Coordination between mitochondria and nucleus is crucial for fertility determination in cytoplasmic male sterility (CMS) plant. Using yeast one-hybrid screening, we identified a transcription factor ZmDREB1.7 that is highly expressed in sterile microspores at the large vacuole stage and activates CMS gene orf355 expression in mitochondria. Δpro, a weak allele of ZmDREB1.7 promoter due to the loss of

The hexaploid species Echinochloa crus-galli is one of the most detrimental weeds in crop fields, especially in rice paddies. Its evolutionary history is similar to that of bread wheat, arising through polyploidization after hybridization between a tetraploid and a diploid species. Here we generated and analyzed high quality genome sequences of diploid (E. haploclada), tetraploid (E. oryzicola) and

Seed germination and seedling establishment are important for the reproductive success of plants, but seeds and seedlings typically encounter constantly changing environmental conditions. By inhibiting seed germination and postgerminative growth through the PYR1/PYL/RCAR ABA receptors and PP2C co-receptors, the phytohormone abscisic acid (ABA) prevents premature germination and seedling growth under

The regulation of stomatal lineage cell development has been extensively investigated. However a comprehensive characterization of this biological process based on single-cell transcriptome analysis has not yet been reported. Here, we performed RNA-seq on 12,844 individual cells from the cotyledons of five-day-old Arabidopsis seedlings. We identified 11 cell clusters corresponding mostly to cells at

The rapid development of high-throughput sequencing (HTS) techniques has led biology into the big-data era. Data analyses using various bioinformatics tools rely on programming and command-line environments, which are challenging and time-consuming for most wet-lab biologists. Here, we present TBtools (a Toolkit for Biologists integrating various biological data handling tools), a stand-alone software

CRISPR-Cas9 is a powerful tool for generating targeted mutations and genomic deletions. However, precise gene insertion or sequence replacement remains a major hurdle before application of CRISPR-Cas9 technology is fully realized in plant breeding. Here we report high frequency, selectable marker-free intra-genomic gene targeting (GT) in maize. Heat shock-inducible Cas9 was used for generating targeted

Tomato (Solanum lycopersicum) is a major horticultural crop worldwide and has emerged as a preeminent model for metabolic research. Although many research efforts have focused on analyzing metabolite variants between varieties and species, the dynamics of metabolic changes during the tomato growth cycle and the regulatory networks underlying these changes are poorly understood. In this study, we integrated

Leaf senescence is driven by the expression of senescence-associated genes (SAGs). Development-specific genes often undergo DNA demethylation in their promoter and other regions to regulate gene expression. Whether and how DNA demethylation regulates SAGs, thus leaf senescence, remain elusive. Whole genome bisulfite sequencing (WGBS) analyses of wild type (WT) and demeter-like 3 (dml3) in Arabidopsis

Adventitious roots form from non-root tissues as part of normal development or in response to stress or wounding. The root primordia form with the source tissue and during emergence, the adventitious roots penetrate the inner cell layers and the epidermis; however, the mechanisms underlying this emergence remain largely unexplored. Here, we reveal that a regulatory module composed of the AP2/ERF transcription

Non-conventional peptides (NCPs), which include small open reading frame-encoded peptides, play critical roles in fundamental biological processes. Here we developed an integrated peptidogenomic pipeline using high-throughput mass spectra to probe a customized six-frame translation database and applied it to large-scale identification of NCPs in plants. Altogether, 1,993 and 1,860 NCPs were unambiguously

The ability of climbing plants to grow upward along others to reach canopy for photosynthesis is hypothesized as a key innovation in flowering plants. Cucurbitaceae, a family containing ∼1000 species and many important crops, are mostly climbers and have characteristic tendrils and pepo fruits. Here, we present 127 newly sequenced transcriptomes and genomes along with other datasets for a total of

Salt-Overly-Sensitive (SOS) signaling module comprising the sodium-transport protein SOS1 and the regulatory proteins SOS2 and SOS3, is well known as the central salt excretion system that helps plants against salt accumulation. Here we report that VPS23A, a component of the endosomal sorting complex required for transport (ESCRT), plays an essential role in the function of the SOS module to confer

Fatty acids and their derivatives are essential building blocks for anther cuticle and pollen wall formation. Disruption of lipid metabolism in anther and pollen development often leads to genic male sterility (GMS). Up to now, lots of lipid metabolism-related GMS genes have been identified and characterized, which are involved in formation of anther cuticle, pollen wall, and subcellular organelle

Both plants and humans require mineral elements for their healthy growth and development. Mineral elements in the soil are taken up by the plant roots and transported to the edible parts for human consumption through various different transporters. An ideal future crop for human health should be rich in essential mineral elements but with less toxic elements in the edible parts. However, due to the

Plant cell growth involves a complex interplay among cell wall expansion, biosynthesis, and in specific tissues secondary cell wall (SCW) deposition, yet their coordination remains elusive. The cotton fiber cells are developmentally synchronous, highly elongated and contain nearly pure cellulose when mature. Here, we report that the transcription factor GhTCP4 plays an important role in balancing the

Mulberry (Morus spp.) is the sole plant consumed by the domesticated silkworm. However, the genome of domesticated mulberry has not yet been sequenced, and the ploidy level of this species remains unclear. Here, we assembled a high-quality, chromosome-level domesticated mulberry (Morus alba L) genome and confirmed that it is diploid with 28 chromosomes (2n=2x=28). Population genomic analysis based

Current cell-wall models assume no covalent bonding between cellulose and hemicelluloses such as xyloglucan or mixed-linkage β-d-glucan (MLG). However, Equisetum hetero-trans-β-glucanase (HTG) grafts cellulose onto xyloglucan oligosaccharides (XGOs) - and, we now show, xyloglucan polysaccharide - in vitro, thus exhibiting CXE (cellulose:xyloglucan endotransglucosylase) activity. HTG additionally catalyses

Tea plant is an important economic crop, which produces the world's oldest and widely consumed tea beverages. We here present a high-quality reference genome of the tea plant (Camellia sinensis var. sinensis) consisting of 15 pseudo-chromosomes, 70.38% of which are LTR retrotransposons. We show the evidence that LTR-RTs play critical roles in the genome size expansion and transcriptional diversification

Lipid catabolism in germinating seeds provides energy and substrates for initial seedling growth, but how this process is regulated is not well understood. Here, we show that an AT-hook motif-containing nuclear localized (AHL) protein regulates lipid mobilization and fatty acid β-oxidation during seed germination and seedling establishment. AHL4 was identified to directly interact with the lipid mediator

Growth inhibition and cold-acclimation strategies help plants withstand cold stress, which adversely affects growth and survival. PHYTOCHROME B (phyB) regulates plant growth through perceiving both light and ambient temperature signals. However, the mechanism by which phyB mediates the plant response to cold stress remains elusive. Here, we show that the key transcription factors mediating cold acclimation

While the structures of plant primary metabolic pathways are generally well defined and highly conserved across species, those defining specialized metabolism are less well characterized and more highly variable across species. In this study, we investigated polyphenolic metabolism in the lycopersicum complex by characterizing the underlying biosynthetic and decorative reactions that constitute the

In response to far-red light (FR), FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) transports the photoactivated phytochrome A (phyA), the primary FR photoreceptor, into the nucleus, where it initiates FR signaling in plants. Light promotes the 26S proteasome-mediated degradation of FHY1, which desensitizes FR signaling, but the underlying regulatory mechanism remains largely unknown. Here, we show that reversible

Chromoplasts are colored plastids that synthesize and store massive amounts of carotenoids. Chromoplast number and size define the sink strength for carotenoid accumulation in plants. However, nothing is known about the mechanisms controlling chromoplast number. Previously, a natural allele of Orange (OR), ORHis, was found to promote carotenoid accumulation by activating chromoplast differentiation

Plant architecture is a complex agronomic trait and a major factor of crop yield, which is affected by several important hormones. Strigolactones (SLs) are identified as a new class hormoneinhibiting branching in many plant species and have been shown to be involved in various developmental processes. Genetical and chemical modulation of the SL pathway is recognized as a promising approach to modify

Plants utilize nucleotide-binding, leucine-rich repeat receptors (NLRs) to detect pathogen effectors, leading to effector-triggered immunity. The NLR ZAR1 indirectly recognizes the Xanthomonas campestris pv. campestris effector AvrAC and Pseudomonas syringae effector HopZ1a by associating with closely related receptor-like cytoplasmic kinase subfamily XII-2 (RLCK XII-2) members RKS1 and ZED1, respectively

Soybean (Glycine max), as an economically important food and oilseedcrop, is a major source of plant proteins and oils. Although considerable progress has been made in increasing the yields of rice, wheat, and maize through the "Green Revolution", little improvements have been made for soybean. With the increasing demand of soybean production and the rapid development of crop breeding technologies

Linking natural genetic variation to trait variation can help determine the functional roles ofdifferent genes. Variations of one or several traits are often assessed separately. High-throughput phenotyping and data mining can capture dozens or hundreds of traits from the same individuals. Here, we test the association between markers within a gene and many traits simultaneously. This genome–phenome

Non-damaging ultraviolet B (UV-B) light promotes photomorphogenic development and stress acclimation through UV-B-specific signal transduction in Arabidopsis. UV-B irradiation induces monomerization and nuclear translocation of the UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8). However, it is not clear how the nuclear localization of UVR8 leads to changes in global gene expression. Here, we reveal

The circadian clocks of plants and animals are recruiting similar cellular systems to regulate PTMs of circadian clock proteins, but distinctions remain. Circadian clocks in both autotrophic and heterotrophic organisms can be refined by PTM cascades, but the same PTMs can have different functional outcomes. The role of protein glycosylation is a clear example of this dichotomy, where circadian clock

Light is arguably one of the most important environmental factors that determines virtually all aspects of plant growth and development, but the molecular link between light signaling and the autophagy pathway has not been elucidated in plants. In this study, we demonstrate that autophagy is activated during light-to-dark conversion though transcriptional upregulation of autophagy-related genes (ATGs)

Optimizing the perception of external cues and regulating physiology accordingly help plants to cope with the constantly changing environmental conditions to which they are exposed. An array of photoreceptors and intricate signaling pathways allow plants to convey the surrounding light information and synchronize an endogenous timekeeping system known as the circadian clock. This biological clock integrates

PHOTOPERIODIC CONTROL OF HYPOCOTYL 1 (PCH1) and PCH1-LIKE (PCHL) were shown to directly bind to phytochrome B (phyB) and suppress phyB thermal reversion, resulting in plants with dramatically enhanced light sensitivity. Here, we show that PCH1 and PCHL also positively regulate various light responses, including seed germination, hypocotyl gravitropism, and chlorophyll biosynthesis, by physically interacting

The ubiquitin-proteasome system (UPS) is an important post-translational regulatory mechanism that controls many cellular functions in eukaryotes. Here, we show that stable expression of P3 protein encoded by Rice grassy stunt virus (RGSV), a negative-strand RNA virus in the Bunyavirales, causes developmental abnormities similar to the disease symptoms caused by RGSV, such as dwarfing and excess tillering

Tillering is a major determinant of rice plant architecture and grain yield. Here, we report that depletion of rice OsNRPD1a and OsNRPD1b, two orthologs of the largest subunit of RNA polymerase IV, leads to a high-tillering phenotype, in addition to dwarfism and smaller panicles. OsNRPD1a and OsNRPD1b are required for the production of 24-nt small interfering RNAs that direct DNA methylation at transposable

Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible

Temperature is a key factor governing the growth and development, distribution, and seasonal behavior of plants. The entire plant lifecycle is affected by environmental temperatures. Plants grow rapidly and exhibit specific changes in morphology under mild average temperature conditions, a response termed thermomorphogenesis. When exposed to chilling or moist chilling low temperatures, flowering or