Expression of the MYB transcription factor gene BplMYB46 affects abiotic stress tolerance and secondary cell wall deposition in Betula platyphylla

Identification and Expression Profiling of Nonphosphorus Glycerolipid Synthase Genes in Response to Abiotic Stresses in Dendrobium catenatum

Dendrobium catenatum, a valuable Chinese herb, frequently experiences abiotic stresses, such as cold and drought, under natural conditions. Nonphosphorus glycerolipid synthase (NGLS) genes are closely linked to the homeostasis of membrane lipids under abiotic stress in plants. However, there is limited information on NGLS genes in D. catenatum. In this study, a total of eight DcaNGLS genes were identified from the D. catenatum genome; these included three monogalactosyldiacylglycerol synthase (DcaMGD1, 2, 3) genes, two digalactosyldiacylglycerol synthase (DcaDGD1, 2) genes, and three sulfoquinovosyldiacylglycerol synthase (DcaSQD1, 2.1, 2.2) genes. The gene structures and conserved motifs in the DcaNGLSs showed a high conservation during their evolution. Gene expression profiling showed that the DcaNGLSs were highly expressed in specific tissues and during rapid growth stages. Furthermore, most DcaNGLSs were strongly induced by freezing and post-freezing recovery. DcaMGD1 and DcaSQDs were greatly induced by salt stress in leaves, while DcaDGDs were primarily induced by salt stress in roots. Under drought stress, most DcaNGLSs were regulated by circadian rhythms, and DcaSQD2 was closely associated with drought recovery. Transcriptome analysis also revealed that MYB might be regulated by circadian rhythm and co-expressed with DcaNGLSs under drought stress. These results provide insight for the further functional investigation of NGLS and the regulation of nonphosphorus glycerolipid biosynthesis in Dendrobium.

Out of the Qinghai-Tibetan Plateau and rapid radiation across Eurasia for Allium section Daghestanica (Amaryllidaceae)

The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidated the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the Qinghai-Tibetan Plateau (QTP) and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4-3 million years ago (Mya). Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.

Resveratrol Alleviates the KCl Salinity Stress of Malus hupehensis Rhed

Applying large amounts of potash fertilizer in apple orchards for high apple quality and yield aggravates KCl stress. As a phytoalexin, resveratrol (Res) participates in plant resistance to biotic stress. However, its role in relation to KCl stress has never been reported. Herein we investigated the role of Res in KCl stress response of Malus hupehensis Rehd., a widely used apple rootstock in China which is sensitive to KCl stress. KCl-stressed apple seedlings showed significant wilting phenotype and decline in photosynthetic rate, and the application of 100 μmol Res alleviated KCl stress and maintained photosynthetic capacity. Exogenous Res can strengthen the activities of peroxidase and catalase, thus eliminating reactive oxygen species production induced by KCl stress. Moreover, exogenous Res can decrease the electrolyte leakage by accumulating proline for osmotic balance under KCl stress. Furthermore, exogenous Res application can affect K+/Na+ homeostasis in cytoplasm by enhancing K+ efflux outside the cells, inhibiting Na+ efflux and K+ absorption, and compartmentalizing K+ into vacuoles through regulating the expression of K+ and Na+ transporter genes. These findings provide a theoretical basis for the application of exogenous Res to relieve the KCl stress of apples.

Transcriptome Sequence Reveals Candidate Genes Involving in the Post-Harvest Hardening of Trifoliate Yam Dioscorea dumetorum

Storage ability of trifoliate yam (Dioscorea dumetorum) is restricted by a severe post-harvest hardening (PHH) phenomenon, which starts within the first 24 h after harvest and renders tubers inedible. Previous work has only focused on the biochemical changes affecting PHH in D. dumetorum. To the best of our knowledge, the candidate genes responsible for the hardening of D. dumetorum have not been identified. Here, transcriptome analyses of D. dumetorum tubers were performed in yam tubers of four developmental stages: 4 months after emergence (4MAE), immediately after harvest (AH), 3 days after harvest (3DAH) and 14 days after harvest (14DAH) of four accessions (Bangou 1, Bayangam 2, Fonkouankem 1, and Ibo sweet 3) using RNA-Seq. In total, between AH and 3DAH, 165, 199, 128 and 61 differentially expressed genes (DEGs) were detected in Bayangam 2, Fonkouankem 1, Bangou 1 and Ibo sweet 3, respectively. Functional analysis of DEGs revealed that genes encoding for CELLULOSE SYNTHASE A (CESA), XYLAN O-ACETYLTRANSFERASE (XOAT), CHLOROPHYLL A/B BINDING PROTEIN1, 2, 3, 4 (LHCB1, LHCB2, LHCB3, and LCH4) and an MYB transcription factor were predominantly and significantly up-regulated 3DAH, implying that these genes were potentially involved in the PHH as confirmed by qRT-PCR. A hypothetical mechanism of this phenomenon and its regulation has been proposed. These findings provide the first comprehensive insights into gene expression in yam tubers after harvest and valuable information for molecular breeding against the PHH.

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.

Synergies and Entanglement in Secondary Cell Wall Development and Abiotic Stress Response in Trees

A major challenge for sustainable food, fuel, and fiber production is simultaneous genetic improvement of yield, biomass quality, and resilience to episodic environmental stress and climate change. For Populus and other forest trees, quality traits involve alterations in the secondary cell wall (SCW) of wood for traditional uses, as well as for a growing diversity of biofuels and bioproducts. Alterations in wood properties that are desirable for specific end uses can have negative effects on growth and stress tolerance. Understanding of the diverse roles of SCW genes is necessary for the genetic improvement of fast-growing, short-rotation trees that face perennial challenges in their growth and development. Here, we review recent progress into the synergies and antagonisms of SCW development and abiotic stress responses, particularly, the roles of transcription factors, SCW biogenesis genes, and paralog evolution.

Potato NAC Transcription Factor StNAC053 Enhances Salt and Drought Tolerance in Transgenic Arabidopsis

The NAC (NAM, ATAF1/2, and CUC2) transcription factors comprise one of the largest transcription factor families in plants and play important roles in stress responses. However, little is known about the functions of potato NAC family members. Here we report the cloning of a potato NAC transcription factor gene StNAC053, which was significantly upregulated after salt, drought, and abscisic acid treatments. Furthermore, the StNAC053-GFP fusion protein was found to be located in the nucleus and had a C-terminal transactivation domain, implying that StNAC053 may function as a transcriptional activator in potato. Notably, Arabidopsis plants overexpressing StNAC053 displayed lower seed germination rates compared to wild-type under exogenous ABA treatment. In addition, the StNAC053 overexpression Arabidopsis lines displayed significantly increased tolerance to salt and drought stress treatments. Moreover, the StNAC053-OE lines were found to have higher activities of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) under multiple stress treatments. Interestingly, the expression levels of several stress-related genes including COR15A,DREB1A, ERD11, RAB18, ERF5, and KAT2, were significantly upregulated in these StNAC053-overexpressing lines. Taken together, overexpression of the stress-inducible StNAC053 gene could enhance the tolerances to both salt and drought stress treatments in Arabidopsis, likely by upregulating stress-related genes.

Dynamics of cell wall structure and related genomic resources for drought tolerance in rice

Cell wall plasticity plays a very crucial role in vegetative and reproductive development of rice under drought and is a highly potential trait for improving rice yield under drought. Drought is a major constraint in rice (Oryza sativa L.) cultivation severely affecting all developmental stages, with the reproductive stage being the most sensitive. Rice plants employ multiple strategies to cope with drought, in which modification in cell wall dynamics plays a crucial role. Over the years, significant progress has been made in discovering the cell wall-specific genomic resources related to drought tolerance at vegetative and reproductive stages of rice. However, questions remain about how the drought-induced changes in cell wall made by these genomic resources potentially influence the vegetative and reproductive development of rice. The possibly major candidate genes underlying the function of quantitative trait loci directly or indirectly associated with the cell wall plasticization-mediated drought tolerance of rice might have a huge promise in dissecting the putative genomic regions associated with cell wall plasticity under drought. Furthermore, engineering the drought tolerance of rice using cell wall-related genes from resurrection plants may have huge prospects for rice yield improvement. Here, we review the comprehensive multidisciplinary analyses to unravel different components and mechanisms involved in drought-induced cell wall plasticity at vegetative and reproductive stages that could be targeted for improving rice yield under drought.

Overexpression of ThMYB8 mediates salt stress tolerance by directly activating stress-responsive gene expression

MYB transcription factors are important in abiotic stress responses; however, the detailed mechanisms are unclear. Tamarix hispida contains multiple MYB genes. The present study characterized T. hispida MYB8 (ThMYB8) during salt stress using transgenic T. hispida and Arabidopsis assays. ThMYB8 overexpression and ThMYB8 RNAi analysis demonstrated that ThMYB8 enhanced the salt stress tolerance. Transgenic Arabidopsis ectopic expression of ThMYB8 significantly increased root growth, fresh weight, and seed germination rate compared with that of the wild-type under salt stress. Physiological parameters analysis in T. hispida and Arabidopsis showed that ThMYB8 overexpressing plants had the lowest levels of O², H₂O₂, cell death, malondialdehyde, and electrolyte leakage. Overexpression of ThMYB8 regulated Na⁺ and K⁺ concentrations in plant tissues while maintaining K⁺/Na⁺ homeostasis. Analysis using qRT-PCR and ChIP-PCR identified possible downstream ThMYB8-regulated genes. ThMYB8 regulated the expression of ThCYP450-2 (cytochrome p450-2), Thltk (leucine-rich repeat transmembrane protein kinase), and ThTIP (aquaporin TIP) by binding to the MBSI motif ('CAACTG') in their promoters. The results indicated that ThMYB8 enhanced salt stress tolerance in T. hispida by regulating gene expression related to the activation of stress-associated physiological changes, such as enhanced reactive oxygen species scavenging capability, maintaining K⁺/Na⁺ homeostasis, and decreasing the malondialdehyde content and lipid peroxidation cell membranes.

PagERF16 of Populus Promotes Lateral Root Proliferation and Sensitizes to Salt Stress

The aggravation of soil salinization limits the growth and development of plants. The AP2/ERF transcription factors (TFs) have been identified and play essential roles in plant development and stress response processes. In this study, the function of PagERF16 was detected using the overexpressing (OX) and RNAi transgenic poplar 84K hybrids. Plant growth, stomatal conductance, antioxidant enzymes activity, and PagERF16 co-expressed TFs were analyzed using morphological, physiological, and molecular methods. OX showed a more robust lateral root system with a bigger diameter and volume compared to the wild-type plants (WT). Physiological parameters indicated the bigger stomatal aperture and lower stomatal density of OX along with the lower Catalase (CAT) activity and higher malondialdehyde (MDA) content contributed to the salt sensitivity. The plant height and rooting rate of OX and RNAi were significantly worse compared to WT. Other than that, the morphology and physiology of RNAi plants were similar to WTs, suggesting that the function of PagERF16 may be redundant with other TFs. Our results indicate that when PagERF16 expression is either too high or too low, poplar growth and rooting is negatively affected. In addition, a downstream target TF, NAC45, involved in Auxin biosynthesis, was identified and PagERF16 could directly bind to its promoter to negatively regulate its expression. These results shed new light on the function of ERF TFs in plant root growth and salt stress tolerance.

Transcriptome analysis and differential gene expression profiling of two contrasting quinoa genotypes in response to salt stress

BACKGROUND

Soil salinity is one of the major abiotic stress factors that affect crop growth and yield, which seriously restricts the sustainable development of agriculture. Quinoa is considered as one of the most promising crops in the future for its high nutrition value and strong adaptability to extreme weather and soil conditions. However, the molecular mechanisms underlying the adaptive response to salinity stress of quinoa remain poorly understood. To identify candidate genes related to salt tolerance, we performed reference-guided assembly and compared the gene expression in roots treated with 300 mM NaCl for 0, 0.5, 2, and 24 h of two contrasting quinoa genotypes differing in salt tolerance.

RESULTS

The salt-tolerant (ST) genotype displayed higher seed germination rate and plant survival rate, and stronger seedling growth potential as well than the salt-sensitive (SS) genotype under salt stress. An average of 38,510,203 high-quality clean reads were generated. Significant Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified to deeper understand the differential response. Transcriptome analysis indicated that salt-responsive genes in quinoa were mainly related to biosynthesis of secondary metabolites, alpha-Linolenic acid metabolism, plant hormone signal transduction, and metabolic pathways. Moreover, several pathways were significantly enriched amongst the differentially expressed genes (DEGs) in ST genotypes, such as phenylpropanoid biosynthesis, plant-pathogen interaction, isoquinoline alkaloid biosynthesis, and tyrosine metabolism. One hundred seventeen DEGs were common to various stages of both genotypes, identified as core salt-responsive genes, including some transcription factor members, like MYB, WRKY and NAC, and some plant hormone signal transduction related genes, like PYL, PP2C and TIFY10A, which play an important role in the adaptation to salt conditions of this species. The expression patterns of 21 DEGs were detected by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-Seq results.

CONCLUSIONS

We identified candidate genes involved in salt tolerance in quinoa, as well as some DEGs exclusively expressed in ST genotype. The DEGs common to both genotypes under salt stress may be the key genes for quinoa to adapt to salinity environment. These candidate genes regulate salt tolerance primarily by participating in reactive oxygen species (ROS) scavenging system, protein kinases biosynthesis, plant hormone signal transduction and other important biological processes. These findings provide theoretical basis for further understanding the regulation mechanism underlying salt tolerance network of quinoa, as well establish foundation for improving its tolerance to salinity in future breeding programs.

In silico identification and characterization of AGO, DCL and RDR gene families and their associated regulatory elements in sweet orange (Citrus sinensis L.)

RNA interference (RNAi) plays key roles in post-transcriptional and chromatin modification levels as well as regulates various eukaryotic gene expressions which are involved in stress responses, development and maintenance of genome integrity during developmental stages. The whole mechanism of RNAi pathway is directly involved with the gene-silencing process by the interaction of Dicer-Like (DCL), Argonaute (AGO) and RNA-dependent RNA polymerase (RDR) gene families and their regulatory elements. However, these RNAi gene families and their sub-cellular locations, functional pathways and regulatory components were not extensively investigated in the case of economically and nutritionally important fruit plant sweet orange (Citrus sinensis L.). Therefore, in silico characterization, gene diversity and regulatory factor analysis of RNA silencing genes in C. sinensis were conducted by using the integrated bioinformatics approaches. Genome-wide comparison analysis based on phylogenetic tree approach detected 4 CsDCL, 8 CsAGO and 4 CsRDR as RNAi candidate genes in C. sinensis corresponding to the RNAi genes of model plant Arabidopsis thaliana. The domain and motif composition and gene structure analyses for all three gene families exhibited almost homogeneity within the same group members. The Gene Ontology enrichment analysis clearly indicated that the predicted genes have direct involvement into the gene-silencing and other important pathways. The key regulatory transcription factors (TFs) MYB, Dof, ERF, NAC, MIKC_MADS, WRKY and bZIP were identified by their interaction network analysis with the predicted genes. The cis-acting regulatory elements associated with the predicted genes were detected as responsive to light, stress and hormone functions. Furthermore, the expressed sequence tag (EST) analysis showed that these RNAi candidate genes were highly expressed in fruit and leaves indicating their organ specific functions. Our genome-wide comparison and integrated bioinformatics analyses provided some necessary information about sweet orange RNA silencing components that would pave a ground for further investigation of functional mechanism of the predicted genes and their regulatory factors.

Genome-wide identification and functional characterization of the Camelina sativa WRKY gene family in response to abiotic stress

Background

WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, there is limited knowledge about the WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance for various stresses. Here, a genome-wide characterization of WRKY proteins is performed to examine their gene structures, phylogenetics, expression, conserved motif organizations, and functional annotation to identify candidate WRKYs that mediate stress resistance regulation in camelinas.

Results

A total of 242 CsWRKY proteins encoded by 224 gene loci distributed unevenly over the chromosomes were identified, and they were classified into three groups by phylogenetic analysis according to their WRKY domains and zinc finger motifs. The 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in the C. sativa and Arabidopsis genomes as well as 282 pairs in the C. sativa and B. napus genomes, respectively. A total of 137 segmental duplication events were observed, but there was no tandem duplication in the camelina genome. Ten major conserved motifs were examined, with WRKYGQK being the most conserved, and several variants were present in many CsWRKYs. Expression analysis revealed that 50% more CsWRKY genes were expressed constitutively, and a set of them displayed tissue-specific expression. Notably, 11 CsWRKY genes exhibited significant expression changes in seedlings under cold, salt, and drought stresses, showing a preferentially inducible expression pattern in response to the stress.

Conclusions

The present article describes a detailed analysis of the CsWRKY gene family and its expression profiles in 12 tissues and under several stress conditions. Segmental duplication is the major force underlying the broad expansion of this gene family, and a strong purifying pressure occurred for CsWRKY proteins during their evolution. CsWRKY proteins play important roles in plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms, were found to be the possible key players in mediating plant responses to various stresses. Overall, our results provide a foundation for understanding the roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance as well as the development of stress tolerance cultivars among Cruciferae crops.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07189-3.

LED Lights Promote Growth and Flavonoid Accumulation of Anoectochilus roxburghii and Are Linked to the Enhanced Expression of Several Related Genes

Anoectochilus roxburghii is a wild edible species and has been traditionally used for a wide range of diseases in many countries. Our research aims to find the optimal light-emitting diode (LED) lighting conditions to improve the growth and development of A. roxburghii seedling at the acclimation stage. Two-month-old explants were cultured under the various lighting conditions including red (R), blue (B), BR (one blue: four red), BRW151 (one blue: five red: one white), BRW142 (one blue: four red: two white), and fluorescent lamp (FL). The results showed that the lighting conditions not only affect the growth and morphology of plants but also the accumulation of total flavonoids. Single wavelengths (B or R LED) inhibited the growth and secondary biosynthesis of A. roxburghii, while the BR LED showed an enhancement in both growth and biomass accumulation. A. roxburghii plants were grown under BR LED light has average plant height (7.18 cm), stem diameter (17.6mm), number of leaves (5.78 leaves/tree), leaf area (4.67 cm²), fresh weight (0.459 g/tree), dry matter percentages (11.69%), and total flavonoid (1.811 mg/g FW) is considered to be superior to FL lamps and other LEDs in the experiment. This indicates that both blue and red wavelengths are required for the normal growth of A. roxburghii. To learn more about how light affects flavonoid biosynthesis, we evaluated the expression of genes involved in this process (pal, chs, chi, and fls) and found that BR LED light enhances the expression level of chi and fls genes compared to fluorescent lamps (1.18 and 1.21 times, respectively), leading to an increase in the flavonoid content of plant. Therefore, applying BR LED during in vitro propagation of A. roxburghii could be a feasible way to improve the medicinal value of this plant.

Plant vascular development: mechanisms and environmental regulation

Plant vascular development is a complex process culminating in the generation of xylem and phloem, the plant transporting conduits. Xylem and phloem arise from specialized stem cells collectively termed (pro)cambium. Once developed, xylem transports mainly water and mineral nutrients and phloem transports photoassimilates and signaling molecules. In the past few years, major advances have been made to characterize the molecular, genetic and physiological aspects that govern vascular development. However, less is known about how the environment re-shapes the process, which molecular mechanisms link environmental inputs with developmental outputs, which gene regulatory networks facilitate the genetic adaptation of vascular development to environmental niches, or how the first vascular cells appeared as an evolutionary innovation. In this review, we (1) summarize the current knowledge of the mechanisms involved in vascular development, focusing on the model species Arabidopsis thaliana, (2) describe the anatomical effect of specific environmental factors on the process, (3) speculate about the main entry points through which the molecular mechanisms controlling of the process might be altered by specific environmental factors, and (4) discuss future research which could identify the genetic factors underlying phenotypic plasticity of vascular development.

EgPHI-1, a PHOSPHATE-INDUCED-1 gene from Eucalyptus globulus, is involved in shoot growth, xylem fiber length and secondary cell wall properties

MAIN CONCLUSION

EgPHI-1 is a member of PHI-1/EXO/EXL protein family. Its overexpression in tobacco resulted in changes in biomass partitioning, xylem fiber length, secondary cell wall thickening and composition, and lignification. Here, we report the functional characterization of a PHOSPHATE-INDUCED PROTEIN 1 homologue showing differential expression in xylem cells from Eucalyptus species of contrasting phenotypes for wood quality and growth traits. Our results indicated that this gene is a member of the PHI-1/EXO/EXL family. Analysis of the promoter cis-acting regulatory elements and expression responses to different treatments revealed that the Eucalyptus globulus PHI-1 (EgPHI-1) is transcriptionally regulated by auxin, cytokinin, wounding and drought. EgPHI-1 overexpression in transgenic tobacco changed the partitioning of biomass, favoring its allocation to shoots in detriment of roots. The stem of the transgenic plants showed longer xylem fibers and reduced cellulose content, while the leaf xylem had enhanced secondary cell wall thickness. UV microspectrophotometry of individual cell wall layers of fibers and vessels has shown that the transgenic plants exhibit differences in the lignification of S2 layer in both cell types. Taken together, the results suggest that EgPHI-1 mediates the elongation of secondary xylem fibers, secondary cell wall thickening and composition, and lignification, making it an attractive target for biotechnological applications in forestry and biofuel crops.

Cell wall remodeling under salt stress: Insights into changes in polysaccharides, feruloylation, lignification, and phenolic metabolism in maize

Although cell wall polymers play important roles in the tolerance of plants to abiotic stress, the effects of salinity on cell wall composition and metabolism in grasses remain largely unexplored. Here, we conducted an in-depth study of changes in cell wall composition and phenolic metabolism induced upon salinity in maize seedlings and plants. Cell wall characterization revealed that salt stress modulated the deposition of cellulose, matrix polysaccharides and lignin in seedling roots, plant roots and stems. The extraction and analysis of arabinoxylans by size-exclusion chromatography, 2D-NMR spectroscopy and carbohydrate gel electrophoresis showed a reduction of arabinoxylan content in salt-stressed roots. Saponification and mild acid hydrolysis revealed that salinity also reduced the feruloylation of arabinoxylans in roots of seedlings and plants. Determination of lignin content and composition by nitrobenzene oxidation and 2D-NMR confirmed the increased incorporation of syringyl units in lignin of maize roots. Salt stress also induced the expression of genes and the activity of enzymes enrolled in phenylpropanoid biosynthesis. The UHPLC-MS-based metabolite profiling confirmed the modulation of phenolic profiling by salinity and the accumulation of ferulate and its derivatives 3- and 4-O-feruloyl quinate. In conclusion, we present a model for explaining cell wall remodeling in response to salinity.

A 2-Cys peroxiredoxin gene from Tamarix hispida improved salt stress tolerance in plants

BACKGROUND

Peroxiredoxins (Prxs) are a large family of antioxidant enzymes that respond to biotic and abiotic stress by decomposing reactive oxygen species (ROS). In this study, the stress tolerance function of the Th2CysPrx gene was further analysed. It lays a foundation for further studies on the salt tolerance molecular mechanism of T. hispida and improved salt tolerance via transgenic plants.

RESULTS

In this study, the stress tolerance function of the Th2CysPrx gene was further analysed. The results of transgenic tobacco showed higher seed germination rates, root lengths, and fresh weight under salt stress than wild-type tobacco. Simultaneously, physiological indicators of transgenic tobacco and T. hispida showed that Th2CysPrx improved the activities of antioxidant enzymes and enhanced ROS removal ability to decrease cellular damage under salt stress. Moreover, Th2CysPrx improved the expression levels of four antioxidant genes (ThGSTZ1, ThGPX, ThSOD and ThPOD).

CONCLUSIONS

Overall, these results suggested that Th2CysPrx enhanced the salt tolerance of the transgenic plants. These findings lay a foundation for further studies on the salt tolerance molecular mechanism of T. hispida and improved salt tolerance via transgenic plants.

Building a Robust Chromatin Immunoprecipitation Method with Substantially Improved Efficiency

Chromatin immunoprecipitation (ChIP) is the gold-standard method for detection of interactions between proteins and chromatin and is a powerful tool for identification of epigenetic modifications. Although ChIP protocols for plant species have been developed, many specific features of plants, especially woody plants, still hinder the efficiency of immunoprecipitation, resulting in inefficient ChIP enrichment and an active demand for a highly efficient ChIP protocol. In this study, using birch (Betula platyphylla) and Arabidopsis (Arabidopsis thaliana) as the research materials, we identified five factors closely associated with ChIP efficiency, including crosslinking, concentration of chromatin using centrifugal filters, use of a different immunoprecipitation buffer, rescue of DNA with proteinase K, and use of Suc to increase immunoprecipitation efficiency. Optimization of any these factors can significantly improve ChIP efficiency. Considering these factors together, we developed a robust ChIP protocol that achieved a 14-fold improvement in ChIP enrichment for birch and a >6-fold improvement for Arabidopsis compared to the standard ChIP method. As this ChIP method works well in both birch and Arabidopsis, it should also be suitable for other woody and herbaceous species. In addition, this ChIP method enables detection of low-abundance transcription factor-DNA interactions and may extend the application of ChIP in the plant kingdom.

The Osmotin-Like Protein Gene PdOLP1 Is Involved in Secondary Cell Wall Biosynthesis during Wood Formation in Poplar

Osmotin-like proteins (OLPs) mediate defenses against abiotic and biotic stresses and fungal pathogens in plants. However, no OLPs have been functionally elucidated in poplar. Here, we report an osmotin-like protein designated PdOLP1 from Populus deltoides (Marsh.). Expression analysis showed that PdOLP1 transcripts were mainly present in immature xylem and immature phloem during vascular tissue development in P. deltoides. We conducted phenotypic, anatomical, and molecular analyses of PdOLP1-overexpressing lines and the PdOLP1-downregulated hybrid poplar 84K (Populus alba × Populus glandulosa) (Hybrid poplar 84K PagOLP1, PagOLP2, PagOLP3 and PagOLP4 are highly homologous to PdOLP1, and are downregulated in PdOLP1-downregulated hybrid poplar 84K). The overexpression of PdOLP1 led to a reduction in the radial width and cell layer number in the xylem and phloem zones, in expression of genes involved in lignin biosynthesis, and in the fibers and vessels of xylem cell walls in the overexpressing lines. Additionally, the xylem vessels and fibers of PdOLP1-downregulated poplar exhibited increased secondary cell wall thickness. Elevated expression of secondary wall biosynthetic genes was accompanied by increases in lignin content, dry weight biomass, and carbon storage in PdOLP1-downregulated lines. A PdOLP1 coexpression network was constructed and showed that PdOLP1 was coexpressed with a large number of genes involved in secondary cell wall biosynthesis and wood development in poplar. Moreover, based on transcriptional activation assays, PtobZIP5 and PtobHLH7 activated the PdOLP1 promoter, whereas PtoBLH8 and PtoWRKY40 repressed it. A yeast one-hybrid (Y1H) assay confirmed interaction of PtoBLH8, PtoMYB3, and PtoWRKY40 with the PdOLP1 promoter in vivo. Together, our results suggest that PdOLP1 is a negative regulator of secondary wall biosynthesis and may be valuable for manipulating secondary cell wall deposition to improve carbon fixation efficiency in tree species.

Wood Architecture and Composition Are Deeply Remodeled in Frost Sensitive Eucalyptus Overexpressing CBF/DREB1 Transcription Factors

Eucalypts are the most planted trees worldwide, but most of them are frost sensitive. Overexpressing transcription factors for CRT-repeat binding factors (CBFs) in transgenic Eucalyptus confer cold resistance both in leaves and stems. While wood plays crucial roles in trees and is affected by environmental cues, its potential role in adaptation to cold stress has been neglected. Here, we addressed this question by investigating the changes occurring in wood in response to the overexpression of two CBFs, taking advantage of available transgenic Eucalyptus lines. We performed histological, biochemical, and transcriptomic analyses on xylem samples. CBF ectopic expression led to a reduction of both primary and secondary growth, and triggered changes in xylem architecture with smaller and more frequent vessels and fibers exhibiting reduced lumens. In addition, lignin content and syringyl/guaiacyl (S/G) ratio increased. Consistently, many genes of the phenylpropanoid and lignin branch pathway were upregulated. Most of the features of xylem remodeling induced by CBF overexpression are reminiscent of those observed after long exposure of Eucalyptus trees to chilling temperatures. Altogether, these results suggest that CBF plays a central role in the cross-talk between response to cold and wood formation and that the remodeling of wood is part of the adaptive strategies to face cold stress.

The TuMYB46L-TuACO3 module regulates ethylene biosynthesis in einkorn wheat defense to powdery mildew

Powdery mildew disease, elicited by the obligate fungal pathogen Blumeria graminis f.sp. tritici (Bgt), causes widespread yield losses in global wheat crop. However, the molecular mechanisms governing wheat defense to Bgt are still not well understood. Here we found that TuACO3, encoding the 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase functioning in ethylene (ET) biosynthesis, was induced by Bgt infection of the einkorn wheat Triticum urartu, which was accompanied by increased ET content. Silencing TuACO3 decreased ET production and compromised wheat defense to Bgt, whereas both processes were enhanced in the transgenic wheat overexpressing TuACO3. TuMYB46L, phylogenetically related to Arabidopsis MYB transcription factor AtMYB46, was found to bind to the TuACO3 promoter region in yeast-one-hybrid and EMSA experiments. TuMYB46L expression decreased rapidly following Bgt infection. Silencing TuMYB46L promoted ET content and Bgt defense, but the reverse was observed when TuMYB46L was overexpressed. Hence, decreased expression of TuMYB46L permits elevated function of TuACO3 in ET biosynthesis in Bgt-infected wheat. The TuMYB46L-TuACO3 module regulates ET biosynthesis to promote einkorn wheat defense against Bgt. Furthermore, we found four chitinase genes acting downstream of the TuMYB46L-TuACO3 module. Collectively, our data shed a new light on the molecular mechanisms underlying wheat defense to Bgt.

Over-expression of poplar NAC15 gene enhances wood formation in transgenic tobacco

BACKGROUND

NAC (NAM/ATAF/CUC) is one of the largest plant-specific transcription factor (TF) families known to play significant roles in wood formation. Acting as master gene regulators, a few NAC genes can activate secondary wall biosynthesis during wood formation in woody plants.

RESULTS

In the present study, firstly, we screened 110 differentially expressed NAC genes in the leaves, stems, and roots of di-haploid Populus simonii×P. nigra by RNA-Seq. Then we identified a nucleus-targeted gene, NAC15 gene, which was one of the highly expressed genes in the stem among 110 NAC family members. Thirdly, we conducted expression pattern analysis of NAC15 gene, and observed NAC15 gene was most highly expressed in the xylem by RT-qPCR. Moreover, we transferred NAC15 gene into tobacco and obtained 12 transgenic lines overexpressing NAC15 gene (TLs). And the relative higher content of hemicellulose, cellulose and lignin was observed in the TLs compared to the control lines containing empty vector (CLs). It also showed darker staining in the culms of the TLs with phloroglucinol staining, compared to the CLs. Furthermore, the relative expression level of a few lignin- and cellulose-related genes was significantly higher in the TLs than that in the CLs.

CONCLUSIONS

The overall results indicated that NAC15 gene is highly expressed in the xylem of poplar and may be a potential candidate gene playing an important role in wood formation in transgenic tobacco.

RNA-Seq identification of candidate defense genes by analyzing Mythimna separata feeding-damage induced systemic resistance in balsas teosinte

BACKGROUND

Armyworm (Mythimna separata) is a destructive herbivore for maize. Balsas teosinte (Zea mays ssp. parviglumis), the direct wild ancestor of cultivated maize, has shown great potential to defend against herbivory. Here, based on armyworm bioassay, we compared responses of teosinte and B73 maize inbred during armyworm attack in their transcriptome profiles to elucidate the gene expression changes involved in teosinte responses to armyworm attack. The goal of this study was to identify novel resistance alleles that could serve as valuable resources for modern maize breeding.

RESULTS

Our bioassay revealed that armyworm larvae grew less on teosinte than on maize. A follow-up transcriptomic comparison showed more down-regulated genes in maize B73 and similar numbers of up-regulated genes in both genotypes under armyworm attack. The up-regulated genes in teosinte were markedly enriched in MAPK cascade-mediated signaling pathway and phytohormone pathway. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that phytohormones jasmonic acid, ethylene, salicylic acid and abscisic acid (ABA) were actively involved in armyworm resistance of teosinte plants, and so were transcription factors such as MYBs, WRKYs and TIFYs. Interestingly, teosinte also showed high regulation in three ABA receptor PYLs. Based on differential expression analysis, we identified 30 candidate defense-related genes in teosinte, which belong to 11 gene families and the majority of the genes were up-regulated, while some of them were nonresponsive in maize.

CONCLUSION

This study demonstrates that teosinte showed more vigorous defense response than maize toward armyworm attack and might be a beneficial genetic resource to improve pest resistance in cultivated maize. © 2019 Society of Chemical Industry.

Functional activation of a novel R2R3-MYB protein gene, GmMYB68, confers salt-alkali resistance in soybean (Glycine max L.)

Soil salinity significantly reduces soybean (Glycine max L.) production worldwide. Plants resistance to stress conditions is a complex characteristic regulated by multiple signaling pathways. The v-Myb avian myeloblastosis viral oncogene homolog (MYB) transcription factor (TF) plays a crucial role in plant development, secondary metabolism, and abiotic stress responses. GmMYB68-overexpression and RNA interference (RNAi) lines were established for examining the function of G. max GmMYB68 in plant responses to abiotic stresses. The predicted amino acid sequence of GmMYB68 was similar to that of R2R3-MYB proteins. Quantitative real-time PCR analysis revealed that GmMYB68 expression varied in response to abiotic stresses. GmMYB68-overexpression lines showed enhanced resistance to salt and alkali stresses and their osmotic adjustment and photosynthetic rates were also stronger than that of GmMYB68-RNAi and wild type plants. Although wild type and transgenic plants showed no significant differences in agronomic traits under normal conditions, the overexpression of GmMYB68 increased grain number and 100-grain weights under salt stress. Our study identified a valuable TF associated with stress response in soybean, as its overexpression might help improve salt and alkali tolerance in soybean and other crops.

MdMYB46 could enhance salt and osmotic stress tolerance in apple by directly activating stress-responsive signals

To expand the cultivation area of apple (Malus×domestica Borkh.) and select resistant varieties by genetic engineering, it is necessary to clarify the mechanism of salt and osmotic stress tolerance in apple. The MdMYB46 transcription factor was identified, and the stress treatment test of MdMYB46-overexpressing and MdMYB46-RNAi apple lines indicated that MdMYB46 could enhance the salt and osmotic stress tolerance in apple. In transgenic Arabidopsis and apple, MdMYB46 promoted the biosynthesis of secondary cell wall and deposition of lignin by directly binding to the promoter of lignin biosynthesis-related genes. To explore whether MdMYB46 could coordinate stress signal transduction pathways to cooperate with the formation of secondary walls to enhance the stress tolerance of plants, MdABRE1A, MdDREB2A and dehydration-responsive genes MdRD22 and MdRD29A were screened out for their positive correlation with osmotic stress, salt stress and the transcriptional level of MdMYB46. The further verification test demonstrated that MdMYB46 could activate their transcription by directly binding to the promoters of these genes. The above results indicate that MdMYB46 could enhance the salt and osmotic stress tolerance in apple not only by activating secondary cell wall biosynthesis pathways, but also by directly activating stress-responsive signals.

Functional characterization of poplar WRKY75 in salt and osmotic tolerance

The WRKY transcription factor family is one of the most important families in plants, playing a significant role in plant growth and development, as well as in stress responses. However, functional studies on the family in response to abiotic stresses are limited in poplar. In the present study, we cloned a WRKY transcription factor gene PagWRKY75, which was down-regulated during early stages of salt and osmotic stresses. The PagWRKY75 protein belongs to the WRKY IIc subfamily. It is located in the nucleus and can bind to the W box. We obtained transgenic poplar lines with PagWRKY75 overexpression or inhibited expression by RNA interference. Stress treatment experiments indicated that the transgenic poplar lines overexpressing PagWRKY75 were more sensitive to salt and osmotic stresses, compared to wild type. The transgenic lines with PagWRKY75 inhibition displayed opposite effects. Furthermore, our results showed that PagWRKY75 can reduce the ability of reactive oxygen species scavenging and the accumulation of proline under stresses, and positively regulate the water loss rate of leaves. These results indicate that the transcription factor PagWRKY75 can negatively regulate salt and osmotic tolerance by modulating various physiological processes.

Physiological and Transcriptional Responses of Industrial Rapeseed (Brassica napus) Seedlings to Drought and Salinity Stress

Abiotic stress greatly inhibits crop growth and reduces yields. However, little is known about the transcriptomic changes that occur in the industrial oilseed crop, rapeseed (Brassica napus), in response to abiotic stress. In this study, we examined the physiological and transcriptional responses of rapeseed to drought (simulated by treatment with 15% (w/v) polyethylene glycol (PEG) 6000) and salinity (150 mM NaCl) stress. Proline contents in young seedlings greatly increased under both conditions after 3 h of treatment, whereas the levels of antioxidant enzymes remained unchanged. We assembled transcripts from the leaves and roots of rapeseed and performed BLASTN searches against the rapeseed genome database for the first time. Gene ontology analysis indicated that DEGs involved in catalytic activity, metabolic process, and response to stimulus were highly enriched. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that differentially expressed genes (DEGs) from the categories metabolic pathways and biosynthesis of secondary metabolites were highly enriched. We determined that myeloblastosis (MYB), NAM/ATAF1-2/CUC2 (NAC), and APETALA2/ethylene-responsive element binding proteins (AP2-EREBP) transcription factors function as major switches that control downstream gene expression and that proline plays a role under short-term abiotic stress treatment due to increased expression of synthesis and decreased expression of degradation. Furthermore, many common genes function in the response to both types of stress in this rapeseed.

Overexpression of BpCUC2 Influences Leaf Shape and Internode Development in Betula pendula

The CUP-SHAPED COTYLEDON 2 (CUC2) gene, which is negatively regulated by microRNA164 (miR164), has been specifically linked to the regulation of leaf margin serration and the maintenance of phyllotaxy in model plants. However, few studies have investigated these effects in woody plants. In this study, we integrated genomic, transcriptomic, and physiology approaches to explore the function of BpCUC2 gene in Betula pendula growth and development. Our results showed that Betula pendula plants overexpressing BpCUC2, which is targeted by BpmiR164, exhibit shortened internodes and abnormal leaf shapes. Subsequent analysis indicated that the short internodes of BpCUC2 overexpressed transgenic lines and were due to decreased epidermal cell size. Moreover, transcriptome analysis, yeast one-hybrid assays, and ChIP-PCR suggested that BpCUC2 directly binds to the LTRECOREATCOR15 (CCGAC), CAREOSREP1 (CAACTC), and BIHD1OS (TGTCA) motifs of a series of IAA-related and cyclin-related genes to regulate expression. These results may be useful to our understanding of the functional role and genetic regulation of BpCUC2.

Novel Maize NAC Transcriptional Repressor ZmNAC071 Confers Enhanced Sensitivity to ABA and Osmotic Stress by Downregulating Stress-Responsive Genes in Transgenic Arabidopsis

NAC TFs play crucial roles in response to abiotic stresses in plants. Here, ZmNAC071 was identified as a nuclear located transcriptional repressor. Overexpression of ZmNAC071 in Arabidopsis enhanced sensitivity of transgenic plants to ABA and osmotic stress. The expression levels of SODs, PODs, P5CSs, and AtMYB61 were inhibited by ZmNAC071, which results in reduced ROS scavenging and proline content, increased ROS level, and water loss. Besides, the expression levels of some ABA or abiotic stress-related genes, like ABIs, RD29A, DREBs, and LEAs were also significantly inhibited by ZmNAC071. Yeast one-hybrid assay demonstrated that ZmNAC071 specifically bound to the cis-acting elements containing CGT[G/A] core sequences in the promoter of stress-related genes, suggesting that ZmNAC071 may participate in the regulation of transcription of these genes through recognizing the core sequences CGT[G/A]. These results will facilitate further studies concerning the cis-elements and downstream genes targeted by ZmNAC071 in maize.

Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant

Gene regulatory networks (GRNs) consist of different molecular interactions that closely work together to establish proper gene expression in time and space. Especially in higher eukaryotes, many questions remain on how these interactions collectively coordinate gene regulation. We study high quality GRNs consisting of undirected protein–protein, genetic and homologous interactions, and directed protein–DNA, regulatory and miRNA–mRNA interactions in the worm Caenorhabditis elegans and the plant Arabidopsis thaliana. Our data-integration framework integrates interactions in composite network motifs, clusters these in biologically relevant, higher-order topological network motif modules, overlays these with gene expression profiles and discovers novel connections between modules and regulators. Similar modules exist in the integrated GRNs of worm and plant. We show how experimental or computational methodologies underlying a certain data type impact network topology. Through phylogenetic decomposition, we found that proteins of worm and plant tend to functionally interact with proteins of a similar age, while at the regulatory level TFs favor same age, but also older target genes. Despite some influence of the duplication mode difference, we also observe at the motif and module level for both species a preference for age homogeneity for undirected and age heterogeneity for directed interactions. This leads to a model where novel genes are added together to the GRNs in a specific biological functional context, regulated by one or more TFs that also target older genes in the GRNs. Overall, we detected topological, functional and evolutionary properties of GRNs that are potentially universal in all species.

The NAC Protein from Tamarix hispida, ThNAC7, Confers Salt and Osmotic Stress Tolerance by Increasing Reactive Oxygen Species Scavenging Capability

Plant specific NAC (NAM, ATAF1/2 and CUC2) transcription factors (TFs) play important roles in response to abiotic stress. In this study, we identified and characterized a NAC protein, ThNAC7, from Tamarix hispida. ThNAC7 is a nuclear localized protein and has transcriptional activation activity. ThNAC7 expression was markedly induced by salt and osmotic stresses. Transiently transformed T. hispida seedlings overexpressing ThNAC7 (OE) or with RNA interference (RNAi) silenced ThNAC7 were generated to investigate abiotic stress tolerance via the gain- and loss- of function. Overexpressing ThNAC7 showed an increased reactive oxygen species (ROS) scavenging capabilities and proline content, which was accomplished by enhancing the activities of superoxide dismutase (SOD) and peroxidase (POD) in transiently transformed T. hispida and stably transformed Arabidopsis plants. Additionally, ThNAC7 activated these physiological changes by regulating the transcription level of P5CS, SOD and PODgenes. RNA-sequencing (RNA-seq) comparison between wild-type and ThNAC7-transformed Arabidopsis showed that more than 40 known salt tolerance genes might regulated by ThNAC7, including stress tolerance-related genes and TF genes. The results indicated that ThNAC7 induces the transcription level of genes associated with stress tolerance to enhance salt and osmotic stress tolerance via an increase in osmotic potential and enhanced ROS scavenging.

A systems biology view of wood formation in Eucalyptus grandis trees submitted to different potassium and water regimes

Wood production in fast-growing Eucalyptus grandis trees is highly dependent on both potassium (K) fertilization and water availability but the molecular processes underlying wood formation in response to the combined effects of these two limiting factors remain unknown. E. grandis trees were submitted to four combinations of K-fertilization and water supply. Weighted gene co-expression network analysis and MixOmics-based co-regulation networks were used to integrate xylem transcriptome, metabolome and complex wood traits. Functional characterization of a candidate gene was performed in transgenic E. grandis hairy roots. This integrated network-based approach enabled us to identify meaningful biological processes and regulators impacted by K-fertilization and/or water limitation. It revealed that modules of co-regulated genes and metabolites strongly correlated to wood complex traits are in the heart of a complex trade-off between biomass production and stress responses. Nested in these modules, potential new cell-wall regulators were identified, as further confirmed by the functional characterization of EgMYB137. These findings provide new insights into the regulatory mechanisms of wood formation under stressful conditions, pointing out both known and new regulators co-opted by K-fertilization and/or water limitation that may potentially promote adaptive wood traits.

Identification of transcription factor binding sites on promoter of RNA dependent RNA polymerases (RDRs) and interacting partners of RDR proteins through in silico analysis

RNA silencing phenomenon in plants provides resistance to various pathogens and also, it maintains genome integrity. The process of RNA silencing is regulated by diverse proteins, among which RNA dependent RNA polymerases (RDRs) are very crucial for the amplification of small RNAs (sRNAs). Out of various RDR proteins present in plants, role of RDR1, RDR2 and RDR6 for providing resistance against various biotic stresses have been well documented. In contrast, very few information is available regarding the role of RDR3, RDR4 and RDR5 proteins in plant biology and stress response. Furthermore, the regulation of RDRs is not yet known. Here, we have carried out in silico studies for identification of the transcription factor (TF) binding sites on the promoter of RDR1-6 genes of various plant species. Among the TFs predicted to bind on the promoter of RDRs, MYB44, AS1/AS2, WRKY1 are the major one. Furthermore, putative interacting protein partners of RDRs proteins of tomato and rice were also predicted by STRING database which suggests that DCL (Dicer-like) proteins are strong candidate proteins as the interacting partners of RDRs. The knowledge of regulation of RDRs and its interacting protein partners might help in developing resistant plants to biotic stresses.

What Makes the Wood? Exploring the Molecular Mechanisms of Xylem Acclimation in Hardwoods to an Ever-Changing Environment

Wood, also designated as secondary xylem, is the major structure that gives trees and other woody plants stability for upright growth and maintains the water supply from the roots to all other plant tissues. Over recent decades, our understanding of the cellular processes of wood formation (xylogenesis) has substantially increased. Plants as sessile organisms face a multitude of abiotic stresses, e.g., heat, drought, salinity and limiting nutrient availability that require them to adjust their wood structure to maintain stability and water conductivity. Because of global climate change, more drastic and sudden changes in temperature and longer periods without precipitation are expected to impact tree productivity in the near future. Thus, it is essential to understand the process of wood formation in trees under stress. Many traits, such as vessel frequency and size, fiber thickness and density change in response to different environmental stimuli. Here, we provide an overview of our current understanding of how abiotic stress factors affect wood formation on the molecular level focussing on the genes that have been identified in these processes.

BplMYB46 from Betula platyphylla Can Form Homodimers and Heterodimers and Is Involved in Salt and Osmotic Stresses

MYB proteins play important roles in the regulation of plant growth, development, and stress responses. Overexpression of BplMYB46 from Betula platyphylla improved plant salt and osmotic tolerances. In the present study, the interaction of eight avian myeloblastosis viral oncogene homolog (MYB) transcription factors with BplMYB46 was investigated using the yeast two-hybrid system, which showed that BplMYB46 could form homodimers and heterodimers with BplMYB6, BplMYB8, BplMYB11, BplMYB12, and BplMYB13. Relative beta-glucuronidase activity and chromatin immunoprecipitation assays showed that the interaction between BplMYB46 and the five MYBs increased the binding of BplMYB46 to the MYBCORE motif. A subcellular localization study showed that these MYBs were all located in the nucleus. Real-time fluorescence quantitative PCR results indicated that the expressions of BplMYB46 and the five MYB genes could be induced by salt and osmotic stress, and the BplMYB46 and BplMYB13 exhibited the most similar expression patterns. BplMYB46 and BplMYB13 co-overexpression in tobacco using transient transformation technology improved tobacco’s tolerance to salt and osmotic stresses compared with overexpressing BplMYB13 or BplMYB46 alone. Taken together, these results demonstrated that BplMYB46 could interact with five other MYBs to form heterodimers that activate the transcription of target genes via an enhanced binding ability to the MYBCORE motif to mediate reactive oxygen species scavenging in response to salt and osmotic stresses.

Proline-rich protein gene PdPRP regulates secondary wall formation in poplar

Proline-rich protein (PRP) is a plant cell wall associated protein. Its distinct patterns of regulation and localization studied in a number of plants indicate that it may play important roles in growth and development. However, the mechanism of how these genes control secondary cell wall development in tree species is largely unknown. Here, we report that a Populus deltoides (Marsh.) proline-rich protein gene PdPRP was preferentially expressed in immature/mature phloem and immature xylem in P. deltoides. PdPRP overexpression increased poplar plant height and diameter as well as the radial width of the phloem and xylem regions, facilitated secondary wall deposition, and induced expression of genes related to microfibril angle (MFA) and secondary wall biosynthesis. Downregulation of PdPRP retarded poplar growth, decreased the radial width of the secondary phloem and secondary xylem regions, reduced secondary wall thickening in fibers and vessels, and decreased the expression of genes related to MFA and secondary wall biosynthesis. These results suggest that PdPRP might positively regulate secondary cell wall formation by promoting secondary wall thickening and expansion in poplar. PdPRP-overexpressing poplar had a lower MFA, indicating that PdPRP may be useful for improving wood stiffness and properties in plants. Together, our results demonstrate that PdPRP is a proline-rich protein associated with cell wall development, playing a critical role in regulating secondary cell wall formation in poplar.

Genome-wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis)

The MYB family, one of the largest transcription factor (TF) families in the plant kingdom, plays vital roles in cell formation, morphogenesis and signal transduction, as well as responses to biotic and abiotic stresses. However, the underlying function of bamboo MYB TFs remains unclear. To gain insight into the status of these proteins, a total of 85 PeMYBs, which were further divided into 11 subgroups, were identified in moso bamboo (Phyllostachys edulis) by using a genome-wide search strategy. Gene structure analysis showed that PeMYBs were significantly different, with exon numbers varying from 4 to 13. Phylogenetic analysis indicated that PeMYBs clustered into 27 clades, of which the function of 18 clades has been predicted. In addition, almost all of the PeMYBs were differently expressed in leaves, panicles, rhizomes and shoots based on RNA-seq data. Furthermore, qRT-PCR analysis showed that 12 PeMYBs related to the biosynthesis and deposition of the secondary cell wall (SCW) were constitutively expressed, and their transcript abundance levels have changed significantly with increasing height of the bamboo shoots, for which the degree of lignification continuously increased. This result indicated that these PeMYBs might play fundamental roles in SCW thickening and bamboo shoot lignification. The present comprehensive and systematic study on the members of the MYB family provided a reference and solid foundation for further functional analysis of MYB TFs in moso bamboo.

Overexpression of OsTF1L, a rice HD-Zip transcription factor, promotes lignin biosynthesis and stomatal closure that improves drought tolerance

Drought stress seriously impacts on plant development and productivity. Improvement of drought tolerance without yield penalty is a great challenge in crop biotechnology. Here, we report that the rice (Oryza sativa) homeodomain-leucine zipper transcription factor gene, OsTF1L (Oryza sativa transcription factor 1-like), is a key regulator of drought tolerance mechanisms. Overexpression of the OsTF1L in rice significantly increased drought tolerance at the vegetative stages of growth and promoted both effective photosynthesis and a reduction in the water loss rate under drought conditions. Importantly, the OsTF1L overexpressing plants showed a higher drought tolerance at the reproductive stage of growth with a higher grain yield than nontransgenic controls under field-drought conditions. Genomewide analysis of OsTF1L overexpression plants revealed up-regulation of drought-inducible, stomatal movement and lignin biosynthetic genes. Overexpression of OsTF1L promoted accumulation of lignin in shoots, whereas the RNAi lines showed opposite patterns of lignin accumulation. OsTF1L is mainly expressed in outer cell layers including the epidermis, and the vasculature of the shoots, which coincides with areas of lignification. In addition, OsTF1L overexpression enhances stomatal closure under drought conditions resulted in drought tolerance. More importantly, OsTF1L directly bound to the promoters of lignin biosynthesis and drought-related genes involving poxN/PRX38, Nodulin protein, DHHC4, CASPL5B1 and AAA-type ATPase. Collectively, our results provide a new insight into the role of OsTF1L in enhancing drought tolerance through lignin biosynthesis and stomatal closure in rice.

Lignin biosynthesis genes play critical roles in the adaptation of Arabidopsis plants to high-salt stress

Salinity is a major abiotic stressor that limits the growth, development, and reproduction of plants. Our previous metabolic analysis of high salt-adapted callus suspension cell cultures from Arabidopsis roots indicated that physical reinforcement of the cell wall is an important step in adaptation to saline conditions. Compared to normal cells, salt-adapted cells exhibit an increased lignin content and thickened cell wall. In this study, we investigated not only the lignin biosynthesis gene expression patterns in salt-adapted cells, but also the effects of a loss-of-function of CCoAOMT1, which plays a critical role in the lignin biosynthesis pathway, on plant responses to high-salt stress. Quantitative real-time PCR analysis revealed higher mRNA levels of genes involved in lignin biosynthesis, including CCoAOMT1, 4CL1, 4CL2, COMT, PAL1, PAL2, and AtPrx52, in salt-adapted cells relative to normal cells, which suggests activation of the lignin biosynthesis pathway in salt-adapted cells. Moreover, plants harboring the CCoAOMT1 mutants, ccoaomt1-1 and ccoaomt1-2, were phenotypically hypersensitive to salt stress. Our study has provided molecular and genetic evidence indicating the importance of enhanced lignin accumulation in the plant cell wall during the responses to salt stress.

Overexpression of Zinc Finger Transcription Factor ZAT6 Enhances Salt Tolerance

The purpose of the present investigation is to examine the function of the C2H2-type zinc finger transcription factor of Arabidopsis thaliana 6 (ZAT6) in salt stress tolerance in cells of rice (Oryza sativa L.), cotton (Gossypium hirsutum L.) and slash pine (Pinus elliottii Engelm.). Cells of O. sativa, G. hirsutum, and P. elliottii overexpressing ZAT6 were generated using Agrobacterium-mediated genetic transformation. Molecular and functional analysis of transgenic cell lines demonstrate that overexpression of ZAT6 increased tolerance to salt stress by decreasing lipid peroxidation and increasing the content of abscisic acid (ABA) and GA₈, as well as enhancing the activities of antioxidant enzymes such as ascorbate peroxidise (APOX), catalase (CAT), glutathione reductase (GR), and superoxide dismutase (SOD). In rice cells, ZAT6 also increased expression of Ca²⁺-dependent protein kinase genes OsCPK9 and OsCPK25 by 5–7 fold under NaCl stress. Altogether, our results suggest that overexpression of ZAT6 enhanced salt stress tolerance by increasing antioxidant enzyme activity, hormone content and expression of Ca²⁺-dependent protein kinase in transgenic cell lines of different plant species.

Identification of novel cis-elements bound by BplMYB46 involved in abiotic stress responses and secondary wall deposition

Transcription factors (TFs) play vital roles in various biological processes by binding to cis-acting elements to control expressions of their target genes. The MYB TF BplMYB46, from Betula platyphylla, is involved in abiotic stress responses and secondary wall deposition. In the present study, we used a TF-centered yeast one-hybrid technology (TF-centered Y1H) to identify the cis-acting elements bound by BplMYB46. We screened a short-insert random library and identified three cis-elements bound by BplMYB46: an E-box (CA(A/T/C)(A/G/C)TG) and two novel motifs, a TC-box (T(G/A)TCG(C/G)) and a GT-box (A(G/T)T(A/C)GT(T/G)C). Chromatin immunoprecipitation (ChIP) and effector-reporter coexpression assays in Nicotiana tabacum confirmed binding of BplMYB46 to the TC-box, GT-box, and E-box motifs in the promoters of the phenylalanine ammonia lyase (PAL), peroxidase (POD), and superoxide dismutase (SOD) genes, which function in abiotic stress tolerance and secondary wall biosynthesis. This finding improves our understanding of potential regulatory mechanisms in the response to abiotic stress and secondary wall deposition of BplMYB46 in B. platyphylla.

Plant cell wall sugars: sweeteners for a bio-based economy

Global warming and the consequent climate change is one of the major environmental challenges we are facing today. The driving force behind the rise in temperature is our fossil-based economy, which releases massive amounts of the greenhouse gas carbon dioxide into the atmosphere. In order to reduce greenhouse gas emission, we need to scale down our dependency on fossil resources, implying that we need other sources for energy and chemicals to feed our economy. Here, plants have an important role to play; by means of photosynthesis, plants capture solar energy to split water and fix carbon derived from atmospheric carbon dioxide. A significant fraction of the fixed carbon ends up as polysaccharides in the plant cell wall. Fermentable sugars derived from cell wall polysaccharides form an ideal carbon source for the production of bio-platform molecules. However, a major limiting factor in the use of plant biomass as feedstock for the bio-based economy is the complexity of the plant cell wall and its recalcitrance towards deconstruction. To facilitate the release of fermentable sugars during downstream biomass processing, the composition and structure of the cell wall can be engineered. Different strategies to reduce cell wall recalcitrance will be described in this review. The ultimate goal is to obtain a tailor-made biomass, derived from plants with a cell wall optimized for particular industrial or agricultural applications, without affecting plant growth and development.

Sucrose transport and carbon fluxes during wood formation

Wood biosynthesis defines the chemical and structural properties of wood. The metabolic pathways that produce the precursors of wood cell wall polymers have a central role in defining wood properties. To make rational design of wood properties feasible, we need not only to understand the cell wall biosynthetic machinery, but also how sucrose transport and metabolism in developing wood connect to cell wall biosynthesis and how they respond to genetic and environmental cues. Here, we review the current understanding of the sucrose transport and primary metabolism pathways leading to the precursors of cell wall biosynthesis in woody plant tissues. We present both old, persistent questions and new emerging themes with a focus on wood formation in trees and draw upon evidence from the xylem tissues of herbaceous plants when it is relevant.

The R2R3MYB Gene Family in Phyllostachys edulis: Genome-Wide Analysis and Identification of Stress or Development-Related R2R3MYBs

The MYB transcription factor (TF) is one of the largest gene families in plants and involved to multiple biological processes. However, little is known about the MYB family and its functional role in the genome of moso bamboo. In the present study, a total of 114 R2R3MYB genes were first identified from moso bamboo genome and full-length non-chimeric (FLNC) reads. Phylogenetic analysis coupled with gene structure analysis and motif determination resulted in the division of these PheR2R3MYBs into 17 subgroups. The position of eight proteins along an external branch in the phylogenetic tree suggested their relatively ancient origin. The genes in this group were all substituted by (Met, M)/(Arg, R) at conservative W residues in both R2 and R3 repeats, and half were found to possess no transcriptional activation activity. The analysis of evolutionary patterns and divergence suggests that the expansion of PheMYBs was mainly attributable to whole genome duplication (WGD) under different selection pressures. Expressional analysis based on microarray and qRT-PCR data performed diverse expression patterns of R2R3MYBs in response to both various abiotic stimuli and flower development. Furthermore, the co-expression analysis of R2R3MYBs suggested an intricate interplay of growth- and stress-related responses. Finally, we found a hub gene, PheMYB4, was involved in a complex proteins interaction network. Further functional analysis indicated that ectopic overexpression of its homologous gene, PheMYB4-1, could increase tolerance to cold treatment and sensitivity to drought and salt treatment of transgenic Arabidopsis seedlings. These findings provide comprehensive insights into the MYB family members in moso bamboo and offer candidate MYB genes for further studies on their roles in stress resistance.

Differential Regulation of Genes Involved in Root Morphogenesis and Cell Wall Modification is Associated with Salinity Tolerance in Chickpea

Salinity is a major constraint for intrinsically salt sensitive grain legume chickpea. Chickpea exhibits large genetic variation amongst cultivars, which show better yields in saline conditions but still need to be improved further for sustainable crop production. Based on previous multi-location physiological screening, JG 11 (salt tolerant) and ICCV 2 (salt sensitive) were subjected to salt stress to evaluate their physiological and transcriptional responses. A total of ~480 million RNA-Seq reads were sequenced from root tissues which resulted in identification of 3,053 differentially expressed genes (DEGs) in response to salt stress. Reproductive stage shows high number of DEGs suggesting major transcriptional reorganization in response to salt to enable tolerance. Importantly, cationic peroxidase, Aspartic ase, NRT1/PTR, phosphatidylinositol phosphate kinase, DREB1E and ERF genes were significantly up-regulated in tolerant genotype. In addition, we identified a suite of important genes involved in cell wall modification and root morphogenesis such as dirigent proteins, expansin and casparian strip membrane proteins that could potentially confer salt tolerance. Further, phytohormonal cross-talk between ERF and PIN-FORMED genes which modulate the root growth was observed. The gene set enrichment analysis and functional annotation of these genes suggests they may be utilised as potential candidates for improving chickpea salt tolerance.

Lignins: Biosynthesis and Biological Functions in Plants

Lignin is one of the main components of plant cell wall and it is a natural phenolic polymer with high molecular weight, complex composition and structure. Lignin biosynthesis extensively contributes to plant growth, tissue/organ development, lodging resistance and the responses to a variety of biotic and abiotic stresses. In the present review, we systematically introduce the biosynthesis of lignin and its regulation by genetic modification and summarize the main biological functions of lignin in plants and their applications. We hope this review will give an in-depth understanding of the important roles of lignin biosynthesis in various plants’ biological processes and provide a theoretical basis for the genetic improvement of lignin content and composition in energy plants and crops.

Identification of SNPs and Candidate Genes Associated With Salt Tolerance at the Seedling Stage in Cotton (Gossypium hirsutum L.)

Salt tolerance in cotton is highly imperative for improvement in the response to decreasing farmland and soil salinization. However, little is known about the genetic basis underlying salt tolerance in cotton, especially the seedling stage. In this study, we evaluated two salt-tolerance-related traits of a natural population comprising 713 upland cotton (Gossypium hirsutum L.) accessions worldwide at the seedling stage and performed a genome-wide association study (GWAS) to identify marker-trait associations under salt stress using the Illumina Infinium CottonSNP63K array. A total of 23 single nucleotide polymorphisms (SNPs) that represented seven genomic regions on chromosomes A01, A10, D02, D08, D09, D10, and D11 were significantly associated with the two salt-tolerance-related traits, relative survival rate (RSR) and salt tolerance level (STL). Of these, the two SNPs i46598Gh and i47388Gh on D09 were simultaneously associated with the two traits. Based on all loci, we screened 280 possible candidate genes showing different expression levels under salt stress. Most of these genes were involved in transcription factors, transporters and enzymes and were previously reported as being involved in plant salt tolerance, such as NAC, MYB, NXH, WD40, CDPK, LEA, and CIPK. We further validated six putative candidate genes by qRT-PCR and found a differential expression level between salt-tolerant and salt-sensitive varieties. Our findings provide valuable information for enhancing the understanding of complicated mechanisms of salt tolerance in G. hirsutum seedlings and cotton salt tolerance breeding by molecular marker-assisted selection.

Comprehensive Analysis of MYB Gene Family and Their Expressions Under Abiotic Stresses and Hormone Treatments in Tamarix hispida

The MYB transcription factors (TFs) is a plant TF families, which involves in hormone signal transduction, and abiotic stress tolerance, etc. However, there are few studies on the MYB TFs family and its regulatory mechanism in Tamarix hispida. In this study, 14 MYB genes (named ThMYB1 - ThMYB14) were cloned and characterized from T. hispida. The transcription profiles of ThMYBs in T. hispida under different abiotic stress conditions were monitored using qRT-PCR. Most of studied ThMYBs were significantly downregulated and/or upregulated by salt and osmotic stress, ABA, GA3 and JA treatments in at least one organ. Especially, ThMYB13 was induced in the leaves and roots of T. hispida when exposed to NaCl treatment at all study periods, indicating that it may involve in salt stress. To further study ThMYB13 function, ThMYB13 overexpression and knock-down plants and control plants transformed with an empty pROKII were obtained using a transient transformation system. Overexpression of ThMYB13 in T. hispida displayed the lowest O^2-, H₂O₂ and MDA accumulation, minimal cell death, the most stable K⁺/Na⁺ ratio and the lowest electrolyte leakage rate among the three kinds of transient expression in T. hispida. Conversely, the RNAi-silencing, transiently transformed plants displayed the opposite physiological changes. Therefore, ThMYB13 might play a role in salt stress tolerance in transgenic T. hispida plants.