Chaofeng Li

CCCH-type zinc finger proteins (C3H transcription factors) play essential roles in plant growth, development, and responses to environmental stresses. Although several maize (Zea mays L.) C3H genes have been reported, a comprehensive genome-wide analysis based on the updated maize reference genome remains lacking. In this study, 64 C3H gene family members were systematically identified from the maize reference genome (Zm-B73-REFERENCE-NAM-5.0) and designated as ZmC3H01 to ZmC3H64 according to their chromosomal locations. Phylogenetic analysis classified the ZmC3H family into four distinct subgroups, exhibiting conserved yet subgroup-specific motif compositions. Synteny analysis revealed that segmental duplication events played an important role in the expansion and evolution of the ZmC3H gene family. Cis-acting regulatory element analysis suggested that ZmC3H genes may participate in multiple stress-responsive and developmental regulatory pathways. Furthermore, transcriptome analysis and quantitative real-time PCR (qRT-PCR) validation identified five candidate ZmC3H genes (ZmC3H33, ZmC3H36, ZmC3H39, ZmC3H52, and ZmC3H57) that exhibited differential expression under low-phosphorus and high-nitrogen conditions in the maize inbred lines 082, Ye107, and B73. These genes were selected based on their differential expression under nutrient stress and their representative distribution across phylogenetic subfamilies, providing preliminary candidates for further functional investigation. Subcellular localization and yeast transcriptional activation assays demonstrated that ZmC3H33, ZmC3H36, and ZmC3H57 are nuclear-localized proteins with transcriptional activation activity. Furthermore, dual-luciferase assays showed that all three proteins activated the maize Phosphate Starvation Response 1 (ZmPHR1) promoter, with ZmC3H57 exhibiting the strongest activation effect, suggesting that these ZmC3H proteins may act as potential upstream regulators of ZmPHR1-mediated low-phosphorus responses. Collectively, these findings provide valuable insights into the evolutionary characteristics and potential biological functions of the maize C3H gene family and identify putative candidate genes for improving phosphorus-use efficiency.

Cytokinin signaling is essential for plant growth, development, and responses to environmental stresses. As key transcription factors in this pathway, type-B response regulators (ARR-Bs) activate the expression of primary cytokinin-responsive genes. However, the systematic identification of the ARR-B family in maize and its functional roles in responses to phosphorus (P) nutritional stress remain largely unclear. In this study, the maize ARR-B (ZmARR-B) transcription factor family was systematically identified and comprehensively characterized at the genome-wide level. A total of 12 ZmARR-B genes were identified and comprehensively characterized in terms of chromosomal localization, physicochemical properties, protein structure, phylogenetic relationships, gene organization, conserved motifs, promoter cis-regulatory elements, and collinearity. Based on systematic measurements of leaf inorganic phosphate (Pi) concentrations in 70 maize inbred lines from southwestern China, the lines 082, B73, and Ye107 were selected as representative materials. By integrating long-term (14 d) and short-term (0.5–12 h) low-P treatments with transcriptome sequencing and qRT-PCR validation, we systematically characterized the expression dynamics of ZmARR-B family members under P deficiency. The results showed that ZmARR-B genes exhibited markedly differentiated low-P-responsive expression patterns among distinct genetic backgrounds. ZmARR-B03 was transiently induced during the early phase of low-P treatment (0–6 h), followed by a rapid decline in transcript abundance. This characteristic pulse-like expression pattern suggests that ZmARR-B03 may function as a rapid-response regulator during early P-starvation signal transduction. In contrast, ZmARR-B06 exhibited sustained transcriptional upregulation throughout the low-P treatment period, suggesting a potential role in long-term adaptive regulation under P-deficient conditions. Notably, the number of low-P-responsive ZmARR-B members was significantly greater in the P-efficient inbred line 082 than in the P-sensitive line Ye107, indicating that ZmARR-B-mediated P-starvation responses are strongly genotype dependent. This study provides an important foundation for elucidating the molecular mechanisms by which cytokinin signaling, through type-B ARRs, regulates phosphate nutritional adaptation in maize. It also identifies potential candidate genes for the genetic improvement of P-efficient maize germplasm.

The three-amino-acid-loop-extension (TALE) gene family encodes a group of plant-specific homeodomain transcription factors that play indispensable roles in plant growth, development, and adaptation to environmental stresses. Although TALE genes have been extensively investigated in several plant species, their genome-wide characteristics and potential functions in maize, particularly in response to phosphorus deficiency, remain poorly understood. In the present study, a comprehensive genome-wide identification and characterization of the maize TALE gene family were conducted using bioinformatics approaches, followed by an investigation of their transcriptional responses to low-phosphorus (LP) stress. A total of 40 ZmTALE genes (ZmTALE1–ZmTALE40) were identified and phylogenetically classified into four subfamilies: BEL1-like, KNOX I, KNOX II, and KNOX III. Members within the same subfamily exhibited highly conserved gene structures and motif compositions, reflecting their evolutionary conservation. Chromosomal localization and synteny analyses demonstrated that segmental duplication has been the predominant force driving the expansion of the ZmTALE gene family during maize evolution. Promoter analysis revealed that the upstream regulatory regions of ZmTALE genes were enriched in light-responsive, phytohormone-responsive, and abiotic stress-related cis-acting regulatory elements, implying their potential involvement in multiple developmental and stress-responsive pathways. Expression profiling under LP conditions revealed pronounced genotype-dependent transcriptional responses among different maize inbred lines. Notably, ZmTALE1/5/12/14/18/30/31/33/36 were significantly induced by LP stress, whereas ZmTALE10 and ZmTALE37 were markedly repressed. These differentially expressed genes represent promising candidates for further functional investigation of phosphorus-deficiency tolerance in maize. Furthermore, ZmTALE10, ZmTALE14, and ZmTALE31 are nuclear-localized transcriptional activators. Taken together, these findings provide valuable insights into the evolutionary characteristics and potential biological functions of the maize TALE gene family and offer candidate genes for developing phosphorus-efficient maize cultivars through molecular breeding.

Gibberellic Acid-Stimulated Arabidopsis (GASA) proteins are cysteine-rich peptides broadly conserved in plants and implicated in growth regulation, stress adaptation, and hormone signaling. Here, we identified 13 GASA genes in the maize genome, distributed across six chromosomes. Comprehensive analyses of their physicochemical properties, subcellular localization, and structural features classified them into three conserved clades. Promoter cis-element analysis suggested roles in developmental regulation, phytohormone responses, abiotic stress adaptation, and light signaling. Comparative synteny revealed close evolutionary relationships between maize and sugarcane GASA genes, implying divergence from a common ancestor. Transcriptomic and qRT-PCR analyses demonstrated that maize GASA genes exhibit tissue-specific and stress-responsive expression under low-phosphorus condition, with ZmGASA06 showing pronounced responsiveness to low-phosphorus stress. This study provides novel insights into the evolutionary dynamics and potential functional roles of the GASA family in maize, laying a foundation for further functional and molecular breeding studies.

YABBY transcription factors (TFs) are key regulators involved in diverse aspects of plant growth, organogenesis, and adaptation to environmental stresses. However, the functional characteristics of YABBY TFs in maize remain largely unexplored. In this study, we systematically identified 12 YABBY genes in the maize genome and characterized their gene structures, physicochemical properties, chromosome location, and genomic collinearity. Phylogenetic analysis classified these genes into five subfamilies, with members of each subfamily exhibiting highly conserved exon–intron structures and motif compositions, indicative of potential functional conservation within subfamilies. Cis-regulatory element analysis indicated that YABBY genes may be involved in developmental processes, abiotic stress responses, and light-mediated signaling pathways. Moreover, transcriptome sequencing combined with qRT-PCR validation demonstrated that several YABBY genes, including ZmYABBY2, ZmYABBY5, ZmYABBY8, and ZmYABBY9, are responsive to low-phosphorus and high-nitrogen conditions, implying their potential roles in nutrient stress adaptation. It is worth mentioning that this study redefined the composition of the maize YABBY gene family by excluding a previously annotated member and, for the first time, established a link between YABBY transcription factors and nutrient stress responses. Meanwhile, this is also the first time that protein structure analysis, cis-regulatory element analysis, interspecific collinearity analysis and subcellular localization have been performed on maize ZmYABBY gene family. In summary, our study provides valuable gene resources for maize molecular breeding and offers new insights into the functions of YABBY TFs.

Isoflavonoids, the major secondary metabolites within the flavonoid biosynthetic pathway, play important roles in plant defense and exhibit free radical scavenging properties in mammals. Recent advancements in understanding the synthesis, transport, and regulation of isoflavonoids have identified their biosynthetic pathways as promising targets for metabolic engineering, offering potential benefits such as enhanced plant resistance, improved biomass, and restoration of soil fertility. This review provides an overview of recent breakthroughs in isoflavonoid biosynthesis, encompassing key enzymes in the biosynthetic pathway, transporters influencing their subcellular localization, molecular mechanisms regulating the metabolic pathway (including transcriptional and post-transcriptional regulation, as well as epigenetic modifications). Metabolic engineering strategies aimed at boosting isoflavonoid content in both leguminous and non-leguminous plants. Additionally, we discuss emerging technologies and resources for precise isoflavonoid regulation. This comprehensive review primarily focuses on model plants and crops, offering insights for more effective and sustainable metabolic engineering approaches to enhance nutritional quality and stress tolerance.

Phosphorus (P) is an essential nutrient for plant growth and yield. Low phosphate-use-efficiency makes it important to clarify the molecular mechanism of low phosphorus stress. In our previous studies, a phosphorus efficiency gene ZmAPRG was identified. Here, we further screened the upstream regulator ZmNF-YC1 of ZmAPRG by yeast one hybrid (Y1H) assay, and found it was a low Pi-inducible gene. The results of dual luciferase assays, expression analysis and ChIP-qPCR assays showed that ZmNF-YC1 is a positive regulator of ZmAPRG. Overexpression of ZmNF-YC1 improved low phosphorus tolerance whereas knockout of ZmNF-YC1 decreased low phosphorus tolerance in maize. Bimolecular fluorescence complementation (BiFC), Y2H and Y3H assay further showed that ZmNF-YC1 can interact with ZmNF-YB14, and recruit ZmNF-YA4/10 to form NF-Y complexes. Transcriptional activation assay confirmed that the NF-Y complexes can activate the promoters of ZmAPRG. Meanwhile, transcriptome and metabolome analyses indicated that overexpression of ZmAPRG improves low P tolerance by regulating lipid composition and photosynthetic capacity, and chlorophyll fluorescence parameters supplied evidence in support of this hypothesis. Furthermore, overexpression of ZmAPRG increased grain yield in inbred and hybrid maize under low P conditions. Taken together, our research revealed the low P tolerance mechanism of ZmNF-YC1-ZmAPRG pathway.

The majority of woody plants are able to form ectomycorrhizal (ECM) symbioses with fungi. During symbiotic development, plants undergo a complex re-programming process involving a series of physiological and morphological changes. MicroRNAs (miRNAs) are important components of the regulatory network underlying symbiotic development. To elucidate the mechanisms of miRNAs and miRNA-mediated mRNA cleavage during symbiotic development, we conducted high-throughput sequencing of small RNAs and degradome tags from roots of Populus tomentosa inoculated with Cenococcum geophilum. This process led to the annotation of 51 differentially expressed miRNAs between non-mycorrhizal and mycorrhizal roots of P. tomentosa, including 13 novel miRNAs. Increased or decreased accumulation of several novel and conserved miRNAs in ECM roots, including miR162, miR164, miR319, miR396, miR397, miR398, novel-miR44 and novel-miR47, suggests essential roles for these miRNAs in ECM formation. The degradome analysis identified root transcripts as miRNA-mediated mRNA cleavage targets, which was confirmed using real-time quantitative PCR. Several of the identified miRNAs and corresponding targets are involved in arbuscular mycorrhizal symbioses. In summary, increased or decreased accumulation of specific miRNAs and miRNA-mediated cleavage of symbiosis-related genes indicate that miRNAs play important roles in the regulatory network underlying symbiotic development.

Cadmium (Cd) displays strong toxicity, high mobility, and cannot be degraded, which poses a serious threat to the environment. Cenococcum geophilum (C. geophilum) is one of the most common ectomycorrhizal fungi (ECMF) in the natural environment. In this study, three Cd sensitive and three Cd tolerant strains of C. geophilum were used to analyze the physiological and molecular responses to Cd exposure. The results showed that Cd inhibited the growth of all strains of C. geophilum but had a less toxic effect on the tolerant strains, which may be correlated to a lower content of Cd and higher activity of antioxidant enzymes in the mycelia of tolerant strains. Comparative transcriptomic analysis was used to identify differentially expressed genes (DEGs) of four selected C. geophilum strains after 2 mg/L Cd treatment. The results showed that the defense response of C. geophilum strain to Cd may be closely related to the differential expression of functional genes involved in cell membrane ion transport, macromolecular compound metabolism, and redox pathways. The results were further confirmed by RT-qPCR analysis. Collectively, this study provides useful information for elucidation of the Cd tolerance mechanism of ECMF.