Expansion and diversification of the Populus R2R3-MYB family of transcription factors

Identification and functional characterization of MYB genes regulating polyphenol biosynthesis in cabbage for resistance to Xanthomonas campestris pv. campestris

Cabbage (Brassica oleracea L. var. capitata) is a vital leafy vegetable, but its production is frequently impacted by Xanthomonas campestris pv. campestris (Xcc). The MYB family is one of the most abundant families involved in plant responses to biotic stresses. However, genome-wide identification of MYB and their roles in regulating phenolic synthesis during Xcc resistance have not been previously reported in cabbage. The present investigation reports a total of 322 BoMYB genes. Transcriptome data revealed that 37 BoMYBs were significantly upregulated upon Xcc infection. Concurrently, an increase in polyphenol content was observed, suggesting a pivotal role of polyphenols in Xcc resistance. Based on phylogenetic relationships and qRT-PCR analysis, BoMYB108 was identified as a candidate gene potentially involved in early resistance to Xcc by regulating polyphenol biosynthesis. Overexpression and silencing experiments were conducted to validate the function of BoMYB108. Overexpression of BoMYB108 significantly enhanced the accumulation of phenolic acids, while silencing resulted in the opposite effect. Furthermore, increased phenolic acid levels were associated with reduced reactive oxygen species (ROS) accumulation. These findings indicate that BoMYB108 promotes phenolic acid biosynthesis and mitigates ROS accumulation under Xcc stress, thereby alleviating Xcc-induced damage. In summary, this study provides a valuable data resource for the MYB gene family in cabbage and establishes a theoretical foundation for understanding the phenolic-based mechanisms of Xcc resistance in brassicaceous vegetables.

gma-miR828a Negatively Regulates Resistance to Tea Leaf Spot Caused by Lasiodiplodia theobromae Through Targeting the CsMYB28-CsRPP13 Module

Leaf spot caused by the fungus Lasiodiplodia theobromae severely affects the quality and production of tea (Camellia sinensis) in plantations across southwestern China. Currently, no effective control measures are available, and the damage to tea leaves is also exacerbated by a lack of understanding regarding the epidemiology of the disease. Previous studies have suggested that gma-miR828a is differentially expressed during L. theobromae infection and may target and cleave the mRNA of CsMYB28. In this study, we characterised CsMYB28 as encoding a transcription factor (TF) that localises to the nucleus, cell membrane, and cytoplasm. This gene was found to be differentially and spatiotemporally expressed in leaf tissues following L. theobromae infection of leaves of the tea plant. Altered CsMYB28 expression, achieved by transient overexpression or stable genetic transformation of Nicotiana benthamiana, or transient silencing using antisense oligonucleotides (AsODN) in the tea plant, indicated that CsMYB28 contributes to resistance against L. theobromae. Using DNA affinity purification sequencing, yeast one-hybrid, and dual-luciferase assays, we also identified that CsMYB28 bound to the AATTAATT motif of CsRPP13, thereby activating the expression of CsRPP13. Additionally, degradome sequencing, β-glucuronidase (GUS) assays, and RNA ligase-mediated rapid amplification of cDNA ends revealed that miR828a cleaved CsMYB28 mRNA, negatively regulating its expression. The results from transient overexpression and stable transformation studies, combined with AsODN-mediated silencing in the tea plant, suggested that miR828a plays a negative regulatory role in modulating the response of the tea plant to L. theobromae infection. This study demonstrates that the miR828a-CsMYB28-CsRPP13 mediates the response of the tea plant to L. theobromae infection.

Gibberellin promotes xylem expansion and cell lignification by regulating sugar accumulation and the expression of JcMYB43 and JcMYB63 in the woody plant Jatropha curcas

Gibberellins (GAs) are a group of diterpene plant hormones that regulate various plant developmental processes, including wood formation. Nevertheless, the regulatory pattern and the downstream targets of GA in the regulation of xylem expansion and cell lignification in woody plants remain unclear. In transgenic Jatropha curcas with significantly increased or decreased bioactive GA content via separate overexpression of JcGA20ox1 or JcGA2ox6, comparative transcriptomic, metabolomic and physiological investigations were conducted on the young stems. Lignin quantification and ultrastructural investigations of the young stems at different development stages revealed that JcGA20ox1 plants presented much faster lignin deposition and xylem expansion even at early development stages. The transcriptomic results revealed that the majority of the differentially expressed genes (DEGs) in the JcGA20ox1 and JcGA2ox6 plants were mainly related to metabolic pathways. Analysis of the DEGs and the gene regulatory network revealed that the increased lignification in JcGA20ox1 plants was due to the activated expression of several key transcription factors and the structural genes in the lignin biosynthesis pathway, which was confirmed by the significantly increased precursors of lignin identified via metabolomic analysis. Interestingly, a total of 15 sugar-related metabolites were differentially regulated, most of which were increased in the xylem of JcGA20ox1, but decreased in JcGA2ox6 plants. Importantly, two key GA-responsive transcription factors JcMYB43 and JcMYB63 were identified to play dual roles in promoting both xylem expansion and cell lignification. Conclusively, this study provides novel insights into the molecular mechanisms of GA-regulated xylem development in the woody plants.

Analysis of the MYB gene family in tartary buckwheat and functional investigation of FtPinG0005108900.01 in response to drought

Tartary buckwheat (Fagopyrum tataricum) is an important crop used for edible food and medicinal usage. Drought annually brings reduction in crop yield and quality, causing enormous economic losses. Transcription factors are often involved in the regulation of plant responses to environmental stresses. In this study, we identified 233 MYB transcription factors in tartary buckwheat and classified them into 13 groups, including 1R, R2R3, 3R, 4R types. Gene structure and conserved motifs of these 233 FtMYBs suggested the relative conservation of these FtMYBs within each group. There is strong collinearity within the genomes of F. tataricum, with identifying syntenic gene pairs of FtMYB. Further, the expansion of FtMYB genes was attributed to whole genome duplication. The enrichment analysis of cis-acting elements in the FtMYB genes indicated that FtMYBs may participate in abiotic stress responses. The transcriptional changes of FtMYB genes in tartary buckwheat were then investigated using public data and qPCR. A number of FtMYB genes exhibited apparent transcript levels in the detected tissues and most of them disturbed their expression after the treatment of PEG6000 or natural treatment of tartary buckwheat seedlings. Some of the FtMYB genes showed a similar expression trend with qPCR validation. FtMYB gene FtPinG0005108900.01 were shown to activated by PEG6000 and natural drought treatment, and its encoded protein localizes to nucleus, revealing it as a typical transcription factor. Overexpression of FtPinG0005108900.01 increase the drought tolerance, and transcriptome analysis indicated that lignin synthesis other than flavonoid biosynthesis pathway was activated in the overexpressing plants following drought treatment. Our results provided detailed evolution and comparative genomic information of FtMYBs in tartary buckwheat and dissected the function of a FtMYB gene FtPinG0005108900.01 in response to drought.

20 years of the Bio-Analytic Resource for Plant Biology

The Bio-Analytic Resource for Plant Biology ('the BAR', at https://bar.utoronto.ca) is celebrating its 20th year in operation in 2025. The BAR encompasses and provides visualization tools for large 'omics data sets from plants. The BAR covers data from Arabidopsis, tomato, wheat, barley and 29 other plant species (with data for 2 others to be released soon). These data include nucleotide and protein sequence data, gene expression data, protein-protein and protein-DNA interactions, protein structures, subcellular localizations, and polymorphisms. The data are stored in more than 200 relational databases holding 186 GB of data and are presented to the researchers via web apps. These web apps provide data analysis and visualization tools. Some of the most popular tools are eFP ('electronic fluorescent pictograph') Browsers, ePlants and ThaleMine (an Arabidopsis-specific instance of InterMine). The BAR was designated a Global Core Biodata Resource in 2023. Like other GCBRs, the BAR has excellent operational stability, provides access without login requirement, and provides an API for researchers to be able to access BAR data programmatically. We present in this update a new overarching search tool called Gaia that permits easy access to all BAR data, powered by machine learning and artificial intelligence.

Transcription factor PdMYB118 in poplar regulates lignin deposition and xylem differentiation in addition to anthocyanin synthesis through suppressing the expression of PagKNAT2/6b gene

R2R3-MYB transcription factors function as the master regulators of the phenylpropanoid pathway in which both lignin and anthocyanin are produced. In poplar, R2R3-MYB transcription factor PdMYB118 positively regulates anthocyanin production to change leaf color. However, the molecular mechanism by which it controls different branches of the phenylpropanoid pathway still remains poorly understood. Here, we reported that in addition to anthocyanin synthesis, lignin deposition and xylem differentiation were regulated by PdMYB118 through inhibiting PagKNAT2/6b gene expression. The transgenic poplar plants overexpressing PdMYB118 accumulated more xylem, lignin and anthocyanin. Transcriptome and reverse transcription quantitative PCR analyses revealed that the expression of PagKNAT2/6b gene which inhibited lignin deposition and xylem differentiation was significantly down-regulated in transgenic poplar plants. Subsequent dual-luciferase reporter and yeast-one-hybrid assays demonstrated that PdMYB118 directly inhibited the transcription of PagKNAT2/6b by binding to the AC elements in its promoter region. Further experiments with transgenic poplar plants overexpressing PagKNAT2/6b demonstrated that overexpression of PagKNAT2/6b in the PdMYB118 overexpression background rescued lignin accumulation and xylem width to the same level of wild type plants. The findings in this work suggest that PdMYB118 is involved in the lignin deposition and xylem differentiation via modulating the expression of PagKNAT2/6b, and the PdMYB118- PagKNAT2/6b model can be used for the genetic breeding of new woody tree with high lignin production.

Comparative genomics analysis of the MYB gene family in barley: preliminary insights into evolution and biological function in Blue Qingke

Background

The Myeloblastosis related (MYB) family is one of the most widely distributed transcription factor families in plants and plays a significant role in plant growth and development, hormone signal transduction, and stress response. There are many reports on MYB family species, but the research on Qingke is still limited.

Methods

This study used comparative genomics methods to analyze gene and protein structure, protein physicochemical properties, chromosome localization, and evolution. A bioinformatics approach was used to systematically analyze the HvMYB gene family. At the milk stage, soft dough stage, and mature stage, White and Blue Qingke grains were selected for RNA sequencing (RNA-seq), among which two proteins interacted (HvMYB and HvMYC). The expression of this gene family was analyzed through RNA-seq, and the expression levels of HvMYB and HvMYC in the grains of two different color varieties were analyzed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Finally, the interaction between HvMYB and HvMYC was verified by bimolecular fluorescence complementation (BiFC) experiments.

Results

A total of 92 Qingke HvMYB genes were identified and analyzed, and 92 HvMYB proteins were classified into five categories. Cis-acting elements associated with abscisic acid response, light response, and methyl jasmonate (MeJA) response were found in the promoter regions of most MYB genes. Using qRT-PCR combined with RNA-seq analysis showed that MYB gene was highly expressed in the soft dough stage and was varietal specific. Subcellular localization indicated that HvMYB was located in the nucleus and cell membrane, HvMYC was located in the nucleus, cell membrane, and cytoplasm. Through BiFC analysis, it has been proven that HvMYB in the MYB family and HvMYC in the basic helix-loop-helix (bHLH) family can interact. This study provides a preliminary theoretical basis for understanding the function and role of the Qingke MYB gene family and provides a reference for the molecular mechanism of Qingke gene evolution.

Lignin lite: Boosting plant power through selective downregulation

This article explores the dual benefits of reducing lignin content in plants, which streamlines biofuel production while maintaining robust defence mechanisms. It discusses how plants compensate for lower lignin levels through alternative defence strategies, recent biotechnological advances in lignin modification, and the implications for agriculture and industry.

Genome-Wide Analysis of the Common Fig (Ficus carica L.) R2R3-MYB Genes Reveals Their Structure, Evolution, and Roles in Fruit Color Variation

The R2R3-MYB transcription factor (TF) family is crucial for regulating plant growth, stress response, and fruit ripening. Although this TF family has been examined in a multitude of plants, the R2R3-MYB TFs in Ficus carica, a Mediterranean fruit species, have yet to be characterized. This study identified and classified 63 R2R3-MYB genes (FcMYB1 to FcMYB63) in the F. carica genome. We analyzed these genes for physicochemical properties, conserved motifs, phylogenetic relationships, gene architecture, selection pressure, and gene expression profiles and networks. The genes were classified into 29 clades, with members of the same clade showing similar exon-intron structures and motif compositions. Of the 54 orthologous gene pairs shared with mulberry (Morus notabilis), 52 evolved under negative selection, while two pairs (FcMYB55/MnMYB20 and FcMYB59/MnMYB31) experienced diversifying selection. RNA-Seq analysis showed that FcMYB26, FcMYB33, and FcMYB34 were significantly overexpressed in fig fruit peel during maturation phase III. Weighted gene co-expression network analysis (WGCNA) indicated that these genes are part of an expression module associated with the anthocyanin pathway. RT-qPCR validation confirmed these findings and revealed that the Tunisian cultivars 'Zidi' and 'Soltani' have cultivar-specific R2R3-FcMYB genes highly overexpressed during the final stage of fruit maturation and color acquisition. These genes likely influence cultivar-specific pigment synthesis. This study provides a comprehensive overview of the R2R3-MYB TF family in fig, offering a framework for selecting genes related to fruit peel color in breeding programs.

In silico analysis of R2R3-MYB transcription factors in the basal eudicot model, Aquilegia coerulea

R2R3-MYBs are an important group of transcription factors that regulate crucial developmental processes across the plant kingdom; yet no comprehensive analysis of the R2R3-MYBs in the early-diverging eudicot clade of Ranunculaceae has been conducted so far. In the present study, Aquilegia coerulea is chosen to understand the extent of conservation and divergence of R2R3-MYBs as a representative of the family by analysing the genomic distribution, organization, gene structure, physiochemical properties, protein architecture, evolution and possible mode of expansion. Genome-wide analysis showed the presence of 82 putative homologues classified into 21 subgroups, based on phylogenetic analysis of full-length protein sequences. The domain has remained largely conserved across all homologues with few differences from the characterized Arabidopsis thaliana R2R3-MYBs. The topology of the phylogenetic tree remains the same when full-length protein sequences are used, indicating that the evolution of R2R3-MYBs is driven by the domain region only. This is supported by the presence of similar structures of exon-intron and conserved motifs within the same subgroup. Furthermore, comparisons of the AqcoeR2R3-MYB members with monocots and core-eudicots revealed the evolutionary expansion of a few functional clades, such as A. thaliana R2R3-MYB subgroup 6 (SG6), the upstream regulatory factors of floral pigment biosynthesis and floral color. The reconstructed evolutionary history of SG6-like genes across angiosperms highlights the occurrence of independent duplication events in the genus Aquilegia. AqcoeR2R3-MYB genes are present in all seven chromosomes of A. coerulea, most of which result from local and segmental duplications. Selection analysis of these duplicated gene pairs indicates purifying selection except one, and the physiochemical analyses of R2R3-MYBs reveal differences among the MYBs signifying their functional diversification. This study paves the way for further investigation of paralogous copies and their probable role in the evolution of different floral traits in A. coerulea. It lays the foundation for functional genomic studies of R2R3-MYBs in the basal eudicots and facilitates comparative studies among angiosperms. The work also provides a framework for deciphering novel genetic regulatory pathways that govern the diversity of floral morphology.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04119-y.

Genome-wide analysis of glutathione S-transferase genes in four Prunus species and the function of PmGSTF2, activated by PmMYBa1, in regulating anthocyanin accumulation in Prunus mume

Glutathione S-transferases (GSTs) are proteases with multiple physiological functions and play an important role in plant responses to abiotic stresses. Nevertheless, there is a paucity of systematic research on GST genes in Prunus genus. Here, 330 GST genes in four Prunus species were identified for the first time and classified into eight subgroups based on protein sequence and conserved structure, among which Tau subfamily genes had the largest number. The amino acid lengths of GST-encoded proteins in the four species ranged from 66 to 1152 aa, most of which were soluble proteins and located in the cytoplasm and chloroplasts. The GST family was propelled by tandem duplications, yet robust purifying selection constrained its divergence. Conserved motif and domain analysis revealed that the majority of PmGSTs exhibited a highly conserved GST-N structure. The expression pattern of PmGSTs exhibited tissue specificity and spatiotemporal specificity. qRT-PCR validated the transcriptome results and 11 genes were differentially expressed in varieties with different flower and stem colors. In addition, we discovered an anthocyanin-related gene PmGSTF2, which can effectively restore the anthocyanin and proanthocyanidin deficiency-related phenotypes of the Arabidopsis tt19 mutant. Recombinant PmGSTF2 enhanced the water solubility of cyanidin and cyanidin-3-O-glucoside in vitro. Moreover, PmMYBa1 could directly bind to the promoter of PmGSTF2 and activate its expression. The findings revealed that GSTs were preserved in Prunus species and that PmGSTF2 was critical in regulating anthocyanin accumulation.

Genome-wide identification of R2R3-MYB transcription factors in Betula platyphylla and functional analysis of BpMYB95 in salt tolerance

The Myeloblastosis (MYB) transcription factor (TF) family is one of the largest transcription factor families in plants and plays an important role in various physiological processes. At present, there are few reports on birch (Betula platyphylla Suk.) of R2R3-MYB-TFs, and most BpMYBs still need to be characterized. In this study, 111 R2R3-MYB-TFs with conserved R2 and R3 MYB domains were identified. Phylogenetic tree analysis showed that the MYB family members of Arabidopsis thaliana and birch were divided into 23 and 21 subgroups, respectively. The latter exhibited an uneven distribution across 14 chromosomes. There were five tandem duplication events and 17 segmental duplication events between BpMYBs, and repeat events play an important role in the expansion of the family. In addition, the promoter region of MYBs was rich in various cis-acting elements, and MYB-TFs were involved in plant growth and development, light responses, biotic stress, and abiotic stress. RNA-sequencing (RNA-seq) and quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) results revealed that most R2R3-MYB-TFs in birch responded to salt stress. In particular, the expression of BpMYBs in the S20 subfamily was significantly induced by salt, drought, abscisic acid, and methyl jasmonate stresses. Based on the weighted co-expression network analysis of physiological and RNA-seq data of birch under salt stress, a key MYB-TF BpMYB95 (BPChr12G24087), was identified in response to salt stress, and its expression level was induced by salt stress. BpMYB95 is a nuclear localization protein with transcriptional activation activity in yeast and overexpression of this gene significantly enhanced salt tolerance in Saccharomyces cerevisiae. The qRT-PCR and histochemical staining results showed that BpMYB95 exhibited the highest expression in the roots, young leaves, and petioles of birch plants. Overexpression of BpMYB95 significantly improved salt-induced browning and wilting symptoms in birch leaves and alleviated the degree of PSII photoinhibition caused by salt stress in birch seedlings. In conclusion, most R2R3-MYB-TFs found in birch were involved in the salt stress response mechanisms. Among these, BpMYB95 was a key regulatory factor that significantly enhanced salt tolerance in birch. The findings of this study provide valuable genetic resources for the development of salt-tolerant birch varieties.

Characterization and functions of Myeloblastosis (MYB) transcription factors in cucurbit crops

Myeloblastosis (MYB) is one of the largest family of transcription factors (TFs) in plants. It plays a key role in plant life activities, such as metabolic regulation, stress resistant, as well as helpful for plant growth and development. In China, cucurbit is an important and nutrients rich vegetable crop, which have high medicinal and socio-economic values. In this review, we discussed the structure and characterization of MYB TFs and how do regulate flower development, fruit maturity, fruit quality, and flavonoid biosynthesis. Furthermore, we highlight the effect and contribution of MYB TFs in the regulation of biotic and abiotic stress resistance. This comprehensive review will provide a new reference for the more effective application of MYB TF in quality control, stress resistance research and molecular breeding of cucurbit crops.

An allometry perspective on crops

Understanding trait-trait coordination is essential for successful plant breeding and crop modeling. Notably, plant size drives variation in morphological, physiological, and performance-related traits, as described by allometric laws in ecology. Yet, as allometric relationships have been limitedly studied in crops, how they influence and possibly limit crop performance remains unknown. Here, we review how an allometry perspective on crops gains insights into the phenotypic evolution during crop domestication, the breeding of varieties adapted to novel conditions, and the prediction of crop yields. As allometry is an active field of research, modeling and manipulating crop allometric relationships can help to develop more resilient and productive agricultural systems to face future challenges.

The Characterization of R2R3-MYB Genes in Water Lily Nymphaea colorata Reveals the Involvement of NcMYB25 in Regulating Anthocyanin Synthesis

Nymphaea colorata, valued for its diverse flower colors and attractive shapes, is a popular ornamental aquatic plant. Anthocyanins provide color to flowers, and their biosynthesis is regulated by the R2R3-MYB transcription factor. In this study, we identified and analyzed the R2R3-MYB genes in N. colorata, focusing on their structure, evolution, expression patterns, regulatory mechanisms, and biological functions. We also investigated the role of the NcMYB25 gene in anthocyanin biosynthesis. There were 59 R2R3-MYB genes in N. colorata, distributed across 14 chromosomes. Among these, 14 genes were involved in segmental duplications and 6 in tandem duplications. Multiple R2R3-MYB transcription factors appeared to play a role in biological processes in N. colorata, including NcMYB48 in flavonoid synthesis, NcMYB33 in lignin synthesis, NcMYB23 in cold stress response, and NcMYB54 in osmotic stress response. Additionally, we identified 92 miRNAs in N. colorata, with 43 interacting with 35 R2R3-MYB genes. The NcMYB25 protein is localized in the nucleus and possesses transcriptional activation activity. Overexpression of the NcMYB25 gene in an apple pericarp resulted in anthocyanin accumulation. These findings provide insight into the evolutionary trajectory of the R2R3-MYB genes in N. colorata and highlight the regulatory function of the NcMYB25 gene in anthocyanin biosynthesis.

Transcriptomic Remodeling Occurs During Cambium Activation and Xylem Cell Development in Taxodium ascendens

Taxodium ascendens has been extensively cultivated in the wetlands of the Yangtze River in south China and has significantly contributed to ecology and timber production. Until now, research on T. ascendens genomics has yet to be conducted due to its large and complex genome, which hinders the development of T. ascendens genomic resources. Combined with the microstructural changes during cambium cell differentiation across various growth periods, we investigate the transcriptome expression and regulatory mechanisms governing cambium activity in T. ascendens. Using RNA sequencing (RNA-Seq) technology, we identified the genes involved in the cambium development of cells at three stages (dormancy, reactivation, and activity). These genes encode the regulatory and control factors associated with the cambial activity, cell division, cell expansion, and biosynthesis of cell wall components. Blast comparison revealed that three genes (TR_DN69961_c0_g1, TRINITY_DN17100_c1_g1, TRINITY_DN111727_c0_g1) from the MYB and NAC families might regulate transcription during lignin formation in wood thickening. These results illustrate the dynamic changes in the transcriptional network during vascular cambium development. Additionally, they shed light on the genetic regulation mechanism of secondary growth in T. ascendens and guide further elucidation of the candidate genes involved in regulating cambium differentiation and wood formation.

Genome-wide identification, expression analysis of the R2R3-MYB gene family and their potential roles under cold stress in Prunus sibirica

BACKGROUND

The R2R3-MYB transcription factors in plants participate in various physiological and biochemical processes and responds to various external stimuli. Prunus sibirica (known as Siberian apricot) is a drupe tree species that produces extremely high nutritional value kernels. However, it is susceptiblility to frost damage during the flowering period, results in a marked reduction in kernel yield.

RESULTS

In this study, the MYB gene family of P. sibirica (PsMYB) was systematically analyzed, and 116 R2R3-MYB genes that were distributed unevenly over eight chromosomes were ultimately screened. Phylogenetic analysis divided these 116 genes into 30 subgroups. We discovered that 37 PsMYBs had cold stress-responsive promoters, and six PsMYBs were annotated to be associated with cold response. Intraspecific homology analysis identified segmental duplication as the primary gene amplification mechanism, and homology analysis of the PsMYB genes with those of five other species revealed phylogenetic relationships with Rosaceae species. Protein interaction studies revealed collaborative regulation of the PsMYB proteins with Arabidopsis protein, and transcriptome analysis identified PsMYB genes that were highly expressed at low temperatures. Additionally, the expression levels of 22 PsMYBs in different tissue parts of P. sibirica and under different low-temperature stress conditions were evaluated using quantitative real-time PCR, with the results verifying that PsMYBs are specifically expressed in different plant parts and may be involved in the growth and development of P. sibirica species. Genes upregulated after exposure to low-temperature stress and likely involved in cold response were identified.

CONCLUSION

This study lays a foundation for understanding the molecular biology of PsMYBs in P. sibirica and provides a theoretical basis for the future study of transgenic lines with cold resistance during the flowering period of this tree.

Genome-wide analysis of flavonoid biosynthetic genes in Musaceae (Ensete, Musella, and Musa species) reveals amplification of flavonoid 3',5'-hydroxylase

Flavonoids in Musaceae are involved in pigmentation and stress responses, including cold resistance, and are a component of the healthy human diet. Identification and analysis of the sequence and copy number of flavonoid biosynthetic genes are valuable for understanding the nature and diversity of flavonoid evolution in Musaceae species. In this study, we identified 71-80 flavonoid biosynthetic genes in chromosome-scale genome sequence assemblies of Musaceae, including those of Ensete glaucum, Musella lasiocarpa, Musa beccarii, M. acuminata, M. balbisiana and M. schizocarpa, checking annotations with BLAST and determining the presence of conserved domains. The number of genes increased through segmental duplication and tandem duplication. Orthologues of both structural and regulatory genes in the flavonoid biosynthetic pathway are highly conserved across Musaceae. The flavonoid 3',5'-hydroxylase gene F3'5'H was amplified in Musaceae and ginger compared with grasses (rice, Brachypodium, Avena longiglumis, and sorghum). One group of genes from this gene family amplified near the centromere of chromosome 2 in the x = 11 Musaceae species. Flavonoid biosynthetic genes displayed few consistent responses in the yellow and red bracts of Musella lasiocarpa when subjected to low temperatures. The expression levels of MlDFR2/3 (dihydroflavonol reductase) increased while MlLAR (leucoanthocyanidin reductase) was reduced by half. Overall, the results establish the range of diversity in both sequence and copy number of flavonoid biosynthetic genes during evolution of Musaceae. The combination of allelic variants of genes, changes in their copy numbers, and variation in transcription factors with the modulation of expression under cold treatments and between genotypes with contrasting bract-colours suggests the variation may be exploited in plant breeding programmes, particularly for improvement of stress-resistance in the banana crop.

PagMYB180 regulates adventitious rooting via a ROS/PCD-dependent pathway in poplar

The formation of adventitious roots (AR) is an essential step in the vegetative propagation of economically woody species. Reactive oxygen species (ROS) function as signaling molecules in regulating root growth and development. Here, we identified an R2R3-MYB transcription factor PagMYB180 as a regulator of AR formation in hybrid poplar (Populus alba × Populus glandulosa). PagMYB180 was specifically expressed in the vascular tissues of poplar roots, stems and leaves, and its protein was localized in the nucleus and acted as a transcriptional repressor. Both dominant repression and overexpression of PagMYB180 resulted in a significant reduction of AR quantity, a substantial increase of AR length, and an elevation of both the quantity and length of lateral roots (LR) compared to the wild type (WT) plants. Furthermore, PagMYB180 regulates programmed cell death (PCD) in root cortex cells, which is associated with elevated levels of ROS. Transcriptome and reverse transcription-quantitative PCR (RT-qPCR) analyses revealed that a series of differentially expressed genes are related to ROS, PCD and ethylene synthesis. Taken together, these results suggest that PagMYB180 may regulate AR development via a ROS/PCD-dependent pathway in poplar.

WUSCHEL-RELATED HOMEOBOX genes are crucial for normal vascular organization and wood formation in poplar

Vascular cambium in tree species is a cylindrical domain of meristematic cells that are responsible for producing secondary xylem (also called wood) inward and secondary phloem outward. The poplar (Populus trichocarpa) WUSCHEL (WUS)-RELATED HOMEOBOX (WOX) family members, PtrWUSa and PtrWOX13b, were previously shown to be expressed in vascular cambium and differentiating xylem cells in poplar stems, but their functions remain unknown. Here, we investigated roles of PtrWUSa, PtrWOX13b and their close homologs in vascular organization and wood formation. Expression analysis showed that like PtrWUSa and PtrWOX13b, their close homologs, PtrWUSb, PtrWUS4a/b and PtrWOX13a/c, were also expressed in vascular cambium and differentiating xylem cells in poplar stems. PtrWUSa also exhibited a high level of expression in developing phloem fibers. Expression of PtrWUSa fused with the dominant EAR repression domain (PtrWUSa-DR) in transgenic poplar caused retarded growth of plants with twisted stems and curled leaves and a severe disruption of vascular organization. In PtrWUSa-DR stems, a drastic proliferation of cells occurred in the phloem region between vascular cambium and phloem fibers and they formed islands of ectopic vascular tissues or phloem fiber-like sclerenchyma cells. A similar proliferation of cells was also observed in PtrWUSa-DR leaf petioles and midveins. On the other hand, overexpression of PtrWOX4a-DR caused ectopic formation of vascular bundles in the cortical region, and overexpression of PtrWOX13a-DR and PtrWOX13b-DR led to a reduction in wood formation without affecting vascular organization in transgenic poplar plants. Together, these findings indicate crucial roles of PtrWUSa and PtrWOX13a/b in regulating vascular organization and wood formation, which furthers our understanding of the functions of WOX genes in regulating vascular cambium activity in tree species.

Study of changes in folding/unfolding properties and stability of Arabidopsis thaliana MYB12 transcription factor following UV-B exposure in vitro

Flavonoids mostly protect plant cells from the harmful effects of UV-B radiation from the sun. In plants, the R2R3-subfamily of the MYB transcription factor, MYB12, is a key inducer of the biosynthesis of flavonoids. Our study involves the biophysical characterization of Arabidopsis thaliana MYB12 protein (AtMYB12) under UV-B exposure in vitro. Tryptophan fluorescence studies using recombinant full-length AtMYB12 (native) and the N-terminal truncated versions (first N-terminal MYB domain absent in AtMYB12Δ1, and both the first and second N-terminal MYB domains absent in AtMYB12Δ2) have revealed prominent alteration in the tryptophan microenvironment in AtMYB12Δ1 and AtMYB12Δ2 protein as a result of UV-B exposure as compared with the native AtMYB12. Bis-ANS binding assay and urea-mediated denaturation profiling showed an appreciable change in the structural conformation in AtMYB12Δ1 and AtMYB12Δ2 proteins as compared with the native AtMYB12 protein following UV-B irradiation. UV-B-treated AtMYB12Δ2 showed a higher predisposition of aggregate formation in vitro. CD spectral analyses revealed a decrease in α-helix percentage with a concomitant increase in random coiled structure formation in AtMYB12Δ1 and AtMYB12Δ2 as compared to native AtMYB12 following UV-B treatment. Overall, these findings highlight the critical function of the N-terminal MYB domains in maintaining the stability and structural conformation of the AtMYB12 protein under UV-B stress in vitro.

Genome-wide analysis of R2R3-MYB transcription factors in poplar and functional validation of PagMYB147 in defense against Melampsora magnusiana

MAIN CONCLUSION

Transcription of PagMYB147 was induced in poplar infected by Melampsora magnusiana, and a decline in its expression levels increases the host's susceptibility, whereas its overexpression promotes resistance to rust disease. Poplars are valuable tree species with diverse industrial and silvicultural applications. The R2R3-MYB subfamily of transcription factors plays a crucial role in response to biotic stresses. However, the functional studies on poplar R2R3-MYB genes in resistance to leaf rust disease are still insufficient. We identified 191 putative R2R3-MYB genes in the Populus trichocarpa genome. A phylogenetic analysis grouped poplar R2R3-MYBs and Arabidopsis R2R3-MYBs into 33 subgroups. We detected 12 tandem duplication events and 148 segmental duplication events, with the latter likely being the main contributor to the expansion of poplar R2R3-MYB genes. The promoter regions of these genes contained numerous cis-acting regulatory elements associated with response to stress and phytohormones. Analyses of RNA-Seq data identified a multiple R2R3-MYB genes response to Melampsora magnusiana (Mmag). Among them, PagMYB147 was significantly up-regulated under Mmag inoculation, salicylic acid (SA) and methyl jasmonate (MeJA) treatment, and its encoded product was primarily localized to the cell nucleus. Silencing of PagMYB147 exacerbated the severity of Mmag infection, likely because of decreased reactive oxygen species (ROS) production and phenylalanine ammonia-lyase (PAL) enzyme activity, and up-regulation of genes related to ROS scavenging and down-regulation of genes related to PAL, SA and JA signaling pathway. In contrast, plants overexpressing PagMYB147 showed the opposite ROS accumulation, PAL enzyme activity, SA and JA-related gene expressions, and improved Mmag resistance. Our findings suggest that PagMYB147 acts as a positive regulatory factor, affecting resistance in poplar to Mmag by its involvement in the regulation of ROS homeostasis, SA and JA signaling pathway.

MYB4, a member of R2R3-subfamily of MYB transcription factor functions as a repressor of key genes involved in flavonoid biosynthesis and repair of UV-B induced DNA double strand breaks in Arabidopsis

Plants accumulate flavonoids as part of UV-B acclimation, while a high level of UV-B irradiation induces DNA damage and leads to genome instability. Here, we show that MYB4, a member of the R2R3-subfamily of MYB transcription factor plays important role in regulating plant response to UV-B exposure through the direct repression of the key genes involved in flavonoids biosynthesis and repair of DNA double-strand breaks (DSBs). Our results demonstrate that MYB4 inhibits seed germination and seedling establishment in Arabidopsis following UV-B exposure. Phenotype analyses of atmyb4-1 single mutant line along with uvr8-6/atmyb4-1, cop1-6/atmyb4-1, and hy5-215/atmyb4-1 double mutants indicate that MYB4 functions downstream of UVR8 mediated signaling pathway and negatively affects UV-B acclimation and cotyledon expansion. Our results indicate that MYB4 acts as transcriptional repressor of two key flavonoid biosynthesis genes, including 4CL and FLS, via directly binding to their promoter, thus reducing flavonoid accumulation. On the other hand, AtMYB4 overexpression leads to higher accumulation level of DSBs along with repressed expression of several key DSB repair genes, including AtATM, AtKU70, AtLIG4, AtXRCC4, AtBRCA1, AtSOG1, AtRAD51, and AtRAD54, respectively. Our results further suggest that MYB4 protein represses the expression of two crucial DSB repair genes, AtKU70 and AtXRCC4 through direct binding with their promoters. Together, our results indicate that MYB4 functions as an important coordinator to regulate plant response to UV-B through transcriptional regulation of key genes involved in flavonoids biosynthesis and repair of UV-B induced DNA damage.

Adaptation mechanism of three Impatiens species to different habitats based on stem morphology, lignin and MYB4 gene

BACKGROUND

Impatiens is an important genus with rich species of garden plants, and its distribution is extremely extensive, which is reflected in its diverse ecological environment. However, the specific mechanisms of Impatiens' adaptation to various environments and the mechanism related to lignin remain unclear.

RESULTS

Three representative Impatiens species,Impatiens chlorosepala (wet, low degree of lignification), Impatiens uliginosa (aquatic, moderate degree of lignification) and Impatiens rubrostriata (terrestrial, high degree of lignification), were selected and analyzed for their anatomical structures, lignin content and composition, and lignin-related gene expression. There are significant differences in anatomical parameters among the stems of three Impatiens species, and the anatomical structure is consistent with the determination results of lignin content. Furthermore, the thickness of the xylem and cell walls, as well as the ratio of cell wall thickness to stem diameter have a strong correlation with lignin content. The anatomical structure and degree of lignification in Impatiens can be attributed to the plant's growth environment, morphology, and growth rate. Our analysis of lignin-related genes revealed a negative correlation between the MYB4 gene and lignin content. The MYB4 gene may control the lignin synthesis in Impatiens by controlling the structural genes involved in the lignin synthesis pathway, such as HCT, C3H, and COMT. Nonetheless, the regulation pathway differs between species of Impatiens.

CONCLUSIONS

This study demonstrated consistency between the stem anatomy of Impatiens and the results obtained from lignin content and composition analyses. It is speculated that MYB4 negatively regulates the lignin synthesis in the stems of three Impatiens species by regulating the expression of structural genes, and its regulation mechanism appears to vary across different Impatiens species. This study analyses the variations among different Impatiens plants in diverse habitats, and can guide further molecular investigations of lignin biosynthesis in Impatiens.

GhMYB52 Like: A Key Factor That Enhances Lint Yield by Negatively Regulating the Lignin Biosynthesis Pathway in Fibers of Upland Cotton (Gossypium hirsutum L.)

In the context of sustainable agriculture and biomaterial development, understanding and enhancing plant secondary cell wall formation are crucial for improving crop fiber quality and biomass conversion efficiency. This is especially critical for economically important crops like upland cotton (Gossypium hirsutum L.), for which fiber quality and its processing properties are essential. Through comprehensive genome-wide screening and analysis of expression patterns, we identified a particularly high expression of an R2R3 MYB transcription factor, GhMYB52 Like, in the development of the secondary cell wall in cotton fiber cells. Utilizing gene-editing technology to generate a loss-of-function mutant to clarify the role of GhMYB52 Like, we revealed that GhMYB52 Like does not directly contribute to cellulose synthesis in cotton fibers but instead represses a subset of lignin biosynthesis genes, establishing it as a lignin biosynthesis inhibitor. Concurrently, a substantial decrease in the lint index, a critical measure of cotton yield, was noted in parallel with an elevation in lignin levels. This study not only deepens our understanding of the molecular mechanisms underlying cotton fiber development but also offers new perspectives for the molecular improvement of other economically important crops and the enhancement of biomass energy utilization.

From swamp to field: how genes from mangroves and its associates can enhance crop salinity tolerance

Salinity stress is a critical challenge in crop production and requires innovative strategies to enhance the salt tolerance of plants. Insights from mangrove species, which are renowned for their adaptability to high-salinity environments, provides valuable genetic targets and resources for improving crops. A significant hurdle in salinity stress is the excessive uptake of sodium ions (Na+) by plant roots, causing disruptions in cellular balance, nutrient deficiencies, and hampered growth. Specific ion transporters and channels play crucial roles in maintaining a low Na+/K+ ratio in root cells which is pivotal for salt tolerance. The family of high-affinity potassium transporters, recently characterized in Avicennia officinalis, contributes to K+ homeostasis in transgenic Arabidopsis plants even under high-salt conditions. The salt overly sensitive pathway and genes related to vacuolar-type H+-ATPases hold promise for expelling cytosolic Na+ and sequestering Na+ in transgenic plants, respectively. Aquaporins contribute to mangroves' adaptation to saline environments by regulating water uptake, transpiration, and osmotic balance. Antioxidant enzymes mitigate oxidative damage, whereas genes regulating osmolytes, such as glycine betaine and proline, provide osmoprotection. Mangroves exhibit increased expression of stress-responsive transcription factors such as MYB, NAC, and CBFs under high salinity. Moreover, genes involved in various metabolic pathways, including jasmonate synthesis, triterpenoid production, and protein stability under salt stress, have been identified. This review highlights the potential of mangrove genes to enhance salt tolerance of crops. Further research is imperative to fully comprehend and apply these genes to crop breeding to improve salinity resilience.

Genome-Wide Analysis of MYB Gene Family in Chrysanthemum ×morifolium Provides Insights into Flower Color Regulation

MYBs constitute the second largest transcription factor (TF) superfamily in flowering plants with substantial structural and functional diversity, which have been brought into focus because they affect flower colors by regulating anthocyanin biosynthesis. Up to now, the genomic data of several Chrysanthemum species have been released, which provides us with abundant genomic resources for revealing the evolution of the MYB gene family in Chrysanthemum species. In the present study, comparative analyses of the MYB gene family in six representative species, including C. lavandulifolium, C. seticuspe, C. ×morifolium, Helianthus annuus, Lactuca sativa, and Arabidopsis thaliana, were performed. A total of 1104 MYBs, which were classified into four subfamilies and 35 lineages, were identified in the three Chrysanthemum species (C. lavandulifolium, C. seticuspe, and C. ×morifolium). We found that whole-genome duplication and tandem duplication are the main duplication mechanisms that drove the occurrence of duplicates in CmMYBs (particularly in the R2R3-MYB subfamily) during the evolution of the cultivated chrysanthemums. Sequence structure and selective pressure analyses of the MYB gene family revealed that some of R2R3-MYBs were subjected to positive selection, which are mostly located on the distal telomere segments of the chromosomes and contain motifs 7 and 8. In addition, the gene expression analysis of CmMYBs in different organs and at various capitulum developmental stages of C. ×morifolium indicated that CmMYBS2, CmMYB96, and CmMYB109 might be the negative regulators for anthocyanin biosynthesis. Our results provide the phylogenetic context for research on the genetic and functional evolution of the MYB gene family in Chrysanthemum species and deepen our understanding of the regulatory mechanism of MYB TFs on the flower color of C. ×morifolium.

Cloning, Expression, and Functional Analysis of the MYB Transcription Factor SlMYB86-like in Tomato

MYB transcription factors (TFs) have been shown to play a key role in plant growth and development and are in response to various types of biotic and abiotic stress. Here, we clarified the structure, expression patterns, and function of a MYB TF, SlMYB86-like (Solyc06g071690) in tomato using an inbred tomato line exhibiting high resistance to bacterial wilt (Hm 2-2 (R)) and one susceptible line (BY 1-2 (S)). The full-length cDNA sequence of this gene was 1226 bp, and the open reading frame was 966 bp, which encoded 321 amino acids; its relative molecular weight was 37.05055 kDa; its theoretical isoelectric point was 7.22; it was a hydrophilic nonsecreted protein; and it had no transmembrane structures. The protein also contains a highly conserved MYB DNA-binding domain and was predicted to be localized to the nucleus. Phylogenetic analysis revealed that SlMYB86-like is closely related to SpMYB86-like in Solanum pennellii and clustered with other members of the family Solanaceae. Quantitative real-time PCR (qRT-PCR) analysis revealed that the expression of the SlMYB86-like gene was tissue specific and could be induced by Ralstonia solanacearum, salicylic acid, and jasmonic acid. The results of virus-induced gene silencing (VIGS) revealed that SlMYB86-like silencing decreased the resistance of tomato plants to bacterial wilt, suggesting that it positively regulates the resistance of tomatoes to bacterial wilt. Overall, these findings indicate that SlMYB86-like plays a key role in regulating the resistance of tomatoes to bacterial wilt.

Genome-wide identification, phylogeny and expression analysis of the R2R3-MYB gene family in quinoa (Chenopodium quinoa) under abiotic stress

The MYB transcription factor (TF) are among the largest gene families of plants being responsible for several biological processes. The R2R3-MYB gene family are integral player regulating plant primary and secondary metabolism, growth and development, and responses to hormones and stresses. The phylogenetic analysis combined with gene structure analysis and motif determination resulted in division of R2R3-MYB gene family into 27 subgroups. Evidence generated from synteny analyses indicated that CqR2R3-MYBs gene family is featured by tandem and segmental duplication events. On the basis of RNA-Seq data, the expression patterns of different tissues under salt treatment were investigated resulting CqR2R3-MYB genes high expression both in roots and stem of quinoa (Chenopodium quinoa ) plants. More than half of CqR2R3-MYB genes showed expression under salt stress. Based on this result, CqR2R3-MYB s may regulate quinoa plant growth development and resistance to abiotic stresses. These findings provided comprehensive insights on role of CqR2R3-MYBs gene family members in quinoa and candidate MYB gene family members can be further studies on their role for abiotic stress tolerance in crop plants.

PtoMYB031, the R2R3 MYB transcription factor involved in secondary cell wall biosynthesis in poplar

Introduction

The biosynthesis of the secondary cell wall (SCW) is orchestrated by an intricate hierarchical transcriptional regulatory network. This network is initiated by first-layer master switches, SCW-NAC transcription factors, which in turn activate the second-layer master switches MYBs. These switches play a crucial role in regulating xylem specification and differentiation during SCW formation. However, the roles of most MYBs in woody plants are yet to be fully understood.

Methods

In this study, we identified and isolated the R2R3-MYB transcription factor, PtoMYB031, from Populus tomentosa. We explored its expression, mainly in xylem tissues, and its role as a transcriptional repressor in the nucleus. We used overexpression and RNA interference techniques in poplar, along with Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays, to analyze the regulatory effects of PtoMYB031.

Results

Overexpression of PtoMYB031 in poplar significantly reduced lignin, cellulose, and hemicellulose content, and inhibited vascular development in stems, resulting in decreased SCW thickness in xylem tissues. Gene expression analysis showed that structural genes involved in SCW biosynthesis were downregulated in PtoMYB031-OE lines. Conversely, RNA interference of PtoMYB031 increased these compounds. Additionally, PtoMYB031 was found to recruit the repressor PtoZAT11, forming a transcriptional inhibition complex.

Discussion

Our findings provide new insights into how PtoMYB031, through its interaction with PtoZAT11, forms a complex that can suppress the expression of key regulatory genes, PtoWND1A and PtoWND2B, in SCW biosynthesis. This study enhances our understanding of the transcriptional regulation involved in SCW formation in poplar, highlighting the significant role of PtoMYB031.

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.

Genome-Wide Analysis of MYB Genes in Primulina eburnea (Hance) and Identification of Members in Response to Drought Stress

Due to periodic water deficiency in karst environments, Primulina eburnea experiences sporadic drought stress in its habitat. Despite being one of the largest gene families and functionally diverse in terms of plant growth and development, MYB transcription factors in P. eburnea have not been studied. Here, a total of 230 MYB genes were identified in P. eburnea, including 67 1R-MYB, 155 R2R3-MYB, six 3R-MYB, and two 4R-MYB genes. The R2R3-type PebMYB genes could be classified into 16 subgroups, while the remaining PebMYB genes (1R-MYB, 3R-MYB, and 4R-MYB genes) were divided into 10 subgroups. Notably, the results of the phylogenetic analysis were further supported by the motif and gene structure analysis, which showed that individuals in the same subgroup had comparable motif and structure organization. Additionally, gene duplication and synteny analyses were performed to better understand the evolution of PebMYB genes, and 291 pairs of segmental duplicated genes were found. Moreover, RNA-seq analysis revealed that the PebMYB genes could be divided into five groups based on their expression characteristics. Furthermore, 11 PebMYB genes that may be involved in drought stress response were identified through comparative analysis with Arabidopsis thaliana. Notably, seven of these genes (PebMYB3, PebMYB13, PebMYB17, PebMYB51, PebMYB142, PebMYB69, and PebMYB95) exhibited significant differences in expression between the control and drought stress treatments, suggesting that they may play important roles in drought stress response. These findings clarified the characteristics of the MYB gene family in P. eburnea, augmenting our comprehension of their potential roles in drought stress adaptation.

PagMYB205 Negatively Affects Poplar Salt Tolerance through Reactive Oxygen Species Scavenging and Root Vitality Modulation

Salt stress is one of the major abiotic stresses that limits plant growth and development. The MYB transcription factor family plays essential roles in plant growth and development, as well as stress tolerance processes. In this study, the cDNA of the 84K poplar (Populus abla × Populus glandulosa) was used as a template to clone the full length of the PagMYB205 gene fragment, and transgenic poplar lines with PagMYB205 overexpression (OX) or inhibited expression (RNAi, RNA interference) were cultivated. The role of PagMYB205 in poplar growth and development and salt tolerance was detected using morphological and physiological methods. The full-length CDS sequence of PagMYB205 was 906 bp, encoding 301 amino acids, and the upstream promoter sequence contained abiotic stress-related cis-acting elements. The results of subcellular localization and transactivation assays showed that the protein had no self-activating activity and was localized in the nucleus. Under salt stress, the rooting rate and root vitality of RNAi were higher than OX and wild type (WT). However, the malondialdehyde (MDA) content of the RNAi lines was significantly lower than that of the wild-type (WT) and OX lines, but the reactive oxygen species (ROS) scavenging ability, such as the peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) enzyme activities, was dramatically more powerful. Most significantly of all, the RNAi3 line with the lowest expression level of PagMYB205 had the lowest MDA content, the best enzyme activity and root vitality, and the best salt stress tolerance compared to the other lines. The above results suggest that the transcription factor PagMYB205 could negatively regulate salt stress tolerance by regulating antioxidant enzyme activity and root vitality.

Comprehensive Time-Course Transcriptome Reveals the Crucial Biological Pathways Involved in the Seasonal Branch Growth in Siberian Elm (Ulmus pumila)

Timber, the most prevalent organic material on this planet, is the result of a secondary xylem emerging from vascular cambium. Yet, the intricate processes governing its seasonal generation are largely a mystery. To better understand the cyclic growth of vascular tissues in elm, we undertook an extensive study examining the anatomy, physiology, and genetic expressions in Ulmus pumila. We chose three robust 15-year-old elm trees for our study. The cultivars used in this study were collected from the Inner Mongolia Autonomous Region in China and nurtured in the tree farm of Shandong Normal University. Monthly samples of 2-year-old elm branches were taken from the tree from February to September. Marked seasonal shifts in elm branch vascular tissues were observed by phenotypic observation: In February, the cambium of the branch emerged from dormancy, spurring growth. By May, elms began generating secondary xylem, or latewood, recognized by its tiny pores and dense cell structure. From June to August, there was a marked increase in the thickness of the secondary xylem. Transcriptome sequencing provides a potential molecular mechanism for the thickening of elm branches and their response to stress. In February, the tree enhanced its genetic responses to cold and drought stress. The amplified expression of CDKB, CYCB, WOX4, and ARF5 in the months of February and March reinforced their essential role in the development of the vascular cambium in elm. Starting in May, the elm deployed carbohydrates as a carbon resource to synthesize the abundant cellulose and lignin necessary for the formation of the secondary wall. Major genes participating in cellulose (SUC and CESA homologs), xylan (UGD, UXS, IRX9, IRX10, and IRX14), and lignin (PAL, C4H, 4CL, HCT, C3H, COMT, and CAD) biosynthetic pathways for secondary wall formation were up-regulated by May or/and June. In conclusion, our findings provided a foundation for an in-depth exploration of the molecular processes dictating the seasonal growth of elm timber.

The Over-Expression of Two R2R3-MYB Genes, PdMYB2R089 and PdMYB2R151, Increases the Drought-Resistant Capacity of Transgenic Arabidopsis

The R2R3-MYB genes in plants play an essential role in the drought-responsive signaling pathway. Plenty of R2R3-MYB S21 and S22 subgroup genes in Arabidopsis have been implicated in dehydration conditions, yet few have been covered in terms of the role of the S21 and S22 subgroup genes in poplar under drought. PdMYB2R089 and PdMYB2R151 genes, respectively belonging to the S21 and S22 subgroups of NL895 (Populus deltoides × P. euramericana cv. 'Nanlin895'), were selected based on the previous expression analysis of poplar R2R3-MYB genes that are responsive to dehydration. The regulatory functions of two target genes in plant responses to drought stress were studied and speculated through the genetic transformation of Arabidopsis thaliana. PdMYB2R089 and PdMYB2R151 could promote the closure of stomata in leaves, lessen the production of malondialdehyde (MDA), enhance the activity of the peroxidase (POD) enzyme, and shorten the life cycle of transgenic plants, in part owing to their similar conserved domains. Moreover, PdMYB2R089 could strengthen root length and lateral root growth. These results suggest that PdMYB2R089 and PdMYB2R151 genes might have the potential to improve drought adaptability in plants. In addition, PdMYB2R151 could significantly improve the seed germination rate of transgenic Arabidopsis, but PdMYB2R089 could not. This finding provides a clue for the subsequent functional dissection of S21 and S22 subgroup genes in poplar that is responsive to drought.

Function of the R2R3-MYB Transcription Factors in Dalbergia odorifera and Their Relationship with Heartwood Formation

R2R3-MYB transcription factors (TFs) form one of the most important TF families involved in regulating various physiological functions in plants. The heartwood of Dalbergia odorifera is a kind of high-grade mahogany and valuable herbal medicine with wide application. However, the role of R2R3-MYB genes in the growth and development of D. odorifera, especially their relevance to heartwood formation, has not been revealed. A total of 126 R2R3-MYBs were screened from the D. odorifera genome and named DodMYB1-126 based on their location on 10 chromosomes. The collinearity results showed that purification selection was the main driving force for the evolution of the R2R3-MYB TFs family, and whole genome/fragment replication event was the main form for expanding the R2R3-MYB family, generating a divergence of gene structure and function. Comparative phylogenetic analysis classified the R2R3-MYB TFs into 33 subfamilies. S3-7,10,12-13,21 and N4-7 were extensively involved in the metabolic process; S9,13,16-19,24-25 and N1-3,8 were associated with the growth and development of D. odorifera. Based on the differential transcriptional expression levels of R2R3-MYBs in different tissues, DodMYB32, DodMYB55, and DodMYB89 were tentatively screened for involvement in the regulatory process of heartwood. Further studies have shown that the DodMYB89, localized in the nucleus, has transcriptional activation activity and is involved in regulating the biosynthesis of the secondary metabolites of heartwood by activating the promoters of the structural genes DodI2'H and DodCOMT. This study aimed to comprehensively analyze the functions of the R2R3-MYB TFs and screen for candidate genes that might be involved in heartwood formation of D. odorifera.

Genome-wide identification of auxin-responsive microRNAs in the poplar stem

BACKGROUND

Wood (secondary xylem) of forests is a material of great economic importance. Wood development is strictly controlled by both the phytohormone auxin and microRNAs (miRNAs). Currently, the regulatory mechanisms underlying wood formation by auxin-associated miRNAs remain unclear.

OBJECTIVE

This report was designed to identify auxin-responsive miRNAs during wood formation.

METHODS

Morphological observation of wood development in the poplar stems was performed under the treatment of different concentrations (0 mg/L, CK; 5 mg/L, Low; 10 mg/L, High) of indol-3-butyric acid (IBA). Using a small RNA sequencing strategy, the effect of IBA treatment on miRNAs expression was genome-widely analyzed.

RESULTS

In this study, we found that wood development of poplar was promoted by low concentration of IBA treatment but inhibited by high concentration of IBA treatment. Stringent bioinformatic analysis led to identification of 118 known and 134 novel miRNAs candidates. Sixty-nine unique developmental-related miRNAs, corresponding to 269 target genes, exhibited specific expression patterns in response to auxin, as was consistent with the influence of auxin application on wood formation. Three novel miRNAs had the most number (≥ 9) of target genes, belonging to SPL, GRF and ARF gene families. The evolutionary relationships and tissue expression patterns of 41 SPL, GRF and ARF genes in poplar were thus analyzed. Of them, four representative members and corresponding miRNAs were confirmed using RT-qPCR.

CONCLUSIONS

Our results may be helpful for a better understanding of auxin-induced regulation of wood formation in tree species.

Jasmonic acid regulates lignin deposition in poplar through JAZ5-MYB/NAC interaction

Jasmonic acid (JA) is a phytohormone involved in plant defense, growth, and development, etc. However, the regulatory mechanisms underlying JA-mediated lignin deposition and secondary cell wall (SCW) formation remain poorly understood. In this study, we found that JA can inhibit lignin deposition and SCW thickening in poplar trees through exogenous MeJA treatment and observation of the phenotypes of a JA synthesis mutant, opdat1. Hence, we identified a JA signal inhibitor PtoJAZ5, belonging to the TIFY gene family, which is involved in the regulation of secondary vascular development of Populus tomentosa. RT-qPCR and GUS staining revealed that PtoJAZ5 was highly expressed in poplar stems, particularly in developing xylem. Overexpression of PtoJAZ5 inhibited SCW thickening and down-regulated the expression of SCW biosynthesis-related genes. Further biochemical analysis showed that PtoJAZ5 interacted with multiple SCW switches NAC/MYB transcription factors, including MYB3 and WND6A, through yeast two-hybrid and bimolecular fluorescent complementation experiments. Transcriptional activation assays demonstrated that MYB3-PtoJAZ5 and WND6A-PtoJAZ5 complexes regulated the expression of lignin synthetic genes. Our results suggest that PtoJAZ5 plays a negative role in JA-induced lignin deposition and SCW thickening in poplar and provide new insights into the molecular mechanisms underlying JA-mediated regulation of SCW formation.

PagMYB151 facilitates proline accumulation to enhance salt tolerance of poplar

Poplar is one of the main urban and rural greening and shade tree species in the northern hemisphere, but its growth and development is always restricted by salt stress. R2R3-MYB transcription factor family is commonly involved in many biological processes during plant growth and stress endurance. In this study, PagMYB151 (Potri.014G035100) one of R2R3-MYB members related to salt stress and expressed in both nucleus and cell membrane was cloned from Populus alba × P. glandulosa to perfect the salt tolerance mechanism. Morphological and physiological indexes regulated by PagMYB151 were detected using the PagMYB151 overexpression (OX) and RNA interference (RNAi) transgenic poplar lines. Under salt stress conditions, compared with RNAi and the non-transgenic wild-type (WT) plants, the plant height, both aboveground and underground part fresh weight of OX was significantly increased. In addition, OX has a longer and finer root structure and a larger root surface area. The root activity of OX was also enhanced, which was significantly different from RNAi but not from WT under salt treatment. Under normal conditions, the stomatal aperture of OX was larger than WT, whereas this phenotype was not obvious after salt stress treatment. In terms of physiological indices, OX enhanced the accumulation of proline but reduced the toxicity of malondialdehyde to plants under salt stress. Combing with the transcriptome sequencing data, 6 transcription factors induced by salt stress and co-expressed with PagMYB151 were identified that may cooperate with PagMYB151 to function in salt stress responding process. This study provides a basis for further exploring the molecular mechanism of poplar PagMYB151 transcription factor under abiotic stress.

Integrating Transcriptional, Metabolic, and Physiological Responses to Drought Stress in Ilex paraguariensis Roots

The appearance of water stress episodes triggers leaf abscission and decreases Ilex paraguariensis yield. To explore the mechanisms that allow it to overcome dehydration, we investigated how the root gene expression varied between water-stressed and non-stressed plants and how the modulation of gene expression was linked to metabolite composition and physiological status. After water deprivation, 5160 differentially expressed transcripts were obtained through RNA-seq. The functional enrichment of induced transcripts revealed significant transcriptional remodelling of stress-related perception, signalling, transcription, and metabolism. Simultaneously, the induction of the enzyme 9-cis-expoxycarotenoid dioxygenase (NCED) transcripts reflected the central role of the hormone abscisic acid in this response. Consequently, the total content of amino acids and soluble sugars increased, and that of starch decreased. Likewise, osmotic adjustment and radical growth were significantly promoted to preserve cell membranes and water uptake. This study provides a valuable resource for future research to understand the molecular adaptation of I. paraguariensis plants under drought conditions and facilitates the exploration of drought-tolerant candidate genes.

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.

Identification of Vitis vinifera MYB transcription factors and their response against grapevine berry inner necrosis virus

BACKGROUND

The myeloblastosis (MYB) superfamily is the largest transcription factor family in plants that play diverse roles during stress responses. However, the biotic stress-responsive MYB transcription factors of the grapevine have not been systematically studied. In China, grapevine berries are often infected with the grapevine berry inner necrosis virus (GINV), which eventually reduces the nutritional quality and commodity value.

RESULTS

The present study identified and characterized 265 VvMYB or VvMYB-related genes of the "Crimson seedless" grapevine. Based on DNA-binding domain analysis, these VvMYB proteins were classified into four subfamilies, including MYB-related, 2R-MYB, 3R-MYB, and 4R-MYB. Phylogenetic analysis divided the MYB transcription factors into 26 subgroups. Overexpression of VvMYB58 suppressed GINV abundance in the grapevine. Further qPCR indicated that among 41 randomly selected VvMYB genes, 12 were induced during GINV infection, while 28 were downregulated. These findings suggest that VvMYB genes actively regulate defense response in the grapevine.

CONCLUSION

A deeper understanding of the MYB TFs engaged in GINV defense response will help devise better management strategies. The present study also provides a foundation for further research on the functions of the MYB transcription factors.

Genome-Wide Identification and Analysis of R2R3-MYB Genes Response to Saline-Alkali Stress in Quinoa

Soil saline-alkalization inhibits plant growth and development and seriously affects crop yields. Over their long-term evolution, plants have formed complex stress response systems to maintain species continuity. R2R3-MYB transcription factors are one of the largest transcription factor families in plants, widely involved in plant growth and development, metabolism, and stress response. Quinoa (Chenopodium quinoa Willd.), as a crop with high nutritional value, is tolerant to various biotic and abiotic stress. In this study, we identified 65 R2R3-MYB genes in quinoa, which are divided into 26 subfamilies. In addition, we analyzed the evolutionary relationships, protein physicochemical properties, conserved domains and motifs, gene structure, and cis-regulatory elements of CqR2R3-MYB family members. To investigate the roles of CqR2R3-MYB transcription factors in abiotic stress response, we performed transcriptome analysis to figure out the expression file of CqR2R3-MYB genes under saline-alkali stress. The results indicate that the expression of the six CqMYB2R genes was altered significantly in quinoa leaves that had undergone saline-alkali stress. Subcellular localization and transcriptional activation activity analysis revealed that CqMYB2R09, CqMYB2R16, CqMYB2R25, and CqMYB2R62, whose Arabidopsis homologues are involved in salt stress response, are localized in the nucleus and exhibit transcriptional activation activity. Our study provides basic information and effective clues for further functional investigation of CqR2R3-MYB transcription factors in quinoa.

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.

Comprehensive Genome-Wide Analyses of Poplar R2R3-MYB Transcription Factors and Tissue-Specific Expression Patterns under Drought Stress

R2R3-type MYB transcription factors are implicated in drought stress, which is a primary factor limiting the growth and development of woody plants. The identification of R2R3-MYB genes in the Populus trichocarpa genome has been previously reported. Nevertheless, the diversity and complexity of the conserved domain of the MYB gene caused inconsistencies in these identification results. There is still a lack of drought-responsive expression patterns and functional studies of R2R3-MYB transcription factors in Populus species. In this study, we identified a total of 210 R2R3-MYB genes in the P. trichocarpa genome, of which 207 genes were unevenly distributed across all 19 chromosomes. These poplar R2R3-MYB genes were phylogenetically divided into 23 subgroups. Collinear analysis demonstrated that the poplar R2R3-MYB genes underwent rapid expansion and that whole-genome duplication events were a dominant factor in the process of rapid gene expansion. Subcellular localization assays indicated that poplar R2R3-MYB TFs mainly played a transcriptional regulatory role in the nucleus. Ten R2R3-MYB genes were cloned from P. deltoides × P. euramericana cv. Nanlin895, and their expression patterns were tissue-specific. A majority of the genes showed similar drought-responsive expression patterns in two out of three tissues. This study provides a valid cue for further functional characterization of drought-responsive R2R3-MYB genes in poplar and provides support for the development of new poplar genotypes with elevated drought tolerance.

Genome-wide characterization of R2R3-MYB gene family in Santalum album and their expression analysis under cold stress

Sandalwood (Santalum album) is a high-value multifunctional tree species that is rich in aromatic substances and is used in medicine and global cosmetics. Due to the scarcity of land resources in tropical and subtropical regions, land in temperate regions is a potential resource for the development of S. album plantations in order to meet the needs of S. album production and medicine. The R2R3-MYB transcription factor family is one of the largest in plants and plays an important role in the response to various abiotic stresses. However, the R2R3-MYB gene family of S. album has not been studied. In this study, 144 R2R3-MYB genes were successfully identified in the assembly genome sequence, and their characteristics and expression patterns were investigated under various durations of low temperature stress. According to the findings, 31 of the 114 R2R3-MYB genes showed significant differences in expression after cold treatment. Combining transcriptome and weighted gene co-expression network analysis (WGCNA) revealed three key candidate genes (SaMYB098, SaMYB015, and SaMYB068) to be significantly involved in the regulation of cold resistance in S. album. The structural characteristics, evolution, and expression pattern of the R2R3-MYB gene in S. album were systematically examined at the whole genome level for the first time in this study. It will provide important information for future research into the function of the R2R3-MYB genes and the mechanism of cold stress response in S. album.

Genome-wide analysis of MYB family in Nicotiana benthamiana and the functional role of the key members in resistance to Bemisia tabaci

MYB transcription factors (TFs) play a key role in plant resistance to abiotic and biotical stresses. However, little is currently known about their involvement in the plant defense to piercing-sucking insects. Here, we studied the MYB TFs that responded to and resisted Bemisia tabaci whitefly in the model plant Nicotiana benthamiana. Firstly, a total of 453 NbMYB TFs in N. benthamiana genome were identified and 182 R2R3-MYB TFs were analyzed for molecular characteristics, phylogenetic analysis, genetic structure, motif composition, and cis-elements. Then, six stress-related NbMYB genes were selected for further study. The expression pattern shows they were highly expressed in mature leaves and intensively induced upon whitefly attack. Combined with bioinformatic analysis, overexpression, β-Glucuronidase (GUS) assay, and virus-induced silencing tests, we determined the transcriptional regulation of these NbMYBs on the genes in lignin biosynthesis and SA-signaling pathways. Meanwhile, we tested the performance of whitefly on plants with increased or silenced NbMYB genes expression and found that NbMYB42, NbMYB107, NbMYB163, and NbMYB423 were resistant to whitefly. Our results contribute to a comprehensive understanding of the MYB TFs in N. benthamiana. Furthermore, our findings will facilitate further studies on the role of MYB TFs in the interaction between plants and piercing-sucking insects.

Identification and Phylogenetic Analysis of the R2R3-MYB Subfamily in Brassica napus

The R2R3-MYB sub-family proteins are composed of most members of MYB (v-Myb avian myeloblastosis viral oncogene homolog) protein, a plant-specific transcription factor (TF) that is classified into four classes depending on the number of MYB repeats. R2R3-MYB TFs are involved in physiological and biochemical processes. However, the functions of the Brassica napus R2R3-MYB genes are still mainly unknown. In this study, 35 Brassica napus MYB (BnaMYB) genes were screened in the genome of Brassica napus, and details about their physical and chemical characteristics, evolutionary relationships, chromosome locations, gene structures, three-dimensional protein structures, cis-acting promoter elements, and gene duplications were uncovered. The BnaMYB genes have undergone segmental duplications and positive selection pressure, according to evolutionary studies. The same subfamilies have similar intron-exon patterns and motifs, according to the genes' structure and conserved motifs. Additionally, through cis-element analysis, many drought-responsive and other stress-responsive cis-elements have been found in the promoter regions of the BnaMYB genes. The expression of the BnaMYB gene displays a variety of tissue-specific patterns. Ten lignin-related genes were chosen for drought treatment. Our research screened four genes that showed significant upregulation under drought stress, and thus may be important drought-responsive genes. The findings lay a new foundation for understanding the complex mechanisms of BnaMYB in multiple developmental stages and pathways related to drought stress in rapeseed.

Genome-Wide Identification Analysis of the R2R3-MYB Transcription Factor Family in Cymbidium sinense for Insights into Drought Stress Responses

Cymbidium sinense represents a distinctive Orchidaceae plant that is more tolerant than other terrestrial orchids. Studies have shown that many members of the MYB transcription factor (TF) family, especially the R2R3-MYB subfamily, are responsive to drought stress. This study identified 103 CsMYBs; phylogenetic analysis classified these genes into 22 subgroups with Arabidopsis thaliana. Structural analysis showed that most CsMYB genes contained the same motifs, three exons and two introns, and showed a helix-turn-helix 3D structure in each R repeat. However, the members of subgroup 22 contained only one exon and no intron. Collinear analysis revealed that C. sinense had more orthologous R2R3-MYB genes with wheat than A. thaliana and rice. Ka/Ks ratios indicated that most CsMYB genes were under purifying negative selection pressure. Cis-acting elements analysis revealed that drought-related elements were mainly focused on subgroups 4, 8, 18, 20, 21, and 22, and Mol015419 (S20) contained the most. The transcriptome analysis results showed that expression patterns of most CsMYB genes were upregulated in leaves in response to slight drought stress and downregulated in roots. Among them, members in S8 and S20 significantly responded to drought stress in C. sinense. In addition, S14 and S17 also participated in these responses, and nine genes were selected for the real-time reverse transcription quantitative PCR (RT-qPCR) experiment. The results were roughly consistent with the transcriptome. Our results, thus, provide an important contribution to understanding the role of CsMYBs in stress-related metabolic processes.

An Arabidopsis family GT106 glycosyltransferase is essential for xylan biosynthesis and secondary wall deposition

We have demonstrated that the Arabidopsis FRA9 (fragile fiber 9) gene is specifically expressed in secondary wall-forming cells and essential for the synthesis of the unique xylan reducing end sequence. Xylan is made of a linear chain of β-1,4-linked xylosyl (Xyl) residues that are often substituted with (methyl)glucuronic acid [(Me)GlcA] side chains and may be acetylated at O-2 and/or O-3. The reducing end of xylan from gymnosperms and dicots contains a unique tetrasaccharide sequence consisting of β-D-Xylp-(1 → 3)-α-L-Rhap-(1 → 2)-α-D-GalpA-(1 → 4)-D-Xylp, the synthesis of which requires four different glycosyltransferase activities. Genetic analysis in Arabidopsis thaliana has so far implicated three glycosyltransferase genes, FRA8 (fragile fiber 8), IRX8 (irregular xylem 8) and PARVUS, in the synthesis of this unique xylan reducing end sequence. Here, we report the essential role of FRA9, a member of glycosyltransferase family 106 (GT106), in the synthesis of this sequence. The expression of the FRA9 gene was shown to be induced by secondary wall master transcriptional regulators and specifically associated with secondary wall-forming cells, including xylem and fiber cells. T-DNA knockout mutation of the FRA9 gene caused impaired secondary cell wall thickening in leaf veins and a severe arrest of plant growth. RNA interference (RNAi) downregulation of FRA9 led to a significant reduction in secondary wall thickening of fibers, a deformation of xylem vessels and a decrease in xylan content. Structural analysis of xylanase-released xylooligomers revealed that RNAi downregulation of FRA9 resulted in a diminishment of the unique xylan reducing end sequence and complete methylation of xylan GlcA side chains, chemotypes reminiscent of those of the fra8, irx8 and parvus mutants. Furthermore, two FRA9 close homologs from Populus trichocarpa were found to be wood-associated functional orthologs of FRA9. Together, our findings uncover a member of the GT106 family as a new player involved in the synthesis of the unique reducing end sequence of xylan.