Promoter is an indispensable regulatory sequence for driving gene expression in higher plants. Different promoter elements cause diverse driving efficiency and space-time specificity. Identifying the structures and functions of promoter elements contributes to a better understanding of the growth and development, multi-stress tolerance, and evolution of plants. With the development of high-throughput sequencing technologies, artificial intelligence and synthetic biology, the techniques for identifying cis-acting elements and constructing artificial biological components that meet the design requirements has gradually emerged, providing a foundation for efficient, precise, and diverse gene regulation in molecular breeding. This article targets on the application of promoter reconstruction in molecular design, introducing the detailed structure and function of higher plant promoters and the methods of cis-acting element identification. We summarized a total of 174 inducible, tissue-specific promoter elements in 27 categories and their applications on artificial modification and synthesis. At the end, we proposed the future directions and methods of the promoter designs. This review will be helpful for the further functional analyses of promoters in higher plants and their applications on molecular design breeding.

In 2024, the numbers of original research articles published by Chinese plant scientists in mainstream plant science journals increased significantly compared with that in 2023, and important advances have been made in the fields of plant hormone regulation, pathology, synthetic biology, stress resistance mechanism, phylogenetics and genomics. Among them, “Characterization and Heterologous Reconstitution of Taxus Biosynthetic Enzymes Leading to Baccatin III”, and “Reciprocal Conversion Between Annual and Polycarpic Perennial Flowering Behavior in the Brassicaceae” were selected as two of the “Top Ten Advances in Life Sciences in China” in 2024. Here we summarize the achievements of plant science research in China in 2024, by briefly introducing 50 representative important research advances, so as to help readers understand the trend of plant science development in China, and evaluate future research direction to meet major national strategic needs.

The external environment severely affects growth and development of plants. In recent years, the increasing extreme climates have posed a serious threat to the growth and development of plants. Understanding the regulatory mechanisms of plant stress tolerance is of great significance for ensuring the survival and development of plants (especially economic crops) and their yields. Alternative splicing is an important post-transcriptional regulatory mechanism and plays an important role in the diversity of plant gene functions and stress resistance. At present, a variety of alternative splicing variants of stress-resistant related genes have been identified in different plant species, and several regulatory mechanisms involved in alternative splicing have been elucidated, effectively advancing the relevant theoretical basis for plant stress resistance in plants. This paper reviews the types and splicing mechanisms of alternative splicing in plants, highlights the recent progress in alternative splicing regulation of plant responses to abiotic stress, and provides a prospect for the future direction of research on alternative splicing in plants.

Maize (Zea mays) is the main crop in China, and drought is a primary abiotic stress during its growth, resulting in direct reduction in grain yield and quality, thereby posing a threat to food security within the global climate context. At present, global climate change leads to extreme weather events, which aggravates the adverse effects on yield. Therefore, it is imperative to identify drought-resistant germplasm resources, elucidate the molecular mechanisms of drought stress response, and breed drought-resistant varieties. Here, we review recent advances in the genetic dissection of drought resistance in maize using methods such as genome-wide association study, quantitative trait locus gene cloning and multi-omics analysis. Additionally, we introduce potential strategies for genetic improvement of drought resistance by leveraging the identified genetic resources while discussing future perspectives within this research area.

Strigolactone (SL) is a novel plant hormone that regulates important growth and developmental processes such as plant branching. In rice, the SL receptor D14 perceives SL signals, binds with the F-box protein D3, and recruits the transcriptional repressor D53, inducing the ubiquitination and degradation of D53, thereby triggering signal transduction and inhibiting tillering. A recent study discovered that nitrogen limitation induces SL biosynthesis in rice to activate the receptor D14, triggering SL signal transduction. Concurrently, nitrogen limitation also induces phosphorylation of the N-terminal disordered region (NTD) of D14, reducing the ubiquitination and degradation of receptor D14, thereby further enhancing SL perception. Through these two synergistic mechanisms, nitrogen limitation stimulates SL signal transduction, strongly inhibiting tillering and enabling rice to adapt to low nitrogen stress conditions. The study also found that the D14-D3 interaction induced by SL promotes the ubiquitination and degradation of D14, thereby mediating the termination of SL signal perception. These significant findings elucidate the mechanisms of activation and termination of SL perception in rice, revealing the crucial regulatory role of SL signals in controlling rice tillering under low nitrogen stress. This would provide key insights into plant adaptation to nutrient scarcity and guide the precise improvement of crop architecture and molecular breeding of rice for reduced fertilizer use and increased yield.

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.

Maize (Zea mays) is a staple crop worldwide, serving as a major source for food, feedstock, and industrial materials. Flowering time, a key agronomic trait determining diverse environmental adaptation and yield potential of crops, is determined by two developmental transitions (namely vegetative phase change and floral transition), and complicatedly regulated by internal factors (such as genetic factors and plant hormones) and external environmental factors. Given the importance of flowering time, in this review, we summarize the research progresses on the regulation of the two-phase transitions in maize, mainly focusing on the aspects of structural basis, physiological basis, genetic basis and molecular mechanisms. We also highlight the contribution of key flowering regulators to geographical adaptation of maize, and discuss future research directions on flowering and application in breeding, aiming to deepen our understanding of the genetic regulation of maize flowering and provide a theoretical basis for genetic improvement of maize cultivars adapting to diverse environmental conditions.

INTRODUCTION: Molecular data is one of the most important bases for many biological studies, including phylogeny, ecology, and biogeography etc. Incomplete sampling may lead to biased results and inadequate conclusions. However, few studies have evaluated current state of sampling density for sequencing DNA data comprehensively. Plastid DNA sequences have been applied in scientific studies of plants extensively due to their easy accessibility, uniparental inheritance, and moderate rate of mutation. Therefore, it is essential to investigate the current state of sampling density for sequencing plastid DNA data in species and geographic area for researchers to better utilize it.

RATIONALE: The GenBank is the biggest and most commonly used database of sequencing DNA data. The data gap of plastid DNA in species and geographic area for vascular plants was investigated based on the GenBank database in this study. Firstly, the plastid DNA data of vascular plant species were downloaded from the GenBank database and cleaned. Secondly, species names were standardized according to the World Checklist of Vascular Plants (WCVP) database. Thirdly, to evaluate the current state of sampling density for plastid DNA data of vascular plants, we counted the number of species with plastid DNA sequenced and the proportion of missing data of lineages representing orders and families. We also mapped the proportion of missing data in each region to evaluate the current state of sampling density of plastid DNA data geographically. To further investigate the potential influencing factors of the plastid DNA data gap, Spearman’s correlations between the proportion of missing data and species diversity among major groups of vascular plants or regions were calculated.

RESULTS: Only 33.75% vascular plant species have at least one record of DNA in GenBank, covering 139 005 vascular plant species (angiosperms: 131 220 species, gymnosperms: 1 154 species, and pteridophytes: 6 631 species). For data gap in species, sequenced species were unevenly sampled among lineages, with the proportion of missing data generally correlated with species richness within the lineages. The top three orders of the highest proportion of missing data were Paracryphiales, Piperales, and Dilleniales, and the top three families were Triuridaceae, Pentaphragmataceae, and Xyridaceae. For data gap in geographic area, the proportion of missing data of plastid DNA of vascular plant species showed a trend of latitudinal gradient, with the degree of missing data decreasing from the equator to the poles. Regions with high proportion of missing data usually possess high biodiversity, including many biodiversity hotspots. In addition, endemic species were generally with the high proportion of missing data in the majority of regions.

CONCLUSION:Our research evaluated the current state of sampling density for plastid DNA data in species and geographic area comprehensively. Our results suggested that about 140 000 vascular plant species have been sequenced for the plastid DNAs. However, there are still large data gaps for the plastid DNA of vascular plants in the following three aspects: (1) Only 1/3 vascular plant species have been sequenced; (2) Ratios of species with plastid DNA sequenced are uneven among lineages; (3) The proportion of missing data decreases from the equator to the poles, with more deficiencies in biodiversity hotspots and endemic species. Based on the results of this study, we propose to give priority to collection and sequencing of vascular plants for groups with high proportion of missing data and regions with high biodiversity, particularly for the endemic species. Our research points out the direction of filling plastid DNA data gap and will be beneficial to biodiversity protection.

INTRODUCTION DNA methylation is one of the important epigenetic modifications involved in the regulation of plant genome stability, development and stress responses. DNA methylation introduces methylation groups into DNA molecules, thereby altering the activity of DNA segments. DNA methylation is catalyzed by DNA methyltransferase, a process by which methyl groups formed from S-adenosyl-L-methionine are transferred via covalent links to specific locations in the DNA sequence to form N4-methylcytosine, 5-methylcytosine, N6-methyladenine, or 7-methylguanine. However, there are few reports about the effects of DNA methyltransferase on leaf variegation formation and stress response of Begonia.


RATIONALE  Studies have shown that DNA methylation is involved in regulating the formation of leaf color, flower color and leaf variegation, as well as responses to stresses and hormones. As an endemic species of Begonia, Begonia masoniana has unique and beautiful leaf markings, pink, dark green and light green in different developmental stages. It has high ornamental value and is an excellent foliage plant. Therefore, based on the genomic data, this study conducted genome-wide identification and expression pattern analysis of DNA methyltransferase genes, aiming to explore the genetic resources that regulate the formation of leaf variegation.


RESULTS  To investigate whether DNA methyltransferase is involved in the regulation of leaf variegation formation and stress response in B. masoniana, bioinformatics analysis was used to identify the genes encoding DNA methyltransferase. Five genes were obtained from the genome of B. masoniana. According to the protein structural characteristics, their encoded proteins were divided into three categories including CMT, MET and DRM. The sequence length and intron number of these genes were significantly categorized into different subgroups, but their structure and conserved domains in the same subgroup were highly conserved. In addition, all the encoded proteins were predicted to locate in the nucleus. The promoters of these genes contain a large number of cis-acting elements such as light response, MYB binding, and plant hormone response elements. Analysis of hormone response patterns showed that the gene expression of CMT3 was significantly decreased under GA, SA and NAA, and the gene expression of CMT2 was significantly decreased under MeJA and NAA, while MET-type and DRM-type genes displayed significantly increased expression under GA and ABA treatments. In addition, tissue specific analysis showed that the expression levels of BmaCMT2-5 and BmaDRM2-2 in leaves were significantly higher than those of other tissues, while the expressions of these two genes and BmaMET1-15 in red part of leaves were significantly higher than that of green part, implying that these three genes may be involved in regulating the formation of leaf variegation.


CONCLUSION The structure and function of DNA methyltransferase genes vary significantly across different categories in B. masoniana. However, within each category, members display high conservation in gene structure, conserved domains, motifs, and evolutionary patterns. These genes are likely to play crucial roles in the growth and development of diverse tissues and organs, as well as in responding to various biological and abiotic stresses. Moreover, based on the differential expression patterns of BmaCMT2-5, BmaMET1-15, and BmaDRM2-2 genes between leaf variegation and non-variegation areas, coupled with the abundance of MYB regulatory elements related to anthocyanin synthesis in their promoters, it is hypothesized that these genes may contribute to the formation of leaf variegation. As the current understanding of the functional roles of these methyltransferase genes is largely speculative, future research should focus on their functional validation, which will involve utilizing reverse genetics techniques coupled with phenotypic observations to determine their involvement in specific biological processes. Additionally, physiological, biochemical, and molecular biological methods should be employed to elucidate the precise mechanisms of their actions.

Relative expression levels of DNA methyltransferase genes in different tissues and organs of Begonia masoniana

Climate change-induced global average temperature rise poses a severe threat to food production, in which maize, one of the three major global staple crops, is particularly susceptible to high temperatures. High temperatures significantly impact maize at various stages of its growth and development, especially during the reproductive growth stage, which can drastically reduce maize yields. Here we summarize the effects of high temperatures on maize at different growth stages, including germination, seedling, late vegetative growth, flowering, and grain-filling stages. We also review the main molecular mechanisms by which maize responds to heat stress, including heat shock and unfolded protein responses. Furthermore, we summarize the latest advances in heat-tolerant maize breeding in China. A batch of heat-tolerant hybrids and inbred lines have been identified through artificial high-temperature treatments and open field trials under natural high-temperature. In addition, we proposed important future research strategies in developing heat-tolerance maize, including new technological methods such as phenomics, genome-wide association studies, and genomic selection-based breeding, combined with intelligent agricultural management measures. We aim to cultivate maize varieties with high heat tolerance to cope with the high-temperature challenges brought about by climate change, thereby ensuring global food security.

Seed desiccation is a key physiological process during plant seed maturation, directly affecting seed moisture content, storage, and quality. In agricultural practice, the kernel dehydration rate (KDR) is a critical determinant of seed water content at harvest and seed quality for mechanical harvesting. Over the past decades, although physiological changes in transcriptome and hormone levels have been linked to seed dehydration, little progress for underlying mechanisms has been achieved. A recent study identified a QTL located in a non-coding region, named qKDR1, which regulates the dehydration rate during maize seed maturation. By recruiting the transcription factors ZmMYBST1 and ZmMYBR43, it suppresses the transcription of the micropeptide-encoding gene RPG upstream of qKDR1, leading to reduced expression of RPG. The encoded micropeptide, microRPG1, regulates the KDR through the ethylene signaling pathway, highlighting its potential in crop breeding and agricultural practices. This study advances our understanding of the molecular mechanisms underlying seed desiccation and provides theoretical support for breeding crops with faster KDR and improved storage qualities.

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.

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.

INTRODUCTION: The cell wall-associated kinase (WAK) family has annotated approximately 130 WAK genes in the genome of rice (Oryza sativa), which play an important role in rice growth and development and stress responses.

RATIONALE: Here, we investigated the regulation and physiological mechanism of OsWAK16, an encoding gene of the cell wall-associated kinase WAK16-RLK, on rice seed vigor and anti-aging ability.

 
RESULTS: The results showed that before and after artificial aging, the seed vigor of OsWAK16 knock out mutants and overexpression lines was significantly lower and higher than that of wild-type seeds, respectively, indicating that OsWAK16 positively regulates the anti-aging ability of seeds. Physiological and biochemical analyses indicated that compared with wild-type seeds before and after artificial aging treatment, malondialdehyde (MDA) content and electrical conductivity (EC) of seed soaking solution of OsWAK16 knock out mutant seeds were significantly increased, while antioxidant enzyme activity was significantly decreased. The reverse was true in overexpression seeds. In addition, the differential expression of OsWAK16 in three types of seeds, whether artificially aged or not, also caused synergistic changes in the expression of other seed vigor-related genes OsPER1A, OsbZIP23, OsPIMT1, OsSdr4, OsMSRB5 and OsHSP18.2.

 
CONCLUSION: Therefore, it is speculated that OsWAK16 may work synergistically with other seed vigor-related genes to clear reactive oxygen species in cells, thereby regulating seed vigor and anti-aging capacity.

Gene editing technology has become an important tool in crop breeding. Maize, one of the globally most important food crops, has been shown with great potential in the use of gene editing technology in genome research and breeding. In this paper, we reviewed the recent progress and applications of gene editing technology in maize research, with a focus on the latest achievements in maize genome editing by CRISPR/Cas. Firstly, we introduced the basic principles and types of gene editing technology, particularly the working mechanism of the CRISPR/Cas systems, and its application advantages in maize. Secondly, we summarized the research progress of gene editing technology in maize breeding, from basic genome editing to the editing of complex multi-gene regulation, aiming at the improvement of key traits such as yield, grain quality, and stress resistance. Finally, the outstanding research work in maize gene editing in China is presented and the existing issues of gene editing technology in maize breeding are discussed, along with an outlook on future development trends.

Plants encounter various abiotic stresses throughout their lifecycle, including heat, drought, and salt stress, all of which have diverse impacts on their growth and development. Global warming has exacerbated the impact of heat stress on crops such as maize, potentially leading to growth retardation and reduced reproductive capacity. As an important staple crop, the yield and quality of maize are severely compromised by heat stress. Plants respond to heat stress through complex molecular mechanisms involving multiple signal transduction pathways and the regulation of gene expression. It is crucial to use advanced techniques such as genetics, genomics, multi-omics analysis, and high-throughput phenotyping to extensively explore and analyze the genes and loci associated to abiotic stress tolerance, including heat stress, in the maize genome. These studies not only deepen our understanding of the biological mechanisms underlying maize stress tolerance but also provide valuable molecular markers and candidate gene resources for breeders to accelerate the development of new maize varieties.

Cryptochromes (CRYs) are blue light receptors that regulate various plant responses. CRYs exist in the dark as an inactive monomer, which absorbs photons and undergo conformational changes and oligomerization. Light alters the affinity between CRYs and interacting proteins, thereby regulating the transcription or stability of photoresponsive proteins to modulate plant growth and development. A recent study has discovered a sophisticated mechanism of CRY2 function, which is not only ‘activated’ by blue light but also by dark signals, thus constructing a more energy-efficient mode of light and dark signal dependent photoreceptor signaling. The authors found that CRY2 can inhibit cell division in root meristematic tissue even in the dark, regulate root elongation and growth, and control the expression of a large number of genes. FL1 and FL3 bind to the chromatin of cell division genes to promote their transcription. It is interesting that only the CRY2 monomer in the dark interacts with FL1/FL3, thereby inhibiting FL1/FL3 to promote root elongation, while blue light releases this inhibitory effect. This discovery reshapes people’s understanding of light receptors, and provides a new perspective for understanding plant perception and response to different signals to regulate growth and adaptability. Moreover, it is highly enlightening for a deeper understanding of sophisticated gene regulation.

INTRODUCTION Tomato (Solanum lycopersicum), a significant warm-season and water-dependent vegetable crop, is extensively cultivated worldwide. Whether grown in open fields or protected environments, tomatoes frequently encounter various environmental stresses, including drought and low temperatures, which significantly impact their yield and quality. Transcription factors play a pivotal role in plant stress responses by modulating the expression of specific target genes, thereby transmitting perceived stress signals downstream. WRKY transcription factors in tomatoes are known to regulate responses to multiple abiotic stresses. However, the specific role of the tomato SlWRKY45 in abiotic stress responses remains unclear.

RATIONALE Studies have demonstrated that WRKY transcription factors play a crucial regulatory role in plant responses to abiotic stress. As an important economic vegetable crop, tomato is susceptible to various environmental stresses during its growth and development. By genetically overexpressing SlWRKY45 in tomato and investigating its function under low-temperature and drought stress conditions, the findings can provide a theoretical foundation for understanding the complex regulatory mechanisms of WRKY transcription factors. Additionally, this research offers valuable candidate genes for breeding stress-resistant tomato varieties.

RESULTS Expression analysis revealed that low-temperature, drought, and abscisic acid (ABA) treatments significantly induced the expression of SlWRKY45. Overexpression of SlWRKY45 enhanced the resistance of tomato plants to drought and low-temperature stresses. Under drought and low-temperature conditions, the photosynthetic indices, antioxidant enzyme activities, and proline (Pro) contents in SlWRKY45 overexpression lines were significantly higher than those in wild-type (WT) plants. Conversely, the accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA) levels in SlWRKY45-OE plants was significantly lower than in WT plants under the same stress conditions. Transcriptome data analysis indicated that SlWRKY45 regulates tomato's response to low-temperature stress primarily by influencing antioxidant enzyme activities and stress response pathways. Dual-luciferase assays demonstrated that SlWRKY45 could directly activate the expression of SlPOD1. Furthermore, the interaction between SlWRKY45 and SlWRKY46 was confirmed through yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays.

CONCLUSION Our findings demonstrate that SlWRKY45 positively regulates drought resistance and low-temperature tolerance in tomato. Additionally, SlWRKY45 can interact with SlWRKY46 and directly activate the expression of SlPOD1. These results offer valuable insights for further research into the regulatory mechanisms underlying abiotic stress responses and provide potential gene resources for genetic improvement through molecular breeding.

Phenotypes of SlWRKY45-overexpressing and wild-type plants under drought and low-temperature treatments

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.

Maize (Zea mays) is the major grain crop with the largest planting area and the highest total yield in China, and it is also a model of heterosis utilization. However, compared with developed countries, China is still facing several outstanding problems in maize production, such as low average yield, lack of breakthrough varieties and high cost of hybrid seed production. The main solution to these problems is the application of male-sterile lines with better heterosis utilization efficiency and thus increase the yield per unit area of maize. In this review, we summarize the latest advances of male sterility research in maize, including its classification, gene cloning and functional analysis, molecular regulatory network construction, and discuss the strategies of creating novel male-sterility systems and their potential/future application in maize breeding. This review provides guidelines for the male-sterility based/assisted hybrid breeding and seed production in maize.

With the sharp change of the global climate, the ecological environment for plant is becoming increasingly harsh, therefore the molecular mechanisms underlying how circadian synergistically interacts with light or temperature receptors to transmit environmental signals and rhythmically regulate various growth and development process received widespread attention. As an endogenous timer of plants, the core oscillator of circadian clock is composed of multiple coupled transcriptional-translational feedback loops (TTFL), and it is modified from transcription, post-transcription, translation, post-translation to epigenetic levels. These multi-precise regulatory mechanisms ensure that the circadian clock can be synchronized and reset by external signals, so that the endogenous rhythm matches with external cycles, thereby endowing plants with the ability to optimize resource utilization and tend towards the optimal growth, which also has an important significance for guiding the genetic improvement and domestication of crops. In this review, we summarized the multi-level of regulatory mechanisms of core oscillator as well as the molecular function of circadian homologous genes in crops, thoroughly described the interaction network between the circadian clock and the light and temperature signal pathways and give prospects for molecular breeding based on the opinion, which provides new ideas for expanding the environmental adaptability and optimizing agronomic traits of crops.

INTRODUCTION Trehalose-6-phosphate synthase (TPS) is a key enzyme involved in the synthesis of trehalose and has been reported to participate in regulating photosynthesis, carbohydrate metabolism, growth and development, and stress responses in various species. Currently, reports on TPS genes in soybean are scarce.

RATIONALE  TPS is a stable non-reducing disaccharide, whose synthesis, decomposition and regulation not only provide energy for plant, but also play an important role in plant growth and development and stress tolerance. The in-depth study of soybean TPS genes and its relationships with salt stress is of great significance in elucidating the molecular mechanism of soybean salt tolerance and improving soybean yield.

RESULTS This study identified 20 soybean TPS genes and their associated 10 conserved protein motifs in the soybean genome. Molecular analysis of the promoter elements revealed that the TPS gene promoters are rich in stress-responsive elements. After salt stress treatment, the expression of 17 TPS genes changed, with 12 genes up-regulated and 5 genes down-regulated. Haplotype and selection analyses revealed two major allelic variations in TPS8, TPS13, TPS15, TPS17, and TPS18. Notably, variants carrying TPS15^H2, TPS13^H2, TPS17^H2, and TPS18^H2 were significantly enriched in improved cultivars that underwent strong artificial selection.

CONCLUSION This study reveals the molecular characteristics of the soybean TPS gene family, their expression patterns under salt stress, and their evolutionary history, providing a theoretical basis and genetic material for further elucidating the functions of soybean TPS genes and breeding salt-tolerant soybean varieties.

TPS genes were subjected to intense artificial selection. The natural variations of TPS8, TPS13, TPS15, TPS17, and TPS18 have been subjected to strong artificial selection during soybean domestication and improvement, with the variants carrying TPS15^H2, TPS13^H2, TPS17^H2, and TPS18^H2 being heavily enriched in improved cultivars.

Non-coding RNA (ncRNA) is a class of RNA molecules that do not have the ability of protein coding but have a variety of biological functions, and widely exist in various organisms. With the continuous improvement of high-throughput sequencing technology, a large number of ncRNAs have been identified, and their functions and mechanisms of action are gradually being elucidated. A large number of studies have shown that ncRNAs play an important role in plant growth, development and response to stress. Although there are many reviews on the regulation of plant growth, development and stress response by a certain class of ncRNAs, it still lacks systematic and comprehensive summaries for all ncRNAs. This review first briefly introduced the classification and characterization of non-coding RNAs, followed by a focus on their roles in various stages of plant growth and development, such as seed dormancy and germination, root and leaf growth and development, flower and fruit development, fruit ripening. Furthermore, we summarized the functions and mechanisms of ncRNAs in response to stress. This review provides some theoretical references for improving varieties and improving the yield and quality of agricultural and forestry production.

Rice (Oryza sativa) is one of the most important food crops in the world. Improving its antioxidant ability and stress resistance is an important way to ensure high and stable yields. In this study, we used the indica rice HZ and the japonica rice Nekken2 as parents and the 120 recombinant inbred line population constructed from them as experimental materials to determine the hydroxyl radical scavenging rate, total phenol content, flavonoid content, and anthocyanin content in sword leaves, glume shells and grains of parents and their progeny at three stages: the tillering stage, the grain filling stage and the maturity stage. Additionally, a total of 62 QTLs related to rice antioxidant damage were identified on the basis of the constructed high-density genetic map for QTL mapping, with an LOD value of up to 4.36. A quantitative analysis of candidate genes related to antioxidant damage ability in these regions revealed that thirteen candidate genes, including LOC_Os06g01850, LOC_Os12g07820, LOC_Os12g07830, and LOC_Os03g60509 were significantly differentially expressed between the two parents at different growth stages. A multitude of QTLs associated with antioxidant damage resistance in rice were identified, providing a foundation for further mapping and cloning of related genes and the development of new rice varieties with increased resistance and nutritional value.

Functional gene expression is a basic life process that connects coding information of a gene to protein products. The level of gene expression is considered as a quantitative trait between genotype and phenotype and plays an important role in plants response to climatic and environmental changes. First, this review systematically comments on regulatory elements of gene expression in plant species and empirical evidence, including the effects of transcription factors and small RNAs on gene expression regulation. Secondly, this review discusses the eQTLs mapping for regulatory elements of gene expression through gene expression-based GWAS analysis and the limitations of this method. This review then analyzes the intraspecific variation of gene expression in theory under the processes of mutation, drift and selection and the testing methods. The review also analyzes the interspecific evolution of gene expression under the mutation and drift processes or under the phylogeny-based drift-selection processes, and the testing methods. Finally, the review discusses the regulation of gene expression by plant mating system. Selfing reduces effective population size, mutation rate, recombination rate and the competition from exogenous pollen, and changes the efficacy of natural selection in gametophytic and sporophytic phases. Selfing regulates intraspecific gene expression variation and interspecific gene expression evolution. The whole review comprehensively comments on theoretical and practical research progress and existing questions, which aids in our deep understanding of plant gene expression regulation and evolution mechanisms.

The phytochrome gene family play a critical role in mediating photothermal responses during Arabidopsis thaliana seed germination. Here we evaluated the germination rates of phyA, phyB, phyC, phyD, and phyE single mutants under 12 different light and temperature regimes, using wild-type (Col-0) seeds as controls. Our results indicate that phyA mutant seeds germinate under red light but are inhibited under far-red light and high temperatures (35°C). phyB mutant seeds germinate at low (15°C) and moderate (25°C) temperatures under both white light and far-red light, but not at high temperatures (35°C). phyC mutant seeds show consistent germination across all conditions except under white light at high temperature (35°C). Both phyD and phyE mutant seeds germinate at low (15°C) and moderate (25°C) temperatures, and under red and white light, but not at high (35°C) temperature, darkness or far-red light. These observations suggest that phyB, phyC, and phyD mutants may have impaired integration of light and temperature cues, whereas phyA and phyE mutants appear to maintain this integrative function. Overall, our findings demonstrate that mutations in phytochrome genes can modify seed germination adaptability to varying environmental conditions.

In this study, the seed embryos of Pyrus calleryana cv. ‘Cleveland’ were used as materials to systematically study the sterilization of seed embryo explants, callus induction, adventitious bud proliferation and rooting medium. The results showed that the germination rate of young embryos stored at 4°C for 21 d was the highest (67.23%) The suitable sterilization treatment of seed embryo explants was 75% alcohol (30 s)+10% H₂O₂ (10 min)+0.1% HgCl₂ (14 min)_. The most suitable medium for seed embryo germination was 1/2MS+4.0 mg·L^-1 6-BA+0.5 mg·L^-1 NAA, and the germination rate was 89.67%. The optimum culture medium for callus induction was 1/2MS+1.0 mg·L^-1 IBA+1.0 mg·L^-1 6-BA, and the callus induction rate was 93.33%. The best differentiation medium was 1/2MS+0.2 mg·L^-1 IBA+2.0 mg·L^-1 6-BA, and the regeneration frequency was 87.44%. Best transgenerational proliferation medium was 1/2MS+1.5 mg·L^-1 6-BA+0.1 mg·L^-1 IBA, and the proliferation rate was 100%. The most suitable medium for root formation was 1/2MS+ 20 g·L^-1 sucrose+1.0 g·L^-1 active carbon+1.5 mg·L^-1 IBA+0.05 mg·L^-1 NAA, and the rooting rate was 82.63%. In summary, the seed embryo regeneration system of P. calleryang cv. ‘Cleveland’ was established, which provides scientific basis and guidan-ce for the efficient reproduction of high-quality pear germplasm resources.

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.

To establish a tissue culture regeneration system for cultivated Chinese yam (Dioscorea polystachya), the effects of different concentrations of plant growth regulators, and stem segments on axillary bud induction and plant regeneration were investigated with different concentrations of plant growth regulators, media types, and shoot tips and stem segments at four different positions under the shoot tip as explants. The results revealed that MS+1.0 mg∙L^-1 6-BA+0.5 mg∙L^-1 KT hormone ratio and 12-20 cm stem segment under the stem tip were the best formulas for the induction of adventitious buds in D. polystachya, and the induction rate reached 90.0%. In the subculture, the optimal concentration was MS+0.5 mg∙L^-1 6-BA+0.05 mg∙L^-1 NAA+0.1 mg∙L^-1 KT, and the proliferation coefficient increased with increasing of 6-BA within a certain range when the low concentration of NAA was constant. With the same concentration of exogenous hormones, DKW medium was significantly better than the conventional 1/2MS medium, and the rooting rate is significantly improved, reaching 92.86%. Adding 1 mg PVP (polyvinylpyrrolidone) and increasing the number of transfers can significantly reduce browning. This study effectively solved the problem of optimizing the explant position for the stable of in vitro propagation of cultivated yam germplasm resources, laying a good foundation for the large-scale production of their high-quality virus-free seedlings.

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.

A rapid propagation system via tissue culture for Rosa multiflora was established using the stem segments with buds of the current-year as the experimental material. The results showed that the best explants were stem segments with axillary buds. The best disinfection method was to soak the explants in 75% ethanol for 30 seconds, and then soak them in 10% sodium hypochlorite solution for 20 minutes. The survival rate can reach 96%. The optimal bud-induction medium was MS+1.0 mg∙L^-1 6-BA+0.01 mg∙L^-1 NAA+0.1 mg∙L^-1 GA₃. The budding rate can reach 98% after 30 days of cultivation. WPM was the best basal medium for the proliferation of sterile regenerated plantlets, and the proliferation coefficient was 2.87. The best medium for rooting was 1/2MS+1.0 mg∙L^-1 6-BA+0.1 mg∙L^-1 NAA, and the rooting rate can reach 93%. The transplanting survival rate of sterile regenerated plantlets was 98%. On this basis, the transient expression system of R. multiflora was established. The results showed that the optimal transformation conditions for transient expression were OD₆₀₀ of 0.8 for the bacterium culture medium, vacuum negative pressure of -0.10 MPa and vacuum suction twice for 15 minutes each time. The transient expression efficiency can reach 96%. The results of this study laid a foundation for the establishment of regeneration and genetic transformation system of R. multiflora, and also provided technical support for studying on the gene function of Rosa plants.

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.

Flow cytometry is a high-throughput technology that allows for the simultaneous and rapid detection of multiple physical and biological characteristics of individual particles. With the significant reduction in sequencing costs, flow cytometry is playing an increasingly prominent role in high-throughput sample acquisition for plant genomics. Taking rice and soybean as examples, this paper describes in detail the application of flow cytometry for fine sorting of plant cell nuclei and the subsequent ATAC-seq and RNA-seq experiments and analysis process, which provides a preferred tool for efficient mining of genes for agrobiological breeding. The key techniques and common problems in the experimental operation, such as the precautions for cell nuclei preparation, the balance between sorting purity and efficiency, and the debugging method for single-cell sorting, were also analyzed and suggested to provide references for the plant scientists in applying flow cytometry to carry out genomics research.

Leaf, as a photosynthetic organ of crops, its senescence process has an important impact on yield formation, but the relationship between leaf senescence and phyllosphere microorganisms has been less studied. In order to explore the impact of the senescence process of maize leaves on the phyllosphere bacterial community, this study used three maize varieties of different maturity time (early-maturation variety Heike Yu 17 (H17), mid-maturation variety Zhongdan 111 (Z111), and late-maturation variety Shen Yu 21 (S21) in Northeast China as the experimental materials, and the leaves of the ear position of the three maize varieties were sampled five times starting from the blooming stage of early- maturation varieties, and the physiological indexes of senescence were determined. And at the same time, the community composition of endogenous and exogenous bacteria in/on the leaves was determined based on high-throughput sequencing technology. The results showed that at the late reproductive stage, leaf water content, POD and SOD activities were significantly higher in the mid- and late-maturation varieties than in the early-maturation varieties. At the phylum level, Cyanobacteria were endemic to mid- and late-maturation cultivars; at the genus level, the relative abundance of the endogenous shared bacteria Sphingomonas, Methylobacterium, and Deinococcus in maize leaves decreased significantly at later stages of maturation (IV and V). The relative abundance of endogenous bacteria Streptomyces and exogenous bacteria P3OB-42 were significantly enriched in the late senescence period, with similar trends and significant differences in relative abundance among the three species. The relative abundance of endogenous and exogenous bacteria differed significantly, with the top 5 exogenous bacteria accounting for more than 60%, while for endogenous bacteria, the top 5 accounted for only more than 30%. Soluble sugar content, photosynthetic pigment content and SOD activity were significantly correlated with bacterial community structure and abundance. In conclusion, mid- and late-maturation varieties were effective in prolonging leaf greening period, maintaining late leaf physiological activity with delaying senescence. The effects of senescence on the composition and diversity of endogenous bacterial communities were significantly greater than those of exogenous bacteria, and there were significantly different genera among three maize varieties studied. Moreover, soluble sugar content, photosynthetic pigment content and SOD activity were the key factors affecting the phyllosphere bacterial communities as well as the dominant species.

Mitochondria and chloroplasts are semi-autonomous organelles harboring their own genomes. RNA editing is essential for the correct expression of organelle genes. The mostly identified RNA editing is cytidine (C)-to-uridine (U). Multiple editing factors have been reported to be involved in RNA C→U editing. The PPR-motifs array in PPR proteins specifically target editing sites, and the DYW domains in PPR-DYW proteins catalyze the deaminase in the C→U editing. This paper aims to review the recent advance of PPR proteins involved in RNA C→U editing, and to discuss the potential application value of synthetic PPR editing factors.

A large number of software applications for plant identification based on plant images have been developed in recent years. However, those applications are mostly used for identifying the common species countrywide, and thus cannot meet the needs of identifying region-specific vegetation types. In this study, we developed an artificial intelligence model for identifying the dominant plants in Hulunbeier and Xilinhot grassland in Inner Mongolia, based on the image datasets in the Plant Photo Bank of China. The Top5 accuracy of this model reaches 94.6% in the actual field identification tests. Our model provides a new method for the intelligent identification of the major plant species in a specific area.

INTRODUCTION:Plant growth regulators are natural or artificially synthesized chemical substances that play an important regulatory role in the growth and development of crops, and can enhance the resistance of plants to stress.

RATIONALE To study the effects of different plant growth regulators on the growth and development of wheat under salt-alkali stress, and to explore methods to increase crop yield in saline-alkali land, we conducted spraying experiments on wheat in saline-alkali soil in the Yellow River Delta Agricultural High-tech Industry Demonstration Zone from 2023 to 2024. The experiment was divided into four groups: a distilled water control group, a 0.5% alginate aligosaccharide group, a Plant Gold group, and a mixed group of 0.5% alginate aligosaccharide and Plant Gold. The wheat was sprayed on March 28, April 12, April 28, and May 12, 2024.

RESULTS: The results showed that after spraying alginate oligosaccharide and its mixture with Plant Gold, the number of grains per ear and the 100-grain weight of wheat significantly increased. In particular, the group that received the mixture of alginate oligosaccharide and Plant Gold achieved a theoretical yield of 1 174.5 kg·hm^-2 for wheat in saline-alkali soil, which was an increase of 14.4% and 46.9% compared to the groups treated with only alginate oligosaccharide and Plant Gold, respectively.

CONCLUSION: Therefore, the combined application of alginate oligosaccharide and Plant Gold can significantly enhance the adaptability of wheat in saline-alkali land, demonstrating its important application potential in wheat production in such environments.

After selecting 1 m × 1 m sample plots within the experimental block and conducting spray tests with different plant growth regulators, the theoretical yields of different groups showed different changes. Among them, the yield of the mixed spray group was significantly higher than that of the control group.

Due to the long flowering cycle, unpredictable flowering period and low seed setting rate of most bamboo plants, bamboo breeding has been a challenge in the research of bamboo plants. Polyploid breeding, as a common mean of plant breeding, is able to obtain progeny with excellent traits through artificial induction. In bamboo breeding, there are fewer studies on polyploid breeding. In this study, based on the existing regeneration system of Dendrocalamus asper, the embryonic calluses of D. asper were treated with colchicine using the liquid suspension method and the solid medium mixed culture method, respectively. The results showed that, based on the differentiation and browning rates of the calluses, the better results were obtained by treating the calluses with 50 mg∙L^-1 colchicine for 48-72 hours using the liquid suspension method. A total of 54 regenerated plants, including 7 control plants, and 16 chromosome doubled plants were successfully obtained from D. asper using flow cytometry to test all the regenerated plants. In terms of chromosomal doubling, treatment with 100 mg∙L^-1 colchicine for 48 h produced the highest number of chromosome-doubled plants with a polyploidy rate of 54.54%. Compared with 6-ploid plants, the 12-ploid plants presented larger and thicker leaves, and larger lower epidermal stomata, implying their superiority in stress tolerance physiology. This study provides an efficient polyploid breeding technique based on the in vitro indirect regeneration system of bamboo, and offers a new solution for breeding new polyploid germplasm of bamboo.

Cytoplasmic male sterility (CMS) is a maternal genetic trait widely found in higher plants. CMS is not only a favorable material for studying the interaction between cytoplasmic and nuclear genomes, but also a crucial foundation for plant heterosis utilization. Maize is one of the most successful example for the utilization of heterosis in crops, and CMS has become a powerful tool for hybrid production to utilize heterosis in maize. Therefore, the molecular mechanism of CMS in maize has always been a research hotspot. In this paper, CMS related genes and fertility restorer genes discovered in the three major types of CMS in maize were summarized, and the problems that needed to be solved in CMS-related research and development prospects in the application of CMS in maize were discussed. This review provided theoretical reference for better understanding of the molecular mechanism of CMS in plant and the application of CMS system for hybrid seed production in the utilization of heterosis in maize.

INTRODUCTION: The CPSF family (cleavage and polyadenylation specificity factor) is a crucial protein family that is responsible for polyadenylation signal recognition in mRNA precursors, cleavage and the addition of poly(A) tails to mRNAs in plants. This family plays crucial roles in the regulation of flowering time, the environmental response, and seed development. Currently, the function of the CPSF family genes in Brassica napus is unclear.

 
RATIONALE: To explore the function and expression patterns of the CPSF gene family, this study cloned BnaA02.CPSF6 from B. napus variety Zhongshuang No.11 and conducted bioinformatics analysis, subcellular localization, expression pattern, and functional characterization of the gene.

 
RESULTS: These results indicate that the coding region of the BnaA02.CPSF6 gene is 1 938 bp in length and encodes 646 amino acids without intron structures. Its promoter region contains multiple cis-acting elements involved in light responses and MYB binding sites. Additionally, there are six genes homologous to BnaA02.CPSF6 in B. napus. The BnaA02.CPSF6 gene expressed in the roots, stems, leaves, flowers and different developmental seeds of B. napus, especially significantly higher in 15-35 d developmental seeds, and its encoded protein was localized in the nucleus. The BnaA02.CPSF6 gene expression is upregulated under salt and drought stress. Under treatment with hormones such as ABA, IAA, GA₃, SA, and MeJA, the expression of BnaA02.CPSF6 gene is initially inhibited and then gradually recovers to normal levels. Under normal conditions, the overexpression of the BnaA02.CPSF6 gene in Arabidopsis thaliana results in an early bolting phenotype, along with a reduced number of rosette leaves.

CONCLUSION: In summary, the above results indicate that the BnaA02.CPSF6 is involved in abiotic stress responses, is regulated by phytohormones, and may also play a promoting role in flowering regulation.