pivotal environmental signal regulating diverse plant developmental and physiological processes, including seed germination, hypocotyl elongation, phototropism, metabolite biosynthesis, stress resistance, temperature response, and circadian rhythms. Multiple signal transduction pathways of ultraviolet, blue light, and red/far-red light as well as related protein interaction networks in…

Crop yield is a focal point in plant breeding. Regulation of lateral budding through apical dominance was a central target of crop domestication, directly affecting crop production. The young fruits of Cucurbita pepo, summer squash, are produced on plants characterized by apical dominance and differentiation of a single flower bud per leaf axil. A single recessive mutation, mf, results in differe…

Plants face constant environmental changes and must integrate external and internal cues to coordinate growth, development, reproduction, and stress responses. A major strategy is perception at the cell surface via a large, diverse network of receptors. Here, we outline how these receptors recognise extracellular signals and assemble active complexes with appropriate co-receptors. Diverse ectodom…