Tandemly duplicated MYB genes are functionally diverged in the regulation of anthocyanin biosynthesis in soybean

Gene duplications have long been recognized as a driving force in the evolution of genes, giving rise to novel functions. The soybean (Glycine max) genome is characterized by a large number of duplicated genes. However, the extent and mechanisms of functional divergence among these duplicated genes in soybean remain poorly understood. In this study, we revealed that 4 MYB genes (GmMYBA5, GmMYBA2, GmMYBA1, and Glyma.09g235000)-presumably generated by tandem duplication specifically in the Phaseoleae lineage-exhibited a stronger purifying selection in soybean compared to common bean (Phaseolus vulgaris). To gain insights into the diverse functions of these tandemly duplicated MYB genes in anthocyanin biosynthesis, we examined the expression, transcriptional activity, induced metabolites, and evolutionary history of these 4 MYB genes. Our data revealed that Glyma.09g235000 is a pseudogene, while the remaining 3 MYB genes exhibit strong transcriptional activation activity, promoting anthocyanin biosynthesis in different soybean tissues. GmMYBA5, GmMYBA2, and GmMYBA1 induced anthocyanin accumulation by upregulating the expression of anthocyanin pathway-related genes. Notably, GmMYBA5 showed a lower capacity for gene induction compared to GmMYBA2 and GmMYBA1. Metabolomics analysis further demonstrated that GmMYBA5 induced distinct anthocyanin accumulation in Nicotiana benthamiana leaves and soybean hairy roots compared to GmMYBA2 and GmMYBA1, suggesting their functional divergence leading to the accumulation of different metabolites accumulation following gene duplication. Together, our data provide evidence of functional divergence within the MYB gene cluster following tandem duplication, which sheds light on the potential evolutionary directions of gene duplications during legume evolution.

Identification and Expression Analysis of R2R3-MYB Transcription Factors Associated with Flavonoid Biosynthesis in Panax quinquefolius

Panax quinquefolius L. is an important medicinal plant, and flavonoids are among its main secondary metabolites. The R2R3-MYB transcription factor plays an irreplaceable role in plant growth, development, and secondary metabolism. In our study, we identified 159 R2R3-MYBs and analyzed their physical and chemical properties in P. quinquefolius. The protein length of 159 PqMYBs varied from 107 to 1050 amino acids. The molecular weight ranged from 12.21 to 116.44 kDa. The isoelectric point was between 4.57 and 10.34. We constructed a phylogenetic tree of P. quinquefolius and Arabidopsis thaliana R2R3-MYB family members, and PqMYB members were divided into 33 subgroups. Transcriptome data analysis showed that the expression patterns of PqMYBs in root, leaf, and flower were significantly different. Following the MeJA treatment of seedlings, five candidate PqMYB genes demonstrated a response. A correlation analysis of PqMYBs and candidate flavonoid pathway genes showed that PqMYB2, PqMYB46, and PqMYB72 had correlation coefficients that were higher than 0.8 with PqCHS, PqANS4, and PqCCoAMT10, respectively. Furthermore, a transient expression assay confirmed that the three PqMYBs were localized in the nucleus. We speculated that these three PqMYBs were related to flavonoid biosynthesis in P. quinquefolius. These results provided a theoretical basis and a new perspective for further understanding the R2R3-MYB gene family and the biosynthesis mechanism of secondary metabolites in P. quinquefolius.

Absence of long-term balancing selection on variation in EuMYB3, an R2R3-MYB gene responsible for the anther-color polymorphism in Erythronium umbilicatum

Balancing selection has been shown to be common in plants for several different types of traits, such as self-incompatibility and heterostyly. Generally, for these traits balancing selection is generated by interactions among individuals or between individuals and other species (e.g., pathogens or pollinators). However, there are phenotypic polymorphisms in plants that do not obviously involve types of interactions that generate balancing selection. Little is known about the extent to which balancing selection also acts to preserve these polymorphisms. Here we ask whether balancing selection preserves an anther-color polymorphism in Erythronium umbilicatum (Liliaceae). We identified a major gene underlying this polymorphism. We then attempted to detect signatures of balancing selection on that gene by developing a new coalescence test for balancing selection. We found that variation in anther color is in large part caused by variation in a paralog of EuMYB3, an anthocyanin-regulating R2R3-MYB transcription factor. However, we found little evidence for balancing selection having acted historically on EuMYB3. Our results thus suggest that plant polymorphisms, especially those not involved in interactions that are likely to generate negative frequency-dependent selection, may reflect a transient state in which one morph will eventually be fixed by either genetic drift or directional selection. Our results also suggest that regulation of the anthocyanin pathway is more evolutionarily labile than is generally believed.

Genome-wide identification of R2R3-MYB family genes and gene response to stress in ginger

Ginger (Zingiber officinale Roscoe) is an important plant used worldwide for medicine and food. The R2R3-MYB transcription factor (TF) family has essential roles in plant growth, development, and stresses resistance, and the number of genes in the family varies greatly among different types of plants. However, genome-wide discovery of ZoMYBs and gene responses to stresses have not been reported in ginger. Therefore, genome-wide analysis of R2R3-MYB genes in ginger was conducted in this study. Protein phylogenetic relations and conserved motifs and chromosome localization and duplication, structure, and cis-regulatory elements were analyzed. In addition, the expression patterns of selected genes were analyzed under two different stresses. A total of 299 candidate ZoMYB genes were discovered in ginger. Based on groupings of R2R3-MYB genes in the model plant Arabidopsis thaliana (L.) Heynh., ZoMYBs were divided into eight groups. Genes were distributed across 22 chromosomes at uneven densities. In gene duplication analysis, 120 segmental duplications were identified in the ginger genome. Gene expression patterns of 10 ZoMYBs in leaves of ginger under abscisic acid (ABA) and low-temperature stress treatments were different. The results will help to determine the exact roles of ZoMYBs in anti-stress responses in ginger.

The R2R3 MYB gene TaMYB305 positively regulates anther and pollen development in thermo-sensitive male-sterility wheat with Aegilops kotschyi cytoplasm

MAIN CONCLUSION

The loss of TaMYB305 function down-regulated the expression of jasmonic acid synthesis pathway genes, which may disturb the jasmonic acid synthesis, resulting in abnormal pollen development and reduced fertility. The MYB family, as one of the largest transcription factor families found in plants, regulates plant development, especially the development of anthers. Therefore, it is important to identify potential MYB transcription factors associated with pollen development and to study its role in pollen development. Here, the transcripts of an R2R3 MYB gene TaMYB305 from KTM3315A, a thermo-sensitive cytoplasmic male-sterility line with Aegilops kotschyi cytoplasm (K-TCMS) wheat, was isolated. Quantitative real-time PCR (qRT-PCR) and promoter activity analysis revealed that TaMYB305 was primarily expressed in anthers. The TaMYB305 protein was localized in the nucleus, as determined by subcellular localization analysis. Our data demonstrated that silencing of TaMYB305 was related to abnormal development of stamen, including anther indehiscence and pollen abortion in KAM3315A plants. In addition, TaMYB305-silenced plants exhibited alterations in the transcriptional levels of genes involved in the synthesis of jasmonic acid (JA), indicating that TaMYB305 may regulate the expression of genes related to JA synthesis and play an important role during anther and pollen development of KTM3315A. These results provide novel insight into the function and molecular mechanism of R2R3-MYB genes in pollen development.

Genome-wide identification of the Pyrus R2R3-MYB gene family and PhMYB62 regulation analysis in Pyrus hopeiensis flowers at low temperature

The R2R3-MYB gene family play an important role in plant growth, development and stress responses. In this study, a total of 122 PcoR2R3-MYB genes were identified and grouped into 26 clades in pear. And these PcoMYBs were unevenly distributed among 17 chromosomes. The sequence characteristics, conversed motifs, exon/intron structures, classification, duplication events and cis-acting elements were also investigated. The gene duplication events showed that segmental duplication may play key roles in expansion of the PcoMYB gene family. Pyrus hopeiensis, which is a valuable wild resource, has strong cold resistance. An integrative analyses of miRNA and mRNA showed that PhMYB62 was involved in regulating low-temperature stress in P. hopeiensis flower organs. Subcellular localization analysis showed that PhMYB62 protein was specifically localized to the nucleus. The result of DAP-seq showed that PhMYB62 responded to low-temperature stress in P. hopeiensis by regulating TFs, which were associated with plant stress resistance, and POD, GAUT12, AUX28 and CHS genes. Subsequently, yeast one-hybrid verified that PhMYB62 could bind and activate the promoter of POD gene. The current study would provide a comprehensive information for further functional research on the stress-responsive R2R3-MYB gene candidates in pear, and may help to identify the genes associated with cold resistance for the cultivation of cold-resistant pear varieties.

Genome-Wide Analysis of Cotton MYB Transcription Factors and the Functional Validation of GhMYB in Response to Drought Stress

MYB transcription factors play important roles during abiotic stress responses in plants. However, little is known about the accurate systematic analysis of MYB genes in the four cotton species, Gossypium hirsutum, G. barbadense, G. arboreum and G. raimondii. Herein, we performed phylogenetic analysis and showed that cotton MYBs and Arabidopsis MYBs were clustered in the same subfamilies for each species. The identified cotton MYBs were distributed unevenly on chromosomes in various densities for each species, wherein genome-wide tandem and segment duplications were the main driving force of MYB family expansion. Synteny analysis suggested that the abundant collinearity pairs of MYBs were identified between G. hirsutum and the other three species, and that they might have undergone strong purification selection. Characteristics of conserved motifs, along with their consensus sequence, promoter cis elements and gene structure, revealed that MYB proteins might be highly conserved in the same subgroups for each species. Subsequent analysis of differentially expressed genes and expression patterns indicated that most GhMYBs might be involved in response to drought (especially) and salt stress, which was supported by the expression levels of nine GhMYBs using real-time quantitative PCR. Finally, we performed a workflow that combined virus-induced gene silencing and the heterologous transformation of Arabidopsis, which confirmed the positive roles of GhMYBs under drought conditions, as validated by determining the drought-tolerant phenotypes, damage index and/or water loss rate. Collectively, our findings not only expand our understanding of the relationships between evolution and function of MYB genes, but they also provide candidate genes for cotton 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 of R2R3-MYB Family Genes and Their Response to Stress in Dendrobium nobile

BACKGROUND

R2R3-MYB genes comprise one of the largest and most important gene families in plants, and are involved in the regulation of plant growth and development as well as responses to abiotic stresses. However, the functions of R2R3-MYB genes in Dendrobium nobile remains largely unknown.

METHODS

Here, a comprehensive genome-wide analysis of D. nobile R2R3-MYB genes was performed, in which phylogenic relationships, gene structures, motif composition, chromosomal locations, collinearity analysis, and cis-acting elements were investigated. Moreover, the expression patterns of selected DnMYB genes were analyzed in various tissues and under different abiotic stresses.

RESULTS

In total, 125 DnMYB genes were identified in the D. nobile genome, and were subdivided into 26 groups based on phylogenetic analysis. Most genes in the same subgroup showed similar exon/intron structure and motif composition. All the DnMYB genes were mapped to 19 chromosomes with the co-linearity relationship. Reverse transcription-quantitative real-time PCR (RT-qPCR) results showed that 8 DnMYBs exhibited different expression patterns in different plant tissues, and were differentially expressed in response to abscisic acid, methyl jasmonate, low-temperature stress.

CONCLUSIONS

This work contributes to a comprehensive understanding of the R2R3-MYB gene family in D. nobile, and provides candidate genes for future research on abiotic stress in this plant.

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.

Identification of MYB gene family in medicinal tea tree Melaleuca alternifolia (Maiden and Betche) cheel and analysis of members regulating terpene biosynthesis

BACKGROUND

The tea tree (Melaleuca alternifolia) is renowned for its production of tea tree oil, an essential oil primarily composed of terpenes extracted from its shoot. MYB transcription factors, which are one of the largest TF families, play a crucial role in regulating primary and secondary metabolite synthesis. However, knowledge of the MYB gene family in M. alternifolia is limited.

METHODS AND RESULTS

Here, we conducted a comprehensive genome-wide analysis of MYB genes in M. alternifolia, referred to as MaMYBs, including phylogenetic relationships, structures, promoter regions, and GO annotations. Our findings classified 219 MaMYBs into four subfamilies: one 5R-MYB, four 3R-MYBs, sixty-one MYB-related, and the remaining 153 are all 2R-MYBs. Seven genes (MYB189, MYB146, MYB44, MYB29, MYB175, MYB162, and MYB160) were linked to terpenoid synthesis based on GO annotation. Phylogenetic analysis with Arabidopsis homologous MYB genes suggested that MYB193 and MYB163 may also be involved in terpenoid synthesis. Additionally, through correlation analysis of gene expression and metabolite content, we identified 42 MYB genes associated with metabolite content.

CONCLUSION

The results provide valuable insights into the importance of MYB transcription factors in essential oil production in M. alternifolia. These findings lay the groundwork for a better understanding of the MYB regulatory network and the development of novel strategies to enhance essential oil synthesis in M. alternifolia.

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.

The Characterization of R2R3-MYB Genes in Ammopiptanthus nanus Uncovers That the miR858-AnaMYB87 Module Mediates the Accumulation of Anthocyanin under Osmotic Stress

R2R3-MYB transcription factors (TFs) participate in the modulation of plant development, secondary metabolism, and responses to environmental stresses. Ammopiptanthus nanus, a leguminous dryland shrub, tolerates a high degree of environmental stress, including drought and low-temperature stress. The systematic identification, structural analysis, evolutionary analysis, and gene profiling of R2R3-MYB TFs under cold and osmotic stress in A. nanus were performed. Up to 137 R2R3-MYB TFs were identified and clustered into nine clades, with most A. nanus R2R3-MYB members belonging to clade VIII. Tandem and segmental duplication events drove the expansion of the A. nanus R2R3-MYB family. Expression profiling revealed that multiple R2R3-MYB genes significantly changed under osmotic and cold stress conditions. MiR858 and miR159 targeted 88 R2R3-MYB genes. AnaMYB87, an miR858-targeted clade VIII R2R3-MYB TF, was up-regulated under both osmotic and cold stress. A transient expression assay in apples showed that the overexpression of AnaMYB87 promoted anthocyanin accumulation. A luciferase reporter assay in tobacco demonstrated that AnaMYB87 positively affected the transactivation of the dihydroflavonol reductase gene, indicating that the miR858-MYB87 module mediates anthocyanin accumulation under osmotic stress by regulating the dihydroflavonol reductase gene in A. nanus. This study provides new data to understand the roles of R2R3-MYB in plant stress responses.

Identification of the MYB gene family in Sorghum bicolor and functional analysis of SbMYBAS1 in response to salt stress

Salt stress adversely affects plant growth and development. It is necessary to understand the underlying salt response mechanism to improve salt tolerance in plants. MYB transcription factors can regulate plant responses to salt stress. However, only a few studies have explored the role of MYB TFs in Sorghum bicolor (L.) Moench. So we decided to make a systematic analysis and research on the sorghum MYB family. A total of 210 MYB genes in sorghum were identified in this study. Furthermore, 210 MYB genes were distributed across ten chromosomes, named SbMYB1-SbMYB210. To study the phylogeny of the identified TFs, 210 MYB genes were divided into six subfamilies. We further demonstrated that SbMYB genes have evolved under strong purifying selection. SbMYBAS1 (SbMYB119) was chosen as the study object, which the expression decreased under salt stress conditions. Further study of the SbMYBAS1 showed that SbMYBAS1 is located in the nucleus. Under salt stress conditions, Arabidopsis plants overexpressed SbMYBAS1 showed significantly lower dry/fresh weight and chlorophyll content but significantly higher membrane permeability, MDA content, and Na+/K+ ratio than the wild-type Arabidopsis plants. Yeast two-hybrid screening result showed that SbMYBAS1 might interact with proteins encoded by SORBI_302G184600, SORBI_3009G247900 and SORBI_3004G59600. Results also showed that SbMYBAS1 could regulate the expression of AtGSTU17, AtGSTU16, AtP5CS2, AtUGT88A1, AtUGT85A2, AtOPR2 and AtPCR2 under salt stress conditions. This work laid a foundation for the study of the response mechanism of sorghum MYB gene family to salt stress.

MYB transcription factors and their roles in the male reproductive development of flowering plants

As one of the largest transcription factor families with complex functional differentiation in plants, the MYB transcription factors (MYB TFs) play important roles in the physiological and biochemical processes of plant growth and development. Male reproductive development, an essential part of sexual reproduction in flowering plants, is undoubtedly regulated by MYB TFs. In this review, we summarize the roles of the MYB TFs involved in the three stages of male reproductive development: pollen grains formation and maturation, filament elongation and anther dehiscence, and fertilization. Also, the potential downstream target genes and upstream regulators of these MYB TFs are discussed. Furthermore, we propose the underlying regulatory mechanisms of these MYB TFs: (1) A complex network of MYB TFs regulates various aspects of male reproductive development; (2) MYB homologous genes in different species may be functionally conserved or differentiated; (3) MYB TFs often form regulatory complexes with bHLH TFs.

Genome-wide identification of the longan R2R3-MYB gene family and its role in primary and lateral root

R2R3-MYB is an important transcription factor family that regulates plant growth and development. Root development directly affects the absorption of water and nutrients by plants. Therefore, to understand the regulatory role of R2R3-MYB transcription factor family in root development of longan, this study identified the R2R3-MYB gene family members at the genome-wide level, and analyzed their phylogenetic characteristics, physical and chemical properties, gene structure, chromosome location and tissue expression. The analysis identified 124 R2R3-MYB family members in the longan genome. Phylogenetic analysis divided these members into 22 subfamilies, and the members of the unified subfamily had similar motifs and gene structures. The result of qRT-PCR showed that expression levels of DlMYB33, DlMYB34, DlMYB59, and DlMYB77 were significantly higher in main roots than in lateral as opposed to those of DlMYB35, DlMYB69, DlMYB70, and DlMYB83, which were significantly lower. SapBase database prediction and miRNAs sequencing results showed that 34 longan miRNAs could cleave R2R3-MYB, including 17 novel miRNAs unique to longan. The qRT-PCR and subcellular localization experiments of DlMYB92 and DlMYB98 showed that DlMYB92 is a key factor that regulates transcription in the nucleus and participates in the regulation of longan lateral root development. Longan also has a conserved miRNA-MYB-lateral root development regulation mechanism. This study provides a reference for further research on the transcriptional regulation of the miRNA-R2R3-MYB module in the root development of longan.

MYB regulates the SUMO protease SENP1 and its novel interaction partner UXT, modulating MYB target genes and the SUMO landscape

SUMOylation is a post-translational modification frequently found on nuclear proteins, including transcription factors (TFs) and coactivators. By controlling the activity of several TFs, SUMOylation may have far-reaching effects. MYB is an example of a developmental TF subjected to SUMO-mediated regulation, through both SUMO conjugation and SUMO binding. How SUMO affects MYB target genes is unknown. Here, we explored the global effect of reduced SUMOylation of MYB on its downstream gene programs. RNA-Seq in K562 cells after MYB knockdown and rescue with mutants having an altered SUMO status revealed a number of differentially regulated genes and distinct gene ontology term enrichments. Clearly, the SUMO status of MYB both quantitatively and qualitatively affects its regulome. The transcriptome data further revealed that MYB upregulates the SUMO protease SENP1, a key enzyme that removes SUMO conjugation from SUMOylated proteins. Given this role of SENP1 in the MYB regulome, we expanded the analysis, mapped interaction partners of SENP1, and identified UXT as a novel player affecting the SUMO system by acting as a repressor of SENP1. MYB inhibits the expression of UXT suggesting that MYB is able not only to control a specific gene program directly but also indirectly by affecting the SUMO landscape through SENP1 and UXT. These findings suggest an autoactivation loop whereby MYB, through enhancing SENP1 and reducing UXT, is itself being activated by a reduced level of repressive SUMOylation. We propose that overexpressed MYB, seen in multiple cancers, may drive this autoactivation loop and contribute to oncogenic activation of MYB.

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 and expression analysis of MYB gene family in Cajanus cajan and CcMYB107 improves plant drought tolerance

MYB transcription factor (TF) is one of the largest superfamilies that play a vital role in multiple plant biological processes. However, the MYB family has not been comprehensively identified and functionally verified in Cajanus cajan, which is the sixth most important legume crop. Here, 170 CcR2R3-MYBs were identified and divided into 43 functional subgroups. Segmental and tandem duplications and alternative splicing events were found and promoted the expansion of the CcR2R3-MYB gene family. Functional prediction results showed that CcR2R3-MYBs were mainly involved in secondary metabolism, cell fate and identity, developmental processes, and responses to abiotic stress. Cis-acting element analysis of promoters revealed that stress response elements were widespread in the above four functional branches, further suggesting CcR2R3-MYBs were extensively involved in abiotic stress response. The transcriptome data and qRT-PCR results indicated that most of the CcR2R3-MYB genes responded to various stresses, of which the expression of CcMYB107 was significantly induced by drought stress. Overexpression of CcMYB107 enhanced antioxidant enzyme activity and increased proline and lignin accumulation, thus improving the drought resistance of C. cajan. Furthermore, Overexpression of CcMYB107 up-regulated the expression of stress-related genes and lignin biosynthesis genes after drought stress. Our findings established a strong foundation for the investigation of biological function of CcR2R3-MYB TFs in C. cajan.

An R2R3 MYB gene GhMYB3 functions in drought stress by negatively regulating stomata movement and ROS accumulation

MYB transcription factors are one of the largest TF families involved in plant growth and development as well as biotic and abiotic stresses. In this study, we report the identification and functional characterization of a stress-responsive MYB gene (GhMYB3) from drought stress related transcriptome of upland cotton. GhMYB3, belonging to the R2R3-type, has high sequence similarity with AtMYB3 and was localized in the nucleus. Silence of GhMYB3 enhanced the drought tolerance of cotton seedlings and plants, reduced the water loss rate, and enhanced stomatal closure. In addition, GhMYB3i lines exhibited less ROS accumulation, as well as higher antioxidant enzyme activity and increased content of anthocyanins and proanthocyanidins than WT plants after drought stress. The expression level of flavonoid biosynthesis- and stress-related genes were up-regulated in GhMYB3i lines under drought stress condition. These results demonstrated that GhMYB3 acted as a negative regulator in upland cotton response to drought stress by regulating stomatal closure and ROS accumulation.

Large-scale analysis of putative Euphorbiaceae R2R3-MYB transcription factors identifies a MYB involved in seed oil biosynthesis

BACKGROUND

MYB transcription factors are widely distributed in the plant kingdom and play key roles in regulatory networks governing plant metabolism and biochemical and physiological processes.

RESULTS

Here, we first determined the R2R3-MYB genes in five Euphorbiaceae genomes. The three Trp (W) residues from the first MYB domain (R2) were absolutely conserved, whereas the first W residue from the second MYB domain (R3) was preferentially mutated. The R2R3-MYBs were clustered into 48 functional subfamilies, of which 34 had both R2R3-MYBs of Euphorbiaceae species and AtMYBs, and four contained only Euphorbiaceae R2R3-MYBs. The whole-genome duplication (WGD) and/or segmental duplication (SD) played key roles in the expansion of the R2R3-MYB family. Unlike paralogous R2R3-MYB family members, orthologous R2R3-MYB members contained a higher selective pressure and were subject to a constrained evolutionary rate. VfMYB36 was specifically expressed in fruit, and its trend was consistent with the change in oil content, indicating that it might be involved in oil biosynthesis. Overexpression experiments showed that VfMYB36 could significantly provide linolenic acid (C18:3) content, which eventually led to a significant increase in oil content.

CONCLUSION

Our study first provides insight into understanding the evolution and expression of R2R3-MYBs in Euphorbiaceae species, and also provides a target for the production of biomass diesel and a convenient way for breeding germplasm resources with high linolenic acid content in the future.

Genome-Wide Analysis of MYB Transcription Factors and Screening of MYBs Involved in the Red Color Formation in Rhododendron delavayi

Flower color is one of the crucial traits of ornamental plants. Rhododendron delavayi Franch. is a famous ornamental plant species distributed in the mountain areas of Southwest China. This plant has red inflorescence and young branchlets. However, the molecular basis of the color formation of R. delavayi is unclear. In this study, 184 MYB genes were identified based on the released genome of R. delavayi. These genes included 78 1R-MYB, 101 R2R3-MYB, 4 3R-MYB, and 1 4R-MYB. The MYBs were divided into 35 subgroups using phylogenetic analysis of the MYBs of Arabidopsis thaliana. The members of the same subgroup in R. delavayi had similar conserved domains and motifs, gene structures, and promoter cis-acting elements, which indicate their relatively conserved function. In addition, transcriptome based on unique molecular identifier strategy and color difference of the spotted petals, unspotted petals, spotted throat, unspotted throat, and branchlet cortex were detected. Results showed significant differences in the expression levels of R2R3-MYB genes. Weighted co-expression network analysis between transcriptome and chromatic aberration values of five types of red samples showed that the MYBs were the most important TFs involved in the color formation, of which seven were R2R3-MYB, and three were 1R-MYB. Two R2R3-MYB (DUH019226.1 and DUH019400.1) had the highest connectivity in the whole regulation network, and they were identified as hub genes for red color formation. These two MYB hub genes provide references for the study of transcriptional regulation of the red color formation of R. delavayi.

Genome-wide identification and expression pattern analysis of R2R3-MYB transcription factor gene family involved in puerarin biosynthesis and response to hormone in Pueraria lobata var. thomsonii

BACKGROUND

R2R3-MYB transcription factors regulate secondary metabolism, stress responses and development in various plants. Puerarin is a bioactive ingredient and most abundant secondary metabolite isolated from Pueraria lobata. The biosynthesis of puerarin proceeds via the phenylpropanoid pathway and isoflavonoids pathway, in which 9 key enzymes are involved. The expression of these structural genes is under control of specific PtR2R3-MYB genes in different plant tissues. However, how PtR2R3-MYB genes regulates structural genes in puerarin biosynthesis remains elusive. This study mined the PtR2R3-MYB genes involved in puerarin biosynthesis and response to hormone in Pueraria lobata var. thomsonii.

RESULTS

A total of 209 PtR2R3-MYB proteins were identified, in which classified into 34 subgroups based on the phylogenetic topology and the classification of the R2R3-MYB superfamily in Arabidopsis thaliana. Furtherly physical and chemical characteristics, gene structure, and conserved motif analysis were also used to further analyze PtR2R3-MYBs. Combining puerarin content and RNA-seq data, speculated on the regulated puerarin biosynthesis of PtR2R3-MYB genes and structural genes, thus 21 PtR2R3-MYB genes and 25 structural genes were selected for validation gene expression and further explore its response to MeJA and GSH treatment by using qRT-PCR analysis technique. Correlation analysis and cis-acting element analysis revealed that 6 PtR2R3-MYB genes (PtMYB039, PtMYB057, PtMYB080, PtMYB109, PtMYB115 and PtMYB138) and 7 structural genes (PtHID2, PtHID9, PtIFS3, PtUGT069, PtUGT188, PtUGT286 and PtUGT297) were directly or indirectly regulation of puerarin biosynthesis in ZG11. It is worth noting that after MeJA and GSH treatment for 12-24 h, the expression changes of most candidate genes were consistent with the correlation of puerarin biosynthesis, which also shows that MeJA and GSH have the potential to mediate puerarin biosynthesis by regulating gene expression in ZG11.

CONCLUSIONS

Overall, this study provides a comprehensive understanding of the PtR2R3-MYB and will paves the way to reveal the transcriptional regulation of puerarin biosynthesis and response to phytohormone of PtR2R3-MYB genes in Pueraria lobata var. thomsonii.

Genome-wide identification and expression analysis of MYB gene family under nitrogen stress in Panax notoginseng

The myeloblastosis (MYB) gene family, involved in regulating many important physiological and biochemical processes, is one of the largest transcript factor superfamilies in plants. Since the identification of genome sequencing of Panax notoginseng has been completed, there was little known about the whole genome of its specific MYB gene family and the response to abiotic stresses, in consideration of the excessive application of nitrogen fertilizers in P. notoginseng. In this study, 123 PnMYB genes (MYB genes of P. notoginseng) have been identified and divided into 3 subfamilies by the phylogenetic analysis. These PnMYB genes were unevenly located on 12 chromosomes. Meanwhile, the gene structure and protein conserved domain were established by MEME Suite. The analysis of collinear relationships reflected that there were 121 homologous genes between P. notoginseng and Arabidopsis and 30 between P. notoginseng and rice. Moreover, cis-acting elements of PnMYB gene promoters were predicted which indicated that PnMYBs are involved in biotic, abiotic stress, and hormone induction. The expressions of PnMYB transcription factors in its roots, flowers, and leaves were detected by qRT-PCR and they had tissue-specific expressions and related to the growth of different tissues. Under nitrogen stress, MYB transcription factors had great feedback. Ten R2R3-MYB subfamily genes were significantly induced and indicated the possible function of protecting P. notoginseng from excess nitrogen. With further knowledge on identification of PnMYB gene related to tissue selectivity and abiotic stresses, this study laid the foundation for the functional development of PnMYB gene family and improved the cultivation of P. notoginseng.

Identification of MYB Transcription Factors Involving in Fruit Quality Regulation of Fragaria × ananassa Duch

The cultivated strawberry (Fragaria × ananassa Duch.) is an important horticultural crop. The economic values of strawberry cultivars are decided by their fruit qualities including taste, color and aroma. The important role of MYB transcription factors in fruit quality regulation is recognized increasingly with the identification of MYB genes involved in metabolism. A total of 407 MYB genes of F. × ananassa (FaMYBs) were identified in the genome-wide scale and named according to subgenome locations. The 407 FaMYBs were clustered into 36 groups based on phylogenetic analysis. According to synteny analysis, whole genome duplication and segmental duplication contributed over 90% of the expansion of the FaMYBs family. A total of 101 FaMYB loci with 1-6 alleles were identified by the homologous gene groups on homologous chromosomes. The differentially expressed FaMYB profiles of three cultivars with different fruit quality and fruit ripe processes provided the 8 candidate loci involved in fruit quality regulation. In this experiment, 7, 5, and 4 FaMYBs were screeded as candidate genes involved in the regulation of metabolism/transportation of anthocyanins, sugars or organic acids and 4-hydroxy-2, 5-dimethyl-3(2H)-furanone, respectively. These results pointed out the key FaMYBs for further functional analysis of gene regulation of strawberry fruit quality and would be helpful in the clarification on ofe roles of MYBs in the metabolism of fruit crops.

Genome-Wide Analysis of Specific PfR2R3-MYB Genes Related to Paulownia Witches' Broom

Paulownia witches' broom (PaWB), caused by phytoplasmas, is the most devastating infectious disease of Paulownia. R2R3-MYB transcription factors (TF) have been reported to be involved in the plant's response to infections caused by these pathogens, but a comprehensive study of the R2R3-MYB genes in Paulownia has not been reported. In this study, we identified 138 R2R3-MYB genes distributed on 20 chromosomes of Paulownia fortunei. These genes were classified into 27 subfamilies based on their gene structures and phylogenetic relationships, which indicated that they have various evolutionary relationships and have undergone rich segmental replication events. We determined the expression patterns of the 138 R2R3-MYB genes of P. fortunei by analyzing the RNA sequencing data and found that PfR2R3-MYB15 was significantly up-regulated in P. fortunei in response to phytoplasma infections. PfR2R3-MYB15 was cloned and overexpressed in Populus trichocarpa. The results show that its overexpression induced branching symptoms. Subsequently, the subcellular localization results showed that PfR2R3-MYB15 was located in the nucleus. Yeast two-hybrid and bimolecular fluorescence complementation experiments showed that PfR2R3-MYB15 interacted with PfTAB2. The analysis of the PfR2R3-MYB15 gene showed that it not only played an important role in plant branching, but also might participate in the biosynthesis of photosystem elements. Our results will provide a foundation for future studies of the R2R3-MYB TF family in Paulownia and other plants.

The R2R3-MYB gene CgMYB4 is involved in the regulation of cell differentiation and fiber development in the stamens of Chelone glabra L

A Plantaginaceae flowering plant, Chelone glabra, is different from Arabidopsis thaliana and cotton (Gossypium hirsutum), as it produces fibers on the anther surface. However, the evolutionary molecular mechanism of how fiber development is controlled in the stamen is unclear. MYB genes are essential transcription factors for trichome and fiber development in plants. In this study, we isolated 29 MYB domain-containing sequences using early-stage anthers and several sets of degenerated primers conserved in the R2R3 domain of the MYB transcription factor. Among them, CgMYB4 is an R2R3-MYB gene encoding 281 amino acids. Phylogenetic analysis showed that CgMYB4 is closely related to GhMYB25L/AmMIXTA, which controls fiber initiation and development in cotton and epidermal cell differentiation in the petals of Antirrhinum. Semiquantitative RT-PCR analysis showed that CgMYB4 is strongly expressed at the stamens and carpels. Overexpression of CgMYB4 significantly enhanced root hair formation in transformed hairy roots, contrary to the root hair numbers, which were reduced in silenced CgMYB4 hairy roots. Moreover, overexpression of CgMYB4 also evidently promoted fiber development at filaments and conical cell-like epidermal cell increases at the anther wall. Our results showed that CgMYB4 is an R2R3-MYB gene and is positively involved in regulating cell division and fiber differentiation in the early stages of stamen development in C. glabra.

Genome-wide analysis of R2R3-MYB transcription factors in Japanese morning glory

The R2R3-MYB transcription factor is one of the largest transcription factor families in plants. R2R3-MYBs play a variety of functions in plants, such as cell fate determination, organ and tissue differentiations, primary and secondary metabolisms, stress and defense responses and other physiological processes. The Japanese morning glory (Ipomoea nil) has been widely used as a model plant for flowering and morphological studies. In the present study, 127 R2R3-MYB genes were identified in the Japanese morning glory genome. Information, including gene structure, protein motif, chromosomal location and gene expression, were assigned to the InR2R3-MYBs. Phylogenetic tree analysis revealed that the 127 InR2R3-MYBs were classified into 29 subfamilies (C1-C29). Herein, physiological functions of the InR2R3-MYBs are discussed based on the functions of their Arabidopsis orthologues. InR2R3-MYBs in C9, C15, C16 or C28 may regulate cell division, flavonol biosynthesis, anthocyanin biosynthesis or response to abiotic stress, respectively. C16 harbors the known anthocyanin biosynthesis regulator, InMYB1 (INIL00g10723), and putative anthocyanin biosynthesis regulators, InMYB2 (INIL05g09650) and InMYB3 (INIL05g09651). In addition, INIL05g09649, INIL11g40874 and INIL11g40875 in C16 were suggested as novel anthocyanin biosynthesis regulators. We organized the R2R3-MYB transcription factors in the morning glory genome and assigned information to gene and protein structures and presuming their functions. Our study is expected to facilitate future research on R2R3-MYB transcription factors in Japanese morning glory.

Convergent loss of anthocyanin pigments is controlled by the same MYB gene in cereals

Loss of anthocyanin pigments is a common transition during cereal domestication, diversification, and improvement. However, the genetic basis for this convergent transition in cereal remains largely unknown. Here, we identified a chromosomal syntenic block across different species that contained R2R3-MYB genes (c1/pl1) responsible for the convergent decoloring of anthocyanins in cereals. Quantitative trait locus (QTL) mapping identified a major QTL for aerial root color corresponding to pl1 and a major QTL for spikelet color corresponding to c1 on maize chromosomes 6 and 9, respectively. One insertion in the regulatory region that led to transcriptional down-regulation was present in maize pl1, and several insertions in the coding region resulting in loss of function occurred in maize c1. A transposable element insertion in the third exon of c1, leading to three new non-functional transcripts, was responsible for decoloring in foxtail millet. The c1/pl1 genes enhanced the transcription of the core enzyme-encoding genes, including pr1, fht1, a1, a2, bz1, and aat1 in the anthocyanin pathway, while they repressed the expression of fnsii1 in flavones, sm2 in maysin, and bx3, bx4, bx5, and bx10 in DIMBOA. Our results indicated that the convergent decoloring of these plants shared the same genetic basis across different cereal species.

Comparative analysis of R2R3-MYB transcription factors in the flower of Iris laevigata identifies a novel gene regulating tobacco cold tolerance

Breeding for flower cold resistance is a priority for flower breeding research in northern China. The identification of cold resistance genes will not only provide genetic resources for cold resistance breeding, but also form a basis for the study of plant cold resistance mechanisms. Based on the flower transcriptome of Iris laevigata, 20 R2R3-MYBs were identified and comprehensive analysis, including conservative domain, phylogenetic analyses and functional distribution, were performed for R2R3-MYBs. Expression patterns of the abiotic stress genes under cold stress were detected, the upregulated gene was genetically transformed into tobacco, and the related physiological indicators of the transgenic tobacco were measured. A novel cold resistance gene, IlMYB306, was obtained. qRT-PCR indicated that IlMYB306 was dramatically induced by cold stress and was significantly upregulated in roots. The free proline content, MDA, SOD and POD activity of the transgenic tobacco improved after cold stress, and the chlorophyll content decreased slowly. In addition, overexpression of IlMYB306 improved cold resistance of the seeds. SEM results showed leaves of transgenic tobacco had obvious folds, more grooves and bulges on the lower leaf surface. Overall, we report a novel cold resistance R2R3-MYB gene, IlMYB306, in the flower of I. laevigata, which could improve tobacco cold stress tolerance by thickening the waxy layer, increasing antioxidant activity and the content of proline.

Conical petal epidermal cells, regulated by the MYB transcription factor MIXTA, have an ancient origin within the angiosperms

Conical epidermal cells occur on the tepals (perianth organs, typically petals and/or sepals) of the majority of animal-pollinated angiosperms, where they play both visual and tactile roles in pollinator attraction, providing grip to foraging insects, and enhancing colour, temperature, and hydrophobicity. To explore the evolutionary history of conical epidermal cells in angiosperms, we surveyed the tepal epidermis in representative species of the ANA-grade families, the early-diverging successive sister lineages to all other extant angiosperms, and analysed the function of a candidate regulator of cell outgrowth from Cabomba caroliniana (Nymphaeales). We identified conical cells in at least two genera from different families (Austrobaileya and Cabomba). A single SBG9 MYB gene was isolated from C. caroliniana and found to induce strong differentiation of cellular outgrowth, including conical cells, when ectopically expressed in Nicotiana tabacum. Ontogenetic analysis and quantitative reverse transcription-PCR established that CcSBG9A1 is spatially and temporally expressed in a profile which correlates with a role in conical cell development. We conclude that conical or subconical cells on perianth organs are ancient within the angiosperms and most probably develop using a common genetic programme initiated by a SBG9 MYB transcription factor.

Genome-Wide Identification and Analysis of the R2R3-MYB Gene Family in Theobroma cacao

The MYB gene family is involved in the regulation of plant growth, development and stress responses. In this paper, to identify Theobroma cacao R2R3-MYB (TcMYB) genes involved in environmental stress and phytohormones, we conducted a genome-wide analysis of the R2R3-MYB gene family in Theobroma cacao (cacao). A total of 116 TcMYB genes were identified, and they were divided into 23 subgroups according to the phylogenetic analysis. Meanwhile, the conserved motifs, gene structures and cis-acting elements of promoters were analyzed. Moreover, these TcMYB genes were distributed on 10 chromosomes. We conducted a synteny analysis to understand the evolution of the cacao R2R3-MYB gene family. A total of 37 gene pairs of TcMYB genes were identified through tandem or segmental duplication events. Additionally, we also predicted the subcellular localization and physicochemical properties. All the studies showed that TcMYB genes have multiple functions, including responding to environmental stresses. The results provide an understanding of R2R3-MYB in Theobroma cacao and lay the foundation for a further functional analysis of TcMYB genes in the growth of cacao.

The R2R3-MYB gene family in Cicer arietinum: genome-wide identification and expression analysis leads to functional characterization of proanthocyanidin biosynthesis regulators in the seed coat

We identified 119 typical CaMYB encoding genes and reveal the major components of the proanthocyanidin regulatory network. CaPARs emerged as promising targets for genetic engineering toward improved agronomic traits in C. arietinum. Chickpea (Cicer arietinum) is among the eight oldest crops and has two main types, i.e., desi and kabuli, whose most obvious difference is the color of their seeds. We show that this color difference is due to differences in proanthocyanidin content of seed coats. Using a targeted approach, we performed in silico analysis, metabolite profiling, molecular, genetic, and biochemical studies to decipher the transcriptional regulatory network involved in proanthocyanidin biosynthesis in the seed coat of C. arietinum. Based on the annotated C. arietinum reference genome sequence, we identified 119 typical CaMYB encoding genes, grouped in 32 distinct clades. Two CaR2R3-MYB transcription factors, named CaPAR1 and CaPAR2, clustering with known proanthocyanidin regulators (PARs) were identified and further analyzed. The expression of CaPAR genes correlated well with the expression of the key structural proanthocyanidin biosynthesis genes CaANR and CaLAR and with proanthocyanidin levels. Protein-protein interaction studies suggest the in vivo interaction of CaPAR1 and CaPAR2 with the bHLH-type transcription factor CaTT8. Co-transfection analyses using Arabidopsis thaliana protoplasts showed that the CaPAR proteins form a MBW complex with CaTT8 and CaTTG1, able to activate the promoters of CaANR and CaLAR in planta. Finally, transgenic expression of CaPARs in the proanthocyanidin-deficient A. thaliana mutant tt2-1 leads to complementation of the transparent testa phenotype. Taken together, our results reveal main components of the proanthocyanidin regulatory network in C. arietinum and suggest that CaPARs are relevant targets of genetic engineering toward improved agronomic traits.

Analyzing lignin biosynthesis pathways in rattan using improved co-expression networks of NACs and MYBs

BACKGROUND

The rattan is a valuable plant resource with multiple applications in tropical forests. Calamus simplicifolius and Daemonorops jenkinsiana are the two most representative rattan species, supplying over 95% of the raw materials for the rattan industry. Hence, the wood properties of both rattans have always attracted researchers' attention.

RESULTS

We re-annotated the genomes, obtained 81 RNA-Seq datasets, and developed an improved pipeline to increase the reliability of co-expression networks of both rattans. Based on the data and pipeline, co-expression relationships were detected in 11 NACs, 49 MYBs, and 86 lignin biosynthesis genes in C. simplicifolius and four NACs, 59 MYBs, and 76 lignin biosynthesis genes in D. jenkinsiana, respectively. Among these co-expression pairs, several genes had a close relationship to the development of wood properties. Additionally, we detected the enzyme gene on the lignin biosynthesis pathway was regulated by either NAC or MYB, while LACCASES was regulated by both NAC and MYB. For D. jenkinsiana, the lignin biosynthesis regulatory network was characterized by positive regulation, and MYB possible negatively regulate non-expressed lignin biosynthesis genes in stem tissues. For C. simplicifolius, NAC may positively regulate highly expressed genes and negatively regulate non-expressed lignin biosynthesis genes in stem tissues. Furthermore, we established core regulatory networks of NAC and MYB for both rattans.

CONCLUSIONS

This work improved the accuracy of rattan gene annotation by integrating an efficient co-expression network analysis pipeline, enhancing gene coverage and accuracy of the constructed network, and facilitating an understanding of co-expression relationships among NAC, MYB, and lignin biosynthesis genes in rattan and other plants.

Over-Expression of an R2R3 MYB Gene, MdMYB108L, Enhances Tolerance to Salt Stress in Transgenic Plants

Plants are affected by various abiotic stresses during their growth and development. In plants, MYB transcription factors are involved in various physiological and biochemical processes, including biotic and abiotic stress responses. In this study, we functionally analyzed MdMYB108L. We examined the transcriptional activity of MdMYB108L under salt stress and determined that the N-terminal domain of MdMYB108L, which was significantly induced under salt stress, has transcriptional activity. MdMYB108L overexpression increased the germination rate, main root length, and the antioxidant activity of catalase and peroxidase in transgenic Arabidopsisthaliana seeds, while reducing reactive oxygen species (ROS) accumulation. MdMYB108L overexpression also increased the photosynthetic capacity of hairy root tissue (leaves) under salt stress. In addition, the MdMYB108L transcription factor bound to the MdNHX1 promoter positively regulated the transcription of the salt tolerance gene MdNHX1 in apples, improving the salt stress tolerance of transgenic plants. These findings have implications for improving the agricultural yields of apple trees under salt stress.

MYB Transcription Factors Becoming Mainstream in Plant Roots

The function of the root system is crucial for plant survival, such as anchoring plants, absorbing nutrients and water from the soil, and adapting to stress. MYB transcription factors constitute one of the largest transcription factor families in plant genomes with structural and functional diversifications. Members of this superfamily in plant development and cell differentiation, specialized metabolism, and biotic and abiotic stress processes are widely recognized, but their roles in plant roots are still not well characterized. Recent advances in functional studies remind us that MYB genes may have potentially key roles in roots. In this review, the current knowledge about the functions of MYB genes in roots was summarized, including promoting cell differentiation, regulating cell division through cell cycle, response to biotic and abiotic stresses (e.g., drought, salt stress, nutrient stress, light, gravity, and fungi), and mediate phytohormone signals. MYB genes from the same subfamily tend to regulate similar biological processes in roots in redundant but precise ways. Given their increasing known functions and wide expression profiles in roots, MYB genes are proposed as key components of the gene regulatory networks associated with distinct biological processes in roots. Further functional studies of MYB genes will provide an important basis for root regulatory mechanisms, enabling a more inclusive green revolution and sustainable agriculture to face the constant changes in climate and environmental conditions.

MicroRNA828 negatively regulates lignin biosynthesis in stem of Populus tomentosa through MYB targets

Lignin biosynthesis in the sclerenchyma cells is strictly controlled by a complex network of genetic and environmental signals. In the last decades, the transcriptional regulation of lignin synthesis in woody species has been established. However, the role of microRNA-mediated post-transcriptional modulation in secondary cell wall biosynthesis remains poorly understood. Here, we identified a microRNA, miR828, involved in the regulation specific to lignin biosynthesis during stem development in Populus tomentosa Carr. miR828 is preferentially expressed in the secondary vascular tissues during stem development. Two MYB genes (MYB171 and MYB011) were validated as direct targets of miR828 by degradome analysis and green fluorescent protein signal detection. Overexpression of miR828 in poplar downregulated genes for lignin biosynthesis, resulting in reduced lignin content in cell walls. Conversely, suppression of miR828 in plants by the short tandem target mimics elevated the expression of lignin biosynthetic genes and increased lignin deposition. We further revealed that poplar MYB171, as the most abundant miR828 target in the stem, is a positive regulator for lignin biosynthesis. Transient expression assays showed that both MYB171 and MYB011 activated PAL1 and CCR2 transcription, whereas the introduction of miR828 significantly suppressed their expression that was induced by MYB171 or MYB011. Collectively, our results demonstrate that the miR828-MYBs module precisely regulates lignin biosynthesis during the stem development in P. tomentosa through transcriptional and post-transcriptional manners.

Genome-wide identification and expression analysis of the R2R3-MYB gene family in tobacco (Nicotiana tabacum L.)

BACKGROUND

The R2R3-MYB transcription factor is one of the largest gene families in plants and involved in the regulation of plant development, hormone signal transduction, biotic and abiotic stresses. Tobacco is one of the most important model plants. Therefore, it will be of great significance to investigate the R2R3-MYB gene family and their expression patterns under abiotic stress and senescence in tobacco.

RESULTS

A total of 174 R2R3-MYB genes were identified from tobacco (Nicotiana tabacum L.) genome and were divided into 24 subgroups based on phylogenetic analysis. Gene structure (exon/intron) and protein motifs were especially conserved among the NtR2R3-MYB genes, especially members within the same subgroup. The NtR2R3-MYB genes were distributed on 24 tobacco chromosomes. Analysis of gene duplication events obtained 3 pairs of tandem duplication genes and 62 pairs of segmental duplication genes, suggesting that segmental duplications is the major pattern for R2R3-MYB gene family expansion in tobacco. Cis-regulatory elements of the NtR2R3-MYB promoters were involved in cellular development, phytohormones, environmental stress and photoresponsive. Expression profile analysis showed that NtR2R3-MYB genes were widely expressed in different maturity tobacco leaves, and however, the expression patterns of different members appeared to be diverse. The qRT-PCR analysis of 15 NtR2R3-MYBs confirmed their differential expression under different abiotic stresses (cold, salt and drought), and notably, NtMYB46 was significantly up-regulated under three treatments.

CONCLUSIONS

In summary, a genome-wide identification, evolutionary and expression analysis of R2R3-MYB gene family in tobacco were conducted. Our results provided a solid foundation for further biological functional study of NtR2R3-MYB genes in tobacco.

Comprehensive analysis of 1R- and 2R-MYBs reveals novel genic and protein features, complex organisation, selective expansion and insights into evolutionary tendencies

Myeloblastosis (MYB) family, the largest plant transcription factor family, has been subcategorised based on the number and type of repeats in the MYB domain. In spite of several reports, evolution of MYB genes and repeats remains enigmatic. Brassicaceae members are endowed with complex genomes, including dysploidy because of its unique history with multiple rounds of polyploidisation, genomic fractionations and rearrangements. The present study is an attempt to gain insights into the complexities of MYB family diversity, understand impacts of genome evolution on gene families and develop an evolutionary framework to understand the origin of various subcategories of MYB gene family. We identified and analysed 1129 MYBs that included 1R-, 2R-, 3R- and atypical-MYBs across sixteen species representing protists, fungi, animals and plants and exclude MYB identified from Brassicaceae except Arabidopsis thaliana; in addition, a total of 1137 2R-MYB genes from six Brassicaceae species were also analysed. Comparative analysis revealed predominance of 1R-MYBs in protists, fungi, animals and lower plants. Phylogenetic reconstruction and analysis of selection pressure suggested ancestral nature of R1-type repeat containing 1R-MYBs that might have undergone intragenic duplication to form multi-repeat MYBs. Distinct differences in gene structure between 1R-MYB and 2R-MYBs were observed regarding intron number, the ratio of gene length to coding DNA sequence (CDS) length and the length of exons encoding the MYB domain. Conserved as well as novel and lineage-specific intron phases were identified. Analyses of physicochemical properties revealed drastic differences indicating functional diversification in MYBs. Phylogenetic reconstruction of 1R- and 2R-MYB genes revealed a shared structure-function relationship in clades which was supported when transcriptome data was analysed in silico. Comparative genomics to study distribution pattern and mapping of 2R-MYBs revealed congruency and greater degree of synteny and collinearity among closely related species. Micro-synteny analysis of genomic segments revealed high conservation of genes that are immediately flanking the surrounding tandemly organised 2R-MYBs along with instances of local duplication, reorganisations and genome fractionation. In summary, polyploidy, dysploidy, reshuffling and genome fractionation were found to cause loss or gain of 2R-MYB genes. The findings need to be supported with functional validation to understand gene structure-function relationship along the evolutionary lineage and adaptive strategies based on comparative functional genomics in plants.

Two R2R3-MYB genes cooperatively control trichome development and cuticular wax biosynthesis in Prunus persica

The fruit surface has an enormous impact on the external appearance and postharvest shelf-life of fruit. Here, we report two functionally redundant genes, PpMYB25 and PpMYB26, involved in regulation of fruit skin texture in peach. PpMYB25 can activate transcription of PpMYB26 and they both induce trichome development and cuticular wax accumulation, resulting in peach fruit with a fuzzy and dull appearance. By contrast, nonfunctional mutation of PpMYB25 caused by an insertional retrotransposon in the last exon in nectarine fails to activate transcription of PpMYB26, resulting in nectarine fruit with a smooth and shiny appearance due to loss of trichome initiation and decreased cuticular wax accumulation. Secondary cell wall biosynthesis in peach fruit pubescence is controlled by a transcriptional regulatory network, including the master regulator PpNAC43 and its downstream MYB transcription factors such as PpMYB42, PpMYB46 and PpMYB83. Our results show that PpMYB25 and PpMYB26 coordinately regulate fruit pubescence and cuticular wax accumulation and their simultaneous perturbation results in the origin of nectarine, which is botanically classified as a subspecies of peach.

Identification of Malus halliana R2R3-MYB gene family under iron deficiency stress and functional characteristics of MhR2R3-MYB4 in Arabidopsis thaliana

Iron (Fe) is an essential element for plant growth and development. Fe deficiency can trigger leaf chlorosis and reduce fruit yield. Therefore, it is necessary to explore transcription factors in response to Fe deficiency stress. A total of 29 MhR2R3-MYB transcription factors were identified based on the transcriptome of Malus halliana under Fe deficiency stress. A comprehensive analysis of physical and chemical properties, gene structures, conserved motif composition, evolutionary relationship and chromosome distribution was performed. Subsequently, based on the transcriptome, 14 genes with the most significant expression under Fe deficiency stress were screened for qRT-PCR verification. Among them,the functional characteristics of MhR2R3-MYB4 (MD05G1089600) were further studied in Arabidopsis thaliana. Expression of 13 out of these 14 genes was upregulated, only one was downregulated. Maximum upregulation of MhR2R3-MYB4 under Fe deficiency was 36.39-fold and 58.21-fold compared with day 0 in leaves and roots, respectively. Overexpression of MhR2R3-MYB4 enhanced tolerance to Fe deficiency in A. thaliana and led to multiple biochemical changes: transgenic lines have higher chl a, chl b and Fe²⁺ content, higher enzyme activity (SOD, POD, CAT and FCR) and lower chlorosis than the wild type in Fe deficiency conditions. We suggest that MhR2R3-MYB4 plays an important part in Fe deficiency stress, which may contribute to improve Fe deficiency tolerance of apple in future.

MYB gene family in the diatom Phaeodactylum tricornutum revealing their potential functions in the adaption to nitrogen deficiency and diurnal cycle

The MYB transcription factor (TF) family is one of the largest and most important TF families, regulating the growth and response of microalgae to stress. However, the gene structure and characteristics of Phaeodactylum tricornutum MYB TFs, and their functions under nitrogen deficiency, have not been explored yet. To identify all P. tricornutum MYB (PtMYB) genes, the MYB gene family was analyzed at the genome-wide level in this study. A total ofm26 PtMYB genes were identified from the genome of P. tricornutum. These PtMYB genes were divided into 5 subfamilies: 5R-MYB, 4R-MYB, R2R3-MYB, R1R2R3-MYB, and MYB-related proteins. Phylogenetical motif and gene structure analyses of MYB genes indicated that the number and proportion of MYB TFs were species-specific, and MYB genes exhibited a lot of duplication events from microalgae to higher plants. Furthermore, the differentially expressed patterns of all 26 PtMYB TFs implied that PtMYB genes might have functional specificity under nitrogen deficiency. Homology analysis of MYB genes revealed that PtMYB3, PtMYB15, and PtMYB21 might play important roles in the regulation of the diurnal cycle and response to nitrogen stress in P. tricornutum. PtMYB3, PtMYB15, and PtMYB21 genes might be used as potential candidate genes for further studying the regulatory mechanisms of P. tricornutum under nitrogen deficiency. This work provides an important foundation for the future research of the potential functions of PtMYB genes and its diurnal regulatory mechanisms under nitrogen deficiency.

[Identification and expression analysis of R2R3-MYB gene family in Andrographis paniculata]

The plant growth, development, and secondary metabolism are regulated by R2 R3-MYB transcription factors. This study identified the R2 R3-MYB genes in the genome of Andrographis paniculata and analyzed the chromosomal localization, gene structure, and conserved domains, phylogenetic relationship, and promoter cis-acting elements of these R2 R3-MYB genes. Moreover, the gene expression profiles of R2 R3-MYB genes under abiotic stress and hormone treatments were generated by RNA-seq and validated by qRT-PCR. The results showed that A. paniculata contained 73 R2 R3-MYB genes on 21 chromosomes. These members belonged to 34 subfamilies, 19 of which could be classified into the known subfamilies in Arabidopsis thaliana. The 73 R2 R3-MYB members included 36 acidic proteins and 37 basic proteins, with the lengths of 148-887 aa. The domains, motifs, and gene structures of R2 R3-MYBs in A. paniculata were conserved. The promoter regions of these genes contains a variety of cis-acting elements related to the responses to environmental factors and plant hormones including light, ABA, MeJA, and drought. Based on the similarity of functions of R2 R3-MYBs in the same subfamily and the transcription profiles, ApMYB13/21/35/67/73(S22) may regulate drought stress through ABA pathway; ApMYB20(S11) and ApMYB55(S2) may play a role in the response of A. paniculata to high temperature and UV-C stress; ApMYB5(S7) and ApMYB33(S20) may affect the accumulation of andrographolide by regulating the expression of key enzymes in the MEP pathway. This study provides theoretical reference for further research on the functions of R2 R3-MYB genes in A. paniculata and breeding of A. paniculata varieties with high andrographolide content.

Full-length transcriptomic identification of R2R3-MYB family genes related to secondary cell wall development in Cunninghamia lanceolata (Chinese fir)

BACKGROUND

R2R3-MYB is a class of transcription factor crucial in regulating secondary cell wall development during wood formation. The regulation of wood formation in gymnosperm has been understudied due to its large genome size. Using Single-Molecule Real-Time sequencing, we obtained full-length transcriptomic libraries from the developmental stem of Cunninghamia lanceolata, a perennial conifer known as Chinese fir. The R2R3-MYB of C. lanceolata (hereafter named as ClMYB) associated with secondary wall development were identified based on phylogenetic analysis, expression studies and functional study on transgenic line.

RESULTS

The evolutionary relationship of 52 ClMYBs with those from Arabidopsis thaliana, Eucalyptus grandis, Populus trichocarpa, Oryza sativa, two gymnosperm species, Pinus taeda, and Picea glauca were established by neighbour-joining phylogenetic analysis. A large number of ClMYBs resided in the woody-expanded subgroups that predominated with the members from woody dicots. In contrast, the woody-preferential subgroup strictly carrying the members of woody dicots contained only one candidate. The results suggest that the woody-expanded subgroup emerges before the gymnosperm/angiosperm split, while most of the woody-preferential subgroups are likely lineage-specific to woody dicots. Nine candidates shared the same subgroups with the A. thaliana orthologs, with known function in regulating secondary wall development. Gene expression analysis inferred that ClMYB1/2/3/4/5/26/27/49/51 might participate in secondary wall development, among which ClMYB1/2/5/26/27/49 were significantly upregulated in the highly lignified compression wood region, reinforcing their regulatory role associated with secondary wall development. ClMYB1 was experimentally proven a transcriptional activator that localised in the nucleus. The overexpression of ClMYB1 in Nicotiana benthamiana resulted in an increased lignin deposition in the stems. The members of subgroup S4, ClMYB3/4/5 shared the ERF-associated amphiphilic repression motif with AtMYB4, which is known to repress the metabolism of phenylpropanoid derived compounds. They also carried a core motif specific to gymnosperm lineage, suggesting divergence of the regulatory process compared to the angiosperms.

CONCLUSIONS

This work will enrich the collection of full-length gymnosperm-specific R2R3-MYBs related to stem development and contribute to understanding their evolutionary relationship with angiosperm species.

Systematic analysis of MYB gene family in Acer rubrum and functional characterization of ArMYB89 in regulating anthocyanin biosynthesis

The v-myb avian myeloblastosis viral oncogene homolog (MYB) family of transcription factors is extensively distributed across the plant kingdom. However, the functional significance of red maple (Acer rubrum) MYB transcription factors remains unclear. Our research identified 393 MYB transcription factors in the Acer rubrum genome, and these ArMYB members were unevenly distributed across 34 chromosomes. Among them, R2R3 was the primary MYB sub-class, which was further divided into 21 sub-groups with their Arabidopsis homologs. The evolution of the ArMYB family was also investigated, with the results revealing several R2R3-MYB sub-groups with expanded membership in woody species. Here, we report on the isolation and characterization of ArMYB89 in red maple. Quantitative real-time PCR analysis revealed that ArMYB89 expression was significantly up-regulated in red leaves in contrast to green leaves. Sub-cellular localization experiments indicated that ArMYB89 was localized in the nucleus. Further experiments revealed that ArMYB89 could interact with ArSGT1 in vitro and in vivo. Overexpression of ArMYB89 in tobacco enhances the anthocyanin content of transgenic plants. In conclusion, our results contribute to the elucidation of a theoretical basis for the ArMYB gene family, and provide a foundation for further characterization of the biological roles of MYB genes in the regulation of Acer rubrum leaf color.

Genome-wide analysis of MYB transcription factors and their responses to salt stress in Casuarina equisetifolia

BACKGROUND

MYB transcription factors are a kind of DNA binding protein that can specifically interact with the promoter region. Members of MYB TFs are widely involved in plant growth and development, secondary metabolism, stress response, and hormone signal transduction. However, there is no report of comprehensive bioinformatics analysis on the MYB family of Casuarina equisetifolia.

RESULTS

In this study, bioinformatics methods were used to screen out 182 MYB transcription factors from the Casuarina equisetifolia genome database, including 69 1R-MYB, 107 R2R3-MYB, 4 R1R2R3-MYB, and 2 4R-MYB. The C. equisetifolia R2R3-MYB genes were divided into 29 groups based on the phylogenetic topology and the classification of the MYB superfamily in Arabidopsis thaliana, while the remaining MYB genes (1R-MYB, R1R2R3-MYB, and 4R-MYB) was divided into 19 groups. Moreover, the conserved motif and gene structure analysis shown that the members of the CeqMYBs were divided into the same subgroups with mostly similar gene structures. In addition, many conserved amino acids in the R2 and R3 domains of CeqMYBs by WebLogo analysis, especially tryptophan residues (W), with 3 conserved W in R2 repeat and 2 conserved W in R3 repeat. Combining promoter and GO annotation analysis, speculated on the various biological functions of CeqMYBs, thus 32 MYB genes were selected to further explore its response to salt stress by using qPCR analysis technique. Most CeqMYB genes were differentially regulated following multiple salt treatments.

CONCLUSIONS

Seven genes (CeqMYB164, CeqMYB4, CeqMYB53, CeqMYB32, CeqMYB114, CeqMYB71 and CeqMYB177) were assigned to the "response to salt stress" by GO annotation. Among them, the expression level of CeqMYB4 was up-regulated under various salt treatments, indicating CeqMYB4 might participated in the response to salt stress. Our results provide important information for the biological function of C. equisetifolia, as well as offer candidate genes for further study of salt stress mechanism.

The R2R3-MYB gene PsMYB58 positively regulates anthocyanin biosynthesis in tree peony flowers

Tree peony (Paeonia suffruticosa Andr.) is a well-known ornamental flower in China with diverse colors. Flower color is one of the most important economic characteristics of tree peony and is mainly determined by anthocyanins. In this study, we cloned a PsMYB58 gene, which contained a 654 bp open reading frame (ORF), encoding a polypeptide of 218 amino acids. Sequence and phylogenetic analysis indicated that PsMYB58 is an anthocyanin regulatory R2R3-MYB gene. The transcription levels of PsMYB58 in different developmental stages of tree peony flowers were similar to those of the anthocyanin biosynthetic genes PsCHS, PsCHI, PsDFR, and PsANS. A bimolecular fluorescence complementation assay showed that PsMYB58 interacted with PsbHLH1 and PsbHLH3 in vivo. The overexpression of PsMYB58 in tobacco enhanced anthocyanin accumulation in various organs. Comparative transcriptome analysis showed that 943 genes were upregulated and 1203 downregulated in PsMYB58 transgenic tobacco, among which genes involved in the anthocyanin pathway were positively activated. Real-time quantitative PCR analysis verified that anthocyanin biosynthetic genes, including NtCHS, NtCHI, NtF3H, NtF3'H, NtDFR, and NtANS, and an anthocyanin regulatory bHLH gene, NtAN1b, were significantly upregulated in PsMYB58 transgenic tobacco. Our results indicated that PsMYB58 is a positive anthocyanin regulator in tree peony flowers. In summary, the functional identification of PsMYB58 furthers our understanding of the mechanism of peony flower color formation, thus providing a foundation for flower color improvement and molecular breeding.

R2R3-MYB genes control petal pigmentation patterning in Clarkia gracilis ssp. sonomensis (Onagraceae)

Petal pigmentation patterning is widespread in flowering plants. The genetics of these pattern elements has been of great interest for understanding the evolution of phenotypic diversification. Here, we investigate the genetic changes responsible for the evolution of an unpigmented petal element on a colored background. We used transcriptome analysis, gene expression assays, cosegregation in F₂ plants and functional tests to identify the gene(s) involved in petal coloration in Clarkia gracilis ssp. sonomensis. We identified an R2R3-MYB transcription factor (CgsMYB12) responsible for anthocyanin pigmentation of the basal region ('cup') in the petal of C. gracilis ssp. sonomensis. A functional mutation in CgsMYB12 creates a white cup on a pink petal background. Additionally, we found that two R2R3-MYB genes (CgsMYB6 and CgsMYB11) are also involved in petal background pigmentation. Each of these three R2R3-MYB genes exhibits a different spatiotemporal expression pattern. The functionality of these R2R3-MYB genes was confirmed through stable transformation of Arabidopsis. Distinct spatial patterns of R2R3-MYB expression have created the possibility that pigmentation in different sections of the petal can evolve independently. This finding suggests that recent gene duplication has been central to the evolution of petal pigmentation patterning in C. gracilis ssp. sonomensis.

A R2R3-MYB gene-based marker for the non-darkening seed coat trait in pinto and cranberry beans (Phaseolus vulgaris L.) derived from 'Wit-rood boontje'

KEY MESSAGE

The gene Phvul.010G130600 which codes for a MYB was shown to be tightly associated with seed coat darkening in Phaseolus vulgaris and a single nucleotide deletion in the allele in Wit-rood disrupts a transcription activation region that likely prevents its functioning in this non-darkening genotype. The beige and white background colors of the seed coats of conventional pinto and cranberry beans turn brown through a process known as postharvest darkening (PHD). Seed coat PHD is attributed to proanthocyanidin accumulation and its subsequent oxidation in the seed coat. The J gene is an uncharacterized classical genetic locus known to be responsible for PHD in common bean (P. vulgaris) and individuals that are homozygous for its recessive allele have a non-darkening (ND) seed coat phenotype. A previous study identified a major colorimetrically determined QTL for seed coat color on chromosome 10 that was associated with the ND trait. The objectives of this study were to identify a gene associated with seed coat postharvest darkening in common bean and understand its function in promoting seed coat darkening. Amplicon sequencing of 21 candidate genes underlying the QTL associated with the ND trait revealed a single nucleotide deletion (c.703delG) in the candidate gene Phvul.010G130600 in non-darkening recombinant inbred lines derived from crosses between ND 'Wit-rood boontje' and a regular darkening pinto genotype. In silico analysis indicated that Phvul.010G130600 encodes a protein with strong amino acid sequence identity (70%) with a R2R3-MYB-type transcription factor MtPAR, which has been shown to regulate proanthocyanidin biosynthesis in Medicago truncatula seed coat tissue. The deletion in the 'Wit-rood boontje' allele of Phvul.010G130600 likely causes a translational frame shift that disrupts the function of a transcriptional activation domain contained in the C-terminus of the R2R3-MYB. A gene-based dominant marker was developed for the dominant allele of Phvul.010G130600 which can be used for marker-assisted selection of ND beans.