MULTIPASS, a rice R2R3-type MYB transcription factor, regulates adaptive growth by integrating multiple hormonal pathways

Unveiling the power of MYB transcription factors: Master regulators of multi-stress responses and development in cotton

Plants, being immobile, are subject to environmental stresses more than other creatures, necessitating highly effective stress tolerance systems. Transcription factors (TFs) play a crucial role in the adaptation mechanism as they can be activated by diverse signals and ultimately control the expression of stress-responsive genes. One of the most prominent plant TFs family is MYB (myeloblastosis), which is involved in secondary metabolites, developmental mechanisms, biological processes, cellular architecture, metabolic pathways, and stress responses. Extensive research has been conducted on the involvement of MYB TFs in crops, while their role in cotton remains largely unexplored. We also utilized genome-wide data to discover potential 440 MYB genes and investigated their plausible roles in abiotic and biotic stress conditions, as well as in different tissues across diverse transcriptome databases. This review primarily summarized the structure and classification of MYB TFs biotic and abiotic stress tolerance and their role in secondary metabolism in different crops, especially in cotton. However, it intends to identify gaps in current knowledge and emphasize the need for further research to enhance our understanding of MYB roles in plants.

Genome-wide identification of R2R3-MYB transcription factor subfamily genes involved in salt stress in rice (Oryza sativa L.)

BACKGROUND

R2R3-MYB transcription factors belong to one of the largest gene subfamilies in plants, and they are involved in diverse biological processes. However, the role of R2R3-MYB transcription factor subfamily genes in the response of rice (Oryza sativa L.) to salt stress has been rarely reported.

RESULTS

In this study, we performed a genome-wide characterization and expression identification of rice R2R3-MYB transcription factor subfamily genes. We identified a total of 117 R2R3-MYB genes in rice and characterized their gene structure, chromosomal location, and cis-regulatory elements. According to the phylogenetic relationships and amino acid sequence homologies, the R2R3-MYB genes were divided into four groups. qRT-PCR of the R2R3-MYB genes showed that the expression levels of 10 genes significantly increased after 3 days of 0.8% NaCl treatment. We selected a high expression gene OsMYB2-115 for further analysis. OsMYB2-115 was highly expressed in the roots, stem, leaf, and leaf sheath. OsMYB2-115 was found to be localized in the nucleus, and the yeast hybrid assay showed that OsMYB2-115 has transcriptional activation activity.

CONCLUSION

This result provides important information for the functional analyses of rice R2R3-MYB transcription factor subfamily genes related to the salt stress response and reveals that OsMYB2-115 may be an important gene associated with salt tolerance in rice.

Regulation of SmEXPA13 expression by SmMYB1R1-L enhances salt tolerance in Salix matsudana Koidz

Expansins, cell wall proteins, play a significant role in plant stress resistance. Our previous study confirmed the expression of the expansin gene SmEXPA13 from Salix matsudana Koidz. enhanced salt tolerance of plants. This report presented an assay that the expression of SmEXPA13 was higher in the salt-resistant willow variety 9901 than in the salt-sensitive variety Yanjiang. In order to understand the possible reasons, a study of the regulation process was conducted. Despite being cloned from both varieties, SmEXPA13 and its promotor showed no significant differences in the structure and sequence. A transcription factor (TF), SmMYB1R1-L, identified through screening the yeast library of willow cDNA, was found to regulate SmEXPA13. Yeast one-hybrid (Y1H) assay confirmed that SmMYB1R1-L could bind to the MYB element at the -520 bp site on the SmEXPA13 promotor. A dual-luciferase reporter assay also demonstrated that SmMYB1R1-L could greatly activate SmEXPA13 expression. The willow calli with over-expression of SmMYB1R1-L exhibited better physiological performance than the wild type under salt stress. Further testing the expression of SmMYB1R1-L displayed it significantly higher in 9901 willow than that in Yanjiang under salt stress. In conclusion, the high accumulation of SmMYB1R1-L in 9901 willow under salt stress led to the high expression of SmEXPA13, resulting in variations in salt stress resistance among willow varieties. The SmMYB1R1-L/SmEXPA13 cascade module in willow offers a new perspective on plant resistance mechanisms.

Mapping of Candidate Genes for Nitrogen Uptake and Utilization in Japonica Rice at Seedling Stage

Nitrogen (N) is one of the essential nutrients for the growth and development of crops. The adequate application of N not only increases the yield of crops but also improves the quality of agricultural products, but the excessive application of N can cause many adverse effects on ecology and the environment. In this study, genome-wide association analysis (GWAS) was performed under low- and high-N conditions based on 788,396 SNPs and phenotypic traits relevant to N uptake and utilization (N content and N accumulation). A total of 75 QTLs were obtained using GWAS, which contained 811 genes. Of 811 genes, 281 genes showed different haplotypes, and 40 genes had significant phenotypic differences among different haplotypes. Of these 40 genes, 5 differentially expressed genes (Os01g0159250, Os02g0618200, Os02g0618400, Os02g0630300, and Os06g0619000) were finally identified as the more valuable candidate genes based on the transcriptome data sequenced from Longjing31 (low-N-tolerant variety) and Songjing 10 (low-N-sensitive variety) under low- and high-N treatments. These new findings enrich the genetic resources for N uptake and utilization in rice, as well as lay a theoretical foundation for improving the efficiency of N uptake and utilization in rice.

Jasmonic acid (JA)-mediating MYB transcription factor1, JMTF1, coordinates the balance between JA and auxin signalling in the rice defence response

The plant hormone jasmonic acid (JA) is a signalling compound involved in the regulation of cellular defence and development in plants. In this study, we investigated the roles of a JA-responsive MYB transcription factor, JMTF1, in the JA-regulated defence response against rice bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo). JMTF1 did not interact with any JASMONATE ZIM-domain (JAZ) proteins. Transgenic rice plants overexpressing JMTF1 showed a JA-hypersensitive phenotype and enhanced resistance against Xoo. JMTF1 upregulated the expression of a peroxidase, OsPrx26, and monoterpene synthase, OsTPS24, which are involved in the biosynthesis of lignin and antibacterial monoterpene, γ-terpinene, respectively. OsPrx26 was mainly expressed in the vascular bundle. Transgenic rice plants overexpressing OsPrx26 showed enhanced resistance against Xoo. In addition to the JA-hypersensitive phenotype, the JMTF1-overexpressing rice plants showed a typical auxin-related phenotype. The leaf divergence and shoot gravitropic responses were defective, and the number of lateral roots decreased significantly in the JMTF1-overexpressing rice plants. JMTF1 downregulated the expression of auxin-responsive genes but upregulated the expression of OsIAA13, a suppressor of auxin signalling. The rice gain-of-function mutant Osiaa13 showed high resistance against Xoo. Transgenic rice plants overexpressing OsEXPA4, a JMTF1-downregulated auxin-responsive gene, showed increased susceptibility to Xoo. JMTF1 is selectively bound to the promoter of OsPrx26 in vivo. These results suggest that JMTF1 positively regulates disease resistance against Xoo by coordinating crosstalk between JA- and auxin-signalling in rice.

Nitrate-responsive OsMADS27 promotes salt tolerance in rice

Salt stress is a major constraint on plant growth and yield. Nitrogen (N) fertilizers are known to alleviate salt stress. However, the underlying molecular mechanisms remain unclear. Here, we show that nitrate-dependent salt tolerance is mediated by OsMADS27 in rice. The expression of OsMADS27 is specifically induced by nitrate. The salt-inducible expression of OsMADS27 is also nitrate dependent. OsMADS27 knockout mutants are more sensitive to salt stress than the wild type, whereas OsMADS27 overexpression lines are more tolerant. Transcriptomic analyses revealed that OsMADS27 upregulates the expression of a number of known stress-responsive genes as well as those involved in ion homeostasis and antioxidation. We demonstrate that OsMADS27 directly binds to the promoters of OsHKT1.1 and OsSPL7 to regulate their expression. Notably, OsMADS27-mediated salt tolerance is nitrate dependent and positively correlated with nitrate concentration. Our results reveal the role of nitrate-responsive OsMADS27 and its downstream target genes in salt tolerance, providing a molecular mechanism for the enhancement of salt tolerance by nitrogen fertilizers in rice. OsMADS27 overexpression increased grain yield under salt stress in the presence of sufficient nitrate, suggesting that OsMADS27 is a promising candidate for the improvement of salt tolerance in rice.

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

Background

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

Results

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

Conclusions

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

Supplementary Information

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

The Characterization of Columnar Apple Gene MdCoL Promoter and Its Response to Abscisic Acid, Brassinosteroid and Gibberellic Acid

Columnar apple was an important germplasm resource to develop compact cultivars for labor-saving cultivation and to study fruit tree architecture. MdCoL is a strong candidate gene for controlling the columnar phenotype in apple. In this study, a 2000 bp upstream region of MdCoL was cloned as a full-length promoter, named MdCoLp1. To gain a better understanding of the characterization of the MdCoL promoter, cis-acting elements and the binding sites of transcription factors were predicted and analyzed, and four binary expression vectors consisting of the GUS reporter gene under the control of the MdCoL promoter was transformed into Arabidopsis thaliana to analyze the response to abscisic acid (ABA), brassinosteroid (BR) and gibberellic acid (GA3) of MdCoL promoters. Multiple transcription factors involving TCP, BEL1 and BES1/BZR1 and other transcription factor (TF) binding sites were predicted on the promoter of MdCoL. Histochemical staining showed that both full-length and 5′ truncated promoters could initiate GUS expression. The GUS activity was the most in leaf and stem, and mainly concentrated in the fibrovascular tissue, followed by root, and the least activity was observed in silique and flower. In addition, MdCoL expression was mainly localized in the quiescent center (QC) and lateral root growing point of root tip and the vascular tissue of stem and leaf by in situ hybridization. The results of exogenous hormones treatment showed that ABA and BR could activate the activity of the MdCoL promoter, while GA3 had opposite effects. In columnar apple seedlings, ABA treatment could upregulate the expression of MdCoL, but GA3 and BR restrained the transcription level of MdCoL. These results provide the foundation for deciphering the regulatory network of hormones affecting MdCoL transcription.

Genome-Wide Identification and Characterization of Chinese Cabbage S1fa Transcription Factors and Their Roles in Response to Salt Stress

The S1fa transcription factor is part of a small family involved in plant growth and development and abiotic stress tolerance. However, the roles of the S1fa genes in abiotic stress tolerance in Chinese cabbage are still unclear. In this study, four S1fa genes in the Chinese cabbage genome were identified and characterized for abiotic stress tolerance. Tissue-specific expression analysis suggested that three of these four S1fa genes were expressed in all tissues of Chinese cabbage, while Bra006994 was only expressed in the silique. Under Hg and Cd stresses, the S1fa genes were significantly expressed but were downregulated under NaCl stresses. The Bra034084 and Bra029784 overexpressing yeast cells exhibited high sensitivity to NaCl stresses, which led to slower growth compared with the wild type yeast cells (EV) under 1 M NaCl stress. In addition, the growth curve of the Bra034084 and Bra029784 overexpressing cells shows that the optical density was reduced significantly under salt stresses. The activities of the antioxidant enzymes, SOD, POD and CAT, were decreased, and the MDA, H₂O₂ and O₂⁻ contents were increased under salt stresses. The expression levels of cell wall biosynthesis genes Ccw14p, Cha1p, Cwp2p, Sed1p, Rlm1p, Rom2p, Mkk1p, Hsp12p, Mkk2p, Sdp1p and YLR194c were significantly enhanced, while Bck1p, and Ptc1p were downregulated under salt stresses. These results suggest that the Bra034084 and Bra029784 genes regulate cell wall biosynthesis and the defense regulatory system under salt stresses. These findings provide a fundamental basis for the further investigation of crop genetic modification to improve crop production and abiotic stress tolerance in Chinese cabbage.

Eutrema EsMYB90 Gene Improves Growth and Antioxidant Capacity of Transgenic Wheat Under Salinity Stress

The ectopic expression of the EsMYB90 transcription factor gene from halophytic Eutrema salsugineum has been reported to enhance the level of anthocyanin and other flavonoid metabolites in transgenic tobacco. In this study, the wheat JW1 overexpressing EsMYB90 showed longer roots and higher fresh weight than that in wild type (WT) under salt stress. In addition, the transgenic wheat plants displayed significantly higher peroxidase (POD) and glutathione S-transferase (GST) activity, as well as markedly lower malondialdehyde (MDA) content than that of the WT during salt stress conditions. The analysis of histochemical staining and H₂O₂ level indicated that the accumulation of reactive oxygen species (ROS) was significantly lower in the roots of transgenic wheat plants compared to the WT under salt stress. Transcriptome analysis revealed that the EsMYB90 gene affected the expression of considerable amounts of stress-related genes that were involved in phenylpropanoid biosynthesis and antioxidant activity in transgenic plants subjected to NaCl treatment. Importantly, the significantly upregulated expression genes in transgenic wheat under salt stress were mainly associated with the antioxidative enzymes POD and GST encoding genes compared with the WT. Furthermore, EsMYB90 is suggested to bind with the MYB-binding elements of pTaANS2 and pTaDFR1 by dual luciferase assay, to activate the transcription of TaANS2 and TaDFR1 genes that are encoding key enzymes of anthocyanin biosynthesis in transgenic wheat plants. All the results indicated that, under salt stress, the EsMYB90 gene plays a crucial role in preventing wheat seedlings from oxidative stress damage via enhancing the accumulation of non-enzymatic flavonoids and activities of antioxidative enzymes, which suggested that EsMYB90 is an ideal candidate gene for the genetic engineering of crops.

Uncovering the Epigenetic Marks Involved in Mediating Salt Stress Tolerance in Plants

The toxic effects of salinity on agricultural productivity necessitate development of salt stress tolerance in food crops in order to meet the escalating demands. Plants use sophisticated epigenetic systems to fine-tune their responses to environmental cues. Epigenetics is the study of heritable, covalent modifications of DNA and histone proteins that regulate gene expression without altering the underlying nucleotide sequence and consequently modify the phenotype. Epigenetic processes such as covalent changes in DNA, histone modification, histone variants, and certain non-coding RNAs (ncRNA) influence chromatin architecture to regulate its accessibility to the transcriptional machinery. Under salt stress conditions, there is a high frequency of hypermethylation at promoter located CpG sites. Salt stress results in the accumulation of active histones marks like H3K9K14Ac and H3K4me3 and the downfall of repressive histone marks such as H3K9me2 and H3K27me3 on salt-tolerance genes. Similarly, the H2A.Z variant of H2A histone is reported to be down regulated under salt stress conditions. A thorough understanding of the plasticity provided by epigenetic regulation enables a modern approach to genetic modification of salt-resistant cultivars. In this review, we summarize recent developments in understanding the epigenetic mechanisms, particularly those that may play a governing role in the designing of climate smart crops in response to salt stress.

CRISPR/Cas9-Mediated SlMYBS2 Mutagenesis Reduces Tomato Resistance to Phytophthora infestans

Phytophthora infestans (P. infestans) recently caused epidemics of tomato late blight. Our study aimed to identify the function of the SlMYBS2 gene in response to tomato late blight. To further investigate the function of SlMYBS2 in tomato resistance to P. infestans, we studied the effects of SlMYBS2 gene knock out. The SlMYBS2 gene was knocked out by CRISPR-Cas9, and the resulting plants (SlMYBS2 gene knockout, slmybs2-c) showed reduced resistance to P. infestans, accompanied by increases in the number of necrotic cells, lesion sizes, and disease index. Furthermore, after P. infestans infection, the expression levels of pathogenesis-related (PR) genes in slmybs2-c plants were significantly lower than those in wild-type (AC) plants, while the number of necrotic cells and the accumulation of reactive oxygen species (ROS) were higher than those in wild-type plants. Taken together, these results indicate that SlMYBS2 acts as a positive regulator of tomato resistance to P. infestans infection by regulating the ROS level and the expression level of PR genes.

Salt Stress Promotes Abscisic Acid Accumulation to Affect Cell Proliferation and Expansion of Primary Roots in Rice

The primary root is the basic component of the root system and plays a key role in early seedling growth in rice. Its growth is easily affected by environmental cues, such as salt stress. Abscisic acid (ABA) plays an essential role in root development, but the molecular mechanism underlying ABA-regulated root growth in response to salt stress remains poorly understood. In this study, we report that salt stress inhibits primary root elongation and promotes primary root swelling. Moreover, salt stress induces the expression of ABA-responsive genes and ABA accumulation in the primary root, revealing that ABA plays an essential role in salt-modulated root growth. Transgenic lines of OsSAPK10-OE and OsABIL2-OE, which constitutively express OsSAPK10 or OsABIL2, with enhanced or attenuated ABA signaling, show increased and decreased sensitivity to salt, correspondingly. Microscopic analysis indicates that salt and ABA inhibits cell proliferation and promotes cell expansion in the root apical meristem. Transcriptome analysis showed that ABA induces the expression of EXPANSIN genes. Further investigations indicate that ABA exerts these effects largely through ABA signaling. Thus, our findings deepen our understanding of the role of ABA in controlling primary root growth in response to salt stress, and this knowledge can be used by breeders to cultivate rice varieties suitable for saline–alkali land.

The Streptochaeta Genome and the Evolution of the Grasses

In this work, we sequenced and annotated the genome of Streptochaeta angustifolia, one of two genera in the grass subfamily Anomochlooideae, a lineage sister to all other grasses. The final assembly size is over 99% of the estimated genome size. We find good collinearity with the rice genome and have captured most of the gene space. Streptochaeta is similar to other grasses in the structure of its fruit (a caryopsis or grain) but has peculiar flowers and inflorescences that are distinct from those in the outgroups and in other grasses. To provide tools for investigations of floral structure, we analyzed two large families of transcription factors, AP2-like and R2R3 MYBs, that are known to control floral and spikelet development in rice and maize among other grasses. Many of these are also regulated by small RNAs. Structure of the gene trees showed that the well documented whole genome duplication at the origin of the grasses (ρ) occurred before the divergence of the Anomochlooideae lineage from the lineage leading to the rest of the grasses (the spikelet clade) and thus that the common ancestor of all grasses probably had two copies of the developmental genes. However, Streptochaeta (and by inference other members of Anomochlooideae) has lost one copy of many genes. The peculiar floral morphology of Streptochaeta may thus have derived from an ancestral plant that was morphologically similar to the spikelet-bearing grasses. We further identify 114 loci producing microRNAs and 89 loci generating phased, secondary siRNAs, classes of small RNAs known to be influential in transcriptional and post-transcriptional regulation of several plant functions.

Transcriptomic Analysis Provides Insights into Foliar Zinc Application Induced Upregulation in 2-Acetyl-1-pyrroline and Related Transcriptional Regulatory Mechanism in Fragrant Rice

The involvement of zinc (Zn) in terms of aroma formation has been rarely investigated. This study shows that the regulation of 2-acetyl-1-pyrroline (2AP) biosynthesis was evaluated in two different rice cultivars under foliar Zn application. The results showed that the 2AP and Zn contents in leaves and grains were improved substantially under foliar Zn application. The 2AP content was positively related to the expression P5CS2 gene, contents of proline, 1-pyrroline, and Δ1-pyrroline-5-carboxylate (P5C), and the activity of pyrroline-5-carboxylate synthase (P5CS) under Zn application in fragrant rice. Multiple transcription factors (TFs) were differently expressed, such as bZIPs, NACs, and MYBs, to play a role under Zn treatments in fragrant rice, suggesting the crucial role of 46 differently expressed TFs in 2AP improvements in fragrant rice. Furthermore, this study showed that the optimal foliar Zn application at a concentration of 30 mg L^-1 could increase the 2AP content of aromatic rice and keep the yield stable or increase the yield. TFs were involved in regulating to promote the 2AP formation in aromatic rice under the foliar Zn application. However, the relationship between 2AP biosynthesis pathway genes and TFs in fragrant rice remains to be further studied.

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.

Scrutinizing the impact of water deficit in plants: Transcriptional regulation, signaling, photosynthetic efficacy, and management

Suboptimal availability of water limits plant growth, development, and performance. Drought is one of the leading factors responsible for worldwide crop yield reduction. In the future, owing to climate changes, more agricultural land will be affected by prolonged periods of water deficit. Thus, understanding the fundamental mechanism of drought response is a major scientific concern for improvement of crop production. To combat drought stress, plants deploy varied mechanistic strategies and alter their morphological, physiochemical, and molecular attributes. This helps plant to enhance water uptake and storage, reduce water loss and avoid wilting. Induction of several transcription factors and drought responsive genes leads to synthesis of stress proteins, regulation of water channels i.e. aquaporins and production of osmolytes that are essential for maintenance of osmotic balance at the cellular level. Self- and hormone-regulated signaling pathways are often stimulated by plants after receiving drought stress signals via secondary messengers, mitogen-activated protein kinases, and stress hormones. These signaling cascades often leads to stomatal closure and reduction in transpiration rates. Reduced carbon dioxide diffusion in chloroplast, lowered efficacy of photosystems, and other metabolic constraints limits the key regulatory photosynthetic process during water deficit. The impact of these stomatal and nonstomatal limitations varies with stress intensity, superimposed stresses and plant species. A clear understanding of the drought resistance process is thus important before adopting strategies for imparting drought tolerance in plants. These management practices at present include exogenous hormone application, breeding, and genetic engineering techniques for combating the water deficit issues.

MYB Transcription Factors and Its Regulation in Secondary Cell Wall Formation and Lignin Biosynthesis during Xylem Development

The secondary wall is the main part of wood and is composed of cellulose, xylan, lignin, and small amounts of structural proteins and enzymes. Lignin molecules can interact directly or indirectly with cellulose, xylan and other polysaccharide molecules in the cell wall, increasing the mechanical strength and hydrophobicity of plant cells and tissues and facilitating the long-distance transportation of water in plants. MYBs (v-myb avian myeloblastosis viral oncogene homolog) belong to one of the largest superfamilies of transcription factors, the members of which regulate secondary cell-wall formation by promoting/inhibiting the biosynthesis of lignin, cellulose, and xylan. Among them, MYB46 and MYB83, which comprise the second layer of the main switch of secondary cell-wall biosynthesis, coordinate upstream and downstream secondary wall synthesis-related transcription factors. In addition, MYB transcription factors other than MYB46/83, as well as noncoding RNAs, hormones, and other factors, interact with one another to regulate the biosynthesis of the secondary wall. Here, we discuss the biosynthesis of secondary wall, classification and functions of MYB transcription factors and their regulation of lignin polymerization and secondary cell-wall formation during wood formation.

Maintenance of Cell Wall Integrity under High Salinity

Cell wall biosynthesis is a complex biological process in plants. In the rapidly growing cells or in the plants that encounter a variety of environmental stresses, the compositions and the structure of cell wall can be dynamically changed. To constantly monitor cell wall status, plants have evolved cell wall integrity (CWI) maintenance system, which allows rapid cell growth and improved adaptation of plants to adverse environmental conditions without the perturbation of cell wall organization. Salt stress is one of the abiotic stresses that can severely disrupt CWI, and studies have shown that the ability of plants to sense and maintain CWI is important for salt tolerance. In this review, we highlight the roles of CWI in salt tolerance and the mechanisms underlying the maintenance of CWI under salt stress. The unsolved questions regarding the association between the CWI and salt tolerance are discussed.

Advances in Sensing, Response and Regulation Mechanism of Salt Tolerance in Rice

Soil salinity is a serious menace in rice production threatening global food security. Rice responses to salt stress involve a series of biological processes, including antioxidation, osmoregulation or osmoprotection, and ion homeostasis, which are regulated by different genes. Understanding these adaptive mechanisms and the key genes involved are crucial in developing highly salt-tolerant cultivars. In this review, we discuss the molecular mechanisms of salt tolerance in rice—from sensing to transcriptional regulation of key genes—based on the current knowledge. Furthermore, we highlight the functionally validated salt-responsive genes in rice.

Contributions of Adaptive Plant Architecture to Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice: Molecular Mechanisms Based on Transcriptional Networks

Genetic novelties are important nucleators of adaptive speciation. Transgressive segregation is a major mechanism that creates genetic novelties with morphological and developmental attributes that confer adaptive advantages in certain environments. This study examined the morpho-developmental and physiological profiles of recombinant inbred lines (RILs) from the salt-sensitive IR29 and salt-tolerant Pokkali rice, representing the total range of salt tolerance including the outliers at both ends of the spectrum. Morpho-developmental and physiological profiles were integrated with a hypothesis-driven interrogation of mRNA and miRNA transcriptomes to uncover the critical genetic networks that have been rewired for novel adaptive architecture. The transgressive super-tolerant FL510 had a characteristic small tiller angle and wider, more erect, sturdier, and darker green leaves. This unique morphology resulted in lower transpiration rate, which also conferred a special ability to retain water more efficiently for osmotic avoidance. The unique ability for water retention conferred by such adaptive morphology appeared to enhance the efficacy of defenses mediated by Na+ exclusion mechanism (SalTol-effects) inherited from Pokkali. The super-tolerant FL510 and super-sensitive FL499 had the smallest proportions of differentially expressed genes with little overlaps. Genes that were steadily upregulated in FL510 comprised a putative cytokinin-regulated genetic network that appeared to maintain robust growth under salt stress through well-orchestrated cell wall biogenesis and cell expansion, likely through major regulatory (OsRR23, OsHK5) and biosynthetic (OsIPT9) genes in the cytokinin signaling pathway. Meanwhile, a constitutively expressed cluster in FL510 prominently featured two transcription factors (OsIBH1, TAC3) that control tiller angle and growth habit through the brassinosteroid signaling pathway. Both the putative cytokinin-mediated and brassinosteroid-mediated clusters appeared to function as highly coordinated network synergies in FL510. In contrast, both networks appeared to be sub-optimal and inferior in the other RILs and parents as they were disjointed and highly fragmented. Transgressively expressed miRNAs (miR169, miR397, miR827) were also identified as prominent signatures of FL510, with functional implications to mechanisms that support robust growth, homeostasis, and osmotic stress avoidance. Results of this study demonstrate how genetic recombination creates novel morphology that complements inducible defenses hence transgressive adaptive phenotypes.

Selenium downregulates auxin and ethylene biosynthesis in rice seedlings to modify primary metabolism and root architecture

Selenium modulates the formation of primary and lateral roots through alterations in auxin and ethylene, leading to new patterns of root architecture in rice seedlings. Selenium (Se) at low concentrations can control root growth through interaction with hormone biosynthesis. Auxin and ethylene have been shown to control the root architecture, with most of the information obtained from the eudicots such Arabidopsis and Nicotiana tabacum. Here, we presented the effects of Se on auxin and ethylene pathways and examined their impact on primary metabolism and root system architecture in rice (Oryza sativa L.) seedlings. Se treatment increased elongation of primary root, but decreased the number and length of lateral roots. Se led to decreased expression of genes associated with the biosynthesis of auxin and ethylene, concomitantly with reduced production of these hormones by the roots. Moreover, Se decreased the abundance of transcripts encoding auxin transport proteins. Indole-3-acetic acid (IAA) treatment overrode the repressive effect of Se on lateral root growth. The ethylene synthesis inhibitor L-α-(2-aminoethoxyvinyl)-glycine (AVG) increased elongation of primary root, whereas the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) resulted in the opposite effect. Soluble sugars accumulate in roots of rice seedlings under Se treatment. Thus, Se modulates the formation of primary and lateral roots through alterations in auxin and ethylene, leading to new patterns of root architecture in rice seedlings.

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

Plants face various stresses during the growth and development processes. The specific transcription factors bind to the cis-acting elements upstream of the stress resistance genes, specifically regulating the expression of the gene in plants and increasing the adaptability of plants to environmental stress. The transcription factor-mediated gene expression regulatory networks play an important role in plant stress response pathways. MYB (v-myb avian myeloblastosis viral oncogene homolog) transcription factor is one of the largest members of the transcription factor family in plants. It participates and has a great influence on all aspects of plant growth and development. It plays an important role in plant secondary metabolic regulation, hormone and environmental factor responses, cell differentiation, organ morphogenesis, and cell cycle regulation. This review mainly introduces the characteristics, structure, and classification of MYB transcription factors, as well as the abiotic stress resistance to drought, salt, temperature, and other functions in breeding, and provides a reference for the research and utilization of transcription factors in the future.

Validation of Yield Component Traits Identified by Genome-Wide Association Mapping in a tropical japonica × tropical japonica Rice Biparental Mapping Population

The Rice Diversity Panel 1 (RDP1) was developed for genome-wide association (GWA) studies to explore five rice ( L.) subpopulations (, , , , and ). The RDP1 was evaluated for over 30 traits, including agronomic, panicle architecture, seed, and disease traits and genotyped with 700,000 single nucleotide polymorphisms (SNPs). Most rice grown in the southern United States is and thus the diversity in this subpopulation is interesting to U.S. breeders. Among the RDP1 accessions, 'Estrela' and 'NSFTV199' are both phenotypically and genotypically diverse, thus making them excellent parents for a biparental mapping population. The objectives were to (i) ascertain the GWA QTLs from the RDP1 GWA studies that overlapped with the QTLs uncovered in an Estrela × NSFTV199 recombinant inbred line (RIL) population evaluated for 15 yield traits, and (ii) identify known or novel genes potentially controlling specific yield component traits. The 256 RILs were genotyped with 132 simple sequence repeat markers and 70 QTLs were found. Perl scripts were developed for automatic identification of the underlying candidate genes in the GWA QTL regions. Approximately 100 GWA QTLs overlapped with 41 Estrela × NSFTV199 QTL (RIL QTL) regions and 47 known genes were identified. Two seed trait RIL QTLs with overlapping GWA QTLs were not associated with a known gene. Segregating SNPs in the overlapping GWA QTLs for RIL QTLs with high values will be evaluated as potential DNA markers useful to breeding programs for the associated yield trait.

Overexpression of a SBP-Box Gene (VpSBP16) from Chinese Wild Vitis Species in Arabidopsis Improves Salinity and Drought Stress Tolerance

Salinity and drought are two major abiotic stresses that limit grape productivity. Responses to stress in grape are known to be regulated by several families of transcription factors. However, little is known about the role of grape Squamosa promoter binding protein (SBP)-box transcription factor genes in response to abiotic stress. To better understand the functions of the grape SBP-box genes in abiotic stress tolerance, a full-length complementary DNA (cDNA) sequence of the putative SBP-box transcription factor gene, VpSBP16 was amplified from Chinese wild grapevine Vitis pseudoreticulata clone "Baihe-35-1". We observed that the VpSBP16 protein fused to the green fluorescent protein (GFP) reporter accumulated in the nucleus when transiently expressed in onion epidermal cells. Moreover, VpSBP16 was shown to have transcriptional activation activity using a yeast trans-activation assay. We performed a VpSBP16 functional analysis through the characterization of transgenic Arabidopsis thaliana plants constitutively over-expressing VpSBP16. The transgenic lines had longer roots and the seeds had a higher germination rate than the wild type (WT) under osmotic stress. In addition, the accumulation of reactive oxygen species (ROS) of transgenic seedlings was significantly lower than WT in the transgenic lines, as was electrolyte leakage. VpSBP16 overexpression also elevated expression levels of stress-response genes involved in the salt overly sensitive (SOS) pathway. These results indicate that overexpression VpSBP16 in A. thaliana enhances tolerance of salt and drought stress during seed germination, as well in seedlings and mature plants, by regulating SOS and ROS signaling cascades.

Engineering abiotic stress response in plants for biomass production

One of the major challenges in today's agriculture is to achieve enhanced plant growth and biomass even under adverse environmental conditions. Recent advancements in genetics and molecular biology have enabled the identification of a complex signaling network contributing toward plant growth and development on the one hand and abiotic stress response on the other hand. As an outcome of these studies, three major approaches have been identified as having the potential to improve biomass production in plants under abiotic stress conditions. These approaches deal with having changes in the following: (i) plant-microbe interactions; (ii) cell wall biosynthesis; and (iii) phytohormone levels. At the same time, employing functional genomics and genetics-based approaches, a very large number of genes have been identified that play a key role in abiotic stress tolerance. Our Minireview is an attempt to unveil the cross-talk that has just started to emerge between the transcriptional circuitries for biomass production and abiotic stress response. This knowledge may serve as a valuable resource to eventually custom design the crop plants for higher biomass production, in a more sustainable manner, in marginal lands under variable climatic conditions.

Genome-wide organization and expression profiling of the R2R3-MYB transcription factor family in pineapple (Ananas comosus)

Background

The MYB proteins comprise one of the largest families of plant transcription factors, which are involved in various plant physiological and biochemical processes. Pineapple (Ananas comosus) is one of three most important tropical fruits worldwide. The completion of pineapple genome sequencing provides a great opportunity to investigate the organization and evolutionary traits of pineapple MYB genes at the genome-wide level.

Results

In the present study, a total of 94 pineapple R2R3-MYB genes were identified and further phylogenetically classified into 26 subfamilies, as supported by the conserved gene structures and motif composition. Collinearity analysis indicated that the segmental duplication events played a crucial role in the expansion of pineapple MYB gene family. Further comparative phylogenetic analysis suggested that there have been functional divergences of MYB gene family during plant evolution. RNA-seq data from different tissues and developmental stages revealed distinct temporal and spatial expression profiles of the AcMYB genes. Further quantitative expression analysis showed the specific expression patterns of the selected putative stress-related AcMYB genes in response to distinct abiotic stress and hormonal treatments. The comprehensive expression analysis of the pineapple MYB genes, especially the tissue-preferential and stress-responsive genes, could provide valuable clues for further function characterization.

Conclusions

In this work, we systematically identified AcMYB genes by analyzing the pineapple genome sequence using a set of bioinformatics approaches. Our findings provide a global insight into the organization, phylogeny and expression patterns of the pineapple R2R3-MYB genes, and hence contribute to the greater understanding of their biological roles in pineapple.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3896-y) contains supplementary material, which is available to authorized users.

Brassinosteroids: A Promising Option in Deciphering Remedial Strategies for Abiotic Stress Tolerance in Rice

Rice is an important staple crop as it feeds about a half of the earth's population. It is known to be sensitive to a range of abiotic stresses which result in significant decline in crop productivity. Recently, the use of phytohormones for abiotic stress amelioration has generated considerable interest. Plants adapt to various environmental stresses by undergoing series of changes at physiological and molecular levels which are cooperatively modulated by various phytohormones. Brassinosteroids (BRs) are a class of naturally occurring steroidal phytohormones, best known for their role in plant growth and development. For the past two decades, greater emphasis on studies related to BRs biosynthesis, distribution and signaling has resulted in better understanding of BRs function. Recent advances in the use of contemporary genetic, biochemical and proteomic tools, with a vast array of accessible biological resources has led to an extensive exploration of the key regulatory components in BR signaling networks, thus making it one of the most well-studied hormonal pathways in plants. The present review highlights the advancements of knowledge in BR research and links it with its growing potential in abiotic stress management for important crop like rice.

Genome-Wide Identification and Analysis of Genes, Conserved between japonica and indica Rice Cultivars, that Respond to Low-Temperature Stress at the Vegetative Growth Stage

Cold stress is very detrimental to crop production. However, only a few genes in rice have been identified with known functions related to cold tolerance. To meet this agronomic challenge more effectively, researchers must take global approaches to select useful candidate genes and find the major regulatory factors. We used five Gene expression omnibus series data series of Affymetrix array data, produced with cold stress-treated samples from the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/), and identified 502 cold-inducible genes common to both japonica and indica rice cultivars. From them, we confirmed that the expression of two randomly chosen genes was increased by cold stress in planta. In addition, overexpression of OsWRKY71 enhanced cold tolerance in 'Dongjin,' the tested japonica cultivar. Comparisons between japonica and indica rice, based on calculations of plant survival rates and chlorophyll fluorescence, confirmed that the japonica rice was more cold-tolerant. Gene Ontology enrichment analysis indicate that the 'L-phenylalanine catabolic process,' within the Biological Process category, was the most highly overrepresented under cold-stress conditions, implying its significance in that response in rice. MapMan analysis classified 'Major Metabolic' processes and 'Regulatory Gene Modules' as two other major determinants of the cold-stress response and suggested several key cis-regulatory elements. Based on these results, we proposed a model that includes a pathway for cold stress-responsive signaling. Results from our functional analysis of the main signal transduction and transcription regulation factors identified in that pathway will provide insight into novel regulatory metabolism(s), as well as a foundation by which we can develop crop plants with enhanced cold tolerance.

OsSGL, a novel pleiotropic stress-related gene enhances grain length and yield in rice

Abiotic stress seriously affects the yield of rice (Oryza sativa L.). Grain yield in rice is multiplicatively determined by the number of panicles, number of grains per panicle, and grain weight. Here, we describe the molecular and functional characterization of STRESS_tolerance and GRAIN_LENGTH (OsSGL), a rice gene strongly up-regulated by a wide spectrum of abiotic stresses. OsSGL encodes a putative member of the DUF1645 protein family of unknown function. Overexpression of OsSGL significantly altered certain development processes greatly and positively affecting an array of traits in transgenic rice plants, including increased grain length, grain weight and grain number per panicle, resulting in a significant increase in yield. Microscopical analysis showed that the enhanced OsSGL expression promoted cell division and grain filling. Microarray and quantitative real-time PCR (qRT-PCR) analyses revealed that a large number of genes involved in stress-response, cell cycle and cytokinin signaling processes were induced or suppressed in OsSGL-overexpressing plants. Together, our results suggest that OsSGL may regulate stress-tolerance and cell growth by acting via a cytokinin signaling pathway. This study not only contributes to our understanding of the underlying mechanism regulating rice stress-tolerance and grain length, but also provides a strategy for tailor-made crop yield improvement.

Cell Wall Metabolism in Response to Abiotic Stress

This review focuses on the responses of the plant cell wall to several abiotic stresses including drought, flooding, heat, cold, salt, heavy metals, light, and air pollutants. The effects of stress on cell wall metabolism are discussed at the physiological (morphogenic), transcriptomic, proteomic and biochemical levels. The analysis of a large set of data shows that the plant response is highly complex. The overall effects of most abiotic stress are often dependent on the plant species, the genotype, the age of the plant, the timing of the stress application, and the intensity of this stress. This shows the difficulty of identifying a common pattern of stress response in cell wall architecture that could enable adaptation and/or resistance to abiotic stress. However, in most cases, two main mechanisms can be highlighted: (i) an increased level in xyloglucan endotransglucosylase/hydrolase (XTH) and expansin proteins, associated with an increase in the degree of rhamnogalacturonan I branching that maintains cell wall plasticity and (ii) an increased cell wall thickening by reinforcement of the secondary wall with hemicellulose and lignin deposition. Taken together, these results show the need to undertake large-scale analyses, using multidisciplinary approaches, to unravel the consequences of stress on the cell wall. This will help identify the key components that could be targeted to improve biomass production under stress conditions.

Antagonistic regulation of Arabidopsis growth by brassinosteroids and abiotic stresses

To withstand ever-changing environmental stresses, plants are equipped with phytohormone-mediated stress resistance mechanisms. Salt stress triggers abscisic acid (ABA) signaling, which enhances stress tolerance at the expense of growth. ABA is thought to inhibit the action of growth-promoting hormones, including brassinosteroids (BRs). However, the regulatory mechanisms that coordinate ABA and BR activity remain to be discovered. We noticed that ABA-treated seedlings exhibited small, round leaves and short roots, a phenotype that is characteristic of the BR signaling mutant, brassinosteroid insensitive1-9 (bri1-9). To identify genes that are antagonistically regulated by ABA and BRs, we examined published Arabidopsis microarray data sets. Of the list of genes identified, those upregulated by ABA but downregulated by BRs were enriched with a BRRE motif in their promoter sequences. After validating the microarray data using quantitative RT-PCR, we focused on RD26, which is induced by salt stress. Histochemical analysis of transgenic Arabidopsis plants expressing RD26pro:GUS revealed that the induction of GUS expression after NaCl treatment was suppressed by co-treatment with BRs, but enhanced by co-treatment with propiconazole, a BR biosynthetic inhibitor. Similarly, treatment with bikinin, an inhibitor of BIN2 kinase, not only inhibited RD26 expression, but also reduced the survival rate of the plant following exposure to salt stress. Our results suggest that ABA and BRs act antagonistically on their target genes at or after the BIN2 step in BR signaling pathways, and suggest a mechanism by which plants fine-tune their growth, particularly when stress responses and growth compete for resources.

Transcriptional control of ROS homeostasis by KUODA1 regulates cell expansion during leaf development

The final size of an organism, or of single organs within an organism, depends on an intricate coordination of cell proliferation and cell expansion. Although organism size is of fundamental importance, the molecular and genetic mechanisms that control it remain far from understood. Here we identify a transcription factor, KUODA1 (KUA1), which specifically controls cell expansion during leaf development in Arabidopsis thaliana. We show that KUA1 expression is circadian regulated and depends on an intact clock. Furthermore, KUA1 directly represses the expression of a set of genes encoding for peroxidases that control reactive oxygen species (ROS) homeostasis in the apoplast. Disruption of KUA1 results in increased peroxidase activity and smaller leaf cells. Chemical or genetic interference with the ROS balance or peroxidase activity affects cell size in a manner consistent with the identified KUA1 function. Thus, KUA1 modulates leaf cell expansion and final organ size by controlling ROS homeostasis.

During plant development, organ size is controlled by cell proliferation and expansion, but the molecular mechanisms involved are unclear. Here, Lu et al. show that leaf cell expansion is controlled by the KUA1 transcription factor that acts in a circadian manner and modulates the expression of genes encoding cell wall-localized peroxidases.

SALT-RESPONSIVE ERF1 is a negative regulator of grain filling and gibberellin-mediated seedling establishment in rice

Grain quality is an important agricultural trait that is mainly determined by grain size and composition. Here, we characterize the role of the rice transcription factor (TF) SALT-RESPONSIVE ERF1 (SERF1) during grain development. Through genome-wide expression profiling and chromatin immunoprecipitation, we found that SERF1 directly regulates RICE PROLAMIN-BOX BINDING FACTOR (RPBF), a TF that functions as a positive regulator of grain filling. Loss of SERF1 enhances RPBF expression resulting in larger grains with increased starch content, while SERF1 overexpression represses RPBF resulting in smaller grains. Consistently, during grain filling, starch biosynthesis genes such as GRANULE-BOUND STARCH SYNTHASEI (GBSSI), STARCH SYNTHASEI (SSI), SSIIIa, and ADP-GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT2 (AGPL2) are up-regulated in SERF1 knockout grains. Moreover, SERF1 is a direct upstream regulator of GBSSI. In addition, SERF1 negatively regulates germination by controlling RPBF expression, which mediates the gibberellic acid (GA)-induced expression of RICE AMYLASE1A (RAmy1A). Loss of SERF1 results in more rapid seedling establishment, while SERF1 overexpression has the opposite effect. Our study reveals that SERF1 represents a negative regulator of grain filling and seedling establishment by timing the expression of RPBF.

The contribution of SERF1 to root-to-shoot signaling during salinity stress in rice

Stress perception and communication play important roles in the adaptation of plants to changing environmental conditions. Plant roots are the first organs to detect changes in the soil water potential induced by salt stress. In the presence of salinity stress, root-to-shoot communication occurs to adjust the growth of the whole plant. So far, the phytohormone abscisic acid (ABA), hydraulic signals and reactive oxygen species (ROS) have been proposed to mediate this communication under salt stress. Recently, we identified the rice transcription factor SALT-RESPONSIVE ERF1 (SERF1), which regulates a ROS-dependent transcriptional cascade in roots required for salinity tolerance. Upon salt stress, SERF1 knockout mutant plants show an increased leaf temperature as compared with wild type. As this occurs within the first 20 min of salt stress, we here evaluated the involvement of SERF1 in the perception of salt stress in the shoot. By metabolic profiling and expression analysis we show that the action of SERF1 in signal communication to the shoot is independent from ABA, but does affect the accumulation of ROS-related metabolites and transcripts under short-term salt stress.

Tolerance to drought and salt stress in plants: Unraveling the signaling networks

Tolerance of plants to abiotic stressors such as drought and salinity is triggered by complex multicomponent signaling pathways to restore cellular homeostasis and promote survival. Major plant transcription factor families such as bZIP, NAC, AP2/ERF, and MYB orchestrate regulatory networks underlying abiotic stress tolerance. Sucrose non-fermenting 1-related protein kinase 2 and mitogen-activated protein kinase pathways contribute to initiation of stress adaptive downstream responses and promote plant growth and development. As a convergent point of multiple abiotic cues, cellular effects of environmental stresses are not only imbalances of ionic and osmotic homeostasis but also impaired photosynthesis, cellular energy depletion, and redox imbalances. Recent evidence of regulatory systems that link sensing and signaling of environmental conditions and the intracellular redox status have shed light on interfaces of stress and energy signaling. ROS (reactive oxygen species) cause severe cellular damage by peroxidation and de-esterification of membrane-lipids, however, current models also define a pivotal signaling function of ROS in triggering tolerance against stress. Recent research advances suggest and support a regulatory role of ROS in the cross talks of stress triggered hormonal signaling such as the abscisic acid pathway and endogenously induced redox and metabolite signals. Here, we discuss and review the versatile molecular convergence in the abiotic stress responsive signaling networks in the context of ROS and lipid-derived signals and the specific role of stomatal signaling.