Domestication of wild plants was crucial for human settlement and the development of civilization, which arose independently in many different geographic areas on different wild species. However, these crops underwent variant domestication process displaying the ‘domestication syndrome’ with a common suite of traits. The systematical analysis of convergent selection at genome level may provide important information and genetic resources for crop breeding. Recently, a team led by Xiaohong Yang and Jiansheng Li from Chinese Agricultural University and Jianbing Yan from Huazhong Agricultural University reported the genetic basis of convergent selection between maize and rice at both single gene and whole genome levels. Particularly, they found the maize KRN2 and rice OsKRN2 genes experienced convergent selection and regulated grain number and yield in a similar pathway. Moreover, they identified a large number of orthologous gene pairs that underwent convergent selection during maize and rice evolution, which were enriched in certain pathways including starch metabolism, sugar and coenzyme synthesis. This significant work not only cloned KRN2/OsKRN2 orthologous gene pairs with great value in maize and rice breeding, but also revealed the convergent selection between maize and rice at the genome level, providing critical foundations for studying the molecular basis of domestication syndrome and their applications in breeding practices.

Genome-wide association study (GWAS) is a general approach for unraveling genetic variations associated with complex traits in both animals and plants. The development of high-throughput genotyping has greatly boosted the development and application of GWAS. GWAS is not only used to identify genes/loci contributing to specific traits from diversenatural populations with high-resolution genome-wide markers, it also systematically reveals the genetic architecture underlying complex traits. During recent years, GWAS has successfully detected a large number of QTLs and candidate genes associated with various traits in plants including Arabidopsis, rice, wheat, soybean and maize. All these findings provided candidate genes controlling the traits and theoretical basis for breeding of high-yield and high-quality varieties. Here we review the methods, the factors affecting the power, and a data analysis pipeline of GWAS to provide reference for relevant research.

Proximity labeling (PL), a recently developed technique to detect protein-protein interactions and subcellular structural proteomes in living cells, has been successfully applied in various animal and plant systems. Proximity labeling is conducted by fusing an engineered enzyme with catalytic activity to a protein of interest (bait protein). With the catalysis of the enzyme, small molecular substrates such as biotin are covalently linked to endogenous proximal proteins, which can be further enriched and analyzed to identify the interactome of the bait protein. TurboID, a biotin ligase produced by directed evolution, has the advantages of non-toxicity and high catalytic efficiency. Using TurboID-based proximity labeling to analyze proximal proteins of bait proteins, we can study transient or weak protein interactions, which helps to understand the complex biological processes occurring inside cells. Here, we describe methods and related tips for TurboID-based proximal labeling in Arabidopsis thaliana, and hope to provide a reference for studying plant protein-protein interactions.

In 2020, the numbers of original research articles published by Chinese plant scientists in international multidisciplinary journals and mainstream plant science journals increased significantly compared with that in 2019, and important advances have been made in the fields of plant development, stress tolerance, crop biology, genomic phylogenetics and evolution. Among them, “Cloning, functional characterization and application in wheat breeding of the Fhb7 resistant gene to Fusarium head blight”, and “A new mechanism to improve the nitrogen-utilization efficiency in crops” were selected as two of the “Top Ten Advances in Life Sciences in China” in 2020. Here we summarize the achievements of plant science research in China in 2020, and briefly introduce 30 representative important research advances, so as to help readers understand the developmental trend of plant sciences in China, and conduct their future research to meet the national needs.

As one of the plant cell wall polysaccharides, pectin has a very complex structure and function. Pectin is mainly composed by homogalacturonan (HG), rhamngalacturonan I (RGI), rhamngalacturonan II (RGII). Pectin plays an important role in maintaining the integrity of cell wall structure, intercellular adhesion and signal transduction. Therefore, studying the structure, distribution and roles of pectin components is of great significance for understanding the construction and function of cell wall. However, it is not clear how these three components of pectin cross-link to form high structure and perform biological function in the cell wall. This review will focus on the biosynthesis, functions of HG, RGI, RGII as well as the microscopic imaging techniques of pectin, aiming to provide a theoretical basis for the study of the structure and function of plant pectin.

Macroautophagy (hereafter termed autophagy) is an evolutionarily conserved cellular degradation and recyc- ling pathway in eukaryotes. In this pathway, cellular substances, such as dysfunctional proteins and damaged organelles, are sequestered by a double-membrane structure, autophagosome, and eventually delivered to the lysosomes or vacuoles for degradation and recycling. Autophagy plays essential roles in plant growth and development, as well as in response to environmental stresses. Up to now, more than 40 autophagy-related (ATG) genes have been identified in model plants such as Arabidopsis thaliana and Oryza sativa. It is well established that a large number of ATG genes are up-regulated during specific developmental stages such as leaf senescence and seed maturation, as well as when plants encounter adverse environmental conditions, for example, nutrient starvation, drought or pathogens infection and so on. However, the transcriptional activation or repression mechanisms of ATG genes during these biological processes are largely unknown and need further study. In this review, we summarized the roles and the well-established transcriptional regulation network of ATG genes during plant growth, development and stress responses.

Auxin is one of the most important plant hormones and plays a key role in regulating plant growth and development. In plants, early auxin responsive gene families, such as Aux/IAA (Auxin/Indole acetic acid repressors), GH3 (Gretchen Hagen3) and SAUR (Small Auxin up RNA), are rapidly induced and up-regulated by auxin treatment. Aux/IAA gene family is generally composed of four conserved domains. Domain I inhibits the expression of downstream genes in the auxin signaling pathway, and domain II is mainly regulated by Transport Inhibitor Response 1 (TIR1) in auxin signal transduction, thus affecting the stability of Aux/IAA. Domain III/IV regulates auxin signaling by interacting with Auxin Response Factor (ARF). Aux/IAA gene family has been reported to play an important role in organ development, root formation, stem elongation and leaf expansion in dicotyledonous Arabidopsis thaliana while in monocotyledonous rice (Oryza sativa) and wheat (Triticum aestivum), Aux/IAA mainly affects root development and plant architecture. However, the functions of most Aux/IAA genes remain unclear and need to further study. In this article, we reviewed the structure and function of Aux/IAA protein, and the auxin signal transduction pathway in Arabidopsis, cereal crops and other plants to provide clues for fully revealing the biofunction of the Aux/IAA gene family.

CRISPR/Cas9 technology is a gene editing strategy using Cas9 nuclease guided by RNA to target an interest gene in genome. Recently, a large number of new-type gene editors based on the CRISPR/Cas9 have been updated rapidly and become more precisely and efficiently in gene editing, which has a great application prospect in crop molecular-designing breeding. This paper summarized the technical principles, editing effects and applications of the CRISPR/cas9 and its related gene editors, and also discussed the aspects of dilemmas, countermeasures and prospects, intending to provide reference for scientific researchers in the related fields.

Xyloglucan (XyG) is a matrix polysaccharide present in the cell wall of all land plants. It is the most abundant hemicellulose in the primary cell walls of dicots (20%-25%, w/w). As a very important plant cell wall component, XyG is not only involved in plant growth and development, but also plays important roles in responses of plants to various abiotic and biotic stresses. The use of genes involved in XyG biosynthesis and degradation possibly improve the tolerance of plants to stresses through influencing the cell wall structure (remodelling) and compositions. In addition, XyG and XyG oligosaccharides likely act as signaling molecules or cooperate with other signaling molecules to induce plant resistance. Here, we review the structure and variety of XyG, the genes involved in XyG biosynthesis and degradation, and advances in potential roles of XyG and XyG-related genes in responses to biotic and abiotic stresses.

The formation pathway of triploid in Poaceae includes 2n gamete fusion, interploidy cross, polyspermy, and endosperm culture. The fusion of reduced male (n) and unreduced female gamete (2n) is the main method for forming natural triploids. Interploidy cross is the main method for synthesizing artificial triploids. The application of ploidy identification methods such as morphological observation, chromosome analysis, flow cytometry and molecular markers in gramineous triploids is introduced, and the advantages and disadvantages of different methods are also discussed. At present, triploid has no direct application value in cereal crops, but it can be used as a genetic bridge to synthetize polyploid and aneuploid, as well as to transfer alien genes from wild species to cultivated species. Gramineous triploids (especially allotriploid) are widely cultivated for forage or biofuel production, suggesting that triploidy breeding may be directly performed in this type of grasses. We discuss the future prospect of research on gramineous triploid, e.g., polyploid- and apomixis-triploid breeding. Particularly, endosperm culture can synthesize triploids in one step, and polyspermy can achieve one-step fusion of three genetically different plant genomes, which should be paid attention to in the triploidy research. Due to rare occurrence of 2n gamete fusion and polyspermy, and frequent chromosomal variation in ploidy hybridization and endosperm culture, the development of high-throughput triploid identification technology will become the key for breakthrough in triploidy generation/breeding.

Seed germination is an important stage in the establishment, growth and propagation of plants, and plays a critical role in the life cycle of seed plants. Seed dormancy is formed during development, and reaches its peak at physiological maturity. The phytohormone regulation of seed dormancy and germination may be a highly conserved mechanism in seed plants. Cytokinin (CK) is one of the most important signal molecules in plants, and regulates many aspects of plant growth and development. The bioactive CK levels are controlled by a balance among biosynthesis, activation, deactivation, re-activation and degradation, and seed development, dormancy and germination are regulated by bioactive CK levels and signaling pathways. Here, we mainly summarize the research progresses of CK biosynthesis and catabolism, signaling, and regulation on seed development, dormancy and germination. In addition, we also propose some scientific questions that need further addressed in this field to provide some information for understanding the molecular mechanism of seed development, dormancy and germination regulated by CK.

Root exudates play an important role in root-soil-microorganism interactions and ecological feedback mechanisms. Root exudates are considered as the medium of “rhizosphere dialogue” in the process of complex plant rhizosphere network interaction, with great impact in regulating plant adaptation to microhabitats, thus alleviating rhizosphere nutrient competition and constructing rhizosphere microbial community structure. Here, we review the recent advances on the effects of root exudates on plant growth, soil microbial characteristics such as soil enzymes, microbial biomass, and microbial community, and soil nutrient circulation. We also propose the important directions and contents of future research on root exudates.

Symbiotic nitrogen fixation between legumes and rhizobia is the most important nitrogen source for sustainable agriculture. As the final accommodation for rhizobia, the specialized lateral organ, root nodule, that provides the essential microenvironments for rhizobia and its proper development, is vital for biological nitrogen fixation. Nodule de novo organogenesis mainly initiates from cortical cell division and it is generally accepted that cortical cells of legumes possess certain identity, which enables them to respond to and establish symbiosis with rhizobia, but the underlying mechanisms remain unknown. Recently a team led by Ertao Wang in Centre for Excellence in Molecular Plant Science, Chinese Academy of Science showed that the SHORTROOT-SCARECROW (SHR-SCR) module predetermines this cortical cell identity in legumes. This study uncovers a novel molecular mechanism for nodule organogenesis, and provides important clues for an evolutionary understanding of root nodule symbiosis, which is both practically and theoretically valuable for improving nitrogen fixation efficiency in legumes and engineering nitrogen symbiosis in non-legumes.

In 2021, the numbers of original research articles published by Chinese plant scientists in international multidisciplinary journals and mainstream plant science journals increased significantly compared with that in 2020, and important advances have been made in the fields of male and female cell recognition and fertilization, stem cell fate determination, mycorrhizal symbiosis, photosynthetic membrane protein complex, nitrogen and phosphorus nutrient utilization, innate immunity, crop de novo domestication and genome design. Among them, ‘rapid de novo domestication of allotetraploid wild rice’ was selected as one of the ‘Top Ten Advances in Life Sciences in China’ in 2021. Here we summarize the achievements of plant science research in China in 2021, and briefly introduce 30 representative important research advances, so as to help readers understand the developmental trend of plant sciences in China, and evaluate how to better connect plant scientific research with major national needs.

As one of the largest transcription factor (TF) families in plants, MYB TFs are involved in various physiological and biochemical processes, such as plant growth, metabolism, and response to various biotic and abiotic stresses. R2R3-MYB is the main form of MYB TFs in higher plants. Pepper is a vegetable crop with important economic value, but the R2R3-MYB TF family has not been systematically studied in pepper. In this study, 94 CaMYB, 92 CbMYB, and 94 CcMYB TFs genes were identified with comparative genomic analysis in Capsicum annuum, C. baccatum, and C. chinense, respectively. These genes were categorized into 28 subfamilies. Collinearity analysis indicated that there were 73 groups of orthologous R2R3-MYB genes among three pepper species. There were five, four, and two unique R2R3-MYB genes in C. annuum, C. baccatum, and C. chinense, respectively. In addition, we identified 12 pairs of duplicated genes, and eight of which are tandemly repeated genes, which already existed before the divergence of three pepper species. Comparative genomics analysis suggested that the homologous R2R3-MYB TFs underwent functionally divergence during the evolution of pepper. Analysis on the expression profile showed that R2R3-MYB genes were expressed in three major patterns: high expression in roots, leaves, stems, and flowers, such as CaMYB13/CbMYB12/- CcMYB13; high expression in flowers, such as CaMYB93/CbMYB86/CcMYB12; high expression in roots, such as CaMYB48/CbMYB47/CcMYB51. These results lay a foundation for further study on the biological functions of R2R3-MYB TFs in the growth and development of pepper.

Cadmium (Cd) is one of the widely distributed and polluted heavy metals. With serious toxicity, Cd not only affects the growth and development of plants, but also endangers human health. This review summarizes recent research advances and underlying mechanisms of physiological and biochemical responses to Cd stress in plants. We also review and discuss plant responses in photosynthetic systems, reactive oxygen species and reactive nitrogen species, antioxidant defense systems, hormones, calcium signals, and their underpinning proteomics and genomics mechanisms. We aim to form a theoretical basis for future research on understanding the physiological and biochemical mechanisms of plant responses to Cd stress.

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.

Nicotiana tabacum (tobacco) is one of the model plants for molecular biology research as well as an important economic crop in the world. A suitable living environment is essential for the growth and reproduction of tobacco. CONSTANS-like (COL) family proteins are not only key regulators for flowering time, but also play important roles in stress response of plants. Our aim was to identify the COL family members, analyze their gene structure, evolutionary relationship, transcriptional regulatory elements and expression patterns, and explore their possible functions in response to cold stress in tobacco. We identified a total of 15 COL genes with similar physiochemical properties in tobacco. Evolutionary analysis divided all COL genes into three categories, and similar intron structure and motif distribution were observed among genes within each category. The promoter regions of tobacco COL genes contain a large number of cis-acting elements related to responses to light, low temperature, drought and phyto hormone. Gene expression analysis showed that low temperature significantly affected the expression of COL genes in tobacco, but the effects on different genes were different. Our study showed different parental (N. sylvestris (maternal) and N. tomentosiformis (paternal)) expression bias between different COL genes in tobacco, and most of the bias patterns were maintained from 6-7 leaf stage to budding stage.

Auxin polar transport regulates plant growth and development. The polar transport of auxin mainly depends on three transporters: AUX/LAX, PIN and ABCB protein families. The direction of auxin flow between cells is closely related to the polar localization of PIN proteins in cells. The PIN protein contains a central hydrophilic loop (HL) and two separated hydrophobic regions, and the multiple phosphorylation sites on HL are the targets of protein kinases. The PIN proteins are fine-tuned at multiple levels, including transcriptional regulation, post-transcriptional modification, intracellular recycling and vacuolar trafficking for degradation, in response to endogenous and exogenous signals. Using genome-wide analysis, 12, 15 and 11 PIN like genes have been identified in rice, maize and sorghum, respectively, but the functions of only a few genes have been reported. Here we reviewed the research progress of PIN protein in Arabidopsis thalianaand cereal crops from the aspects of protein structure, activity regulation and functional verification to provide new ideas and clues for exploring the auxin polar transport mediated by PIN protein family.

Global warming is the most severe environmental challenge that mankind is facing now. In addition to effectively controlling carbon emissions, making the ecosystem work at full capacity of carbon sequestration is an important means to achieve the goal of carbon neutralization. As one of the wetland types with the highest carbon sequestration capacity, peatland is the key terrestrial ecosystem to accelerate the achievement of carbon neutrality goals. As the ‘effective ecosystem engineer’ on peatlands, peat moss (Sphagnum) plays an extremely important role in peatlands, such as carbon sink, freshwater filtering, and land protection from flooding. For more than 100 years, peat mosses, as the most economically valuable group of bryophytes, have been widely used in the fields of medicine and health care, pollution monitoring and wastewater treatment, especially in the horticultural industry as one of the most reliable soil media and moisturizing materials. In the context of global warming and the ‘two-carbon’ goal, peat moss is a research hotspot in life sciences and ecology. This paper mainly reviews the morphology, species diversity and origin, habitat and distribution, reproduction and protection, cultivation and planting, environmental indication and monitoring, usage and applications, capabilities of carbon sequestration, water storage and acidification. It provides a reference for peat moss research, peatland protection and restoration, as well as development, utilization, and industrial development of peat moss.

The leaf morphology of Chinese traditional chrysanthemum varieties is very variable, but it has not been scientifically defined and classified, so it is impossible to make effective use of these morphological traits for variety identification and genetic analysis. The definition and classification of plant morphology by quantitative analysis is the premise of genetic analysis of plant traits. In this study, 24 leaf traits of 436 chrysanthemum varieties were re-defined and measured. The correlation analysis identified 8 relatively independent traits, and principal component analysis further focused on 5 key traits, including the leaf blade length/leaf blade width, widest part length/leaf blade length, right lower leaf lobe length/leaf vein length of right lower lobe, right lower leaf lobe length/right lower leaf lobe width, leaf petiole length/leaf blade length. The leaf shapes were classified into 16 types by Q clustering analysis. This study established a quantitative definition and classification system for the leaves of Chinese traditional chrysanthemum varieties. It provided an effective leaf evaluation standard for the identification of chrysanthemum varieties, and a new method for the analysis of complex traits of ornamental plants.

Reactive oxygen species (ROS) are a ‘double-edged sword’ in plants. On the one hand, ROS, as a signal molecule, plays pivotal roles in many aspects of life activities; on the other hand, excessive accumulation of ROS can cause oxidative damage to biological macromolecules. Accurate detection of ROS is essential to assess its intracellular redox status. Due to the characteristics of short half-life and strong reactivity of ROS components, their qualitative and quantitative analysis are difficult. It is critical to select the appropriate detection method and improve the spatiotemporal accuracy of detection for research in plant sciences and in other fields. At present, fluorescent probe analysis has attracted the attention of researchers because of its advantages of high sensitivity, good selectivity, low detection limit and strong intuition. This article introduces the detailed operation protocol and attentions for ROS detection using 2′,7′-dichlorodi-hydrofluorescein diacetate (H2DCFDA) fluorescent probe based on flow cytometry and confocal microscope. These methods can be used to detect ROS levels and distribution in model plant tissues, including Oryza sativa, Arabidopsis thaliana, Zea mays and Glycine max.

A large area of membrane surface and intracellular immune receptors have been evolved in higher plants to sense various pathogen signals and prevent pathogen invasion. Among them, pattern recognition receptors on the cell surface activate basic immune response after sensing pattern molecules, while nucleotide-bounding leucine-rich repeat proteins (NLRs) activate specific immune response by sensing effector proteins secreted by pathogenic microorganisms, resulting in hypersensitivity and cell death. In this review, the latest research progress of plant immunity is mainly reviewed from the aspects of NLRs on the recognition of effector proteins, plant immune activation and downstream signal regulation.

CRISPR/Cas9-based genome editing technology has been an important tool to study the gene function and genomic modification. Directed by a guide RNA, Cas9 protein can cleavage the genomic DNA at the target site, and produce mutations, including deletion, insertion, substitution and fragment deletion, by DNA double strand break (DSB) repair mechanism. In this protocol, we introduce the method to use CRISPR/Cas9 system to increase the efficiency of genomic DNA fragment deletion with microhomology-mediated end joining, especially the details in target design and detection of mutant plants.

Spatiotemporal heterogeneity is a key factor for functional differentiation in different tissues and plays an important role in regulating cell fate. Spatiotemporal transcriptomic sequencing (stRNA-seq) is an emerging omics technology that combines quantitative transcriptome with high-resolution tissue imaging. It anchors expression data to the physical map of a target organ or tissue and molecularly characterizes tissue sections and cell layers via unbiased bioinformatic analysis, which reflects the spatiotemporal heterogeneity of gene expression abundances within specific cells. Benefiting from the rapid development of high-throughput sequencing, the spatiotemporal heterogeneity of gene expression in various cells can be explored by new experimental approaches. In this review, we first briefly introduce the principle and development process of stRNA-seq, providing readers an overview on the characteristics, advantages and disadvantages of different stRNA-seq techniques. Then, we summarize the applications of stRNA-seq in animals, plants and microorganisms, which provide theoretical references for the systematic research of stRNA-seq in future.

Small RNAs are a type of small nucleotide molecules that are essential for plant growth and development, playing a key role in variety of life processes and in response to stresses. Research on the location of small RNAs could discover their functions in plants. Small RNA FISH is a qualitative or semi-quantitative analysis of small RNA in organisms by fluorescence detection technology. At present, this technology has been widely used in animals, but it is still less applied in plants. This article introduces the specific operation procedures and attentions based on ultra-high resolution microscopy that combines locked nucleic acid (LNA) probe in situ hybridization with immunofluorescence. This protocol can be used to detect the expression and localization of small RNA in plant tissues.

FLOWERING LOCUS C (FLC) is an important repressor of plant flowering. It mainly represses flowering by binding to the promoters of two downstream key floral promoting genes, FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1). It also regulates flowering time by binding to other regulatory genes. While the detailed molecular mechanisms of FLC in the regulation of flowering still need to be deeply investigated. This review summarizes the new research progresses of FLC in recent years in the 8 genetic pathways of flowering regulation, and give an outlook for the future study in this field.

Calcineurin B-like proteins (CBLs) and their CBL-interacting protein kinases (CIPKs) are important regulatory network in response to abiotic stresses. The CBL-CIPK system senses and decodes Ca²⁺-signals through phosphorylation to regulate plant response to abiotic stresses. In this review, the basic structures of CBLs and CIPKs, and their phosphorylation on different substrates, as well as regulatory mechanisms of plants in response to abiotic stresses were summarized. We also put forward a perspective on the future research directions of CBLs and CIPKs, as well as their potential applications in genetic improvement of crops for stress tolerance.

As a small molecule volatile compound released by green plants, trans-2-hexenal plays a vital role in regulating plant growth and resistance to various environmental stresses. Studies have shown that trans-2-hexenal exhibits obvious inhibition on growth of plant root, and defense against bacterial infection and herbivorous feeding. Furthermore, it also displays a ‘messenger’ role in transmitting defense signals among plants. This paper reviewed trans-2-hexenal biosynthesis, metabolism pathway and its important role in defense response to biotic stress, also discussed the current problems in this research field and suggestions for future research, which would be helpful to illustrate defense or growth mechanism in plant response to trans-2-hexenal.

Melatonin (N-acetyl-5-methoxytryptamine) is a small molecule indoleamine that is essential for life. Melatonin is widely present in animals and plants, and plays a vital role in the growth and development. With the study of plant melatonin, its synthesis pathway and roles in plants have become clear. Studies have shown that melatonin has the regulatory effects in improving plant resistance to abiotic and biotic stresses. This review summarizes the research progress of melatonin in plant abiotic and biotic stresses in recent years; it provides reference for in-depth analysis of influence of melatonin on the regulation mechanism of plant resistance to stresses.

Dioecious plants provide ideal materials for studying the sex determination mechanisms and the origin and evolution of sex chromosomes. Cloning of sex determination genes is crucial for revealing the sex-determination mechanism. There are many woody dioecious plant species, which contain two opposite sex determination systems: XY (females are homogametic XX and males are heterogametic XY) and ZW (females are heterogametic ZW and males are homogametic ZZ). Besides, trees of different sexes may have different economic values. Studies on the sex determination of woody plants not only have theoretical significances, but also have potential practical applications. With the development of large-scale sequencing technology, more and more sex determination genes of woody plants have been identified and cloned, which provides strong experimental evidence for the evolutionary history of dioecious plants and sex chromosomes. In this review, we summarized the important research progress on sex determination genes of woody plants, and discussed some future perspectives in this area.

Mitogen-activated protein kinase (MAPK) cascade is an important and highly conserved cellular signal transduction pathway by delivery and amplification of upstream signals through protein kinase cascade phosphorylation in eukaryotes. In plants, MAPK signaling pathways not only mediate plant responses to environment, but also play crucial roles in regulating plant growth and development. A recent study from the Zhaojun Ding’s group of Shandong University uncovered a novel molecular mechanism of MPK14-mediated auxin signaling in lateral root development via ERF13- regulated very-long-chain fatty acids (VLCFAs) biosynthesis. This study reveals the molecular mechanism of the lateral root development from a new perspective, and further confirms the coupling between the vital phytohormone auxin and the ancient MAPKs module. Since lateral roots act as essential organs for plants in response to environment, deciphering the MAPK signaling pathway in regulation of lateral root development will provide a new strategy for how plants integrate development signals and environmental cues.

Crop productivity relies heavily on inorganic nitrogen (N) fertilization, while excess application of N fertilizers results in detrimental effects on ecosystem and plant developmental process. Thus, the improvement of crop N use efficiency (NUE) is critical for the development of sustainable agriculture. Thus far, significant advances in understanding the regulation of NUE have been achieved in rice (Oryza sativa), one of the most important food crops. Several key transporter and regulatory genes involved in N uptake, translocation, and metabolism have been cloned and characterized in rice. However, the genetic mechanisms underlying the geographic adaptation of rice to the change of local soil N status remain elusive. Recently, a team led by Prof. Chengcai Chu, in Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, evaluated the responses to N supplies of rice germplasm resources collected from different eco-geographical regions worldwide. By performing genome-wide association study on rice tillering response to N (TRN), OsTCP19 is identified as a repressor of TRN, and a 29 bp InDel polymorphism in its promoter determines TRN variations among the rice varieties. OsTCP19 regulates TRN by inhibiting the transcription of DLT, a tiller-promoting gene, whilst the transcription of OsTCP19 itself is controlled by a N responsive suppressor LATERAL ORGAN BOUNDARIES DOMAIN (LBD) protein. Notably, OsTCP19 haplotypes were selected among rice germplasms and correlated with local soil N content. This study not only reveals the genetic basis of geographic adaptation of cultivated rice to the changes of soil N environment, but also provides novel genetic candidates for effective breeding of higher NUE rice cultivars.

Dryopteris fragrans is a perennial herb fern with medical and economical values, such as anti-oxidation, bacteriostasis, anti-psoriasis, and anti-tumor. The wild resources of D. fragrans are scarce. Establishing a regeneration system for D. fragrans through tissue culture is needed to enable a sustainable use of this valuable resource. In this experiment, through sterile culture of spores of D. fragrans, the effects of different factors on prothallium proliferation, sporophyte induction, callus induction and proliferation, cluster bud differentiation, and rooting were compared and analyzed to establish a rapid propagation system, which laid the foundation for large-scale production of D. fragrans. The results showed that 1/2MS medium provided optimal growth with green color and a multiplication factor up to 5.67±0.59. The obtained plants have numerous young spores, and the spore induction rate was (37.50±2.04)%. The most efficient callus induction medium contains 1/2MS media supplied with 2.0 mg·L^-1 6-BA, and 1.0 mg·L^-1 2,4-D, which reached an induction rate up to (96.67±5.77)%. The optimal callus proliferation medium we obtained was 1/2MS media supplied with 1.0 mg·L^-1 6-BA, and 0.5 mg·L^-1 2,4-D, which reached a proliferation factor of 13.30. The obtained granular callus produced a large number of cluster buds (53.33±3.33)% in 1/2MS medium, and 1/2MS media supplied with 0.2 mg·L^-1 NAA medium promoted rooting, resulting in a transplanting survival rate of ~60%.

In this study, a simple and stable genetic transformation system of foxtail millet (Seteria italica) was established and optimized, in which shoot tips were used as the explant. We transformed Yugu 1, an elite millet cultivar, by Agrobacterium-mediated transformation, and tested different treatments to boost transformation efficiency. We used a PCR-based assay to screen transformants in third-leaf stage seedlings. We determined an optimal lethal concentration of glufosinate (Basta) when sprayed to millet seedlings, and tested the different PCR-based genotyping methods with or without Basta spary. Using the newly established pipeline, we further optimized various crucial factors that affect genetic transformation efficiency. We found that an optimal concentration of bacterial culture was OD₆₀₀=1.4, an optimal concentration of acetolsyringone was 800 μmol∙L ^-1. We also obtained high transformation efficiency with an infecting pressure at 0.05 MPa, and an infecting time of 40 min. We used the above-mentioned transformation method to transform a Seteria italica calcineurin B-like protein 4 (SiCBL4) overexpression construct. Genetic stability analysis on T₂ generation transformed plants was performed by the combination assay of Basta resistance and real-time quantitative fluorescence RT-PCR, which can save the time of genotyping. Altogether, this study establishes a shoot tip-based stable genetic transformation system for foxtail millets, and also develops a robust pipeline to detect transgenic offsprings.

High yield and good quality of rice are important guarantees for food security in China, as well as the objective which breeders are pursuing. Grain-filling rate (GFR) is an important and complex agronomic trait in rice, directly affecting grain plumpness, weight, and quality. To date, elite rice germplasm with rapid GFR is rare, and valuable gene resources for breeding remain limited, which has become a bottleneck for further improvement of yield and quality in rice breeding. Comparing with other rice agronomic traits, GFR is highly complex for its spatio-temporal dynamics and environment- dependent variability, the research of which has long been concentrated on the physiological and biochemical characteristics and cultivation measure control of grain-filling period. The study on the molecular mechanism and genetic regulation of GFR has arisen relatively recently. Here, focusing on the GFR-related genes in rice identified recently, we reviewed the preliminarily known molecular mechanism and genetic regulation of GFR, including the influence of sugar metabolism and transport-related genes on GFR, the transcriptional and translational regulatory genes in GFR, the function of grain size and weight-related quantitative trait loci (QTLs) of GFR, and the analysis of GFR-related QTLs; we also discussed the future perspective of the research strategies for GFR, especially the application potential of phenomics-related technologies for GFR research, in order to promote the foundational research and application in rice breeding.

Target of rapamycin (TOR) is a highly conserved serine/threonine-protein kinase among all eukaryotes. As a central regulator, TOR integrates nutrient, energy, growth factor and environmental signals to control cell proliferation, growth, and metabolism. With the establishment of TOR research systems in plants, tremendous progress has been made in, both conserved and unique functions of plant TOR have been uncovered in recent years. Here, we reviewed TOR complexes and the mechanisms of plant TOR integrating sugar, nitrogen, phosphate, sulfur, phytohormone and stress signals to orchestrate transcription, translation, metabolism, autophagy, and stress responses. We also highlight a few fundamental questions that will be of great interest to be resolved for fully revealing biofunctions of plant TOR.

Plant cells rely on the receptors on the plasma membrane to sense and transmit environmental signals that mediate by the specific binding of ligands, thus initiating a series of downstream signaling pathways to maintain normal activities of plants and their responses to environmental stimuli. Receptor-like kinases (RLKs) are a group of important receptors composed of extracellular binding domain, transmembrane domain and intracellular kinase domain, which are the important regulatory hubs of plants to respond to environmental stimuli. FERONIA (FER) is a member of CrRLK1L receptor protein kinase family, which was firstly identified to play a role in the recognition between male and female game- tes in higher plants. Subsequently, numerous studies have shown that FER plays an important role in various biological processes, such as plant growth and development, hormonal cross-talk, responses to biotic and abiotic stress. FER has become a “star protein” in the studies of plants signaling transduction in recent years. With the intensification of the studies on plant pathology, the functions of FER in the interaction between plants and pathogens have attracted more attention. In this paper, we summarized the advances in understanding the functions of FER in the plants-pathogen interaction. This review will provide a reference for further understanding the mechanisms of receptor-like protein kinases of plant cells in response to pathogen infection.

In order to establish the regeneration system of Cerasus serrulata var. lannesiana cv. ‘Grandiflora’, the effects of different explants and plant hormone combinations on callus induction, adventitious bud differentiation, proliferation and rooting were studied using perennial mother plant leaflets, annual grafted seedling leaflets, axillary bud induction leaflets and proliferative first-generation leaflets as explants. The results showed that callus could be induced from all four explants, and adventitious buds could be derived from all explants except the leaflets of perennial mother plants. The higher the degree of explants’ juvenility, the greater the success of subsequent culture, with the best explants were the proliferative first generation leaflets. The best medium for callus induction was MS+0.5 mg·L^-1 6-BA+1.0 mg·L^-1 2,4-D, and the induction rate was 96.22%. The optimal medium for differentiation was MS+1.0 mg·L^-1 6-BA+0.1 mg·L^-1 2,4-D+0.1 mg·L^-1 TDZ, and the differentiation rate was 78.14%. The optimal medium for proliferation was MS+1.0 mg·L^-1 6-BA, and the proliferation coefficient reached 7.85. The optimal medium for rooting was 1/2MS without any hormone, and the regenerated plants with 100% rooting rate were obtained. The regenerated plants from different explants grew very differently, and those induced from first generation of proliferative leaflets had the best growth.

Because the genome of an organism determines its primary phenotype, evolutionary principles suggest that genetic variations enhance phenotypic diversity towards increased fitness. Targeted saturation mutagenesis of crop genes could be used to screen for genetic variants with improved agronomic traits. Compared to traditional mutational breeding or directed evolution in heterologous organisms, targeted mutagenesis via dual cytosine and adenine base editors effectively generates endogenous mutagenesis and facilitates in vivo directed evolution of plant genes. In this protocol, we detail the process towards using saturated targeted endogenous mutagenesis editors (STEMEs) to generate targeted, random mutagenesis of plant genes. In particular, we focus on the process of designing targets, screening and genotyping the resulting evolved variants.