Protein post-translational modifications (PTMs) serve as a crucial regulatory mechanism of protein function and play a significant role in rice seed development and endosperm starch biosynthesis. With advancements in proteomics technologies, numerous starch synthesis-related proteins in rice endosperm have been identified to undergo various PTMs. This review summarizes the proteomic analyses, modification sites, pathways, and biological functions of six major types of PTMs in starch synthesis-related proteins in rice endosperm: phosphorylation, lysine acetylation, succinylation, 2-hydroxyisobutyrylation, malonylation, and ubiquitination. Among these, protein phosphorylation has been the most extensively studied and is recognized as a key regulator of plant growth, development, and starch metabolism. Additionally, we discuss the potential roles of PTMs in grain filling, rice starch quality, and appearance. This review provides insights into the regulatory mechanisms of PTMs in starch synthesis-related proteins in rice endosperm, offering a valuable reference for breeding high-yield and high-quality rice varieties.

Charophytes and land plants form a monophyletic group known as Streptophyta. Fossil and molecular evidences suggest that land plants originated from charophytes. This article summarizes the 14 sequenced genomes of 10 species in charophytes and reviews the molecular mechanisms involved in the terrestrialization of plants, revealing the genomic basis for the pre-adaptation of charophytes that included the expansion of gene families regulating plant hormone signal transduction and encoding key transcription factors, as well as horizontal gene transfer. We elucidate with examples the helpful role of the whole-genome data of charophytes in transcriptomic and functional genomic discovery. Moreover, we discuss the importance of telomere-to-telomere genomes and pan-genomes for a deeper understanding of plant terrestrialization and the future directions of integrating genomic data with biological experiments for deciphering the function and origin of charophyte genes.

Biological small molecules, also known as monomeric compounds with relatively low molecular weight found in organisms, encompass a wide array of substances in plants, such as ions, plant hormones and metabolites. Studying the dynamic fluctuations of these small molecules in plants is crucial for analyzing their corresponding physiological functions, regulatory networks, and enhancing the precision of botanical research. Genetically encoded fluorescent biosensors/probes utilizing Förster resonance energy transfer (FRET) technology serves as a valuable tool for real-time monitoring of these small molecules within living organisms. These FRET biosensors/probes allow for the non-invasive visualization of specific small molecule concentrations, providing detailed information at a high resolution. Because of these unique advantages, this technique has been extensively applied in various research fields, including plant physiology, developmental biology, and environmental science. This review provides a comprehensive overview of FRET sensors/probes utilized in plant research in recent years, outlines the key design concepts, and highlights their applications and advances in detecting ions, plant hormones, and metabolites. Furthermore, this review demonstrates practical technological tools and potential research directions for elucidating the functions of small biomolecules in plants.

Cyclic nucleotide-gated channels (CNGCs) are important cation channels that play pivotal roles in the regulation of growth and development, as well as in response to stresses such as cold, heat, salt, and pathogen attacks in plants. In this review, we briefly outline the classification, structure and location of CNGCs in plants, and comprehensively summarize the recent research progress on their ionic selectivity, regulatory mechanisms, and biological functions, in order to enhance our understanding of plant CNGCs and provide a reference for future research.

Single-cell transcriptomics has improved the spatiotemporal resolution from multi-cell to single-cell levels, and notable progress in this technique has facilitated the identification of new rare cell types, exploration of intercellular heterogeneity, and mapping of cell developmental trajectories. Single-cell transcriptomics is currently being widely used in various research fields such as plant growth and development, stress response, and environmental adaptability, which helps to more thoroughly and precisely uncover the molecular regulatory mechanisms underlying plant life processes. However, there are numerous challenges associated with the study and analysis of different plant species. In this review, we compare and evaluate various single-cell transcription techniques and processes, summarize plant single-cell studies in recent years, and explore new single-cell analysis tools to support researchers studying plant biology with high precision and dynamics. In addition, we propose future directions in using single-cell transcriptomics technologies to address some of the key challenges in plant research and breeding. Furthermore, some important methods for addressing plant research and breeding with single-cell transcriptomics are discussed, along with their difficulties and potential applications.

Nicotinamide adenine dinucleotide (NAD⁺) and nicotinamide adenine dinucleotide phosphate (NADP⁺) act as an integral regulator of plant core energy metabolism, growth and development, and stress response, which can directly and indirectly influence many key cellular functions. As the cornerstone of cell metabolism, NAD(P)⁺ homeostasis is crucial for normal plant growth and development, and stress response. Impaired synthesis of NAD(P)⁺ or deficiency can trigger metabolic disorders and a series of defective phenotypes, and may even lead to plant death in severe cases. Currently, NAD(P)⁺ biosynthesis pathway and its key enzymes have been well studied in plants, but its homeostatic regulation in plants and the mechanism of coordinating plant growth and stress response are still unclear. Therefore, isolating NAD(P)⁺ deficiency-related mutants is crucial for exploring the regulatory mechanisms of NAD(P)⁺ homeostasis and its balancing in plant growth and stress response. This review summarizes the biosynthetic metabolic pathways of plant NAD(P)⁺, focuses on the participation of NAD(P)⁺ in plant growth and stress response processes, and looks into the future on the research prospects of NAD(P)⁺ in plants.

Rice (Oryza sativa) is a globally important cereal crop, and the rational application of fertilizers is necessary agricultural practice to ensure its sustainable and stable yield. Phosphorus is one of the essential nutrients for rice, primarily absorbed through the rice roots. Since rice is mostly grown in flooded conditions, the root surface of rice generally forms iron plaques rich in iron oxides, which play a crucial role in the migration of inorganic phosphorus in the rhizosphere of rice. This paper reviews the impact of biotic and abiotic factors on the formation of iron plaques in rice and discusses the effect of iron plaques on the absorption and transport of phosphorus in plant nutrition. Furthermore, we discuss the prospects of future research on iron plaques, aiming to provide clues for our further understanding of the interactions between iron and phosphorus in the rhizosphere of rice.

China is rich in the resources of tall gramineous grass which is widely distributed and extensively cultivated. Here we review the research progress on the characteristics, cultivation techniques, and main usage of the common species of tall gramineous grass. We also give prospections on the techniques which could improve the breeding and cultivation techniques, as well as the collection, storage and transport technology systems of tall gramineous grass. We hope our work could promote the industrial application of tall gramineous grass.

Herba Epimedii is a traditional Chinese herb medicine (TCM) with a long history. Research on Herba Epimedii has attracted much attention in China due to its high medicinal value. C8-prenylated flavonol glycosides (PFGs) have been demonstrated to be the main bioactive components in Epimedium brevicornu, and their content determines the medicinal quality. Understanding the biosynthesis pathway of PFGs, exploring genes related to PFGs content, and elucidating the regulatory mechanisms of PFGs biosynthesis pathway is fundamental and essential for improving the quality of E. brevicornu. Here, we provide a comprehensive review of the research on structural and transcriptional factor genes related to the biosynthesis of PFGs, which not only contributes to unravel the regulatory mechanisms related to PFGs content, but also lay a foundation for research on molecular breeding and the synthetic biology in Epimedium plants.

Abiotic stresses such as drought, extreme temperatures, salinity, and heavy metals can cause a decrease in plant yield and quality. miRNAs are a class of endogenous non-coding small RNA with a length of about 20-24 nucleotides. By forming miRNA-mediated silencing complexes (RISCs), they cleave target mRNAs and inhibit the translation of target genes, negatively regulating eukaryotic gene expression at the post-transcriptional level. The development of high-throughput sequencing technology has enabled the identification and characterization of a large number of miRNAs that respond to abiotic stress in various plant species. Under abiotic stress, plant miRNAs bind to their target genes, forming a large gene regulatory network that controls various life activities, including growth and development, nutrient absorption and distribution, signal transduction, and oxidative stress, thereby improving plant stress resistance. Understanding the function and regulatory mechanisms of miRNAs is crucial for crop improvement and stress-resistant breeding through genetic engineering. This review summarized the advances in the biosynthesis and mechanisms of plant miRNAs in recent years, with emphasis on the identification and function of miRNAs involved in regulating plant response to abiotic stress. Possible future research directions in this field are also discussed.

Global warming is now a major trend, in which temperature stress due to abnormal climate occurs frequently, posing a great challenge to the high-yield and stable agricultural production. The circadian clock, an endogenous, heritable timekeeping mechanism, endows plants with the ability to anticipate and respond rapidly to cyclic changes in external factors, which ensures that physiological and biochemical pathways are synchronized with the environment and greatly enhances plant’s ability to survive and reproduce. The temperature responses and temperature compensation are not only related to the key scientific issue of “synchronization” of the circadian clock with environmental signals, but also to the application of crop adaptation to temperature stress in agriculture. Temperature compensation refers to the fact that within a broad range of physiological temperatures, through transcriptional and post-transcriptional architecture, the clock can essentially maintain the circadian period length unchanged, ensuring that the timekeeping mechanism operates accurately. Light, temperature and humidity are closely coupled in the natural environment, and they act as timing factors, transmitting external cues to the core oscillators via the input pathway, which affects almost all processes of plant growth and development. In this review, we summarize the historical research of temperature response and compensation mechanism of plant circadian clocks, and describe the latest research progress, and also look forward to its application in crop genetic breeding and field management. We seek to provide new idea and solution to the problem of temperature stress adaptation in crops.

The plant hormone auxin regulates many processes of plant growth and development, including embryonic development, organogenesis, and tropism, as well as environmental adaptation. To perform these functions, auxin mainly depends on the typical TIR1/AFB-auxin-Aux/IAA-ARF signaling pathway. In this pathway, the canonical Aux/IAA proteins composed of four conserved domains play a key role in auxin signaling as co-receptor with TIR1/AFB. Recently, some non-canonical Aux/IAA proteins lacking conserved domain(s) were also found to be involved in the auxin response. This review focuses on the research advances of non-canonical Aux/IAA proteins on their structure, biological function and roles in auxin signal transduction, and discusses the future research directions of these proteins.

Heavy metal-associated isoprenylated plant proteins (HIPPs) are a class of proteins characterized by the presence of heavy metal-associated domains (HMA) and C-terminal isoprenylation motifs in plants. Here, we introduce the structural characteristics of the HIPPs, review their potential roles in plant development and response to environmental changes (including biotic and abiotic stresses) as well as discuss their working mechanisms underlying their participation in heavy-metal homeostasis and detoxification. This comprehensive overview aims to provide valuable insights for future research on the HIPP family across diverse plant species.

The survive of plants is mainly attributed to their complex and sophisticated immune defense system that has evolved through the process of battles against pathogens. The cloning and functional research of disease resistance (R) genes have greatly facilitated people’s understanding of plant immune defense systems. Executor (E) genes, as a new type of plant disease resistance genes, has unique disease resistance characteristics and is also an important resource for disease resistance genes, making it a research hotspot in the field of plant immunity. In recent years, significant progress has been made in the cloning and functional mechanism research of E genes, however, there is no Chinese review about them. This article comprehensively summarizes the protein sequence characteristics, interaction mechanisms with pathogens, biological functions and breeding applications of the E genes, aiming to provide important references for understanding the molecular mechanisms of plant-pathogen interactions and disease-resistant breeding of crops.