Genome-Wide Identification and Characterization of GARP Transcription Factor Gene Family Members Reveal Their Diverse Functions in Tea Plant (Camellia sinensis)

Optimizing plant phosphate uptake: Advances in the core regulatory mechanisms of phosphate starvation response proteins and their macromolecular partners: A review

Phosphorus (P), essential for plant survival, is primarily absorbed as inorganic phosphate (Pi), yet soil Pi scarcity severely limits plant growth and agricultural productivity. This review synthesizes current research on plant adaptations to Pi scarcity, with a focus on the root system as the primary site of Pi absorption and the role of MYB transcription factors, particularly PHOSPHATE STARVATION RESPONSE 1 (PHR1), a core regulatory biological macromolecule. PHR1 orchestrates a wide array of genetic responses that modify root architecture to enhance Pi acquisition under nutrient-poor conditions. This review delves into the biological activities, molecular associations, chemical and biological modifications, and functional properties of PHR1 and related MYB transcription factors, examining how these regulatory macromolecular proteins interact with other molecular components to form complexes that coordinate adaptive root development. By integrating findings from diverse plant species, the review highlights the potential of leveraging molecular breeding techniques to develop cultivars with enhanced phosphate uptake efficiency by targeting these regulatory macromolecular proteins. Such advancements promise to mitigate the impacts of Pi deficiency, supporting sustainable agricultural and forestry practices. The insights provided aim to inform and guide future research in plant nutrient management, focusing on the intricate interplay of biological and molecular factors that regulate phosphate uptake.

Decoding PHR-Orchestrated Stress Adaptation: A Genome-Wide Integrative Analysis of Transcriptional Regulation Under Abiotic Stress in Eucalyptus grandis

The phosphate starvation response (PHR) transcription factor family play central regulatory roles in nutrient signaling, but its relationship with other abiotic stress remains elusive. In the woody plant Eucalyptus grandis, we characterized 12 EgPHRs, which were phylogenetically divided into three groups, with group I exhibiting conserved structural features (e.g., unique motif composition and exon number). Notably, a protein-protein interaction network analysis revealed that EgPHR had a species-specific protein-protein interaction network: EgPHR6 interacted with SPX proteins of multiple species, while Eucalyptus and poplar PHR uniquely bound to TRARAC-kinesin ATPase, suggesting functional differences between woody and herbaceous plants. A promoter sequence analysis revealed a regulatory network of 59 transcription factors (TFs, e.g., BPC, MYBs, ERFs and WUS), mainly associated with tissue differentiation, abiotic stress, and hormonal responses that regulated EgPHRs' expression. Transcriptomics and RT-qPCR gene expression analyses showed that all EgPHRs dynamically responded to phosphate (Pi) starvation, with the expression of EgPHR2 and EgPHR6 exhibiting sustained induction, and were also regulated by salt, cold, jasmonic acid, and boron deficiency. Strikingly, nitrogen starvation suppressed most EgPHRs, highlighting crosstalk between nutrient signaling pathways. These findings revealed the multifaceted regulatory role of EgPHRs in adaptation to abiotic stresses and provided insights into their unique evolutionary and functional characteristics in woody plants.

Genome-Wide Identification and Comprehensive Analysis of the GARP Transcription Factor Superfamily in Populus deltoides

Background/Objectives: The GARP transcription factor superfamily is crucial for plant growth, development, and stress responses. This study systematically identified and analyzed the GARP family genes in Populus deltoides to explore their roles in plant development and abiotic stress responses. Methods: A total of 58 PdGARP genes were identified using bioinformatics tools. Their physicochemical properties, genomic locations, conserved motifs, gene structures, and phylogenetic relationships were analyzed. Expression patterns under phosphorus and nitrogen deficiency, as well as tissue-specific expression, were investigated using RT-qPCR. Transgenic RNAi lines were generated to validate the function of GLK genes in chlorophyll biosynthesis. Results: The 58 PdGARP genes were classified into five subfamilies based on their evolutionary relationships and protein sequence similarity. Segmental duplication was found to be the primary driver of the PdGARP family's expansion. Cis-regulatory elements (CREs) related to light, hormones, and abiotic stresses were identified in the promoters of PdGARP genes. Differential expression patterns were observed for NIGT1/HRS1/HHO and PHR/PHL subfamily members under phosphorus and nitrogen deficiency, indicating their involvement in stress responses. KAN subfamily members exhibited tissue-specific expression, particularly in leaves. Structural analysis of the GLK subfamily revealed conserved α-helices, extended chains, and irregular coils. Transgenic RNAi lines targeting GLK genes showed significant reductions in chlorophyll and carotenoid content. Conclusions: This study provides a comprehensive analysis of the GARP transcription factor superfamily in P. deltoides, highlighting their potential roles in nutrient signaling and stress response pathways. The findings lay the foundation for further functional studies of PdGARP genes and their application in stress-resistant breeding of poplar.

Genome-Wide Identification of GLK Family Genes in Phoebe bournei and Their Transcriptional Analysis Under Abiotic Stresses

GOLDEN2-LIKE (GLK) transcription factors are crucial regulators of chloroplast development and stress responses in plants. In this study, we investigated the GLK gene family in Phoebe bournei (Hemsl.) Yen C. Yang, a near-threatened species important for forestry and wood utilization in China. We identified 61 PbGLK genes which were classified into seven subfamilies. Our analyses of their phylogenetic relationships, gene structures, and chromosomal distribution revealed diverse characteristics. Expression profiling under different tissues and abiotic stresses showed that PbGLK25 and PbGLK30 were particularly responsive to drought, heat, light, and shade stresses, with significant upregulation. These findings highlight the potential role of PbGLK genes in stress adaptation and provide insights for the genetic improvement of P. bournei.

Identification of Cold Tolerance Transcriptional Regulatory Genes in Seedlings of Medicago sativa L. and Medicago falcata L

Alfalfa species Medicago sativa L. (MS) and Medicago falcata L. (MF), globally prominent perennial leguminous forages, hold substantial economic value. However, our comprehension of the molecular mechanisms governing their resistance to cold stress remains limited. To address this knowledge gap, we scrutinized and compared MS and MF cold-stress responses at the molecular level following 24 h and 120 h low-temperature exposure (4 °C). Our study revealed that MF had superior physiological resilience to cold stress compared with MS, and its morphology was healthier under cold stress, and its malondialdehyde content and superoxide dismutase activity increased, first, and then decreased, while the soluble sugar content continued to accumulate. Transcriptome analysis showed that after 120 h of exposure, there were different gene-expression patterns between MS and MF, including 1274 and 2983 genes that were continuously up-regulated, respectively, and a total of 923 genes were included, including star cold-resistant genes such as ICE1 and SIP1. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed numerous inter-species differences in sustained cold-stress responses. Notably, MS-exclusive genes included a single transcription factor (TF) gene and several genes associated with a single DNA repair-related pathway, whereas MF-exclusive genes comprised nine TF genes and genes associated with 14 pathways. Both species exhibited high-level expression of genes encoding TFs belonging to AP2-EREBP, ARR-B, and bHLH TF families, indicating their potential roles in sustaining cold resistance in alfalfa-related species. These findings provide insights into the molecular mechanisms governing cold-stress responses in MS and MF, which could inform breeding programs aimed at enhancing cold-stress resistance in alfalfa cultivars.

Genome-wide characterization of RR gene family members in Zanthoxylum armatum and the subsequent functional characterization of the C-type RR

Response Regulators (RRs) are crucial regulators in plant development and stress responses, comprising A-type, B-type, C-type, and pseudo-RR subfamilies. However, previous studies have often focused on specific subfamilies, which restricts our understanding of the complete RR gene family. In this study, we conducted a comprehensive analysis of 63 RR members from Zanthoxylum armatum, using phylogenetic relationships, motif composition, cis-acting elements, gene duplication and collinearity analyses. Segmental repeats among ZaRR genes enhanced the various environmental adaptabilities of Z. armatum, and the B-type ZaRR exhibited significant collinearity with the RRs in P. trichocarpa and C. sinensis. Cis-element analysis indicated ZaRRs play a significant role in abiotic stress and phytohormone pathways, particularly in light, drought, cold, abscisic acid (ABA) and salicylic acid (SA) responses. Abundant Ethylene Response Factor (ERF) and reproduction-associated binding sites in ZaRR promoters suggested their roles in stress and reproductive processes. A-type ZaRRs were implicated in plant vegetative and reproductive growth, whereas B-type ZaRRs contributed to both growth and stress responses. C-type ZaRRs were associated with plant reproductive growth, whereas pseudo-RRs may function in plant stress responses, such as water logging, cold, and response to ethylene (ETH), SA, and jasmonic acid (JA). Ectopic expression of ZaRR24, a C-type RR, inhibits growth, induces early flowering, and shortens fruit length in Arabidopsis. ZaRR24 overexpression also affected the expression of A- and B-type RRs, as well as floral meristem and organ identity genes. These findings establish a solid and comprehensive foundation for RR gene research in Z. armatum, and provide a platform for investigating signal transduction in other woody plants.

Transcriptome-Based Screening of Candidate Low-Temperature-Associated Genes and Analysis of the BocARR-B Transcription Factor Gene Family in Kohlrabi (Brassica oleracea L. var. caulorapa L.)

Low temperature is a significant abiotic stress factor that not only impacts plant growth, development, yield, and quality but also constrains the geographical distribution of numerous wild plants. Kohlrabi (Brassica oleracea L. var. caulorapa L.) belongs to the Brassicaceae family and has a short growing period. In this study, a total of 196,642 unigenes were obtained from kohlrabi seedlings at low temperatures; of these, 52,836 unigenes were identified as differentially expressed genes. Transcription factor family members ARR-B, C3H, B3-ARF, etc. that had a high correlation with biochemical indicators related to low temperature were identified. A total of nineteen BocARR-B genes (named BocARR-B1-BocARR-B19) were obtained, and these genes were distributed unevenly across seven chromosomes. Nineteen BocARR-B genes searched four conserved motifs and were divided into three groups. The relative expression level analysis of 19 BocARR-B genes of kohlrabi showed obvious specificity in different tissues. This study lays a foundation and provides new insight to explain the low-temperature resistance mechanism and response pathways of kohlrabi. It also provides a theoretical basis for the functional analysis of 19 BocARR-B transcription factor gene family members.

Marchantia polymorpha GOLDEN2-LIKE transcriptional factor; a central regulator of chloroplast and plant vegetative development

The GOLDEN2-LIKE (GLK) transcription factors act as a central regulatory node involved in both developmental processes and environmental responses. Marchantia polymorpha, a basal terrestrial plant with strategic evolutionary position, contains a single GLK representative that possesses an additional domain compared to spermatophytes. We analyzed the role of MpGLK in chloroplast biogenesis and development by altering its levels, preforming transcriptomic profiling and conducting chromatin immunoprecipitation. Decreased MpGLK levels impair chloroplast differentiation and disrupt the expression of photosynthesis-associated nuclear genes, while overexpressing MpGLK leads to ectopic chloroplast biogenesis. This demonstrates the MpGLK functions as a bona fide GLK protein, likely representing an ancestral GLK architecture. Altering MpGLK levels directly regulates the expression of genes involved in Chl synthesis and degradation, similar to processes observed in eudicots, and causes various developmental defects in Marchantia, including the formation of dorsal structures such as air pores and gemma cups. MpGLK, also directly activates MpMAX2 gene expression, regulating the timing of gemma cup development. Our study shows that MpGLK functions as a master regulator, potentially coupling chloroplast development with vegetative reproduction. This illustrates the complex regulatory networks governing chloroplast function and plant development communication and highlight the evolutionary conservation of GLK-mediated regulatory processes across plant species.

Integrated transcriptomics and metabolomics provide insights into the biosynthesis of militarine in the cell suspension culture system of Bletilla striata

Militarine is a monomer molecule with abundant and distinctive biological properties, also the lead member of secondary metabolites in Bletilla striata, while its biosynthesis mechanism is still unknown. To improve the production efficiency of militarine, sodium acetate and salicylic acid (SA) were introduced as elicitors into the suspension-cultured callus of B. striata. Subsequently, samples were taken from callus at different culturing stages to investigate the synthesis mechanisms of militarine in B. striata through integrated metabolomics and transcriptomics. Metabolomics analysis revealed that acetate ions promoted militarine synthesis, while SA had an inhibitory effect. Additionally, regulators such as ferulic acid, 2-hydroxy-3-phenylpropionic acid, and cis-beta-D-Glucosyl-2-hydroxycinnamate were identified as influencing militarine synthesis. Transcriptomics analysis indicated that the expression levels of genes involved in phenylalanine metabolism, phenylpropanoid biosynthesis, and tyrosine metabolism were correlated with militarine content. This study sheds light on the regulatory mechanism of militarine biosynthesis in plants. The results suggested that acetate ions and SA impact militarine synthesis through specific metabolic pathways and gene expression changes. This knowledge serves as a foundation for future research on militarine biosynthesis and its industrial production.

Phosphorus uptake, transport, and signaling in woody and model plants

Phosphorus (P), a critical macronutrient for plant growth and reproduction, is primarily acquired and translocated in the form of inorganic phosphate (Pi) by roots. Pi deficiency is widespread in many natural ecosystems, including forest plantations, due to its slow movement and easy fixation in soils. Plants have evolved complex and delicate regulation mechanisms on molecular and physiological levels to cope with Pi deficiency. Over the past two decades, extensive research has been performed to decipher the underlying molecular mechanisms that regulate the Pi starvation responses (PSR) in plants. This review highlights the prospects of Pi uptake, transport, and signaling in woody plants based on the backbone of model and crop plants. In addition, this review also highlights the interactions between phosphorus and other mineral nutrients such as Nitrogen (N) and Iron (Fe). Finally, this review discusses the challenges and potential future directions of Pi research in woody plants, including characterizing the woody-specific regulatory mechanisms of Pi signaling and evaluating the regulatory roles of Pi on woody-specific traits such as wood formation and ultimately generating high Phosphorus Use Efficiency (PUE) woody plants.

The GARP family transcription factor MtHHO3 negatively regulates salt tolerance in Medicago truncatula

High salinity is one of the detrimental environmental factors restricting plant growth and crop production throughout the world. This study demonstrated that the GARP family transcription factor MtHHO3 is involved in response to salt stress and abscisic acid (ABA) signaling in Medicago truncatula. The transcription of MtHHO3 was repressed by salt, osmotic stress, and ABA treatment. The seed germination assay showed that, overexpression of MtHHO3 in Arabidopsis thaliana caused hypersensitivity to salt and osmotic stress, but increased resistance to ABA inhibition. Overexpression of MtHHO3 in M. truncatula resulted in decreased tolerance of salinity, while loss-of-function mutants mthho3-1 and mthho3-2 were more resistant to salt stress compared with wild-type plants. qRT-PCR analyses showed that MtHHO3 downregulated the expression of genes in stress and ABA responsive pathways. We further demonstrated that MtHHO3 repressed the transcription of the pathogenesis-related gene MtPR2 by binding to its promoter. Overall, these results indicate that MtHHO3 negatively regulates salt stress response in plants and deepen our understanding of the role of the GARP subfamily transcription factors in modulating salt stress and ABA signaling.

Structural and Functional Analysis of the MADS-Box Genes Reveals Their Functions in Cold Stress Responses and Flower Development in Tea Plant (Camellia sinensis)

MADS-box genes comprise a large family of transcription factors that play crucial roles in all aspects of plant growth and development. However, no detailed information on the evolutionary relationship and functional characterization of MADS-box genes is currently available for some representative lineages, such as the Camellia plant. In this study, 136 MADS-box genes were detected from a reference genome of the tea plant (Camellia sinensis) by employing a 569 bp HMM (Hidden Markov Model) developed using nucleotide sequencing including 73 type I and 63 type II genes. An additional twenty-seven genes were identified, with five MIKC-type genes. Truncated and/or inaccurate gene models were manually verified and curated to improve their functional characterization. Subsequently, phylogenetic relationships, chromosome locations, conserved motifs, gene structures, and gene expression profiles were systematically investigated. Tea plant MIKC genes were divided into all 14 major eudicot subfamilies, and no gene was found in Mβ. The expansion of MADS-box genes in the tea plant was mainly contributed by WGD/fragment and tandem duplications. The expression profiles of tea plant MADS-box genes in different tissues and seasons were analyzed, revealing widespread evolutionary conservation and genetic redundancy. The expression profiles linked to cold stress treatments suggested the wide involvement of MADS-box genes from the tea plant in response to low temperatures. Moreover, a floral 'ABCE' model was proposed in the tea plant and proved to be both conserved and ancient. Our analyses offer a detailed overview of MADS-box genes in the tea plant, allowing us to hypothesize the potential functions of unknown genes and providing a foundation for further functional characterizations.

Genome-Scale Investigation of GARP Family Genes Reveals Their Pivotal Roles in Nutrient Stress Resistance in Allotetraploid Rapeseed

The GARP genes are plant-specific transcription factors (TFs) and play key roles in regulating plant development and abiotic stress resistance. However, few systematic analyses of GARPs have been reported in allotetraploid rapeseed (Brassica napus L.) yet. In the present study, a total of 146 BnaGARP members were identified from the rapeseed genome based on the sequence signature. The BnaGARP TFs were divided into five subfamilies: ARR, GLK, NIGT1/HRS1/HHO, KAN, and PHL subfamilies, and the members within the same subfamilies shared similar exon-intron structures and conserved motif configuration. Analyses of the Ka/Ks ratios indicated that the GARP family principally underwent purifying selection. Several cis-acting regulatory elements, essential for plant growth and diverse biotic and abiotic stresses, were identified in the promoter regions of BnaGARPs. Further, 29 putative miRNAs were identified to be targeting BnaGARPs. Differential expression of BnaGARPs under low nitrate, ammonium toxicity, limited phosphate, deficient boron, salt stress, and cadmium toxicity conditions indicated their potential involvement in diverse nutrient stress responses. Notably, BnaA9.HHO1 and BnaA1.HHO5 were simultaneously transcriptionally responsive to these nutrient stresses in both hoots and roots, which indicated that BnaA9.HHO1 and BnaA1.HHO5 might play a core role in regulating rapeseed resistance to nutrient stresses. Therefore, this study would enrich our understanding of molecular characteristics of the rapeseed GARPs and will provide valuable candidate genes for further in-depth study of the GARP-mediated nutrient stress resistance in rapeseed.

Chromosome-scale genome assembly of Camellia sinensis combined with multi-omics provides insights into its responses to infestation with green leafhoppers

The tea plant (Camellia sinensis) is an important economic crop, which is becoming increasingly popular worldwide, and is now planted in more than 50 countries. Tea green leafhopper is one of the major pests in tea plantations, which can significantly reduce the yield and quality of tea during the growth of plant. In this study, we report a genome assembly for DuyunMaojian tea plants using a combination of Oxford Nanopore Technology PromethION™ with high-throughput chromosome conformation capture technology and used multi-omics to study how the tea plant responds to infestation with tea green leafhoppers. The final genome was 3.08 Gb. A total of 2.97 Gb of the genome was mapped to 15 pseudo-chromosomes, and 2.79 Gb of them could confirm the order and direction. The contig N50, scaffold N50 and GC content were 723.7 kb, 207.72 Mb and 38.54%, respectively. There were 2.67 Gb (86.77%) repetitive sequences, 34,896 protein-coding genes, 104 miRNAs, 261 rRNA, 669 tRNA, and 6,502 pseudogenes. A comparative genomics analysis showed that DuyunMaojian was the most closely related to Shuchazao and Yunkang 10, followed by DASZ and tea-oil tree. The multi-omics results indicated that phenylpropanoid biosynthesis, α-linolenic acid metabolism, flavonoid biosynthesis and 50 differentially expressed genes, particularly peroxidase, played important roles in response to infestation with tea green leafhoppers (Empoasca vitis Göthe). This study on the tea tree is highly significant for its role in illustrating the evolution of its genome and discovering how the tea plant responds to infestation with tea green leafhoppers will contribute to a theoretical foundation to breed tea plants resistant to insects that will ultimately result in an increase in the yield and quality of tea.