The biological functions of epitranscriptomic modification N6-methyladenosine (m6A) in plants have not been fully understood. CPSF30-L is a predominant isoform of polyadenylation factor CPSF30 and consists of CPSF30-S and m6A-binding YTH domain. Little is known about the biological roles of CPSF30-L and the molecular mechanism underlying its m6A binding function in alternative polyadenylation (APA)

N6-methyladenosine (m6A), a ubiquitous internal modification of eukaryotic mRNAs, plays a vital role in almost every aspect of mRNA metabolism. However, evidence regarding the role of m6A in regulating alternative polyadenylation (APA) is limited. APA is controlled by a large protein-RNA complex with many components, including CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30 (CPSF30). Arabidopsis

Phosphorus is an essential nutrient for plants. It is stored as inorganic phosphate (Pi) in vacuoles of land plants but as inorganic polyphosphate (polyP) in chlorophyte algae. Although it has been known that the SPX-MFS and VPE proteins are respectively responsible for Pi influx and efflux across the tonoplast in land plants, the mechanisms underlying polyP homeostasis and the transition of phosphorus

Abscisic acid (ABA) transport plays an important role in systemic plant responses to environmental factors. In this study, we showed that C-terminally encoded peptide receptor 2 (CEPR2) directly interacts with the ABA transporter NRT1.2/NPF4.6. Using transgenic seedlings, we demonstrated that NRT1.2/NPF4.6 positively regulated the ABA response, and that NRT1.2/NPF4.6 was epistatically and negatively

Mitogen-activated protein kinase (MAPK) cascades regulate a myriad of plant biological processes, including disease resistance. Plant genomes encode large numbers of MAPK kinase kinases (MAPKKKs) that can be divided into two subfamilies, namely MEKK-like kinases and Raf-like kinases. Thus far, the functions of MEKK-like MAPKKKs have been relatively well characterised, but the roles of Raf-like MAPKKKs

Many important crops (e.g., tuber, root and tree crops) have the cross-pollination nature. In these crops, no inbred lines are available for genetic study and breeding due to self-incompatibility, clonal propagation way or long generation time, which makes the identifications of agronomically important genes difficult, particularly in crops with complex autopolyploid genome. Here we developed a method

Similar to other complex organisms, plants consist of diverse and specialized cell types. The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-type-specific transcriptional programs. As a necessary step in gaining a deeper understanding of the regulatory mechanisms controlling plant gene expression, we report the use of single nucleus

The unprecedented wheat yield increases during the Green Revolution were achieved through the introduction of the Reduced height (Rht)-B1b and Rht-D1b semi-dwarfing alleles. These Rht-1 alleles encode growth repressing DELLA genes containing a stop codon within their open reading frame, that confers gibberellin (GA)-insensitive semi-dwarfism. In this study, we successfully took the hurdle of detecting

Crop domestication has fundamentally altered the course of human history, causing a shift from hunter-gatherer to agricultural societies and stimulating the rise of modern civilization. A greater understanding of crop domestication would provide a theoretical basis for how we could improve current crops and develop new crops to deal with environmental challenges in a sustainable manner. Here, we provide

More than half of the calories consumed by humans are provided by three major cereal crops (rice, maize, and wheat). Orphan crops are usually well adapted to low-input agricultural conditions, and they not only play vital roles in local areas but can also contribute to food and nutritional needs worldwide. Interestingly, many wild relatives of orphan crops are important weeds of major crops. Although

Micronutrient deficiencies include shortages of vitamins and minerals. They affect billions of people and are associated with long-range effects on health, learning ability, and huge economic losses. Biofortification of multiple micronutrients can play an important role in combating malnutrition. The challenge, however, is to balance plant growth with nutrient requirements for humans. Here, we summarize

Plants detect and respond to the proximity of competitors using light signals perceived by photoreceptor proteins. A low ratio of red to far-red radiation (R:FR ratio) is a key signal of competition that is sensed by the photoreceptor phytochrome B (phyB). Low R:FR ratios increase the synthesis of growth-related hormones, including auxin and gibberellins, promoting stem elongation and other shade-avoidance

The functional genes underlying phenotypic variation and their interactions represent “genetic mysteries”. Understanding and utilizing these genetic mysteries are key solutions for mitigating the current threats to agriculture posed by population growth and individual food preferences. Due to advances in high-throughput multi-omics technologies, we are stepping into an Interactome Big Data era that

The endoplasmic reticulum, chloroplasts, and mitochondria are major plant organelles for protein synthesis, photosynthesis, metabolism, and energy production. Protein homeostasis in these organelles, maintained by a balance between protein synthesis and degradation, is essential for cell functions during plant growth, development, and stress resistance. Nucleus-encoded chloroplast- and mitochondrion-targeted

The rapid and enthusiastic adoption of single-cell RNA sequencing (scRNA-seq) has demonstrated that this technology is far more than just another way to perform transcriptome analysis. It is not an exaggeration to say that the advent of scRNA-seq is revolutionizing the details of whole-transcriptome snapshots from a tissue to a cell. With this disruptive technology, it is now possible to mine heterogeneity

The central dogma (CD) of molecular biology is the transfer of genetic information from DNA to RNA to protein. Major CD processes governing genetic flow include the cell cycle, DNA replication, chromosome packaging, epigenetic changes, transcription, posttranscriptional alterations, translation, and posttranslational modifications. The CD processes are tightly regulated in plants to maintain genetic

The phytohormone auxin plays a central role in shaping plant growth and development. With decades of genetic and biochemical studies, numerous core molecular components and their networks, underlying auxin biosynthesis, transport, and signaling, have been identified. Notably, protein phosphorylation, catalyzed by kinases and oppositely hydrolyzed by phosphatases, has been emerging to be a crucial type

Cell-to-cell and cell-to-environment communications are critical to the growth and development of plants. Cell surface-localized receptor-like kinases (RLKs) are mainly involved in sensing various extracellular signals to initiate their corresponding cellular responses. As important vegetative organs for higher plants to adapt to a terrestrial living situation, roots play a critical role for the survival

N-hydroxy-pipecolic acid (NHP) activates plant systemic acquired resistance (SAR). Enhanced defense responses are typically accompanied by deficiency in plant development and reproduction. Albeit extensive studies of SAR induction, the effect of NHP metabolism on plant growth is presently unexplored. Here, we discovered that NHP glycosylation is a critical factor that fine-tunes the tradeoff between

Post-transcriptional gene silencing mediated by microRNAs (miRNAs) modulates numerous developmental and stress response pathways. For the last two decades, HASTY (HST), the ortholog of human Exportin-5, has been considered as a candidate protein that exports plant miRNAs from the nucleus to the cytoplasm. Here, we report HST functions in the miRNA pathway independent of its cargo-exporting activity

The complexity of epigenome landscape and transcriptional regulation is significantly increased during plant polyploidy, which drives genome evolution and contributes to the increased adaptability to diverse environments. However, the comprehensive epigenomic mapping of Brassica napus remains unexplored. In this study, we performed integrative analysis of five histone modifications, RNA polymerase

Streptococcus pyogenes Cas9 (SpCas9) is the most widely used genome editing system in plants. The editing induced by SpCas9 strictly require a canonical NGG protospacer-adjacent motif (PAM), thus limiting the scope of application. Recently, five SpCas9 variants, including SpCas9-NRRH, SpCas9-NRCH, SpCas9-NRTH, SpG and SpRY, were developed to recognize non-canonical PAMs in human cells. Here, these

Legumes establish symbiotic associations with rhizobia for biological nitrogen fixation. This process is highly regulated by various abiotic stresses, but the underlying genetic and molecular mechanisms are largely unknown. Here, we established that the glycogen synthase kinase 3 (GSK3)-like kinase, GmSK2-8, plays an important role in inhibiting symbiotic signaling and nodule formation in soybean (Glycine

There are two main types of root systems in flowering plants, namely taproot systems of dicots and fibrous root systems found in monocots. Despite this fundamental split, our current knowledge of cellular and molecular mechanism driving root development is mainly based on studies of the dicot model Arabidopsis. However, the world major crops are monocots and little is known about the transcriptional

The coordinated utilization of nitrogen (N) and phosphorus (P) is vital to maintain nutrient balance and achieve an optimal growth for plants. Previously, we revealed a mechanism by which nitrate induces genes for phosphate utilization depending on NRT1.1B-facilitated degradation of cytoplasmic SPX4, thus promoting cytoplasmic-nuclear shuttling of PHR2, the central transcription factor of phosphate

Seed oil content (SOC) is a highly important and complex trait in oil crops. Here we report deciphering of the genetic basis of natural variation of SOC in Brassica napus by genome- and transcriptome-wide association studies using 505 inbred lines. We mapped reliable quantitative trait loci (QTLs) controlling SOC in eight environments, evaluated the effect of each QTL on SOC, and analyzed the selection

Plants establish symbioses with mutualistic fungi, such as arbuscular mycorrhizal (AM) fungi, and bacteria, such as rhizobia, to exchange key nutrients and thrive. The plants and symbionts have coevolved and represent vital components of terrestrial ecosystems. Plants employ an ancestral AM signaling pathway to establish intracellular symbioses, including the legume-rhizobia symbiosis, in their roots

Rice grain oil is a valuable nutrient source. However, the genetic basis of oil biosynthesis in rice grains remains unclear. In this study, we performed a genome-wide association study on oil composition and oil concentration in a diverse panel of 533 cultivated rice accessions. High variation for eleven oil-related traits was observed and oil composition was found to differentiate in rice grains among

The eukaryotic genome has a hierarchical three-dimensional (3D) organization with functional implications for DNA replication, DNA repair, and transcriptional regulation. Over the past decade, scientists have endeavored to elucidate the spatial characteristics and functions of plant genome architecture using high-throughput chromatin conformation capturing technologies such as Hi-C, ChIA-PET, and HiChIP

Proteome remodeling is a fundamental adaptive response, and proteins in complexes and functionally related proteins are often co-expressed. Using a deep sampling strategy we define core proteomes of Arabidopsis thaliana tissues with around 10 000 proteins per tissue, and absolutely quantify (copy numbers per cell) nearly 16 000 proteins throughout the plant lifecycle. A proteome-wide survey of global

Trichomes are universally present in plants and their development is delicately regulated. Trichomes are responsible for pubescence, whose density is associated with some agronomic traits such as insect resistance, evapotranspiration, and yield. Almost a century ago, three dominant alleles related to pubescence density in soybean, namely Pd1 (dense pubescence), Ps (sparse pubescence), and P1 (glabrous)

Rice tillering is an important agronomic trait affecting grain yield. Here, we identified a high-tillering mutant tillering20 (t20), which could be restored to the wild type by treatment with the strigolactone (SL) analog rac-GR24. T20 encodes a chloroplast ζ-carotene isomerase (Z-ISO), which is involved in the biosynthesis of carotenoids and their metabolites, SL and abscisic acid (ABA). The t20 mutant

Several photorespiratory bypasses have been introduced into plants and shown to improve photosynthesis by increasing chloroplastic CO2 concentrations or optimizing energy balance. We recently reported that an engineered GOC bypass could increase photosynthesis and productivity in rice. However, the grain yield of GOC plants was unstable, fluctuating in different cultivation seasons because of varying

Low temperature is a major environmental factor limiting plant growth and productivity. Although transient elevation of cytoplasmic calcium has long been recognized as a critical signal for plant cold tolerance, the calcium channels responsible for this process have remained largely elusive. Here, we reported that OsCNGC9, a cyclic nucleotide-gated channel, positively regulates chilling tolerance by

Salinity severely reduces plant growth and limits agricultural productivity. Dynamic changes and rearrangement of the plant cell wall is an important response to salt stress, but relatively little is known about the biological importance of specific cell wall components in the response. Here, we demonstrate a specific function of β-1,4-galactan in salt hypersensitivity. Salt stress induced the accumulation

Tip growth is a special polarization in which a single and unique polarization site is established and maintained. Rho of Plants (ROPs) represent the only class of Rho GTPases in plants, regulating tip growth. Dynamic and asymmetric distribution of ROPs, critical for the establishment and maintenance of tip growth, requires at least one positive feedback loop, which is still elusive. We report a positive

Soybean as an important legume crop displays classic shade avoidance syndrome (SAS) including exaggerated stem elongation that leads to lodging and yield reduction under density farming conditions. Here we compared the effects of two shade signals, low red light to far-red light ratio (R:FR) and low blue light (LBL), on soybean status and revealed that LBL predominantly induces excessive stem elongation

Heading date (or flowering time) is one of the most important agronomic traits in rice, which influences the regional adaptability and crop yield. Many major-effect genes have been identified on rice heading date, which influence heading date to a large extent, and they are hard to utilize in rice molecular breeding. While minor-effect genes on heading date which are more desirable for fine-tuning

Auxin plays a critical role in lateral root (LR) formation. The signaling module composed of auxin responsive factors (ARFs)-lateral organ boundaries-domain transcription factors (LBDs) mediates auxin signaling to control almost every stage of LR development. Here, we show that auxin-induced degradation of the APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factor ERF13, dependent on MITOGEN-ACTIVATED

Plants are vulnerable to heat stress especially during reproductive development. HSR (Heat shock response) in cytosol and nucleus as well as UPR (Unfolded protein response) in ER (Endoplasmic reticulum) are two mechanisms that enable plants to survive heat stress. Excessive heat or ER stresses lead to cell death when UPR cannot repair stress damages, but how the outcome of being survival being death

Under conditions of labor or resource scarcity, direct seeding, rather than transplantation, is a preferred mode of rice (Oryza sativa. L) cultivation. This approach requires varieties that exhibit uniform seedling emergence. Mesocotyl elongation (ME), the main driver of rice seedling rapid emergence from soil, is enhanced by darkness and inhibited by light. Plant polyamine oxidases (PAOs) oxidate

It is increasingly realized that homoploid hybrid speciation (HHS), involving no change in chromosome number, is an important mechanism of speciation likely to increase in frequency as ecological and geographical barriers between species continue to be disrupted by human activities into the future. HHS requires the establishment of reproductive isolation between a hybrid and its parents. However, the

Nucleotide-binding leucine-rich repeat (NLR) proteins play critical roles in plant immunity. However, how NLRs are regulated and activate defense signaling is not fully understood. The rice (Oryza sativa) NLR receptor Piz-t confers broad-spectrum resistance to the fungal pathogen Magnaporthe oryzae and the RING-type E3 ligase AVRPIZ-T INTERACTING PROTEIN 10 (APIP10) negatively regulates Piz-t accumulation

Transposable elements (TEs) regularly capture fragments of genes. When the host silences these TEs, siRNAs homologous to the captured regions may also target the genes. This epigenetic cross-talk establishes an intragenomic conflict: silencing the TEs has the cost of silencing the genes. If genes are important, however, natural selection may maintain function by moderating the silencing response, which

Plants often encounter light intensities exceeding the capacity of photosynthesis (excessive light) mainly due to biotic and abiotic factors, which lower CO2 fixation and reduce light energy sinks. Under excessive light, the photosynthetic electron transport chain generates damaging molecules, hence leading to photooxidative stress and eventually to cell death. In this review, we summarize the mechanisms

A myriad of abiotic stress responses in plants are controlled by abscisic acid (ABA) signaling. ABA receptors can be degraded by both the 26S proteasome pathway and vacuolar degradation pathway after processing via the endosomal sorting complex required for transport (ESCRT) proteins. Despite being essential for ABA signaling, the upstream regulators of ESCRTs remain unknown. Here, we report that the

Photosynthetic rate at the present atmospheric condition is limited by the CO2-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) because of its extremely low catalytic rate (kcat) and poor affinity for CO2 (Kc) and specificity for CO2 (Sc/o). Rubisco in C4 plants generally shows higher kcat than that in C3 plants. Rubisco consists of eight large subunits and eight small subunits

In angiosperms, the process of pollination relies on species-specific interaction and signaling between the male (pollen) and female (pistil) counterparts where the interplay between several pollen and stigma proteins decides the fate of the pollen. In Brassicaceae, the dry stigmatic papillary cells control pollen germination by releasing resources only to compatible pollen thereby allowing pollen

Root growth is maintained by the continuous division of cells in the apical meristem. ROOT MERISTEM GROWTH FACTOR 1 (RGF1) is a critical peptide hormone regulating root stem cell niche maintenance. Previous studies discovered that five closely related leucine-rich repeat receptor-like protein kinases (LRR-RLKs), named RGF1 INSENSITIVES (RGIs) or RGF1 RECEPTORS (RGFRs), are able to perceive the RGF1

The mitotic activity of root apical meristem (RAM) is critical to primary root growth and development. Previous studies have identified the roles of ROOT GROWTH FACTOR 1 (RGF1), a peptide ligand, and its receptors, RGF1 INSENSITIVEs (RGIs), a clade of five leucine-rich-repeat receptor-like kinases, in promoting cell division in the RAM, which determines the primary root length. However, the downstream

Genic male sterility (GMS) is critical for heterosis utilization and hybrid seed production. Although GMS mutants and genes have been studied extensively in plants, it has remained unclear whether chloroplast-associated photosynthetic and metabolic activities are involved in the regulation of anther development. In this study, we characterized the function of ZmMs33/ZmGPAT6, which encodes a member

Temperature-sensitive phase separation is reversibly and rapidly controlled by the prion domain (PrD)-containing EARLY FLOWERING 3 (ELF3) protein. Disordered protein-driven liquid-liquid phase separation underlies a ratio-metric thermosensing in plants.

Ribosome biogenesis, taking place mainly in the nucleolus, involves coordinated expression of pre-ribosomal RNAs (pre-rRNAs) and ribosomal proteins, pre-rRNA processing, and subunit assembly with the aid of numerous assembly factors. Our previous study showed that the Arabidopsis thaliana protein arginine methyltransferase AtPRMT3 regulates pre-rRNA processing; however, the molecular mechanism remains

After three decades of the amazing progress made on molecular studies of plant–microbe interactions (MPMI), we have begun to ask ourselves “what are the major questions still remaining?” as if the puzzle has only a few pieces missing. Such an exercise has ultimately led to the realization that we still have many more questions than answers. Therefore, it would be an impossible task for us to project

Vector-borne plant diseases have significant ecological and economic impacts, affecting farm profitability and forest composition throughout the world. Bacterial vector-borne pathogens have evolved sophisticated strategies to interact with their hemipteran insect vectors and plant hosts. These pathogens reside in plant vascular tissue, and their study represents an excellent opportunity to uncover

Looking forward includes looking back every now and then. In 2007, David Weller looked back at 30 years of biocontrol of soil-borne pathogens by Pseudomonas and signified that the progress made over decades of research has provided a firm foundation to formulate current and future research questions. It has been recognized for more than a century that soil-borne microbes play a significant role in

Crop diseases are major factors responsible for substantial yield losses worldwide, which affects global food security. The use of resistance (R) genes is an effective and sustainable approach to controlling crop diseases. Here, we review recent advances on R gene studies in the major crops and related wild species. Current understanding of the molecular mechanisms underlying R gene activation and

Mycoviruses are viruses that infect fungi, and hypovirulence-associated mycoviruses have the potential to control fungal diseases. However, it is unclear how mycovirus-mediated hypovirulent strains live and survive in the field, and no mycovirus has been applied for field crop protection. In this study, we found that a previously identified small DNA mycovirus (SsHADV-1) can convert its host, Sclerotinia