Bioactive compounds play an increasingly prominent role in breeding functional and nutritive fruit crops such as citrus. However, the genomic and metabolic bases for the selection and differentiation underlying bioactive compound variations in citrus remain poorly understood. In this study, we constructed a species-level variation atlas of genomes and metabolomes using 299 citrus accessions. A total

The pursuit of complete telomere-to-telomere (T2T) genome assembly in plants, challenged by genomic complexity, has been advanced by Oxford Nanopore Technologies (ONT), which offers ultra-long, real-time sequencing. Despite its promise, sequencing length and gap filling remain significant challenges. This study optimized DNA extraction and library preparation, achieving DNA lengths exceeding 485 kb;

Theoretical research on plant immunity and disease resistance is an important foundation for crop disease resistance breeding. AI-based protein engineering is of great significance in accelerating the precise design of crop disease resistance and realizing broad-spectrum crop disease resistance.

Keeping immune responses in an off state in the absence of a threat is essential to avoid the deleterious consequences of autoimmunity, while their timely activation upon perception of non-self determines the capacity of an organism to defend against potential pathogens. In plants, constitutive or untimely activation of immune responses dramatically limits growth and reproduction, highlighting the

Obligate biotrophs depend on living hosts for nutrient acquisition to complete their life cycle, yet the mechanisms by which hosts restrict nutrient availability to pathogens remain largely unknown. The fungal pathogen Sporisorium reilianum infects maize seedlings and causes head smut disease in inflorescences at maturity, while a cell wall-associated kinase, ZmWAK, provides quantitative resistance

Rice (Oryza sativa) provides >20% of the consumed calories in the human diet. However, rice is also a leading source of dietary cadmium (Cd) that seriously threatens human health. Deciphering the genetic network that underlies the grain-Cd accumulation will benefit the development of low-Cd rice and mitigate the effects of Cd accumulation in the rice grain. In this study, we identified a QTL gene,

In plants, sugars are the key source of energy and metabolic building blocks. The systemic transport of sugars is essential for plant growth and morphogenesis. Plants evolved intricate molecular networks to effectively distribute sugars. The dynamic distribution of these osmotically active compounds is a handy tool for regulating cell turgor pressure, an instructive force in developmental biology.

Thousands of nuclear-encoded proteins are transported into chloroplasts through the TOC–TIC translocon that spans the chloroplast envelope membranes. A motor complex pulls the translocated proteins out of the TOC–TIC complex into the chloroplast stroma by hydrolyzing ATP. The Orf2971–FtsHi complex has been suggested to serve as the ATP-hydrolyzing motor in Chlamydomonas reinhardtii, but little is known

Most coexisting insect species exhibit stunted growth compared to individual species on plants. This phenomenon reflects an interspecific antagonism drawing extensive attention, while the underlying mechanisms remain largely uncharacterized. Mirids (Apolygus lucorum) and cotton bollworms (Helicoverpa armigera) are two common cotton pests. We identified a secretory protein, ASP1, from the oral secretion

Bread wheat (Triticum aestivum) became a globally dominant crop after incorporating the D genome from the donor species Aegilops tauschii, but the evolutionary history that shaped the D genome during this process remains to be clarified. Here, we propose a renewed evolutionary model linking Ae. tauschii and the hexaploid wheat D genome by constructing an ancestral haplotype map covering 762 Ae. tauschii

Maize (Zea mays) is one of the most important crops in the world, but its yield and quality are seriously affected by diverse diseases. Identifying broad-spectrum resistance genes is crucial for developing effective strategies to control the disease in maize. In a genome-wide study in maize, we identified a G-type lectin receptor kinase ZmLecRK1, as a new resistance protein against Pythium aphanidermatum

Plants are frequently exposed to herbivory and mechanical damage that result in wounding. Two fundamental strategies, regeneration and healing, are employed by plants upon wounding. How plants make different decisions and how wound healing is sustained until the damaged tissues recover are not fully understood. In this study, we found that local auxin accumulation patterns, determined by wounding modes

Fusing three-dimensional (3D) and multispectral (MS) imaging data holds promise for high-throughput and comprehensive plant phenotyping to decipher genome-to-phenome knowledge. Acquiring high-quality 3D MS point clouds (3DMPCs) of plants remains challenging because of poor 3D data quality and limited radiometric calibration methods for plants with a complex canopy structure. Here, we present a novel

Drought is a major environmental stress limiting crop yields worldwide. Upland rice (Oryza sativa) has evolved complex genetic mechanisms for adaptative growth under drought stress. However, few genetic variants that mediate drought resistance in upland rice have been identified, and little is known about the evolution of this trait during rice domestication. In this study, using a genome-wide association

High seed lint fibre density is proposed as one of the breeding objectives for boosting cotton fibre yield. We identify the sources of potential lint fibre cells and discuss the opportunities and challenges involved in realizing the goal.

The life cycle of many plants including our most important crops is short, with weeks to months between germination and death. Monocarpic plants flower only once, with seed/grain filling dependent on nutrient remobilization from senescing parental plants. A mature crop stand such as a harvest-ready wheat field is the result of mass suicide, with only the seeds/grains as living entities.

For over 60 years, salicylic acid (SA) has been known as a plant immune signal required for basal and systemic acquired resistance. SA activates these immune responses by reprogramming ∼20% of the transcriptome through NPR1. However, components in the NPR1 signaling hub, which appears as nuclear condensates, and the NPR1 signaling cascade have remained elusive due to difficulties in studying this transcriptional

Optimal plant height is crucial in modern agriculture, influencing lodging resistance and facilitating mechanized crop production. Upland cotton (Gossypium hirsutum) is the most important fiber crop globally; however, the genetic basis underlying plant height remains largely unexplored. In this study, we conducted a genome-wide association study to identify a major locus controlling plant height (PH1)

Cold stress is one of the major abiotic stress factors affecting rice growth and development, leading to significant yield loss in the context of global climate change. Exploring natural variants that confer cold resistance and the underlying molecular mechanism responsible for this is the major strategy to breed cold-tolerant rice varieties. Here, we show that natural variations of a SIMILAR to RCD

Root-knot nematodes (RKNs) are plant pests that infect the roots of host plants. Bacillus thuringiensis (Bt) nematicidal proteins exhibited toxicity to nematodes. However, the application of nematicidal proteins for plant protection is hampered by the lack of effective delivery systems in transgenic plants. In this study, we discovered the accumulation of leucoplasts (root plastids) in galls and RKN-induced

Hyperforin is the compound responsible for the effectiveness of St. John’s wort () as an antidepressant, but its complete biosynthetic pathway remains unknown. Gene discovery based on co-expression analysis of bulk RNA-sequencing data or genome mining failed to discover the missing steps in hyperforin biosynthesis. In this study, we sequenced the 1.54-Gb tetraploid . genome assembled into 32 chromosomes

Understanding how maize () responds to cold stress is crucial for facilitating breeding programs of cold-tolerant varieties. Despite extensive utilization of the genome-wide association study (GWAS) approach for exploring favorable natural alleles associated with maize cold tolerance, few studies have successfully identified candidate genes that contribute to maize cold tolerance. In this study, we

Combinatorial interactions between different regulators diversify and enrich the chance of transcriptional regulation in eukaryotic cells. However, a dose-dependent functional switch of homologous transcriptional repressors has rarely been reported. Here, we show that SHY2, an auxin/indole-3-acetic acid (Aux/IAA) repressor, exhibits a dose-dependent bimodal role in auxin-sensitive root-hair growth

Suppressor of G2 allele of skp1 (SGT1) is a highly conserved eukaryotic protein that plays a vital role in growth, development, and immunity in both animals and plants. Although some SGT1 interactors have been identified, the molecular regulatory network of SGT1 remains unclear. SGT1 serves as a co-chaperone to stabilize protein complexes such as the nucleotide-binding leucine-rich repeat (NLR) class

Under warm temperatures, plants adjust their morphologies for environmental adaption via precise gene expression regulation. However, the function and regulation of alternative polyadenylation (APA), an important fine-tuning of gene expression, remains unknown in plant thermomorphogenesis. In this study, we found that SUMOylation, a critical post-translational modification, is induced by a long-term

Gene upregulation through genome editing is important for plant research and breeding. Targeted insertion of short transcriptional enhancers (STEs) into gene promoters may offer a universal solution akin to transgene-mediated overexpression while avoiding the drawbacks associated with transgenesis. Here, we introduce an “ activation” technique in rice that leverages well-characterized STEs for refined

Plant cell walls are a critical site where plants and pathogens continuously struggle for physiological dominance. Here we show that dynamic remodeling of pectin methylesterification of plant cell walls is a component of the physiological and co-evolutionary struggles between hosts and pathogens. A pectin methylesterase (PsPME1) secreted by decreases the degree of pectin methylesterification, thus

Plants exploit phenotypic plasticity to adapt their growth and development to prevailing environmental conditions. Interpretation of light and temperature signals is aided by the circadian system, which provides a temporal context. Phenotypic plasticity provides a selective and competitive advantage in nature but is obstructive during large-scale, intensive agricultural practices since economically

Plant immunity is a multilayered process that includes recognition of patterns or effectors from pathogens to elicit defense responses. These include the induction of a cocktail of defense metabolites that typically restrict pathogen virulence. Here, we investigate the interaction between barley roots and the fungal pathogens () and () at the metabolite level. We identify hordedanes, a previously undescribed

Monocarpic senescence, characterized by whole-plant senescence following a single flowering phase, is widespread in seed plants, particularly in crops, determining seed harvest time and quality. However, how external and internal signals are systemically integrated into monocarpic senescence remains largely unknown. Here, we report that the transcription factor WRKY1 plays essential roles in multiple

The discovery of a wild abortive-type (WA) cytoplasmic male sterile (CMS) line and breeding its restorer line have led to the commercialization of three-line hybrid rice, contributing considerably to global food security. However, the molecular mechanisms underlying fertility abortion and the restoration of CMS-WA lines remain largely elusive. In this study, we cloned a restorer gene, , following a

Over the past few decades, significant improvements in maize yield have been largely attributed to increased plant density of upright hybrid varieties rather than increased yield per plant. However, dense planting triggers shade avoidance responses (SARs) that optimize light absorption but impair plant vigor and performance, limiting yield improvement through increasing plant density. In this study

Steroidal glycoalkaloids (SGAs) are specialized metabolites produced by hundreds of species, including important vegetable crops such as tomato, potato, and eggplant. Although it has been known that SGAs play important roles in defense in plants and “anti-nutritional” effects (e.g., toxicity and bitterness) to humans, many of these molecules have documented anti-cancer, anti-microbial, anti-inflammatory

Xenia, the phenomenon in which the pollen genotype directly affects the phenotypic characteristics of maternal tissues (i.e., fruit ripening), has applications in crop production and breeding. However, the underlying molecular mechanism has yet to be elucidated. Here, we investigated whether mobile mRNAs from the pollen affect the ripening and quality-related characteristics of the fruit using cross-pollination

Plants are sessile organisms that have acquired highly plastic developmental strategies to adapt to the environment. Among these processes, the floral transition is essential to ensure reproductive success and is finely regulated by several internal and external genetic networks. The photoperiodic pathway, which controls plant response to day length, is one of the most important pathways controlling

Maize develops separate ear and tassel inflorescences with initially similar morphology but ultimately different architecture and sexuality. The detailed regulatory mechanisms underlying these changes still remain largely unclear. In this study, through analyzing the time-course meristem transcriptomes and floret single-cell transcriptomes of ear and tassel, we revealed the regulatory dynamics and

Doubled haploid (DH) technology and synthetic apomixis approaches can considerably shorten breeding cycles and enhance breeding efficiency. Compared with traditional breeding methods, DH technology offers the advantage of rapidly generating inbred lines, while synthetic apomixis can effectively fix hybrid vigor. In this review, we focus on (i) recent advances in identifying and characterizing genes