Autophagy is an evolutionarily conserved self-degradation process in eukaryotes. It not only plays a role in plant growth and development but also is involved in plant responses to biotic and abiotic stresses. Plants can initiate autophagy to degrade the surplus or damaged cytoplasmic materials and organelles, thus coping with abiotic and biotic stresses. The initiation of autophagy depends on autophagy-related genes (ATGs). The transcription factors can directly bind to the promoters of ATGs to activate autophagy and regulate their transcriptional levels and post-translational modifications. Furthermore, ATGs can directly or indirectly interact with plant hormones to regulate plant responses to stresses. When plants are exposed to salinity, drought, extreme temperatures, nutrient deficiencies, and pathogen stress, ATGs are significantly induced, which enhances the autophagy activity to facilitate the degradation of the denatured and misfolded proteins, thereby enhancing plant tolerance to adversity stresses. This article summarizes the discovery, structures, and classification of plant ATGs, reviews the research progress in the mechanisms of ATGs in plant responses to abiotic and biotic stresses, and prospects the future research directions. This review is expected to provide the genetic resources and a theoretical foundation for the genetic improvement of crops in responses to stress tolerance.
Autophagy/physiology* ; Stress, Physiological/genetics* ; Gene Expression Regulation, Plant ; Plants/metabolism* ; Transcription Factors/metabolism* ; Plant Proteins/genetics* ; Genes, Plant ; Plant Physiological Phenomena ; Droughts

In recent years, the spread of clubroot disease caused by Plasmodiophora brassicae infection has seriously affected the yield and quality of Brassica juncea (L.) Czern.. The cascade of mitogen-activated protein kinases (MAPKs), a highly conserved signaling pathway, plays an important role in plant responses to both biotic and abiotic stress conditions. To mine the MAPK genes related to clubroot disease resistance in B. juncea, we conducted a genome-wide analysis on this vegetable, and we analyzed the phylogenetic evolution and gene structure of the MAPK gene family in mustard. The 66 BjuMAPK genes identified by screening the whole genome sequence of B. juncea were unevenly distributed on 17 chromosomes. At the genomic scale, tandem repeats led to an increase in the number of MAPK genes in B. juncea. It was found that members of the same subfamily had similar gene structures, and there were great differences among different subfamilies. These predicted cis-acting elements were related to plant hormones, stress resistance, and plant growth and development. The expression of BjuMAPK02, BjuMAPK15, BjuMAPK17, and BjuMAPK19 were down-regulated or up-regulated in response to P. brassicae infection. The above results lay a theoretical foundation for further studying the functions of BjuMAPK genes in B. juncea in response to the biotic stress caused by clubroot disease.
Mustard Plant/parasitology* ; Plasmodiophorida/pathogenicity* ; Plant Diseases/genetics* ; Mitogen-Activated Protein Kinases/metabolism* ; Phylogeny ; Disease Resistance/genetics* ; Gene Expression Regulation, Plant ; Genome, Plant ; Plant Proteins/genetics*

Lateral organ boundaries (LOB) domain (LBD) genes encode a family of transcription factors ubiquitous in higher plants, playing crucial roles in the growth, development, and stress responses. Hippophae rhamnoides, known for its drought, cold, and saline-alkali tolerance, offers significant economic benefits and ecological values. Utilizing the whole genome data and bioinformatics approaches, this study identified and analyzed the LBD gene family in H. rhamnoides. Additionally, we examined the expression pattern of HrLBD genes by integrating the transcriptome data from male and female flower buds in development. Eleven LBD genes were identified in H. rhamnoides, and these genes were distributed on five chromosomes. The HrLBD proteins showed the lengths ranging from 159 aa to 302 aa, the molecular weights between 18 249.91 Da and 33 202.01 Da, and the subcellular localization in the nucleus or chloroplasts. LBD protein domains and gene structures were highly conserved, featuring similar motifs. The phylogenetic analysis of HrLBD genes and the LBD genes in Arabidopsis thaliana and Hordeum vulgare revealed that HrLBD genes falled into two major categories: Class Ⅰ and Class Ⅱ. The transcriptome data and RT-qPCR showed that HrLBD genes were highly expressed in male flower buds, with up-regulated expression levels throughout bud development, indicating a role in the specific stage of male flower bud development. This study lays a theoretical foundation for exploring the roles of HrLBD genes in the growth, development, and sex differentiation of H. rhamnoides flower buds.
Flowers/genetics* ; Hippophae/metabolism* ; Phylogeny ; Gene Expression Regulation, Plant ; Plant Proteins/genetics* ; Transcription Factors/genetics* ; Multigene Family ; Genes, Plant

Docynia delavayi (Franch.) Schneid. is an economic fruit plant with high medicinal and edible values. The TCP gene family plays a vital role in plant growth and development. To explore the function of the TCP gene family in the growth and development of D. delavayi. In this study, the TCP gene family (DdeTCP) members were identified from the D. delavayi genome and their expression levels at different stages of seed germination and fruit development were analyzed. The results showed that a total of 18 DdeTCP genes were identified from the D. delavayi genome, with uneven location on 11 chromosomes. The phylogenetic tree showed that the 18 DdeTCPs could be classified into class Ⅱ (3) and class Ⅱ (15), suggesting that functional differentiation occurred among the DdeTCP family members. DdeTCP11 highly homologous to AtTCP14 was highly expressed in the early stage of seed germination, which suggested that this gene played a key role in seed germination. In addition, DdeTCP16 in class Ⅱ had a high expression level during the fruit ripening stage, which indicated that it might be related to fruit ripening. The findings lay a foundation for probing into the roles of the DdeTCP gene family in the growth and development of D. delavayi.
Phylogeny ; Gene Expression Regulation, Plant ; Multigene Family ; Genome, Plant/genetics* ; Plant Proteins/genetics* ; Transcription Factors/genetics* ; Germination/genetics* ; Fruit/growth & development* ; Genes, Plant

Rice is the world's largest food crop, and its yield and quality are directly related to food security and human health. Grain size, as one of the important factors determining the rice yield, has been widely concerned by breeders and researchers for a long time. To decipher the regulatory mechanism of rice grain size, we obtained a multi-tiller, dwarf, and small-grain mutant htd1 by ethyl methanesulfonate (EMS) mutation from the Japonica rice cultivar 'Zhonghua 11' ('ZH11'). Genetic analysis indicated that the phenotype of htd1 was controlled by a single recessive gene. Using the mutation site map (Mutmap) method, we identified the candidate gene OsHTD1, which encoded a carotenoid cleavage dioxygenase involved in the biosynthesis of strigolactone (SL). The SL content in htd1 was significantly lower than that in 'ZH11'. Cytological analysis showed that the grain size of the mutant decreased due to the reductions in the length and width of glume cells. The function of htd1 was further verified by the CRISPR/cas9 gene editing technology. The plants with the gene knockout exhibited similar grain size to the mutant. In addition, gene expression analysis showed that the expression levels of multiple grain size-related genes in the mutant changed significantly, suggesting that HTD1 may interact with other genes regulating grain size. This study provides a new theoretical basis for research on the regulatory mechanism of rice grain size and potential genetic resources for breeding the rice cultivars with high yields.
Oryza/growth & development* ; Mutation ; Edible Grain/growth & development* ; Alleles ; Plant Proteins/genetics* ; Dioxygenases/genetics* ; Lactones/metabolism* ; Gene Expression Regulation, Plant ; Genes, Plant ; Gene Editing ; CRISPR-Cas Systems ; Phenotype

Rice (Oryza sativa L.) is an important food crop. The appearance of lesion mimics in rice leads to phytohormone disorders, which affects rice adaptation to environmental stresses and ultimately reduces the yield and quality. To explore whether the changes in the adaptability of rice lesion-mimic mutants to stressful environments are caused by the disorder of phytohormone metabolism in plants. In this study, we screened an ethyl methane sulfonate-treated population of the japonica cultivar 'Taipei 309' for a mutant with rust-like spots on leaves at the early tillering stage and brown-red spots at maturity and named it rsl1 (rust spotted leaf 1). Compared with the wild type, rsl1 showed decreases in plant height, panicle length, primary branch number, secondary branch number, filled grains per panicle, seed-setting rate, and 1 000-grain weight, and an increase in number of effective panicles. Genetic analysis indicated that rsl1 was controlled by a single recessive nuclear gene. RSL1 was localized between two molecular markers, B7-7 and B7-9, on rice chromosome 7 by map-based cloning. PCR sequencing of the annotated genes in this interval revealed a mutation of C1683A on the eighth exon of SPL5 (LOC_Os07g10390) in rsl1, which resulted in premature termination of protein translation. Exogenous phytohormone treatments showed that rsl1 was less sensitive to salicylic acid (SA), abscisic acid (ABA), and indo-3-acetic acid (IAA) and more sensitive to methyl jasmonate (MeJA) and gibberellin acid (GA) than the wild type. In addition, the survival rate of rsl1 was lower than that of the wild type under salt, alkali, drought, and high temperature stresses, and it was higher than that of the wild type under cold stress. Quantitative real-time polymerase chain reaction (qRT-PCR) results showed that RSL1 was involved in the regulation of ABA, SA, MeJA, IAA, and GA-related genes under abiotic stresses. The present study showed that the RSL1 mutation led to the appearance of lesion mimics and affected the growth, development, and stress resistance of rsl1 under abiotic stresses. The study of the functional mechanism of this gene can provide theoretical guidance for the research on rice stress resistance.
Oryza/microbiology* ; Stress, Physiological/genetics* ; Plant Diseases/genetics* ; Cloning, Molecular ; Chromosome Mapping ; Plant Growth Regulators/metabolism* ; Plant Proteins/genetics* ; Mutation ; Cyclopentanes ; Genes, Plant ; Plant Leaves/genetics* ; Oxylipins

The plant AT-rich sequence and zinc-binding protein (PLATZ) family is composed of plant-specific zinc finger-like transcription factors, which play important roles in plant growth, development, and stress tolerance. In this study, to gain a better understanding of the PLATZ gene in C. sinensis and elucidate its response under drought and high temperature conditions, the PLATZ gene family of the C. sinensis cultivar 'Tieguanyin' was systematically identified, and a total of 12 CsPLATZ family members were identified. Expasy online and other bioinformatics tools were used to analyze the members of the PLATZ gene family in terms of protein physicochemical properties, phylogenetic relationships, cis-acting elements, gene structures, and intra- and inter-species collinearity. The results of phylogenetic analysis classified the CsPLATZ family members into 2 subfamilies. The conserved domains and gene structures of PLATZ family members within the same subfamily had a high degree of consistency, whereas a certain degree of diversity was observed among the subfamilies. Twelve PLATZ genes were unevenly distributed across 7 chromosomes of C. sinensis and the promoter regions of these genes had multiple cis-acting elements related to hormone and stress responses. The collinearity analysis showed that there were 4 pairs of duplication events in the CsPLATZ gene family, all of which were segmental duplications. Based on this gene family, C. sinensis had a closer evolutionary relationship with A. thaliana than with O. sativa. The transcriptome analysis showed that the expression levels of CsPLATZ family members varied in different tissue samples of C. sinensis. 6 genes (CsPLATZ-1, CsPLATZ-2, CsPLATZ-3, CsPLATZ-4, CsPLATZ-6, and CsPLATZ-8) with high expression in shoots, young leaves, and roots were selected for high temperature and drought stress treatments, and their expression was quantified by qRT-PCR. The results indicated that the six genes might play important roles in the response to drought stress. In addition, CsPLATZ-2 and CsPLATZ-8 might have important functions in the response to high temperature stress. The results of this study will contribute to a better understanding of the biological functions of PLATZ genes and their possible roles in the growth, development, and stress responses of C. sinensis.
Droughts ; Camellia sinensis/physiology* ; Phylogeny ; Gene Expression Regulation, Plant ; Plant Proteins/genetics* ; Stress, Physiological/genetics* ; Multigene Family ; Transcription Factors/genetics* ; Hot Temperature ; Genes, Plant

Filamentous fungi represent an important group of eukaryotic microorganisms with diverse ecological functions and ubiquitous distribution in various ecosystems. Among them, many species are closely associated with agriculture, functioning as major plant pathogens that cause yield losses and produce mycotoxins to compromise both the quality and safety of agricultural products. In recent years, the CRISPR/Cas system has emerged as a powerful and programmable genome editing tool, and it has been extensively applied to the genetic study of plant pathogenic fungi. This technology has greatly facilitated the investigation of pathogenic mechanisms, mycotoxin biosynthetic pathways and key gene functions, antifungal resistance, and rapid pathogen detection. This review summarizes the development of CRISPR/Cas systems and the key strategies for their application in plant pathogenic fungi and makes an outlook on the practical deployment. With the continuous advancement of gene editing technologies, emerging fungal-adapted editing systems hold great promise for advancing functional genomics and enabling innovations in disease-resistant breeding and sustainable crop protection.
Gene Editing/methods* ; Fungi/pathogenicity* ; CRISPR-Cas Systems/genetics* ; Plant Diseases/microbiology* ; Plants/microbiology* ; Genome, Fungal/genetics*

Trihelix transcription factors play important roles in plant light responses, growth and development, and stress responses. However, Trihelix has not yet been reported in Eucommia ulmoides. In this study, bioinformatics methods were used to comprehensively identify and analyze the expression patterns of the Trihelix gene family in E. ulmoides, aiming to provide a basis for further functional studies of EuGTs genes. A total of 9 Trihelix gene family members were identified in E. ulmoides, encoding proteins with 339 to 883 amino acids, with isoelectric points ranging from 5.13 to 9.39 and relative molecular weights between 36 992.06 and 97 871.61. Subcellular localization results showed that only EuGT-2 was localized in chloroplasts, while the others were located in the nucleus. The Trihelix gene family was categorized into six subfamilies: GT-1, GT-2, SH4, SIP1, GTγ, and GTδ. EuGTs were distributed among three subfamilies: SH4, GT-1, and GT-2, containing 1, 6, and 2 Trihelix proteins, respectively, with 2 to 17 exons. The promoters of EuGTs contained various cis-acting elements related to hormones, stress, photoperiod, and growth and development. Collinearity analysis revealed 5 collinear gene pairs between E. ulmoides and Arabidopsis thaliana, and 14 collinear gene pairs between E. ulmoides and Populus. Expression pattern analysis showed that EuGTs exhibited tissue-specific expression: EuGT-1, EuGT-2 had the highest expression levels in leaves, EuGT-4, EuGT-6, EuGT-9 had the highest transcriptional levels in marginal peel, and EuGT-5、EuGT-8 were predominantly expressed in the xylem. As leaves developed, EuGTs showed a trend of asynchronous changes. No significant differences in EuGTs expression were observed between male and female flowers, with high expression levels mainly during the induction stage of flowering. The qRT-PCR analysis indicated that most EuGTs genes were most highly expressed in the leaves of E. ulmoides, while EuGT-5 was highly expressed in the stems. Under 200 mmol·L~(-1) NaCl treatment, most EuGTs genes exhibited an initial increase followed by a decrease in expression, significantly responding to salt stress. This study provides important genetic resources for further exploration of EuGTs gene functions and germplasm innovation in E. ulmoides.
Plant Proteins/metabolism* ; Gene Expression Regulation, Plant ; Eucommiaceae/chemistry* ; Phylogeny ; Multigene Family/genetics* ; Gene Expression Profiling ; Transcription Factors/metabolism* ; Genome, Plant/genetics*

Based on whole genome data, the identification and expression pattern analysis of the Atropa belladonna WRKY transcription factor family were conducted to provide a theoretical foundation for studying the biological functions and mechanisms of these transcription factors. In this study, bioinformatics methods were employed to identify members of the A. belladonna WRKY gene family and to predict their physicochemical properties, conserved motifs, promoter cis-acting elements, and chromosomal localization. Additionally, the expression patterns of the A. belladonna WRKY gene family under the regulation of environmental factors such as light quality and temperature were analyzed. The results revealed a total of 28 AbWRKY transcription factors, randomly distributed across 16 chromosomes, encoding 324-707 amino acids. Most AbWRKY proteins were acidic, unstable, and hydrophilic. Based on multiple sequence alignment and phylogenetic analysis, the WRKY gene family members were classified into two subfamilies. Conserved motif and domain analysis indicated that WRKY transcription factors in the same subfamily possessed conserved structural features. Promoter analysis predicted that the A. belladonna WRKY family contained light-responsive elements, hormone-responsive elements, and stress-responsive elements. Collinearity analysis showed that AbWRKY24 plays a crucial role in the expansion of the AbWRKY gene family. Then qRT-PCR results indicated that AbWRKY6, AbWRKY8, AbWRKY14, and AbWRKY24 responded to red light stress, while AbWRKY8, AbWRKY14, and AbWRKY24 responded to yellow light/low-temperature combined stress. AbWRKY6 and AbWRKY8 were significantly expressed in leaves and stems, AbWRKY27 and AbWRKY28 were significantly expressed in fibrous roots, and AbWRKY25 was significantly expressed in flowers. This study is the first to identify and analyze the WRKY gene family in A. belladonna and to examine its expression patterns under light and temperature regulation, laying a foundation for in-depth analysis and functional validation of the molecular mechanisms of A. belladonna WRKY transcription factors in responding to light quality and temperature environmental factors.
Transcription Factors/chemistry* ; Plant Proteins/metabolism* ; Phylogeny ; Gene Expression Regulation, Plant ; Light ; Temperature ; Atropa belladonna/metabolism* ; Multigene Family/genetics* ; Promoter Regions, Genetic/genetics* ; Sequence Alignment ; Amino Acid Sequence ; Genome, Plant/genetics*