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.

Functional gene expression is a basic life process that connects the 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 response to climatic and environmental changes. First, we systematically summarize regulatory elements of gene expression in plant species and empirical evidence, including the effects of transcription factors and small RNAs on gene expression regulation. Second, this review discusses the eQTL mapping for regulatory elements of gene expression through gene expression-based genome-wide association study (GWAS) and the limitations of this method. This review analyzes the intraspecific variation in gene expression in theory under the processes of mutation, drift and selection and the testing methods. This 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, this review discusses the regulation of gene expression by the plant mating system. Selfing reduces the effective population size, mutation rate, recombination rate and competition from exogenous pollen, and changes the efficacy of natural selection in the gametophytic and sporophytic phases. Selfing regulates intraspecific gene expression variation and interspecific gene expression evolution. This 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.

INTRODUCTION Chrysanthemum × morifolium is one of the ten most famous traditional flowers in China, and it has a rich variety of cultivars with diverse floral colour and shapes. However, varieties with blue floral colour have not been found in the natural chrysanthemum, therefore, breeding blue chrysanthemums has always been a goal pursued by researchers.

RATIONALE The total flavonoid extract of C. × morifolium ‘Wandai Fengguang’ could turn blue when adding appropriate concentration of Fe³⁺, and its living petal cells could also turn blue with the participation of Fe³⁺, which proved the feasibility of breeding blue chrysanthemums with Fe³⁺. Meanwhile, C. × morifolium ‘Wandai Fengguang’ can bloom both in summer and autumn, with early flowering and long flowering period, which is also an important material for the study of flowering period. Therefore, in order to cultivate blue chrysanthemums and achieve the targeted improvement of flowering period, it is particularly important to establish an efficient and stable regeneration and genetic transformation system for the C. × morifolium ‘Wandai Fengguang’. However, chrysanthemum has a long history of cultivation and complex genetic background, so the regeneration and genetic transformation system is not universal among different varieties.

RESULTS In this study, C. × morifolium ‘Wandai Fengguang’ was used as the experimental material to study the effects of different explant types with different combinations of plant growth regulators on its regeneration, and to investigate the effects of relevant factors on the efficiency of genetic transformation with the Agrobacterium-mediated genetic transformation method. The experimental results showed that the most suitable explants for the regeneration of C. × morifolium ‘Wandai Fengguang’ was the transverse thin cell layers (tTCLs), and the optimal culture medium was MS+1.5 mg∙L^-1 6-BA+0.6 mg∙L^-1 NAA. The highest differentiation rate was 70.06% and an adventitious bud coefficient was 3.37. The kanamycin selection pressures for the differentiation of the tTCLs and the adventitious bud rooting were 7.5 mg∙L^-1 and 5.0 mg∙L^-1, respectively. The optimal procedure for genetic transformation was pre-culture for 1 day, OD₆₀₀=0.8, treatment for 5 minutes, and co-culture in the dark for 3 days. Fifteen resistant plantlets were screened on kanamycin medium, and two positive plantlets were confirmed by PCR amplification, with a transformation efficiency of 13.33%.

CONCLUSION This study laid the foundation for the gene function analysis and targeted improvement molecular breeding of chrysanthemum by using this kind of unique variety resource, and provided reference for the establishment of regeneration and transformation system for other chrysanthemum varieties.

SWEETs are a recently discovered family of bidirectional sugar transporters that are widely present in all organisms. Their high substrate specificity for hexoses (such as glucose, fructose and galactose) and sucrose in different clades underlines their significance in regulating sugar signaling during various developmental and physiological processes in plants. This review primarily focuses on how SWEETs precisely respond to various biotic and abiotic stresses. We summarized systematically the regulatory mechanisms of SWEETs in response to environmental stresses at both the transcriptional level and the post-translational level and in multiple signal transduction pathways. This review aims to provide a novel perspective and deeper understanding of the complex biological functions and regulating mechanisms of SWEET transporters, and provides valuable information for future research on plant stress resistance and molecular breeding crops with high yield and disease resistance.

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.

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.

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.

Iron-sulfur [Fe-S] clusters, which act as cofactors for iron-sulfur proteins, are ubiquitously implicated in a diverse array of biological processes, such as photosynthesis, respiration, electron transport, and the biosynthesis of essential vitamins and cofactors. Their intracellular biogenesis is modulated by a suite of proteins that catalyze and regulate the process, with compartmentalization occurring within discrete subcellular compartments. Mitochondria, as the central organelles for cellular energy metabolism, harbor numerous key metabolic enzymes that are iron-sulfur proteins, necessitating the provision of iron-sulfur clusters by the mitochondrial assembly machinery, the iron-sulfur cluster (ISC). Advancements in research, particularly from bacteria and yeast systems, have facilitated significant strides in the identification and functional characterization of pivotal catalytic and regulatory proteins within the plant mitochondrial ISC system. Additionally, considerable progress has been made in the research of the role in iron-sulfur clusters in the plant growth and development. The elucidation of plant-specific components within the iron-sulfur cluster synthesis machinery and the mechanisms by which this system responds to environmental stress are areas of growing interest. This manuscript provides a comprehensive review of the current state of research on the mechanism of iron-sulfur cluster synthesis in plants, with a particular focus on the mitochondrial ISC assembly system. It also provides a succinct synopsis of the role of key genes within the ISC system in plant growth and development, as well as their involvement in the response to abiotic stressors.

In recent years, significant progresses have been made in plant stress biology, particularly in elucidating the mechanisms underlying responses to extreme temperatures and salinity-alkalinity stresses. These advancements have not only broadened our understanding of plant resilience but also provided a wealth of potential targets for molecular breeding, paving new avenues for developing climate-resilient crop varieties that maintain high yield potential under both optimal and adverse conditions. This review concisely summarizes current knowledge on signal perception and transduction mechanisms during plant adaptation to extreme temperature and saline-alkali stresses, discusses the balance regulation between growth/development and stress tolerance, particularly highlights recent breakthroughs by Chinese scientists in discovering key genes and deciphering mechanisms that synergistically improve crop stress resistance and yield. We also provide future prospects for breeding strategies.

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.

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

Salicylic acid (SA) is a natural phenolic compound in plants that plays a crucial regulatory role in plant immune responses. Plants primarily synthesize SA through two pathways: the isochorismate synthase (ICS) pathway and the phenylalanine ammonia-lyase (PAL) pathway. The synthesized SA is perceived by receptors such as nonexpressor of pathogenesis-related genes 1 (NPR1), which subsequently activate immune responses. In Brassicaceae species like Arabidopsis thaliana, SA is mainly synthesized via the ICS pathway, whereas monocots and non-Brassicaceae dicots predominantly rely on the PAL pathway. For a long time, understanding of SA biosynthesis via the PAL pathway has been incomplete, hindering research on SA-mediated immunity in crops and significantly limiting progress in crop disease-resistant breeding. Recently, three research groups from China independently elucidated the PAL-mediated SA biosynthesis pathway in crops. Building on these breakthroughs, this review summarizes recent advances in the study of SA-mediated plant immune responses. We primarily focus on the biosynthetic pathways of SA within plants, the mechanisms by which SA is perceived and activates immune responses, and discuss current challenges and future directions in SA-mediated immunity research. We hope this review provides new insights and perspectives for both theoretical studies and practical applications in crop disease-resistant breeding.

INTRODUCTION: The AT-hook motif nuclear localized (AHL) gene family is a highly conserved transcription factors involved in plant growth, development, and stress responses, but their roles in spinach are still unknown.

RATIONALE:To reveal the basic characteristics of the AHL family in spinach, members of the spinach SoAHLfamily were identified at the whole-genome level, and their physicochemical properties, gene structure, conserved motifs, promoter elements, and salicylic acid-responsive expression profiles were analyzed in this study.

RESULTS: The results revealed 19 SoAHL family members in the spinach genome, which were unevenly distributed across six chromosomes. These SoAHL members can be classified into three branches, with 10 members in subfamily I and 9 members in subfamily II. The sequence composition of PPC and AT-hook conserved motifs varies among subfamilies; most of the SoAHL genes are located in the nucleus, cytoplasm, and mitochondrion. Members of subfamily I of SoAHL have no introns, whereas members of subfamily II contain 4-5 introns. The varying numbers of cis-acting elements relate to phytohormones and abiotic stress responses were distributed upstream of the promoters of the SoAHL members. The SoAHL genes can be expressed in roots, leaves, and petioles, with most genes expressed at relatively high levels in roots. The expression of two SoAHL genes (SOV6g041850.1 and SOV2g038950.1) was significantly induced by salicylic acid treatment. The expression profiles and salicylic acid-induced expression levels of SOV2g031340.1 and SOV4g018880.1 were highly correlated with the folic acid content, which may play a role in the spinach response to the salicylic acid signaling pathway. The transient overexpression of SOV4g018880.1 increased the folate content of spinach leaves by 1.75 times.

CONCLUSION: The results from the sequence characteristics, expression profiles and exogenous salicylic acid treatment revealed that the SoAHLs had potential functional diversity and that specific members may have positive effects on spinach folate accumulation. Our results will lay the foundation for further resolving the function of spinach AT-hook genes.

Phenotype (A), total folate content (B) and expression analysis of SoAHL (C) under 50 μmol∙L^-1 salicylic acid (SA) treatment for 5 days (D5) and 7 days (D7). CK: Control

RATIONALE: In this study, 11 peanut varieties were selected, and the cotyledonary leaflets from the variety with the highest bud cluster induction rate were screened out as experimental materials. By screening and optimizing influencing factors such as Agrobacterium strains, the optical density (OD) value of the bacterial suspension, the concentration of acetosyringone (AS), the concentration of surfactants, the infection method and duration, and the co-culture time, transgenic plants of peanut cotyledonary leaflets were obtained.

RESULTS: The results showed that using the embryo leaflet of Huayu 9133 as the receptor, the recombinant Agrobacterium containing eGFP (green fluorescent protein) and GUS (β-glucosidase) protein was used to infect and transform. It was found that when the infection solution was MS liquid+LBA4404 strain+100 μmol∙L^-1 AS+150 mg∙L^-1 surfactant Silwet-77 + bacterial solution OD600 was 0.7, the infection method was vacuuming for 15 min + soaking for 20 min + co-culture for 4 d, the peanut conversion rate was the highest. The positive rates of CaMV 35S:eGFP and AhUBQ4:GUS were 52.67% and 57.67%, respectively.The transgenic plants were induced by tissue culture method. The transgenic plants containing eGFP protein were identified as transgenic positive plants by eGFP green fluorescence and PCR detection, and the transgenic plants containing GUS protein were identified as transgenic positive plants by GUS staining and PCR detection.

CONCLUSION: This experiment successfully established and optimized the peanut genetic transformation system, which provided a reference for the study of peanut gene function, the cultivation of resistant varieties, quality improvement and biotechnology research.

CaMV 35S:eGFP侵染材料荧光示意图(a: 再生芽丛明场, b: 再生芽丛荧光, c: 再生苗明场, d: 再生苗荧光)

INTRODUCTION:An efficient Agrobacterium rhizogenes-mediated transformation system for Pueraria lobata was established.

RATIONALE: In this study, tissue-cultured plantlets of P. lobata were used as explants to investigate the effects of different genotypes, A. rhizogenes strains, explants, precultivation times, infection times, culture days, subculture times, and culture methods on the efficiency of hairy root genetic transformation in P. lobata.

RESULTS: The results indicated that the induction rate of hairy root formation was the highest when the immature leaves of YG-19 were used as the explant material, reaching 10.2%. A. rhizogenes K599 was identified as the most suitable strain. The optimal explant material was immature leaves that had just unfolded from the first to second nodes of the 5^th to 13^th generation tissue culture plantlets subcultured for 8 days. After 3 days of pre-culture and 15 minutes of bacterial infection, the highest induction rate of hairy roots reached 22.4%. The optimal type of culture medium for the proliferation of hairy roots in P. lobatawas solid medium culture, and the fresh weight of hairy roots grown on solid medium was 75 times greater than that of hairy roots grown in liquid medium. PCR detection and fluorescence microscopy assays revealed that the expression of GFP and rolB genes in the hairy roots of P. lobata was stable, and the rate of cotransformation was 80%.

CONCLUSION: Genotype, A. rhizogenes strain, and culture duration were the most critical factors for the efficient genetic transformation of hairy roots in P. lobata.

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.

INTRODUCTION Mahonia (Berberidaceae), a basal eudicot lineage, ranks as the second largest genus in the family, comprising approximately 100 species distributed across subtropical to temperate regions of East Asia and North America. The genus exhibits a classic East Asia-Western North America (EA/WNA) disjunction. Notably, Mahonia preserves abundant leaf fossil records in Cenozoic strata of the Northern Hemisphere, reflecting its prolonged evolutionary history. Characterized by distinctive foliar architecture that differs markedly from other angiosperm groups, this genus holds significant potential as a invaluable biological proxy or model plant for investigating the formation of intercontinental disjunct distribution patterns. Its unique morphological traits and biogeographic history provide critical opportunities to trace genus-level morphological evolution and spatio-temporal dynamics against the backdrop of global tectonic movements and climatic shifts.

RATIONALE Through comprehensive morphological surveys of extant Mahonia species, we established a novel leaf architecture classification framework designed for application to fossil leaf typology. This system aims to elucidate the genus’ foliar evolutionary trajectory since the Cenozoic and unravel the historical processes underlying its intercontinental disjunct distribution.

RESULTS Traditionally taxonomist divides Mahonia into two groups based on venation patterns: the palmately veined Group Orientales and the pinnately veined Group Occidentales. Building upon previous studies, we analyzed leaf architecture across 46 extant species and developed a refined subclade classification system using four diagnostic traits: leaflet margin type, serration density (teeth per edge), serration height, and leaflet length-to-width ratio. The Group Oriental was subdivided into seven foliar types (Microphylla, Japonica, Cardiophylla, Bodinieri, Polyodonta, Fortunei, and Nervosa), while the Occidental clade yielded six types (Chochoco, Dictyota, Volcania, Pumila, Lanceolata, and Aquifolium), accompanied by a diagnostic key. Distributional analyses revealed that within Group Orientales, geographic range expands with increasing serration height, whereas in Group Occidentales, distribution range correlates positively with serration density. The framework’s utility was further validated through taxonomic reclassification of two disputed fossil specimens, demonstrating its applicability to paleobotanical studies.

CONCLUSION Our refined foliar classification system for Mahonia represents a significant advancement in precision and granularity over previous systems. This framework holds substantial promise for standardizing Cenozoic leaf fossil typology across the Northern Hemisphere, while providing critical insights into the genus’ foliar evolution and the historical assembly of its intercontinental disjunct distribution pattern.

Retrieval and line drawings of leaf architecture of Mahonia

Rice (Oryza sativa) is one of the most vital food crops globally, and its yield plays a crucial role in ensuring food security. However, various diseases affecting rice pose significant threats to this security. Among these, rice blast, bacterial blight, and sheath blight are the three predominant diseases impacting global rice production. Consequently, there is an urgent need to breed and cultivate rice varieties with broad-spectrum disease resistance. In recent years, substantial advancements have been made in understanding the regulatory mechanisms underlying disease resistance in rice. This paper reviews these mechanisms from multiple perspectives, including the plant’s intrinsic immune responses and the functional dynamics of resistance genes. Furthermore, it highlights pressing issues that require immediate attention to facilitate broad-spectrum disease-resistant breeding efforts for rice.

INTRODUCTION: As the main grain crop, rice plays an important role in ensuring food security of China. Rise in global average temperature is detrimental to crop yield and heat stress is currently one of the major abiotic threats on rice production. There are significant variations in heat tolerance among different rice varieties. As a typical quantitative trait, heat tolerance of rice is controlled by multiple genes. Identification of new QTLs and genes related to heat tolerance is very important for the genetic research and the breeding of new heat-tolerant rice varieties.

RATIONALE:In recent years, many heat tolerant QTLs had been identified with different genetic populations and evaluation indicators at different growth stages. Most of those QTLs were mapped in large intervals due to the limited population sizes, simplified experimental designs and inaccurately controlled environments. The heat tolerance level identification in a population is very difficult for mature plants. Therefore, we developed a population of recombinant inbred lines (RILs) with 186 lines derived from japonica rice TD70 and indica rice Kasalath, which showed large variations in seedling survival rates under high temperature stress (HTSR). QTLs associated with HTSR were mapped by the high-density linkage Bin-map and candidate genes were identified.

RESULTS: Twenty-six QTLs related to the HTSR were mapped on 11 of the 12 chromosomes, with the exception of 3. The LOD values of single QTL ranged from 2.59-16.15, four of which with LOD values greater than 10. Seven QTLs were located within the same interval or adjacent to known heat tolerance QTLs. The major locus of qHTSR5.2 was located in the 26.25-26.38 Mb region of Chr. 5 with an LOD value of 12.07, which explained 7.18% of the total phenotypic variation in the HTSR. According to the annotation and sequence analysis of the genes located in the region of four major QTLs,we found that twenty-seven annotated genes with non-synonymous mutations in the coding regions between TD70 and Kasalath. Five of them were identified as potential candidate genes because the RILs sharing each of the distinct haplotypes of their parents for each gene exhibited significant different HTSR resistance level. Among them, three candidate genes encode heat shock proteins HSP20 or HSP17.5.

CONCLUSION: We detected 26 QTLs controlling seedling heat tolerance based on a high-density Bin map in a RIL population. Some of the QTLs were overlapped with known heat tolerance loci, indicating their strong effects on regulating heat tolerance of rice. Five candidate genes were identified through gene annotation, parental sequence comparison, effect analysis of heat tolerance between RILs with different haplotypes. The candidate genes identified in our study could be used for molecular mechanism research on high temperature tolerance of rice in the future.

Mapping of QTL for heat tolerance at seedling stage in rice based on a high-density Bin map. Heat tolerance of parents and RILs population during seedling stage. Location of QTLs contributing to heat tolerance at seedling stage.

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.

The organs abscission is a phenomenon in which parts of organs are separated from the body. It is an adaptive strategy evolved by plants in the process of growth and response to environmental changes, which ensures the normal growth and adaptation of plants to the environment. This process involves the abscission zone formation, signal activation, cell separation, and is regulated by both internal (in vivo) physiological processes and external environmental factors including light, temperature, and humidity. In agricultural production, the abscission of plant organs directly affects crop yield. Understanding the regulatory mechanisms of plant organ abscission is greatly important for improving crop yield. In recent years, tremendous progress has been made in the study of organ abscission mechanisms. The studies showed that the mechanisms of organ abscission in plants are largely conservative between species, but also with significant variations. This review delved into the physiological and biochemical mechanisms of plant organ abscission, and summarized the effects of both the environmental factors and the hormones and enzymes in the process. The review provides a solid theoretical support and practical guidance for crop genetic breeding and agricultural production improvement in connection with organ abscission.

UV-B, as an inherent constituent of sunlight, exerts a crucial influence on the growth and development of plants. Recent studies showed that UV-B is not merely an environmental stressor, but also a functional signal molecule that is able to promote plant growth under moderate radiation level. The protein UVR8, as a unique photoreceptor specific to UV-B, plays an irreplaceable role in the plant's response to UV-B, whose functions are regulated by both upstream and downstream transcription factors. At present, a variety of transcription factors such as BBXs, WRKYs, MYBs, and PIFs have been reported to be involved in UV-B regulated processes like hypocotyl elongation, primary root length, leaf size and shape, flowering cycle, and anthocyanin synthesis. This article reviews the molecular mechanisms of UVR8 in the UV-B signaling pathway and summarizes the regulatory mechanisms of the transcription factors during the UV-B radiation process, to provide reference for relevant research.

Coumarins are a class of phenolic compounds with benzopyrones as the parent ring structure, categorized into simple and complex coumarins, and widely distributed in higher plants. In recent years, studies have shown that root-secreted coumarins can promote iron absorption in plants. Here, the recent progress in the discovery and identification of genes related to the biosynthesis and regulation of plant iron deficiency-induced coumarins is reviewed, and the molecular mechanisms of the biosynthesis, storage, secretion, and regulation of iron deficiency-induced coumarins are further elaborated. The mechanism by which coumarins could promote plant iron uptake has also been discussed. Finally, this paper provides a preliminary outlook on the future research directions to gain knowledge of these mechanisms, which could offer novel opportunities to generate iron deficiency-tolerant crops and iron-biofortified crops.

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.

INTRODUCTION: Galactinol synthase (GolS) is a key enzyme in the biosynthetic pathway of raffinose family oligosaccharides (RFOs), providing the activated galactosyl group for the biosynthesis and accumulation of RFOs in plants. It plays an important role in plant responses to abiotic stresses.

RATIONALE: Although the role of GolS in plant stress responses has been extensively studied, little is known about the molecular characteristics of the GolSgene family in Lagerstroemia indica. This study aims to identify the members of the LiGolS gene family, analyze their physicochemical properties, gene structure, and expression patterns, and explore their potential functions in salt stress response.

RESULTS: A total of 13 LiGolS gene family members were identified at the whole-genome level. These genes were unevenly distributed across 10 chromosomes. The isoelectric points of the 13 LiGolS proteins ranged from 4.75 to 9.45, with molecular weights varying from 37.69 to 46.12 kDa, and amino acid counts ranging from 327 to 404. Subcellular localization prediction revealed that six proteins were localized to chloroplasts, one to mitochondria, five to the cytoplasm, and one to vacuoles. Additionally, the number of exons in the 13 gene members ranged from 0 to 4. Expression analysis under salt stress showed that all LiGolS genes were upregulated to various degrees after salt treatment, suggesting their potential involvement in salt stress response in L. indica.

CONCLUSION: This study systematically identified and characterized the LiGolS gene family members in L. indica, including their physicochemical properties, gene structure, and expression patterns. These results lay the foundation for further functional analysis of LiGolS genes and provide theoretical insights into their roles in stress responses.

Expression patterns of LiGolS genes in Lagerstroemia indica under salt treatment

(A) Cloud and rain map of LiGolS gene expression in salt-sensitive L. indica cultivars under normal and salt treatment conditions; (B) Cloud and rain map of LiGolS gene expression in salt-tolerant L. indica cultivars under normal and salt treatment conditions; (C) LiGolS gene expression in different varieties of L. indica under normal and salt treatment conditions; (D) Heatmap of LiGolS gene expression patterns before and under salt treatment, this heatmap illustrated the log₂-transformed expression levels of LiGolS genes before and after salt treatment (yellow modules indicate higher expression levels, while green modules indicate lower expression levels). M-CK and N-CK indicate salt-sensitive and salt-tolerant cultivars under normal conditions, respectively; M-T and N-T indicate salt-sensitive and salt-tolerant groups under salt treatment conditions, respectively.

In recent years, we have witnessed transformative breakthroughs in plant disease resistance research, particularly in deciphering the intricate interplay between hosts and pathogens. Cutting-edge discoveries span pathogen recognition mechanisms, immune signaling cascades, and multi-layered interactions integrating plants, pathogens, vectors, and environmental variables. Notably, pioneering studies from domestic research institutions have driven progress across pathogen-sensing systems, secondary metabolite-mediated defense, immune module engineering in crops, and artificial intelligence (AI)-powered solutions for pathogen-resistant peptide design. The rapid development of CRISPR/ Cas9-based gene editing and AI technologies has further empowered researchers to engineer disease-resistant crop varieties with unprecedented precision. Such progress holds profound implications for ensuring national food security and advancing strategic priorities in disease-resistant crop breeding, marking a transformative era in agricultural biotechnology and sustainable agriculture.

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.

INTRODUCTION Genetic diversity is the natural attribute of organisms formed in the long-term evolution process, which refers to the sum of all genetic variations of different individuals within a species or a group. Pepper (Capsicumspp.), a popular vegetable crop in China, is cultivated extensively with a substantial annual yield. Nevertheless, the widespread adoption of commercial pepper varieties has led to a gradual reduction in its genetic diversity, resulting in an increasing homogenization of germplasm resources. Given that germplasm forms the foundation for crop genetic improvement, maintaining rich genetic diversity is crucial for effective breeding.

RATIONALE On the other hand, morphological markers serve as a fundamental approach for investigating plant phenotypic diversity, as they allow researchers to evaluate the variations in marked samples through the observation of plant agronomic traits. On the other hand, molecular markers, particularly SSR (simple sequence repeat) markers, have gained widespread application in the breeding of new crop varieties and related fields due to their accuracy and reliability. This study focused on analyzing the diversity of 146 pepper germplasms in Inner Mongolia by employing both morphological traits and SSR markers.

RESULTS  We assessed 34 morphological traits of 146 pepper germplasms and evaluated their genetic diversity using 22 pairs of SSR primers. Our analysis revealed a high degree of diversity in the traits of these pepper lines. The results of phenotypic trait diversity analysis showed that the coefficient of variation of quality traits and quantitative traits ranged from 8.22% to 267.58% and 14.35% to 72.51%, respectively, and the Shannon-Wiener diversity index ranged from 0.04 to 1.91 and 1.58 to 2.02, respectively. The genetic diversity of pepper germplasm resources was rich. A total of 102 alleles were detected by 22 pairs of SSR fluorescent molecular markers, with an average of 4.636 alleles per pair of primers. The effective allelic variation ranged from 1.191 to 5.311, the Shannon-Wiener diversity index ranged from 0.345 to 2.056, and the polymorphic information content (PIC) ranged from 0.153 to 0.795. The average genetic distance of 146 pepper germplasm resources was 0.429. Phenotypic value clustering and principal component analysis categorized the 146 accessions into six distinct groups, while the analysis of the SSR marker data divided them into seven groups. Population genetic structure analysis further delineated the 146 pepper germplasms into two main groups. Most of these germplasms were high-generation breeding lines with high homozygosity. However, gene introgression was observed within Group1 and Group2.

CONCLUSION This study is the systematic analysis of the morphological characteristics, genetic diversity and population structure of 146 pepper germplasms, particularly by utilizing SSR fluorescent molecular markers. The high diversity in both morphological traits and genetic markers of these pepper germplasm resources indicated significant genetic differences in them. Consequently, this study provides a better understanding of the germplasm diversity and population genetic structure of these 146 pepper germplasms, establishing a theoretical foundation for future variety breeding efforts.

Genetic diversity analysis of 146 pepper germplasms. 146 pepper germplasms were categorized into six groups based on phenotypic markers and seven groups based on molecular markers, but the correlation between these clusters was weak (r=0.3967). Population genetic structure analysis further divided the germplasms into two distinct groups.

INTRODUCTION: Genetic diversity is considered as a crucial aspect in assessment and conservation of rare and endangered species. Brachystachyum densiflorum is a species endemic to eastern China. In recent years, with rapid economic development, accelerated urbanization, and escalating pollutant emissions, the habitat of B. densiflorum has been continuously degraded, habitat fragmentation has intensified, and its populations have shown a tendency to decline.

RATIONALE: Genetic diversity endows species with abundant genetic resources and plays a pivotal role in shaping their capacity to adapt to new environments. To elucidate the genetic diversity of B. densiflorum and evaluate the influence of climate change on its genetic variation, reduced-representation genome sequencing technology was employed to obtain single nucleotide polymorphisms (SNPs), and subsequently population genetics and landscape genetics together with species distribution modelling were analyzed.

RESULTS: B. densiflorum had a moderate level of genetic diversity. Six populations were divided into two groups, and there was moderate differentiation (F_ST=0.102) and high gene flow (Nm=2.442) between them. Genotype-environment association analysis indicated that the two groups were diverged attributable to local adaptation to the climate. Temperature differences and low-temperature regimes interacting together with precipitation gave rise to genetic variation of this species. In total, 544 adaptive loci were identified, which displayed significant correlations with temperature difference, low-temperature factors (Bio2, Bio6, Bio11, and Bio7), and precipitation factors (Bio19). B. densiflorum migrated evidently northward from the Last Glacial Maximum to the current, with its distribution area increased by 89.5%. However, during the period from 2061 to 2080, the extent of the suitable area for this species will be contracted, and there will be partial degradation and fragmentation occurring in highly suitable areas within Anhui Province.

CONCLUSION: B. densiflorum showed a moderate level of genetic diversity and a moderate degree of genetic differentiation. Local adaptation drove the formation of the current genetic pattern of B. densiflorum, and temperature differences, low-temperature, and precipitation led to genetic variation. B. densiflorum has evidently migrated northward from the Last Glacial Maximum to the current with increase of distribution area. However, niche modelling indicated that during the period from 2061 to 2080, the suitable habitat area of B. densiflorum would be contracted, with partial degradation and fragmentation occurring in highly suitable areas within Anhui Province. These results provide the basis for conservation and utilization of B. densiflorum.

Population genetic structure analysis of Brachystachyum densiflorum

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.

INTRODUCTION: Verticillium wilt (VW), caused by Verticillium dahliae, severely reduces cotton yield and fiber quality. Previous transcriptomic analysis in V. dahliae-inoculated Arabidopsis thaliana identified the pathogen-induced DIR1-like gene AT3G53980.2. In cotton, we discovered a homologous gene, GhDIR1 (Gh_A09G180700.1), encoding a lipid transfer protein. This study investigates its role in cotton resistance to V. dahliae.

RATIONALE: We characterized GhDIR1’s molecular features, expression patterns under pathogen stress, and functional impact using bioinformatics, subcellular localization, qRT-PCR, and virus-induced gene silencing (VIGS) analyses. Transcriptomic analysis of wild-type and GhDIR1-silenced plants were conducted to unravel downstream regulatory networks, focusing on metabolic pathways linked to plant immunity.

RESULTS: The results showed that GhDIR1 contains a 351 bp ORF encoding 116 amino acids. Subcellular localization confirmed its presence on the cell membrane. qRT-PCR showed rapid induction of GhDIR1 by V. dahliae. Silencing GhDIR1 increased cotton susceptibility to the pathogen. Transcriptomic data revealed that differentially expressed genes in silenced plants were enriched in flavonoid biosynthesis, sesquiterpene/triterpene biosynthesis, and α-linolenic acid metabolism. Key genes (GhCHS, GhDFR, GhCAD, GhSEQ, GhLOX, and GhAOC) in these pathways were downregulated, suggesting impaired synthesis of protective metabolites.

CONCLUSION: It is speculated that GhDIR1 positively regulates cotton resistance to VW by modulating flavonoid and terpenoid biosynthesis and jasmonic acid-related signaling. Its silencing disrupts critical defense pathways, highlighting its role in coordinating immune responses. These findings propose GhDIR1 as a potential target for enhancing disease resistance in cotton.

The induced expression pattern of GhDIR1 and related genes after inoculation with Verticillium dahliae.

INTRODUCTION: Identification of salt-alkali tolerant germplasm in faba bean lays the foundation for the exploration of salt-alkali tolerant genes and for the selection and breeding of salt-alkali tolerant varieties, which is of great significance for the utilization of saline-alkali land.

RATIONALE: Most of the studies on the salt-alkali tolerance of faba beans were focused on the morphological and physiological traits of the aboveground parts, while there are few studies on the phenotypic traits of the roots. The root plays a crucial role in resisting salt-alkali stress. Deep research on the relationship between the phenotypic traits of the root and the salt-alkali tolerance of faba beans will help to comprehensively understand the physiological mechanism of the salt-alkali tolerance.

RESULTS: The results showed that: (1) Under salt-alkali stress, the root overlap number was mostly affected, it was followed by the coila number, while the average diameter of root was affected slightly; (2) Between the overlap number and total number of connection points, among the bifurcation number and the overlap number and total number of connection points, most of indicators were significant positively correlation (P<0.01), while there were significant negatively correlation (P<0.01) among the average diameter of root and total number of root, the number of root tip, total length of root, endpoint number, coila number, linking number, bifurcation number, overlap number and total number of connection points; (3) Total root surface area of root, total projected area of root, total length of root and total volume of root could be used as the key indicators to identify the salt-alkali tolerance of faba bean during the germination period; (4) Two salt-alkali tolerant accessions H0000809 and H0000653, and two salt-alkali sensitive accessions H0001714 and H0002622 were screened out; and (5) The 399 faba bean accessions were divided into 4 groups: group I, salt-alkali tolerance germplasm, accounting for 0.75%; group II, moderately salt-alkali tolerant germplasm, accounting for 8%; group III, weakly saline-tolerant germplasm, accounting for 52.88%; and group IV, salt-alkali sensitive germplasm, constituting 38.35%.

CONCLUSION: Variation and correlation of each index, and the key indicators used to identify salt-alkali tolerance were determined, extreme materials can be selected and used for future study of salt-alkali tolerance mechanisms in faba bean and the excavation of salt-alkali tolerance genes.

Phenotypic differences of faba bean germplasms with different levels of salt-alkali tolerance at different growth stages (A) Root phenotype differences of faba bean germplasms with different levels of salt-alkali tolerance at germination stage (bar=5 cm); (B) Plant phenotype differences of faba bean germplasms with different levels of salt-alkali tolerance at flowering stage (bars=1 cm).

Rice bacterial leaf streak (BLS), caused by Xanthomonas oryzae pv. oryzicola (Xoc), is a significant quarantine disease. The pathogen exhibits both high genetic diversity and strong transmission capabilities. Driven by agricultural intensification and global warming, BLS has been progressively expanding across major indica rice-producing regions in southern China. This review systematically summarizes recent advances in Xoc-rice interaction mechanisms: (1) Pathogen perspective: elucidating pathogenic mechanisms of virulence factors (including T2SS, T3SS, and extracellular polysaccharides (EPS)) and pathovar differentiation patterns; (2) Host perspective: clarifying advances in PTI/ETI-mediated immunity signaling pathways, resistance (R) gene cloning, and susceptibility (S) gene editing; and (3) Future directions: proposing multi-omics approaches to decode Xoc pathogenicity networks, leveraging pan-genomics for large-scale mining of durable and broad-spectrum R genes, and constructing synergistic systems integrating S gene editing with immune activation to establish systematic solutions for sustainable BLS management.

The plant cell wall, which is composed of cellulose, hemicellulose, pectin and lignin, is a dynamically changing network structure, that not only plays the role of a key line of defense in the process of plant resistance to external pressure and adaptation to environmental changes, but also plays the role of an information hub in the process of signal transmission. When the cell wall is damaged, cells sense cell wall changes and initiate early immune responses, such as hormonal changes, alterations in wall composition and modifications, and the production of disease-resistant secondary metabolites. Although the importance of the cell wall in plant immunity is widely recognized, the specific molecular mechanisms by which cell wall damage triggers immune responses remain poorly understood. The application of in situ unlabeled imaging techniques in plant cells is gradually increasing and has become an important tool for studying cell wall structure and function. This paper describes the interaction mechanism between the plant cell wall and the immune response to provide a scientific basis for a deeper understanding of plant life activities and improve crop disease resistance, and describes in situ non-labeled imaging of the cell wall to provide more technological options for advancing the study of the cell wall in the immune response.

Unraveling the mechanisms of plant disease resistance and immunity is crucial for breeding disease-resistant crops and safeguarding national food security. Photoreceptors, which are central for perceiving environmental signals, not only fine-tune plant growth and development, but also serve as key signaling hubs in plant-pathogen interactions. Studies have demonstrated that photoreceptor interact directly or indirectly with the COP1/SPA complex, HY5, PIFs, and other light-signaling components. By regulating the spatiotemporal expression of resistance-related defense genes and controlling the synthesis and response networks of defense-related hormones, photoreceptors precisely integrate light signals with pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), thereby balancing plant growth and immunity. In recent years, research into the interaction between light signaling and plant immune systems has become a hot topic in the field of plant biology. Elucidating these underlying mechanisms offers new directions for breeding disease-resistant crops. This paper focuses on the molecular mechanisms of plant disease resistance regulated by photoreceptors, particularly the immune activation mechanisms mediated by photoreceptors and their spatiotemporal integration with immune-related hormone signals. Additionally, it delves into the potential application of optogenetic technology in studying this interaction. The aim is to provide new theoretical and technical avenues for future molecular breeding of disease-resistant crops, which will be based on photoreceptor modification and signal transduction pathways.

INTRUDUCTION: Xanthopappus subacaulis, endemic to the Qinghai-Xizang Plateau, is a perennial medicinal plant from the genus Xanthopappus of the family Asteraceae, with important economic, ecological and medicinal values. However, genomic information for this species remains limited, hindering further genetic studies and resource utilization. Determining an appropriate sequencing strategy for its whole genome is a key prerequisite for subsequent genomic studies.
RATIONALE: In order to determine the appropriate sequencing strategy for the whole genome of X. subacaulis, we analyzed and evaluated its genome size, heterozygosity, repeat and GC content using flow cytometry and genome survey analysis based on BGI sequencing.
RESULTS: Flow cytometry analyses using Opisthopappus longilobus and Solanum lycopersicum as reference genomes indicated that X. subacaulis was a diploid, with an estimated genome size of 1.94 G and 1.75 G respectively, and a DNA-C value of 0.99 pg. We generated approximately 100.3 G of clean short read sequencing data, with a GC content of 38.5%. K-mer analysis indicated that the genome size of X. subacaulis was 2 198.50 Mb, with a heterozygosity rate of 0.69%, and repeat content of 80.15%. The analysis of the long terminal repeat retrotransposons (LTR-RTs) indicated that the LTR/Copia was the most abundant LTR family, accounting for 30.72% of the whole genome, while the Gypsy family and the unknown LTRs accounted for 33.66% and 16.54%, respectively. Moreover, their peak insertion time began approximately three million years ago (Mya), with a marked amplification occurring within the last 1 Mya. These results suggested that the large-scale insertion of LTR elements was (most) likely one of the important factors leading to the genomic complexity of X. subacaulis.
CONCLUSION: This study clarifies the key genomic characteristics of X. subacaulis, which provides valuable reference data resources for subsequent genetic map construction and functional gene mining of X. subacaulis, and also lays a foundation for determining its whole-genome sequencing strategy.

Growth morphology and genomic characteristics of Xanthopappus subacaulis. (A) Growth morphology of X. subacaulis (bar=5 cm); (B) Depth and frequency distribution of K-mer and insertion time analysis of long terminal repeat retrotransposons (LTR-RTs)

INTRODUCTION Aronia melanocarpa also known as black chokeberry, belongs to the genus Aronia (Rosaceae). In addition to A. melanocarpa, Aronia includes A. arbutifolia or red chokeberry and A. prunifolia or purple chokeberry, both distributed naturally in North American, and an additional cultivated taxon, A. mitschurinii or Mitschurin’s chokeberry, originating from Europe. However, the species boundaries and relationships among the species of Aronia are not clear. Moreover, the taxonomic history of Aroniais complex, as species of this genus have formerly been placed in many different genera, such as Mespilus, Pyrus, Adenorachis, Sorbus, and Photinia. In the present study, we first sequenced and characterized the complete chloroplast (cp) genome of A. melanocarpa and compared its sequence with those of the cp genomes from 13 species of the family Rosaceae. The aims of this study were: (1) to increase our understanding of the structural patterns of complete cp genome of A. melanocarpa; (2) to investigate the phylogenetic relationships of A. melanocarpa with other Rosaceae species based on their cp genomes.

RATIONALE The chloroplast is a unique and essential organelle in green plants with vital roles in photosynthesis and carbon fixation. Comparative analyses of cp genomes between different plant species reveal intra- and inter-species rearrangements that have occurred during evolution, such as inverted repeat (IR) contraction and expansion. Based on these characteristics, the cp genome has been wildly used for species identification, phylogenetic analysis, and exploring the genetic basis of environmental adaptation.

RESULTS The complete A. melanocarpa cp genome was sequenced, analyzed, and compared with that from 13 other species in the Rosaceae. The cp genome is 159 772 bp and has a total guanine-cytosine (GC) content of 36.6%. It exhibits a typical quadripartite structure with four separate regions, including a large single copy (LSC) region of 87 810 bp and a small single copy (SSC) region of 19 200 bp separated by two inverted repeats (IRa and IRb) regions of 26 381 bp each. A total of 132 genes were annotated, including 87 protein-coding genes, 37 tRNAs, and eight rRNAs, with 22 duplicates in the IR regions. In total, 76 simple sequence repeats (SSRs) and 50 long repeats were detected. Phylogenetic analysis indicated that A. melanocarpa is most closely related to A. arbutifolia and forms a sister clade to Cydonia oblonga with weak support.

CONCLUSION We analyzed the complete cp genome of A. melanocarpa by using Illumina high-throughput sequencing technology. The sequence of A. melanocarpa cp genome could be further used for the development of molecular markers. Highly variable regions were detected in intergenic regions, such as trnK-rps16, rps16-trnQ, trnG-atpA, petN-psbM, trnT-psbD, psbZ-trnG, trnT-trnL, ndhC-trnV and accD-psaI, which might be useful for broad applications in genetic research studies as well as phylogenetic studies. Phylogenetic construction results strongly supported that A. melanocarpa was closest related to A. arbutifolia, followed by C. oblonga with weak support. This newly available genomic data for A. melanocarpa will provide a basis for future research on the population genetics and phylogenomics and will benefit the breeding studies and utilization of the genus Aronia.

Map of the chloroplast genome of Aronia melanocarpa and phylogenetic analyses among the 60 Rosaceae species using their complete chloroplast genomes. Aronia formed a clade with Dichotomanthes and Pourthiaea based on cpDNA tree. Moreover, A. melanocarpa is most closely related to A. arbutifolia and forms a sister clade to Cydonia oblonga with weak support.

INTRODUCTION Due to differences in breeding objectives, northeast japonica rice (Oryza sativa subsp. geng or japonica) is more advantageous than Japanese japonica rice in terms of yield level, whereas Japanese japonica rice is significantly better than Chinese japonica rice in terms of eating quality. Clarifying the genetic basis of the differences in eating quality between Chinese and Japanese japonica rice is highly valuable for the cultivation of high-yield and high-quality japonica rice.

RATIONALEA total of 274 Chinese and Japanese japonica rice varieties were used as research materials to quantify the eating quality of the rice and to analyze the genetic basis of the taste differences between Chinese and Japanese japonica rice by combining genome-wide association analysis with the downscaling of many parameters.

RESULTSThe results revealed that the significant differences in the taste values of Chinese and Japanese japonica rice were reflected in three textural parameters: the adhesion force (ADF), first recoverable deformation cycle (FRDC), and elasticity index (EI). Moreover, the correlation analysis between the taste values and 30 textural characters showed that 24 characters were significantly correlated with the taste value of rice. The 30 metrics of textural characterization were downscaled to four principal components that explained 80% of the phenotypic variation in the population, and the genome-wide associations of their eigenvalues were mined to two primary effector loci affecting the textural characterization of Chinese-Japanese japonica rice, qFPC4.3 and qFPC9.2.

CONCLUSION In this study, we quantified the parameters of eating quality from a qualitative perspective, and thus analyzed the genetic basis of the differences in eating quality between Chinese and Japanese rice, which provided valuable genetic information and a theoretical basis for the genetic improvement of the eating quality of japonica rice in China.

PCA analysis and genome-wide association studies based on principal component eigenvalues of texture characteristics indicators. PCA analysis was performed using 2021 data.