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

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 Salicylic acid (SA) plays an important role in the plant immune system. The quantitative analysis of SA in plants is fundamental to studying SA metabolism and its biological functions. Although high-performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC/MS) are widely used for SA determination, their low throughput limits their suitability for large-scale analysis. However, the SA biosynthetic pathway in rice is not well understood, highlighting the need for efficient methods to screen SA-related mutants and elucidate SA metabolic pathways.

RATIONALECurrent methods for measuring endogenous SA levels, such as HPLC and LC/MS, involve labor-intensive sample preparation, making them unsuitable for high-throughput analysis. While a lux gene-based SA biosensor has been successfully used in tobacco and Arabidopsis, a reliable and efficient method for SA detection in rice remains unavailable. To address this problem, we optimized sample processing and operational workflows to enable high- throughput SA quantification in rice plants.

RESULTS We developed a streamlined, high-throughput method for SA quantification in rice, eliminating time-consuming steps such as sample weighing, tissue grinding, and centrifugation. This approach significantly simplifies the process while maintaining efficiency and accuracy. We validated the method’s feasibility using published rice SA metabolic mutants. We then applied it to screen a Cobalt-60 induced rice mutant library, identifying mutants with altered SA metabolism. Endogenous SA levels in these mutants were confirmed using HPLC. The results demonstrate the method’s effectiveness in screening SA-related metabolic mutants, providing a valuable tool for studying SA metabolism and its roles in rice and other crops. The method was validated using known SA genetic materials. SA content-altered mutants were successfully isolated for further research.

CONCLUSION This study establishes a rapid and cost-effective method for measuring SA content in rice tissues using the SA biosensor Acinetobacter sp. ADPWH_lux. Given the pivotal role of SA in plant defense, our method adopts streamlined sampling process, requiring only leaf clipping and boiling in LB medium, and dramatically reduces the time and effort associated with tissue collection and processing. This high-throughput approach is well-suited for large-scale screening of greenhouse-grown or hydroponic plants, providing a powerful platform for advancing research on SA metabolism and its biological functions in crops.

Modified manipulating process for high-throughput determination of salicylic acid (SA) content using SA biosensor Acinetobacter sp. ADPWH_lux strain in rice

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.

INTRODUCTION A preliminary tissue culture system for Phyllanthus acidus was established.

RATIONALE In this study, the stem tips of P. acidus were used as explants, and the schemes of primary culture, secondary proliferation culture and rooting culture were screened.

RESULTS The results showed that the optimal medium for primary culture was MS+2.0 mg·L^-1 6-BA+0.2 mg·L^-1 NAA, and the induced germination rate of explants reached 81.11%. The optimal medium for subculture was MS+1.0 mg·L^-1 6-BA+0.2 mg·L^-1 IBA, and the proliferation coefficient was 1.86. The optimal medium for rooting was MS+1.5 mg·L^-1 IBA, and the rooting rate reached 83.00%. After 7 days of cultivation, the plantlets were transplanted with perlite, peat soil and humus=1:1:1 (v/v/v), and the survival rate was 90%.

CONCLUSION The most suitable medium for primary culture using the stem tip of P. acidus as explant was MS medium and the phytohormones were 2.0 mg·L^-1 6-BA and 0.2 mg·L^-1 NAA; the optimal phytohormones for subculture were 1.0 mg·L^-1 6-BA and 0.2 mg·L^-1 IBA; the optimal phytohormone for rooting culture was 1.5 mg·L^-1 IBA.

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.

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.

With the mission of fostering talented graduates with innovative skills and knowledge, colleges and universities are the primary base for providing innovative educational models. The traditional high-education model in the field of plant science is not well suited for innovative student talent development due to its structural deficiencies such as obsolete teaching forms and contents, the dissociation between theoretical teaching and practice, non-standardized training processes, and irrational evaluation systems. As an important vehicle for promoting in depth teaching reform, subject teaching competitions exert a remarkable impact in stimulating students’ innovative potential and practicing their innovative skills at four levels: consciousness, thinking, spirit, and quality. This paper takes the undergraduate training program in College of Life Sciences in Zhejiang Normal University as an example to explore how to incorporate teaching competitions into the innovative talent training programs in plant science. Specific implementation strategies were proposed from multiple perspectives such as curriculum construction, management system, teaching staff, incentive and evaluation mechanisms. The effects of our college’s educational practice is summarized. This work provides a reference for the training of innovative student talents in plant science in similar institutions.

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: 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.