Research advances of MYB transcription factors in plant stress resistance and breeding

Genome-Wide Analysis of R2R3-MYB Genes and Functional Characterization of SmMYB75 in Eggplant Fruit Implications for Crop Improvement and Nutritional Enhancement

R2R3-MYB represents a substantial gene family that plays diverse roles in plant development. In this study, 102 SmR2R3-MYB genes were identified from eggplant fruit and classified into 31 subfamilies. Analysis indicated that segmental duplication events played a pivotal role in the expansion of the SmR2R3-MYB gene family. Furthermore, the prediction of miRNAs targeting SmR2R3-MYB genes revealed that 60 SmR2R3-MYBs are targeted by 57 miRNAs, with specific miRNAs displaying varying numbers of target genes, providing valuable insights into the regulatory functions of miRNAs in plant growth, development, and responses to stress conditions. Through expression profile analysis under various treatment conditions, including low temperature (4 °C), plant hormone (ABA, Abscisic acid), and drought stress (PEG, Polyethylene glycol), diverse and complex regulatory mechanisms governing SmR2R3-MYB gene expression were elucidated. Notably, EGP21875.1 and EGP21874.1 exhibited upregulation in expression under all treatment conditions. Transcriptome and metabolome analyses demonstrated that, apart from anthocyanins (delphinidin-3-O-glucoside, cyanidin-3-O-(6-O-p-coumaroyl)-glucoside, and malvidin-3-O-(6-O-p-coumaroyl)-glucoside), overexpression of SmMYB75 could also elevate the content of various beneficial compounds, such as flavonoids, phenolic acids, and terpenes, in eggplant pulp. This comprehensive study enhances our understanding of SmR2R3-MYB gene functions and provides a strong basis for further research on their roles in regulating anthocyanin synthesis and improving eggplant fruit quality.

Genome-wide identification, classification and expression analysis of MYB gene family in coconut (Cocos nucifera L.)

MYB transcription factors regulate the growth, development, and secondary metabolism of plant species. To investigate the origin of color variations in coconut pericarp, we identified and analyzed the MYB gene family present in coconut. According to the sequence of MYB genes in Arabidopsis thaliana, homologous MYB gene sequences were found in the whole genome database of coconut, the conserved sequence motifs within MYB proteins were analyzed by Motif Elicitation (MEME) tool, and the sequences without conservative structure were eliminated. Additionally, we employed RNA-seq technology to generate gene expression signatures of the R2R3-MYB genes across distinctive coconut parts exhibiting diverse colors. To validate these profiles, we conducted quantitative PCR (qPCR). Through comprehensive genome-wide screening, we successfully identified a collection of 179 MYB genes in coconut. Subsequent phylogenetic analysis categorized these 179 coconut MYB genes into 4-subfamilies: 124 R2R3-MYB, 4 3R-MYB types, 4 4R-MYB type, and 47 unknown types. Furthermore, these genes were further divided into 34 subgroups, with 28 of these subgroups successfully classified into known subfamilies found in Arabidopsis thaliana. By mapping the CnMYB genes onto the 16 chromosomes of the coconut genome, we unveiled a collinearity association between them. Moreover, a preservation of gene structure and motif distribution was observed across the CnMYB genes. Our research encompassed a thorough investigation of the R2R3-MYB genes present in the coconut genome, including the chromosomal localization, gene assembly, conserved regions, phylogenetic associations, and promoter cis-acting elements of the studied genes. Our findings revealed a collection of 12 R2R3-MYB candidate genes, namely CnMYB8, CnMYB15, CnMYB27, CnMYB28, CnMYB61, CnMYB63, CnMYB68, CnMYB94, CnMYB101, CnMYB150, CnMYB153, and CnMYB164. These genes showed differential expressions in diverse tissues and developmental stages of four coconut species, such as CnMYB68, CnMYB101, and CnMYB28 exhibited high expression in majority of tissues and coconut species, while CnMYB94 and CnMYB164 showed lower expression. These findings shed light on the crucial functional divergence of CnMYB genes across various coconut tissues, suggesting these genes as promising candidate genes for facilitating color development in this important crop.

Genome-Wide Identification and Characterization of MYB Gene Family and Analysis of Its Sex-Biased Expression Pattern in Spinacia oleracea L

The members of the myeloblastosis (MYB) family of transcription factors (TFs) participate in a variety of biological regulatory processes in plants, such as circadian rhythm, metabolism, and flower development. However, the characterization of MYB genes across the genomes of spinach Spinacia oleracea L. has not been reported. Here, we identified 140 MYB genes in spinach and described their characteristics using bioinformatics approaches. Among the MYB genes, 54 were 1R-MYB, 80 were 2R-MYB, 5 were 3R-MYB, and 1 was 4R-MYB. Almost all MYB genes were located in the 0-30 Mb region of autosomes; however, the 20 MYB genes were enriched at both ends of the sex chromosome (chromosome 4). Based on phylogeny, conserved motifs, and the structure of genes, 2R-MYB exhibited higher conservation relative to 1R-MYB genes. Tandem duplication and collinearity of spinach MYB genes drive their evolution, enabling the functional diversification of spinach genes. Subcellular localization prediction indicated that spinach MYB genes were mainly located in the nucleus. Cis-acting element analysis confirmed that MYB genes were involved in various processes of spinach growth and development, such as circadian rhythm, cell differentiation, and reproduction through hormone synthesis. Furthermore, through the transcriptome data analysis of male and female flower organs at five different periods, ten candidate genes showed biased expression in spinach males, suggesting that these genes might be related to the development of spinach anthers. Collectively, this study provides useful information for further investigating the function of MYB TFs and novel insights into the regulation of sex determination in spinach.

Comparative transcriptome analysis revealed that auxin and cell wall biosynthesis play important roles in the formation of hollow hearts in cucumber

BACKGROUND

Hollow heart is a kind of physiological defect that seriously affects the yield, quality, and economic value of cucumber. However, the formation of hollow hearts may relate to multiple factors in cucumber, and it is necessary to conduct analysis.

RESULTS

In this study, hollow and non-hollow fruits of cucumber K07 were used for comparative transcriptome sequencing and analysis. 253 differentially expressed genes and 139 transcription factors were identified as being associated with the formation of hollow hearts. Hormone (auxin) signaling and cell wall biosynthesis were mainly enriched in GO and KEGG pathways. Expression levels of key genes involved in indole-3-acetic acid biosynthesis in carpel were lower in the hollow fruits than non-hollow fruits, while there was no difference in the flesh. The concentration of indole-3-acetic also showed lower in the carpel than flesh. The biosynthetic pathway and content analysis of the main components of the cell wall found that lignin biosynthesis had obvious regularity with hollow heart, followed by hemicellulose and cellulose. Correlation analysis showed that there may be an interaction between auxin and cell wall biosynthesis, and they collectively participate in the formation of hollow hearts in cucumber. Among the differentially expressed transcription factors, MYB members were the most abundant, followed by NAC, ERF, and bHLH.

CONCLUSIONS

The results and analyses showed that the low content of auxin in the carpel affected the activity of enzymes related to cell wall biosynthesis at the early stage of fruit development, resulting in incomplete development of carpel cells, thus forming a hollow heart in cucumber. Some transcription factors may play regulatory roles in this progress. The results may enrich the theory of the formation of hollow hearts and provide a basis for future research.

A novel PGPR strain homologous to Beijerinckia fluminensis induces biochemical and molecular changes involved in Arabidopsis thaliana salt tolerance

The use of PGPR is widely accepted as a promising tool for a more sustainable agricultural production and improved plant abiotic stress resistance. This study tested the ability of PVr_9, a novel bacterial strain, homologous to Beijerinckia fluminensis, to increase salt stress tolerance in A. thaliana. In vitro plantlets inoculated with PVr_9 and treated with 150 mM NaCl showed a reduction in primary root growth inhibition compared to uninoculated ones, and a leaf area significantly less affected by salt. Furthermore, salt-stressed PVr_9-inoculated plants had low ROS and 8-oxo-dG, osmolytes, and ABA content along with a modulation in antioxidant enzymatic activities. A significant decrease in Na+ in the leaves and a corresponding increase in the roots were also observed in salt-stressed inoculated plants. SOS1, NHX1 genes involved in plant salt tolerance, were up-regulated in PVr_9-inoculated plants, while different MYB genes involved in salt stress signal response were down-regulated in both roots and shoots. Thus, PVr_9 was able to increase salt tolerance in A. thaliana, thereby suggesting a role in ion homeostasis by reducing salt stress rather than inhibiting total Na+ uptake. These results showed a possible molecular mechanism of crosstalk between PVr_9 and plant roots to enhance salt tolerance, and highlighted this bacterium as a promising PGPR for field applications on agronomical crops.

Genetic and Epigenetic Responses of Autochthonous Grapevine Cultivars from the 'Epirus' Region of Greece upon Consecutive Drought Stress

Within the framework of preserving and valorizing the rich grapevine germplasm of the Epirus region of Greece, indigenous grapevine (Vitis vinifera L.) cultivars were characterized and assessed for their resilience to abiotic stresses in the context of climate change. The cultivars 'Debina' and 'Dichali' displayed significant differences in their response to drought stress as judged by morpho-physiological analysis, indicating higher drought tolerance for Dichali. Hence, they were selected for further study aiming to identify genetic and epigenetic mechanisms possibly regulating drought adaptability. Specifically, self-rooted and heterografted on 'Richter 110' rootstock plants were subjected to two phases of drought with a recovery period in between. Gene expression analysis was performed for two stress-related miRNAs and their target genes: (a) miRNA159 and putative targets, VvMYB101, VvGATA-26-like, VvTOPLESS-4-like and (b) miRNA156 and putative target gene VvCONSTANS-5. Overall, grafted plants exhibited a higher drought tolerance than self-rooted plants, suggesting beneficial rootstock-scion interactions. Comparative analysis revealed differential gene expression under repetitive drought stresses between the two cultivars as well as between the self-rooted and grafted plants. 'Dichali' exhibited an up-regulation of most of the genes examined, which may be associated with increased tolerance. Nevertheless, the profound down-regulation of VvTOPLESS-4-like (a transcriptional co-repressor of transcription factors) upon drought and the concomitant up-regulation of miRNA159 highlights the importance of this 'miRNA-target' module in drought responsiveness. DNA methylation profiling using MSAP analysis revealed differential methylation patterns between the two genotypes in response to drought. Further investigations of gene expression and DNA methylation will contribute to our understanding of the epigenetic mechanisms underlying grapevine tolerance to drought stress.

Research progress on the roles of actin-depolymerizing factor in plant stress responses

Actin-depolymerizing factors (ADFs) are highly conserved small-molecule actin-binding proteins found throughout eukaryotic cells. In land plants, ADFs form a small gene family that displays functional redundancy despite variations among its individual members. ADF can bind to actin monomers or polymerized microfilaments and regulate dynamic changes in the cytoskeletal framework through specialized biochemical activities, such as severing, depolymerizing, and bundling. The involvement of ADFs in modulating the microfilaments' dynamic changes has significant implications for various physiological processes, including plant growth, development, and stress response. The current body of research has greatly advanced our comprehension of the involvement of ADFs in the regulation of plant responses to both biotic and abiotic stresses, particularly with respect to the molecular regulatory mechanisms that govern ADF activity during the transmission of stress signals. Stress has the capacity to directly modify the transcription levels of ADF genes, as well as indirectly regulate their expression through transcription factors such as MYB, C-repeat binding factors, ABF, and 14-3-3 proteins. Furthermore, apart from their role in regulating actin dynamics, ADFs possess the ability to modulate the stress response by influencing downstream genes associated with pathogen resistance and abiotic stress response. This paper provides a comprehensive overview of the current advancements in plant ADF gene research and suggests that the identification of plant ADF family genes across a broader spectrum, thorough analysis of ADF gene regulation in stress resistance of plants, and manipulation of ADF genes through genome-editing techniques to enhance plant stress resistance are crucial avenues for future investigation in this field.

Characteristics and Functions of MYB (v-Myb avivan myoblastsis virus oncogene homolog)-Related Genes in Arabidopsis thaliana

The MYB (v-Myb avivan myoblastsis virus oncogene homolog) transcription factor family is one of the largest families of plant transcription factors which plays a vital role in many aspects of plant growth and development. MYB-related is a subclass of the MYB family. Fifty-nine Arabidopsis thaliana MYB-related (AtMYB-related) genes have been identified. In order to understand the functions of these genes, in this review, the promoters of AtMYB-related genes were analyzed by means of bioinformatics, and the progress of research into the functions of these genes has been described. The main functions of these AtMYB-related genes are light response and circadian rhythm regulation, root hair and trichome development, telomere DNA binding, and hormone response. From an analysis of cis-acting elements, it was found that the promoters of these genes contained light-responsive elements and plant hormone response elements. Most genes contained elements related to drought, low temperature, and defense and stress responses. These analyses suggest that AtMYB-related genes may be involved in A. thaliana growth and development, and environmental adaptation through plant hormone pathways. However, the functions of many genes do not occur independently but instead interact with each other through different pathways. In the future, the study of the role of the gene in different pathways will be conducive to a comprehensive understanding of the function of the gene. Therefore, gene cloning and protein functional analyses can be subsequently used to understand the regulatory mechanisms of AtMYB-related genes in the interaction of multiple signal pathways. This review provides theoretical guidance for the follow-up study of plant MYB-related genes.

Overexpression of Lolium multiflorum LmMYB1 Enhances Drought Tolerance in Transgenic Arabidopsis

Lolium multiflorum is one of the world-famous forage grasses with rich biomass, fast growth rate and good nutritional quality. However, its growth and forage yield are often affected by drought, which is a major natural disaster all over the world. MYB transcription factors have some specific roles in response to drought stress, such as regulation of stomatal development and density, control of cell wall and root development. However, the biological function of MYB in L. multiflorum remains unclear. Previously, we elucidated the role of LmMYB1 in enhancing osmotic stress resistance in Saccharomyces cerevisiae. Here, this study elucidates the biological function of LmMYB1 in enhancing plant drought tolerance through an ABA-dependent pathway involving the regulation of cell wall development and stomatal density. After drought stress and ABA stress, the expression of LmMYB1 in L. multiflorum was significantly increased. Overexpression of LmMYB1 increased the survival rate of Arabidopsis thaliana under drought stress. Under drought conditions, expression levels of drought-responsive genes such as AtRD22, AtRAB and AtAREB were up-regulated in OE compared with those in WT. Further observation showed that the stomatal density of OE was reduced, which was associated with the up-regulated expression of cell wall-related pathway genes in the RNA-Seq results. In conclusion, this study confirmed the biological function of LmMYB1 in improving drought tolerance by mediating cell wall development through the ABA-dependent pathway and thereby affecting stomatal density.

Sequence Characterization of Extra-Chromosomal Circular DNA Content in Multiple Blackgrass (Alopecurus myosuroides) Populations

Alopecurus myosuroides (blackgrass) is a problematic weed of Western European winter wheat, and its success is largely due to widespread multiple-herbicide resistance. Previous analysis of F2 seed families derived from two distinct blackgrass populations exhibiting equivalent non-target site resistance (NTSR) phenotypes shows resistance is polygenic and evolves from standing genetic variation. Using a CIDER-seq pipeline, we show that herbicide-resistant (HR) and herbicide-sensitive (HS) F3 plants from these F2 seed families as well as the parent populations they were derived from carry extra-chromosomal circular DNA (eccDNA). We identify the similarities and differences in the coding structures within and between resistant and sensitive populations. Although the numbers and size of detected eccDNAs varied between the populations, comparisons between the HR and HS blackgrass populations identified shared and unique coding content, predicted genes, and functional protein domains. These include genes related to herbicide detoxification such as Cytochrome P450s, ATP-binding cassette transporters, and glutathione transferases including AmGSTF1. eccDNA content was mapped to the A. myosuroides reference genome, revealing genomic regions at the distal end of chromosome 5 and the near center of chromosomes 1 and 7 as regions with a high number of mapped eccDNA gene density. Mapping to 15 known herbicide-resistant QTL regions showed that the eccDNA coding sequences matched twelve, with four QTL matching HS coding sequences; only one region contained HR coding sequences. These findings establish that, like other pernicious weeds, blackgrass has eccDNAs that contain homologs of chromosomal genes, and these may contribute genetic heterogeneity and evolutionary innovation to rapidly adapt to abiotic stresses, including herbicide treatment.

Genome-wide identification of GH9 gene family and the assessment of its role during fruit abscission zone formation in Vaccinium ashei

KEY MESSAGE

The genomic location and stage-specific expression pattern of GH9 genes reveal their critical roles during fruit abscission zone formation in Vaccinium ashei. Glycosyl hydrolase family 9 (GH9) cellulases play a crucial role in both cellulose synthesis and hydrolysis during plant growth and development. Despite this importance, there is currently no study on the involvement of GH9-encoding genes, specifically VaGH9s, in abscission zone formation of rabbiteye blueberries (Vaccinium ashei). In this study, we identified a total of 61 VaGH9s in the genome, which can be classified into 3 subclasses based on conserved motifs and domains, gene structures, and phylogenetic analyses. Our synteny analysis revealed that VaGH9s are more closely related to the GH9s of Populus L. than to those of Arabidopsis, Vitis vinifera, and Citrus sinensis. In silico structural analysis predicted that most of VaGH9s are hydrophilic, and localized in cell membrane and/or cell wall, and the variable sets of cis-acting regulatory elements and functional diversity with four categories of stress response, hormone regulation, growth and development, and transcription factor-related elements are present in the promoter sequence of VaGH9s genes. Transcriptomic analysis showed that there were 22 differentially expressed VaGH9s in fruit abscission zone tissue at the veraison stage, and the expression of VaGH9B2 and VaGH9C10 was continuously increased during fruit maturation, which were in parallel with the increasing levels of cellulase activity and oxidative stress indicators, suggesting that they are involved in the separation stage of fruit abscission in Vaccinium ashei. Our work identified 22 VaGH9s potentially involved in different stages of fruit abscission and would aid further investigation into the molecular regulation of abscission in rabbiteye blueberries fruit.

A multi-level approach reveals key physiological and molecular traits in the response of two rice genotypes subjected to water deficit at the reproductive stage

Rice is more vulnerable to drought than maize, wheat, and sorghum because its water requirements remain high throughout the rice life cycle. The effects of drought vary depending on the timing, intensity, and duration of the events, as well as on the rice genotype and developmental stage. It can affect all levels of organization, from genes to the cells, tissues, and/or organs. In this study, a moderate water deficit was applied to two contrasting rice genotypes, IAC 25 and CIRAD 409, during their reproductive stage. Multi-level transcriptomic, metabolomic, physiological, and morphological analyses were performed to investigate the complex traits involved in their response to drought. Weighted gene network correlation analysis was used to identify the specific molecular mechanisms regulated by each genotype, and the correlations between gene networks and phenotypic traits. A holistic analysis of all the data provided a deeper understanding of the specific mechanisms regulated by each genotype, and enabled the identification of gene markers. Under non-limiting water conditions, CIRAD 409 had a denser shoot, but shoot growth was slower despite better photosynthetic performance. Under water deficit, CIRAD 409 was weakly affected regardless of the plant level analyzed. In contrast, IAC 25 had reduced growth and reproductive development. It regulated transcriptomic and metabolic activities at a high level, and activated a complex gene regulatory network involved in growth-limiting processes. By comparing two contrasting genotypes, the present study identified the regulation of some fundamental processes and gene markers, that drive rice development, and influence its response to water deficit, in particular, the importance of the biosynthetic and regulatory pathways for cell wall metabolism. These key processes determine the biological and mechanical properties of the cell wall and thus influence plant development, organ expansion, and turgor maintenance under water deficit. Our results also question the genericity of the antagonism between morphogenesis and organogenesis observed in the two genotypes.

MIR159 regulates multiple aspects of stamen and carpel development and requires dissection and delimitation of differential downstream regulatory network for manipulating fertility traits

Unravelling genetic networks regulating developmental programs are key to devising and implementing genomics assisted trait modification strategies. It is crucial to understand the role of small RNAs, and the basis of their ability to modify traits. MIR159 has been previously reported to cause defects in anther development in Arabidopsis; however, the complete spectrum and basis of the defects remained unclear. The present study was therefore undertaken to comprehensively investigate the role of miR159 from Brassica juncea in modulating vegetative and reproductive traits. Owing to the polyploid nature of Brassica, paralogous and homeologous copies of MIR159A, MIR159B, and, MIR159C were identified and analysis of the precursor uncovered extensive structural and sequence variation. The MIR159 locus with mature miR159 with perfect target complimentarily with MYB65, was cloned from Brassica juncea var. Varuna for functional characterization by generating constitutively over-expressing lines in Arabidopsis thaliana Col-0. Apart from statistically significant difference in multiple vegetative traits, drastic differences were observed in stamen and pistil. Over-expression of miR159a led to shortening of filament length and loss of tetradynamous condition. Anthers were apiculate, with improper lobe formation, and unsynchronized cellular growth between connective tissue and another lobe development. Analysis revealed arrested meiosis/cytokinesis in microspores, and altered lignin deposition pattern in endothecial walls thus affecting anther dehiscence. In the gynoecium, flaccid, dry stigmatic papillae, and large embryo sac in the female gametophyte was observed. Over-expression of miR159a thus severely affected pollination and seed-set. Analysis of the transcriptome data revealed components of regulatory networks of anther and carpel developmental pathway, and lignin metabolism that are affected. Expression analysis allowed us to position the miR159a-MYB65 module in the genetic network of stamen development, involved in pollen-grain maturation; in GA-mediated regulation of stamen development, and in lignin metabolism. The study, on one hand indicates role of miR159a-MYB65 in regulating multiple aspects of reproductive organ development that can be manipulated for trait modification, but also raises several unaddressed questions such as relationship between miR159a and male-meiosis, miR159a and filament elongation for future investigations. Accession numbers: KC204951-KC204960. Project number PRJNA1035268.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01377-7.

Function of Transcription Factors PoMYB12, PoMYB15, and PoMYB20 in Heat Stress and Growth of Pleurotus ostreatus

MYB transcription factors (TFs) have been extensively studied in plant abiotic stress responses and growth and development. However, the role of MYB TFs in the heat stress response and growth and development of Pleurotus ostreatus remains unclear. To investigate the function of PoMYB12, PoMYB15, and PoMYB20 TFs in P. ostreatus, mutant strains of PoMYB12, PoMYB15, and PoMYB20 were generated using RNA interference (RNAi) and overexpression (OE) techniques. The results indicated that the mycelia of OE-PoMYB12, OE-PoMYB20, and RNAi-PoMYB15 mutant strains exhibited positive effects under heat stress at 32 °C, 36 °C, and 40 °C. Compared to wild-type strains, the OE-PoMYB12, OE-PoMYB20, and RNAi-PoMYB15 mutant strains promoted the growth and development of P. ostreatus. These mutant strains also facilitated the recovery of growth and development of P. ostreatus after 24 h of 36 °C heat stress. In conclusion, the expression of PoMYB12 and PoMYB20 supports the mycelium's response to heat stress and enhances the growth and development of P. ostreatus, whereas PoMYB15 produces the opposite effect.

The ARF2-MYB6 module mediates auxin-regulated petal expansion in rose

In cut rose (Rosa hybrida), the flower-opening process is closely associated with vase life. Auxin induces the expression of transcription factor genes that function in petal growth via cell expansion. However, the molecular mechanisms underlying the auxin effect during flower opening are not well understood. Here, we identified the auxin-inducible transcription factor gene RhMYB6, whose expression level is high during the early stages of flower opening. Silencing of RhMYB6 delayed flower opening by controlling petal cell expansion through down-regulation of cell expansion-related genes. Furthermore, we demonstrated that the auxin response factor RhARF2 directly interacts with the promoter of RhMYB6 and represses its transcription. Silencing of RhARF2 resulted in larger petal size and delayed petal movement. We also showed that the expression of genes related to ethylene and petal movement showed substantial differences in RhARF2-silenced petals. Our results indicate that auxin-regulated RhARF2 is a critical player that controls flower opening by governing RhMYB6 expression and mediating the crosstalk between auxin and ethylene signaling.

Seed Halopriming: A Promising Strategy to Induce Salt Tolerance in Indonesian Pigmented Rice

Unfavorable environmental conditions and climate change impose stress on plants, causing yield losses worldwide. The Indonesian pigmented rice (Oryza sativa L.) cultivars Cempo Ireng Pendek (black rice) and Merah Kalimantan Selatan (red rice) are becoming popular functional foods due to their high anthocyanin contents and have great potential for widespread cultivation. However, their ability to grow on marginal, high-salinity lands is limited. In this study, we investigated whether seed halopriming enhances salt tolerance in the two pigmented rice cultivars. The non-pigmented cultivars IR64, a salt-stress-sensitive cultivar, and INPARI 35, a salt tolerant, were used as control. We pre-treated seeds with a halopriming solution before germination and then exposed the plants to a salt stress of 150 mM NaCl at 21 days after germination using a hydroponic system in a greenhouse. Halopriming was able to mitigate the negative effects of salinity on plant growth, including suppressing reactive oxygen species accumulation, increasing the membrane stability index (up to two-fold), and maintaining photosynthetic pigment contents. Halopriming had different effects on the accumulation of proline, in different rice varieties: the proline content increased in IR64 and Cempo Ireng Pendek but decreased in INPARI 35 and Merah Kalimantan Selatan. Halopriming also had disparate effects in the expression of stress-related genes: OsMYB91 expression was positively correlated with salt treatment, whereas OsWRKY42 and OsWRKY70 expression was negatively correlated with this treatment. These findings highlighted the potential benefits of halopriming in salt-affected agro-ecosystems.

Insights into the molecular mechanisms underlying responses of apple trees to abiotic stresses

Apple (Malus[Formula: see text]domestica) is a popular temperate fruit crop worldwide. However, its growth, productivity, and quality are often adversely affected by abiotic stresses such as drought, extreme temperature, and high salinity. Due to the long juvenile phase and highly heterozygous genome, the conventional breeding approaches for stress-tolerant cultivars are time-consuming and resource-intensive. These issues may be resolved by feasible molecular breeding techniques for apples, such as gene editing and marker-assisted selection. Therefore, it is necessary to acquire a more comprehensive comprehension of the molecular mechanisms underpinning apples' response to abiotic stress. In this review, we summarize the latest research progress in the molecular response of apples to abiotic stressors, including the gene expression regulation, protein modifications, and epigenetic modifications. We also provide updates on new approaches for improving apple abiotic stress tolerance, while discussing current challenges and future perspectives for apple molecular breeding.

Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry

Strawberry is an emerging model for studying polyploid genome evolution and rapid domestication of fruit crops. Here we report haplotype-resolved genomes of two wild octoploids (Fragaria chiloensis and Fragaria virginiana), the progenitor species of cultivated strawberry. Substantial variation is identified between species and between haplotypes. We redefine the four subgenomes and track the genetic contributions of diploid species by additional sequencing of the diploid F. nipponica genome. We provide multiple lines of evidence that F. vesca and F. iinumae, rather than other described extant species, are the closest living relatives of these wild and cultivated octoploids. In response to coexistence with quadruplicate gene copies, the octoploid strawberries have experienced subgenome dominance, homoeologous exchanges and coordinated expression of homoeologous genes. However, some homoeologues have substantially altered expression bias after speciation and during domestication. These findings enhance our understanding of the origin, genome evolution and domestication of strawberries.

Metabolomic and transcriptomice analyses of flavonoid biosynthesis in apricot fruits

Introduction

Flavonoids, as secondary metabolites in plants, play important roles in many biological processes and responses to environmental factors.

Methods

Apricot fruits are rich in flavonoid compounds, and in this study, we performed a combined metabolomic and transcriptomic analysis of orange flesh (JN) and white flesh (ZS) apricot fruits.

Results and discussion

A total of 222 differentially accumulated flavonoids (DAFs) and 15855 differentially expressed genes (DEGs) involved in flavonoid biosynthesis were identified. The biosynthesis of flavonoids in apricot fruit may be regulated by 17 enzyme-encoding genes, namely PAL (2), 4CL (9), C4H (1), HCT (15), C3'H (4), CHS (2), CHI (3), F3H (1), F3'H (CYP75B1) (2), F3'5'H (4), DFR (4), LAR (1), FLS (3), ANS (9), ANR (2), UGT79B1 (6) and CYP81E (2). A structural gene-transcription factor (TF) correlation analysis yielded 3 TFs (2 bHLH, 1 MYB) highly correlated with 2 structural genes. In addition, we obtained 26 candidate genes involved in the biosynthesis of 8 differentially accumulated flavonoids metabolites in ZS by weighted gene coexpression network analysis. The candidate genes and transcription factors identified in this study will provide a highly valuable molecular basis for the in-depth study of flavonoid biosynthesis in apricot fruits.

DREB1 and DREB2 Genes in Garlic (Allium sativum L.): Genome-Wide Identification, Characterization, and Stress Response

Dehydration-responsive element-binding (DREB) transcription factors (TFs) of the A1 and A2 subfamilies involved in plant stress responses have not yet been reported in Allium species. In this study, we used bioinformatics and comparative transcriptomics to identify and characterize DREB A1 and A2 genes redundant in garlic (Allium sativum L.) and analyze their expression in A. sativum cultivars differing in the sensitivity to cold and Fusarium infection. Eight A1 (AsaDREB1.1-1.8) and eight A2 (AsaDREB2.1-2.8) genes were identified. AsaDREB1.1-1.8 genes located in tandem on chromosome 1 had similar expression patterns, suggesting functional redundancy. AsaDREB2.1-2.8 were scattered on different chromosomes and had organ- and genotype-specific expressions. AsaDREB1 and AsaDREB2 promoters contained 7 and 9 hormone- and stress-responsive cis-regulatory elements, respectively, and 13 sites associated with TF binding and plant development. In both Fusarium-resistant and -sensitive cultivars, fungal infection upregulated the AsaDREB1.1-1.5, 1.8, 2.2, 2.6, and 2.8 genes and downregulated AsaDREB2.5, but the magnitude of response depended on the infection susceptibility of the cultivar. Cold exposure strongly upregulated the AsaDREB1 genes, but downregulated most AsaDREB2 genes. Our results provide the foundation for further functional analysis of the DREB TFs in Allium crops and could contribute to the breeding of stress-tolerant varieties.

Physiological response and transcriptome analyses of leguminous Indigofera bungeana Walp. to drought stress

Objective

Indigofera bungeana is a shrub with high quality protein that has been widely utilized for forage grass in the semi-arid regions of China. This study aimed to enrich the currently available knowledge and clarify the detailed drought stress regulatory mechanisms in I. bungeana, and provide a theoretical foundation for the cultivation and resistance breeding of forage crops.

Methods

This study evaluates the response mechanism to drought stress by exploiting multiple parameters and transcriptomic analyses of a 1-year-old seedlings of I. bungeana in a pot experiment.

Results

Drought stress significantly caused physiological changes in I. bungeana. The antioxidant enzyme activities and osmoregulation substance content of I. bungeana showed an increase under drought. Moreover, 3,978 and 6,923 differentially expressed genes were approved by transcriptome in leaves and roots. The transcription factors, hormone signal transduction, carbohydrate metabolism of regulatory network were observed to have increased. In both tissues, genes related to plant hormone signaling transduction pathway might play a more pivotal role in drought tolerance. Transcription factors families like basic helix-loop-helix (bHLH), vian myeloblastosis viral oncogene homolog (MYB), basic leucine zipper (bZIP) and the metabolic pathway related-genes like serine/threonine-phosphatase 2C (PP2C), SNF1-related protein kinase 2 (SnRK2), indole-3-acetic acid (IAA), auxin (AUX28), small auxin up-regulated rna (SAUR), sucrose synthase (SUS), sucrosecarriers (SUC) were highlighted for future research about drought stress resistance in Indigofera bungeana.

Conclusion

Our study posited I. bungeana mainly participate in various physiological and metabolic activities to response severe drought stress, by regulating the expression of the related genes in hormone signal transduction. These findings, which may be valuable for drought resistance breeding, and to clarify the drought stress regulatory mechanisms of I. bungeana and other plants.

The pivotal role of MYB transcription factors in plant disease resistance

MAIN CONCLUSION

MYB transcription factors are essential for diverse biology processes in plants. This review has focused on the potential molecular actions of MYB transcription factors in plant immunity. Plants possess a variety of molecules to defend against disease. Transcription factors (TFs) serve as gene connections in the regulatory networks controlling plant growth and defense against various stressors. As one of the largest TF families in plants, MYB TFs coordinate molecular players that modulate plant defense resistance. However, the molecular action of MYB TFs in plant disease resistance lacks a systematic analysis and summary. Here, we describe the structure and function of the MYB family in the plant immune response. Functional characterization revealed that MYB TFs often function either as positive or negative modulators towards different biotic stressors. Moreover, the MYB TF resistance mechanisms are diverse. The potential molecular actions of MYB TFs are being analyzed to uncover functions by controlling the expression of resistance genes, lignin/flavonoids/cuticular wax biosynthesis, polysaccharide signaling, hormone defense signaling, and the hypersensitivity response. MYB TFs have a variety of regulatory modes that fulfill pivotal roles in plant immunity. MYB TFs regulate the expression of multiple defense genes and are, therefore, important for increasing plant disease resistance and promoting agricultural production.

Integrated IBD Analysis, GWAS Analysis and Transcriptome Analysis to Identify the Candidate Genes for White Spot Disease in Maize

Foundation parents (FPs) play an irreplaceable role in maize breeding practices. Maize white spot (MWS) is an important disease in Southwest China that always seriously reduces production. However, knowledge about the genetic mechanism of MWS resistance is limited. In this paper, a panel of 143 elite lines were collected and genotyped by using the MaizeSNP50 chip with approximately 60,000 single nucleotide polymorphisms (SNPs) and evaluated for resistance to MWS among 3 environments, and a genome-wide association study (GWAS) and transcriptome analysis were integrated to reveal the function of the identity-by-descent (IBD) segments for MWS. The results showed that (1) 225 IBD segments were identified only in the FP QB512, 192 were found only in the FP QR273 and 197 were found only in the FP HCL645. (2) The GWAS results showed that 15 common quantitative trait nucleotides (QTNs) were associated with MWS. Interestingly, SYN10137 and PZA00131.14 were in the IBD segments of QB512, and the SYN10137-PZA00131.14 region existed in more than 58% of QR273's descendants. (3) By integrating the GWAS and transcriptome analysis, Zm00001d031875 was found to located in the region of SYN10137-PZA00131.14. These results provide some new insights for the detection of MWS's genetic variation mechanisms.

The Contribution of PGPR in Salt Stress Tolerance in Crops: Unravelling the Molecular Mechanisms of Cross-Talk between Plant and Bacteria

Soil salinity is a major abiotic stress in global agricultural productivity with an estimated 50% of arable land predicted to become salinized by 2050. Since most domesticated crops are glycophytes, they cannot be cultivated on salt soils. The use of beneficial microorganisms inhabiting the rhizosphere (PGPR) is a promising tool to alleviate salt stress in various crops and represents a strategy to increase agricultural productivity in salt soils. Increasing evidence underlines that PGPR affect plant physiological, biochemical, and molecular responses to salt stress. The mechanisms behind these phenomena include osmotic adjustment, modulation of the plant antioxidant system, ion homeostasis, modulation of the phytohormonal balance, increase in nutrient uptake, and the formation of biofilms. This review focuses on the recent literature regarding the molecular mechanisms that PGPR use to improve plant growth under salinity. In addition, very recent -OMICs approaches were reported, dissecting the role of PGPR in modulating plant genomes and epigenomes, opening up the possibility of combining the high genetic variations of plants with the action of PGPR for the selection of useful plant traits to cope with salt stress conditions.

Kiwifruit bZIP transcription factor AcePosF21 elicits ascorbic acid biosynthesis during cold stress

Cold stress seriously affects plant development, resulting in heavy agricultural losses. L-ascorbic acid (AsA, vitamin C) is an antioxidant implicated in abiotic stress tolerance and metabolism of reactive oxygen species (ROS). Understanding whether and how cold stress elicits AsA biosynthesis to reduce oxidative damage is important for developing cold-resistant plants. Here, we show that the accumulation of AsA in response to cold stress is a common mechanism conserved across the plant kingdom, from single-cell algae to angiosperms. We identified a basic leucine zipper domain (bZIP) transcription factor (TF) of kiwifruit (Actinidia eriantha Benth.), AcePosF21, which was triggered by cold and is involved in the regulation of kiwifruit AsA biosynthesis and defense responses against cold stress. AcePosF21 interacted with the R2R3-MYB TF AceMYB102 and directly bound to the promoter of the gene encoding GDP-L-galactose phosphorylase 3 (AceGGP3), a key conduit for regulating AsA biosynthesis, to up-regulate AceGGP3 expression and produce more AsA, which neutralized the excess ROS induced by cold stress. On the contrary, VIGS or CRISPR-Cas9-mediated editing of AcePosF21 decreased AsA content and increased the generation of ROS in kiwifruit under cold stress. Taken together, we illustrated a model for the regulatory mechanism of AcePosF21-mediated regulation of AceGGP3 expression and AsA biosynthesis to reduce oxidative damage by cold stress, which provides valuable clues for manipulating the cold resistance of kiwifruit.

Evaluating the Differential Response of Transcription Factors in Diploid versus Autotetraploid Rice Leaves Subjected to Diverse Saline-Alkali Stresses

Saline-alkali stress is a significant abiotic stress factor that impacts plant growth, development, and crop yield. Consistent with the notion that genome-wide replication events can enhance plant stress resistance, autotetraploid rice exhibited a higher level of tolerance to saline-alkali stress than its donor counterparts, which is reflected by differential gene expression between autotetraploid and diploid rice in response to salt, alkali, and saline-alkali stress. In this study, we investigated the expression of the transcription factors (TFs) in the leaf tissues of autotetraploid and diploid rice under different types of saline-alkali stress. Transcriptome analysis identified a total of 1040 genes from 55 TF families that were altered in response to these stresses, with a significantly higher number in autotetraploid rice compared to diploid rice. Contrarily, under these stresses, the number of expressed TF genes in autotetraploid rice was greater than that in diploid rice for all three types of stress. In addition to the different numbers, the differentially expressed TF genes were found to be from significantly distinct TF families between autotetraploid and diploid rice genotypes. The GO enrichment analysis unraveled that all the DEGs were distributed with differentially biological functions in rice, in particular those that were enriched in the pathways of phytohormones and salt resistance, signal transduction, and physiological and biochemical metabolism in autotetraploid rice compared to its diploid counterpart. This may provide useful guidance for studying the biological roles of polyploidization in plant resilience in response to saline-alkali stress.

Two Medicago truncatula growth-promoting rhizobacteria capable of limiting in vitro growth of the Fusarium soil-borne pathogens modulate defense genes expression

MAIN CONCLUSION

PGPRs: P. fluorescens Ms9N and S. maltophilia Ll4 inhibit in vitro growth of three legume fungal pathogens from the genus Fusarium. One or both trigger up-regulation of some genes (CHIT, GLU, PAL, MYB, WRKY) in M. truncatula roots and leaves in response to soil inoculation. Pseudomonas fluorescens (referred to as Ms9N; GenBank accession No. MF618323, not showing chitinase activity) and Stenotrophomonas maltophilia (Ll4; GenBank accession No. MF624721, showing chitinase activity), previously identified as promoting growth rhizobacteria of Medicago truncatula, were found, during an in vitro experiment, to exert an inhibitory effect on three soil-borne fungi: Fusarium culmorum Cul-3, F. oxysporum 857 and F. oxysporum f. sp. medicaginis strain CBS 179.29, responsible for serious diseases of most legumes including M. truncatula. S. maltophilia was more active than P. fluorescens in suppressing the mycelium growth of two out of three Fusarium strains. Both bacteria showed β-1,3-glucanase activity which was about 5 times higher in P. fluorescens than in S. maltophilia. Upon soil treatment with a bacterial suspension, both bacteria, but particularly S. maltophilia, brought about up-regulation of plant genes encoding chitinases (MtCHITII, MtCHITIV, MtCHITV), glucanases (MtGLU) and phenylalanine ammonia lyases (MtPAL2, MtPAL4, MtPAL5). Moreover, the bacteria up-regulate some genes from the MYB (MtMYB74, MtMYB102) and WRKY (MtWRKY6, MtWRKY29, MtWRKY53, MtWRKY70) families which encode TFs in M. truncatula roots and leaves playing multiple roles in plants, including a defense response. The effect depended on the bacterium species and the plant organ. This study provides novel information about effects of two M. truncatula growth-promoting rhizobacteria strains and suggests that both have a potential to be candidates for PGPR inoculant products on account of their ability to inhibit in vitro growth of Fusarium directly and indirectly by up-regulation of some defense priming markers such as CHIT, GLU and PAL genes in plants. This is also the first study of the expression of some MYB and WRKY genes in roots and leaves of M. truncatula upon soil treatment with two PGPR suspensions.

PpMYB1 and PpNPR1 interact to enhance the resistance of peach fruit to Rhizopus stolonifer infection

MYB transcription factors play important role in stress-resistance of plants. Nevertheless, the function of MYB TFs in peach Rhizopus rot remains poorly understood. Herein, Pichia guilliermondii treatment activated resistance against Rhizopus stolonifer, as illustrated by reductions in the incidence rate and severity of Rhizopus rot disease, increased enzyme activities and gene expression of chitinase (CHI) and β-1,3-glucanase (GLU), and enhancement of energy production by inducing the activities and expression of H⁺-ATPase and Ca²⁺-ATPase, succinate dehydrogenase (SDH), and cytochrome c oxidase (CCO). Moreover, an R1-type MYB, PpMYB1, from peach fruit was induced during R. stolonifer infection and in response to P. guilliermondii treatment. PpMYB1 activated the transcription of PpCHI-EP3 and PpGLU-like genes and the energy metabolism-related gene PpH⁺-ATPase1 by directly targeting the MBS element. Importantly, PpMYB1 interacted with PpNPR1 to form a heterodimer, which was conducive to enhancing the activation of target gene transcription. Collectively, our findings suggest that PpMYB1 cooperates with PpNPR1 to positively regulate disease resistance by activating the disease defense system and energy metabolism in peaches.

A translatome-transcriptome multi-omics gene regulatory network reveals the complicated functional landscape of maize

BACKGROUND

Maize (Zea mays L.) is one of the most important crops worldwide. Although sophisticated maize gene regulatory networks (GRNs) have been constructed for functional genomics and phenotypic dissection, a multi-omics GRN connecting the translatome and transcriptome is lacking, hampering our understanding and exploration of the maize regulatome.

RESULTS

We collect spatio-temporal translatome and transcriptome data and systematically explore the landscape of gene transcription and translation across 33 tissues or developmental stages of maize. Using this comprehensive transcriptome and translatome atlas, we construct a multi-omics GRN integrating mRNAs and translated mRNAs, demonstrating that translatome-related GRNs outperform GRNs solely using transcriptomic data and inter-omics GRNs outperform intra-omics GRNs in most cases. With the aid of the multi-omics GRN, we reconcile some known regulatory networks. We identify a novel transcription factor, ZmGRF6, which is associated with growth. Furthermore, we characterize a function related to drought response for the classic transcription factor ZmMYB31.

CONCLUSIONS

Our findings provide insights into spatio-temporal changes across maize development at both the transcriptome and translatome levels. Multi-omics GRNs represent a useful resource for dissection of the regulatory mechanisms underlying phenotypic variation.

Genome-Wide Identification and Analysis of MYB Transcription Factor Family in Hibiscus hamabo

MYB transcription factors constitute one of the largest gene families in plants and play essential roles in the regulation of plant growth, responses to stress, and a wide variety of physiological and biochemical processes. In this study, 204 MYB proteins (HhMYBs) were identified in the Hibiscus hamabo Sieb. et Zucc (H. hamabo) genome and systematically analyzed based on their genomic sequence and transcriptomic data. The candidate HhMYB proteins and MYBs of Arabidopsis thaliana were divided into 28 subfamilies based on the analysis of their phylogenetic relationships and their motif patterns. Expression analysis using RNA-seq and quantitative real-time PCR (qRT-PCR) indicated that most HhMYBs are differentially regulated under drought and salt stresses. qRT-PCR analysis of seven selected HhMYBs suggested that the HhMYB family may have regulatory roles in the responses to stress and hormones. This study provides a framework for a more comprehensive analysis of the role of MYBs in the response to abiotic stress in H. hamabo.

AgMYB5, an MYB transcription factor from celery, enhanced β-carotene synthesis and promoted drought tolerance in transgenic Arabidopsis

BACKGROUND

Water shortage caused by global warming seriously affects the yield and quality of vegetable crops. β-carotene, the lipid-soluble natural product with important pharmacological value, is abundant in celery. Transcription factor MYB family extensively disperses in plants and plays regulatory roles in carotenoid metabolism and water scarcity response.

RESULTS

Here, the AgMYB5 gene encoding 196 amino acids was amplified from celery cv. 'Jinnanshiqin'. In celery, the expression of AgMYB5 exhibited transactivation activity, tissue specificity, and drought-condition responsiveness. Further analysis proved that ectopic expression of AgMYB5 increased β-carotene content and promoted drought tolerance in transgenic Arabidopsis thaliana. Moreover, AgMYB5 expression promoted β-carotene biosynthesis by triggering the expression of AtCRTISO and AtLCYB, which in turn increased antioxidant enzyme activities, and led to the decreased contents of H2O2 and MDA, and the inhibition of O2- generation. Meanwhile, β-carotene accumulation promoted endogenous ABA biosynthesis of transgenic Arabidopsis, which resulted in ABA-induced stomatal closing and delayed water loss. In addition, ectopic expression of AgMYB5 increased expression levels of AtERD1, AtP5CS1, AtRD22, and AtRD29.

CONCLUSIONS

The findings indicated that AgMYB5 up-regulated β-carotene biosynthesis and drought tolerance of Arabidopsis.

Genome-wide characterization of ubiquitin-conjugating enzyme gene family explores its genetic effects on the oil content and yield of Brassica napus

Ubiquitin-conjugating enzyme (UBC) is a critical part of the ubiquitin-proteasome pathway and plays crucial roles in growth, development and abiotic stress response in plants. Although UBC genes have been detected in several plant species, characterization of this gene family at the whole-genome level has not been conducted in Brassica napus. In the present study, 200 putative BnUBCs were identified in B. napus, which were clustered into 18 subgroups based on phylogenetic analysis. BnUBCs within each subgroup showed relatively conserved gene architectures and motifs. Moreover, the gene expression patterns in various tissues as well as the identification of cis-acting regulatory elements in BnUBC promoters suggested further investigation of their potential functions in plant growth and development. Furthermore, three BnUBCs were predicted as candidate genes for regulating agronomic traits related to oil content and yield through association mapping. In conclusion, this study provided a wealth of information on the UBC family in B. napus and revealed their effects on oil content and yield, which will aid future functional research and genetic breeding of B. napus.

Genome-wide characterization and expression analysis of MYB transcription factors in Chrysanthemum nankingense

BACKGROUND

Chrysanthemum is a popular ornamental plant worldwide. MYB (v-myb avian myeloblastosis viral oncogene homolog) transcription factors play an important role in everything from stress resistance to plant growth and development. However, the MYB family of chrysanthemums has not been the subject of a detailed bioinformatics and expression investigation.

RESULTS

In this study, we examined 324 CnMYB transcription factors from Chrysanthemum nankingense genome data, which contained 122 Cn1R-MYB, 183 CnR2R3-MYB, 12 Cn3R-MYB, 2 Cn4R-MYB, and 5 atypical CnMYB. The protein motifs and classification of CnMYB transcription factors were analyzed. Among them, motifs 1, 2, 3, and 4 were found to encode the MYB DNA-binding domain in R2R3-MYB proteins, while in other-MYB proteins, the motifs 1, 2, 3, 4, 5, 6, 7, and 8 encode the MYB DNA-binding domain. Among all CnMYBs, 44 genes were selected due to the presence of CpG islands, while methylation is detected in three genes, including CnMYB9, CnMYB152, and CnMYB219. We analyzed the expression levels of each CnMYB gene in ray floret, disc floret, flower bud, leaf, stem, and root tissues. Based on phylogenetic analysis and gene expression analysis, three genes appeared likely to control cellulose and lignin synthesis in stem tissue, and 16 genes appeared likely to regulate flowering time, anther, pollen development, and flower color. Fifty-one candidate genes that may be involved in stress response were identified through phylogenetic, stress-responseve motif of promoter, and qRT-PCR analyses. According to genes expression levels under stress conditions, six CnMYB genes (CnMYB9, CnMYB172, CnMYB186, CnMYB199, CnMYB219, and CnMYB152) were identified as key stress-responsive genes.

CONCLUSIONS

This research provides useful information for further functional analysis of the CnMYB gene family in chrysanthemums, as well as offers candidate genes for further study of cellulose and lignin synthesis, flowering traits, salt and drought stress mechanism.

Overexpression of a Fragaria vesca 1R-MYB Transcription Factor Gene (FvMYB114) Increases Salt and Cold Tolerance in Arabidopsis thaliana

The MYB (v-MYB avian myeloblastosis viral oncogene homolog) transcription factor (TF) family has numerous members with complex and diverse functions, which play an indispensable role in regulating the response of plants to stress. In this study, a new 1R-MYB TF gene was obtained from Fragaria vesca (a diploid strawberry) by cloning technology and given a new name, FvMYB114. According to the subcellular localization results, FvMYB114 protein was a nuclear localization protein. Overexpression of FvMYB114 greatly enhanced the adaptability and tolerance of Arabidopsis thaliana to salt and low temperature. Under salt and cold stress, the transgenic plants had greater proline and chlorophyll contents and higher activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) than the wild-type (WT) and unloaded-line (UL) A. thaliana. However, malondialdehyde (MDA) was higher in the WT and UL lines. These results suggested that FvMYB114 may be involved in regulating the response of A. thaliana to salt stress and cold stress. FvMYB114 can also promote the expression of genes, such as the genes AtSOS1/3, AtNHX1 and AtLEA3 related to salt stress and the genes AtCCA1, AtCOR4 and AtCBF1/3 related to cold stress, further improving the tolerance of transgenic plants to salt and cold stress.

Overexpression of MYB-like transcription factor SiMYB30 from foxtail millet (Setaria italica L.) confers tolerance to low nitrogen stress in transgenic rice

Nitrogen fertilizers significantly increase crop yield; however, the negative impact of excessive nitrogen use on the environment and soil requires urgent attention. Improving crop nitrogen use efficiency (NUE) is crucial to increase yields and protect the environment. Foxtail millet (Setaria italica L.), a gramineous crop with significant tolerance to barren croplands, is an ideal model crop for studying abiotic stress resistance in gramineous crops. However, knowledge of the regulatory network for NUE in foxtail millet is fragmentary. Herein, we identified an R2R3-like MYB transcription factor in foxtail millet, SiMYB30, which belongs to MYB subfamily 17. The expression of SiMYB30 is responsive to low nitrogen (LN) concentration. Compared with wildtype Kitaake, seedlings of rice lines overexpressing SiMYB30 showed significantly increased shoot fresh and dry weights, plant height, and root area under LN treatment indoors. Consistently, overexpression of SiMYB30 in field experiments significantly increased grain and stem nitrogen contents, grain yield per plant, and stem weight in rice. Furthermore, qRT-PCR revealed that SiMYB30 effectively activated the expression of nitrogen uptake-related genes-OsNRT1, OsNRT1.1B, and OsNPF2.4-and nitrogen assimilation-related genes-OsGOGAT1, OsGOGAT2, and OsNIA2. Notably, SiMYB30 directly bound to the promoter of OsGOGAT2 and regulated its expression. These results highlight the novel and pivotal role of SiMYB30 in improving crop NUE.

Genome-wide analysis of R2R3-MYB transcription factors reveals their differential responses to drought stress and ABA treatment in desert poplar (Populus euphratica)

The R2R3-MYB transcription factors are widely involved in the regulation of plant growth, biotic and abiotic stress responses. Meanwhile, seed germination, which is stimulated by internal and external environments, is a critical stage in the plant life cycle. However, the identification, characterization, and expression profiling of the Populus euphratica R2R3-MYB family in drought response during seed germination have been unknown. Our study attempted to identify and characterize the R2R3-MYB genes in P. euphratica (PeR2R3-MYBs) and explore how R2R3-MYBs trigger the drought and abscisic acid (ABA) response mechanism in its seedlings. Based on the analysis of comparative genomics, 174 PeR2R3-MYBs were identified and expanded driven by whole genome duplication or segment duplication events. The analysis of Ka/Ks ratios showed that, in contrast to most PeR2R3-MYBs, the other PeR2R3-MYBs were subjected to positive selection in P. euphratica. Further, the expression data of PeR2R3-MYBs under drought stress and ABA treatment, together with available functional data for Arabidopsis thaliana MYB genes, supported the hypothesis that PeR2R3-MYBs involved in response to drought are dependent or independent on ABA signaling pathway during seed germination, especially PeR2R3-MYBs with MYB binding sites (MBS) cis-element and/or tandem duplication. This study is the first report on the genome-wide analysis of PeR2R3-MYBs, as well as the other two Salicaceae species. The duplication events and differential expressions of PeR2R3-MYBs play important roles in enhancing the adaptation to drought desert environment. Our results provide a reference for prospective functional studies of R2R3-MYBs of poplars and lay the foundation for new breeding strategies to improve the drought tolerance of P. euphratica.

Genome-wide identification, characterization, and expression profile ofNBS-LRRgene family in sweet orange (Citrussinensis)

BACKGROUND

The NBS-LRR (nucleotide-binding site-leucine-rich repeat gene) gene family, known as the plant R (resistance) gene family with the most members, plays a significant role in plant resistance to various external adversity stresses. The NBS-LRR gene family has been researched in many plant species. Citrus is one of the most vital global cash crops, the number one fruit group, and the third most traded agricultural product world wild. However, as one of the largest citrus species, a comprehensive study of the NBS-LRR gene family has not been reported on sweet oranges.

METHODS

In this study, NBS-LRR genes were identified from the Citrus sinensis genome (v3.0), with a comprehensive analysis of this gene family performed, including phylogenetic analysis, gene structure, cis-acting element of a promoter, and chromosomal localization, among others. The expression pattern of NBS-LRR genes was analyzed when sweet orange fruits were infected by Penicillium digitatum, employing experimental data from our research group. It first reported the expression patterns of NBS-LRR genes under abiotic stresses, using three transcript data from NCBI (National Center for Biotechnology Information).

RESULTS

In this study, 111 NBS-LRR genes were identified in the C. sinensis genome (v3.0) and classified into seven subfamilies according to their N-terminal and C-terminal domains. The phylogenetic tree results indicate that genes containing only the NBS structural domain are more ancient in the sweet orange NBS-LRR gene family. The chromosome localization results showed that 111 NBS-LRR genes were distributed unevenly on nine chromosomes, with the most genes distributed on chromosome 1. In addition, we identified a total of 18 tandem duplication gene pairs in the sweet orange NBS-LRR gene family, and based on the Ka/Ks ratio, all of the tandem duplication genes underwent purifying selection. Transcriptome data analysis showed a significant number of NBS-LRR genes expressed under biotic and abiotic stresses, and some reached significantly different levels of expression. It indicates that the NBS-LRR gene family is vital in resistance to biotic and abiotic stresses in sweet oranges.

CONCLUSION

Our study provides the first comprehensive framework on the NBS-LRR family of genes, which provides a basis for further in-depth studies on the biological functions of NBS-LRR in growth, development, and response to abiotic stresses in sweet orange.

Insights into the Genetic Determination of the Autotetraploid Potato Plant Height

Plant height is an important characteristic, the modification of which can improve the ability of stress adaptation as well as the yield. In this study, genome-wide association analysis was performed for plant height traits in 370 potato cultivars using the tetraploid potato genome as a reference. A total of 92 significant single nucleotide polymorphism (SNP) loci for plant height were obtained, which were particularly significant in haplotypes A3 and A4 on chromosome 1 and A1, A2, and A4 on chromosome 5. Thirty-five candidate genes were identified that were mainly involved in the gibberellin and brassinolide signal transduction pathways, including the FAR1 gene, methyltransferase, ethylene response factor, and ubiquitin protein ligase. Among them, PIF3 and GID1a were only present on chromosome 1, with PIF3 in all four haplotypes and GID1a in haplotype A3. This could lead to more effective genetic loci for molecular marker-assisted selection breeding as well as more precise localization and cloning of genes for plant height traits in potatoes.

Comparative physiological and transcriptomic analyses reveal the mechanisms of CO2 enrichment in promoting the growth and quality in Lactuca sativa

The increase in the concentration of CO2 in the atmosphere has attracted widespread attention. To explore the effect of elevated CO2 on lettuce growth and better understand the mechanism of elevated CO2 in lettuce cultivation, 3 kinds of lettuce with 4 real leaves were selected and planted in a solar greenhouse. One week later, CO2 was applied from 8:00 a.m. to 10:00 a.m. on sunny days for 30 days. The results showed that the growth potential of lettuce was enhanced under CO2 enrichment. The content of vitamin C and chlorophyll in the three lettuce varieties increased, and the content of nitrate nitrogen decreased. The light saturation point and net photosynthetic rate of leaves increased, and the light compensation point decreased. Transcriptome analysis showed that there were 217 differentially expressed genes (DEGs) shared by the three varieties, among which 166 were upregulated, 44 were downregulated, and 7 DEGs were inconsistent in the three materials. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these DEGs involved mainly the ethylene signaling pathway, jasmonic acid signaling pathway, porphyrin and chlorophyll metabolism pathway, starch and sucrose metabolism pathway, etc. Forty-one DEGs in response to CO2 enrichment were screened out by Gene Ontology (GO) analysis, and the biological processes involved were consistent with KEGG analysis. which suggested that the growth and nutritional quality of lettuce could be improved by increasing the enzyme activity and gene expression levels of photosynthesis, hormone signaling and carbohydrate metabolism. The results laid a theoretical foundation for lettuce cultivation in solar greenhouses and the application of CO2 fertilization technology.

Transcriptomic and metabolic regulatory network characterization of drought responses in tobacco

Drought stress usually causes huge economic losses for tobacco industries. Drought stress exhibits multifaceted impacts on tobacco systems through inducing changes at different levels, such as physiological and chemical changes, changes of gene transcription and metabolic changes. Understanding how plants respond and adapt to drought stress helps generate engineered plants with enhanced drought resistance. In this study, we conducted multiple time point-related physiological, biochemical,transcriptomic and metabolic assays using K326 and its derived mutant 28 (M28) with contrasting drought tolerance. Through integrative analyses of transcriptome and metabolome,we observed dramatic changes of gene expression and metabolic profiles between M28 and K326 before and after drought treatment. we found that some of DEGs function as key enzymes responsible for ABA biosynthesis and metabolic pathway, thereby mitigating impairment of drought stress through ABA signaling dependent pathways. Four DEGs were involved in nitrogen metabolism, leading to synthesis of glutamate (Glu) starting from NO-3 /NO-2 that serves as an indicator for stress responses. Importantly, through regulatory network analyses, we detected several drought induced TFs that regulate expression of genes responsible for ABA biosynthesis through network, indicating direct and indirect involvement of TFs in drought responses in tobacco. Thus, our study sheds some mechanistic insights into how plant responding to drought stress through transcriptomic and metabolic changes in tobacco. It also provides some key TF or non-TF gene candidates for engineering manipulation for breeding new tobacco varieties with enhanced drought tolerance.

Integration of meta-analysis, machine learning and systems biology approach for investigating the transcriptomic response to drought stress in Populus species

In Populus, drought is a major problem affecting plant growth and development which can be closely reflected by corresponding transcriptomic changes. Nevertheless, how these changes in Populus are not fully understood. Here, we first used meta-analysis and machine learning methods to identify water stress-responsive genes and then performed a systematic approach to discover important gene networks. Our analysis revealed that large transcriptional variations occur during drought stress. These changes were more associated with the response to stress, cellular catabolic process, metabolic pathways, and hormone-related genes. The differential gene coexpression analysis highlighted two acetyltransferase NATA1-like and putative cytochrome P450 genes that have a special contribution in response to drought stress. In particular, the findings showed that MYBs and MAPKs have a prominent role in the drought stress response that could be considered to improve the drought tolerance of Populus. We also suggest ARF2-like and PYL4-like genes as potential markers for use in breeding programs. This study provides a better understanding of how Populus responses to drought that could be useful for improving tolerance to stress in Populus.

Genome-wide characterization and functional identification of MYB genes in Malus sieversii infected by Valsa mali

Among the most important transcription factors in plants, the v-myb avian myeloblastosis viral oncogene homolog (MYB) regulates the expression network of response genes under stresses such as fungal infection. In China, the canker disease Valsa mali threatens the survival of Malus sieversii, an ancestor of cultivated apples. Using the M. sieversii genome, we identified 457 MsMYB and 128 R2R3-MsMYB genes that were randomly distributed across 17 chromosomes. Based on protein sequence and structure, the R2R3-MsMYB genes were phylogenetically divided into 29 categories, and 26 conserved motifs were identified. We further predicted cis-elements in the 2000-kb promoter region of R2R3-MsMYBs based on the genome. Transcriptome analysis of M. sieversii under V. mali infection showed that 27 R2R3-MsMYBs were significantly differentially expressed, indicating their key role in the response to V. mali infection. Using transient transformation, MsMYB14, MsMYB24, MsMYB39, MsMYB78, and MsMYB108, which were strongly induced by V. mali infection, were functionally identified. Among the five MsMYBs, MsMYB14 and MsMYB78 were both important in enhancing resistance to diseases, whereas MsMYB24 inhibited resistance. Based on the results of this study, we gained a better understanding of the MsMYB transcription factor family and laid the foundation for a future research program on disease prevention strategies in M. sieversii.

Genome-wide analysis of R2R3-MYB transcription factors in Boehmeria nivea (L.) gaudich revealed potential cadmium tolerance and anthocyanin biosynthesis genes

Gene family, especially MYB as one of the largest transcription factor family in plants, the study of its subfunctional characteristics is a key step in the study of plant gene function. The sequencing of ramie genome provides a good opportunity to study the organization and evolutionary characters of the ramie MYB gene at the whole genome level. In this study, a total of 105 BnGR2R3-MYB genes were identified from ramie genome and subsequently grouped into 35 subfamilies according to phylogeny divergence and sequences similarity. Chromosomal localization, gene structure, synteny analysis, gene duplication, promoter analysis, molecular characteristics and subcellular localization were accomplished using several bioinformatics tools. Collinearity analysis showed that the segmental and tandem duplication events is the dominant form of the gene family expansion, and duplications prominent in distal telomeric regions. Highest syntenic relationship was obtained between BnGR2R3-MYB genes and that of Apocynum venetum (88). Furthermore, transcriptomic data and phylogenetic analysis revealed that BnGMYB60, BnGMYB79/80 and BnGMYB70 might inhibit the biosynthesis of anthocyanins, and UPLC-QTOF-MS data further supported the results. qPCR and phylogenetic analysis revealed that the six genes (BnGMYB9, BnGMYB10, BnGMYB12, BnGMYB28, BnGMYB41, and BnGMYB78) were cadmium stress responsive genes. Especially, the expression of BnGMYB10/12/41 in roots, stems and leaves all increased more than 10-fold after cadmium stress, and in addition they may interact with key genes regulating flavonoid biosynthesis. Thus, a potential link between cadmium stress response and flavonoid synthesis was identified through protein interaction network analysis. The study thus provided significant information into MYB regulatory genes in ramie and may serve as a foundation for genetic enhancement and increased productivity.

Transcriptome-wide analysis reveals core transcriptional regulators associated with culm development and variation in Dendrocalamus sinicus, the strongest woody bamboo in the world

Transcription factors (TFs) play indispensable roles in plant development and stress responses. As the largest woody bamboo species in the world, Dendrocalamus sinicus is endemic to Yunnan Province, China, and possesses two natural variants characterized by culm shape, namely straight or bent culms. Understanding the transcriptional regulation network of D. sinicus provides a unique opportunity to clarify the growth and development characteristics of woody bamboos. In this study, 10,236 TF transcripts belonging to 57 families were identified from transcriptome data of two variants at different developmental stages, from which we constructed a transcriptional regulatory network and unigene-coding protein-TFs interactive network of culm development for this attractive species. Gene function enrichment analysis revealed that hormone signaling and MAPK signaling pathways were two most enriched pathways in TF-regulated network. Based on PPI analysis, 50 genes interacting with nine TFs were screened as the core regulation components related to culm development. Of them, 18 synergistic genes of seven TFs, including nuclear cap-binding protein subunit 1, transcription factor GTE9-like, and ATP-dependent DNA helicase DDX11 isoform X1, involved in culm-shape variation. Most of these genes would interact with MYB, C3H, and ARF transcription factors. Six members with two each from ARF, C3H, and MYB transcription factor families and six key interacting genes (IAA3, IAA19, leucine-tRNA ligase, nuclear cap-binding protein subunit 1, elongation factor 2, and coiled-coil domain-containing protein 94) cooperate with these transcription factors were differentially expressed at development stage of young culms, and were validated by quantitative PCR. Our results represent a crucial step towards understanding the regulatory mechanisms of TFs involved in culm development and variation of D. sinicus.

Candidate Genes Associated with Abiotic Stress Response in Plants as Tools to Engineer Tolerance to Drought, Salinity and Extreme Temperatures in Wheat: An Overview

Wheat represents one of the most important staple food crops worldwide and its genetic improvement is fundamental to meeting the global demand of the growing population. However, the environmental stresses, worsened by climate change, and the increasing deterioration of arable land make it very difficult to fulfil this demand. In light of this, the tolerance of wheat to abiotic stresses has become a key objective of genetic improvement, as an effective strategy to ensure high yields without increasing the cultivated land. Genetic erosion related to modern agriculture, whereby elite, high-yielding wheat varieties are the product of high selection pressure, has reduced the overall genetic diversity, including the allelic diversity of genes that could be advantageous for adaptation to adverse environmental conditions. This makes traditional breeding a less effective or slower approach to generating new stress-tolerant wheat varieties. Either mining for the diversity of not-adapted large germplasm pools, or generating new diversity, are the mainstream approaches to be pursued. The advent of genetic engineering has opened the possibility to create new plant variability and its application has provided a strong complement to traditional breeding. Genetic engineering strategies such as transgenesis and genome editing have then provided the opportunity to improve environmental tolerance traits of agronomic importance in cultivated species. As for wheat, several laboratories worldwide have successfully produced transgenic wheat lines with enhanced tolerance to abiotic stresses, and, more recently, significant improvements in the CRISPR/Cas9 tools available for targeted variations within the wheat genome have been achieved. In light of this, the present review aims to provide successful examples of genetic engineering applications for the improvement of wheat adaptation to drought, salinity and extreme temperatures, which represent the most frequent and most severe events causing the greatest losses in wheat production worldwide.

An R3-MYB repressor, BnCPC forms a feedback regulation with MBW complex to modulate anthocyanin biosynthesis in Brassica napus

BACKGROUND

Anthocyanins are metabolites of phenylpropanoid pathway, and involves in diverse processes of plant development and adaptation, which are regulated by the MYB-bHLH-WD40 (MBW) protein complexes. Many R2R3-MYB activators have been well characterized, but the MYB repressors in anthocyanin biosynthesis were recognized recently, which are also important in modulating phenylpropanoid metabolism in plants. The regulatory mechanism of anthocyanin biosynthesis in oil crop Brassica napus remains to be revealed.

RESULTS

In this study, we identified an anthocyanin repressor BnCPC in B. napus. BnCPC encoded a typical R3-MYB protein containing a conserved [D/E]Lx2[R/K]x3Lx6Lx3R motif for interaction with bHLH proteins. Overexpression of BnCPC in B. napus inhibited anthocyanin accumulation, especially under anthocyanin inducible conditions. Protein-protein interaction and dual-luciferase assays confirmed that BnCPC could compete with BnPAP1 to interact with bHLHs (BnTT8 and BnEGL3), and repress the expression of anthocyanin biosynthetic genes (e.g., BnDFR) that activated by MBW complexes. Moreover, we found BnCPC inhibited the MBW complex-induced BnCPC activity.

CONCLUSIONS

Overall, this research demonstrated that BnCPC repressed anthocyanin biosynthesis by affecting the formation of MBW complex, and formed a feedback loop to regulate anthocyanin accumulation in B. napus.

A R2R3 MYB Transcription Factor, TaMYB391, Is Positively Involved in Wheat Resistance to Puccinia striiformis f. sp. tritici

A biotrophic fungus, Puccinia striiformis f.sp. tritici (Pst), which causes stripe rust disease in wheat is the most yield-limiting factor in wheat production. Plants have complex defense mechanisms against invading pathogens. Hypersensitive response (HR), a kind of programmed cell death (PCD) at the infection site, is among these defense mechanisms. Transcription factors (TFs) play a crucial role in plant defense response against invading pathogens. Myeloblastosis (MYB) TFs are among the largest TFs families that are involved in response to both biotic and abiotic stresses. However, little is known about the mechanisms of MYB TFs during the interaction between wheat and the stripe rust fungus. Here, we identified an R2R3 MYB TF from wheat, designated as TaMYB391, and characterized its functional role during wheat-Pst interaction. Our data indicated that TaMYB391 is induced by Pst infection and exogenous application of salicylic acid (SA) and abscisic acid (ABA). TaMYB391 is localized in the nucleus of both wheat and Nicotiana benthamiana. Transient overexpression of TaMYB391 in N. benthamiana triggered HR-related PCD accompanied by increased electrolyte leakage, high accumulation of reactive oxygen species (ROS), and transcriptional accumulation of SA defense-related genes and HR-specific marker genes. Overexpression of TaMYB391 in wheat significantly enhanced wheat resistance to stripe rust fungus through the induction of pathogenesis-related (PR) genes, ROS accumulation and hypersensitive cell death. On the other hand, RNAi-mediated silencing of TaMYB391 decreased the resistance of wheat to Pst accompanied by enhanced growth of the pathogen. Together our findings demonstrate that TaMYB391 acts as a positive regulator of HR-associated cell death and positively contributes to the resistance of wheat to the stripe rust fungus by regulating certain PR genes, possibly through SA signaling pathways.

Identification and Analysis of Stress-Associated Proteins (SAPs) Protein Family and Drought Tolerance of ZmSAP8 in Transgenic Arabidopsis

Stress-associated proteins (SAPs), a class of A20/AN1 zinc finger proteins, play vital roles in plant stress response. However, investigation of SAPs in maize has been very limited. Herein, to better trace the evolutionary history of SAPs in maize and plants, 415 SAPs were identified in 33 plant species and four species of other kingdoms. Moreover, gene duplication mode exploration showed whole genome duplication contributed largely to SAP gene expansion in angiosperms. Phylogeny reconstruction was performed with all identified SAPs by the maximum likelihood (ML) method and the SAPs were divided into five clades. SAPs within the same clades showed conserved domain composition. Focusing on maize, nine ZmSAPs were identified. Further promoter cis-elements and stress-induced expression pattern analysis of ZmSAPs indicated that ZmSAP8 was a promising candidate in response to drought stress, which was the only AN1-AN1-C2H2-C2H2 type SAP in maize and belonged to clade I. Additionally, ZmSAP8 was located in the nucleus and had no transactivation activity in yeast. Overexpressing ZmSAP8 enhanced the tolerance to drought stress in Arabidopsis thaliana, with higher seed germination and longer root length. Our results should benefit the further functional characterization of ZmSAPs.

Dehydration response in Stylosanthes scabra: Transcriptional, biochemical, and physiological modulations

Stylosanthes scabra, popularly known as stylo, is native to the Brazilian Caatinga semiarid region and stands out as a drought-tolerant shrub forage crop. This work provides information about the plant response during the first 48 h of water deficit, followed by a rehydration treatment. Besides root transcriptomics data, 13 physiological or biochemical parameters were scrutinized. Additionally, RNA-Seq annotated transcripts not associated with the "Viridiplantae" clade were taxonomically categorized. It was found that S. scabra quickly perceives and recovers from the oscillations of the imposed water regime. Physiologically, mechanisms that minimize evapotranspiration or protect the photosynthetic apparatus stood out. Biochemically, it was found that the root tissue invests in synthesizing compounds that can act as osmolytes (proline and sugars), emphasizing the importance of osmoregulation to water deficit acclimation. Consistently, transcriptome and qPCR analyses showed that a set of enriched biological processes with upregulated (UR) transcripts were involved in protective functions against reactive oxygen species or encoding enzymes of important metabolic pathways, which might contribute to S. scabra response to water deficit. Additionally, several UR kinases and transcription factors were identified. Finally, in an innovative approach, some naturally occurring microbial groups (such as Schizosaccharomyces, Bradyrhizobium, etc.) were identified in the S. scabra roots. This study reveals insights into the physiological, biochemical, and molecular mechanisms underlying the S. scabra response to water deficit and provides candidate genes that may be useful in developing drought-tolerant crop varieties through biotechnological applications.

Transcription factor FfMYB15 regulates the expression of cellulase gene FfCEL6B during mycelial growth of Flammulina filiformis

Background

Cellulose degradation can determine mycelial growth rate and affect yield during the growth of Flammulina filiformis. The degradation of cellulose requires the joint action of a variety of cellulases, and some cellulase-related genes have been detected in mushrooms. However, little is known about the transcriptional regulatory mechanisms of cellulose degradation.

Results

In this study, FfMYB15 that may regulate the expression of cellulase gene FfCEL6B in F. filiformis was identified. RNA interference (RNAi) showed that FfCEL6B positively regulated mycelial growth. Gene expression analyses indicated that the expression patterns of FfCEL6B and FfMYB15 in mycelia cultured on the 0.9% cellulose medium for different times were similar with a correlation coefficient of 0.953. Subcellular localization and transcriptional activity analyses implied that FfMYB15 was located in the nucleus and was a transcriptional activator. Electrophoretic mobility shift assay (EMSA) and dual-luciferase assays demonstrated that FfMYB15 could bind and activate FfCEL6B promoter by recognizing MYB cis-acting element.

Conclusions

This study indicated that FfCEL6B played an active role in mycelial growth of F. filiformis and was regulated by FfMYB15.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01932-z.