Lignin Synthesis Research Articles

Unveiling Molecular Mechanisms of Nitric Oxide-Induced Low-Temperature Tolerance in Cucumber by Transcriptome Profiling.

Cucumber (Cucumis sativus L.) is one of the most popular cultivated vegetable crops but it is intrinsically sensitive to cold stress due to its thermophilic nature. To explore the molecular mechanism of plant response to low temperature (LT) and the mitigation effect of exogenous nitric oxide (NO) on LT stress in cucumber, transcriptome changes in cucumber leaves were compared. The results showed that LT stress regulated the transcript level of genes related to the cell cycle, photosynthesis, flavonoid accumulation, lignin synthesis, active gibberellin (GA), phenylalanine metabolism, phytohormone ethylene and salicylic acid (SA) signaling in cucumber seedlings. Exogenous NO improved the LT tolerance of cucumber as reflected by increased maximum photochemical efficiency (Fv/Fm) and decreased chilling damage index (CI), electrolyte leakage and malondialdehyde (MDA) content, and altered transcript levels of genes related to phenylalanine metabolism, lignin synthesis, plant hormone (SA and ethylene) signal transduction, and cell cycle. In addition, we found four differentially expressed transcription factors (MYB63, WRKY21, HD-ZIP, and b-ZIP) and their target genes such as the light-harvesting complex I chlorophyll a/b binding protein 1 gene (LHCA1), light-harvesting complex II chlorophyll a/b binding protein 1, 3, and 5 genes (LHCB1, LHCB3, and LHCB5), chalcone synthase gene (CSH), ethylene-insensitive protein 3 gene (EIN3), peroxidase, phenylalanine ammonia-lyase gene (PAL), DNA replication licensing factor gene (MCM5 and MCM6), gibberellin 3 beta-dioxygenase gene (GA3ox), and regulatory protein gene (NPRI), which are potentially associated with plant responses to NO and LT stress. Notably, HD-ZIP and b-ZIP specifically responded to exogenous NO under LT stress. Taken together, these results demonstrate that cucumber seedlings respond to LT stress and exogenous NO by modulating the transcription of some key transcription factors and their downstream genes, thereby regulating photosynthesis, lignin synthesis, plant hormone signal transduction, phenylalanine metabolism, cell cycle, and GA synthesis. Our study unveiled potential molecular mechanisms of plant response to LT stress and indicated the possibility of NO application in cucumber production under LT stress, particularly in winter and early spring.

Modulation of class III peroxidase pathways and phenylpropanoids in Arundo donax under salt and phosphorus stress

Arundo donax L. is an invasive species that has been recently employed for biomass production due to its well-known ability to colonize harsh environment. Based on previous observations, the present study investigated the potential role of phenylpropanoids and class III peroxidases to confer adaptation through biochemical and transcriptomic analysis in A. donax after Na+ and P excess supply, both in single stress and in combination, and after growth at low P level.The levels of hydrogen peroxide, flavonoids (i.e., quercetin, apigenin and kaempferol derivatives) and the activity of class III peroxidases, as well as the expression of several genes encoding for their enzymes involved in their biosynthesis, increased when Na+ was supplied in combination with P. These results suggest that those biomolecules are involved in the response of A. donax, to the presence of +Na and P in the soil. Moreover, even though at the sampling time no significant accumulation of lignin has been determined, the trend of accumulation of such metabolite and most of all the increase of several transcripts involved in its synthesis was found. This work for the first time indicates the need for further investigation devoted to elucidating whether the strengthening of cell walls via lignin synthesis is one of the mechanisms used by A. donax to adapt to harsh environments.

Analysis of the β-Glucosidase Family Reveals Genes Involved in the Lignification of Stone Cells in Chinese White Pear (Pyrus bretschneideri Rehd.).

BGLU β-glucosidases in glycoside hydrolase family 1 (GH1) are involved in many processes of plant secondary metabolism. In particular, its de-glycosylation function plays an important role in the transport of lignin monolignols. No comprehensive study of the BGLU family in Chinese pear (Pyrus bretschneideri Rehd.) has been reported yet. In this study, the 50 BGLU family members from Chinese white pear were identified. Three candidate genes, PbBGLU1, PbBGLU15, and PbBGLU16, that may be involved in lignin synthesis were screened by bioinformatics analysis and qRT-PCR. Subcellular localization showed that all three of these candidate genes were expressed in the extracellular region. Then, we analyzed the functions of PbBGLU1 and PbBGLU16. In situ hybridization analysis showed that PbBGLU1 transcripts were not only localized to some pulp cell walls, lignin deposition, and stone cell areas of a pear fruit, but that was also a small amount of enrichment in normal pear flesh cells. PbBGLU16 transcripts were only enriched in lignin deposition and stone cell areas of pear fruit. Enzyme activity analysis revealed that GST-PbBGLU1 and GST-PbBGLU16 had a stronger activity and higher catalytic efficiency for coniferin than syringin. In addition, GST-PbBGLU16 exhibited the higher activity and catalytic efficiency for the two substrates compared with GST-PbBGLU1. The transformation of PbBGLU1 and PbBGLU16 into Arabidopsis identified that the lignin contents of Arabidopsis BGLU-45 mutant, PbBGLU1-RE, and PbBGLU16-RE were not changed than that of wild-type. However, compared with wild-type Arabidopsis, the overexpression of the plant’s lignin increased in varying degrees. The effect of PbBGLU16 on the lignin increment was greater than that of PbBGLU1 in Arabidopsis. In pear fruits, with transient overexpression of PbBGLU1, the contents of lignin and stone cells were significantly higher (0.01 < P < 0.05) than those with empty vector injection pear fruits. After transient expression of PbBGLU16, lignin in pear fruit increased significantly (0.01 < P < 0.05) and stone cells showed a very significant difference (P < 0.01) compared with the control group. However, RNA interference silenced these two genes in pear fruit, which seemed to have no impression on lignin and stone cells. This study provides a molecular biological basis for improving pear fruit quality at the molecular level.

BRITTLE CULM17, a Novel Allele of TAC4, Affects the Mechanical Properties of Rice Plants.

Lodging resistance of rice (Oryza sativa L.) has always been a hot issue in agricultural production. A brittle stem mutant, osbc17, was identified by screening an EMS (Ethylmethane sulfonate) mutant library established in our laboratory. The stem segments and leaves of the mutant were obviously brittle and fragile, with low mechanical strength. Examination of paraffin sections of flag leaf and internode samples indicated that the number of cell layers in mechanical tissue of the mutant was decreased compared with the wild type, Pingtangheinuo, and scanning electron microscopy revealed that the mechanical tissue cell walls of the mutant were thinner. Lignin contents of the internodes of mature-stage rice were significantly lower in the mutant than in the wild type. By the MutMap method, we found candidate gene OsBC17, which was located on rice chromosome 2 and had a 2433 bp long coding sequence encoding a protein sequence of 810 amino acid residues with unknown function. According to LC-MS/MS analysis of intermediate products of the lignin synthesis pathway, the accumulation of caffeyl alcohol in the osbc17 mutant was significantly higher than in Pingtangheinuo. Caffeyl alcohol can be polymerized to the catechyl lignin monomer by laccase ChLAC8; however, ChLAC8 and OsBC17 are not homologous proteins, which suggests that the osbc17 gene is involved in this process by regulating laccase expression.

Transcriptomic and metabolomic analyses reveal defense mechanism in ‘Beta’ grapevine root border cells under ρ-hydroxybenzoic acid stress

Autotoxins are a major cause of grapevine replant disease. Root border cells (RBCs) of ‘Beta’ grapevine seedlings were selected to investigate the mechanism underlying the changes in the composition of grapevine root secretions mediated by autotoxins ρ-hydroxybenzoic acid (4-HBA) and their effect on harmful soil fungi (Fusarium solani). The results showed that, compared with control, the root length and number of RBCs were increased under 50 μg·mL–1 4-HBA treatment but inhibited under 200 μg·mL–1 treatment (T200), and no significant difference was found under 100 μg·mL–1 treatment (T100). In the T100 vs CK group, RBCs enhanced metabolites involved in the respiratory pathway and released carbon source substances, such as saccharides and organic acids. In addition, most metabolites of the flavonoid biosynthesis pathway and gallic acid (GA) of tannins were abundant in the RBC mucilage possibly due to the action of shikimate dehydrogenase (SDH). In the T200 vs CK group, abundance of some metabolites of the respiratory pathway decreased, and dihydroquercetin (DHQ), catechin (C), epicatechin gallate (ECG), quercetin derivative, and hesperetin derivative abundances of flavonoid biosynthesis pathway were inhibited possibly due to the declined expression level of PAL and CHS genes. Tannins [such as GA and ellagic acid (EA)] were also decreased in the mucilage of RBCs. Plate confrontation experiments showed that flavonoids [C, DHQ, and naringenin (NAR)] and tannin (GA) inhibited the growth of Fusarium solani to some extent. RBCs may also resist 4-HBA stress by increasing the expression level of lignin synthesis and SOD genes. Our research indicates that RBCs and their mucilage play an important role in protecting the root tips of grapevine against 4-HBA stress.

H-lignin can be deposited independently of CINNAMYL ALCOHOL DEHYDROGENASE C and D in Arabidopsis.

Lignin contributes substantially to the recalcitrance of biomass toward saccharification. To circumvent this problem, researchers have genetically altered lignin, although, in a number of cases, these efforts have resulted in an undesirable yield penalty. Recent findings have shown that by knocking out two subunits (MED5A and MED5B) of the transcriptional regulatory complex Mediator, the stunted growth phenotype of mutants in p-coumaroyl shikimate 3'-hydroxylase, reduced epidermal fluorescence 8-1 (ref8-1), can be alleviated. Furthermore, these plants synthesize a lignin polymer almost entirely derived from p-coumaryl alcohol. Plants deficient in cinnamyl alcohol dehydrogenase (CAD) are notable in that they primarily incorporate coniferaldehyde and sinapaldehyde into their lignin. We tested the hypothesis that by stacking mutations in the genes encoding for the CAD paralogs C and D on an Arabidopsis (Arabidopsis thaliana) med5a/5b ref8-1 genetic background, the biosynthesis of p-coumaryl alcohol would be blocked, making p-coumaraldehyde available for polymerization into a novel kind of lignin. The med5a/5b ref8-1 cadc cadd plants are viable, but lignin analysis demonstrated that they continue to synthesize p-hydroxyphenyl lignin despite being mutated for the CADs typically considered to be required for monolignol biosynthesis. In addition, enzyme activity tests showed that even in the absence of CADC and CADD, there is high CAD activity in stems. We tested the potential involvement of other CADs in p-coumaraldehyde biosynthesis in the quintuple mutant by mutating them using the CRISPR/Cas9 system. Lignin analysis demonstrated that the resulting hextuple mutant plants continue to deposit p-coumaryl alcohol-derived lignin, demonstrating a route for the synthesis of p-hydroxyphenyl lignin in Arabidopsis independent of four CAD isoforms.

Integrated Transcriptome and Proteome Analyses of Maize Inbred lines in Response to Salt Stress

To better understand the resistance of maize (Zea mays L.) to salt stress, maize inbred lines 8723 and P138, which are salt-tolerant and salt-sensitive, respectively, were investigated using the transcriptional and proteomic profiling of seedling roots under normal conditions and 180 mM NaCl stress. The screening criteria for differentially expressed proteins (DEPs) were a fold change (FC) ≥1.20 (up-regulated) or ≤0.83 (down-regulated). Additionally, the screening criteria for differentially expressed genes (DEGs) were FC &gt;2 or &lt;0.5. We analyzed the correlation between the protein and mRNA levels of two maize inbred lines under salt stress and found that a total of 3152 associated genes/proteins were identified in line 8723 under salt stress. However, only 14 DEGs were also identified by their corresponding DEPs, with a correlation coefficient of 0.07. A similar comparison of the 3159 genes/proteins affected by salt stress in line P138 identified just 8 DEGs with corresponding DEPs, with a correlation coefficient of 0.05. This indicates major differences in the regulation of transcriptional and translational processes in response to salt stress. In addition, in line 8723, we identified just eight DEGs with the same expression trend as their corresponding DEPs and six DEGs that behaved in contrast to their DEPs under salt stress. Compared to P138, the root response to salt stress in line 8723 involved the following processes. First, the up-regulation of lipid transporters and the lipid transfer-like protein VAS resulted in an increased lipid metabolism. Next, the increased expression of CAD6, as well as PRP1 and PRP10 under salt stress, promoted lignin synthesis and activated the abscisic acid signal pathway, respectively. In addition, the up-regulation of ADK2 and adenylate kinase expression regulated the concentration of purine ribonucleoside to help maintain dynamic energy balance in the maize cells. Furthermore, reactive oxygen species (ROS) scavenging and protective mechanisms were effectively enhanced by the up-regulation of peroxidase 12, peroxidase 67, glutathione transferase 9 and the putative laccase family protein, and the down-regulation of peroxidase 72. Therefore, maize enhances its salt tolerance by enhancing its lipid metabolism, promoting lignin biosynthesis, activating the abscisic acid signaling pathway, maintaining the dynamic energy balance of the maize cells, and enhancing the ROS clearance and protection mechanisms. Our study identified some genes and proteins related to salt tolerance in maize, and has thus provided new and important clues to better understand the resistance of maize to salt stress.

Genomic and Transcriptomic Analyses Reveal Pathways and Genes Associated With Brittle Stalk Phenotype in Maize.

The mechanical strength of the stalk affects the lodging resistance and digestibility of the stalk in maize. The molecular mechanisms regulating the brittleness of stalks in maize remain undefined. In this study, we constructed the maize brittle stalk mutant (bk5) by crossing the W22:Mu line with the Zheng 58 line. The brittle phenotype of the mutant bk5 existed in all of the plant organs after the five-leaf stage. Compared to wild-type (WT) plants, the sclerenchyma cells of bk5 stalks had a looser cell arrangement and thinner cell wall. Determination of cell wall composition showed that obvious differences in cellulose content, lignin content, starch content, and total soluble sugar were found between bk5 and WT stalks. Furthermore, we identified 226 differentially expressed genes (DEGs), with 164 genes significantly upregulated and 62 genes significantly downregulated in RNA-seq analysis. Some pathways related to cellulose and lignin synthesis, such as endocytosis and glycosylphosphatidylinositol (GPI)-anchored biosynthesis, were identified by the Kyoto Encyclopedia of Gene and Genomes (KEGG) and gene ontology (GO) analysis. In bulked-segregant sequence analysis (BSA-seq), we detected 2,931,692 high-quality Single Nucleotide Polymorphisms (SNPs) and identified five overlapped regions (11.2 Mb) containing 17 candidate genes with missense mutations or premature termination codons using the SNP-index methods. Some genes were involved in the cellulose synthesis-related genes such as ENTH/ANTH/VHS superfamily protein gene (endocytosis-related gene) and the lignin synthesis-related genes such as the cytochrome p450 gene. Some of these candidate genes identified from BSA-seq also existed with differential expression in RNA-seq analysis. These findings increase our understanding of the molecular mechanisms regulating the brittle stalk phenotype in maize.

Integrated mRNA and Small RNA Sequencing Reveals microRNAs Associated With Xylem Development in Dalbergia odorifera.

Dalbergia odorifera is a rare and precious rosewood specie, whose wood is a very high-quality material for valuable furniture and carving crafts. However, limited information is available about the process of wood formation in D. odorifera. To determine genes that might be closely associated with the xylem differentiation process, we analyzed the differentially expressed genes (DEGs) and microRNAs (miRNAs) from specific xylem tissues of D. odorifera by RNA sequencing (RNA-seq) and small RNA sequencing (small RNA-seq). In total, we obtained 134,221,955 clean reads from RNA-seq and 90,940,761 clean reads from small RNA-seq. By comparing the transition zone (Dotz) and sapwood (Dosw) samples, a total of 395 DEGs were identified. Further analysis revealed that DEGs encoded for WRKY transcription factors (eight genes), lignin synthesis (PER47, COMT, CCR2), cell wall composition (UXS2), gibberellin synthesis (KAO2, GA20OX1), jasmonic acid synthesis (OPR2, CYP74A), and synthesis of flavonoids (PAL2) and terpenoids (CYP71A1). Subsequently, a preliminary analysis by small RNA-seq showed that the expressions of 14 miRNAs (such as miR168a-5p, miR167f-5p, miR167h-5p, miR167e, miR390a, miR156g, novel_52, and novel_9) were significantly different between Dotz and Dosw. Further analysis revealed that the target genes of these differentially expressed miRNAs were enriched in the GO terms “amino acid binding,” “cellulase activity,” and “DNA beta-glucosyltransferase activity”. Further, KEGG pathway annotation showed significant enrichment in “fatty acid elongation” and “biosynthesis of unsaturated fatty acids”. These processes might be participating in the xylem differentiation of D. odorifera. Next, expression correlation analysis showed that nine differentially expressed miRNAs were significantly negatively associated with 21 target genes, which encoded for proteins such as pyrH, SPL6, SPL12, GCS1, and ARF8. Overall, this is the first study on miRNAs and their potential functions in the xylem development of D. odorifera, which provides a stepping stone for a detailed functional investigation of D. odorifera miRNAs.

Methionine enhances disease resistance of jujube fruit against postharvest black spot rot by activating lignin biosynthesis

The present research is focused on the effect of methionine on black spot rot caused by Alternaria alternata on jujube fruit and the possible mechanism involved. The results showed that 0.1 g L−1 methionine could induce disease resistance against A. alternata in jujube fruit; however, 0.1 g L−1 methionine did not directly inhibit the growth of A. alternata in vitro. According to the transcriptome analysis, it was observed that the enzymatic activities (PAL, 4CL, COMT, POD, and LAC), the expression of the corresponding genes, and the MYB genes related to lignin synthesis increased by 0.1 g L−1 methionine treatment. Moreover, a higher lignin content was observed in jujube fruit treated with 0.1 g L−1 methionine. These results suggest that 0.1 g L−1 of methionine increased jujube resistance against black spot rot, primarily by activating lignin biosynthesis, rather than directly inhibiting the pathogen. The present research indicates that methionine can potentially be used as a safe and reliable alternative fungicide for the control of postharvest infection in fruit.

Comparative analysis of anatomical structure, assimilate accumulation and gene expression in lignin and carbohydrate metabolism pathway during taproot thickening of taicai and pak choi

Taicai (Brassica rapa L.ssp. chinensis Makino var. tai-tsai Hort) is a type of brassica vegetable that can form edible fleshy roots, and is a variant of pak choi (Brassica rapa L. ssp. chinensis (L.) Hanelt). Its expanded taproot is an important nutrient storage organ. To better understand the changes and their regulation during taproot formation in taicai, we compared and analyzed the anatomical structure, lignin synthesis, carbohydrate accumulation and mRNA expression profile in the axial roots of taicai and pak choi, respectively. Compared with pak choi, the taproot of taicai had more developed phloem, a more scattered distribution of xylem vessels, and more sucrose and amylopectin accumulation. Comparison results based on RNA-seq data and qRT-PCR also reflected a greater reduction in lignin synthesis in taicai. Two genes encoding α-glucan phosphorylase 2 (BrPHS2) and glucan-6-phosphate/phosphate translocator 2 (BrGPT2) were suggested to play a noteworthy role in the starch accumulation during the taproot formation in taicai. Weighted gene co-expression network analysis (WGCNA) analysis identified two modules highly associated with the increase of root diameter; these modules contain genes related to sucrose starch metabolism as well as cell proliferation. Several transcription factors from four families in the module may regulate the genes related to carbohydrate metabolism and cell development in taicai taproot. These results contributed to a better understanding of the differences in root development among brassicas, and provide valuable resources for further exploring the regulation of the formation of modified organ in brassicas.

Transposon Insertion Drove the Loss of Natural Seed Shattering during Foxtail Millet Domestication.

Loss of seed shattering was a key step during cereal domestication, and it greatly facilitated seed harvest of the staple cereal foxtail millet (Setaria italica) because the cereal has very small seeds. However, the genetic basis for this loss has been largely unknown. Here, we combined comparative and association mapping to identify an 855-bp Harbinger transposable element insertion in the second exon of the foxtail millet gene shattering1 (sh1) that was responsible for the loss of seed shattering. The sh1 gene encodes zinc finger and YABBY domains. The insert prevents transcription of the second exon, causing partial loss of the zinc finger domain and then loss of natural seed shattering. Specifically, sh1 functions as a transcription repressor and represses the transcription of genes associated with lignin synthesis in the abscission zone, including CAD2. The diversity of sh1 is highly reduced in foxtail millet, consistent with either a severe domestication bottleneck or a selective sweep. Phylogenetic analysis of sh1 further revealed a single origin of foxtail millet in China. Our results support the theories that transposons were the most active factors in genome evolution driving loss of natural seed shattering during foxtail millet domestication and that sh1 underwent parallel selection during domestication across different cereal species.

Integrated analysis of the lncRNA/circRNA-miRNA-mRNA expression profiles reveals novel insights into potential mechanisms in response to root-knot nematodes in peanut

BackgroundPeanut is the most essential oil and food crop globally due to its high oil and protein content. Root-knot nematode infects peanut roots, causing poor development and severely limiting peanut yields worldwide. The discovery of peanut genome identified a considerable number of genetic loci controlling the peanut root-knot nematode; however, the molecular mechanism of root-knot nematode remains unknown.ResultsThe heterogeneous response to root-knot nematode stress in peanut roots was identified using whole-transcriptome RNA-seq. A total of 430 mRNAs, 111 miRNAs, 4453 lncRNAs, and 123 circRNAs were found to have differential expression between infected and non-infected peanuts. The expression profiles of the lncRNA/circRNA-miRNA-mRNA network were developed to understand the potential pathways that lead to root-knot nematodes in peanut roots. During root-knot nematodes stress, a total of 10 lncRNAs, 4 circRNAs, 5 miRNAs, and 13 mRNAs can create competing endogenous RNA and participate in the oxidation–reduction process as well as other biological metabolism processes in peanuts. The findings will highlight the role of peanut ceRNAs in response to root-knot nematodes.ConclusionThe GO classification and KEGG pathway enrichment study of core regulatory networks revealed that ceRNAs are involved in oxidation–reduction, peroxidase activity, lignin synthesis in the xylem, and flavonoid synthesis. Overall, these findings may help researchers better understand the role of non-coding RNAs in response to root-knot nematodes.

Exogenous Salicylic Acid Modifies Cell Wall Lignification, Total Phenolic Content, PAL-Activity in Wheat (Triticum aestivum L.) and Buckwheat (Fagopyrum esculentum Moench) Plants under Cadmium Chloride Impact

Salicylic acid (SA) is considered one of the most important plant signaling molecules involved in abiotic and biotic stress tolerance. Application of 0,05 mM SA enhanced plants’ tolerance to cadmium stress by modulating levels of several metabolites, including components of antioxidative defense, osmolytes, secondary metabolites, and metal-chelating compounds. Seeds of bread wheat (Triticum aestivum L.) and buckwheat (Fagopyrum esculentum Moench) were presoaked in 0,05 mM SA/or distilled water for 5 h, with the following germination in a dark thermostat for 3 d. Uniform seedlings were planted into +Cd / or -Cd-containing substrate and grown for 16/8 h light/dark. It was revealed that seed pretreatment with SA alone caused a 3-5-fold decrease in phenylalanine ammonia-lyase (PAL) activity and total phenolic content compared to the control water treatment. Seed pretreatment with SA alleviated the negative impact of Cd on plant growth, PAL activity, and total phenolic content. These results indicate that salicylate treatment alleviates Cd toxicity by modifying lignin synthesis and accumulation of flavonoids in wheat and buckwheat plants. Protective effects were more pronounced for buckwheat with the studied variables' high total phenolic content.

Systematic Analysis and Expression Profiles of the 4-Coumarate: CoA Ligase (4CL) Gene Family in Pomegranate (Punica granatum L.).

4-Coumarate:CoA ligase (4CL, EC6.2.1.12), located at the end of the phenylpropanoid metabolic pathway, regulates the metabolic direction of phenylpropanoid derivatives and plays a pivotal role in the biosynthesis of flavonoids, lignin, and other secondary metabolites. In order to understand the molecular characteristics and potential biological functions of the 4CL gene family in the pomegranate, a bioinformatics analysis was carried out on the identified 4CLs. In this study, 12 Pg4CLs were identified in the pomegranate genome, which contained two conserved amino acid domains: AMP-binding domain Box I (SSGTTGLPKGV) and Box II (GEICIRG). During the identification, it was found that Pg4CL2 was missing Box II. The gene cloning and sequencing verified that this partial amino acid deletion was caused by genome sequencing and splicing errors, and the gene cloning results corrected the Pg4CL2 sequence information in the ‘Taishanhong’ genome. According to the phylogenetic tree, Pg4CLs were divided into three subfamilies, and each subfamily had 1, 1, and 10 members, respectively. Analysis of cis-acting elements found that all the upstream sequences of Pg4CLs contained at least one phytohormone response element. An RNA-seq and protein interaction network analysis suggested that Pg4CL5 was highly expressed in different tissues and may participate in lignin synthesis of pomegranate. The expression of Pg4CL in developing pomegranate fruits was analyzed by quantitative real-time PCR (qRT-PCR), and the expression level of Pg4CL2 demonstrated a decreasing trend, similar to the trend of flavonoid content, indicating Pg4CL2 may involve in flavonoid synthesis and pigment accumulation. Pg4CL3, Pg4CL7, Pg4CL8, and Pg4CL10 were almost not expressed or lowly expressed, the expression level of Pg4CL4 was higher in the later stage of fruit development, suggesting that Pg4CL4 played a crucial role in fruit ripening. The expression levels of 4CL genes were significantly different in various fruit development stages. The results laid the foundation for an in-depth analysis of pomegranate 4CL gene functions.

Genome-Wide Development of Polymorphic Microsatellite Markers and Association Analysis of Major Agronomic Traits in Core Germplasm Resources of Tartary Buckwheat.

Tartary buckwheat (TB; Fagopyrum tataricum Gaertn.) is an important multigrain crop and medicinal plant, but functional genomics and molecular breeding research in this species have been lacking for quite some time. Here, genome-wide screening was performed to develop simple sequence repeat (SSR) markers associated with six major agronomic traits and the rutin contents of 97 core germplasm resources. A total of 40,901 SSR loci were identified; they were uniformly distributed throughout the TB genome, with a mean distance of 11 kb between loci. Based on these loci, 8,089 pairs of SSR primers were designed, and 101 primer pairs for polymorphic SSR loci were used to genotype the 97 core germplasm resources. The polymorphic SSR loci showed high genetic variation in these core germplasm resources, with an average polymorphic information content (PIC) value of 0.48. In addition, multiple SSR markers, such as SXAU8002 [100-grain weight (HGW)] and SXAU8006 [stem diameter (SD)], were found to be associated with agronomic traits in the two environments. Finally, based on gene functional annotation and homology analysis, a candidate gene, FtPinG0007685500, that may affect the node number and SD of the main stem by participating in lignin synthesis was identified. This study reports the mining of genome-wide SSR loci and the development of markers in TB, which can be used for molecular characterization of the germplasm in its gene pool. In addition, the detected markers and candidate genes could be used for marker-assisted breeding and functional gene cloning in TB.

Silicon Nanoparticles Enhance Ginger Rhizomes Tolerance to Postharvest Deterioration and Resistance to Fusarium solani.

Postharvest deterioration of ginger rhizome caused by microorganisms or wound infections causes significant economic losses. Fusarium solani is one of the important causal agents of prevalent ginger disease soft rot across the world. The massive and continuous use of chemical fungicides in postharvest preservation pose risks to human health and produce environmental contamination. Hence, new alternative tools are required to reduce postharvest deterioration and extend the postharvest life of ginger. In this study, the use of silicon nanoparticles (SiNPs) on the storability of ginger rhizomes during postharvest storage and their resistance to Fusarium solani was investigated. The results showed that 50, 100, and 150 mg L−1 of SiNPs increased the firmness of the ginger rhizome during storage but decreased the decay severity, water loss, total color difference, and the reactive oxygen species (ROS; H2O2 and superoxide anion) accumulation. Specifically, 100 mg L−1 (SiNP100) demonstrated the best effect in the extension of postharvest life and improved the quality of the ginger rhizomes. SiNP100 application increased the activities of antioxidant enzymes (SOD and CAT) and the total phenolics and flavonoid contents, thereby reducing the ROS accumulation and malondialdehyde (MDA) content. Meanwhile, SiNP100 treatment negatively impacts the peroxidase (POD) and polyphenol oxidase (PPO) activities, which may have contributed to the lower level of lignin and decreased total color difference. SiNP100 likely decreased water loss and the transfer of water by altering the expression of aquaporin genes. Moreover, SiNP100 modulated the expression of lignin synthesis and phytopathogenic responses genes including MYB and LysM genes. Furthermore, SiNP100 inhibited Fusarium solani by preventing the penetration of hyphae into cells, thus decreasing the severity of postharvest pathogenic decay. In summary, this study revealed the physiology and molecular mechanisms of SiNPs-induced tolerance to postharvest deterioration and resistance to disease, which provides a foundation for using SiNPs resources as a promising alternative tool to maintain ginger quality and control postharvest diseases.

Impact of ethanol vapor treatment on the quality of water bamboo ( Zizania caduciflora L.) shoots during cold storage

This study evaluated the effect of ethanol vapor treatments on the physicochemical characteristics and quality of postharvest water bamboo shoots (WBS) (Zizania caduciflora L.). WBS were treated with ethanol vapor at doses of 0 (control), 500, 750, and 1000 μl/L at 0 ± 1°C for 35 days. The fruit were evaluated for weight loss, firmness, color, total soluble solids, soluble sugars, malondialdehyde, lignin, and lignification-related enzyme activities. The results revealed that all ethanol treatments could inhibit the weight loss and softening of WBS, reduce the reduction of soluble solids and soluble sugars content, inhibit the lignification-associated enzymes peroxidase and phenylalanine ammonia lyase activities, and reduce the synthesis of lignin. Among them, the 750 μl/L ethanol vapor treatment had a significant effect on all tested parameters and maintained the storage quality of WBS better than other treatments. Practical applications Water bamboo shoot is a nutritionally rich aquatic vegetable. However, its quality deteriorates rapidly after harvest due to wilting, softening, and lignification. The ethanol vapor treatment in this study significantly reduced the softening and lignification of WBS. The ethanol vapor treatment is simple and has less residue, which is effective in maintaining the fruit quality and reducing the nutritional loss of WBS after harvest. It is a safe and environmentally friendly preservation method for WBS.

Synthesis, characterization, and utilization of poly-amino acid-functionalized lignin for efficient and selective removal of lead ion from aqueous solution

Effectively removing heavy metals from the wastewater using a green low-cost natural polymer-based adsorbent received a great deal of attention. In this study, natural γ-polyglutamic acid (γ-PGA) and ε-poly-L-lysine (ε-PL) functionalized lignin (DLGS and DLLS) were synthesized through demethylation/phenolation and amination to increase its intrinsic reactivity and adsorption sites, which were used to remove heavy metals from aqueous solutions. DLGS and DLLS were comprehensively characterized by 31P, 2D HSQC NMR, and elemental analysis (EA). The adsorption property of DLGS and DLLS for Pb2+ have been systematically investigated. The adsorption kinetics and isotherms were compliant with the pseudo-second-order model and Langmuir isotherm model, respectively. The maximum adsorption capacity of DLGS and DLLS for Pb2+ was 275.9 and 231.8 mg g−1 at 298 K, respectively, which is higher than that of most of the lignin-based adsorbent reported. Furthermore, it is confirmed that DLGS and DLLS exhibit excellent selectivity for removing Pb2+ through competitive adsorption experiments. Based on the Fourier transform infrared spectrum (FTIR) and X-ray photoelectron spectroscopy (XPS) and the density functional theory (DFT) calculations, the hydroxyl, carboxyl, amino, methoxyl, and dithiocarbamate groups are contributed to the binding with Pb2+, and density functional theory calculation further suggested dithiocarbamate and the carboxyl group are the primary active sites.

Global analysis of switchgrass (Panicum virgatum L.) transcriptomes in response to interactive effects of drought and heat stresses

BackgroundSustainable production of high-quality feedstock has been of great interest in bioenergy research. Despite the economic importance, high temperatures and water deficit are limiting factors for the successful cultivation of switchgrass in semi-arid areas. There are limited reports on the molecular basis of combined abiotic stress tolerance in switchgrass, particularly the combination of drought and heat stress. We used transcriptomic approaches to elucidate the changes in the response of switchgrass to drought and high temperature simultaneously.ResultsWe conducted solely drought treatment in switchgrass plant Alamo AP13 by withholding water after 45 days of growing. For the combination of drought and heat effect, heat treatment (35 °C/25 °C day/night) was imposed after 72 h of the initiation of drought. Samples were collected at 0 h, 72 h, 96 h, 120 h, 144 h, and 168 h after treatment imposition, total RNA was extracted, and RNA-Seq conducted. Out of a total of 32,190 genes, we identified 3912, as drought (DT) responsive genes, 2339 and 4635 as, heat (HT) and drought and heat (DTHT) responsive genes, respectively. There were 209, 106, and 220 transcription factors (TFs) differentially expressed under DT, HT and DTHT respectively. Gene ontology annotation identified the metabolic process as the significant term enriched in DTHT genes. Other biological processes identified in DTHT responsive genes included: response to water, photosynthesis, oxidation-reduction processes, and response to stress. KEGG pathway enrichment analysis on DT and DTHT responsive genes revealed that TFs and genes controlling phenylpropanoid pathways were important for individual as well as combined stress response. For example, hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HCT) from the phenylpropanoid pathway was induced by single DT and combinations of DTHT stress.ConclusionThrough RNA-Seq analysis, we have identified unique and overlapping genes in response to DT and combined DTHT stress in switchgrass. The combination of DT and HT stress may affect the photosynthetic machinery and phenylpropanoid pathway of switchgrass which negatively impacts lignin synthesis and biomass production of switchgrass. The biological function of genes identified particularly in response to DTHT stress could further be confirmed by techniques such as single point mutation or RNAi.