Skip to main content
Download PDF

Genome-wide analysis of MYB transcription factor family and AsMYB1R subfamily contribution to ROS homeostasis regulation in Avena sativa under PEG-induced drought stress

BMC Plant Biology volume 24, Article number: 632 (2024) Cite this article

Abstract

Background

The myeloblastosis (MYB) transcription factor (TF) family is one of the largest and most important TF families in plants, playing an important role in a life cycle and abiotic stress.

Results

In this study, 268 Avena sativa MYB (AsMYB) TFs from Avena sativa were identified and named according to their order of location on the chromosomes, respectively. Phylogenetic analysis of the AsMYB and Arabidopsis MYB proteins were performed to determine their homology, the AsMYB1R proteins were classified into 5 subgroups, and the AsMYB2R proteins were classified into 34 subgroups. The conserved domains and gene structure were highly conserved among the subgroups. Eight differentially expressed AsMYB genes were screened in the transcriptome of transcriptional data and validated through RT-qPCR. Three genes in AsMYB2R subgroup, which are related to the shortened growth period, stomatal closure, and nutrient and water transport by PEG-induced drought stress, were investigated in more details. The AsMYB1R subgroup genes LHY and REV 1, together with GST, regulate ROS homeostasis to ensure ROS signal transduction and scavenge excess ROS to avoid oxidative damage.

Conclusion

The results of this study confirmed that the AsMYB TFs family is involved in the homeostatic regulation of ROS under drought stress. This lays the foundation for further investigating the involvement of the AsMYB TFs family in regulating A. sativa drought response mechanisms.

Peer Review reports

Background

Over the last decade, intensified climate change has seriously impacted profitability of agricultural production systems severely impacting crops growth and yields. One of the major constraints is a drought stress that cause crop yields to decrease by 50–70% [1]. Drought stress affects growth and development of plants by reducing water availability. The most significant manifestations of this process are reduced leaf water potential and associated stomatal closure; reduced photosynthesis leading to an imbalance in the source-sink relationship; and increased production of reactive oxygen species (ROS), leading to membrane ester peroxidation and electrolyte leakage. All these processes further disturb plant’s osmotic balance, eventually leading (in severe cases) to plant death [2]. Plants adapt to drought stress by employing a broad range of anatomical (e.g. leaf shape and angle; root system architecture; shoot pubescence and glaucousness) and physiological traits. One of the critical traits in the latter groups is efficient osmotic adjustment that can be achieved by combination of enhanced uptake of inorganic ions (K+, Na+, Cl-) [2] and de novo synthesis of organic osmolytes (proline, soluble sugars, alcohols, betaines, etc.) [3]. Plants also synthesize ABA to close stomata and reduce water loss [4] as well as control water loss by adjusting stomatal density [5]. In addition, plants regulate ROS homeostasis by synthesizing antioxidant enzymes and antioxidants to scavenge ROS [6]. All above processes are controlled at both transcriptional and post-translational levels and rely heavily on numerous transcriptional factors (TFs). Among major classes of TFs are MYB, APETALA2/ethylene-responsive element binding protein (AP2/EREBP), basic helix-loop-helix (bHLH), basic region/leucine zipper motif (bZIP), NAM, ATAF1, ATAF2 and CUC2 (NAC), WRKYGQK sequence (WRKY) and zinc finger protein (ZFP) [7].

Avena sativa (A. sativa) is an allohexaploid crop (AACCDD, 2n = 6x = 42) of the family Poaceae in the genus Avena, which ranks sixth in world cereal production [8]. A. sativa is an important grain and forage grass, functionally classified as a food rich in soluble fiber, β-glucan, lipid, protein, and antioxidants [8,9,10] A. sativa also possesses good adaptability to various soil environments [10, 11]. Although A. sativa has relatively high abiotic stress tolerance, it is usually grown in areas where other crops cannot cope with climate extremes [12], and therefore, its yield is affected by environmental stress. Therefore, more strategies are needed to improve the stress resistance of A. sativa, especially drought resistance, because most areas where A. sativa is grown are prone to severe drought stress [12, 13]. Therefore, studying the molecular mechanisms of drought tolerance in A. sativa is particularly important for breeding programs and coping with future climate environments.

Under drought stress, oats synthesize ABA to reduce stomatal conductance and close stomata to reduce water loss [14]. This comes with some penalties such as reduced photosynthetic efficiency, reduce nutrient consumption, reduction in growth rate, shortened life cycle and accelerated aging [13]. Oats also synthesize organic compounds such as proline and glycine betaine (GB) to osmotically adjust to drought conditions [15]; this process, however, comes with high carbon cost and also on expense of growth [16]. However, little is known about the regulation of these pathways by TFs.

The recently reported high-quality genome and annotation data of A. sativa allohexaploid provide important references for the study of TFs [9, 17]. Of a specific interest are MYB TFs, as MYB genes play important roles in cell cycle, metabolism, abiotic stress response [18,19,20,21,22]. MYB TFs possess highly conserved MYB DNA binding domain at N-terminal, which typically consists of one to four imperfect tandem repeats (R). The repeats consist of 51–53 amino acid residues that form a helix-turn-helix (HTH) structure that interacts with target DNA [23]. In addition, this conserved structure of repeats comprises regularly interval triplet tryptophan residues, which aggregate to form a hydrophobic core. The repeats of MYB DNA binding domain are named as R1, R2, and R3 based on the similarity to Myb-c protein [24]. The MYB genes can be classified into four categories according to the number of MYB repeat and the characteristic of MYB sequences, including MYB-related (MYB1R), R2R3-MYB (MYB2R), R1R2R3-MYB (MYB3R), and atypical MYB (MYB4R) [25]. The MYB genes have been systematically studied in Arabidopsis thaliana [25], Diospyros oleifera [26], and Melastoma candidum [27].

As commented above, drought tolerance traits are closely associated with plant’s ability to maintain redox balance and prevent oxidative stress damage. Drought stress leads to overaccumulation of various types of ROS in plant cells, such as superoxide (O2-), hydrogen peroxide (H2O2), singlet oxygen (1O2), and hydroxyl radicals (OH∙) [28], causing damage to cellular components (proteins, nucleic acids, and lipids) and triggering programmed cell death. Plant scavenge ROS through the synergistic action of enzymatic and non-enzymatic antioxidant mechanisms. The enzymatic antioxidants include superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), and ascorbate peroxidase (APX). Non-enzymatic antioxidants include β-carotene, α-tocopherol, ascorbic acid, glutathione, anthocyanins, and flavonoids [2, 29, 30]. Importantly, ROS plays a double-edged sword role, acting as a signaling molecule in mild abiotic stress signal transduction [31, 32] and causing oxidative stress to key macromolecules under more severe conditions.

It was shown that expression of CIRCADIAN CLOCK ASSOCIATED (CCA1) gene was closely related to redox regulation, and mutations in the core clock regulatory factor CCA1 have been shown to affect ROS homeostasis and the transcriptionally regulated expression of tolerance to oxidative stress of ROS responsive ROS-responsive genes [18]. It was suggested that CCA1 is the main regulator of ROS homeostasis, and ROS functions as an input signal that affects the transcriptional output of the clock. CCA1 belongs to REV family, alongside with some other proteins related to the biological clock such as LATE ELONGATED HYPOCOTYL (LHY), and 9 REVEILLE (RVE) genes. This family consists of two subgroups: the first subgroup includes CCA1, LHY, RVE 1, 2, 7, and RVE 7-like, and the second subgroup includes RVE 3, 4, 5, 6, and 8 [33], with all proteins having a single highly conserved MYB/SANT domain.

Herein, 268 members of AsMYB TFs were identified based on the genome and annotation data of A. sativa. Further, comprehensive bioinformatic analysis was performed in terms of chromosome location, phylogenetic analysis, conserved domain, gene structure, and gene duplication of the AsMYB genes. The expression levels of 8 AsMYB genes in A. sativa roots under PEG-induced drought stress at different time points were analyzed based on transcriptome data and RT-qPCR, with consistent results between two data sets. Three genes in AsMYB2R subgroup, which are related to the shortened growth period, stomatal closure, and nutrient and water transport by PEG-induced drought stress, were investigated in more details. These findings demonstrate that circadian clock key genes LHY and RVE1 of the AsMYB1R subfamily, along with non-enzymatic antioxidant GST genes, jointly regulate ROS homeostasis in A. sativa plants.

Results

Identification of MYB TFs and physicochemical properties in A. sativa

AsMYB genes were initially screened by aligning the HMM and alignment file of MYB (PF00249) against the protein data using HMMER software. Subsequently, CD-HIT software, NCBI-CDD, and SMART database were successively used to obtain 268 AsMYB TFs which removed redundant sequences and possessed complete MYB structure. Based on the number and characteristics of MYB DNA binding repeats, the AsMYB genes were classified into three categories: 112 AsMYB1R TFs, 151 AsMYB2R TFs, and 5 AsMYB3R TFs. Since R1, R2, and R3 are different in amino acid structure and R2 and R3 are highly conservative, the conserved region of AsMYB2R proteins was aligned and visualized, as shown in Fig. 1. The characteristic sequence of R2 domain was [-W-(X19)-W-(X19)-W-], and R3 domain was [-F/I/L/W-(X18)-W-(X18)-W-]. Highly conservative structure of R2 and R3 were consistent with previous reports in A. thaliana, which proved the accuracy of AsMYB2R genes. It was notability that the first tryptophan (W) residue of the R3 repeat was replaced by Leucine (L), Isoleucine (I), or Phenylalanine (F) residues, which was a common phenomenon in plant R2R3-MYBs [34]. Hydrophobic residues of L, I, and F have proved that they can substitute for W and maintain the function of the MYB domain, at least in terms of DNA binding, which has been proved in animals [35]. The multiple sequence alignment plot of AsMYB2R proteins showed that they are highly conserved (Fig. 1) and similar to other species such as Hibiscus cannabinus [36], Linum usitatissimum [37], and Pyrus bretschneideri [38], indicating the conserved nature of MYB genes during the evolution of the plant lineage. The physicochemical properties of AsMYB proteins are shown in Table S2. The size of AsMYB proteins ranges from 126 to 1942 amino acids, with a predicted molecular weight ranging from 13.87 to 208.67 KDa. Since only 6 AsMYB proteins have a protein size of more than 1000 amino acids, the average molecular weight was 40.33 KDa. The predicted isoelectric point (pI) ranges from 4.51 to 11.69, with an average pI of 7.06. Surprisingly, only circa 41.4% of AsMYB proteins translated basic proteins. Only 9 AsMYB proteins were predicted to belong to stable proteins (instability index less than 40), indicating that the AsMYB proteins as a whole was in an unstable state and the proteins were easily degraded. The grand average of hydropathicity of AsMYB proteins was less than 0 (-1.155 to -0.154) except AsMYB1R035 protein (0.065), which indicated that almost all of AsMYB proteins were hydrophilic. By using the WOLF PSORT online tool, subcellular localization analysis showed that the majority of the AsMYB genes were predicted in the nucleus, with a small set of them were predicted to localize in other subcellular locations, such as chloroplast, cytoplasm, and mitochondrion (Table S2).

Fig. 1
figure 1

The conserved amino acid sequences logo of AsMYB2R proteins. (A) The sequence logo of the R2 conserved domain includes three conserved tryptophan residues. (B) The sequence logo of the R3 conserved domain. The typically conserved tryptophan amino acid sites were labeled by black *, and red * represents the substituted amino acid site in the R3 domain. (C) The detail information of AsMYB1R TFs conserved motifs includes E-value, site and width. (D) The detail information of AsMYB2R TFs conserved motifs includes E-value, site and width

Full size image

Chromosome localization and phylogenetic tree construction in A. sativa

AsMYB genes localization plot was mapped according to the annotation data of A. sativa. AsMYB genes of three categories were named according to their order of location on the chromosomes, respectively. Genes that were not assembled onto the chromosome were defined as ChrUn [39]. In AsMYB genes localization plot (Fig. 2), AsMYB1R TFs were named as AsMYB1R001-AsMYB1R112, with six genes located on ChrUn. AsMYB2R TFs were named as AsMYB2R001-AsMYB2R151, and AsMYB3R TFs were named as AsMYB3R001-AsMYB3R005. Particular chromosomes were found; of these, Chr1C had the lowest gene density and Chr4D had the highest gene density, AsMYB TFs were unevenly distributed in each chromosome [40]. The detailed information on the number of AsMYB genes in different chromosomes is shown in Table S3. The result indicated that the AsMYB TFs underwent duplication events (Fig. S1). Since 98.13% AsMYB TFs were made up of AsMYB1R TFs and AsMYB2R TFs, the Neighbor-Joining phylogenetic trees were constructed using MEGA software, respectively. As shown in Figs. 3A and 112 AsMYB1R proteins and 59 AtMYB1R proteins were aligned, and phylogenetic tree of MYB-related revealed 5 subgroups (CCK1-like, CPC-like, TBP-like, I-box-binding-like, and R-R), of which TBP-like and I-box-binding-like in A. sativa contracted more than double. Similar to A. thaliana, the CCK1-like subgroup has the most members of 22 AsMYB1R TFs, and the I-box-binding-like subgroup has the least members of 1 AsMYB1R TFs. The phylogenetic tree of AsMYB2R proteins was shown in Fig. 3B, which contained 151 AsMYB2R proteins and 126 AtMYB2R proteins. In Figs. 3B and 34 subgroups were divided and the amount of AsMYB2R genes were varied in each subgroup (the number from 1 to 17). The distribution of A. sativa and A. thaliana for the same subgroups was also greatly different. Five subgroups (S4, S8, S11, S16, and S33) of A. sativa expanded more than two-fold, while S3 of A. sativa contracted more than twice. In addition, the subgroups included the member of A. thaliana (S5, S9, S14, S15, and S30) and the member of A. sativa (S23 and S34). This implied ancestral gene duplication and loss events [41]. More information is available from Table S4.

Fig. 2
figure 2

Distribution of AsMYB TFs on A. sativa chromosomes. The chromosomal position of each AsMYB TFs was mapped to the A. sativa genome. ChrUn represents genes that have failed to assemble onto the chromosomes

Full size image
Fig. 3
figure 3

The phylogenetic tree plots of AtMYB and AsMYB TFs. (A) The phylogenetic tree plot of AsMYB1R and AtMYB1R TFs. The AsMYB1R TFs are divided into 5 subgroups (CCK1-like, CPC-like, TBP-like, I-box-binding-like, and R-R). (B) The phylogenetic tree plot of AsMYB2R and AtMYB2R TFs. The AsMYB2R TFs are divided into 34 subgroups (S1-S34). Yellow and green dots represent AtMYB TFs and AsMYB TFs, respectively

Full size image

Conserved motif, gene structure, and cis-acting in A. sativa

To further understand the diversity of AsMYB1R and AsMYB2R TFs, the conserved motifs were analyzed by using the MEME online program, and ten conserved motifs were investigated. The motif and structure plots of AsMYB genes are shown in Fig. 4. For AsMYB1R genes (Fig. 4A), the number of conserved motifs varied greatly among subgroups (from 1 to 6), the subgroups (I-box-binding-like and R-R) constituted motifs 1, 2, and 6 in common. CCK1-like subgroup constituted of motifs 1 and 2, which indicate that the members in the same subgroups have a similar function. The motif and structure plot of AsMYB2R genes (Fig. 4B) showed more motifs than AsMYB1R genes, and all numbers of AsMYB2R genes have more than three motifs besides AsMYB2R094. The gene structure analysis showed some incomplete UTRs or too-long regions of some genes, which may be caused by genome assembly. The cis-acting elements of AsMYB genes were analysed (Fig S2), 24 cis-elements mainly related to auxin response, abscisic acid response, gibberellin response, and light response were identified.

Fig. 4
figure 4

Conserved motif, gene structure, and phylogenetic tree plots of AsMYB TFs. (A) The plot of AsMYB1R TFs; (B) The plot of AsMYB2R TFs. Conserved motifs are highlighted with different colored backgrounds and numbers, and their position in each MYB sequence was determined. The CDS, UTR and Myb DNA-binding site were mapped on the genes and indicated by different colors, respectively

Full size image

Gene duplication and collinearity information in A. sativa

Gene duplication is a common phenomenon in the process of plant evolution that played an important role in the gene expansion [42]. Here, the duplication event plots of the AsMYB1R TFs, AsMYB2R TFs, and AsMYB3R TFs were identified by MCScanx methods to determine the gene duplication events, respectively. The gene segmental duplication event could serve as an important access for plants to acquire new genes and contribute to the gene family expansion as well. As shown in Fig. 5, a total of 91 AsMYB1R genes were identified to form 192 segmental duplication pairs. The ends of 61 gene pairs were comprised by AsMYB1R genes, where 12 gene pairs were connected by AsMYB1R and AsMYB2R genes, residual gene pairs were one end being AsMYB1R genes, and the other joined the gene of non-AsMYB genes. The gene duplication events of 129 AsMYB2R genes are shown in Fig. 6. In addition, 308 gene pairs were discovered, where 167 gene pairs consisted of AsMYB2R genes, the ends of the 12 gene pairs are AsMYB1R and AsMYB2R genes, and the ends of 2 gene pairs are AsMYB2R and AsMYB3R genes. Furthermore, Fig. 7 shows 11 segmental duplication pairs formed by 5 AsMYB3R genes belonging to AsMYB3R TFs, including 1 gene pair for AsMYB3R genes, and 2 gene pairs comprised of AsMYB2R and AsMYB3R genes. At the same time, the Ka/Ks values of all gene pairs were less than 1, indicating that AsMYB genes in A. sativa underwent purify selection during evolution [43]. More information is given in Table S5.

Fig. 5
figure 5

Gene duplication plots of AsMYB1R TFs. The gray line represents all duplication events in A. sativa genome, the yellow line represents the AsMYB1R TFs duplication events, and the heat map represents the gene density in A. sativa genome

Full size image
Fig. 6
figure 6

Gene duplication plots of AsMYB2R TFs. The gray line represents all duplication events in A. sativa genome, the red line represents the AsMYB2R TFs duplication events, and the heat map represents the gene density in A. sativa genome

Full size image
Fig. 7
figure 7

Gene duplication plots of AsMYB3R TFs. The gray line represents all duplication events in A. sativa genome, the blue line represents the AsMYB3R TFs duplication events, and the heat map represents the gene density in A. sativa genome

Full size image

Expression of AsMYB TFs under drought stress in A. sativa

There is always an association between gene expression patterns and function, and how AsMYB genes can regulate gene expression when plants suffer from environmental changes. To explore AsMYB genes related to drought response, transcriptional abundance of AsMYB genes under drought stress was studied using transcriptome data (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1056521/). During the growth and development of roots under drought conditions, the data of 44 AsMYB genes was not detected in all treatment groups, and there was no significant difference in the expression pattern of the other 216 AsMYB genes. Finally, eight differentially expressed AsMYB genes (DEGs) were detected. This included five AsMYB1R TFs (AsMYB1R022, AsMYB1R078, AsMYB1R079, AsMYB1R088, and AsMYB1R098) and three AsMYB2R TFs (AsMYB2R039, AsMYB2R043, and AsMYB2R045). Figure 8 shows the expression levels of 268 AsMYB genes transcriptome data. The expression patterns of different AsMYB1R genes, AsMYB2R and AsMYB3R genes show significant differences at all time stages (Fig. 8A and B). The 8 DEGs of AsMYB genes were extracted to display detailed transcriptome abundance information. As shown in Fig. 8C, AsMYB2R and AsMYB1R genes exhibit differential gene expression patterns at different time points of PEG treatment. For AsMYB2R genes, the AsMYB2R039 was only upregulated in the middle stage (24 h) of drought stress treatment, while AsMYB2R043 and AsMYB2R045 show a downward trend at all five time points after drought treatment. In AsMYB1R genes, AsMYB1R022, AsMYB1R078, and AsMYB1R079 were upregulated in the early stage (12 h) of drought treatment, followed by a decrease in the expression levels of the three genes. However, AsMYB1R088 and AsMYB1R098 were significantly upregulated in the middle stage (24 h) of drought treatment, followed by a decrease in expression levels in the later stages (48 and 72 h) of drought treatment.

Fig. 8
figure 8

Transcriptional abundance plots of AsMYB TFs. (A) The heatmap showed the expression profile of AsMYB1R TFs; (B) The heatmap showed the expression profile of AsMYB2R and AsMYB3R TFs; (C) The heatmap showed the expression profile of 8 differential expression genes. Rows represent the different time samples (0–72 h), the columns represent the different AsMYB genes

Full size image

We then used RT-qPCR approach to validate this data. It was found that AsMYB2R genes, AsMYB2R043 and AsMYB2R045 had lower transcriptional levels at 5 time points after PEG treatment compared to 0 h (Fig. 9), which is consistent with the transcriptome data (Fig. 8C). The gene expression trend of AsMYB2R039 gene at 5 time points after PEG treatment was also similar to that from the transcriptome (Fig. 8C). For AsMYB1R genes, the gene expression levels of AsMYB1R022 were upregulated at 5 time points after PEG treatment (Fig. 9), which was consistent with the trend in the transcriptome (Fig. 8C). However, the gene expression levels of AsMYB1R078, AsMYB1R079, AsMYB1R088, and AsMYB1R098 were basically consistent with the trend in the transcriptome (Fig. 8C). Hence, despite the RT-qPCR validation of AsMYB1R and AsMYB2R gene expressions were not completely consistent with the multiples in the transcriptome (Fig. 8C), the overall trends were similar.

Fig. 9
figure 9

The RT-qPCR plots of 8 differentially expressed genes. Relative expression level plots of 8 AsMYB genes following PEG treatment as determined by RT-qPCR. The Y-axis and X-axis indicated relative expression level and six time points of PEG treatment, respectively. The relative expression level of genes at 0 h was taken as 1, and were calculated by normalization method. Mean ± SD (Standard Deviation) was obtained from three biological and three technical replicates. The error bars indicate standard deviation. Different letters indicate significant differences, and the same letters represent no significant differences at the 0.05 level

Full size image

Stomatal aperture, H2O2 and GST quantification

After 6 h of PEG treatment, it was observed that the guard cells of A. sativa began to contract, and the stomata began to closure. They continued to closure at the following 12, 24, and 48 h. However, after 72 h, the stomata were almost closed (Fig. 10A). The stomata size data also showed a decrease (Fig S3B).

Fig. 10
figure 10

Stomatal aperture, H2O2 content and GST activity plots. (A) The stomatal aperture state at 6 time points (0–72 h) of A. sativa; The size of scale bar is 10 μm. (B) The analytic result of H2O2 content. Mean ± SD (Standard Deviation) was obtained from six biological replicates. The error bars indicate standard deviation. Different letters indicate significant differences, and the same letters represent no significant differences at the 0.05 level; (C) The analytic result of GST activity. Mean ± SD (Standard Deviation) was obtained from six biological replicates. The error bars indicate standard deviation. Different letters indicate significant differences, and the same letters represent no significant differences at the 0.05 level

Full size image

The H2O2 content in the roots of A. sativa showed some fluctuation at 5 time points after PEG treatment, mimicking diurnal patters, with the overall trend for increase, with 5-fold higher H2O2 content at 72 h compared to 0 h (Fig. 10B). The GST activity in the roots also increased significantly (Fig. 10C), with highest value recorded for 72 h timepoint.

Changes in the expression levels of GST family genes by PEG treatment

In transcriptome data, the expression level of the non-enzymatic antagonists GST family genes with ROS scavenging function increased after 6 h of PEG treatment, and the expression level of GST genes increased starting from 6 h of PEG treatment. Most GST genes were upregulated at 12 and 24 h of PEG treatment, but their expression was suppressed at 48 h, only AVESA.00010b.r2.7AG1218190 gene expression significantly increased. Most genes showed increased expression at 72 h (Fig. 11).

Fig. 11
figure 11

Transcriptional abundance plots of GST genes. The heatmap showed the expression profile of AsMYB1R TFs. Rows represent the different time samples (0–72 h), the columns represent the different GST genes

Full size image

Discussion

Plants scavenge ROS accumulation due to drought stress through enzymatic and non-enzymatic antioxidant systems, reducing membrane ester peroxidation and avoiding damage to biomolecules such as DNA and proteins [44]. Drought-exposed plants also retain water by increasing amounts of osmolytes to maintain cell turgor pressure and reducing stomatal size to avoid water loss [45]. Reducing stomatal density and increasing the thickness of the wax layer are also essential to reduce water loss via residual (non-stomatal) transpiration [5, 7]. TFs may play an important roles in these processes.

TFs specifically bind to the nucleotide sequence in the promoter region of downstream target genes to activate gene transcription and expression, and then participate in signal transduction and gene expression regulation under abiotic stress. The MYB family is one of the largest TFs families in plants [44]. Studies have shown that OsMYB2 regulates accumulation of organic osmolytes in rice [46], and OsMYB48-1 and BnMYB2-1 were essential for regulation of ABA synthesis in rice [47] and wheat [48], respectively. The OsMYB60 regulates cuticle wax synthesis in rice [49], and overexpression of GbMYB5 enhanced the accumulation of proline and antioxidant enzymes in transgenic tobacco, while reducing the production of MDA and improving tobacco drought tolerance [45]. A. sativa contain a large number of MYB transcription factors [9, 17], but it is unknown whether the MYB family contribute to drought tolerance. 268 AsMYB TFs were identified from the A. sativa genome data. Among them, 8 AsMYB TFs differentially expressed under drought stress were identified and analyzed by bioinformatics.

The AsMYB2R subfamily genes in A. sativa are related to the shortened growth period, stomatal closure, and nutrient and water transport by PEG-induced drought stress

AsMYB2R039 is homologous with AtMYB2R56 in Arabidopsis. AtMYB2R56 is one of the important members of S31 subfamily (Fig. 3), which is confirmed to code carbon starred anthers (CSA). Its role is to promote sugar transport to pollen by binding to the MST8 sugar transporter promoter to control carbon allocation during anther and pollen maturation during rice flowering [50], and it is further confirmed to regulate the size and shape of Arabidopsis seeds during seed maturation [51]. Studies have also shown that the interaction between MYB56 and MATH-BTB/POZ (BPM) protein acts as a negative regulator of flowering in Arabidopsis [52]. It is interesting that the expression of AsMYB2R039 began to increase after PEG treatment, which we believe may be evidence that A. sativa prepared to escape drought stress by early initiation of flowering and fruiting mechanisms, and completing the growth cycle ahead of schedule. The results of this study are more likely to be that AtMYB2R56 promotes sugar transport to reproductive organs, promotes early flowering, and shortens the growth cycle in response to drought stress.

The amino acid sequences were analyzed using the Blastp tool on the NCBI website, and the results showed that AsMYB2R043 and AtMYB2R61 sequences were highly homologous, with AtMYB2R61 being a member of the Arabidopsis S16 subfamily (Fig. 3). Effective control of stomatal aperture may be one of the key means for plants to adapt to drought [53]. It was shown that AtMYB2R61 can reduce stomatal aperture and water loss to resist drought stress [54]. Based on RT-qPCR results, this study found that the expression of AsMYB2R043 in roots showed a decreasing trend during PEG treatment, while the expression slightly increased at 72 h. However, after drought treatment, the expression of AsMYB2R043 was inhibited in the leaves (Fig S4). The observation of stomata further confirmed that stomatal aperture continued to decrease with the increase of PEG treatment time, and until 72 h of PEG treatment, the stomata were almost completely closed, thereby reducing excessive water loss. It has been reported that some genes of the MYB family are involved in or regulate stomatal closure. Overexpression of AtMYB61 enhances stomatal closure [55], ABA can induce the expression of AtMYB44 to promote stomatal closure [56], and overexpression of AtMYB96 promotes stomatal closure. The stomatal aperture of leaves becomes smaller [57]. AtMYB60 is involved in regulating stomatal movement, and AtMYB60 mutants promote stomatal closing [58]. Interestingly though, in the transcriptome data of this study, no above-mentioned homologous genes were differentially expressed (Fig. 10A, Fig S3A and S3B). Therefore, we conclude that the closure of A. sativa stomata under drought stress is not regulated by AsMYB2R043 gene. These conclusions may be one of the important reasons why A. sativa can maintain long-term drought resistance.

The AsMYB2R045 is homologous to AtMYB2R036 and is a member of the S11 subfamily (Fig. 3). AtMYB2R036 has been shown to regulate the formation of Casparian strips in the root endothelial layer, which can transport essential nutrients and water for plant growth and development [59]. The AsMYB2R045 in A. sativa roots showed a higher expression level at 0 h, which is consistent with the normal growth and development process of plants that regulate nutrient and water transport through positive regulation of Casparian strips. However, after PEG treatment, the AsMYB2R045 showed a declining trend in transcriptional levels, indicating that drought inhibited the absorption of nutrients and water in A. sativa roots.

The AsMYB1R subfamily genes of A. sativa and GST regulation of ROS homeostasis confer signal transduction and scavenge excess ROS to avoid oxidative damage

PEG-induced drought stress upregulated the expression of 5 genes in the AsMYB1R subfamily of A. sativa (Fig. 9), all of which are key genes in the circadian clock. Among them, AsMYB1R022, AsMYB1R079, and AsMYB1R088 are homologous to REVEILLE 1 (REV 1), AsMYB1R078 is homologous to REVEILLE 6 (REV 6), and AsMYB1R098 is homologous to LHY. REVEILLE 6 (REV 6) which, as an activator of the nocturnal clock, promotes downregulation of the Arabidopsis clock gene complex LHY/CCA1 expression [60]. Upregulation of AsMYB1R078 (REV 6) gene expression may be used to regulate the expression of the A. sativa clock complex LHY/CCA1 genes under drought stress. However, the MYB1R subfamily genes are closely related to ROS, studies have shown that the loss of function of the MYB1R subfamily genes CCA1 and LHY impairs the production and clearance of ROS in Arabidopsis mutants at specific times of the day, suggesting regulatory effects of CCA1 and LHY on basal ROS levels [18], LHY/CCA1 is one of the main components of the core circular clock machinery complex [61]. The upregulation of A. sativa REV 1 genes AsMYB1R022, AsMYB1R079, and AsMYB1R088 after PEG treatment may be similar in function to the Arabidopsis MYB1R subfamily RVE 1, acting as clock output genes in Arabidopsis and regulating auxin production [62, 63]. It is worth noting that the RVE 1 gene binds directly to the protochlorophyllide oxidoreductase (PORA) promoter through the EE [(A) AATATCT] - box cis regulatory element. By regulating the catalytic activity of PORA, RVE 1 promotes the reduction of protochlorophyll (Pchlide) to chlorophyll, avoiding excessive accumulation of Pchlide or a decrease in POR activity during the dark period, thus preventing excessive production of ROS under light stimulation and the ROS-induced oxidative damage [64]. Therefore, the key genes LHY (AsMYB1R098) and RVE 1 (AsMYB1R022, AsMYB1R079, and AsMYB1R088) in A. sativa circadian clock may be involved in regulation of ROS homeostasis, of which the latter is a key signaling substance regulating plant circadian clock [65]. Changes in ROS content may serve as evidence for A. sativa response to drought stress signaling substances.

Through physiological evidence, we further confirmed that the content of H2O2 in the roots, one of the major types of ROS species, exhibited oscillatory changes in response to PEG treatment (Fig. 10B), which may be used to stabilize the impact of drought stress on the circadian clock system. On the other hand, changes in H2O2 content are used to provide signal molecules for circadian rhythms and other physiological processes [18, 31, 32, 65]. Furthermore, if H2O2 content continues to increase, it can oxidize and damage A. sativa cell membranes and chloroplasts, induce membrane lipid peroxidation, produce toxic metabolites such as malondialdehyde, damage proteins, lipids, and nucleic acids, and lead to cell death [66]. However, the H2O2 content in A. sativa decreased after 12 and 48 h of PEG treatment (Fig. 10B), which may be partly due to the upregulation of the AsMYB1R subfamily genes LHY (AsMYB1R098) and RVE 1 (AsMYB1R022, AsMYB1R079, and AsMYB1R088) on the steady-state regulation of ROS.

We found that genes encoding enzymatic antioxidants such as CAT, SOD, APX did not show differential expression (data not shown). However, the expressions of non-enzymatic antioxidant GST genes were significantly upregulated at 12 and 24 h after PEG treatment (Fig. 11), which may be mainly used to scavenge excess ROS produced by sudden outbreaks in the early stages of drought stress. Interestingly, the expression level of GST genes showed an up-regulated down-regulated up-regulated oscillation pattern after PEG treatment (Fig. 11), and GST activity in the roots also shows an oscillatory upward pattern (Fig. 10C). These two correlated results are consistent with the long-term changes in the wave pattern of H2O2 content (in units of h) (Fig. 10B), which not only confirms the continuous regulation of H2O2 by A. sativa GST family genes from transcription to expression, but also matches the signal transduction pattern of ROS waves [32, 67]. It can be, therefore, suggested that GST family genes and MYB1R subfamily genes jointly regulate H2O2 levels. An appropriate amount of H2O2 is used for signal transmission in plants, while excessive H2O2 can cause oxidative damage to plants. Therefore, we infer that the GST gene family plays a major role in regulating H2O2 content. The MYB1R subfamily genes CCA1, LHY and REV1 are important clock genes, and there is evidence that a loss of CCA1 and LHY function impairs ROS production and scavenging in Arabidopsis mutants at specific times of the day, and that the RVE1 gene can bind to the promoter of protochlorophyllide oxidoreductase (PORA) to regulate ROS levels [64]. Therefore, we infer that the respectively up-regulated expression of LHY (AsMYB1R098) and RVE 1 (AsMYB1R022, AsMYB1R079 and AsMYB1R088) of A. sativa may be involved in the regulation of ROS homeostasis.

Conclusions

In this study, a genome-wide identification of MYB genes in A. sativa was performed and a total of 268 AsMYB genes were identified. The expression levels of eight TFs in A. sativa roots by PEG-induced drought stress at different time points were analyzed based on transcriptome data and RT-qPCR. Of these, three genes from AsMYB2R subfamily (AsMYB2R039, AsMYB2R043, AsMYB2R045) played essential role in the shortening growth period, triggering stomatal closure, and controlling nutrient and water transport under PEG drought stress. The results confirmed that the upregulation of key AsMYB1R subfamily genes LHY (AsMYB1R098) and RVE 1 (AsMYB1R022, AsMYB1R079, and AsMYB1R088) in A. sativa under PEG stress may be used to regulate ROS homeostasis, and ROS may be a key signaling substance for the circadian clock. GST, as a non-enzymatic antioxidant, works together with the key genes LHY (AsMYB1R098) and RVE 1 (AsMYB1R022, AsMYB1R079, and AsMYB1R088) in A. sativa to regulate ROS homeostasis and maintain the basal H2O2 level required for signal transduction while avoiding oxidative damage to cells.

Materials and methods

Screening of the AsMYB TFs and physicochemical properties analysis

The genome and annotation data of A. sativa were downloaded from the GrainGenes database (https://wheat.pw.usda.gov/GG3/content/avena-sang-download). Characteristic Hidden Markov Model (HMM) and alignment files of the MYB protein structural domain (PF00249) from the PFAM database (https://pfam-legacy.xfam.org) were used as search files to initially identify the candidate AsMYB genes (E-values < 1 × 10− 5) by HMMER software (Version 3.0). Then, to remove redundant sequences, AsMYB genes were further screened by using CD-HIT software (Version 4.8.1) with the parameters c = 0.9, n = 5. In some cases, multiple transcripts of AsMYB genes were noticed, and only the longest transcript corresponding to each AsMYB gene was retained for further studies [68]. Finally, the candidate AsMYB genes were further manually examined for the completeness of the conserved domain in the protein sequence using the NCBI conserved domain database (https://www.ncbi.nlm.nih.gov/cdd/) and search against the simple modular architecture research tool (SMART) website (https://smart.embl.de) with default parameters (E-values < 1 × 10− 5). Only genes with intact MYB conserved domain can be used for subsequent analysis. Based on the number and the characteristic of AsMYB genes imperfect tandem repeat, AsMYB genes were classified into different categories. Alignment file of amino acid sequences aligned by Clustal X software (Version 2.1) were submitted to Weblogo online website (https://weblogo.berkeley.edu/logo.cgi) to exhibit the MYB imperfect tandem repeat sequences. The physicochemical properties of AsMYB proteins, including protein size, molecular weight, isoelectric point, instability index, and grand average of hydropathicity, were analyzed by using the online program ExPASy-ProtParam (https://www.expasy.org/resources/protparam). Furthermore, the subcellular localization of the AsMYB genes was predicted using the online tool WOLF PSORT (https://wolfpsort.hgc.jp).

Chromosome localization and phylogenetic tree construction

The location of AsMYB genes in different categories on the chromosomes were obtained from the A. sativa annotation data using the Gene Location Visualize program of TBtools software (Version 2.003) [69]. To facilitate the subsequent research, the location of AsMYB genes were ensured and systematically named according to the order on the chromosome. Subsequently, to examine the phylogenetic relationship and evolutionary history of AsMYB genes, the identified AsMYB proteins were combined with the reported MYB proteins of A. thaliana [70], which were obtained from TAIR database (http://www.arabidopsis.org/) to construct protein alignment files by using Clustal X software. Subsequently, the Neighbor-Joining phylogenetic tree was built from the alignment files using MEGA software (Version 11.0) with the following parameters: p-distance, partial deletion (50%), and bootstrap analysis with 1000 replicates, respectively. Finally, the phylogenetic tree was modified using the Interaction Tree of Life (iTOL) online website (https://itol.embl.de).

Conserved motif, gene structure, and cis-acting analysis

To further investigate conserved motifs of AsMYB proteins, the conserved motifs of amino acid sequences were analyzed by using the MEME online program (https://meme-suite.org/meme/tools/meme). The number of conserved motifs searched was 10, and the rest of the settings were left unchanged. For a visual visualization, the evolutionary tree file, conserved motifs, genome annotation data, and the positions of MYB binding site which extracted by CD-search tool (https://www.ncbi.nlm.nih.gov/cdd/) were submitted to Gene Structure View program of TBtools software.

To analyze the cis-acting elements in the promoter region, the 2000 bp length of the upstream DNA sequences of AsMYB TFs were submitted to the PlantCARE database (https://bioinformatics.psb.ugent.be/webtools/plantcare/html/).

Gene duplication and collinearity analysis

Gene duplication events of AsMYB genes were detected using One Step MCScanX program (E-values < 1 × 10–10) of TBtools software with default parameters and visualized the location of AsMYB genes, gene density, and collinearity information of AsMYB genes, the Advance Circos program was chosen to perform the work. The selection pressure in biological evolution can be represented by the rate of nonsynonymous and synonymous (Ka/Ks) [71]. Relevant files were entered into Simple Ka/Ks Calculator program of TBtools software to obtain the calculation results.

Plant materials and treatment

A crop seed detector (BIO seed M-P, Research Center of Information Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China) was used to screen A. sativa seeds with consistent phenotypes. Seeds were surface sterilized with sodium hypochlorite (1.5%) for 20 min, then placed in a germination box and cultured in a growth chamber at 25 ± 1℃ until the seedling height was 2–3 cm. Plants were then transferred to a 1/2 Hoagland nutrient solution for further growth [72]. Once the seedlings had two true leaves, nutrient solutions that contain 15% (w/v) polyethylene glycol 6000 (PEG 6000) were supplied [68]. This concentration of PEG has osmotic potential of about 1.2 MPa and was usually used in numerous studies to mimic drought stress. After the certain treated time points (0/6/12/24/48/72 h), the roots were rinsed with sterile water and the residual water droplets were removed, followed by flash freezing with liquid nitrogen. Finally, the roots were stored at -80℃ for further analysis.

Templet preparation and RT-qPCR

Total RNA was extracted from all roots of A. sativa using the RNAiso Plus Kit (Takara, Japan) as the manufacturer’s guidelines. The concentration and purity of isolated total RNA were estimated by Nanodrop spectrometer (Thermo Fisher Scientific, USA). First-strand complementary DNA (cDNA) which using 1 µg of total RNA as the template was synthesized using the PrimeScript™ RT reagent kit with gDNA Eraser (Takara, Japan). Gene specific primers for RT-qPCR were designed by Primer Premier software (Version 5.0) and shown in Table S1. RT-qPCR was performed with CFX Connect (Bio-Rad, USA) using ArtiCanCEO SYBR qPCR Mix (Tsingke, China). The reaction system (20 µL) was performed as follows: 10 µL ArtiCanCEO SYBR qPCR Mix, 0.4 µL of each primer (10 µM), 2 µL cDNA (Ten-fold dilution was performed with water), the rest of the volume were replenished by water. The thermal cycle program was set as follows: initial denaturation at 95℃ for 5 min, followed by 40 cycles of 95℃ for 10 s and 60℃ for 30 s, the melt curve of built-in program was set to verify the specificity of the primers. The primer of GAPDH gene was chosen as the internal reference gene to normalize cDNA concentrations [73]. The relative expression levels of AsMYB genes was calculated by utilizing 2-ΔΔCq algorithm.

Physiological traits

The A. sativa leaves were excised from 6 time point samples, and an EVOS microscope (Thermo Fisher Scientific, USA) was used to observe the plant stomatal status in the abaxial surface of the blade. In Fig S3A, the stomatal width of differential photos was measured by ImageJ program [74]. The content in the roots of H2O2 was determined using Hydrogen Peroxide (H2O2) Content Assay Kit (Solarbio, China) following the manufacturer’s protocol. The roots (0.1 g) were homogenized in 1 mL of cold acetone, multiple regents were added to mixture and its absorbance was measured at 415 nm. The TissueLyser II machine (QIAGEN, Germany) was used for tissue fragmentation [75]. GST activity in roots was determined following the protocol of the Glutathione S-transferase (GST) Activity Assay Kit (Solarbio, China) [76]. The roots (0.1 g) were homogenized on ice with 1 mL regent 1 of GST Activity Assay Kit. The absorbance was measured at 340 nm after multiple reagent treatments.

Statistical analysis

Three independent sample replicates were used for RT-qPCR analysis at each time point, and six independent sample replicates were used for H2O2 content and GST activity analysis at each time point. All the statistical analyses were performed using GraphPad Prism9 (GraphPad Software Inc.; San Diego, CA, USA). The reported data are presented as mean ± SD (Standard Deviation). One-way ANOVA is used to analyze the significance of different treatments (p < 0.05 significance level).

Data availability

All RNA-Seq data were deposited in the NCBI SRA database under the project PRJNA1056521 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1056521).

References

  1. Verma A, Deepti S. Abiotic stress and crop improvement: current scenario. Adv Plants Agric Res. 2016; 4(4):345–6.

  2. Hou P, Wang F, Luo B, Li A, Wang C, Shabala L et al. Antioxidant enzymatic activity and osmotic adjustment as components of the drought tolerance mechanism in Carex duriuscula. Plants. 2021;10(3).

  3. Irigoyen JJ, Einerich DW, Sánchez-Díaz M. Water stress induced changes in concentrations of proline and total soluble sugars in nodulated alfalfa (Medicago sativa) plants. Physiol Plant. 1992;84(1):55–60.

    Article  CAS  Google Scholar 

  4. Daszkowska-Golec A, Szarejko I. Open or close the gate - stomata action under the control of phytohormones in drought stress conditions. Front Plant Sci. 2013;4.

  5. Hasanuzzaman M, Zhou MX, Shabala S. How does stomatal density and residual transpiration contribute to osmotic stress tolerance? Plants. 2023;12(3).

  6. Nadarajah KK. ROS homeostasis in abiotic stress tolerance in plants. Int J Mol Sci. 2020;21(15).

  7. Geng A, Lian W, Wang Y, Liu M, Zhang Y, Wang X et al. Molecular mechanisms and regulatory pathways underlying drought stress response in rice. Int J Mol Sci. 2024;25(2).

  8. Rasane P, Jha A, Sabikhi L, Kumar A, Unnikrishnan VS. Nutritional advantages of oats and opportunities for its processing as value added foods - a review. J Food Sci Technol. 2015;52(2):662–75.

    Article  CAS  PubMed  Google Scholar 

  9. Kamal N, Tsardakas Renhuldt N, Bentzer J, Gundlach H, Haberer G, Juhász A et al. The mosaic oat genome gives insights into a uniquely healthy cereal crop. Nature. 2022;606(7912):113–9.

  10. Isidro-Sánchez J, Prats E, Howarth CJ, Langdon T, Montilla-Bascón G. Genomic approaches for climate resilience breeding in oats. 2020: 133–69.

  11. Han L, Liu H, Yu S, Wang W, Liu J. Potential application of oat for phytoremediation of salt ions in coastal saline-alkali soil. Ecol Eng. 2013;61:274–81.

    Article  Google Scholar 

  12. Wu B, Hu Y, Huo P, Zhang Q, Chen X, Zhang Z. Transcriptome analysis of hexaploid hulless oat in response to salinity stress. PLoS ONE. 2017;12(2):e0171451.

    Article  PubMed  PubMed Central  Google Scholar 

  13. Hou P, Qu M, Yun P, Li A, Ahmed HAI, Peng Y, et al. Avena sativa under drought stress. Boca Raton: CRC; 2023.

    Book  Google Scholar 

  14. Peltonen-Sainio P, Mäkelä PSA. Comparison of physiological methods to assess drought tolerance in oats. Acta Agr Scand B-S P. 1995;45:32–8.

    Google Scholar 

  15. Gong D-S, Xiong Y, Ma B-L, Wang T-M, Ge J-P, Qin X, et al. Early activation of plasma membrane H+-ATPase and its relation to drought adaptation in two contrasting oat (Avena sativa L.) genotypes. Environ Exp Bot. 2010;69:1–8.

    Article  CAS  Google Scholar 

  16. Munns R, Day DA, Fricke W, Watt M, Arsova B, Barkla BJ, et al. Energy costs of salt tolerance in crop plants. New Phytol. 2020;225(3):1072–90.

    Article  CAS  PubMed  Google Scholar 

  17. Peng Y, Yan H, Guo L, Deng C, Wang C, Wang Y, et al. Reference genome assemblies reveal the origin and evolution of allohexaploid oat. Nat Genet. 2022;54(8):1248–58.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Lai AG, Doherty CJ, Mueller-Roeber B, Kay SA, Schippers JHM, Dijkwel PP. CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses. Proc Natl Acad Sci USA. 2012;109(42):p17129–17134.

    Article  Google Scholar 

  19. Ma D, Constabel CP. MYB repressors as regulators of phenylpropanoid metabolism in plants. Trends Plant Sci. 2019;24(3):275–89.

    Article  CAS  PubMed  Google Scholar 

  20. Jiménez A, Sevilla F, Martí MC. Reactive oxygen species homeostasis and circadian rhythms in plants. J Exp Bot. 2021;72(16):5825–40.

    Article  PubMed  Google Scholar 

  21. Li X, Guo C, Li Z, Wang G, Yang J, Chen L, et al. Deciphering the roles of tobacco MYB transcription factors in environmental stress tolerance. Front Plant Sci. 2022;13:998606.

    Article  PubMed  PubMed Central  Google Scholar 

  22. Liu D, Tang D, Xie M, Zhang J, Zhai L, Mao J, et al. Agave REVEILLE1 regulates the onset and release of seasonal dormancy in Populus. Plant Physiol. 2023;191(3):1492–504.

    Article  CAS  PubMed  Google Scholar 

  23. Azuara-Liceaga EI, Sanchez-Buena S, Meneses E, Brieba LG, Orozco E. Identification of myb transcription factors in Entamoeba histolytica. Faseb J. 2007;21(6):A1031–1031.

    Google Scholar 

  24. Kundan M, Gani U, Fayaz M, Angmo T, Kesari R, Rahul VP, et al. Two R2R3-MYB transcription factors, CsMYB33 and CsMYB78 are involved in the regulation of anthocyanin biosynthesis in Cannabis sativa L. Ind Crops Prod. 2022;188:115546.

    Article  CAS  Google Scholar 

  25. Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L. MYB transcription factors in Arabidopsis. Trends Plant Sci. 2010;15(10):573–81.

    Article  CAS  PubMed  Google Scholar 

  26. Ji K, Liu CY, Wu KY, Yue ZH, Dong Y, Gong BC et al. Genome-wide characterization of the R2R3-MYB gene family in Diospyros oleifera. Agriculture. 2023;13(5).

  27. Li H, Wen X, Wei M, Huang X, Dai S, Ruan L et al. Genome-Wide identification, characterization, and expression pattern of MYB gene family in Melastoma candidum. Horticulturae. 2023;9(6):708.

  28. Munné-Bosch S, Peñuelas J. Photo- and antioxidative protection, and a role for salicylic acid during drought and recovery in field-grown Phillyrea Angustifolia plants. Planta. 2003;217(5):758–66.

    Article  PubMed  Google Scholar 

  29. Smirnoff N. The role of active oxygen in the response of plants to water deficit and desiccation. New Phytol. 1993;125(1):27–58.

    Article  CAS  PubMed  Google Scholar 

  30. Rudenko NN, Vetoshkina DV, Marenkova TV, Borisova-Mubarakshina MM. Antioxidants of non-enzymatic nature: their function in higher plant cells and the ways of boosting their biosynthesis. Antioxidants. 2023;12(11).

  31. Ma L, Zhang H, Sun L, Jiao Y, Zhang G, Miao C, et al. NADPH oxidase AtrbohD and AtrbohF function in ROS-dependent regulation of Na+/K+homeostasis in Arabidopsis under salt stress. J Exp Bot. 2012;63(1):305–17.

  32. Baxter A, Mittler R, Suzuki N. ROS as key players in plant stress signalling. J Exp Bot. 2014;65(5):1229–40.

    Article  CAS  PubMed  Google Scholar 

  33. Linde AM, Eklund DM, Kubota A, Pederson ERA, Holm K, Gyllenstrand N, et al. Early evolution of the land plant circadian clock. New Phytol. 2017;216(2):576–90.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Martin C, Paz-Ares J. MYB transcription factors in plants. Trends Genet. 1997;13(2):67–73.

    Article  CAS  PubMed  Google Scholar 

  35. Zargarian L, Le Tilly V, Jamin N, Chaffotte A, Gabrielsen OS, Toma F et al. Myb-DNA recognition: role of tryptophan residues and structural changes of the minimal DNA binding domain of c-Myb. Biochemistry. 1999;38(6):1921–9.

  36. Li H, Yang X, Niyitanga S, He Q, Chen S, Xu J, et al. Transcriptomes of different tissues for expression characteristics analysis of MYB gene family in kenaf (Hibiscus cannabinus L). Trop Plant Biology. 2022;15(4):261–75.

    Article  CAS  Google Scholar 

  37. Tombuloglu H. Genome-wide identification and expression analysis of R2R3, 3R- and 4R-MYB transcription factors during lignin biosynthesis in flax (Linum usitatissimum). Genomics. 2020;112(1):782–95.

    Article  CAS  PubMed  Google Scholar 

  38. Li X, Xue C, Li J, Qiao X, Li L, Yu L, et al. Genome-wide identification, evolution and functional divergence of MYB transcription factors in Chinese white pear (Pyrus Bretschneideri). Plant Cell Physiol. 2016;57(4):824–47.

    Article  CAS  PubMed  Google Scholar 

  39. Xu Q, He J, Dong J, Hou X, Zhang X. Genomic survey and expression profiling of the MYB gene family in watermelon. Hortic Plant J. 2018;4(1):1–15.

    Article  Google Scholar 

  40. Li Z, Peng R, Tian Y, Han H, Xu J, Yao Q. Genome-wide identification and analysis of the MYB transcription factor superfamily in Solanum lycopersicum. Plant Cell Physiol. 2016;57(8):1657–77.

    Article  CAS  PubMed  Google Scholar 

  41. Li SJ, Huang H, Ma XN, Hu ZK, Li JY, Yin HF. Characterizations of MYB transcription factors in Camellia Oleifera reveal the key regulators involved in oil biosynthesis. Horticulturae. 2022;8(8).

  42. Hajiebrahimi A, Owji H, Hemmati S. Genome-wide identification, functional prediction, and evolutionary analysis of the R2R3-MYB superfamily in Brassica napus. Genome. 2017;60(10):797–814.

    Article  CAS  PubMed  Google Scholar 

  43. Si Z, Wang L, Ji Z, Zhao M, Zhang K, Qiao Y. Comparative analysis of the MYB gene family in seven Ipomoea species. Front Plant Sci. 2023;14:1155018.

    Article  PubMed  PubMed Central  Google Scholar 

  44. Yao C, Li X, Li Y, Yang G, Liu W, Shao B et al. Overexpression of a Malus baccata MYB transcription factor gene MbMYB4 increases cold and drought tolerance in Arabidopsis thaliana. Int J Mol Sci. 2022;23(3).

  45. Chen T, Li W, Hu X, Guo J, Liu A, Zhang B. A cotton MYB transcription factor, GbMYB5, is positively involved in plant adaptive response to drought stress. Plant Cell Physiol. 2015;56(5):917–29.

    Article  CAS  PubMed  Google Scholar 

  46. Yang A, Dai X, Zhang WH. A R2R3-type MYB gene, OsMYB2, is involved in salt, cold, and dehydration tolerance in rice. J Exp Bot. 2012;63(7):2541–56.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Xiong H, Li J, Liu P, Duan J, Zhao Y, Guo X, et al. Overexpression of OsMYB48-1, a novel MYB-related transcription factor, enhances drought and salinity tolerance in rice. PLoS ONE. 2014;9(3):e92913.

    Article  PubMed  PubMed Central  Google Scholar 

  48. Gao S, Xu J, Song W, Dong J, Xie L, Xu B. Overexpression of BnMYBL2-1 improves plant drought tolerance via the ABA-dependent pathway. Plant Physiol Biochem. 2023;207:108293.

    Article  PubMed  Google Scholar 

  49. Jian L, Kang K, Choi Y, Suh MC, Paek NC. Mutation of OsMYB60 reduces rice resilience to drought stress by attenuating cuticular wax biosynthesis. Plant J. 2022;112(2):339–51.

    Article  CAS  PubMed  Google Scholar 

  50. Zhang H, Liang W, Yang X, Luo X, Jiang N, Ma H, et al. Carbon starved anther encodes a MYB domain protein that regulates sugar partitioning required for rice pollen development. Plant Cell. 2010;22(3):672–89.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Zhang H, Xu C, He Y, Zong J, Yang X, Si H, et al. Mutation in CSA creates a new photoperiod-sensitive genic male sterile line applicable for hybrid rice seed production. Proc Natl Acad Sci U S A. 2013;110(1):76–81.

    Article  PubMed  Google Scholar 

  52. Chen L, Bernhardt A, Lee J, Hellmann H. Identification of Arabidopsis MYB56 as a novel substrate for CRL3BPM E3 ligases. Mol Plant. 2014.

  53. Chen X, Zhao C, Yun P, Yu M, Zhou M, Chen ZH et al. Climate-resilient crops: lessons from xerophytes. Plant J. 2023.

  54. Liang Y-K, Dubos C, Dodd IC, Holroyd GH, Hetherington AM, Campbell MM. AtMYB61, an R2R3-MYB transcription factor controlling stomatal aperture in Arabidopsis thaliana. Curr Biol. 2005;15(13):1201–6.

    Article  CAS  PubMed  Google Scholar 

  55. Liang Y-K, Dubos C, Dodd IC, Holroyd GH, Hetherington AM, Campbell MM. AtMYB61, an R2R3-MYB transcription factor controlling stomatal aperture in Arabidopsis thaliana. Curr Biol. 2005;15:1201–6.

    Article  CAS  PubMed  Google Scholar 

  56. Jung C, Seo JS, Han SW, Koo YJ, Kim C-H, Song SI, et al. Overexpression of AtMYB44 enhances stomatal closure to confer abiotic stress tolerance in transgenic Arabidopsis 1. Plant Physiol. 2007;146:623–35.

    PubMed  Google Scholar 

  57. Seo PJ, Xiang F, Qiao M, Park JY, Lee YN, Kim SG, et al. The MYB96 transcription factor mediates abscisic acid signaling during drought stress response in Arabidopsis. Plant Physiol. 2009;151(1):275–89.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Cominelli E, Galbiati M, Vavasseur A, Conti L, Sala T, Vuylsteke M, et al. A guard-cell-specific MYB transcription factor regulates stomatal movements and plant drought tolerance. Curr Biol. 2005;15:1196–200.

    Article  CAS  PubMed  Google Scholar 

  59. Kamiya T, Borghi M, Wang P, Danku JM, Kalmbach L, Hosmani PS, et al. The MYB36 transcription factor orchestrates casparian strip formation. Proc Natl Acad Sci U S A. 2015;112(33):10533–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. De Leone MJ, Hernando CE, Romanowski A, García-Hourquet M, Careno D, Casal J et al. The LNK gene family: at the crossroad between light signaling and the circadian clock. Genes. 2018;10(1).

  61. Dubois M, Claeys H, Van den Broeck L, Inzé D. Time of day determines Arabidopsis transcriptome and growth dynamics under mild drought. Plant Cell Environ. 2017;40(2):180–9.

    Article  CAS  PubMed  Google Scholar 

  62. Rawat R, Schwartz J, Jones MA, Sairanen I, Cheng Y, Andersson CR, et al. REVEILLE1, a myb-like transcription factor, integrates the circadian clock and auxin pathways. Proc Natl Acad Sci USA. 2009;106(39):16883–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Yin H, Guo HB, Weston DJ, Borland AM, Ranjan P, Abraham PE, et al. Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave. BMC Genomics. 2018;19(1):588.

    Article  PubMed  PubMed Central  Google Scholar 

  64. Xu G, Guo H, Zhang D, Chen D, Jiang Z, Lin R. REVEILLE1 promotes NADPH: protochlorophyllide oxidoreductase A expression and seedling greening in Arabidopsis. Photosynth Res. 2015;126(2–3):331–40.

    Article  CAS  PubMed  Google Scholar 

  65. Luklová M, Novák J, Kopecká R, Kameniarová M, Gibasová V, Brzobohatý B et al. Phytochromes and their role in diurnal variations of ROS metabolism and plant proteome. Int J Mol Sci. 2022;23(22).

  66. Hou P, Qu M, Yun P, Li A, Ahmed HAI, Peng Y, et al. Avena sativa under Drought stress. Boca Raton: CRC; 2023.

    Book  Google Scholar 

  67. Mittler R, Vanderauwera S, Suzuki N, Miller G, Tognetti VB, Vandepoele K, et al. ROS signaling: the new wave? Trends Plant Sci. 2011;16(6):300–9.

    Article  CAS  PubMed  Google Scholar 

  68. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22(13):1658–9.

    Article  CAS  PubMed  Google Scholar 

  69. Chen C, Wu Y, Li J, Wang X, Zeng Z, Xu J, et al. TBtools-II: a one for all, all for one bioinformatics platform for biological big-data mining. Mol Plant. 2023;16(11):1733–42.

    Article  CAS  PubMed  Google Scholar 

  70. Yanhui C, Xiaoyuan Y, Kun H, Meihua L, Jigang L, Zhaofeng G, et al. The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family. Plant Mol Biol. 2006;60(1):107–24.

    Article  PubMed  Google Scholar 

  71. Wang Y, Zhang Y, Fan C, Wei Y, Meng J, Li Z, et al. Genome-wide analysis of MYB transcription factors and their responses to salt stress in Casuarina equisetifolia. BMC Plant Biol. 2021;21(1):328.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Gong W, Ju Z, Chai J, Zhou X, Lin D, Su W, et al. Physiological and transcription analyses reveal the regulatory mechanism in oat (Avena sativa) seedlings with different drought resistance under PEG-Induced drought stress. Agronomy. 2022;12(5):1005.

    Article  CAS  Google Scholar 

  73. Yin H, Yin D, Zhang M, Gao Z, Tuluhong M, Li X et al. Validation of appropriate reference genes for qRT-PCR normalization in Oat (Avena sativa L.) under UV-B and high-light stresses. Int J Mol Sci. 2022;23(19).

  74. Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Methods. 2012;9(7):671–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Guo X, Niu J, Cao X. Heterologous expression of Salvia miltiorrhiza microRNA408 enhances tolerance to salt stress in Nicotiana Benthamiana. Int J Mol Sci. 2018;19(12).

  76. Guan L, Haider MS, Khan N, Nasim M, Jiu S, Fiaz M et al. Transcriptome sequence analysis elaborates a complex defensive mechanism of grapevine (Vitis vinifera L.) in response to salt stress. Int J Mol Sci. 2018;19(12).

Download references

Acknowledgements

Not applicable.

Funding

This study was supported by the Guangdong Provincial Key Areas R&D Programs (2022B0202110003).

Author information

Author notes

  1. Yang Chen and Aixue Li contributed equally to this work.

Authors and Affiliations

  1. Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100083, China

    Yang Chen, Aixue Li, Quan Chen, Dayu Pan, Rui Guo, Han Zhang, Cheng Wang, Hongtu Dong, Chaoyang Qiu, Bin Luo & Peichen Hou

  2. Intelligent Equipment Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100083, China

    Yang Chen, Aixue Li, Quan Chen, Dayu Pan, Rui Guo, Han Zhang, Cheng Wang, Hongtu Dong, Chaoyang Qiu, Bin Luo & Peichen Hou

  3. School of Biological Sciences, University of Western Australia, Crawley, WA, 6009, Australia

    Ping Yun, Lana Shabala & Sergey Shabala

  4. International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, 528000, China

    Lana Shabala & Sergey Shabala

  5. Department of Botany, Faculty of Science, Port Said University, Port Said, 42526, Egypt

    Hassan Ahmed Ibraheem Ahmed

  6. College of Forestry and Prataculture, Ningxia University, Yinchuan, 750021, China

    Haiying Hu

  7. State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 625014, China

    Yuanying Peng

  8. College of Life Scienc, Jilin Agricultural University, Changchun, 130118, China

    Yang Chen

Authors
  1. Yang Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Aixue Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ping Yun
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Quan Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Dayu Pan
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Rui Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Han Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Hassan Ahmed Ibraheem Ahmed
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Haiying Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Yuanying Peng
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Cheng Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Hongtu Dong
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Chaoyang Qiu
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Lana Shabala
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Sergey Shabala
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Bin Luo
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Peichen Hou
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Y.C., A.L. conceived and designed the research. B.L. and P.H. guided the experiment. Y.C. and P.H. conducted the experiments. Y.C. and P.H. wrote the manuscript. Q.C., H.Z., D.P., R.G., H.A.IA., H.H., P.Y., Y.P., C.W., H.D., C.Q. and L.S. provided technical assistance. P.Y. and S.S. critically reviewed and revised the manuscript. All authors have read and agreed to the published version of the manuscript.

Corresponding authors

Correspondence to Sergey Shabala, Bin Luo or Peichen Hou.

Ethics declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Material 1

Supplementary Material 2

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chen, Y., Li, A., Yun, P. et al. Genome-wide analysis of MYB transcription factor family and AsMYB1R subfamily contribution to ROS homeostasis regulation in Avena sativa under PEG-induced drought stress. BMC Plant Biol 24, 632 (2024). https://doi.org/10.1186/s12870-024-05251-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1186/s12870-024-05251-w

Keywords

BMC Plant Biology

ISSN: 1471-2229

Contact us