Genome-wide identification and characterization of bHLH family genes from orchardgrass and the functional characterization of DgbHLH46 and DgbHLH128 in drought and salt tolerance

Combined Genome-Wide Association Study and Transcriptome Analysis Reveal Candidate Genes for Resistance to Rust (Puccinia graminis) in Dactylis glomerata

Rust disease is a common plant disease that can cause wilting, slow growth of plant leaves, and even affect the growth and development of plants. Orchardgrass (Dactylis glomerata L.) is native to temperate regions of Europe, which has been introduced as a superior forage grass in temperate regions worldwide. Orchardgrass has rich genetic diversity and is widely distributed in the world, which may contain rust resistance genes not found in other crops. Therefore, we collected a total of 333 orchardgrass accessions from different regions around the world. Through a genome-wide association study (GWAS) analysis conducted in four different environments, 91 genes that overlap or are adjacent to significant single nucleotide polymorphisms (SNPs) were identified as potential rust disease resistance genes. Combining transcriptome data from susceptible (PI292589) and resistant (PI251814) accessions, the GWAS candidate gene DG5C04160.1 encoding glutathione S-transferase (GST) was found to be important for orchardgrass rust (Puccinia graminis) resistance. Interestingly, by comparing the number of GST gene family members in seven species, it was found that orchardgrass has the most GST gene family members, containing 119 GST genes. Among them, 23 GST genes showed significant differential expression after inoculation with the rust pathogen in resistant and susceptible accessions; 82% of the genes still showed significantly increased expression 14 days after inoculation in resistant accessions, while the expression level significantly decreased in susceptible accessions. These results indicate that GST genes play an important role in orchardgrass resistance to rust (P. graminis) stress by encoding GST to reduce its oxidative stress response.

Genome-wide identification of bHLH transcription factors and functional analysis in salt gland development of the recretohalophyte sea lavender (Limonium bicolor)

Transcription factors with basic helix-loop-helix (bHLH) structures regulate plant growth, epidermal structure development, metabolic processes, and responses to stress extensively. Sea lavender (Limonium bicolor) is a recretohalophyte with unique salt glands in the epidermis that make it highly resistant to salt stress, contributing to the improvement of saline lands. However, the features of the bHLH transcription factor family in L. bicolor are largely unknown. Here, we systematically analyzed the characteristics, localization, and phylogenetic relationships of 187 identified bHLH family genes throughout the L. bicolor genome, as well as their cis-regulatory promoter elements, expression patterns, and key roles in salt gland development or salt tolerance by genetic analysis. Nine verified L. bicolor bHLH genes are expressed and the encoded proteins function in the nucleus, among which the proteins encoded by Lb2G14060 and Lb1G07934 also localize to salt glands. Analysis of CRISPR-Cas9-generated knockout mutants and overexpression lines indicated that the protein encoded by Lb1G07934 is involved in the formation of salt glands, salt secretion, and salt resistance, indicating that bHLH genes strongly influence epidermal structure development and stress responses. The current study lays the foundation for further investigation of the effects and functional mechanisms of bHLH genes in L. bicolor and paves the way for selecting salt-tolerance genes that will enhance salt resistance in crops and for the improvement of saline soils.

Systematic identification and expression analysis of bHLH gene family reveal their relevance to abiotic stress response and anthocyanin biosynthesis in sweetpotato

BACKGROUND

bHLH transcription factors play significant roles in regulating plant growth and development, stress response, and anthocyanin biosynthesis. Sweetpotato is a pivotal food and industry crop, but little information is available on sweetpotato bHLH genes.

RESULTS

Herein, 227 putative IbbHLH genes were defined on sweetpotato chromosomes, and fragment duplications were identified as the dominant driving force for IbbHLH expansion. These IbbHLHs were divided into 26 subfamilies through phylogenetic analysis, as supported by further analysis of exon-intron structure and conserved motif composition. The syntenic analysis between IbbHLHs and their orthologs from other plants depicted evolutionary relationships of IbbHLHs. Based on the transcriptome data under salt stress, the expression of 12 IbbHLHs was screened for validation by qRT-PCR, and differential and significant transcriptions under abiotic stress were detected. Moreover, IbbHLH123 and IbbHLH215, which were remarkably upregulated by stress treatments, had obvious transactivation activity in yeasts. Protein interaction detections and yeast two-hybrid assays suggested an intricate interaction correlation between IbbHLHs. Besides, transcriptome screening revealed that multiple IbbHLHs may be closely related to anthocyanin biosynthesis based on the phenotype (purple vs. white tissues), which was confirmed by subsequent qRT-PCR analysis.

CONCLUSIONS

These results shed light on the promising functions of sweetpotato IbbHLHs in abiotic stress response and anthocyanin biosynthesis.

Basic helix-loop-helix (bHLH) gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses

BACKGROUND

Rye (Secale cereale), one of the drought and cold-tolerant crops, is an important component of the Triticae Dumortier family of Gramineae plants. Basic helix-loop-helix (bHLH), an important family of transcription factors, has played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. However, no systemic analysis of the bHLH transcription factor family has yet been reported in rye.

RESULTS

In this study, 220 bHLH genes in S. cereale (ScbHLHs) were identified and named based on the chromosomal location. The evolutionary relationships, classifications, gene structures, motif compositions, chromosome localization, and gene replication events in these ScbHLH genes are systematically analyzed. These 220 ScbHLH members are divided into 21 subfamilies and one unclassified gene. Throughout evolution, the subfamilies 5, 9, and 18 may have experienced stronger expansion. The segmental duplications may have contributed significantly to the expansion of the bHLH family. To systematically analyze the evolutionary relationships of the bHLH family in different plants, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. Finally, the gene expression response characteristics of 22 ScbHLH genes in various biological processes and stress responses were analyzed. Some candidate genes, such as ScbHLH11, ScbHLH48, and ScbHLH172, related to tissue developments and environmental stresses were screened.

CONCLUSIONS

The results indicate that these ScbHLH genes exhibit characteristic expression in different tissues, grain development stages, and stress treatments. These findings provided a basis for a comprehensive understanding of the bHLH family in rye.

Transcriptome Profiling Provides Insights into the Early Development of Tiller Buds in High- and Low-Tillering Orchardgrass Genotypes

Orchardgrass (Dactylis glomerata L.) is among the most economically important perennial cool-season grasses, and is considered an excellent hay, pasture, and silage crop in temperate regions worldwide. Tillering is a vital feature that dominates orchardgrass regeneration and biomass yield. However, transcriptional dynamics underlying early-stage bud development in high- and low-tillering orchardgrass genotypes are unclear. Thus, this study assessed the photosynthetic parameters, the partially essential intermediate biomolecular substances, and the transcriptome to elaborate the early-stage profiles of tiller development. Photosynthetic efficiency and morphological development significantly differed between high- (AKZ-NRGR667) and low-tillering genotypes (D20170203) at the early stage after tiller formation. The 206.41 Gb of high-quality reads revealed stage-specific differentially expressed genes (DEGs), demonstrating that signal transduction and energy-related metabolism pathways, especially photosynthetic-related processes, influence tiller induction and development. Moreover, weighted correlation network analysis (WGCNA) and functional enrichment identified distinctively co-expressed gene clusters and four main regulatory pathways, including chlorophyll, lutein, nitrogen, and gibberellic acid (GA) metabolism pathways. Therefore, photosynthesis, carbohydrate synthesis, nitrogen efficient utilization, and phytohormone signaling pathways are closely and intrinsically linked at the transcriptional level. These findings enhance our understanding of tillering in orchardgrass and perennial grasses, providing a new breeding strategy for improving forage biomass yield.

Genome-Wide Identification and Functional Analysis of RF2 Gene Family and the Critical Role of GhRF2-32 in Response to Drought Stress in Cotton

Cotton is an important natural fiber crop. The RF2 gene family is a member of the bZIP transcription factor superfamily, which plays an important role in plant resistance to environmental stresses. In this paper, the RF2 gene family of four cotton species was analyzed genome-wide, and the key gene RF2-32 was cloned for functional verification. A total of 113 RF2 genes were identified in the four cotton species, and the RF2 family was relatively conserved during the evolution of cotton. Chromosome mapping and collinear analysis indicated that fragment replication was the main expansion mode of RF2 gene family during evolution. Cis-element analysis showed that there were many elements related to light response, hormone response and abiotic stress response in the promoters of RF2 genes. The transcriptome and qRT-PCR analysis of RF2 family genes in upland cotton showed that RF2 family genes responded to salt stress and drought stress. GhRF2-32 protein was localized in the cell nucleus. Silencing the GhRF2-32 gene showed less leaf wilting and increased total antioxidant capacity under drought and salt stress, decreased malondialdehyde content and increased drought and salt tolerance. This study revealed the evolutionary and functional diversity of the RF2 gene family, which laid a foundation for the further study of stress-resistant genes in cotton.

Genome-wide identification of SrbHLH transcription factors highlights its potential role in rebaudioside A (RA) biosynthesis in Stevia rebaudiana

Stevia rebaudiana Bertoni is a valuable medicinal plant and an essential source of natural sweetener, steviol glycosides (SGs), with rebaudioside A (RA) being one of the main components of SGs. bHLH transcription factors play a crucial role in plant development and secondary metabolism. In this study, 159 SrbHLH genes were identified from the S. rebaudiana genome, and each gene was named based on its chromosome location. The SrbHLH proteins were then clustered into 18 subfamilies through phylogenetic analysis. The analysis of conserved motifs and gene structure further supported the classification of the SrbHLH family. Chromosomal location and gene duplication events of SrbHLH genes were also studied. Moreover, based on the RNA-Seq data of different tissues of S. rebaudiana, 28 SrbHLHs were co-expressed with structural genes involved in RA biosynthesis. The expression pattern of candidate SrbHLH genes were confirmed by qPCR. Finally, dual luciferase reporter assays (DLAs) and subcellular localization analysis verified SrbHLH22, SrbHLH111, SrbHLH126, SrbHLH142, and SrbHLH152 are critical regulators of RA biosynthesis. This study provides new insights into the function of SrbHLHs in regulating SGs biosynthesis and lays the foundation for future applications of SrbHLH genes in molecular breeding of S. rebaudiana.

Strigolactone signaling gene from soybean GmMAX2a enhances the drought and salt-alkaline resistance in Arabidopsis via regulating transcriptional profiles of stress-related genes

Strigolactone (SL) is a new plant hormone, which not only plays an important role in stimulating seed germination, plant branching, and regulating root development, but also plays an important role in the response of plants to abiotic stresses. In this study, the full-length cDNA of a soybean SL signal transduction gene (GmMAX2a) was isolated, cloned and revealed an important role in abiotic stress responses. Tissue-specific expression analysis by qRT-PCR indicated that GmMAX2a was expressed in all tissues of soybean, but highest expression was detected in seedling stems. Moreover, upregulation of GmMAX2a transcript expression under salt, alkali, and drought conditions were noted at different time points in soybean leaves compared to roots. Additionally, histochemical GUS staining studies revealed the deep staining in P_GmMAX2a: GUS transgenic lines compared to WT indicating active involvement of GmMAX2a promoter region to stress responses. To further investigate the function of GmMAX2a gene in transgenic Arabidopsis, Petri-plate experiments were performed and GmMAX2a OX lines appeared with longer roots and improved fresh biomass compared to WT plants to NaCl, NaHCO₃, and mannitol supplementation. Furthermore, the expression of several stress-related genes such as RD29B, SOS1, NXH1, AtRD22, KIN1, COR15A, RD29A, COR47, H+-APase, NADP-ME, NCED3, and P5CS were significantly high in GmMAX2a OX plants after stress treatment compared to WT plants. In conclusion, GmMAX2a improves soybean tolerance towards abiotic stresses (salt, alkali, and drought). Hence, GmMAX2a can be considered a candidate gene for transgenic breeding against various abiotic stresses in plants.

Supplementation of the Plant Conditioner ELICE Vakcina® Product with β-Aminobutyric Acid and Salicylic Acid May Lead to Trans-Priming Signaling in Barley (Hordeum vulgare)

Plant immunological memory, priming, is a defense mechanism that can be triggered by external stimuli, leading to the activation of biochemical pathways and preparing plants for disease resistance. Plant conditioners improve yield and crop quality through nutrient efficiency and abiotic stress tolerance, which is enhanced by the addition of resistance- and priming-induced compounds. Based on this hypothesis, this study aimed to investigate plant responses to priming actives of different natures, including salicylic acid and beta-aminobutyric acid, in combination with the plant conditioning agent ELICE Vakcina^®. Phytotron experiments and RNA-Seq analyses of differentially expressed genes using the combinations of these three investigated compounds were performed in a barley culture to investigate possible synergistic relationships in the genetic regulatory network. The results indicated a strong regulation of defense responses, which was enhanced by supplemental treatments; however, both synergistic and antagonistic effects were enhanced with one or two components, depending on the supplementation. The overexpressed transcripts were functionally annotated to assess their involvement in jasmonic acid and salicylic acid signaling; however, their determinant genes were highly dependent on the supplemental treatments. Although the effects overlapped, the potential effects of trans-priming the two supplements tested could be largely separated.

The resilient cotton plant: uncovering the effects of stresses on secondary metabolomics and its underlying molecular mechanisms

Cotton is an important fiber crop cultivated around the world under diverse climate conditions and generates billions of dollars in annual revenue globally. Biotic and abiotic stresses have caused reduction in yield and productivity of cotton crops. In this review, we comprehensively analyzed and summarized the effect of biotic and abiotic stress on secondary metabolite production in cotton. The development of cotton varieties with improved tolerance against abiotic and biotic stress can play an important role in sustainable cotton production. Under stress conditions, plants develop a variety of defense mechanisms such as initiating signaling functions to upregulate defense responsive genes and accumulation of secondary metabolites. Understanding the impact of stress on secondary metabolite production in cotton is crucial for developing strategies to alleviate the negative effects of stress on crop yield and quality. Further, the potential industrial applications of these secondary metabolites in cotton, such as gossypol, could provide new opportunities for sustainable cotton production and the development of value-added products. Additionally, transgenic and genome-edited cotton cultivars can be developed to provide tolerance to both abiotic and biotic stress in cotton production.

OsMBTB32, a MATH-BTB domain-containing protein that interacts with OsCUL1s to regulate salt tolerance in rice

MATH-BTB proteins are involved in a variety of cellular processes that regulate cell homeostasis and developmental processes. Previous studies reported the involvement of BTB proteins in the development of various organs in plants; however, the function of BTB proteins in salt stress is less studied. Here, we found a novel MATH-BTB domain-containing OsMBTB32 protein that was highly expressed in leaf, root, and shoot. The up-regulation of the OsMBTB32 transcript in 2-week-old seedlings under salt stress suggests the significant role of the OsMBTB32 gene in salinity. The OsMBTB32 transgenic seedlings (OE and RNAi) exhibited significant differences in various phenotypes, including plumule, radical, primary root, and shoot length, compared to WT seedlings. We further found that OsCUL1 proteins, particularly OsCUL1-1 and OsCUL1-3, interact with OsMBTB32 and may suppress the function of OsMBTB32 during salt stress. Moreover, OsWRKY42, a homolog of ZmWRKY114 which negatively regulates salt stress in rice, directly binds to the W-box of OsCUL1-1 and OsCUL1-3 promoters to promote the interaction of OsCUL1-1 and OsCUL1-3 with OsMBTB32 protein in rice. The overexpression of OsMBTB32 and OsCUL1-3 further confirmed the function of OsMBTB32 and OsCUL1s in salt tolerance in Arabidopsis. Overall, the findings of the present study provide promising knowledge regarding the MATH-BTB domain-containing proteins and their role in enhancing the growth and development of rice under salt stress.MATH-BTB proteins are involved in a variety of cellular processes that regulate cell homeostasis and developmental processes. Previous studies reported the involvement of BTB proteins in the development of various organs in plants; however, the function of BTB proteins in salt stress is less studied. Here, we found a novel MATH-BTB domain-containing OsMBTB32 protein that was highly expressed in leaf, root, and shoot. The up-regulation of the OsMBTB32 transcript in 2-week-old seedlings under salt stress suggests the significant role of the OsMBTB32 gene in salinity. The OsMBTB32 transgenic seedlings (OE and RNAi) exhibited significant differences in various phenotypes, including plumule, radical, primary root, and shoot length, compared to WT seedlings. We further found that OsCUL1 proteins, particularly OsCUL1-1 and OsCUL1-3, interact with OsMBTB32 and may suppress the function of OsMBTB32 during salt stress. Moreover, OsWRKY42, a homolog of ZmWRKY114 which negatively regulates salt stress in rice, directly binds to the W-box of OsCUL1-1 and OsCUL1-3 promoters to promote the interaction of OsCUL1-1 and OsCUL1-3 with OsMBTB32 protein in rice. The overexpression of OsMBTB32 and OsCUL1-3 further confirmed the function of OsMBTB32 and OsCUL1s in salt tolerance in Arabidopsis. Overall, the findings of the present study provide promising knowledge regarding the MATH-BTB domain-containing proteins and their role in enhancing the growth and development of rice under salt stress.

Genome-Wide Identification of bHLH Transcription Factor Family in Malus sieversii and Functional Exploration of MsbHLH155.1 Gene under Valsa Canker Infection

Xinjiang wild apple (Malus sieversii) is an ancient relic; a plant with abundant genetic diversity and disease resistance. Several transcription factors were studied in response to different biotic and abiotic stresses on the wild apple. Basic/helix-loop-helix (bHLH) is a large plant transcription factor family that plays important roles in plant responses to various biotic and abiotic stresses and has been extensively studied in several plants. However, no study has yet been conducted on the bHLH gene in M. sieversii. Based on the genome of M. sieversii, 184 putative MsbHLH genes were identified, and their physicochemical properties were studied. MsbHLH covered 23 subfamilies and lacked two subfamily genes of Arabidopsis thaliana based on the widely used classification method. Moreover, MsbHLH exon-intron structures matched subfamily classification, as evidenced by the analysis of their protein motifs. The analysis of cis-acting elements revealed that many MsbHLH genes share stress- and hormone-related cis-regulatory elements. These MsbHLH transcription factors were found to be involved in plant defense responses based on the protein-protein interactions among the differentially expressed MsbHLHs. Furthermore, 94 MsbHLH genes were differentially expressed in response to pathogenic bacteria. The qRT-PCR results also showed differential expression of MsbHLH genes. To further verify the gene function of bHLH, our study used the transient transformation method to obtain the overexpressed MsbHLH155.1 transgenic plants and inoculated them. Under Valsa canker infection, the lesion phenotype and physiological and biochemical indexes indicated that the antioxidant capacity of plants could increase and reduce the damage caused by membrane peroxidation. This study provides detailed insights into the classification, gene structure, motifs, chromosome distribution, and gene expression of bHLH genes in M. sieversii and lays a foundation for a better understanding disease resistance in plants, as well as providing candidate genes for the development of M. sieversii resistance breeding.

Basic Helix-Loop-Helix Transcription Factors: Regulators for Plant Growth Development and Abiotic Stress Responses

Plant basic helix-loop-helix (bHLH) transcription factors are involved in many physiological processes, and they play important roles in the abiotic stress responses. The literature related to genome sequences has increased, with genome-wide studies on the bHLH transcription factors in plants. Researchers have detailed the functionally characterized bHLH transcription factors from different aspects in the model plant Arabidopsis thaliana, such as iron homeostasis and abiotic stresses; however, other important economic crops, such as rice, have not been summarized and highlighted. The bHLH members in the same subfamily have similar functions; therefore, unraveling their regulatory mechanisms will help us to identify and understand the roles of some of the unknown bHLH transcription factors in the same subfamily. In this review, we summarize the available knowledge on functionally characterized bHLH transcription factors according to four categories: plant growth and development; metabolism synthesis; plant signaling, and abiotic stress responses. We also highlight the roles of the bHLH transcription factors in some economic crops, especially in rice, and discuss future research directions for possible genetic applications in crop breeding.