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.

With the increase in atmospheric CO₂ concentration caused by human activities, the global climate continues to warm. The past five years have been the hottest since the record of temperature. High temperature stress has become one of the main adverse factors affecting plant growth and development. Photosynthesis is the basis of life activities on earth, and it is highly sensitive to fluctuation in environmental factors. Understanding the response of plant photosynthesis under high temperature stress can provide a scientific basis for exploring the physiological and ecological mechanisms of plant tolerance to high temperature stress, cultivating new heat-tolerant varieties and taking reasonable measures to adapt to extreme climate in the future. In this paper, the effects of high temperature stress on the process of photosynthetic electron transfer and carbon fixation in plants were reviewed, and the effects of light on photosynthesis under high temperature stress were comprehensively analyzed from the perspective of light quality and light intensity. This paper also expounded the ways and mechanisms to improve the tolerance of plants to high temperature stress from the aspects of plants themselves and exogenous mitigating substances. Meanwhile, the research direction of plant photosynthesis response to high temperature stress and the application of multi-histology combined analysis in the comprehensive study of the mechanism of plant tolerance to high temperature stress were prospected.

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.

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.

Multidrug and toxic compound extrusion (MATE) transporters are also known as detoxification efflux carriers (DTXs) that are ubiquitously present in prokaryotes and eukaryotes. MATE transporters are membrane proteins usually with twelve transmembrane regions arranged in a "V" shape. MATE/DTX transporters are mainly involved in the modulation of iron homeostasis, transport of inorganic anions and secondary metabolites, the detoxification of heavy metals and xenobiotics, regulation of growth and development, and response to diseases and abiotic stress in plants. This review summarizes the research progress for the discovery, phylogeny, structure, and function of MATE/DTX family proteins and may provide a reference for the stress tolerance improvement of crops and forages with MATE/DTXs.

Phylogenetics is a discipline reconstructing evolutionary relationships of organisms. With improvements in sequencing technique, analytic methods, and computation power, the molecular data have been used widely and have promoted greatly the rapid development of molecular phylogenetics. The phylogenetic tree has become a powerful tool in many areas of biology, such as ecology and comparative biology. Currently, phylogenetic studies mainly focus on phylogenetic tree reconstructions by using various software, however, some fundamental principles or matters that should be paid attention when performing phylogenetic analyses are sometimes weakened or even ignored. Here, we present the workflow and methods in details for phylogenetic tree reconstruction based on molecular data, including taxon sampling, molecular marker selection, sequence alignment, partitioning and model selection, combined analysis of multiple markers, and topological test. Currently, the widely used methods of phylogenetic reconstructions are maximum parsimony, maximum likelihood, and Bayesian inference. We thereby provide the detailed operating flows and corresponding commands for these three methods, respectively. We expect this paper will provide a reference for relevant researches.

Receptor-like kinases (RLKs) are a large family of transmembrane protein kinases, which play an important role in the regulation of cell communication and signal transduction under different environmental conditions. The extracellular region of RLKs can sense and transmit extracellular and environmental signals that mediate by the specific binding of ligands, which in turn initiates a series of downstream signaling pathways through the interaction with its co-receptors, thus regulating plant growth, development, and environmental adaptation. The rice (Oryza sativa) genome contains at least 1 131 RLKs, nearly twice the number found in Arabidopsis thaliana. RLKs are further divided into more than 20 subfamilies based on the characteristic motifs and structural domains of their extracellular regions. Although ligands and interacting proteins of some RLKs have been identified, the biological functions of most RLKs remain unclear in rice. In this review, we summarize current advances in understanding the mechanisms of RLKs-mediated signaling pathways and their contributions to plant growth and environmental adaptations in rice. The progress in understanding of RLKs and function roles in regulating plant growth, development and their adaptations to environments will facilitate breeding strategies for future sustainable agriculture and a new Green Revolution.

In 2022, the numbers of original research articles published by Chinese plant scientists in mainstream plant science journals increased significantly compared with that in 2021, and important advances have been made in the fields of preventing “polyspermy fertilization” mechanisms, extracellular pH receptors, chloroplast protein transport channel structures, mechanisms of crop yield, quality, stress tolerance, disease resistance, and symbiotic nitrogen fixation, the origin and evolution mechanisms of self-incompatibility in angiosperms, and the evolution of sugarcane and maize germplasm resources. Among them, “New Mechanisms for Mining and Regulating High Temperature Resistance Genes in Rice” was selected as one of the “Top Ten Advances in Life Sciences in China” in 2022. Here we summarize the achievements of plant science research in China in 2022, by briefly introducing 30 representative important research advances and sorting out the experimental materials used in plant science research, so as to help readers understand the trend of plant science development in China, and evaluate future research direction to meet national needs.

Self-incompatibility (SI) is an intraspecific reproductive barrier widely occurring in flowering plants to prevent inbreeding depression by promoting outcrossing. However, this trait severely restricts the production of homozygous lines in hybrid breeding, especially for the forage crops mostly belonging to Fabaceae, Asteraceae and Poaceae with unclear molecular mechanisms of SI. Therefore, SI has become one of the major barriers limiting the development of forage industry in China and even in the world. So far, large progresses have been made in the biochemical and evolutionary mechanisms of five different SI types, providing a good foundation for further exploring the SI mechanisms of Fabaceae, Asteraceae and Poaceae forage crops. Here, we briefly review the mechanisms of the five reported SI types and the research progress of SI and inbreeding depression in Fabaceae, Asteraceae and Poaceae.

Life science is entering into the era of big data due to the rapid development of high-throughput omics technology. Multi-omics data such as genome, transcriptome, proteome, metabolome have greatly facilitated dissecting the complex and sophisticated regulatory networks of organisms. Recently, a collaborative team led by Lin Li, Fang Yang and Jianbing Yan from Huazhong Agricultural University constructed the first multi-omics integrative network map of maize. This map comprises over 30 000 genes and 2.8 million network edges at the levels of genome, transcriptome, translatome, and proteome, finally forming 1 412 regulatory modules. Using the integrative network map, the research team successfully predicted and confirmed five new functional genes regulating the development of tiller, lateral organ, and kernel in maize. Based on the integrative map and machine learning, the research team identified 2 651 maize flowering time genes that are enriched in eight candidate subnetworks. The biological functions of 20 flowering candidate genes were further validated using CRISPR/Cas9 gene editing technology and EMS mutants. Furthermore, evolutionary analysis of the integrative network map showed that the two subgenomes of maize had undergone a progressive functional differentiation from the levels of co-expression, co-translation to interactome. The construction of the multi-omics integrative network map represents an important breakthrough in maize functional genomics, which provides a new tool for cloning new genes, identifying novel molecular regulatory pathways, and revealing maize genome evolutionary features. This multi-omics integrative network map is a new key to decode maize functional genomics.

Since the 1960s, the utilization of semi-dwarfing genes Rht-B1b and Rht-D1b has significantly improved the lodging resistance and harvest index of wheat (Triticum aestivum), leading to a doubling of global wheat production and triggering the “Green Revolution” in agriculture. Rht-B1b and Rht-D1b encode plant growth-inhibiting factors, DELLA proteins, which are negative regulatory factors in the gibberellin (GA) signaling pathway. Accumulation of DELLA proteins not only inhibits cell division and elongation, leading to a dwarf phenotype, but also suppresses photosynthesis and nitrogen use efficiency, resulting in semi-dwarf varieties requiring higher fertilizer inputs to achieve high yields. Addressing the challenge of “reducing fertilizer inputs while increasing efficiency” is a crucial issue for achieving green and low-carbon agriculture. Recently, Zhongfu Ni and his colleagues from China Agricultural University identified a novel “semi-dwarfing” regulatory module with potential breeding applications and demonstrated that reducing brassinosteroid (BR) signaling could enhance grain yield of wheat “Green Revolution” varieties (GRVs). They isolated and characterized a major QTL responsible for plant height and 1000-grain weight in wheat. Positional cloning and functional analysis revealed that this QTL was associated with a ~500 kb fragment deletion in the Heng597 genome, designated as r-e-z, which contains Rht-B1 and ZnF-B (encoding a RING E3 ligase). ZnF-B was found to positively regulate BR signaling by triggering the degradation of BR signaling repressor BRI1 Kinase Inhibitor (TaBKI1). Further experiments showed that deletion of ZnF-B not only caused the semi-dwarf phenotypes in the absence of Rht-B1b and Rht-D1b alleles, but also enhanced grain yield at low nitrogen fertilization levels. Thus, manipulation of GA and BR signaling provides a new breeding strategy to improve grain yield and nitrogen use efficiency of wheat GRVs without affecting beneficial semi-dwarfism, which will drive toward a new “Green Revolution” in wheat.

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.

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.

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.

Broomcorn millet (Panicum miliaceum) has a short growth period, high water use efficiency, resistance to salt, alkali, and insect pests. It is an important crop in the adjustment of planting structure. Broomcorn millet is rich in starch, protein, essential amino acids, unsaturated fatty acids, vitamins (niacin, B vitamins, folic acid, etc.), minerals (phosphorus, calcium, zinc, iron), dietary fiber, phenolics, etc. It is also gluten-free, an ideal food for people who are allergy to gluten. In addition, broomcorn millet has the functions of lowering blood sugar, anti-inflammatory, and preventing cardiovascular and cerebrovascular diseases. Therefore, broomcorm millet is an environmental friendly crop and beneficial to human health. It can be used as a future smart food for our country to deal with hidden hunger. This paper summarizes the research progress on the quality of broomcorn millet from the perspectives of appearance quality, nutritional quality and processing quality, and provides a reference for the quality research, processing and utilization of broomcorn millet.

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.

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.

The genera of Lolium and Festuca include many cool season forage grasses and turf species, such as Italian ryegrass (L. multiflorum), perennial ryegrass (L. perenne), tall fescue (F. arundinacea) and meadow fescue (F. pratensis). The ryegrass can be used as hay and silage, due to its high yield, broad adaptability, rich nutrition, good palatability, and high digestibility; and it was considered as a high-quality feed. But because its cultivation region in China is limited by geography factors, the current proportion of ryegrass in China’s grass pasture industry is still very small. In order to increase the proportion of ryegrass cultivation, the use of molecular breeding methods to breed excellent varieties maybe one of the key directions. In this review, we summarized recent progress in the Lolium-Festuca complex, especially in Lolium, including classification and evolution study, molecular marker development, linkage map construction, quantitative trait locus (QTL) and genome wide association study (GWAS) for important agronomic traits, genome sequences, transcriptome analysis, gene cloning and variety breeding. We also brought up some biological issues in Lolium species that need to be resolved, and try to provide some reference for further strengthening the basic biological research and molecular breeding of ryegrass.

Xylan is a major component of hemicellulose that widely present in the cell walls of various types of plants and is essential for the growth and development of plants. Many studies have shown that the content and structure of xylan in the cell wall have a significant impact on the processing characteristics of biomass. Hence, understanding the mechanism of xylan biosynthesis will enable us to modify the cell wall through genetic engineering. During last decade, many genes involved in xylan biosynthesis have been characterized in the model plant Arabidopsis and some important grain and cash crops. This article reviews these recent findings and discusses the potential applications of xylan biosynthesis genes in biomass energy and related fields.

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.

Rhododendron is famous for its diversity and ornamental value. Rhododendron ovatum has unique flower type and low-altitude adaptability, thus possessing landscape application prospect in southern China. In this study, we analyzed evolutionary pattern within Ericales based on recently published genomes, and identified key genes underlying flower development of R. ovatum. Phylogenetic analysis showed that the number of MADS-box genes in three representative species of Rhododendron (R. ovatum, R. simsii, and R. delavayi) was relatively consistent and can be divided into 19 subfamilies, including AP1, AP3, PI, AG, and SEP. MADS-box gene have expanded, especially SVP, ANR1, Mα, Mβ, and Mγ. Multiple copies were retained in AG and SEP clades in R. ovatum. While a few copies of AP3/PI gene, indicating a more conservative evolutionary pattern. The transcriptome data illustrated tissue-specific expression pattern in MADS-box genes, among which AP1, AP3/PI, AG, SEP and MIKC* genes are specifically expressed in floral organs. Overall, we discussed evolutionary history of MADS-box gene family in R. ovatum and proposed functions, providing reference for further study the flower development and functional analysis of MADS-box genes in R. ovatum.

Modern science and technology have just been entering the field of grass-based livestock husbandry, and “less input, low output and poor platform” restrict the development of forage breeding and industry in China. Although the development of grass-based livestock husbandry is ready to take off, the lack of scientific and technological innovation is difficult to ensure China’s food security; furthermore, there are few institutions and teams that focus on forage breeding research in China. Therefore, we organize the special issue ‘Forage Biology’, aiming to promote public awareness of the scientific and technological innovation, industrial development and national forage seed industry safety.

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.

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.

In China, the demand for high-quality forage is continuously increasing. Improving the yield and quality of various forages, especially alfalfa (Medicago sativa), has been an important scientific and economic goal for plant breeders. Fixation of carbon dioxide by photosynthesis is the basis for the formation of forage biomass. Nitrogen absorption, fixation, transport and assimilation are important biological processes that affect the crude protein content of forage and determine its quality. Both biological processes are interdependent to each other. Therefore, we propose the new breeding ideas for efficient fixation, transport and assimilation of carbon and nitrogen in alfalfa, and summarize the latest progress in efficient fixation and transport of carbon dioxide, nitrogen fixation and absorption, as well as nitrogen transport and assimilation in recent years, so as to shed some light on molecular design breeding for forage with high biomass and high protein content in the future.

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.

Atraphaxis spinosa, A. jrtyschensis, and A. decipiens are three species with sympatric distribution in northern Xinjiang, China. In this study, their chloroplast genomes were assembled and annotated with the second-generation high-throughput sequencing technology (NGS). We compared the nucleotide sequences of the chloroplast (cp) genomes of these three Atraphaxis species and carried out the phylogenetic analysis. The results showed that the cp genomes of the three species ranged from 164 106 bp to 164 216 bp, similar to that of other green plants, all including a pair of inverted repeats separated by a large single-copy and a small single-copy region. We detected a total of 48-49 tandem repeats and 59-63 simple sequence repeats (SSRs) from the three cp genomes. The mean value of nucleotide diversity of the three species was 0.000 96, the average score of K_a/K_s ratio was 0.030 3, and the mean genetic distance value was 0.001 0. A comparative analysis showed that the coding regions were more conserved than the non-coding regions. The phylogenetic analysis showed that the three species were closely related. This study reveals the phylogenetic relationships among the three sympatric distribution species of Atraphaxis based on complete chloroplast genomes, and the phylogenetic position of Atraphaxis in the family Polygonaceae. This work may provide a reference for taxonomic, systematic and biogeographical studies of Atraphaxis.

The F₂ and F₃ populations derived from the cross between Sulv16-10 and Weilv11 were used to explore the genetic loci controlling yield-related traits in mungbean, and the phenotype identification and correlation analysis between yield-related traits were completed. The genetic linkage map was constructed and used for QTL analysis. The yield per plant was positively correlated with the number of pods per plant, the number of seeds per pod, hundred-seed weight and the number of branches on main stem. The correlation between the yield per plant and the number of pods per plant was the highest, and the correlation coefficient between these two traits were 0.950 and 0.914 in F₂ and F₃ population, respectively. A total of 8 QTLs for yield-related traits were detected in the F₂ population. Among them, three traits including the number of pods per plant, number of seeds per pod and yield per plant were found only on one related QTL, and each QTL accounting for 11.09% (qNPP3), 17.93% (qNSP3) and 14.18% (qYP3) of phenotype variance, respectively. Two QTLs, qBMS3 and qBMS11 related to the branch number on main stem were detected, which could explain 18.51% and 7.06% of phenotype variance, respectively. Three QTLs, qHSW3, qHSW7 and qHSW10 controlling hundred-seed weight were identified, which could explain 5.33%, 46.07% and 4.24% of phenotype variance, respectively. qNSP3 and qHSW7 were detected again in the F₃ population, demonstrating that the two QTLs were genetically stable. The InDel molecular marker R7-13.4 which closely linked to the major-effect QTL qHSW7 for hundred-seed weight was developed, and the validation of molecular marker-assisted selection was verified in natural populations. These studies provide reference for mapping, cloning of genes associated with yield-related traits as well as molecular marker-assisted selection in mungbean.

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

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.

Common bean (Phaseolus vulgaris) is an important bean crop but it is highly susceptible to salt stress which causes yield decrease. Melatonin can improve the salt tolerance of plants. However, the mechanism of exogenous melatonin in regulating the salt tolerance of common bean has not been explored. In this study, the common bean variety Naihua common bean (GZ-YD014) was used as materials, and three treatments were set for comparisons, including water (W, control), salt stress (S), and salt stress+100 µmol∙L^-1 melatonin (M+S). The results showed that salt stress inhibited the growth of sprouts, whose length, surface area, volume and diameter decreased significantly under salt stress conditions. Exogenous melatonin alleviated the inhibition of salt stress on the growth of common bean sprouts by signi-ficantly reducing the accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA) content, increasing protective enzymes such as peroxidase, superoxide dismutase, catalase and ascorbate peroxidase, osmotic regulators including soluble sugar and soluble protein content, auxin (IAA), gibberellin (GA), zeatin (ZT) content, and decreasing abscisic acid (ABA) content. Transcriptome analysis discovered 217 differentially expressed genes (DEGs), which were significantly enriched (P-value<0.05) in the nucleic acid-related entries by GO enrichment analysis and also in the nucleic acid damage repair (including base excision repair, mismatch repair and nucleotide excision repair) pathways by KEGG enrichment analysis (P-value<0.05). Real-time quantitative PCR and random amplified polymorphism analysis proved that the nucleic acid damage repair was a mechanism of exogenous melatonin regulating the salt tolerance of common bean. The study revealed the mechanism of exogenous melatonin regulating the salt tolerance of common bean sprouts, and provided a theoretical basis for the application of melatonin in common bean to increase yield under salt stress.

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.

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.

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.

In 2023, the numbers of original research articles published by Chinese plant scientists in mainstream plant science journals increased significantly improved compared with that in 2022, and important advances have been made in the fields of regulation of intraspecific and interspecific reproductive isolation in Brassicaceae by stigma receptors, supercomplex structure of chloroplast TOC-TIC, mechanisms of crop yield, disease resistance, stress tolerance, the origin and spread of grapes and citrus plants, and the evolution of modern maize, millet and potato germplasm resources. Among them, “Crop Salt and Alkali Tolerance Mechanisms and Applications”, and “A New Method for Precise Manipulation of Single Base to Large Fragment DNA” in 2023 were selected as two of the “Top Ten Advances in Plant Sciences in China”; “The Molecular Mechanism of Mentor Pollen Effect in Plant Distant Hybridization” was selected as one of the “Top Ten Advances in Life Sciences in China” in 2023. Here we summarize the achievements of plant science research in China in 2023, by briefly introducing 30 representative important research advances and sorting out the experimental materials used in plant science research, so as to help readers understand the trend of plant science development in China, and evaluate future research direction to meet major national strategic needs.

The cell is the basic structural and functional unit of living organisms, its complex internal organizational structure, interaction and process dynamics determine the life form and life process of the entire organism. The study of cell structure and function in the living state is of great significance for exploring and grasping the essence of life. With the continuous advances in science and technology, a series of new live cell labeling technologies have been innovated. In recent years, the Halo-tag labeling technology has gradually been developed into a widely used new molecular labeling technology, playing an increasingly important role in the field of living cell imaging analysis and tracking research. It has been gradually applied in plant cell imaging. In this review, we focus on the definition, classification and development process of Halo-tag technology, and introduce the reaction mechanism of the dehydrohalogenation of Halo-tag labeling technology and the types of fluorescent ligands in detail. Finally, we introduce the latest progress of this technology in the application of living cell imaging in plants is emphatically expounded from three aspects: observing the fine localization of molecules, tracking the real-time motion of molecules and detecting the interactions between molecules. Taken together, this study provides theoretical foundation and technical support for the potential application of the subsequent Halo-tag labeling technology in plants.

Gene editing technology can manipulate the genome of organisms precisely and directionally. It is one of the most eye-catching subversive technologies in the field of life sciences, and has become the key technology in breeding of agriculture and animal husbandry. Recently, the demand for high-yield and high-quality forage grass are increasing in China, therefore, it is urgent to cultivate high-quality forage grass varieties with independent intellectual property rights. Here, we briefly reviewed the development of gene editing technology and its application in agricultural breeding, summarized the research progress in genome editing of gramineous and leguminous forage, and prospected the future direction of molecular module-based technology in forage grass breeding using genome editing.

Oat (Avena sativa) is an annual grass species grown as either a grain or a forage crop. Its valuable nutrition and excellent forage quality make its market demand increase year by year, which brings forth new requirements for innovative oat cultivars. Molecular breeding is the ideal technology for oat improvement with its high precision and efficiency. Genomic study of oat is the very important basis for the analysis of important agronomic traits, the precise utilization of excellent germplasm and molecular design breeding of oats. This article mainly reviews the important achievements of world-wide oat germplasm resources collection and preservation, genome composition and chromosome ploidy level variations in the genus Avena, oat genetic linkage map construction and oat genome sequencing, as well as oat molecular breeding. Furthermore, this article discusses the future directions of oat genomic study and molecular breeding in the post genomic era.

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