A gene that underwent adaptive evolution, LAC2 (LACCASE), in Populus euphratica improves drought tolerance by improving water transport capacity

MicroRNA408 negatively regulates drought tolerance by controlling lignin synthesis in potato

Potato is an important food crop in China, and its growth and development are vulnerable to abiotic stresses. The effect of drought on potato growth and development is more dramatic. In this study, StLAC12 was verified as target gene of potato Stu-miR408. It was demonstrated that Stu-miR408 negatively regulated expression of StLAC12. The effect of Stu-miR408 on plant drought resistance was also investigated, and it was found that down-regulated expression of Stu-miR408 can enhance drought resistance of potato. It was also found that lignin synthesis was affected by Stu-miR408, and miR408-LAC12 can affect xylem development by regulating lignin synthesis in response to drought stress. In conclusion, this study demonstrated that Stu-miR408 negatively regulates potato drought tolerance and provided valuable new insights into Stu-miR408-mediated lignin synthesis pathway in response to potato drought stress.

Comprehensive analysis of the NAC transcription factor gene family in Sophora tonkinensis Gagnep

BACKGROUND

Sophora tonkinensis Gagnep. has long been utilized in the treatment of anti-inflammatory and pain-relieving, with its principal active compounds being alkaloids and flavonoids. NAC transcription factors, a large family of plant-specific regulators, play pivotal roles in growth, development, stress responses, and secondary metabolism. However, comprehensive genome-wide characterization of S. tonkinensis NAC gene family (StNAC) remains unexplored.

RESULTS

This study identified 85 NAC proteins from the S. tonkinensis genome database. Phylogenetic analysis revealed that StNAC proteins were categorized into 15 subgroups based on their homology with Arabidopsis thaliana NAC proteins. Gene structure analysis demonstrated a variation in intron numbers ranging from 1 to 7, with a majority of StNAC genes containing 2-3 introns. Chromosomal distribution analysis indicated an uneven spread of StNAC genes across 9 chromosomes, with the highest number of StNAC genes on Chr3. Detection of 4 tandem duplicates and 32 segmental duplicates revealed that segmental duplication primarily drive StNAC genes amplification. Prediction of cis-regulatory elements suggested the involvement of StNAC genes in growth, stress responses, and hormone regulation. Gene expression analysis showed substantial variability expression of StNAC genes across different tissues. Notably, eight StNAC genes were identified as significantly associated alkaloid and flavonoid levels. qRT-PCR validation indicated that five genes were highly expressed in tissues, corroborating transcriptome data.

CONCLUSION

These findings offer valuable insights for further functional characterization of NAC genes and their potential roles in alkaloid and flavonoid biosynthesis in S. tonkinensis.

The LoMYB26/LoJAZ4-LoCOMT module regulates anther dehiscence via Jasmonic acid-mediated endothecium lignification in lily

INTRODUCTION

Timely anther dehiscence is a key step for successful sexual reproduction in plants. Secondary cell wall thickening of anther endothecium is a vital process during anther dehiscence that provides an indispensable mechanical force for successful dehiscence. Anther dehiscence depends on anther lignification, and it is a timely and sophisticated process regulated by phytohormones and transcription factors. However, whether endothecium lignification occurs during anther dehiscence in lily and underlying mechanisms are still largely unclear.

OBJECTIVES

Our work focuses on identifying the course of endothecium lignification during anther dehiscence and elucidating the molecular mechanisms underlying endothecium lignification-dependent anther dehiscence in lily.

METHODS

Lignin fluorescence analysis and ultraviolet spectrophotometry were employed to elucidate the endothecium lignification process. Target genes were isolated from the transcriptomic data of anther dehiscence and lignification process. Virus-induced gene silencing (VIGS) and transient overexpression in lily anthers were used to analyze the LoMYB26 function. Yeast one-hybrid (Y1H), electrophoretic mobility shift assay (EMSA), and dual-luciferase (LUC) assay analyzed the regulatory mechanisms. Yeast two-hybrid (Y2H), luciferase complementation imaging (LCI), and bimolecular fluorescence complementation (BiFC) assays illustrated the interaction between LoMYB26 and LoJAZ4.

RESULTS

Our results showed that endothecium lignification occurred in S6-S7 stages when anther dehiscence had not yet occurred. The R2R3-type MYB transcription factor, LoMYB26, was found to promote endothecium lignification. LoMYB26 directly bound to the Caffeic Acid O-methyltransferase (LoCOMT) promoter and activated its transcription. Meanwhile, LoMYB26 interacted with jasmonate-ZIM domain protein 4 (LoJAZ4), which repressed the LoMYB26-mediated activation of LoCOMT transcription. Additionally, the exogenous application of methyl-jasmonate (Me-JA) induced LoMYB26 transcription and promoted endothecium lignification.

CONCLUSION

Our findings demonstrate that LoMYB26 promotes endothecium lignification and anther dehiscence. LoMYB26 interacted with LoJAZ4, forming a heterodimer that participates in JA-mediated endothecium lignification and anther dehiscence. This study offers valuable insights and a theoretical foundation for the breeding of anther-indehiscent lily.

Lignin synthesis plays an essential role in the adaptation of Haloxylon ammodendron to adverse environments

Haloxylon ammodendron is a desert shrub exhibiting remarkable tolerance to adverse environments, making it an excellent model for studying the mechanisms by which plants adapt to harsh environmental conditions. Lignin, a crucial component of plants, has been shown to play an important role in the adaptation of H. ammodendron to osmotic and salt stress. Therefore, this study was focused on the role of lignin synthesis by H. ammodendron in its adaptation to osmotic and salt stress (imposed by 0.4 % sorbitol and 350 mM NaCl, respectively). We investigated lignin deposition, the polymerization of lignin monomers, water content and adjustment of osmotic potential in assimilating branches of H. ammodendron, as well as gene expression and small molecules related to lignin biosynthesis. The results indicated that osmotic and salt stress induced the activity of peroxidase (POD) and laccase (LAC), while H2O2 concentration also increased. The genes encoding functions associated with lignin biosynthesis in both shoots and roots were upregulated and lignin accumulation in H. ammodendron increased, thereby maintaining osmotic potential and shoot water content under stress. These results showed that osmotic and salt stresses significantly increased lignin production in H. ammodendron, polymerization of lignin monomers, and the expression of genes encoding functions correlated to lignin synthesis. In addition, under osmotic stress, phenylalanine and p-coumaric acid increased in the shoots and roots, as did coniferyl alcohol and sinapyl alcohol. Overall, this study confirmed the role of lignin biosynthesis in the stress resistance of H. ammodendron, providing further insights into its adaptive strategies to adversity, and suggesting new ideas for improving the resistance of cultivated plants.

Genome-wide analysis of the laccase gene family in Arachis hypogaea and functional characterization of AhLAC63 involved in lignin biosynthesis and abiotic stress

Plant laccases (LACs) play a vital role in lignification and participate in multiple biotic/abiotic stress responses. However, little is known about their role in lignin deposition and stress resistance in cultivated peanut (Arachis hypogaea L.). In this study, 80 putative peanut laccase genes (AhLACs) were identified and clustered into seven distinct phylogenetic groups. While the AhLAC members of group VI were lost, a novel specific group VIII was discovered in peanut. AhLACs within same group generally have similar gene structures and protein motif organizations. Expression pattern and subcellular cellular analysis revealed that AhLAC63 is a candidate gene involved in lignification and abiotic stress response. In addition, introducing AhLAC63 into the Arabidopsis laccase mutant (lac4 lac11) restored its lignin contents and abiotic stress tolerance. Moreover, the overexpression of AhLAC63 significantly altered phenylpropanoid metabolism flux and increased lignin content in peanut hairy roots. This study not only enables the further exploration of LAC biological functions in peanut, but also provides new gene resources for improving stress resistance in crops.

Genome-wide identification, classification, and expression profiling of LAC gene family in sesame

BACKGROUND

Laccases (LACs) are vital plant growth and development enzymes, participating in lignin biopolymerization and responding to stress. However, the role of LAC genes in plant development as well as stress tolerance, is still not well understood, particularly in sesame (Sesamum indicum L.), an important oilseed crop.

RESULTS

In this study, 51 sesame LAC genes (SiLACs) were identified, which were unevenly distributed across different chromosomes. The phylogeny of Arabidopsis LAC (AtLACs) subdivided the SiLAC proteins into seven subgroups (Groups I-VII), of which Group VII contained only sesame LACs. Within the same subgroup, SiLACs exhibit comparable structures and conserved motifs. The promoter region of SiLACs harbors various cis-acting elements that are related to plant growth, phytohormones, and stress responses. Most SiLACs were expressed in the roots and stems, whereas some were expressed specifically in flowers or seeds. RNA-seq analysis revealed that 19 SiLACs exhibited down-regulation and three showed up-regulation in response to drought stress, while 15 SiLACs were down-regulated and four up-regulated under salt stress. Additionally, qRT-PCR analysis showcased that certain SiLAC expression was significantly upregulated as a result of osmotic and salt stress. SiLAC5 and SiLAC17 exhibited the most significant changes in expression under osmotic and salt stresses, indicating that they may serve as potential targets for improving sesame resistance to various stresses.

CONCLUSIONS

Our study offers a thorough comprehension of LAC gene structure, classification, evolution, and abiotic stress response in sesame plants. Furthermore, we provide indispensable genetic resources for sesame functional characterization to enhance its tolerance to various abiotic stresses.

CsLAC4, regulated by CsmiR397a, confers drought tolerance to the tea plant by enhancing lignin biosynthesis

Drought is a prevalent abiotic stress that commonly affects the quality and yield of tea. Although numerous studies have shown that lignin accumulation holds significant importance in conferring drought tolerance to tea plants, the underlying molecular regulatory mechanisms governing the tea plant's response to drought remain largely elusive. LACCASEs (LACs), which belong to the class of plant copper-containing polyphenol oxidases, have been widely reported to participate in lignin biosynthesis in plants and are implicated in numerous plant life processes, especially in the context of adverse conditions. In this study, we detected the upregulation of CsLAC4 in response to drought induction. Remarkably, the overexpression of CsLAC4 not only substantially increased the lignin content of transgenic Arabidopsis thaliana but also simulated the development of vascular tissues, consequently leading to a significant enhancement in drought tolerance. Moreover, via dual-luciferase assays and transient overexpression in tea leaves, we revealed that CsLAC4 was negatively regulated by the upstream CsmiR397a. Interestingly, the expression of CsmiR397a was downregulated during drought stress in tea plants. Arabidopsis thaliana overexpressing CsmiR397a showed increased sensitivity to drought stress. By transient overexpression of CsmiR397a and CsLAC4 in tea plant leaves, we verified that CsLAC4, which is regulated by CsmiR397a, conferred drought tolerance to tea plants by enhancing lignin biosynthesis. These findings enhance our understanding of the molecular regulatory mechanisms underlying the response of tea plants to drought stress.

Genome-Wide Identification and Characterization of the Laccase Gene Family in Fragaria vesca and Its Potential Roles in Response to Salt and Drought Stresses

Laccase (LAC, EC 1.10.3.2) is integral to the formation of lignin synthesis, flavonoid production, and responses to both biotic and abiotic stresses. While recent studies have characterized numerous LAC gene families and their functions across various plants, information regarding LAC genes in woodland strawberry (Fragaria vesca) remains limited. In this study, we identified a total of 57 FvLAC genes in the Fragaria vesca genome, which were phylogenetically categorized into five distinct groups. Analysis of the gene structures revealed a uniformity in the exon-intron structure among the subgroups, while conserved motifs identified unique motifs specific to certain subgroups, suggesting functional variations. Chromosomal localization studies indicated that FvLACs are distributed across seven chromosomes, and collinearity analysis demonstrated that FvLACs exhibit collinearity within the species. Additionally, cis-acting element analysis suggested that FvLAC genes are involved in stress responses, hormone responses, light responses, and the growth and development of plants. qRT-PCR demonstrated that FvLACs responded to salt, drought, and hormone stresses, with the expression levels of FvLAC24, FvLAC32, and FvLAC51 continuously increasing under these stress conditions. Furthermore, transgenic yeast experiments revealed that FvLAC51 enhanced yeast tolerance to both salt and drought stresses, while FvLAC24 and FvLAC32 negatively regulated yeast tolerance under these same conditions. These findings provide a theoretical foundation for further investigation into the functions of FvLAC genes in woodland strawberry.

Cadmium-induced protein AS8: A protein to improve Cd accumulation and transport via Cd uptake in poplar

The pollution of soil with heavy metals (HMs) has become an environmental problem of global concern. Phytoremediation, whereby plants extract HMs from soil, can efficiently and substantially reduce HM pollution in soil in an environmentally friendly manner. Cadmium-induced protein AS8 (CIPAS8) is present in many plants and its expression is induced by HMs. In this study, PeCIPAS8 and SlCIPAS8 were transformed into 84K poplar to study their effects on tolerance to, and translocation of, cadmium (Cd) in woody plants. Localization analyses showed that two CIPAS8 proteins were localized at the plasma membrane when transiently expressed in tobacco leaf epidermal cells. Compared with wild-type 84K poplar seedlings, transgenic poplar lines overexpressing PeCIPAS8 or SlCIPAS8 showed increased Cd contents and decreased Cd tolerance. Transgenic poplar lines overexpressing PeCIPAS8 or SlCIPAS8 accumulated more Cd in the roots, stems, and leaves, but the plant height did not differ significantly, compared with wild-type 84K poplar under Cd stress during the vegetative stage. CIPAS8 increased the Cd influx rate of transgenic poplar roots compared with that of the wild type, and affected the transcription levels of other metal transporters. These findings show that CIPAS8 increases Cd flux into plant tissues and demonstrate moderate Cd sensitivity of the plant. Therefore, CIPAS8 is an influx transporter with the potential to increase the uptake of toxic HMs by woody plants growing in HM-contaminated soils.

Bioengineering for robust tolerance against cold and drought stresses via co-overexpressing three Cu-miRNAs in major food crops

Environmental stresses threaten global food security by reducing major crop productivity. MicroRNAs (miRNAs), a class of small non-coding RNAs, function as master regulators of gene expression in plants. In this study, we co-overexpressed three copper-miRNAs (miR397, miR408, and miR528) in three major food crops (referred to as 3miR-OE), which simultaneously silenced several target laccase genes, resulting in reduced lignin contents but increased flavonoid metabolites. Importantly, we observed that, compared to wild-type and single miRNA overexpression lines, the 3miR-OE transgenic Japonica and Indica rice exhibited significantly enhanced tolerance against cold and drought stresses throughout the growth period. In addition, 3miR-OE transgenic maize and wheat also exhibited robust resistance to cold and water-deficit conditions, suggesting that co-overexpressing three Cu-miRNAs is a powerful tool for improving resilience to abiotic stresses across diverse crops. Altogether, we have developed a bioengineering strategy to maintain crop growth and yield under unfavorable environmental conditions.

Molecular characterization and transcriptional response of Lactuca sativa seedlings to co-exposure to graphene nanoplatelets and titanium dioxide nanoparticles

The widespread use of nanomaterials in agriculture may introduce multiple engineered nanoparticles (ENPs) into the environment, posing a combined risk to crops. However, the precise molecular mechanisms explaining how plant tissues respond to mixtures of individual ENPs remain unclear, despite indications that their combined toxicity differs from the summed toxicity of the individual ENPs. Here, we used a variety of methods including physicochemical, biochemical, and transcriptional analyses to examine the combined effects of graphene nanoplatelets (GNPs) and titanium dioxide nanoparticles (TiO2 NPs) on hydroponically exposed lettuce (Lactuca sativa) seedlings. Results indicated that the presence of GNPs facilitated the accumulation of Ti as TiO2 NPs in the seedling roots. Combined exposure to GNPs and TiO2 NPs caused less severe oxidative damage in the roots compared to individual exposures. Yet, GNPs and TiO2 NPs alone and in combination did not cause oxidative damage in the shoots. RNA sequencing data showed that the mixture of GNPs and TiO2 NPs led to a higher number of differentially expressed genes (DEGs) in the seedlings compared to exposure to the individual ENPs. Moreover, the majority of the DEGs encoding superoxide dismutase displayed heightened expression levels in the seedlings exposed to the combination of GNPs and TiO2 NPs. The level of gene ontology (GO) enrichment in the seedlings exposed to the mixture of GNPs and TiO2 NPs was found to be greater than the level of GO enrichment observed after exposure to isolated GNPs or TiO2 NPs. Furthermore, the signaling pathways, specifically the "MAPK signaling pathway-plant" and "phenylpropanoid biosynthesis," exhibited a close association with oxidative stress. This study has provided valuable insights into the molecular mechanisms underlying plant resistance against multiple ENPs.

RNA-seq reveals the gene expression in patterns in Populus × euramericana 'Neva' plantation under different precision water and fertilizer-intensive management

BACKGROUND

Populus spp. is a crucial fast-growing and productive tree species extensively cultivated in the mid-latitude plains of the world. However, the impact of intensive cultivation management on gene expression in plantation remains largely unexplored.

RESULTS

Precision water and fertilizer-intensive management substantially increased key enzyme activities of nitrogen transport, assimilation, and photosynthesis (1.12-2.63 times than CK) in Populus × euramericana 'Neva' plantation. Meanwhile, this management approach had a significant regulatory effect on the gene expression of poplar plantations. 1554 differential expression genes (DEGs)were identified in drip irrigation (ND) compared with conventional irrigation. Relative to ND, 2761-4116 DEGs, predominantly up-regulated, were identified under three drip fertilization combinations, among which 202 DEGs were mainly regulated by fertilization. Moreover, drip irrigation reduced the expression of cell wall synthesis-related genes to reduce unnecessary water transport. Precision drip and fertilizer-intensive management promotes the synergistic regulation of carbon and nitrogen metabolism and up-regulates the expression of major genes in nitrogen transport and assimilation processes (5 DEGs), photosynthesis (15 DEGs), and plant hormone signal transduction (11 DEGs). The incorporation of trace elements further enhanced the up-regulation of secondary metabolic process genes. In addition, the co-expression network identified nine hub genes regulated by precision water and fertilizer-intensive management, suggesting a pivotal role in regulating the growth of poplar.

CONCLUSION

Precision water and fertilizer-intensive management demonstrated the ability to regulate the expression of key genes and transcription factor genes involved in carbon and nitrogen metabolism pathways, plant hormone signal transduction, and enhance the activity of key enzymes involved in related processes. This regulation facilitated nitrogen absorption and utilization, and photosynthetic abilities such as light capture, light transport, and electron transport, which faintly synergistically regulate the growth of poplar plantations. These results provide a reference for proposing highly efficient precision intensive management to optimize the expression of target genes.

Comparative Analysis of the Effect of Gamma-, Electron, and Proton Irradiation on Transcriptomic Profile of Hordeum vulgare L. Seedlings: In Search for Molecular Contributors to Abiotic Stress Resilience

The development of adaptation strategies for crops under ever-changing climate conditions is a critically important food security issue. Studies of barley responses to ionising radiation showed that this evolutionarily ancient stress factor can be successfully used to identify molecular pathways involved in adaptation to a range of abiotic stressors. In order to identify potential molecular contributors to abiotic stress resilience, we examined the transcriptomic profiles of barley seedlings after exposure to γ-rays, electrons, and protons. A total of 553 unique differentially expressed genes with increased expression and 124 with decreased expression were detected. Among all types of radiation, the highest number of differentially expressed genes was observed in electron-irradiated samples (428 upregulated and 56 downregulated genes). Significant upregulation after exposure to the three types of radiation was shown by a set of ROS-responsive genes, genes involved in DNA repair, cell wall metabolism, auxin biosynthesis and signalling, as well as photosynthesis-related genes. Most of these genes are known to be involved in plant ROS-mediated responses to other abiotic stressors, especially with genotoxic components, such as heavy metals and drought. Ultimately, the modulation of molecular pathways of plant responses to ionising radiation may be a prospective tool for stress tolerance programmes.

Transcriptomic and Phenotypic Analyses Reveal the Molecular Mechanism of Dwarfing in Tetraploid Robinia pseudoacacia L

Polyploid breeding techniques aid in the cultivation of new forestry cultivars, thus expanding the suite of strategies for the improvement of arboreal traits and innovation within the field of forestry. Compared to diploid Robinia pseudoacacia L. (black locust) 'D26-5①' (2×), its dwarfed homologous tetraploid 'D26-5②' (4×) variety has better application prospects in garden vegetation guardrails and urban landscape. However, the molecular mechanism of the generation and growth of this dwarf variety is still unclear. Here, plant growth and development as well as histological differences between the diploid and its autotetraploid were investigated. Levels of endogenous hormones at three different developmental stages (20, 40, and 70 days) of 2× and homologous 4× tissue culture plantlets were assessed, and it was found that the brassinosteroid (BR) contents of the former were significantly higher than the latter. Transcriptome sequencing data analysis of 2× and homologous 4× showed that differentially expressed genes (DEGs) were significantly enriched in plant hormone synthesis and signal transduction, sugar and starch metabolism, and the plant circadian rhythm pathway, which are closely related to plant growth and development. Therefore, these biological pathways may be important regulatory pathways leading to dwarfism and slow growth in tetraploids. Additionally, utilizing weighted gene coexpression network analysis (WGCNA), we identified three crucial differentially expressed genes (DEGs)-PRR5, CYP450, and SPA1-that potentially underlie the observed ploidy variation. This study provides a new reference for the molecular mechanism of dwarfism in dwarfed autotetraploid black locusts. Collectively, our results of metabolite analysis and comparative transcriptomics confirm that plant hormone signaling and the circadian rhythm pathway result in dwarfism in black locusts.

GhTLP1, a thaumatin-like protein 1, improves Verticillium wilt resistance in cotton via JA, ABA and MAPK signaling pathway-plant pathways

Verticillium wilt of cotton is a very serious soil-borne disease and there is no effective control method. The mechanism of Gossypium hirsutum thaumatin-like protein 1(GhTLP1) in upland cotton regulating Verticillium wilt resistance has been an uncovered research approach. GhTLP1 is mainly localized in the cell wall. Overexpression of GhTLP1 significantly enhanced Arabidopsis plants resistance to Verticillium dahliae, while its homologous mutant tlp1 in Arabidopsis was more susceptible to the pathogen, and the heterologous complement line (EC) recovered resistance to V. dahliae. GhTLP1 responds to jasmonate acid (JA) and abscisic acid (ABA) hormones and regulates mitogen-activated protein kinase (MAPK) signaling pathway-plant pathway to enhance Arabidopsis plants resistance to V. dahliae. Silencing GhTLP1 resulted decrease in cotton plants resistance to V. dahliae. Moreover, the mutation of GhTLP1 at site Tyr97 and Tyr199 with the phosphorylation also decreased plant resistance to V. dahliae. Therefore, GhTLP1 phosphorylation was observed important in cotton plants against V. dahliae. Further analysis demonstrated that GhTLP1 interacted with gossypium hirsutum laccase 14 (GhLAC14) to enhance plants resistance to V. dahliae. Silencing GhLAC14 resulted decrease in cotton plants resistance to V. dahliae. Here, we propose that GhTLP1 is a potential molecular target for improving resistance to Verticillium wilt in cotton.

The Euphrates Poplar Responses to Abiotic Stress and Its Unique Traits in Dry Regions of China (Xinjiang and Inner Mongolia): What Should We Know?

At the moment, drought, salinity, and low-temperature stress are ubiquitous environmental issues. In arid regions including Xinjiang and Inner Mongolia and other areas worldwide, the area of tree plantations appears to be rising, triggering tree growth. Water is a vital resource in the agricultural systems of countries impacted by aridity and salinity. Worldwide efforts to reduce quantitative yield losses on Populus euphratica by adapting tree plant production to unfavorable environmental conditions have been made in response to the responsiveness of the increasing control of water stress. Although there has been much advancement in identifying the genes that resist abiotic stresses, little is known about how plants such as P. euphratica deal with numerous abiotic stresses. P. euphratica is a varied riparian plant that can tolerate drought, salinity, low temperatures, and climate change, and has a variety of water stress adaptability abilities. To conduct this review, we gathered all available information throughout the Web of Science, the Chinese National Knowledge Infrastructure, and the National Center for Biotechnology Information on the impact of abiotic stress on the molecular mechanism and evolution of gene families at the transcription level. The data demonstrated that P. euphratica might gradually adapt its stomatal aperture, photosynthesis, antioxidant activities, xylem architecture, and hydraulic conductivity to endure extreme drought and salt stress. Our analyses will give readers an understanding of how to manage a gene family in desert trees and the influence of abiotic stresses on the productivity of tree plants. They will also give readers the knowledge necessary to improve biotechnology-based tree plant stress tolerance for sustaining yield and quality trees in China's arid regions.

Functional Diversification and the Plant Secondary Cell Wall

Much evidence exists suggesting the presence of genetic functional diversification in plants, though literature associated with the role of functional diversification in the evolution of the plant secondary cell wall (SCW) has sparsely been compiled and reviewed in a recent context. This review aims to elucidate, through the examination of gene phylogenies associated with its biosynthesis and maintenance, the role of functional diversification in shaping the critical, dynamic, and characteristic organelle, the secondary cell wall. It will be asserted that gene families resulting from gene duplication and subsequent functional divergence are present and are heavily involved in SCW biosynthesis and maintenance. Furthermore, diversification will be presented as a significant driver behind the evolution of the many functional characteristics of the SCW. The structure and function of the plant cell wall and its constituents will first be explored, followed by a discussion on the phenomenon of gene duplication and the resulting genetic functional divergence that can emerge. Finally, the major constituents of the SCW and their individual relationships with duplication and divergence will be reviewed to the extent of current knowledge on the subject.

PaLectinL7 enhances salt tolerance of sweet cherry by regulating lignin deposition in connection with PaCAD1

Lectin receptor-like kinases (LecRLKs), a large family of plant receptor-like kinases, play an important role in plant response to abiotic stresses. However, little information is available about the roles of LecRLKs in the salt stress response of sweet cherry (Prunus avium). Here, an L-type LecRLK gene (PaLectinL7) was characterized from sweet cherry. Subcellular localization analysis revealed that PaLectinL7 is a plasma membrane protein. The expression of PaLectinL7 was up-regulated by salt, drought and exogenously gibberellin treatments. Overexpression of PaLectinL7 in the roots of Gisela 6 enhanced its tolerance to salt stress. Additionally, transcriptome analysis showed that lignin metabolic-related genes were regulated by PaLectinL7 overexpression. Meanwhile, the lignin contents and associated enzymes (CAD and COMT) rose concurrently with PaLectinL7 overexpression under salt stress. We also found that PaCAD1, a key enzyme involved in lignin metabolism, interacted with PaLectinL7 and could be phosphorylated by PaLectinL7 in vitro, suggesting that PaLectinL7 may regulate the enzyme activity of PaCAD1. Therefore, these results indicated that PaLectinL7, as a membrane-bound regulator, promoted lignin deposition by regulating the activities of enzymes related to lignin metabolism, thus enhancing salt tolerance.

Chromosome-level genome assembly and population genomics of Robinia pseudoacacia reveal the genetic basis for its wide cultivation

Urban greening provides important ecosystem services and ideal places for urban recreation and is a serious consideration for municipal decision-makers. Among the tree species cultivated in urban green spaces, Robinia pseudoacacia stands out due to its attractive flowers, fragrances, high trunks, wide adaptability, and essential ecosystem services. However, the genomic basis and consequences of its wide-planting in urban green spaces remains unknown. Here, we report the chromosome-level genome assembly of R. pseudoacacia, revealing a genome size of 682.4 Mb and 33,187 protein-coding genes. More than 99.3% of the assembly is anchored to 11 chromosomes with an N50 of 59.9 Mb. Comparative genomic analyses among 17 species reveal that gene families related to traits favoured by urbanites, such as wood formation, biosynthesis, and drought tolerance, are notably expanded in R. pseudoacacia. Our population genomic analyses further recover 11 genes that are under recent selection. Ultimately, these genes play important roles in the biological processes related to flower development, water retention, and immunization. Altogether, our results reveal the evolutionary forces that shape R. pseudoacacia cultivated for urban greening. These findings also present a valuable foundation for the future development of agronomic traits and molecular breeding strategies for R. pseudoacacia.

Effects of long-term irrigation on soil phosphorus fractions and microbial communities in Populus euphratica plantations

Irrigation has been demonstrated to be effective in managing Populus euphratica plantations, but its impacts on phosphorus (P) availability and the soil microbiome have not been fully elucidated. In this study, we compared soil properties, P fractions, phosphatase activities, and microbial communities in the surface soil (0-20 cm) of P. euphratica plantations under both drought and irrigation conditions. We found that total P, labile P and moderately labile P all increased significantly under irrigation by 12.3%, 70.1%, and 3.0%, respectively. The increased levels of labile P were primarily driven by higher levels of NaHCO3-Pi, which increased from 1.9 to 12.3 mg·kg-1. Furthermore, irrigation markedly altered labile P composition and the relative levels of resin P, NaHCO3-Pi, and NaHCO3-Po were all impacted. Improved soil moisture increased soil phosphatase activity, suggesting that soil organic P (Po) mineralization was positively affected by irrigation. Moreover, we observed that bacterial diversity, fungal diversity, and alkaline phosphatase gene communities, rather than total microbial biomass carbon or total phospholipid fatty acids, were most explained in the dynamics of soil P fractions. Furthermore, we found positive correlations among inorganic P (Pi) and Bradyrhizobiaceae, Nocardiaceae, and Sphingomonadaceae, whereas negative correlations were found between Burkholderiaceae and Pi, highlighting the diverse functional bacteria involved in P cycling. Our study demonstrates that irrigation can increase soil P availability and supply capacity, with shifts in P composition closely linked to changes in soil microbial characteristics. Water management strategies that target the restoration of soil microbial communities may therefore improve soil quality and enhance soil P cycling.

Chromatin accessibility dynamics insight into crosstalk between regulatory landscapes in poplar responses to multiple treatments

Perennial trees develop and coordinate endogenous response signaling pathways, including their crosstalk and convergence, to cope with various environmental stresses which occur simultaneously in most cases. These processes are involved in gene transcriptional regulations that depend on dynamic interactions between regulatory proteins and corresponding chromatin regions, but the mechanisms remain poorly understood in trees. In this study, we detected chromatin regulatory landscapes of poplar under abscisic acid, methyl jasmonate, salicylic acid and sodium chloride (NaCl) treatment, through integrating ATAC-seq and RNA-seq data. Our results showed that the degree of chromatin accessibility for a given gene is closely related to its expression level. However, unlike the gene expression that shows treatment-specific response patterns, changes in chromatin accessibility exhibit high similarities under these treatments. We further proposed and experimentally validated that a homologous gene copy of RESPONSIVE TO DESICCATION 26 mediates the crosstalk between jasmonic acid and NaCl signaling pathways by directly regulating the stress-responsive genes and that circadian clock-related transcription factors like REVEILLE8 play a central role in response of poplar to these treatments. Overall, our study provides a chromatin insight into the molecular mechanism of transcription regulatory networks in response to different environmental stresses and raises the key roles of the circadian clock of poplar to adapt to adverse environments.

Genomic characterization of the NAC transcription factors, directed at understanding their functions involved in endocarp lignification of iron walnut (Juglans sigillata Dode)

The NAC (NAM, ATAF1/2, and CUC2) transcription factors (TF), one of the largest plant-specific gene families, play important roles in the regulation of plant growth and development, stress response and disease resistance. In particular, several NAC TFs have been identified as master regulators of secondary cell wall (SCW) biosynthesis. Iron walnut (Juglans sigillata Dode), an economically important nut and oilseed tree, has been widely planted in the southwest China. The thick and high lignified shell derived endocarp tissues, however, brings troubles in processing processes of products in industry. It is indispensable to dissect the molecular mechanism of thick endocarp formation for further genetic improvement of iron walnut. In the present study, based on genome reference of iron walnut, 117 NAC genes, in total, were identified and characterized in silico, which involves only computational analysis to provide insight into gene function and regulation. We found that the amino acids encoded by these NAC genes varied from 103 to 1,264 in length, and conserved motif numbers ranged from 2 to 10. The JsiNAC genes were unevenly distributed across the genome of 16 chromosomes, and 96 of these genes were identified as segmental duplication genes. Furthermore, 117 JsiNAC genes were divided into 14 subfamilies (A-N) according to the phylogenetic tree based on NAC family members of Arabidopsis thaliana and common walnut (Juglans regia). Furthermore, tissue-specific expression pattern analysis demonstrated that a majority of NAC genes were constitutively expressed in five different tissues (bud, root, fruit, endocarp, and stem xylem), while a total of 19 genes were specifically expressed in endocarp, and most of them also showed high and specific expression levels in the middle and late stages during iron walnut endocarp development. Our result provided a new insight into the gene structure and function of JsiNACs in iron walnut, and identified key candidate JsiNAC genes involved in endocarp development, probably providing mechanistic insight into shell thickness formation across nut species.

The C2 H2 -type zinc finger transcription factor OSIC1 positively regulates stomatal closure under osmotic stress in poplar

Salt and drought impair plant osmotic homeostasis and greatly limit plant growth and development. Plants decrease stomatal aperture to reduce water loss and maintain osmotic homeostasis, leading to improved stress tolerance. Herein, we identified the C₂ H₂ transcription factor gene OSMOTIC STRESS INDUCED C₂ H₂ 1 (OSIC1) from Populus alba var. pyramidalis to be induced by salt, drought, polyethylene glycol 6000 (PEG6000) and abscisic acid (ABA). Overexpression of OSIC1 conferred transgenic poplar more tolerance to high salinity, drought and PEG6000 treatment by reducing stomatal aperture, while its mutant generated by the CRISPR/Cas9 system showed the opposite phenotype. Furthermore, OSIC1 directly up-regulates PalCuAOζ in vitro and in vivo, encoding a copper-containing polyamine oxidase, to enhance H₂ O₂ accumulation in guard cells and thus modulates stomatal closure when stresses occur. Additionally, ABA-, drought- and salt-induced PalMPK3 phosphorylates OSIC1 to increase its transcriptional activity to PalCuAOζ. This regulation of OSIC1 at the transcriptional and protein levels guarantees rapid stomatal closure when poplar responds to osmotic stress. Our results revealed a novel transcriptional regulatory mechanism of H₂ O₂ production in guard cells mediated by the OSIC1-PalCuAOζ module. These findings deepen our understanding of how perennial woody plants, like poplar, respond to osmotic stress caused by salt and drought and provide potential targets for breeding.

Genome-wide association study in two-row spring barley landraces identifies QTL associated with plantlets root system architecture traits in well-watered and osmotic stress conditions

Water availability is undoubtedly one of the most important environmental factors affecting crop production. Drought causes a gradual deprivation of water in the soil from top to deep layers and can occur at diverse stages of plant development. Roots are the first organs that perceive water deficit in soil and their adaptive development contributes to drought adaptation. Domestication has contributed to a bottleneck in genetic diversity. Wild species or landraces represent a pool of genetic diversity that has not been exploited yet in breeding program. In this study, we used a collection of 230 two-row spring barley landraces to detect phenotypic variation in root system plasticity in response to drought and to identify new quantitative trait loci (QTL) involved in root system architecture under diverse growth conditions. For this purpose, young seedlings grown for 21 days in pouches under control and osmotic-stress conditions were phenotyped and genotyped using the barley 50k iSelect SNP array, and genome-wide association studies (GWAS) were conducted using three different GWAS methods (MLM GAPIT, FarmCPU, and BLINK) to detect genotype/phenotype associations. In total, 276 significant marker-trait associations (MTAs; p-value (FDR)< 0.05) were identified for root (14 and 12 traits under osmotic-stress and control conditions, respectively) and for three shoot traits under both conditions. In total, 52 QTL (multi-trait or identified by at least two different GWAS approaches) were investigated to identify genes representing promising candidates with a role in root development and adaptation to drought stress.

An R2R3-MYB network modulates stem strength by regulating lignin biosynthesis and secondary cell wall thickening in herbaceous peony

Stem strength is an important agronomic trait affecting plant lodging, and plays an essential role in the quality and yield of plants. Thickened secondary cell walls in stems provide mechanical strength that allows plants to stand upright, but the regulatory mechanism of secondary cell wall thickening and stem strength in cut flowers remains unclear. In this study, first, a total of 11 non-redundant Paeonia lactiflora R2R3-MYBs related to stem strength were identified and isolated from cut-flower herbaceous peony, among which PlMYB43, PlMYB83 and PlMYB103 were the most upregulated differentially expressed genes. Then, the expression characteristics revealed that these three R2R3-MYBs were specifically expressed in stems and acted as transcriptional activators. Next, biological function verification showed that these P. lactiflora R2R3-MYBs positively regulated stem strength, secondary cell wall thickness and lignin deposition. Furthermore, yeast-one-hybrid and dual luciferase reporter assays demonstrated that they could bind to the promoter of caffeic acid O-methyltransferase gene (PlCOMT2) and/or laccase gene (PlLAC4), two key genes involved in lignin biosynthesis. In addition, the function of PlLAC4 in increasing lignin deposition was confirmed by virus-induced gene silencing and overexpression. Moreover, PlMYB83 could also act as a transcriptional activator of PlMYB43. The findings of the study propose a regulatory network of R2R3-MYBs modulating lignin biosynthesis and secondary cell wall thickening for improving stem lodging resistance, and provide a resource for molecular genetic engineering breeding of cut flowers.

Characterization of plant laccase genes and their functions

Laccase is a copper-containing polyphenol oxidase found in different organisms. The multigene family that encodes laccases is widely distributed in plant genomes. Plant laccases oxidize monolignols to produce lignin which is important for plant growth and stress responses. Industrial applications of fungal and bacterial laccases are extensively explored and addressed. Recently many studies have focused on the significance of plant laccase, particularly in crop yield, and its functions in different environmental conditions. This review summarizes the transcriptional and posttranscriptional regulation of plant laccase genes and their functions in plant growth and development. It especially describes the responses of laccase genes to various stresses and their contributions to plant biotic and abiotic stress resistance. In-depth explanations and scientific advances will serve as foundations for research into plant laccase genes' function, mechanism, and possible applications.

Genome-wide analysis of the Populus trichocarpa laccase gene family and functional identification of PtrLAC23

INTRODUCTION

Biofuel is a kind of sustainable, renewable and environment friendly energy. Lignocellulose from the stems of woody plants is the main raw material for "second generation biofuels". Lignin content limits fermentation yield and is therefore a major obstacle in biofuel production. Plant laccase plays an important role in the final step of lignin formation, which provides a new strategy for us to obtain ideal biofuels by regulating the expression of laccase genes to directly gain the desired lignin content or change the composition of lignin.

METHODS

Multiple sequence alignment and phylogenetic analysis were used to classify PtrLAC genes; sequence features of PtrLACs were revealed by gene structure and motif composition analysis; gene duplication, interspecific collinearity and Ka/Ks analysis were conducted to identify ancient PtrLACs; expression levels of PtrLAC genes were measured by RNA-Seq data and qRT-PCR; domain analysis combine with cis-acting elements prediction together showed the potential function of PtrLACs. Furthermore, Alphafold2 was used to simulate laccase 3D structures, proLAC23::LAC23-eGFP transgenic Populus stem transects were applied to fluorescence observation.

RESULTS

A comprehensive analysis of the P. trichocarpa laccase gene (PtLAC) family was performed. Some ancient PtrLAC genes such as PtrLAC25, PtrLAC19 and PtrLAC41 were identified. Gene structure and distribution of conserved motifs clearly showed sequence characteristics of each PtrLAC. Combining published RNA-Seq data and qRT-PCR analysis, we revealed the expression pattern of PtrLAC gene family. Prediction results of cis-acting elements show that PtrLAC gene regulation was closely related to light. Through above analyses, we selected 5 laccases and used Alphafold2 to simulate protein 3D structures, results showed that PtrLAC23 may be closely related to the lignification. Fluorescence observation of proLAC23::LAC23-eGFP transgenic Populus stem transects and qRT-PCR results confirmed our hypothesis again.

DISCUSSION

In this study, we fully analyzed the Populus trichocarpa laccase gene family and identified key laccase genes related to lignification. These findings not only provide new insights into the characteristics and functions of Populus laccase, but also give a new understanding of the broad prospects of plant laccase in lignocellulosic biofuel production.

Identification and Expression Analysis of Calcium-Dependent Protein Kinases Gene Family in Potato Under Drought Stress

Calcium-dependent protein kinases (CDPKs) are a class of serine/threonine protein kinases encoded by several gene families that play key roles in stress response and plant growth and development. In this study, the BLAST method was used to search for protein sequences of the potato Calcium-dependent protein kinase gene family. The chromosome location, phylogeny, gene structures, gene duplication, cis-acting elements, protein-protein interaction, and expression profiles were analyzed. Twenty-five CDPK genes in the potato genome were identified based on RNA-seq data and were clustered into four groups (I-IV) based on their structural features and phylogenetic analysis. The result showed the composition of the promoter region of the StCDPKs gene, including light-responsive elements such as Box4, hormone-responsive elements such as ABRE, and stress-responsive elements such as MBS. Four pairs of segmental duplications were found in StCDPKs genes and the Ka/Ks ratios were below 1, indicating a purifying selection of the genes. The protein-protein interaction network revealed defense-related proteins such as; respiratory burst oxidase homologs (RBOHs) interacting with potato CDPKs. Transcript abundance was measured via RT-PCR between the two cultivars and their relative expression of CDPK genes was analyzed after 15, 20, and 25 days of drought. There were varied expression patterns of StCDPK3/13/21 and 23, between the two potato cultivars under mannitol induced-drought conditions. Correlation analysis showed that StCDPK21/22 and StCDPK3 may be the major differentially expressed genes involved in the regulation of malondialdehyde (MDA) and proline content in response to drought stress, opening a new research direction for genetic improvement of drought resistance in potato.

Lignin Synthesis, Affected by Sucrose in Lotus (Nelumbo nucifera) Seedlings, Was Involved in Regulation of Root Formation in the Arabidopsis thanliana

Adventitious roots (ARs) have an unmatched status in plant growth and metabolism due to the degeneration of primary roots in lotuses. In the present study, we sought to assess the effect of sucrose on ARs formation and observed that lignin synthesis was involved in ARs development. We found that the lignification degree of the ARs primordium was weaker in plants treated with 20 g/L sucrose than in 50 g/L sucrose treatment and control plants. The contents of lignin were lower in plants treated with 20 g/L sucrose and higher in plants treated with 50 g/L sucrose. The precursors of monomer lignin, including p-coumaric acid, caffeate, sinapinal aldehyde, and ferulic acid, were lower in the GL50 library than in the GL20 library. Further analysis revealed that the gene expression of these four metabolites had no novel difference in the GL50/GL20 libraries. However, a laccase17 gene (NnLAC17), involved in polymer lignin synthesis, had a higher expression in the GL50 library than in the GL20 library. Therefore, NnLAC17 was cloned and the overexpression of NnLAC17 was found to directly result in a decrease in the root number in transgenic Arabidopsis plants. These findings suggest that lignin synthesis is probably involved in ARs formation in lotus seedlings.

The Laccase Gene Family Mediate Multi-Perspective Trade-Offs during Tea Plant (Camellia sinensis) Development and Defense Processes

Laccase (LAC) plays important roles in different plant development and defense processes. In this study, we identified laccase genes (CsLACs) in Camellia sinensis cv ‘Longjing43′ cultivars, which were classified into six subclades. The expression patterns of CsLACs displayed significant spatiotemporal variations across different tissues and developmental stages. Most members in subclades II, IV and subclade I exhibited contrasting expression patterns during leaf development, consistent with a trade-off model for preferential expression in the early and late developmental stages. The extensive transcriptional changes of CsLACs under different phytohormone and herbivore treatment were observed and compared, with the expression of most genes in subclades I, II and III being downregulated but genes in subclades IV, V and VI being upregulated, suggesting a growth and defense trade-off model between these subclades. Taken together, our research reveal that CsLACs mediate multi-perspective trade-offs during tea plant development and defense processes and are involved in herbivore resistance in tea plants. More in-depth research of CsLACs upstream regulation and downstream targets mediating herbivore defense should be conducted in the future.

A Cotton Lignin Biosynthesis Gene, GhLAC4, Fine-Tuned by ghr-miR397 Modulates Plant Resistance Against Verticillium dahliae

Plant lignin is a component of the cell wall, and plays important roles in the transport potential of water and mineral nutrition and plant defence against biotic stresses. Therefore, it is necessary to identify lignin biosynthesis-related genes and dissect their functions and underlying mechanisms. Here, we characterised a cotton LAC, GhLAC4, which participates in lignin biosynthesis and plant resistance against Verticillium dahliae. According to degradome sequencing and GUS reporter analysis, ghr-miR397 was identified to directedly cleave the GhLAC4 transcript through base complementary. GhLAC4 knockdown and ghr-miR397 overexpression significantly reduced basal lignin content compared to the control, whereas ghr-miR397 silencing significantly increased basal lignin levels. Based on staining patterns and GC/MS analysis, GhLAC4 acted in G-lignin biosynthesis. Under V. dahliae infection, we found that G-lignin content in ghr-miR397-knockdowned plants significantly increased, compared to these plants under the mock treatment, while G-lignin contents in GhLAC4-silenced plants and ghr-miR397-overexpressed plants treated with pathogen were comparable with these plants treated with mock, indicating that GhLAC4 participates in defence-induced G-lignin biosynthesis in the cell wall. Knockdown of ghr-miR397 in plants inoculated with V. dahliae promoted lignin accumulation and increased plant resistance. The overexpression of ghr-miR397 and knockdown of GhLAC4 reduced lignin content and showed higher susceptibility of plants to the fungal infection compared to the control. The extract-free stems of ghr-miR397-knockdowned plants lost significantly less weight when treated with commercial cellulase and V. dahliae secretion compared to the control, while the stems of ghr-miR397-overexpressed and GhLAC4-silenced plants showed significantly higher loss of weight. These results suggest that lignin protects plant cell walls from degradation mediated by cellulase or fungal secretions. In summary, the ghr-miR397-GhLAC4 module regulates both basal lignin and defence-induced lignin biosynthesis and increases plant resistance against infection by V. dahliae.