Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae

Genetic analysis and molecular mapping of the purple leaf sheath in barley (Hordeum vulgare)

Although anthocyanin is frequently found in various barley organs, the genetic basis of the pigmentation is still poorly understood. In this study, we examined the development of anthocyanin in GemCraft, a malting barley cultivar showing purple leaf sheath (PLS), and found that the pigmentation became visible on the leaf sheath at the early tillering stage. This study employed single nucleotide polymorphism (SNP) array genotyping data in two F2 populations developed using GemCraft and two barley lines with green leaf sheath throughout the plant development. Genetic and quantitative trait locus (QTL) analyses suggested regulation of the purple pigment accumulation by a single major QTL that was inherited as a dominant allele, which was necessary for the phenotype to develop. A major QTL, named qPLS2 (purple leaf sheath2 locus), was found on chromosome 2H and explained >70% of the trait variation. Nonetheless, the genetic model in the two mapping populations resonated between multiple loci and a single locus that determines the trait variation. Accordingly, in one of the populations, three minor QTL were also detected on chromosomes 1H and 5H: each of these QTL explained <5% variation and showed influence in regulation of the purple pigment intensity. In the qPLS2 QTL interval, comparative genomic analysis of annotated genes that are widely known to regulate anthocyanin development in plants identified a single candidate gene encoding a basic helix-loop-helix (bHLH) transcription factor. The study identified a new major QTL associated with the purple leaf sheath and generated further information for validation and cloning the causal gene for effective utilization of anthocyanin in barley genetic improvement.

OsPIL15-Induced Delay in Rice Heading Date via Direct Binding to the OsLF Promoter is Dependent on Functional Phytochrome B

Heading date of rice (Oryza sativa) is a key factor determining rice production and regional adaptability. We analysed the molecular mechanism of OsPIL15, encoding phytochrome-interacting factor-like protein, in delaying rice heading date. Overexpression of OsPIL15 delayed rice heading date by upregulating Hd1 and inhibiting Hd3a and RFT1 expression. OsLF, encoding one rice heading repressor, was found to be the putative candidate regulated by OsPIL15 through a chromatin immunoprecipitation sequencing assay and a transcriptome sequencing assay. OsPIL15 could directly bind to the OsLF promoter and activated its expression. Knocking-out OsLF in OsPIL15-overexpressing lines resulted in flowering 2-3 days earlier, partially rescuing the delayed phenotype. This indicates that overexpression of OsPIL15 overexpression delays heading date partially through OsLF. Protein-protein interaction assay of OsPIL15 or OsPIL15-∆APB (OsPIL15 lacking the active phytochrome B [phyB]-binding [APB] motif) with PHYB showed that the APB motif was required for the interaction between OsPIL15 and PHYB. Furthermore, overexpression of either OsPIL15-∆APB in the wild type or OsPIL15 in the phyB mutant did not delay rice heading date under natural long-day conditions, suggesting that phyB influences OsPIL15-mediated delay in rice heading date.

Genome-wide identification of five fern bHLH families and functional analysis of bHLHs in lignin biosynthesis in Alsophila spinulosa

BACKGROUND

The basic helix-loop-helix (bHLH) transcription factors are involved in the biosynthesis of various secondary metabolites. However, genome-wide studies on the bHLH gene family in ferns and their role in lignin biosynthesis remain limited. As the second largest group of vascular plants, ferns are of significant interest for understanding plant evolution and secondary metabolism. Among ferns, Alsophila spinulosa stands out as one of the few tree ferns with a distinctive trunk structure. Investigating the genes potentially regulating lignin biosynthesis in A. spinulosa offers valuable insights into the growth and development mechanisms of its trunk, which is pivotal for the overall architecture and function of the plant.

RESULTS

In this study, we conducted a systematic study of bHLH gene families in five ferns, including 186 in A. spinulosa, 130 in A. capillus, 107 in A. filiculoides, 71 in S. cucullata, and 67 in C. richardii. Based on phylogenetic analysis, all bHLH genes were classified into 28 subgroups. The number of bHLH members in different ferns was closely related to their growth patterns and life habits, with the number in tree ferns being much larger than in other ferns. In addition, we identified tandem duplication in C. richardii and A. capillus as a key driver of their bHLH gene diversity, whereas in A. spinulosa, segmental duplication contributed more to gene expansion and evolution. Most of the bHLH genes in ferns are in a state of purifying selection. Additionally, tissue-specific expression patterns of AspbHLH genes suggest diverse functional roles in plant growth, development, and metabolite synthesis. We further focused on three genes, AspbHLH80, AspbHLH120, and AspbHLH185, which are specifically highly expressed in xylem. Results from weighted gene co-expression network analysis (WGCNA) and downstream target gene prediction indicate their potential regulatory roles in lignin biosynthesis.

CONCLUSION

This study presents a comprehensive genomic analysis of the bHLH gene family in five fern species. We found a strong correlation between bHLH gene number and fern growth morphology, with tree ferns exhibiting a significantly higher number of bHLH genes. Tandem duplications were key to bHLH gene diversity in C. richardii, A. capillus, and A. spinulosa, while segmental duplications contributed more to bHLH gene expansion in A. spinulosa. Evolutionary analysis indicated most fern bHLH genes are under purifying selection. Tissue-specific expression patterns of AspbHLH genes suggest roles in growth, development, and secondary metabolism. Furthermore, WGCNA and target gene predictions highlight three genes (AspbHLH80, AspbHLH120, and AspbHLH185) potentially involved in lignin biosynthesis. Overall, this work provides key insights into the mechanisms of wood formation in ferns and advances our understanding of plant secondary metabolism.

AmbHLH091 is released by AmNAC035 and drives Salt Overly Sensitive 1 and Pyrroline-5-Carboxylate Synthase expression to mediate salt tolerance in mangrove Avicennia marina

Avicennia marina is the pioneer species of mangroves suffering from high-saline environment. bHLH is the second largest family of transcription factors (TFs) in plants, and involves in various stress responses. So far, the bHLH family members are not identified and bio-functionally characterized in A. marina. In this study, the 228 AmbHLH family members were identified from A. marina genome. Through bioinformatics analysis, the AmbHLH091 was specifically chosen to elucidate its biological function in salt tolerance. Expression pattern analysis exhibited AmbHLH091 was mainly expressed in leaf, root, and stem tissues, and AmbHLH091 was significantly up-regulated under salinity treatment. Additionally, subcellular localization analysis showed AmbHLH091 was mainly expressed in cell nucleus. The transient overexpression and protein-DNA interaction analysis revealed AmbHLH091 is likely to promote Na+ transport and proline accumulation by interacting with the promoters of Salt Overly Sensitive 1 (AmSOS1) and Pyrroline-5-Carboxylate Synthase (AmP5CS). In yeast expression analysis, the AmbHLH091 enhanced the salt tolerance via promoting the AmSOS1 and AmP5CS expression. Besides, another TF AmNAC035 interacts with AmbHLH091 and negatively regulates AmbHLH091 transcriptional activity, thereby modulating the expression of AmSOS1 and AmP5CS. Summarily, our results revealed AmbHLH091-AmNAC035 macromolecule participates the salt tolerance of A. marina in the coastal saline intertidal habitats.

Potential regulation of cleistogamy in pigeonpea through jasmonic acid and bHLH transcription factor interactions

KEY MESSAGE

This study provides insights into the molecular and hormonal control of cleistogamy in pigeonpea, focusing on bHLH transcription factors and jasmonic acid pathway. Pigeonpea, an annual diploid (2n = 22) grain legume, holds significant nutritional value in cereal-dominated diets. The chasmogamous flowers of pigeonpea have a typical 9 + 1 diadelphous stamen where flowers open pre-fertilization resulting in cross-pollination. In contrast, a cleistogamous genotype characterized by polyadelphous stamens and flowers that open post-fertilization ensuring seed purity was analyzed for identifying causal pathways. Subsequent analysis focused on a set of transcription factors and their interaction with the hormonal networks associated with cleistogamy. Genes of the Jasmonic acid (JA) signaling pathway have been established to play a significant role in inducing cleistogamy and one of the key regulators of the JA pathway is bHLH (basic helix loop helix). A genome-wide survey identified 176 bHLH genes in the pigeonpea genome. Phylogenetic analysis classified 176 bHLH genes into 21 subfamilies distributed randomly across the genome. Gene ontology, cis-motifs analysis in the upstream region, and protein-protein interaction network implied the involvement of these genes in various biological processes. Expression analysis of key genes of the jasmonic acid pathway which includes MYC2 (Cc_bHLH135) along with its interacting partners TIFY/JAZ in chasmogamous and cleistogamous floral tissues revealed their potential role in flower opening. The results of UHPLC-MS/MS quantitation of Jasmonic acid and its bioactive form JA-Ile align with the expression analysis. The congruence of gene expression and hormone profiling highlights the involvement of the JA pathway in regulating flower opening, implying their potential role in cleistogamy in pigeonpea.

Identification of the bHLH Transcription Factor Family in Orah Mandarin and the Response of CrbHLH46 to Low-Temperature Stress

As the second largest family of transcription factors (TFs) in plants, basic helix-loop-helices (bHLHs) play key roles in regulating plant growth and development and responding to environmental stress. As the fastest growing Citrus variety in China in recent years, Orah mandarin has vital economic and nutritional value. Although a comprehensive genome-wide analysis of the bHLH TF family has been performed in many plants, a systematic study of the genes of this family has not been carried out in Orah mandarin. In this study, 114 bHLH TFs were identified in Orah mandarin via genome-wide analysis and were classified into 27 subfamilies according to the evolutionary tree. The gene expression profile revealed that five genes were significantly upregulated at 12 h and 24 h after low-temperature stress treatment. In addition, soluble sugars, soluble proteins, and proline contents increased with increasing low-temperature stress, which promoted the expression of the CrbHLH46 gene, thus mediating the interconversion pathway of pentose and glucose to improve the cold tolerance of Orah mandarin. The results help explore the characteristics and functions of CrbHLH genes and provide a basis for further research on the Orah mandarin resistance to low-temperature stress.

A novel bHLH transcription factor, FabHLH110, is involved in regulation of anthocyanin synthesis in petals of pink-flowered strawberry

The pink-flowered strawberry is a kind of perennial herb that serves as both an ornamental plant with a range of red-colored petals and a food crop, which was produced by distant hybridization of Fragaria × Potentilla. Although there have been numerous reports on anthocyanin synthesis in strawberry fruits, the mechanism by which bHLH transcription factors regulate anthocyanin synthesis in strawberry red petals remains unclear. In this study, a total of 376 FabHLHs were finally identified, which were divided into 25 subfamilies. According to transcriptome sequencing, phylogenetic tree construction, correlation analysis and real-time fluorescence quantitative analysis, the differential gene FabHLH110 was screened out to regulate the synthesis of flower petal anthocyanin of pink-flowered strawberry. Specifically, transient overexpression of FabHLH110 in petals of pink-flowered strawberry increased anthocyanin accumulation, while virus-induced FabHLH110 gene silencing had the opposite effect, indicating FabHLH110 functioned as a positive regulator of anthocyanin biosynthesis. In addition, it was found that FabHLH110 could not bind to the promoter of FaDFR, FaANS, FaUGT and FaGST, which should interact with FaMYB10, FaMYB90 and FaMYB114 to form MBW complex to promote anthocyanin accumulation in fruit and petals of pink-flowered strawberry, respectively. Our findings provide new insight into the regulatory network of anthocyanin synthesis in petal of pink-flowered strawberry and a new strategy for breeding rich anthocyanin.

A candidate association study of transcription factors in maize revealed the ZmPLATZ15-ZmEREB200 module as a key regulator of waterlogging tolerance at the seedling stage

Soil waterlogging is a major abiotic stress that severely impairs maize growth and development by inducing hypoxic conditions that disrupt essential physiological processes. Transcription factors (TFs) play crucial roles in modulating plant responses to waterlogging stress by regulating the expression of stress-related genes that enhance or diminish stress tolerance. In this study, we conducted an association analysis to identify 11 TFs closely associated with waterlogging stress in maize. Notably, the PLATZ family emerged as a novel and significant contributor to waterlogging stress. Overexpression of ZmPLATZ15 resulted in increased sensitivity to waterlogging at maize seedlings. Conversely, ZmEREB200, a member of the maize Group VII ERF (ZmERFVII) family, was significantly downregulated in the ZmPLATZ15 overexpression lines under waterlogging stress. Promoter analysis revealed that ZmPLATZ15 regulates ZmEREB200 by binding to the A/T-rich motifs in the ZmEREB200 promoter. Interestingly, overexpression of ZmEREB200 was found to enhance waterlogging tolerance at maize seedlings. To further elucidate their roles, we analyzed the transcriptomic profiles of ZmPLATZ15 and ZmEREB200 overexpression lines under waterlogging stress. The overlapping differentially expressed genes in both ZmPLATZ15 and ZmEREB200 overexpression lines were significantly enriched in pathways associated with redox balance and salicylic acid metabolism, both of which are crucial for modulating waterlogging tolerance at maize seedlings. Metabolomic analysis revealed that antioxidant enzyme activity, salicylic acid, and glutathione levels were decreased in OE-ZmPLATZ15, while these metabolites were significantly increased in OE-ZmEREB200. These contrasting metabolic responses in overexpression lines may underlie their different tolerances to waterlogging stress. Our findings provide valuable insights into the regulatory mechanisms underlying maize's response to waterlogging stress and highlight the potential of TFs as tools for developing maize varieties with enhanced waterlogging tolerance.

Genome-wide characterization and expression analysis of the bHLH gene family in response to abiotic stresses in Zingiber officinale Roscoe

BACKGROUND

The basic helix-loop-helix (bHLH) transcription factors play important physiological functions in the processes of plant growth, development, and response to abiotic stresses. However, a comprehensive genome-scale study of the ginger bHLH gene family has not been documented.

RESULTS

In this study, 142 ZobHLH genes were identified in the ginger genome. Using Arabidopsis bHLH proteins as a reference, ZobHLH genes were classified into 15 subfamilies and unevenly distributed on 11 chromosomes of ginger. Sequence characterization, multiple sequence alignment, phylogenetic analysis, conserved protein motifs and exon-intron distribution patterns were conducted to further analyze the evolutionary relationships among these ZobHLH proteins. The results of the duplicated event analysis demonstrated that the pivotal role of segment duplication in promoting the expansion of the ZobHLH gene family. Additionally, analysis of cis-regulatory elements as well as protein interaction networks indicated the potential involvement of ginger ZobHLH family proteins in plant growth and development, and response to adversity stress. RNA-seq and RT-qPCR results showed that ZobHLH083 and ZobHLH108 play key roles in response to salt stress and waterlogging stress, respectively.

CONCLUSION

In this study, we systematically analyzed the characteristics of ZobHLH proteins in ginger, discovering that these genes play critical roles in ginger rhizome expansion and response to salt and waterlogging stresses. The present study provides a theoretical foundation for the further research on ZobHLHs and will help to explore the functional properties of ZobHLH genes.

Characterization and Expression Analysis of the bHLH Gene Family During Developmental Stages and Under Various Abiotic Stresses in Sanghuangporus baumii

BACKGROUND

Basic helix-loop-helix (bHLH) transcription factors (TFs) widely exist in eukaryotic organisms and play a key role in plant growth and development in response to environmental stresses. Sanghuangporus baumii, an important medicinal mushroom known for its anticancer properties, has limited research on the bHLH gene family.

METHODS

This research utilized the genomic data from S. baumii to identify bHLH family members, and their gene structure, conserved motifs, and phylogenetic relationship were characterized. Additionally, we conducted an analysis of promoter cis-elements and predicted protein interaction networks. We also examined the expression profiles of bHLH genes during different developmental stages and in response to four abiotic stresses: heat, cold, oxidative stress, and heavy metal exposure. Finally, we overexpressed the candidate gene SbbHLH3 in yeast to assess its tolerance to these different stress conditions.

RESULTS

A total of 12 SbbHLH genes were identified in S. baumii, and the members of the bHLH gene family displayed a variety of physicochemical characteristics, reflecting their diverse array of functions. Based on homology, the SbbHLH proteins are more closely related to those found in Lentinula edodes and Pleurotus ostreatus. The analysis of promoter cis-elements showed that SbbHLHs contain several elements associated with abiotic stress response, and a network prediction identified 28 bHLH-interacting proteins. Expression pattern analysis revealed that most SbbHLH genes exhibited a positive response to different developmental stages and abiotic stresses. Notably, the overexpression of SbbHLH3 significantly enhanced stress tolerance in yeast.

CONCLUSIONS

This study provides a comprehensive assessment of the bHLH family in S. baumii, delivering new genetic resources for breeding resistant varieties.

Genome-wide identification of the bHLH gene family and the mechanism regulation of anthocyanin biosynthesis by ChEGL1 in Cerasus humilis

Cerasus humilis is a fruit tree with enormous potential economic value, and its fruit is rich in various bioactive substances. The basic helix loop helix (bHLH) gene family plays an important role in the biosynthesis of plant anthocyanins. However, there was no research on the ChbHLH gene family in C. humilis. In this study, 114 ChbHLH genes were identified from the C. humilis genome and divided into 17 subgroups. Then, evolutionary relationships, conserved motifs, gene structures, and cis-acting elements were analyzed. By predicting the interaction network between ChbHLH proteins and ChMYB1, it was found that ChbHLH44 (here named as ChEGL1) was located at the core of the interaction network. Further experiments revealed that ChEGL1 and ChMYB1 could interact with each other both in vivo and in vitro. In addition, ChEGL1 significantly increased the anthocyanin content in transgenic tomato plants. This study provides a comprehensive understanding of the ChbHLH gene family and supports further enrichment of the regulation mechanism of anthocyanin biosynthesis in C. humilis fruit.

A bHLH transcription factor RrUNE12 regulates salt tolerance and promotes ascorbate synthesis

KEY MESSAGE

RrUNE12 binds to the RrGGP2 promoter to facilitate biosynthesis of AsA in Rosa roxburghii fruit. Furthermore, RrUNE12 upregulates antioxidant-related genes and maintains ROS homeostasis, thereby improving tolerance to salt stress. L-ascorbic acid (AsA) plays an essential role in stress defense as a major antioxidant in plant cells. GDP-L-galactose pyrophosphatase 2 (RrGGP2) has been previously identified as the key structural gene operating in AsA overproduction in Rosa roxburghii fruit. However, the transcriptional regulation of RrGGP2 in response to abiotic stress is not fully elucidated. In this study, we identified a bHLH transcription factor, RrUNE12, whose transcription level significantly correlated with RrGGP2 abundance and AsA accumulation in developing fruit. RrUNE12 is localized in the nucleus and specifically binds to the promoter of RrGGP2 to promote its transcription. The overexpression or silencing of RrUNE12 in R. roxburghii fruit and fruit callus further confirmed that RrUNE12 positively regulated RrGGP2 transcription and AsA level. Different abiotic stress treatments indicated that RrUNE12 was greatly induced by salt. Exogenous NaCl treatment on the RrUNE12-overexpressing or RrUNE12-silencing fruits also led to enhanced transcripts abundance of both RrUNE12 and RrGGP2, compared to the treatment without adding NaCl. RrUNE12 overexpression in fruit callus alleviated salt stress damage by upregulating the expression of RrGGP2 and antioxidant-related genes. Additionally, stable overexpression of RrUNE12 in tomato plants resulted in a significant increase in AsA content and antioxidant capacity, accompanied by an increased resistance to the salt stress. Collectively, the results suggest that RrUNE12 functions as an activator of AsA biosynthesis in R. roxburghii fruit and plays a positive role in mitigating salt stress by increasing both AsA level and the oxidation resistance.

Genome-wide identification of the bHLH gene family in Scutellaria baicalensis and their relationship with baicalin biosynthesis under drought stress

The bHLH gene family plays a critical role in regulating internal responses in plants. Although the pharmacological properties of Scutellaria baicalensis have been extensively studied, its bHLH gene family remains poorly investigated. In this study, 142 SbbHLH genes were identified using the complete genome data of S. baicalensis. Phylogenetic and conserved motif analyses were performed. Gene duplication events were analyzed, and cis-element analysis was conducted to explore regulatory factors. The expression patterns of these genes in different tissues and under drought stress were investigated using transcriptome data and qRT-PCR analysis. Phylogenetic and conserved motif analyses revealed that the gene structures within each SbbHLH clade are relatively conserved. Gene duplication analysis identified 29 duplication events in the SbbHLH gene family, most of which involved gene pairs under purifying selection. Cis-element analysis revealed that these genes are regulated by various environmental and hormonal factors. Transcriptomic data and qRT-PCR results demonstrated tissue-specific expression patterns for the 142 SbbHLH genes. Additionally, bHLH genes potentially involved in baicalin biosynthesis were identified under drought stress. The findings suggest that under drought stress, SbbHLH74, SbbHLH98, and SbbHLH142 are regulated by a network centered on SbbHLH53, which enhances baicalin biosynthesis. In conclusion, this study provides a comprehensive analysis of the bHLH gene family in S. baicalensis and identifies 4 potential SbbHLH genes involved in regulating baicalin biosynthesis under drought stress.

Genome-wide identification and expression analysis of bHLH gene family revealed their potential roles in abiotic stress response, anthocyanin biosynthesis and trichome formation in Glycyrrhiza uralensis

Introduction

Licorice stands out as an exceptional medicinal resource with a long history of application, attributed to its substantial pharmacological potential. The basic helix-loop-helix (bHLH) transcription factors (TFs) gene family, being the second-largest in plants, is vital for plant development and adapting to environmental shifts. Despite this, the comprehensive characteristics of licorice bHLH gene family are not well-documented.

Results

In this study, a detailed and thorough genome-wide identification and expression analysis of Glycyrrhiza uralensis bHLH gene family was carried out, resulting in the identification of 139 licorice bHLH members. Our duplication analysis highlighted the significant contribution of segmental duplications to the expansion of G. uralensis bHLH genes, with GubHLH genes experiencing negative selection throughout evolution. It was discovered that GubHLH64 and GubHLH38 could be importantly linked to the licorice trichome initiation and anthocyanin biosynthesis and GubHLH64 was also involved in the abiotic stress response. Additionally, certain subfamily III (d+e) GubHLH members could be implicated in the licorice drought response. GubHLH108, GubHLH109, and GubHLH116 were suggested to form a tightly related cluster, initiating transcriptional responses via JA signaling pathway.

Discussion

In summary, our findings furnish a foundational understanding for future investigations of GubHLH gene functions and regulation mechanisms, shedding light on the potential applications of licorice in medicine and agriculture.

Regulation of Flavonoid Biosynthesis by the MYB-bHLH-WDR (MBW) Complex in Plants and Its Specific Features in Cereals

Flavonoids are a large group of secondary metabolites, which are responsible for pigmentation, signaling, protection from unfavorable environmental conditions, and other important functions, as well as providing numerous benefits for human health. Various stages of flavonoid biosynthesis are subject to complex regulation by three groups of transcription regulators-MYC-like bHLH, R2R3-MYB and WDR which form the MBW regulatory complex. We attempt to cover the main aspects of this intriguing regulatory system in plants, as well as to summarize information on their distinctive features in cereals. Published data revealed the following perspectives for further research: (1) In cereals, a large number of paralogs of MYC and MYB transcription factors are present, and their diversification has led to spatial and biochemical specialization, providing an opportunity to fine-tune the distribution and composition of flavonoid compounds; (2) Regulatory systems formed by MBW proteins in cereals possess distinctive features that are not yet fully understood and require further investigation; (3) Non-classical MB-EMSY-like complexes, WDR-independent MB complexes, and solely acting R2R3-MYB transcription factors are of particular interest for studying unique regulatory mechanisms in plants. More comprehensive understanding of flavonoid biosynthesis regulation will allow us to develop cereal varieties with the required flavonoid content and spatial distribution.

Pangenome and pantranscriptome as the new reference for gene-family characterization: A case study of basic helix-loop-helix (bHLH) genes in barley

Genome-wide identification and comparative gene-family analyses have commonly been performed to investigate species-specific evolution linked to various traits and molecular pathways. However, most previous studies have been limited to gene screening in a single reference genome, failing to account for the gene presence/absence variations (gPAVs) in a species. Here, we propose an innovative pangenome-based approach for gene-family analyses based on orthologous gene groups (OGGs). Using the basic helix-loop-helix (bHLH) transcription factor family in barley as an example, we identified 161-176 bHLHs in 20 barley genomes, which can be classified into 201 OGGs. These 201 OGGs were further classified into 140 core, 12 softcore, 29 shell, and 20 line-specific/cloud bHLHs, revealing the complete profile of bHLH genes in barley. Using a genome-scanning approach, we overcame the genome annotation bias and identified an average of 1.5 un-annotated core bHLHs per barley genome. We found that whole-genome/segmental duplicates are predominant mechanisms contributing to the expansion of most core/softcore bHLHs, whereas dispensable bHLHs are more likely to result from small-scale duplication events. Interestingly, we noticed that the dispensable bHLHs tend to be enriched in the specific subfamilies SF13, SF27, and SF28, implying the potentially biased expansion of specific bHLHs in barley. We found that 50% of the bHLHs contain at least 1 intact transposon element (TE) within the 2-kb upstream-to-downstream region. bHLHs with copy-number variations (CNVs) have 1.48 TEs on average, significantly more than core bHLHs without CNVs (1.36), supporting a potential role of TEs in bHLH expansion. Analyses of selection pressure showed that dispensable bHLHs have experienced clear relaxation of selection compared with core bHLHs, consistent with their conservation patterns. We also integrated the pangenome data with recently available barley pantranscriptome data from 5 tissues and discovered apparent transcriptional divergence within and across bHLH subfamilies. We conclude that pangenome-based gene-family analyses can better describe the previously untapped, genuine evolutionary status of bHLHs and provide novel insights into bHLH evolution in barley. We expect that this study will inspire similar analyses in many other gene families and species.

Dressed Up to the Nines: The Interplay of Phytohormones Signaling and Redox Metabolism During Plant Response to Drought

Plants must effectively respond to various environmental stimuli to achieve optimal growth. This is especially relevant in the context of climate change, where drought emerges as a major factor globally impacting crops and limiting overall yield potential. Throughout evolution, plants have developed adaptative strategies for environmental stimuli, with plant hormones and reactive oxygen species (ROS) playing essential roles in their development. Hormonal signaling and the maintenance of ROS homeostasis are interconnected, playing indispensable roles in growth, development, and stress responses and orchestrating diverse molecular responses during environmental adversities. Nine principal classes of phytohormones have been categorized: auxins, brassinosteroids, cytokinins, and gibberellins primarily oversee developmental growth regulation, while abscisic acid, ethylene, jasmonic acid, salicylic acid, and strigolactones are the main orchestrators of environmental stress responses. Coordination between phytohormones and transcriptional regulation is crucial for effective plant responses, especially in drought stress. Understanding the interplay of ROS and phytohormones is pivotal for elucidating the molecular mechanisms involved in plant stress responses. This review provides an overview of the intricate relationship between ROS, redox metabolism, and the nine different phytohormones signaling in plants, shedding light on potential strategies for enhancing drought tolerance for sustainable crop production.

Genome- and Transcriptome-Wide Characterization and Expression Analyses of bHLH Transcription Factor Family Reveal Their Relevance to Salt Stress Response in Tomato

The bHLH (basic helix-loop-helix) transcription factors function as crucial regulators in numerous biological processes including abiotic stress responses and plant development. According to our RNA-seq analysis of tomato seedlings under salt stress, we found that, although the bHLH gene family in tomato has been studied, there are still so many tomato bHLH genes that have not been identified and named, which will hinder the later study of SlbHLHs. In total, 195 SlbHLHs that were unevenly distributed onto 12 chromosomes were identified from the tomato genome and were classified into 27 subfamilies based on their molecular features. The collinearity between SlbHLHs and interrelated orthologs from 10 plants further revealed evolutionary insights into SlbHLHs. Cis-element investigations of SlbHLHs promotors further suggested the potential roles of SlbHLHs in tomato development and stress responses. A total of 30 SlbHLHs were defined as the differentially expressed genes in response to salt stress by RNA-seq. The expression profiles of selected SlbHLHs were varyingly and markedly induced by multiple abiotic stresses and hormone treatments. These results provide valuable information to further understand the significance and intricacy of the bHLH transcription factor family, and lay a foundation for further exploring functions and possible regulatory mechanisms of SlbHLH members in abiotic stress tolerance, which will be significant for the study of tomato stress resistance and agricultural productivity.

The StbHLH47 transcription factor negatively regulates drought tolerance in potato (Solanum tuberosum L.)

BACKGROUND

Drought stress is a major environmental constraint affecting crop yields. Plants in agricultural and natural environments have developed various mechanisms to cope with drought stress. Identifying genes associated with drought stress tolerance in potato and elucidating their regulatory mechanisms is crucial for the breeding of new potato germplasms. The bHLH transcription factors involved play crucial roles not only in plant development and growth but also in responsesresponse to abiotic stress.

RESULTS

In this study, the StbHLH47 gene, which is highly expressed in potato leaves, was cloned and isolated. Subcellular localization assays revealed that the gene StbHLH47 performs transcriptional functions in the nucleus, as evidenced by increased malondialdehyde (MDA) content and relative conductivity under drought stress. These findings indicate that overexpressing plants are more sensitive to drought stress. Differential gene expression analysis of wild-type plants (WT) and plants overexpressing StbHLH47 (OE-StbHLH47) under drought stress revealed that the significantly differentially expressed genes were enriched in metabolic pathways, biosynthesis of various plant secondary metabolites, biosynthesis of metabolites, plant hormone signal transduction, mitogen-activated protein kinase (MAPK) signalling pathway-plant, phenylpropanoid biosynthesis, and plant‒pathogen interactions. Among these pathways, the phenylalanine and abscisic acid (ABA) signal transduction pathways were enriched in a greater number of differentially expressed genes, and the expression trends of these differentially expressed genes (DEGs) were significantly different between WT and OE-StbHLH47. Therefore, it is speculated that StbHLH47 may regulate drought resistance mainly through these two pathways. Additionally, RT‒qPCR was used for fluorescence quantification of the expression of StNCED1 and StERD11, which are known for their drought resistance, and the results revealed that the expression levels were much lower in OE-StbHLH47 than in WT plants.

CONCLUSION

RNA-seq, RT‒qPCR, and physiological index analyses under drought conditions revealed that overexpression of the StbHLH47 gene increased the sensitivity of potato plants to drought stress, indicating that StbHLH47 negatively regulates drought tolerance in potato plants. In summary, our results indicate that StbHLH47 is a negative regulator of drought tolerance and provide a theoretical basis for further studies on the molecular mechanism involved.

Malus xiaojinensis MxbHLH30 Confers Iron Homeostasis Under Iron Deficiency in Arabidopsis

Iron stress adversely impacts plants' growth and development. Transcription factors (TFs) receive stress signals and modulate plant tolerance by influencing the expression of related functional genes. In the present study, we investigated the role of an apple bHLH transcription factor MxbHLH30 in the tolerance to iron stresses. The expression of MxbHLH30 was induced significantly by low-iron and high-iron treatments and MxbHLH30-overexpressed Arabidopsis plants displayed iron-stress-tolerant phenotypes. A determination of physiological and biochemical indexes associated with abiotic stress responses showed that overexpression of MxbHLH30 increased the activities of antioxidant enzymes superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) in Arabidopsis plants treated with iron stress, and decreased the contents of H2O2 and malondialdehyde (MDA), which contribute to reduce cell membrane lipid peroxidation. Meanwhile, the accumulation of proline in transgenic plant cells increased, regulating cell osmotic pressure. Furthermore, quantitative expression analysis indicated that overexpression of MxbHLH30 improved the expression levels of positive functional genes' responses to iron stress, improving plant resistance. Interestingly, MxbHLH30 may have the ability to balance the homeostasis of iron and other metal ions for the iron homeostasis of Arabidopsis cell under low-iron environments. This research demonstrates that MxbHLH30 is a key regulator of cell iron homeostasis in Arabidopsis plants under iron deficiency, providing new knowledge for plant resistance regulation.

Synthetic alleles to study MUTE-dependent molecular transitions in stomatal development

Stomatal abundance sets plants' potential for gas exchange, impacting photosynthesis and transpiration and, thus, plant survival and growth. Stomata originate from cell lineages initiated by asymmetric divisions of protodermal cells, producing meristemoids that develop into guard cell pairs. The transcription factors SPEECHLESS, MUTE, and FAMA are essential for stomatal lineage development, sequentially driving cell division and differentiation events. Their absence produces stomataless epidermis, hindering analysis of their roles during lineage development. MUTE drives the transition from proliferating meristemoids to guard mother cells, committed to stomatal fate. We aim to explore the molecular mechanisms underlying MUTE activity, using partial loss-of-function alleles predicted to impair DNA-binding and to potentially alter MUTE transcriptional activity. We engineered mutant allele coding sequences, generated Arabidopsis lines carrying them and analyzed their epidermal and transcriptional phenotypes using microscopy and RNA-seq. Synthetic alleles driven by the MUTE promoter rescued the stomata less phenotype of the seedling-lethal mute-3 mutant, enabling stomata differentiation and resulting in viable, fertile plants. Further examination of the developmental consequences of MUTE partial loss-of-function revealed arrested lineages, reduced stomatal abundance and altered stomatal spacing. Transcriptomic analysis of very young cotyledons from complemented lines indicated that only some MUTE targets require an intact MUTE bHLH domain. Comparison with existing lineage cell-specific transcriptional profiles showed that lineage development in the mutant lines was delayed compared to the wild-type but followed similar gene networks. These synthetic alleles provide new insight into MUTE ability to accurately and timely specify stomata formation.

The brassinosteroid signaling-related ILI-OsAIF-OsbHLH92 transcription factor module antagonistically controls leaf angle and grain size in rice

Atypical basic helix-loop-helix (bHLH) transcription factors, which lack the basic region for DNA binding, are important elements of brassinosteroid (BR) signaling. Recently, our systematic characterization of the rice (Oryza sativa) INCREASED LEAF INCLINATION (ILI) subfamily of atypical bHLHs revealed their indispensable roles in BR-mediated growth and development. Here, we reported the isolation of two additional rice ILI-interacting atypical bHLHs, ATBS1-INTERACTING FACTOR 1 (OsAIF1)/OsbHLH176 and OsAIF2/OsbHLH178. Genetic and cytological analyses of the OsAIFs knockout mutants and overexpression lines revealed that OsAIF1 and OsAIF2 negatively regulate rice leaf inclination and grain size in a synergistic and redundant manner. Compared to the wild-type, osaif knockout mutants exhibited hypersensitivity to BR, while OsAIF1 and OsAIF2 overexpression lines showed greatly reduced sensitivity or complete insensitivity to BR, indicating that these two OsAIFs act as major negative regulators of rice BR signaling. As ILI-interacting negative atypical HLHs, OsAIF1 and OsAIF2 genetically counteracted the positive ILI subfamily of atypical HLHs. Moreover, OsAIF1 and OsAIF2 physically interacted with and antagonized OsbHLH92, a positive regulator of BR signaling, thereby modulating rice development and gene transcription. These findings suggested that the atypical HLHs (ILIs and OsAIF1/OsAIF2) and the bHLH (OsbHLH92) transcription factors form a triantagonistic cascade in rice, counteracting each other to fine-tune leaf angle and grain size through BR signaling. Our results provide insights into the mechanisms balancing BR signaling and growth in rice.

OsbHLH6, a basic helix-loop-helix transcription factor, confers arsenic tolerance and root-to-shoot translocation in rice

Arsenic (As) is extremely toxic to plants, posing a serious concern for food safety. Identification of genes responsive to As is significative for figuring out this issue. Here, we identified a bHLH transcription factor OsbHLH6 that was involved in mediating the processes of As tolerance, uptake, and root-to-shoot translocation in rice. The expression of OsbHLH6 gene was strongly induced after 3 and 48 h of arsenite [As(III)] treatment. The OsbHLH6-overexpressed transgenic rice (OE-OsbHLH6) was sensitive to, while the knockout mutant of OsbHLH6 gene (Osbhlh6) was tolerant to As(III) stress by affecting the contents of reactive oxygen species (ROS) and non-protein thiols (NPT), etc. Knockout of OsbHLH6 gene increased significantly the As concentration in roots, but decreased extensively As accumulation in shoots, compared to that in OE-OsbHLH6 and WT plants. The transcripts of phytochelatins (PCs) synthetase encoding genes OsPCS1 and OsPCS2, as well as As(III) transporter encoding genes OsLsi1 and OsABCC1 were greatly abundant in Osbhlh6 mutants than in OE-OsbHLH6 and WT plants under As(III) stress. In contrast, the expression of OsLsi2 gene was extensively suppressed by As(III) in Osbhlh6 mutants. OsbHLH6 acted as a transcriptional activator to bind directly to the promoter and regulate the expression of OsPrx2 gene that encodes a peroxidase precursor. Moreover, overexpression of OsbHLH6 gene resulted in significant change of expression of amounts of abiotic stress-related genes, which might partially contribute to the As sensitivity of OE-OsbHLH6 plants. These findings may broaden our understanding of the molecular mechanism of OsbHLH6-mediated As response in rice and provide novel useful genes for rice As stress-resistant breeding.

bHLH19 and bHLH20 repress jasmonate-mediated plant defense against insect herbivores in Arabidopsis

Plants are attacked by various insect herbivores. Upon attack-triggered biosynthesis of the phytohormone jasmonates (JAs), the JA receptor CORONATINE INSENSITIVE 1 recruits the JA-ZIM domain (JAZ) repressors for ubiquitination, releases the MYC-MYB transcription factor (TF) complexes, and enhances glucosinolates (GSs) biosynthesis to promote defense against insects in Arabidopsis. However, the negative regulation of JA-regulated defense remains largely unclear. Here, we found that Arabidopsis IVa bHLH TFs bHLH19 and bHLH20 interacted with JAZs. The bhlh19/20 mutations enhanced defense against the insects Spodoptera frugiperda and S. exigua, while their overexpression inhibited defense. bHLH19/20 repressed defense via at least two layers of regulation: first, bHLH19/20 interacted with the members MYC2/3/4/5 and MYB34/51/122 of MYC-MYB complexes, and inhibited the interaction/transcription activity of MYC2-MYB34; second, bHLH19/20 activated the RNA level of nitrile-specifier protein 1, which converts GSs into the less toxic nitriles. bhlh19/20 exhibited no penalty in JA-regulated growth inhibition. Collectively, our findings reveal the molecular mechanism for negatively regulating JA-mediated defense against insects in Arabidopsis without growth penalty by the pair of bHLH19/20 TFs.

Genome-wide identification and expression analysis of the glutathione transferase gene family and its response to abiotic stress in rye (Secale cereale)

BACKGROUND

Glutathione S-transferases (GSTs) are a crucial class of plant enzymes, playing pivotal roles in plant growth, development, and stress responses. However, studies on the functions and regulatory mechanisms of GSTs in plants remain relatively limited.

RESULTS

This study aimed to comprehensively identify and analyze GST proteins in rye. A total of 171 rye GST genes were identified and classified into four subfamilies, Tau, Phi, Theta, and Zeta, based on their sequence similarity and structural features. Notably, genes classified under the Tau subfamily were the most abundant at 118, while only one gene was under the Theta subfamily. Subsequent phylogenetic and collinearity analysis revealed 29 tandem duplications and 6 segmental duplication events. There were 13 collinear genes between rye and wheat, maize, and rice, demonstrating the expansion and evolution of the GST gene family. An analysis of the expression profiles of 20 representative ScGST genes in different tissues and under various environmental stresses was performed to further understand the functions and expression patterns of ScGST genes. The results showed that these genes exhibited the highest expression levels in stems, followed by fruits and leaves.

CONCLUSIONS

This study provides a comprehensive identity, classification, and analysis of rye GST genes, which offer valuable insights into the functionality and regulatory mechanisms of the GST gene family in rye. Especially, ScGST39 was identified as a candidate gene because it was significantly upregulated under multiple stress conditions, indicating its potential crucial role in plant stress tolerance mechanisms.

Genome expression analysis of basic helix-loop-helix transcription factors in Sea buckthorn (Hippophae rhamnoides L.)

Introduction

The basic helix-loop-helix (bHLH) transcription factor family is one of the largest gene families in plants, extensively involved in plant growth, organ development, and stress responses. However, limited studies of this family are available in sea buckthorn (Hippophae rhamnoides).

Methods

In this study, we identified 144 bHLH genes in H. rhamnoides (HrbHLH) through a genome-wide search method, then explored their DNA and protein sequences and physicochemical properties.

Results and discussion

According to the sequence similarities, we classified them into 15 groups with specific motif structures. To explore their expressions, we performed gene expression profiling using RNA-Seq and identified 122 HrbHLH mRNAs were highly expressed, while the remaining 22 HrbHLH genes were expressed at very low levels in all 21 samples. Among these HrbHLH genes, HrbHLH47, HrbHLH74, HrbHLH90, HrbHLH131 showed the highest expression level in the root nodule, root, leaf, stem and fruit tissues. Furthermore, eleven HrbHLH genes displayed increased expressions during the fruit development process of sea buckthorn. Finally, we validated the expression patterns of HrbHLH genes using reverse transcription quantitative real-time PCR (QPCR). This comprehensive analysis provides a useful esource that enables further investigation of the physiological roles and molecular functions of the HrbHLH TFs.

Genome-Wide Identification of Basic Helix-Loop-Helix (bHLH) Family in Peanut: Potential Regulatory Roles in Iron Homeostasis

The basic helix-loop-helix (bHLH) superfamily is the second-largest transcription factor family that participates in a wide range of biological processes in plants, including iron homeostasis. Although the family has been studied in several plant species, a comprehensive investigation is still needed for peanut (Arachis hypogaea). Here, a genome-wide analysis identified 373 AhbHLH genes in peanut, which were divided into 14 groups or subfamilies according to phylogenetic analysis. Clustered members generally share similar gene/protein structures, supporting the evolutionary relationships among AhbHLH proteins. Most AhbHLHs experienced whole-genome or segmental duplication. The majority of AhbHLH proteins had a typical bHLH domain, while several phylogenetic groups, including Group VI, X, XIII, and XIV, had the HLH domain. The expression of several AhbHLH genes, including AhbHLH001.3, AhbHLH029.1/.2, AhbHLH047.1/.2, AhbHLH115.1/.2, AhbHLH097.1/.2, AhbHLH109.4, and AhbHLH135.1, was induced by Fe deficiency for both cultivars, or at least in Silihong, suggesting an important role in the Fe deficiency response in peanut. Nine genes (AhbHLH001.3, AhbHLH029.1/.2, AhbHLH047.1/.2, AhbHLH097.1/.2, and AhbHLH115.1/.2) were specifically induced by Fe deficiency in Silihong, and their expression was higher in Silihong than that in Fenghua 1. These genes might be responsible for higher tolerance to Fe deficiency in Silihong. Our findings provide comprehensive information for further elucidating the regulatory mechanism of Fe homeostasis in peanut.

The SlbHLH92 transcription factor enhances salt stress resilience by fine-tuning hydrogen sulfide biosynthesis in tomato

Ongoing soil salinization severely hampers plant growth and the sustainability of global crops production. Hydrogen sulfide (H2S), acting as a critical gaseous signaling molecule, plays a vital role in plant response to various environmental cues such as salt stress. Nonetheless, it is not well understood how the transcriptional network regulates H2S production in response to salt stress in tomato. Herein, we determine that the bHLH transcription factor SlbHLH92 functions as a transcriptional activator in tomato (Solanum lycopersicum L.), upregulating the expression of the L-CYSTEINE DESULFHYDRASE 1 (SlLCD1) gene involved in H2S biosynthesis, thereby enhancing the plants' tolerance to salt stress. When exposed to salt stress, overexpression of SlbHLH92 in tomato leads to enhanced salt tolerance compared to wild-type plants. In contrast, suppression of SlbHLH92 expression with RNAi silencing results in increased sensitivity to salt stress. Subsequent molecular and biochemical investigations confirm that the salt-induced SlbHLH92 upregulates the expression of SlLCD1, leading to an increase in H₂S levels, as well as other salt-responsive genes (SlCBL10 and SlVQ16), by directly binding to specific cis-elements in their promoter regions. Furthermore, the VQ-motif containing protein SlVQ16 physically interacts with SlbHLH92, thereby promoting an increase in its transcriptional activity. Taken together, our study reveals an emerging mechanism in which the SlbHLH92-SlVQ16-H2S signaling cascade contributes to enhancing salt tolerance in tomato, presenting potential genetic targets for breeding salt-tolerant tomato cultivars.

Genome-Wide Identification of the bHLH Gene Family in Callerya speciosa Reveals Its Potential Role in the Regulation of Isoflavonoid Biosynthesis

Callerya speciosa (Champ. ex Benth.) Schot is a significant leguminous plant valued for its edible tuberous roots, which are a plentiful source of isoflavonoids. Basic helix-loop-helix (bHLH) transcription factors (TFs) have been reported to regulate secondary metabolism in plants, especially flavonoid biosynthesis. However, the bHLH genes in C. speciosa have not yet been reported, and their regulatory role in isoflavonoid biosynthesis remains unexplored. Here, 146 CsbHLH genes were identified in the C. speciosa genome, classifying them into 23 subfamilies based on the gene structures and phylogenetic relationships. All the CsbHLH proteins contained both motifs 1 and 2, whereas motif 8 was only distributed in subgroup III (d + e). Collinearity analysis demonstrated that fragmental replications are the primary driver of CsbHLH evolution, with the majority of duplicated CsbHLH gene pairs experiencing selective pressure. Nine candidate CsbHLH genes were found to play a potential role in regulating isoflavonoid biosynthesis through a combination of gene-to-metabolite correlation analysis and weighted gene co-expression network analysis (WGCNA). Additionally, the cis-regulatory elements and response to MeJA of these nine genes were characterized and confirmed through quantitative real-time PCR (qRT-PCR) analysis. Among them, three CsbHLHs (CsbHLH9, CsbHLH89, and CsbHLH95) were selected for further investigation. Yeast two-hybrid (Y2H), dual-luciferase (LUC) assays, bimolecular fluorescence complementation (BiFC) assays, and transient transformation demonstrated that CsbHLH9 acted as a transcriptional activator through its interaction with CsMYB36 and binding to the promoters of isoflavonoid biosynthesis genes in a MeJA-induced manner, such as CsIFR2, CsI3'H2, and CsCHS4, to promote isoflavonoid (calycosin, calycosin-7-o-glucoside, and formononetin) accumulation. Our results establish a basis for the functional analysis of bHLH genes and investigations into the molecular mechanisms underlying isoflavonoid biosynthesis in C. speciosa.

Genome-wide analysis of calmodulin binding Protein60 candidates in the important crop plants

BACKGROUND

Efficient management of environmental stresses is essential for sustainable crop production. Calcium (Ca²⁺) signaling plays a crucial role in regulating responses to both biotic and abiotic stresses, particularly during host-pathogen interactions. In Arabidopsis thaliana, calmodulin-binding protein 60 (CBP60) family members, such as AtCBP60g, AtCBP60a, and AtSARD1, have been well characterized for their involvement in immune regulation. However, a comprehensive understanding of CBP60 genes in major crops remains limited.

METHODS

In this study, we utilized the Phytozome v12.1 database to identify and analyze CBP60 genes in agriculturally important crops. Expression patterns of a Oryza sativa (rice) CBP60 gene, OsCBP60bcd-1, were assessed in resistant and susceptible rice genotypes in response to infection by the bacterial pathogen Xanthomonas oryzae. Localization of CBP60 proteins was analyzed to predict their functional roles, and computational promoter analysis was performed to identify stress-responsive cis-regulatory elements.

RESULTS

Phylogenetic analysis revealed that most CBP60 genes in crops belong to the immune-related clade. Expression analysis showed that OsCBP60bcd-1 was significantly upregulated in the resistant rice genotype upon pathogen infection. Subcellular localization studies suggested that the majority of CBP60 proteins are nuclear-localized, indicating a potential role as transcription factors. Promoter analysis identified diverse stress-responsive cis-regulatory elements in the promoters of CBP60 genes, highlighting their regulatory potential under stress conditions.

CONCLUSION

The upregulation of OsCBP60bcd-1 in response to Xanthomonas oryzae and the presence of stress-responsive elements in its promoter underscore the importance of CBP60 genes in pathogen defense. These findings provide a basis for further investigation into the functional roles of CBP60 genes in crop disease resistance, with implications for enhancing stress resilience in agricultural species.

Comprehensive analysis of transcription factor binding sites and expression profiling of rice pathogenesis related genes (OsPR1)

Pathogenesis-related (PR) proteins, found in plants, play a crucial role in responding to both biotic and abiotic stresses and are categorized into 17 distinct families based on their properties and functions. We have conducted a phylogenetic analysis of OsPR1 genes (rice PR1 genes) in conjunction with 58 putative PR1 genes identified in Brachypodium distachyon, Hordeum vulgare, Brassica rapa, and Zea mays through BLASTP predictions. We extensively investigated the responses of the remaining 11 rice PR1 genes, using OsPR1a as a reference, under various stress conditions, including phytohormone treatments (salicylic acid and brassinosteroid [BR]), wounding, and heat stress (HS). In rice, of the 32 predicted OsPR1 genes, 12 have been well-characterized for their roles in disease resistance, while the functions of the remaining genes have not been studied extensively. In our study, we selected an additional 11 OsPR1 genes for further analysis and constructed a phylogenetic tree based on the presence of a 10-amino-acid-long conserved motif within these proteins. The phylogenetic analysis revealed that both OsPR1a from earlier studies and OsPR1-74 from our current study belong to the same clade. These genes consistently exhibit upregulation in response to diverse stress treatments such as biotic stress and abiotic stresses such as heat, drought, and salinity, indicating their potential roles in enhancing stress tolerance in rice. Significantly, this study delves into the previously unexplored role of OsPR1 genes in responding to Brassinosteroid (BR) and heat stress (HS) treatments, confirming their involvement in stress responses through qRT-PCR analysis. We found that seven genes were upregulated by EBR treatment. During heat stress (HS), six and seven genes were upregulated at 1hand 4h HS, respectively. The remaining genes OsPR1-22 and OsPR1-75 were upregulated at 1h but downregulated at 4h HS and under EBR treatment. In contrast, OsPR1-76 was upregulated at both 1h and 4h HS, but downregulated under EBR treatment. Promoters of PR1 genes in rice and other crops are rich in transcription factor binding sites (TFBSs) and feature a conserved Cysteine-rich secretory protein (SCP or CAP) motif. This study advances our understanding of PR1 gene regulation and its potential to enhance stress tolerance in rice.

Drought-inducible HpbHLH70 enhances drought tolerance and may accelerate floral bud induction in pitaya

Floral bud induction is of great importance for fruit crops, which may substantially affect fruit yield. Previously, a FLOWERING BHLH (FBH) transcription factor gene HpbHLH70 was identified in pitaya (Hylocereus polyrhizus) as subjected to drought stress. In present work, HpbHLH70 was found predominantly activated in pitaya anthers. GUS fusing reporter assay showed its selective activation in anthers and vasculatures of transgenic Arabidopsis. Moreover, HpbHLH70 is drought inducible, which was further supported by the deepened GUS staining under drought condition, indicating a HpbHLH70-mediated crosstalk between drought response and floral bud induction, which partially explained the advanced floral bud induction in pitaya by drought stress. Overexpression of HpbHLH70 in pitaya improved the drought tolerance by enhancing the water-holding capacity and the ROS-scavenging activity. Meanwhile, overexpression of HpbHLH70 in Arabidopsis improved their behaviors under drought stress. Intriguingly, the transgenic Arabidopsis flowered earlier than the wild-type. In addition, HpbHLH70 was verified to heterodimerize with HpbHLH59 and transactivate the floral-bud-induction regulator HpSOC1 via direct binding to the promoter. Overexpression of HpbHLH70 up-regulated the expression of HpSOC1 in pitaya. Collectively, our data uncover that drought-induced HpbHLH70 enhances drought tolerance and may accelerate floral bud induction in pitaya via heterodimerization with HpbHLH59 and transactivation of HpSOC1.

Protein kinase SnRK2.6 phosphorylates transcription factor bHLH3 to regulate anthocyanin homeostasis during strawberry fruit ripening

Strawberry (Fragaria × ananassa) is a model plant for studying non-climacteric fruit ripening regulated by abscisic acid (ABA); however, the signaling of ABA in the regulation of fruit coloration is not fully understood. In this study, we identified the transcription factor BASIC HELIX-LOOP-HELIX 3 (bHLH3) as being key to fruit coloration via yeast two-hybrid library screening using the bait SUCROSE NONFERMENTING 1 (SNF1)-RELATED PROTEIN KINASE 2 (SnRK2.6), which is a core ABA signaling component that negatively regulates ripening. The interaction was also confirmed by firefly luciferase complementation assays and pull-down assays. RT-qPCR and western blot analysis confirmed that bHLH3 is expressed ubiquitously in strawberry tissues, and it is expressed stably during fruit development. Overexpression and RNAi of both bHLH3 and SnRK2.6 demonstrated that bHLH3 and SnRK2.6 promote and inhibit strawberry fruit coloration, respectively. Using EMSAs, we showed that bHLH3 promotes the expression of UDP-GLUCOSE: FLAVONOL-O-GLUCOSYLTRANSFERASE (UFGT), a key gene for anthocyanin biosynthesis, by directly binding to its promoter. We determined that SnRK2.6 can phosphorylate bHLH3 and that this inhibits its binding to the UFGT promoter, consequently suppressing expression. Altogether, we propose that increased ABA content during strawberry fruit ripening leads to decreased expression of SnRK2.6, which in turn releases the phosphorylation of bHLH3 and thereby enhances UFGT expression, ultimately promoting the coloration of the fruit.

Comparative genomics and transcriptomics analysis of the bHLH gene family indicate their roles in regulating flavonoid biosynthesis in Sophora flavescens

The basic helix-loop-helix (bHLH) transcription factors play crucial roles in various processes, such as plant development, secondary metabolism, and response to biotic/abiotic stresses. Sophora flavescens is a widely used traditional herbal medicine in clinical practice, known for its abundant flavonoids as the main active compounds. However, there has been no comprehensive analysis of S. flavescens bHLH (SfbHLH) gene family reported currently. In this study, we identified 167 SfbHLH genes and classified them into 23 subfamilies based on comparative genomics and phylogenetic analysis. Furthermore, widespread duplications significantly contributed to the expansion of SfbHLH family. Notably, SfbHLH042 was found to occupy a central position in the bHLH protein-protein interaction network. Transcriptome analysis of four tissues (leaf, stem, root and flower) revealed that most SfbHLH genes exhibited high expression levels exclusively in specific tissues of S. flavescens. The integrated analysis of transcriptomics and metabolomics during pod development stages revealed that SfbHLH042 may play a central role in connecting SfbHLH genes, flavonoids, and key enzymes involved in the biosynthesis pathway. Moreover, we also checked the expression of 8 SfbHLH genes using RT-qPCR analysis to realize the expression profiles of these genes among various tissues at different cultivated periods and root development. Our study would aid to understand the phylogeny and expression profile of SfbHLH family genes, and provide a promising candidate gene, SfbHLH042, for regulating the biosynthesis of flavonoids in S. flavescens.

Metabolic characterization and transcriptional profiling of polyphenols in Cannabis sativa L. inflorescences with different chemical phenotypes

MAIN CONCLUSION

After the most comprehensive analysis of the phenolic composition in Cannabis reported to date, a total of 211 compounds were identified, phenolic profiles were able to discriminate cannabis varieties and a complex regulatory network for phenolics accumulation in Cannabis chemovars was highlighted. Female inflorescences of Cannabis sativa L. are plenty of secondary metabolites, of which flavonoids and phenolic acids have been investigated by far less than phytocannabinoids and terpenoids. Understanding the biochemical composition in phenylpropanoids of Cannabis inflorescences, the molecular basis of flavonoid synthesis and how their content can be modulated by specific transcription factors will shed light on the variability of this trait in the germplasm, allowing the identification of biologically active metabolites that can be of interest to diverse industries. In this work, an untargeted metabolomic approach via UHPLC-HRMS was adopted to investigate the composition and variability of phenylpropanoids in thirteen Cannabis genotypes differentiated for their profile in phytocannabinoids, highlighting that phenolic profiles can discriminate varieties, with characteristic, unique genotype-related patterns. Moreover, the transcription profile of candidate phenolics regulatory MYB and bHLH transcription factors, analyzed by RT-qPCR, appeared strongly genotype-related, and specific patterns were found to be correlated between biochemical and transcriptional levels. Results highlight a complex regulatory network for phenolic accumulation in Cannabis chemovars that will need further insights from the functional side.

Functions and Regulatory Mechanisms of bHLH Transcription Factors during the Responses to Biotic and Abiotic Stresses in Woody Plants

Environmental stresses, including abiotic and biotic stresses, have complex and diverse effects on the growth and development of woody plants, which have become a matter of contention due to concerns about the outcomes of climate change on plant resources, genetic diversity, and world food safety. Plant basic helix-loop-helix (bHLH) transcription factors (TFs) are involved in a variety of physiological processes and play an important role in biotic and abiotic stress responses of woody plants. In recent years, an increasing body of studies have been conducted on the bHLH TFs in woody plants, and the roles of bHLH TFs in response to various stresses are increasingly clear and precise. Therefore, it is necessary to conduct a systematic and comprehensive review of the progress of the research of woody plants. In this review, the structural characteristics, research history and roles in the plant growth process of bHLH TFs are summarized, the gene families of bHLH TFs in woody plants are summarized, and the roles of bHLH TFs in biotic and abiotic stresses in woody plants are highlighted. Numerous studies mentioned in this review have shown that bHLH transcription factors play a crucial role in the response of woody plants to biotic and abiotic stresses. This review serves as a reference for further studies about enhancing the stress resistance and breeding of woody plants. Also, the future possible research directions of bHLH TFs in response to various stresses in woody plants will be discussed.

A bamboo bHLH transcription factor PeRHL4 has dual functions in enhancing drought and phosphorus starvation tolerance

ROOTHAIRLESS (RHL) is a typical type of basic helix-loop-helix (bHLH) transcription factor (TF), which has been reported to participate in various aspects of plant growth and in response to stress. However, the functions of RHL subfamily members in moso bamboo (Phyllostachys edulis) remain unknown. In this study, we identified 14 bHLH genes (PeRHL1-PeRHL14) in moso bamboo. Phylogenetic tree and conserved motif analyses showed that PeRHLs were clustered into three clades. The expression analysis suggested that PeRHL4 was co-expressed with PeTIP1-1 and PePHT1-1 in moso bamboo. Moreover, these three genes were all up-regulated in moso bamboo under drought stress and phosphate starvation. Y1H, DLR and EMSA assays demonstrated that PeRHL4 could activate the expression of PeTIP1-1 and PePHT1-1. Furthermore, overexpression of PeRHL4 could increase both drought and phosphate starvation tolerance in transgenic rice, in which the expression of OsTIPs and OsPHT1s was significantly improved, respectively. Overall, our results indicated that drought stress and phosphate starvation could induce the expression of PeRHL4, which in turn activated downstream genes involved in water and phosphate transport. Collectively, our findings reveal that PeRHL4 acting as a positive regulator contributes to enhancing the tolerance of moso bamboo under drought stress and phosphate starvation.

Investigating the regulatory role of HvANT2 in anthocyanin biosynthesis through protein-motif interaction in Qingke

Background

Currently, there are no reports on the HvbHLH gene family in the recent barley genome (Morex_V3). Furthermore, the structural genes related to anthocyanin synthesis that interact with HvANT2 have yet to be fully identified.

Methods

In this study, a bioinformatics approach was used to systematically analyze the HvbHLH gene family. The expression of this gene family was analyzed through RNA sequencing (RNA-seq), and the gene with the most significant expression level, HvANT2, was analyzed using quantitative reverse transcription polymerase chain reaction (qRT-PCR) in different tissues of two differently colored varieties. Finally, structural genes related to anthocyanin synthesis and their interactions with HvANT2 were verified using a yeast one-hybrid (Y1H) assay.

Results

The study identified 161 bHLH genes, designated as HvbHLH1 to HvbHLH161, from the most recent barley genome available. Evolutionary tree analysis categorized barley bHLH TFs into 21 subfamilies, demonstrating a pronounced similarity to rice and maize. Through RNA-Seq analysis of purple and white grain Qingke, we discovered a significant transcription factor (TF), HvANT2 (HvbHLH78), associated with anthocyanin biosynthesis. Subsequently, HvANT2 protein-motifs interaction assays revealed 41 interacting motifs, three of which were validated through Y1H experiments. These validated motifs were found in the promoter regions of key structural genes (CHI, F3'H, and GT) integral to the anthocyanin synthesis pathway. These findings provide substantial evidence for the pivotal role of HvANT2 TF in anthocyanin biosynthesis.

Genome-Wide Identification of Sorghum Paclobutrazol-Resistance Gene Family and Functional Characterization of SbPRE4 in Response to Aphid Stress

Sorghum (Sorghum bicolor), the fifth most important cereal crop globally, serves as a staple food, animal feed, and a bioenergy source. Paclobutrazol-Resistance (PRE) genes play a pivotal role in the response to environmental stress, yet the understanding of their involvement in pest resistance remains limited. In the present study, a total of seven SbPRE genes were found within the sorghum BTx623 genome. Subsequently, their genomic location was studied, and they were distributed on four chromosomes. An analysis of cis-acting elements in SbPRE promoters revealed that various elements were associated with hormones and stress responses. Expression pattern analysis showed differentially tissue-specific expression profiles among SbPRE genes. The expression of some SbPRE genes can be induced by abiotic stress and aphid treatments. Furthermore, through phytohormones and transgenic analyses, we demonstrated that SbPRE4 improves sorghum resistance to aphids by accumulating jasmonic acids (JAs) in transgenic Arabidopsis, giving insights into the molecular and biological function of atypical basic helix-loop-helix (bHLH) transcription factors in sorghum pest resistance.

AabHLH48, a novel basic helix-loop-helix transcription factor from Adonis amurensis, promotes early flowering in Arabidopsis by activating FRUITFULL expression

Basic helix-loop-helix (bHLH) transcription factors play various important roles in plant growth and development. In this study, a AabHLH48 was identified in the floral organ of Adonis amurensis, a perennial herb that can naturally complete flowering at extreme low temperatures. AabHLH48 was widely expressed in various tissues or organs of A. amurensis and was localized in the nucleus. Overexpression of AabHLH48 promotes early flowering in Arabidopsis under both photoperiod (12 h light/12 h dark and 16 h light/8 h dark) and temperature (22 and 18 °C) conditions. Transcriptome sequencing combined with quantitative real-time PCR analysis showed that overexpression of AabHLH48 caused a general upregulation of genes involved in floral development in Arabidopsis, especially for AtAGAMOUS-LIKE 8/FRUITFULL (AtAGL8/FUL). The yeast one-hybrid assay revealed that AabHLH48 has transcriptional activating activity and can directly bind to the promoter region of AtAGL8/FUL. These results suggest that the overexpression of AabHLH48 promoting early flowering in Arabidopsis is associated with the upregulated expression of AtAGL8/FUL activated by AabHLH48. This indicates that AabHLH48 can serve as an important genetic resource for improving flowering-time control in other ornamental plants or crops.

The arabidopsis bHLH transcription factor family

Basic helix-loop-helices (bHLHs) are present in all eukaryotes and form one of the largest families of transcription factors (TFs) found in plants. bHLHs function as transcriptional activators and/or repressors of genes involved in key processes involved in plant growth and development in interaction with the environment (e.g., stomata and root hair development, iron homeostasis, and response to heat and shade). Recent studies have improved our understanding of the functioning of bHLH TFs in complex regulatory networks where a series of post-translational modifications (PTMs) have critical roles in regulating their subcellular localization, DNA-binding capacity, transcriptional activity, and/or stability (e.g., protein-protein interactions, phosphorylation, ubiquitination, and sumoylation). Further elucidating the function and regulation of bHLHs will help further understanding of the biology of plants in general and for the development of new tools for crop improvement.

Genome-wide identification of bHLH gene family and its response to cadmium stress in Populus × canescens

The basic helix-loop-helix (bHLH) gene family is integral to various aspects of plant development and the orchestration of stress response. This study focuses on the bHLH genes within Populus × canescens, a poplar species noted for its significant tolerance to cadmium (Cd) stress. Through our comprehensive genomic analysis, we have identified and characterized 170 bHLH genes within the P. canescens genome. These genes have been systematically classified into 22 distant subfamilies based on their evolutionary relationships. A notable conservation in gene structure and motif compositions were conserved across these subfamilies. Further analysis of the promoter regions of these genes revealed an abundance of essential cis-acting element, which are associated with plant hormonal regulation, development processes, and stress response pathway. Utilizing quantitative PCR (qPCR), we have documented the differential regulation of PcbHLHs in response to elevated Cd concentrations, with distinct expression patterns observed across various tissues. This study is poised to unravel the molecular mechanism underpinning Cd tolerance in P. canescens, offering valuable insights for the development of new cultivars with enhanced Cd accumulation capacity and tolerance. Such advancements are crucial for implementing effective phytoremediation strategies to mitigate soil pollution caused by Cd.

Functions of Basic Helix-Loop-Helix (bHLH) Proteins in the Regulation of Plant Responses to Cold, Drought, Salt, and Iron Deficiency: A Comprehensive Review

Abiotic stresses including cold, drought, salt, and iron deficiency severely impair plant development, crop productivity, and geographic distribution. Several bodies of research have shed light on the pleiotropic functions of BASIC HELIX-LOOP-HELIX (bHLH) proteins in plant responses to these abiotic stresses. In this review, we mention the regulatory roles of bHLH TFs in response to stresses such as cold, drought, salt resistance, and iron deficiency, as well as in enhancing grain yield in plants, especially crops. The bHLH proteins bind to E/G-box motifs in the target promoter and interact with various other factors to form a complex regulatory network. Through this network, they cooperatively activate or repress the transcription of downstream genes, thereby regulating various stress responses. Finally, we present some perspectives for future research focusing on the molecular mechanisms that integrate and coordinate these abiotic stresses. Understanding these molecular mechanisms is crucial for the development of stress-tolerant crops.

Transcription factors as molecular switches regulating plant responses to drought stress

Plants often experience abiotic stress, which severely affects their growth. With the advent of global warming, drought stress has become a pivotal factor affecting crop yield and quality. Increasing numbers of studies have focused on elucidating the molecular mechanisms underlying plant responses to drought stress. As molecular switches, transcription factors (TFs) are key participants in drought-resistance regulatory networks in crops. TFs regulate the transcription of downstream genes and are regulated by various upstream regulatory factors. Therefore, understanding the mechanisms of action of TFs in regulating drought stress can help enhance the adaptive capacity of crops under drought conditions. In this review, we summarize the structural characteristics of several common TFs, their multiple drought-response pathways, and recently employed research strategies. We describe the application of new technologies such as analysis of stress granule dynamics and function, multi-omics data, gene editing, and molecular crosstalk between TFs in drought resistance. This review aims to familiarize readers with the regulatory network of TFs in drought resistance and to provide a reference for examining the molecular mechanisms of drought resistance in plants and improving agronomic traits.

TARGET OF MONOPTEROS: key transcription factors orchestrating plant development and environmental response

Plants have an incredible ability to sustain root and vascular growth after initiation of the embryonic root and the specification of vascular tissue in early embryos. Microarray assays have revealed that a group of transcription factors, TARGET OF MONOPTEROS (TMO), are important for embryonic root initiation in Arabidopsis. Despite the discovery of their auxin responsiveness early on, their function and mode of action remained unknown for many years. The advent of genome editing has accelerated the study of TMO transcription factors, revealing novel functions for biological processes such as vascular development, root system architecture, and response to environmental cues. This review covers recent achievements in understanding the developmental function and the genetic mode of action of TMO transcription factors in Arabidopsis and other plant species. We highlight the transcriptional and post-transcriptional regulation of TMO transcription factors in relation to their function, mainly in Arabidopsis. Finally, we provide suggestions for further research and potential applications in plant genetic engineering.

Genome-wide characterization of the bHLH gene family in Gynostemma pentaphyllum reveals its potential role in the regulation of gypenoside biosynthesis

BACKGROUND

Gynostemma pentaphyllum, an ancient Chinese herbal medicine, serves as a natural source of gypenosides with significant medicinal properties. Basic helix-loop-helix (bHLH) transcription factors play pivotal roles in numerous biological processes, especially in the regulation of secondary metabolism in plants. However, the characteristics and functions of the bHLH genes in G. pentaphyllum remain unexplored, and their regulatory role in gypenoside biosynthesis remains poorly elucidated.

RESULTS

This study identified a total of 111 bHLH members in G. pentaphyllum (GpbHLHs), categorizing them into 26 subgroups based on shared conserved motif compositions and gene structures. Collinearity analysis illustrated that segmental duplications predominately lead to the evolution of GpbHLHs, with most duplicated GpbHLH gene pairs undergoing purifying selection. Among the nine gypenoside-related GpbHLH genes, two GpbHLHs (GpbHLH15 and GpbHLH58) were selected for further investigation based on co-expression analysis and functional prediction. The expression of these two selected GpbHLHs was dramatically induced by methyl jasmonate, and their nuclear localization was confirmed. Furthermore, yeast one-hybrid and dual-luciferase assays demonstrated that GpbHLH15 and GpbHLH58 could bind to the promoters of the gypenoside biosynthesis pathway genes, such as GpFPS1, GpSS1, and GpOSC1, and activate their promoter activity to varying degrees.

CONCLUSIONS

In conclusion, our findings provide a detailed analysis of the bHLH family and valuable insights into the potential use of GpbHLHs to enhance the accumulation of gypenosides in G. pentaphyllum.

MYC2 regulates stomatal density and water use efficiency via targeting EPF2/EPFL4/EPFL9 in poplar

Although polyploid plants have lower stomatal density than their diploid counterparts, the molecular mechanisms underlying this difference remain elusive. Here, we constructed a network based on the triploid poplar transcriptome data and triple-gene mutual interaction algorithm and found that PpnMYC2 was related to stomatal development-related genes PpnEPF2, PpnEPFL4, and PpnEPFL9. The interactions between PpnMYC2 and PagJAZs were experimentally validated. PpnMYC2-overexpressing poplar and Arabidopsis thaliana had reduced stomatal density. Poplar overexpressing PpnMYC2 had higher water use efficiency and drought resistance. RNA-sequencing data of poplars overexpressing PpnMYC2 showed that PpnMYC2 promotes the expression of stomatal density inhibitors PagEPF2 and PagEPFL4 and inhibits the expression of the stomatal density-positive regulator PagEPFL9. Yeast one-hybrid system, electrophoretic mobility shift assay, ChIP-qPCR, and dual-luciferase assay were employed to substantiate that PpnMYC2 directly regulated PagEPF2, PagEPFL4, and PagEPFL9. PpnMYC2, PpnEPF2, and PpnEPFL4 were significantly upregulated, whereas PpnEPFL9 was downregulated during stomatal formation in triploid poplar. Our results are of great significance for revealing the regulation mechanism of plant stomatal occurrence and polyploid stomatal density, as well as reducing stomatal density and improving plant water use efficiency by overexpressing MYC2.

Rice ILI atypical bHLH transcription factors antagonize OsbHLH157/OsbHLH158 during brassinosteroid signaling

Brassinosteroids (BRs) are a group of steroid hormones that play crucial roles in plant growth and development. Atypical bHLH transcription factors that lack the basic region for DNA binding have been implicated in BR signaling. However, the underlying mechanisms of atypical bHLHs in regulation of rice (Oryza sativa) BR signaling are still largely unknown. Here, we describe a systematic characterization of INCREASED LEAF INCLINATION (ILI) subfamily atypical bHLH transcription factors in rice. A total of 8 members, ILI1 to ILI8, with substantial sequence similarity were retrieved. Knockout and overexpression analyses demonstrated that these ILIs play unequally redundant and indispensable roles in BR-mediated growth and development in rice, with a more prominent role for ILI4 and ILI5. The ili3/4/5/8 quadruple and ili1/3/4/7/8 quintuple mutants displayed tremendous BR-related defects with severe dwarfism, erect leaves, and sterility. Biochemical analysis showed that ILIs interact with OsbHLH157 and OsbHLH158, which are also atypical bHLHs and have no obvious transcriptional activity. Overexpression of OsbHLH157 and OsbHLH158 led to drastic BR-defective growth, whereas the osbhlh157 osbhlh158 double mutant developed a typical BR-enhanced phenotype, indicating that OsbHLH157 and OsbHLH158 play a major negative role in rice BR signaling. Further transcriptome analyses revealed opposite effects of ILIs and OsbHLH157/OsbHLH158 in regulation of downstream gene expression, supporting the antagonism of ILIs and OsbHLH157/OsbHLH158 in maintaining the balance of BR signaling. Our results provide insights into the mechanism of BR signaling and plant architecture formation in rice.

bHLH-regulated routes in anther development in rice and Arabidopsis

Anther development is a complex process essential for plant reproduction and crop yields. In recent years, significant progress has been made in the identification and characterization of the bHLH transcription factor family involved in anther regulation in rice and Arabidopsis, two extensively studied model plants. Research on bHLH transcription factors has unveiled their crucial function in controlling tapetum development, pollen wall formation, and other anther-specific processes. By exploring deeper into regulatory mechanisms governing anther development and bHLH transcription factors, we can gain important insights into plant reproduction, thereby accelerating crop yield improvement and the development of new plant breeding strategies. This review provides an overview of the current knowledge on anther development in rice and Arabidopsis, emphasizing the critical roles played by bHLH transcription factors in this process. Recent advances in gene expression analysis and functional studies are highlighted, as they have significantly enhanced our understanding of the regulatory networks involved in anther development.

Transcriptome-Wide Identification and Expression Analysis of bHLH Family Genes in Iris domestica under Drought and Cu Stress

The role of bHLH transcription factors in plant response to abiotic stress and regulation of flavonoid metabolism is well documented. However, to date, the bHLH transcription factor family in Iris domestica remains unreported, impeding further research on flavonoid metabolism in this plant. To address this knowledge gap, we employed bioinformatics to identify 39 IdbHLH genes and characterised their phylogenetic relationships and gene expression patterns under both drought and copper stress conditions. Our evolutionary tree analysis classified the 39 IdbHLHs into 17 subfamilies. Expression pattern analysis revealed that different IdbHLH transcription factors had distinct expression trends in various organs, suggesting that they might be involved in diverse biological processes. We found that IdbHLH36 was highly expressed in all organs (Transcripts Per Million (TPM) > 10), while only 12 IdbHLH genes in the rhizome and four in the root were significantly upregulated under drought stress. Of these, four genes (IdbHLH05, -37, -38, -39) were co-upregulated in both the rhizome and root, indicating their potential role in drought resistance. With regards to copper stress, we found that only 12 genes were upregulated. Further co-expression analysis revealed that most bHLH genes were significantly correlated with key enzyme genes involved in isoflavone biosynthesis. Thereinto, IdbHLH06 showed a significant positive correlation with IdC4H1 and Id4CL1 (p < 0.05). Furthermore, a transient expression assay confirmed that the IdbHLH06 protein was localised in the nucleus. Our findings provide new insights into the molecular basis and regulatory mechanisms of bHLH transcription factors in isoflavone biosynthesis in I. domestica.