As an important environmental factor, light not only provides energy for plant photosynthesis, but also acts as a signal to regulate plant growth and development. Here, we summarize the regulatory effects of red light and far-red light on plant growth and development and abiotic stress responses. This review focuses on the mechanism of phytochrome and light signaling factor regulation of seed germination, hypocotyl growth, bud development, and flowering in plants through integration with endogenous signal transduction, such as hormones. In addition, the regulatory mechanisms of red light and far-red light on plant responses to salt, drought and temperature stress were elucidated. It is expected that on the basis of exploring the mechanism of plant’ perception and response to the light environment, we can accurately supplement light for crops to improve crop yield, quality and stress resistance by using LED spectrum technology while promoting the goal of “dual carbon” to reduce energy consumption and environmental pollution.

Riboflavin is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) that serve as an indispensable cofactor to maintain normal metabolism, which plays pivotal roles in mitochondrial electron transport chain, citric acid cycle, β-oxidation of fatty acids, branched-chain amino acid catabolism, redox homeostasis, chromatin remodeling, DNA repair, apoptosis and secondary metabolite biosynthesis. Riboflavin deficiency will cause metabolic disorders and a series of defective phenotypes, and death in the most severe cases. Among the living organisms, microorganisms and plants can de novo synthesize riboflavin, but humans and animals can only obtain it from food. At present, the regulation of riboflavin biosynthesis in microorganisms has been clearly studied, but the mechanism of riboflavin transport and metabolism in plants is still not clear. Isolating riboflavin deficient mutants is crucial for analyzing the molecular mechanisms of riboflavin biosynthesis, transport, and metabolism in plants and the effect of riboflavin on plant growth and development. Here we review first the riboflavin biosynthetic pathway and its key enzymes, and then the processes of riboflavin involved in plant growth and development in detail, and finally give prospects for plant riboflavin research.

Tn5 is a bacterial transposon. The engineered Tn5 can efficiently tag DNA while adding the adapter sequences. Therefore, it has been widely used in the preparation of high-throughput sequencing libraries. Cleavage Under Target & Tagmentation (CUT&Tag) is an improved technology for studying the interaction between protein and DNA, which has the advantages of good repeatability, high signal-to-noise ratio, and easy operation. This technology uses Protein A (pA) or Protein G (pG) and Tn5 to form a fusion protein, which can locate specific antibodies (the antibody is used to identify the target protein) and break the DNA near the target site while introducing sequencing adapters. Then, DNA was extracted, followed by PCR amplification to obtain the sequencing library. However, different types of antibodies have different affinities for pA and pG, thus limiting the application of CUT&Tag for some antibodies. To overcome this limitation, the expression vector of pG-Tn5 was constructed by recombination, and pG-Tn5 recombinant protein was obtained by prokaryotic expression and affinity purification. We used RNA polymerase II (Pol II)-specific antibodies (Pol II Ser5P, mouse IgG1 and rabbit IgG) to compare the efficiency of pA-Tn5 and pG-Tn5 in library preparation of CUT&Tag in Arabidopsis. The results showed that the IgG1 antibody had higher affinity for pG-Tn5, and the quality of the constructed library was better when pG-Tn5 was used. The rabbit IgG antibody has comparable affinities to the two enzymes. A lower starting amount of plant material can be applicable in CUT&Tag. This study provides a reference for the selection of Tn5 fusion proteins against different antibodies in future CUT&Tag experiments.

Nitrogen, the essential macronutrient in plants, plays a critical role in regulating plant growth and development, especially for crops production. To gain high crop yield, a large amount N fertilizer is usually applied to the planting field. However, the excessive use of chemical fertilizers has aggravated the agricultural non-point source pollution (NSP). Increasing crop yield under reduced fertilizer consumption can be achieved by increasing nitrogen use efficiency (NUE), which is crucial for promoting sustainable agriculture and for achieving agriculture and food security. In response to nitrogen-deficiency condition under natural environments, high-affinity nitrate transporter 2 (NRT2) proteins have evolved in plants. Among them, NRT2.1 subfamily acts as the main component of nitrate uptake in roots under conditions of nitrate deficiency. Here we summarize the latest progresses of the function and molecular mechanism of the NRT2 proteins, particularly of the NRT2.1 subfamily in Arabidopsis and several important crops and discuss the future directions of NRT2 research. This review aims to provide an important basis for the subsequent exploration of the potential of NRT2 proteins in increasing crop yield and the underlying molecular mechanisms.

The amide-synthase encoded by the auxin early response gene GH3 in plants could catalyze the combination of auxin, jasmonic acid and benzoic acid derivatives with amino acids respectively to form the corresponding amino acid complex. Under the high auxin concentration in plants, GH3 protein catalyzes the combination of auxin and amino acid, which acts as the auxin sink in plants. Under the low auxin concentration, the auxin-amino acid complex is hydrolyzed to auxin by proteolytic enzymes and re-participates in the auxin signaling pathway, thus regulating the dynamic balance of auxin levels in plants. When plants are subjected to biological or abiotic stress, GH3 protein catalyzes jasmonic acid and salicylic acid to bind to amino acids and participate in plant stress response. In this study, we summarized the research progress of GH3 gene in dicotyledonous model plant Arabidopsis thaliana, monocotyledonous model plant rice, and the other plants from the aspects of GH3 protein structure, GH3 gene family classification and its function, and provided some references for further study of GH3 gene family in plants.

The PLATZ transcription factor family is a class of plant-specific zinc-dependent DNA-binding proteins that play an indispensable role in plant growth and development and stress resistance. However, the PLATZ family genes have not been systematically analyzed in foxtail millet (Setaria italica). In this study, 17 PLATZ genes in the foxtail millet genome were identified and systematically named. The SiPLATZ genes were divided into five subfamilies by phylogenetic analysis, and members of the same subfamily have similar gene structures and motifs. Cis-acting element analysis demonstrated that the SiPLATZ genes may play a role in endosperm development and various stress-resistant responses. The K_a/K_s ratio analysis indicates that duplicated genes are subject to purifying selection. There were significant differences in the expression of SiPLATZ genes in different tissues and developmental stages, which were mainly divided into two categories: high expression in roots, leaves, and stems, and in spikes and seeds. This reflects the complexity of the physiological functions of SiPLATZ genes and their possible involvement in regulating seed growth and multiple stress responses. In addition, the co-expression network constructed in combination with WGCNA analysis revealed that SiPLATZ6, SiPLATZ8, SiPLATZ9 and SiPLATZ11 may be the candidates for genetic improvement of foxtail millet yield and functional gene research. These results lay the foundation for further studies on the biological functions of PLATZ transcription factors in foxtail millet growth and development.

Aluminum (Al) is one of the common metal contaminants in acidic soils. To reveal the effects of exogenous organic acids on the physiological characteristics and root DNA damage of Helianthus tuberosus under Al stress, we used Al resistant H. tuberosus cv. ‘Xuzhou’ and Al sensitive H. tuberosus cv. ‘Ziyang’ as materials. The effects of exogenous organic acids on the physiological responses and DNA damage of H. tuberosus at various periods (7, 14, and 21 d) under Al stress were investigated by setting 0, 350 and 700 µmol∙L^-1 Al concentration treatments and applying 0, 30, 60 and 90 µmol∙L^-1 compound organic acids, respectively. The results showed that Al stress inhibits root elongation and root activity, severely inhibited the photosynthetic and antioxidant systems of H. tuberosus, and the DNA damage in the root system increased with the increase of Al concentration. In contrast, the application of compound organic acid effectively alleviated Al stress. 60 µmol∙L^-1 compound organic acid improved the activity of the antioxidant system, maximum photochemical efficiency and organic acid secretion in root tips, secretion of citric acid was 2 times (H. tuberosus cv. ‘Xuzhou’) and 0.75 times (H. tuberosus cv. ‘Ziyang’) higher than the control, reduced root tip Al content and improved root activity. Besides, H. tuberosus cv. ‘Xuzhou’ and H. tuberosus cv. ‘Ziyang’ oliver tail moment decreased by 51.53% and 35.10%, and compound organic acid reduced the DNA trailing phenomenon and repaired DNA breaks to a greater extent. In conclusion, high concentration of Al causes serious damage to H. tuberosus, which is difficult to mitigate. 60 µmol∙L^-1 compound organic acid could enhance the H. tuberosus physiological responses under low Al stress, reduce DNA damage and thus improve the stress resistance. The alleviation effect was better in H. tuberosus cv. ‘Ziyang’. This study reveals the regulatory role of exogenous organic acids on the physiological responses of H. tuberosus under Al stress, and provides a theoretical basis for planting and production of H. tuberosus and production of other cash crops in the acid-aluminium areas of southern China.

Starch is the major storage material of rice (Oryza sativa) endosperm, and its accumulation process affects the subsequent growth and development of plants. As one of the main nutrients absorbed by human beings from rice, the synthesis and accumulation process of starch in rice has attracted increasing attention. This review mainly discusses the latest progress of endogenous factors affecting starch synthesis and accumulation, such as sucrose unloading from phloem, key enzymes of starch synthesis and hormones, and points out the unsettled questions in the field of endosperm starch accumulation to provide some reference ideas for further research in the future.

Soil cadmium (Cd) pollution seriously restricts the yield and quality of facility vegetables. Melatonin (MT) can enhance the resistance to various stresses in plants. However, the downstream signals, which regulated by MT during tomato seed germination under Cd²⁺ stress remains unclear. The effects of Cd²⁺ stress and exogenous MT on seed germination were investigated using tomato (Solanum lycopersicum) wild-type Alisa Craig seeds. The results showed that the germination of tomato seeds and seedling growth were significantly inhibited by Cd²⁺ treatment with more than 0.5 mmol·L^-1. Exogenous MT (0.15 mmol·L^-1) reduced the content of Cd²⁺ in the underground and above-ground tissues of seedlings, effectively alleviating the inhibitory effect of Cd²⁺ stress on tomato seed germination and seedling length. The expression of phytochelatin and transporters-related genes (PCS, NRAMP1, ABCC3, HMA3, and ABCG5) in tomato radicles were significantly increased by MT under Cd²⁺ stress, showing the positive regulation of MT in transmembrane transport and vacuolar sequestration of Cd²⁺. In addition, MT alleviated the oxidative damage induced by Cd²⁺ stress, which was related to the enhanced activities of CAT, APX, and ALDH enzymes apart from its own scavenging ability. Furthermore, MT significantly down-regulated the expressions of abscisic acid (ABA) synthesis genes (NCED1 and NCED2) under Cd²⁺ stress, and up-regulated the expression of ABA decomposition gene ABA8ox1, leading to the decrease of ABA content, which effectively regulated the GA/ABA ratio and promoted the germination of tomato seeds under Cd²⁺ stress.

In this study, we used the leaflets of marigold (Tagetes erecta) Milestone Yellow as explants to investigate the major factors impacting the transformation efficiency of Agrobacterium-mediated method. The factors included antibiotic concentration, strain type, bacterial concentration, infection time, co-culture time, acetosyringone concentration and anti-browning agent type. We found that the suitable concentrations of cefotaxim sodium salt and kanamycin sulfate were 100 mg·L^-1 and 10 mg·L^-1, respectively. We also found that the strain EHA105 had the highest transformation efficiency up to 4%. The best infection conditions for EHA105 were at bacterial concentration of 0.1 for OD₆₀₀, infected for 5 minutes, and co-cultured for 1 day. In addition, the bud germination rate could be improved by both applying 100 μmol·L^-1 acetosyringone during the infection process and adding 0.2 g·L^-1 polyvinyl pyrrolidone in the screening medium. This study laid a foundation for marigold gene function research and transgenic breeding.

Squamosa promoter binding protein-like (SPL) family is a class of plant-specific transcription factors, which contain a highly conserved SBP domain consisting of two zinc finger structures and a short nuclear localization sequence. The expression of most SPL genes is regulated by microRNAs at transcription level. Based on the current research progress of SPL transcription factors, this paper summarizes the biological functions of SPLs in plant growth, development, and environmental adaptation, and discusses the future research directions of SPLs.

The development of drought-resistant tree varieties is of great significance for maintaining forest productivity in arid and semi-arid regions of China and addressing the challenges of global climate change. Populus laurifolia is distributed in the Irtysh River Basin in Xinjiang, China, has excellent characteristics such as fast growth and cold resistance. P. simonii has the characteristics of drought resistance and barren resistance, and is widely planted in northern China. In this study, the drought resistance characteristics of P. laurifolia × P. simonii F₁ progeny were comprehensively analyzed and evaluated. We investigated seven growth parameters such as high growth and relative leaf water content, six photosynthetic parameters such as net photosynthetic rate and intercellular CO₂ concentration, and five biochemical characteristics such as SOD activity and MDA content. Based on the drought resistance coefficient and membership function analysis of 18 trait parameters, the parent and 23 F₁ progeny were divided into three drought resistance types: high, medium and low. Compared to other two drought resistance types seedlings, the highly drought-resistant F₁ progeny seedlings had larger leaf thickness, upper and lower epidermis thickness, palisade tissue thickness, and leaf tissue compactness. For highly drought-resistant F₁ progeny seedlings, the expression levels of key drought resistance genes under drought stress were significantly higher than other two drought resistance types. This study provides theoretical guidance and material basis for breeding drought-resistant poplar.

Plants can coordinate the growth direction of their various organs upon the gravity stimulus. In the process of plant gravitropism, gravity sensing and gravity signal transduction have always been the focus of attention in the field of plants. The classical “starch-statolith” hypothesis proposes that plants sense gravity through the sedimentation of amyloplasts that contain starch granules. In addition, previous studies have shown that LAZY proteins regulate plant gravitropism by mediating the asymmetric distribution of auxin. However, the molecular mechanism underlying how sedimentation of amyloplasts triggers gravity signal transduction and its coordination with LAZY proteins remains unclear. Recently, Professor Haodong Chen’s team from Tsinghua University reveals that gravistimulation induces the phosphorylation of LAZY proteins via MKK5-MPK3 kinase pathway in Arabidopsis, which modulates the phosphorylation of LAZY proteins. The phosphorylated LAZY proteins can enhance their interaction with the TOC proteins on the surface of amyloplasts, leading to the enrichment of LAZY proteins on the surface of amyloplasts and the polarity relocation on the new bottom of plasma membrane. This study illustrates the molecular mechanism underlying gravity signal transduction in plants and establishes the molecular connection between gravity sensing and LAZY mediated auxin asymmetric distribution, which is a major breakthrough in the field of plant gravitropism.

Chimeric soybean plants with transgenic hairy roots is very important for soybean functional genomics. In this study, we used three soybean genotypes to compare their hairy root induction rate and plant survival rate under different co-cultivation conditions. Our results showed that co-culturing the explants infected by Agrobacterium rhizogenes for 1 d under dark conditions was an effective strategy to induce hairy roots. We also found that removing the adventitious roots (AR) at hypocotyl significantly increased number of hairy roots, enhanced their growth and subsequently improved the positive rate of transgenic hairy roots. Furthermore, we found that the inoculation with rhizobium at 14 d of induction was able to enhance the contact between the bacteria and the transgenic hairy roots at early growth stages, and thus improved the soybean’s nodulation efficiency. Taken together, we successfully established a simple and efficient method to generate chimeric soybean plants with transgenic hairy roots. This method can be widely used in soybean gene functional studies.

The erection of rice leaf is one of the important agronomic traits that determine plant architecture, photosynthetic efficiency, and crop yield. Cytokinin is one of the most important plant hormones that regulate crop morphology, stress resistance and yield, but its role in the lamina joint development and leaf angle is still need to be further studied. Here, we report that rice CYTOKININ OXIDASE/DEHYDROGENASE9 (OsCKX9) controls lamina joint development and positively regulates leaf angle. Histological sections indicated that the leaf inclination changes in the WT and osckx9 resulted from the asymmetric proliferation of cells and vascular bundles in lamina joint. qRT-PCR showed that OsCKX9 was highly expressed in lamina joint. Quantification of cytokinin content in osckx9 mutant lamina joint showed that there were a mass of cytokinin accumulated. Moreover, the osckx9 showed insensitive to eBL. Therefore, our results revealed that OsCKX9 played a positive role in regulating leaf erectness, which provides genetic resources for analyzing the genetic basis of leaf angle and molecular-breeding of the ideal plant architecture rice.

Photosynthesis of plants depends on the green leaves, and the most intuitive feature of leaf growth and development is its color. At present, more than 200 genes related to rice leaf color have been cloned. The regulatory mechanisms of rice leaf color are complex and diverse, which involve multiple regulatory pathways, including biosynthesis and degradation of photosynthetic pigments, pathway of nucleus-plastid signaling, and heme synthesis. In addition, external environment such as temperature and light intensity can also affect the color changes of rice leaves. Here we reviewed the molecular pathways of rice leaf color, environmental factors and leaf color related genes, as well as the genetic regulatory mechanisms of rice leaf color was revealed, which will provide theoretical basis for rice high photosynthetic breeding and application, and future research in addressing some scientific problems in this field.

Plant epidermis is crucial in regulating photosynthesis, respiration, heat dissipation, and water utilization. Significant progress has been made in the study of stomatal development in dicotyledonous plants, such as Arabidopsis thaliana. Three important bHLH transcription factors (SPCH, MUTE, and FAMA) have been reported to be specifically expressed at different stages of cell division and differentiation in the stomatal lineage. They form heterodimers with another transcription factors SCRM/ICE1 and SCRM2/ICE2 to regulate the morphological transformation and changes of stomatal lineage cells across three stages of division, finally forming the stomatal complex. However, in monocots, especially in Poaceae plants such as maize (Zea mays), studies on genes regulating epidermal morphogenesis are less reported. In this study, two single-gene recessive mutants, Zmice1-1 (inducer of cbf expression1-1) and Zmice2-1, were isolated using reverse genetics approaches. Compared to the control B73, Zmice2-1 exhibited dwarfism, leaf chlorosis, reduced fertility, significantly lower stomatal density and index, disrupted arrangement of epidermal long cells, and absence of spacing between stomata. Zmice1-1 leaves gradually turned yellow from the five-leaf stage and displayed complete chlorosis at later stages. The homozygous Zmice1-1 plants are growth-arrested and sterile, but the stomatal density showed no significant difference compared to the control. Different allels of Zmice2 were obtained using CRISPR-Cas9 genome editing technology. Phenotypic identification showed that Zmice2-2 had an abnormal stomatal phenotype similar to Zmice2-1, indicating that ZmICE2 is involved in the regulation of stomatal development. Transcriptome analysis of B73 and Zmice2-1 revealed that ZmICE2 primarily regulated stomatal development by affecting cell division and differentiation, participating in the formation of maize epidermal morphology. These results contribute to a better understanding of the mechanisms of epidermal morphogenesis in maize and provide valuable genetic resources for improving crop resilience and yield traits.

Lutein can effectively reduce incidence of atherosclerosis, diabetes, cancer and multiple eye diseases. The lutein biofortification through food crop has gained more attention with improvement of daily diet. In this paper, 194 Shanxi wheat cultivars planted in three environments were used to extract lutein by organic solvent extraction, and the content of lutein in different germplasms was determined by high performance liquid chromatography (HPLC). The broad-sense heritability of lutein content in wheat and its relationship with grain color, winter/spring types, geographical origin, accession types, and main agronomic traits were analyzed, and the genetic loci associated with lutein content were identified through genome-wide association analysis. Results showed that significant variation in lutein contents occurred among Shanxi wheat accessions, the coefficient of variation was 33.12%-48.57%. Genotype was the main factor affecting lutein content. The average lutein content in three environments was 0.67-4.03 μg·g^-1, 0.16-5.05 μg·g^-1 and 0.16-3.63 μg·g^-1, respectively. The average lutein content of winter types and irrigated-wheat accessions were higher than those of spring types and dryland-wheat, respectively. There was no significant effect of grain color and released years on lutein content. Heading date, plant height and 1 000 kernel weight were significantly negative correlated with lutein content. The other agronomic traits had no significant effect on lutein. Genome-wide association analysis found four major loci related to lutein content on chromosomes 1B, 3A and 7A, among them, QLuc.3A and QLuc.7A.1 are new loci affecting the lutein content. These results provide valuable information for breeding and cultivation of wheat lutein bioaugmentation varieties.

Angiosperm fertilization has been a hot topic in the field of sexual plant reproduction. In recent years, great advances have been made in the studies on some critical steps, such as pollen tube guidance, polytubey block, and fertilization recovery system. However, most of these known mechanisms are synergid cell-based for ensuring successful double fertilization, the counterpart system based on central cell remains poorly understood. A recently published paper from Hongju Li’s lab revealed that the central cell could also secrete peptides as pollen tube attractants to guide the pollen tube entering embryo sac to ensure double fertilization. Interestingly, this mechanism is not synergid-dependent. Thus, the authors revealed a novel fertilization recovery system and bridged a gap in understanding the mechanism underlying double fertilization.

Plant roots can acquire water and nutrients selectively from soil and transport them upwards to the aerial parts for plant growth and development. These functions are closely related to their anatomical structures. The radial transport of water and solutes absorbed by roots mainly includes three different pathways, namely, the apoplastic pathway, the symplastic pathway and the transcellular pathway. The endodermis is the innermost cell layer that surrounds the central vasculature. For a long time, endodermal differentiation formed the Casparian strips has been considered to play a decisive role in blocking water and solutes transport through the apoplastic pathway. However, in recent years, it has been found that suberin lamellae formed by endodermal differentiation plays no less important role in the radial transport of water and solutes than Casparian strips, and even that suberization is the second life of an endodermal cell. In this paper, we reviewed the latest research progress on the physiological function of suberin lamellae in water and solutes transport in recent years, and discussed the relationship between suberin lamellae and drought, salt, nutrient and heavy metal stress of crops, in order to provide a reference for the theory and practice of endodermal plasticity in the regulation of plant physiological function.

Temperature is one of the major environmental determinants of plant geographical distribution. Plants distri-

buted at high latitudes or altitudes usually suffer a period of sub-zero temperature during their life cycle. When the ambient temperature drops to the freezing point, the water molecules in plants form ice crystals, causing fatal damage to plant tissue structure. In order to adapt to the freezing environment, the pathogenesis-related protein PR (PR) and its related WRKY transcription factors in cold climate plants have evolved into antifreeze proteins (AFPs) that can bind specifically to the ice surface and effectively inhibit the formation and growth of ice crystals. Currently, AFPs have been identified in nearly 100 plant species, such as winter rye (Secale cereale). Compared with insect AFPs, plant AFPs have extremely high recrystallization inhibition activity, which can effectively prevent the formation of large ice crystals in vivo. Both low temperature and pathogens can induce AFP synthesis in cold climate plants. Interestingly, only the cold-induced AFPs have dual molecular functions as hydrolase/antifreeze activity. The PR-AFPs, however, possess only one of hydrolase/antifreeze activites, whose conversion is controlled/regulated by post-translational peptide differential folding, as suggested with growing evidence. AFP has gradually become one of the hot targets in botanical research due to its unique molecular function and its promising applications. This paper will provide a systematic review of recent progress in this area.

Stress associated proteins (SAPs) are a group of A20/AN1 zinc-finger domain-containing proteins which play regulatory roles in plant response to adverse stresses. Although many studies have elucidated the functions of plant SAPs during these processes, their action mechanisms have not been systematically summarized. In this review, we briefly summarized the structural characteristics and classification of plant SAPs, with a focus on elucidating their action mechanisms. Further, we summarized the research progress on their response to environmental stress, with the aim of enhancing our understanding of plant SAPs and providing a reference for future research.

Both biological conservation practices and utilization of biological resources need accurate identification. Traditional species identification relies on taxonomic specialists, but the training of taxonomic specialists is time-consuming, which leads to a bottleneck in the utilization of taxonomic knowledge. Interactive keys and Apps based on artificial intelligence are often unable to accurately identify species because of developmental stage differences and morphological variation. DNA barcoding is an effective identification technique, its identification results based on DNA sequences are not dependent upon developmental stages and morphological polymorphism, which makes it an ideal solution to rapid species identification. Here we reviewed the types and development trends of DNA barcoding. The development of DNA barcoding can be divided into two main phases: (1) The initial phase of a single marker or combination of a few markers based on the Sanger-sequencing method; (2) The ultra-barcoding phase based on the Next-generation sequencing method. We compared the main characteristics, research methods, and species identification power of different DNA barcoding methods in these two development phases. In general, the ultra-barcoding based on plastomes performs better in species identification than normal barcodes of the first phase, and is likely to become the main method of DNA barcode research. This review summarized the difficulties and solutions of DNA barcoding development. Research material availability remains the key limitation for developing ultra-barcodes of plants. Herbariomics can capture genomic data from herbarium specimens and is thus a time-saving, highly efficient and economical approach for ultra-barcoding studies. Botanists can also obtain single-copy or low-copy nuclear genes by mining herbariomic data, and thus can apply the nuclear genes in barcoding analyses to improve the species discrimination resolution and resolve the identification problems of those plant groups with complicated evolutionary history including incomplete lineage sorting and hybridization. We thus propose to mine the treasures of herbarium specimens and establish the reference database of ultra-barcoding.

Auxin plays an important role in plant growth and development and its signal transduction has always been the focus of attention in the field of plant biology. AUXIN BINDING PROTEIN 1 (ABP1)-TRANSMEMBRANE KINASE (TMK) molecular module is involved in the extracellular auxin perception. In recent years, ABP1 has been controversial as an auxin receptor. Recently, Tongda Xu’s team and Zhenbiao Yang’s team from Fujian Agriculture and Forestry University identified ABP1-LIKE PROTEIN (ABL) as the auxin binding proteins involved in the extracellular auxin perception. Different from traditional functional redundancy, ABL and ABP1 achieve functional compensation effect through protein structure similarity, and then form complex with TMK at the plasma membrane, acting as co-receptors of apoplastic auxin to mediate auxin driven rapid response. This study deeply dissects the mechanism of extracellular auxin sensing, which is a breakthrough in the field of auxin signaling transduction.

Chitin, a major component of the fungal cell wall, is a kind of typical microbe associated molecular pattern (MAMP) that is recognized by two plasma membrane located LysM receptors, CERK1 and LYK5, and trigger immune response in plants. In this study, the intracellular kinase domain of CERK1 was cloned and used to screen the yeast cDNA library, and identify its interaction with HSP1. Using CRISPR-Cas-mediated gene editing technology, we knocked out the HSP1 gene in wild-type Arabidopsis thaliana Col-0 and obtained hsp1 v63 deletion mutant. We showed that the expression of downstream defense-related genes and the phosphorylation pathway of mitogen-activated protein kinase were inhibited in the hsp1 v63 deletion mutant compared to the wild type Col-0. We also showed that the protein level of CERK1 in hsp1 v63 mutants was lower than that in the Col-0, and that reduced CERK1 levels in this mutant were associated with the endoplasmic reticulum degradation system. These results indicate that HSP1 is a key gene in the chitin-induced defense response pathway, thus revealing the important roles of molecular chaperone in regulating receptor protein level and improvement in crop resistance.

(reed) is a cosmopolitan species, with huge biomass and high environmental adaptability. Restricted by its polyploidy genome, it is very difficult to study its unique properties at the genetic level. Using third-generation sequencing and multiple methods, we comprehensively studied the type, structure, expression, and localization patterns of RCA genes (encoding Rubisco activating enzyme) in two reed ecotypes (2n=8x). There are four types of RCA genes in Phragmites genome, all belonging to the RCA2β category. At the transcriptional and protein levels, we adopted immunogold method to detect the localization of RCA proteins. We found that RCAs have obvious ecotype specificity. Compared with swamp reeds (SR), desert-dune reeds (DR) have low RCA expression and RCA2-β2 are preferentially expressed. Six highly expressed RCA isoforms were identified though two-dimensional electrophoresis (2-DE) and mass spectrometry (MS), and were distributed in a high proportion in membrane fraction in DR. This result supports the hypothesis that RCA may transfer to the membrane area as the environment deteriorates, thereby giving RCA a protective function on the chloroplast membrane.

The secondary metabolites produced by plants provide human beings with a wealth of pharmaceutical, perfume and industrial raw materials. With the rapid development of molecular biology and genomics research, the biosynthetic gene clusters (BGCs) of secondary metabolites of various plants have been analyzed, which opens a new path for us to quickly obtain the biosynthetic pathways of target products and discover novel natural products. This paper focuses on the definition and characteristics of plant secondary metabolite biosynthesis gene clusters, and its basic structural models, evolution and regulatory mechanisms, in order to provide theoretical basis and reference for related research.

Borneol is one of the most important pharmacodynamic components in Artemisia argyi, which has antibacterial, anti-inflammatory, analgesic and other pharmacological activities. The synthesis and metabolism of borneol are affected by many kinds of enzymes, and borneol dehydrogenase is one of the key enzymes that oxidize borneol to camphor. In this study, the contents of borneol and camphor in 35 germplasm of A. argyi leaves were determined by Gas chromatograph-mass spectrometer (GC-MS). We found that the amount of borneol and camphor was highly varied among the varieties, and some germplasm contained more camphor than borneol, indicating that a large proportion of borneol was oxidized to camphor in A. argyi leaves. Based on the full-length transcriptome of A. argyi and homology comparison analysis, we cloned the first borneol dehydrogenase encoding gene AArBDH1 in A. argyi. The AArBDH1 contained 2 exons and 1 intron, and encoded a protein of 289 amino acids. The AArBDH1 gene expression levels were measured by real-time quantitative reverse transcription PCR (qRT-PCR) technology, which showed that AArBDH1 was differentially expressed in different tissues and in leaves at different development stages, and highly expressed in stem and 30 days old leaves. The enzymatic reactions of AArBDH1 with borneol as substrate and NAD⁺ as coenzyme showed that AArBDH1 could catalyze the dehydrogenation of borneol to camphor. Our study provides a theoretical basis and gene resource for further analyzing the regulation and potential improvement of borneol accumulation in A. argyi leaves.

miRNAs are involved in plant growth and response to stress by regulating the expression of target genes. We conducted a functional study on a single miRNA identified by our group, Bna-miR43. The function of Bna-miR43 under drought stress was investigated by constructing a Bna-miR43 overexpression vector. Degradation group sequencing has predicted that the four target genes of Bna-miR43 belonged to the F-box protein family. Under simulated drought conditions, the expression of Bna-miR43 in J572 roots decreased gradually, while the expression pattern of target genes was shown to be opposite to that of Bna-miR43. With the increaseing time of drought treatment, the expression of target genes increased gradually. Expression pattern analysis showed that Bna-miR43 could respond to drought stress by negatively regulating the expression of target genes. Transgenic experiment showed that under drought stress, the Bna-miR43 overexpressed lines were extremely sensitive to drought. It was shown that the germination rate of the overexpressed lines decreased significantly, the plant dehydration was serious, and more MDA and H₂O₂ were accumulated in the body. After drought treatment, three coding superoxide dismutase (SOD), catalase (CAT) and glycolate oxidase (GOX) were identified in the Bna-miR43 overexpressed lines, and their expressions were down-regulated in the Bna-miR43 overexpressed lines. The results showed that Bna-miR43 plays a key role in regulating plant drought tolerance by regulating the osmotic accumulation and ROS homeostasis in Brassica napus.

Phytochrome is an important receptor for red and far-red light sensing in plants, and it plays a vital role in regulating the plant flowering period, improving crop yield potential and regulating plant stress resistance. Identification of PHY family genes in Gossypium, exploration of the patterns of inheritance and regulatory network of domestication and improvement, and identification of the key phytochrome genes in Gossypium, provides insights into the de novo domestication and breeding of early maturing Gossypium species. To identify the phytochrome genes of Gossypium, we used bioinformatics methods to analyze 5 phytochrome genes in Arabidopsis thaliana. Phylogenetic analysis showed that the PHY genes in Malvaceae species consisted of 4 subfamilies (PHYA, PHYB, PHYC and PHYE). Moreover, the domestication selection analysis of PHY genes among different populations of G. hirsutum showed that the domestication process of PHY genes could be divided into two stages: domestication and improvement. Furthermore, the gene expression of the PHY gene family was analyzed using leaf RNA-sequencing data obtained from wild and cultivar genotypes of G. hirsutum under short-day (SD) and long-day (LD) conditions. The results showed that the expression of GhPHYA1Dt and GhPHYB1Dt were significantly different between SD and LD conditions. After 14 hours of long-day treatment, the expression of GhPHYC1At and GHPHYE1At in the cultivar was significantly lower than that in wild species. These results lay a foundation for further study on domestication selection and functional mechanisms of Gossypium PHY genes and provide a theoretical basis for breeding new early maturing Gossypium varieties and de novo domestication.

Due to their nanoscale effects and excellent physicochemical properties, engineering nanomaterials (ENMs) have been increasingly applied in various fields during the last decade. The biological effects of these ENMs on higher plants and the risk assessment of their ecological effects have become research hotspots. To comprehensively understand the effects of ENMs on higher plants in ecosystems, this paper reviews the effects of several ENMs (metal nanomaterials, metal oxide nanomaterials, carbon-based nanomaterials) on the growth of higher plants and their mechanisms. These ENMs could inhibit plant growth by reducing the seed germination rate, inducing relative reactive oxygen production, enhancing cell membrane permeability and directly damaging roots and can also promote plant growth by enhancing photosynthesis, increasing root activity, strengthening water absorption and enhancing plant metabolic enzyme activity. The influencing factors of ENMs on plant biological effects were further analyzed, including plant species, nanomaterial size and shape, nanomaterial surface characteristics, nanomaterial concentration and treatment time, and plant growth medium. Finally, based on the real soil environment, long-term and low-dose effects, and plant absorption and transportation, we propose the future research associated with the interaction between ENMs and higher plants, aiming to provide a reference for the efficient use of ENMs in agricultural production.

In this study, a plant regeneration system via somatic embryogenesis was established in Alocasia genus. We obtained embryogenic cell suspension cultures of A. reginula through embryogenic calli induced from petioles, and achieved a high frequency of plant regeneration using embryogenic cell aggregates. Efficiency of embryogenic calli induced from petiole explants was highest (81.3%) on a Murashige and Skoog (MS) medium supplemented with 2.0 mg·L^-1 2,4-dichlorophenoxyacetic acid (2,4-D) and 1.0 mg·L^-1 thidiazuron (TDZ). The embryogenic calli were crushed into cell aggregates and then transferred to liquid MS media supplemented with 2.0 mg·L^-1 2,4-D and 1.0 mg·L^-1 TDZ for suspension cultivation. By subculturing biweekly, lots of cell aggregates were gained from embryogenic suspension cultures after 12 weeks. The cell aggregates within 28 weeks of suspension culture were transferred to solid 1/2MS media without plant growth regulator for differentiation culture, with an average of 2.3-2.5 plantlets regenerated from each cell aggregate. The formation and germination of somatic embryos were observed by optical microscopy and scanning electron microscopy (SEM). After the regenerated plantlets were transplanted to a greenhouse for 4 months, the achieved survival ratio was 95.3%. Flow cytometry (FCM) demonstrated that there was no chromosome ploidy variation in randomly selected 50 surviving plants. In addition, the nuclear DNA content was estimated at 10.94 pg·(2C)^-1, and the genome size was 5 290.12 Mb·C^-1. There was no significant variation in their phenotypes from the time the plants were transplanted to the greenhouse until they bloomed spontaneously. These results provide good technical support for the commercial production of seedlings and biotechnological breeding of A. reginula.

Rehmannia henryi is an important plant with great medicinal value, but no research of CRISPR/Cas9 has been done on this species. To establish the gene editing system of R. henryi, the gene encoding phytoene desaturase (PDS) in carotenoid biosynthesis was screened, and the CRISPR/Cas9 vector of RhPDS1 was constructed and transformed into R. henryi genome by Agrobacterium-mediated transformation method. The transcript of RhPDS1 with a 1 764 bp open reading frame (ORF) of RhPDS1 was obtained, the deduced amino acid sequence of RhPDS1 has the typical structural domains of phytoene desaturase. RhPDS1 showed higher expression levels in bud, flower and new leaf. Using CRISPR/Cas9 method, three regenerated shoots with albino phenotype were finally obtained, the differentiation rate of albino shoot was 3.7%. Sequencing analysis revealed that the three albino shoots belong to 2 editing events, in which deletion of 1 bp or (and) 5 bp occurred, respectively, which caused frame shift mutations. The contents of chlorophylls and carotenoids were significantly decreased in the albino mutants as compared to wild type, and the expression levels of RhPDS1 were also decreased in the albino mutants. Taken together, the RhPDS1 gene was cloned and knocked out by using CRISPR/Cas9 method, which laid down the foundations for functional genomics studies and de novo domestication of R. henryi.

In order to establish the regeneration system of Citrus australasica, the effects of different plant growth regulators combinations, medium types and dark culture time on callus induction and plant regeneration of C. australasica were studied using stem segments as explants. The results showed that the best medium for adventitious bud induction was 1/2MS+4.0 mg∙L^-1 ZT+30.0 g∙L^-1 sucrose. Dark culture for 14 days and then light culture had the best promoting effect. The induction rate of callus and adventitious bud was 100%, and the average number of adventitious bud regeneration per explants was 4.83. The optimal rooting medium was 1/2MS+0.5 mg∙L^-1 NAA, and the regenerated plants with the 94.43% rooting rate were obtained, and the average number of roots was 3.9. In the mixture of grass carbon:perlite: vermiculite=2:1:1 (v/v/v), tissue culture seedlings had the best growth, and the survival rate was more than 90%. This study established in vitro regeneration system of C. australasica, which laid the foundation for the genetic improvement and rapid propagation of C. australasica fine varieties.

The domestication of crops was a significant event in human history, which led to the emergence and prosperity of agricultural civilization. Maize is an important global food crop, and its domestication origin has long attracted the attention of both the biological and historical communities. The mainstream view in the past was that modern maize originated from the parviglumis type of teosinte. Recently, Yan Jianbing and his collaborators systematically collected and sorted various types of wild and cultivated maize resources, and comprehensively applied genomics, population genetics, and quantitative genetics methods, along with the use of archaeological findings. They found that modern maize also has the gene introgression of the mexicana type of teosinte, which has influenced many agronomic traits. A new model for the origin of modern maize has been proposed based on these findings.

Taxus contains the anti-cancer ingredient paclitaxel, is the top-protected endangered plant in China, and has great medicinal value but scarce resources. To solve the problem of paclitaxel source shortage, in this study, an in vitro culture of a taxane-rich Taxus system was established. The results showed that MS+2 mg·L^-1 6-BA+0.4 mg·L^-1 NAA+0.7 g·L^-1 Pro was the optimal treatment for absorption surface expansion, and the expansion rate reached 90%. The adventitious bud high-frequency synchronous growth induction was in the DCR+1 mg·L^-1 6-BA+0.1 mg·L^-1 NAA+5 mg·L^-1 Glu+1 g·L^-1 AC. The best biomass amplification phase I was in MS+0.7 mg·L^-1 6-BA+0.07 mg·L^-1 NAA+0.1 mg·L^-1 Phe+50 mg·L^-1 PG, in which the biomass reached 542 mg. The optimized biomass amplification phase II was obtained in MS+0.5 mg·L^-1 6-BA+0.05 mg·L^-1 NAA+0.1 mg·L^-1 Phe+2 g·L^-1 AC, in which the biomass reached 1 612 mg. The content of taxanes in tissue culture materials is much higher than that of natural materials. The content of paclitaxel in tissue culture materials was 6.1 times that of natural materials. The contoent of baccatin III in tissue culture materials was 8.2 times that of natural materials. The content of 10-DAB in tissue culture materials was 68.1 times that of natural materials. This study established an in vitro culture system of taxane-rich Taxus, and solved the problem of paclitaxel drug shortage.

Pinoresinol-lariciresinol reductases (PLRs) are key enzymes involved in the lignan biosynthesis in plants, which convert pinoresinol to lariciresinol and then to secoisolariciresinol. PLRs are NADPH-dependent reductases with substrate stereoselectivity. The catalytic products of PLR are the sources of different types of 8-8′ lignans, and the substrate selectivity directly determines the skeleton types of lignans, such as furano, dibenzylbutane, dibenzylbutyrolactone and aryltetrahydronaphthalene lignans. Therefore, the catalytic and expression characteristics of PLRs play an important role in the composition and biodiversity of lignans in plants. This paper reviewed the research progress on the important role of PLRs in lignans biosynthesis, as well as its enantioselectivity and catalytic mechanism, thus to lay the foundation for further study on the biological function and catalytic mechanism of PLR genes, and point out the direction for the precise biosynthesis of different types of lignans enantiomers through synthetic biology.

To solve the problem of breeding excellent seedlings of Erythropalum scandens, research has been conducted on the establishment and optimization of tissue culture and rapid propagation systems of E. scandens by taking apical bud-induced aseptic seedlings as the material. Explant sterilization, callus induction, callus differentiation, test-tube rooting and transplanting and domestication were studied. The results are as follows: the best ratio of sterilization was 60 seconds of 75% alcohol+10 minutes of 0.1% HgCl₂, and the success rate was 48.89%. The best formula for callus induction by aseptic seedling leaf was MS+0.5 mg·L^-1 6-BA+1.0 mg·L^-1 2,4-D+1.0 mg·L^-1 IBA, for 30 days, and the induction rate was 71.11%, with compact green and strong differentiation potential. The best formula for callus induction by aseptic seedling shoot was MS+1.0 mg·L^-1 6-BA+0.5 mg·L^-1 2,4-D+1.0 mg·L^-1 IBA, for 30 days, and the induction rate was 70.00%; The most suitable medium for induction of callus propagation and differentiation was MS+2.0 mg·L^-1 6-BA+0.5 mg·L^-1 TDZ+1.0 mg·L^-1 IBA, bud differentiation rate was 98.89%, and coefficient of propagation was 3.33. The most suitable medium for rootage was MS+1.5 mg·L^-1 6-BA+0.5 mg·L^-1 IBA, achieving a 100% rootage rate with 2.2 of the average number. Plantlets were transplanted to small particle peat soil, and 88.89% of rooted plants survived. The research has established the tissue culture and rapid propagation system of E. scandens, which can be applied in production and serve as a foundation for providing seedlings and factory production.

The sirtuin protein family of plants is a class of enzymes that depend on β-nicotinamide adenine dinucleotide (β-NAD⁺) to catalyze the removal of N^ε-acetyl and N^ε-acyl (acetyl, crotonyl, butylyl and 2-hydroxy-isobutylyl) from non-histone and histone lysine, respectively, and has the function of regulating the activity of non-histone protein and gene expression. Members of the sirtuin protein family have been shown to play important epigentic regulatory roles in the growth and development of rice (Oryza sativa), soybean (Glycine max) and tomato (Solanum lycopersicum), and in response to salt, cold, heat and pathogen stresses. Here we summarized the recent research advances in the enzyme activity, catalytic substrates, cell localization and function of plant sirtuins, which will serve as a reference for understanding the epigenetic regulation mechanism and studying the new function of sirtuin.

Aphids and the viruses transmitted by them cause some of the most devastating plant diseases across the globe. Once infected by aphids, plants can produce and release volatile organic compounds (VOCs), which are transmitted through air and elicit defense in neighboring plants (airborne defense, AD). However, the mechanisms underlying AD remained largely elusive. Dr. Yule Liu’s group at Tsinghua University, China, recently reports a new study and they identify a new signaling circuit, comprising methyl-salicylate (MeSA), salicylic-acid (SA)-binding protein-2 (SABP2), a transcription factor NAC2 and SA-carboxylmethyltransferase-1 (SAMT1) converting SA to MeSA, that mediate interplant communication and airborne defense against aphids and viruses. Furthermore, some virus-encoded virulence proteins could interact with NAC2 transcription factor to reduce the nuclear localization and promotes the degradation of NAC2, thereby suppressing the interplant AD and promoting viral transmission. This comprehensive study provides new mechanistic insights into airborne defense of plants and unravels an amazing aphid/virus co-evolutionary mutualism. It also sets the foundation for new approaches of using AD to control aphid and virus diseases in agriculturally-important plants.