Lignins: Biosynthesis and Biological Functions in Plants

Heinz-resistant tomato cultivars exhibit a lignin-based resistance to field dodder (Cuscuta campestris) parasitism

Cuscuta species (dodders) are agriculturally destructive, parasitic angiosperms. These parasitic plants use haustoria as physiological bridges to extract nutrients and water from hosts. Cuscuta campestris has a broad host range and wide geographical distribution. While some wild tomato relatives are resistant, cultivated tomatoes are generally susceptible to C. campestris infestations. However, some specific Heinz tomato (Solanum lycopersicum) hybrid cultivars exhibit resistance to dodders in the field, but their defense mechanism was previously unknown. Here, we discovered that the stem cortex in these resistant lines responds with local lignification upon C. campestris attachment, preventing parasite entry into the host. Lignin Induction Factor 1 (LIF1, an AP2-like transcription factor), SlMYB55, and Cuscuta R-gene for Lignin-based Resistance 1, a CC-NBS-LRR (CuRLR1) are identified as factors that confer host resistance by regulating lignification. SlWRKY16 is upregulated upon C. campestris infestation and potentially negatively regulates LIF1 function. Intriguingly, CuRLR1 may play a role in signaling or function as an intracellular receptor for receiving Cuscuta signals or effectors, thereby regulating lignification-based resistance. In summary, these four regulators control the lignin-based resistance response in specific Heinz tomato cultivars, preventing C. campestris from parasitizing resistant tomatoes. This discovery provides a foundation for investigating multilayer resistance against Cuscuta species and has potential for application in other essential crops attacked by parasitic plants.

Necessity of rice resistance to planthoppers for OsEXO70H3 regulating SAMSL excretion and lignin deposition in cell walls

The planthopper resistance gene Bph6 encodes a protein that interacts with OsEXO70E1. EXO70 forms a family of paralogues in rice. We hypothesized that the EXO70-dependent trafficking pathway affects the excretion of resistance-related proteins, thus impacting plant resistance to planthoppers. Here, we further explored the function of EXO70 members in rice resistance against planthoppers. We used the yeast two-hybrid and co-immunoprecipitation assays to identify proteins that play roles in Bph6-mediated planthopper resistance. The functions of the identified proteins were characterized via gene transformation, plant resistance evaluation, insect performance, cell excretion observation and cell wall component analyses. We discovered that another EXO70 member, OsEXO70H3, interacted with BPH6 and functioned in cell excretion and in Bph6-mediated planthopper resistance. We further found that OsEXO70H3 interacted with an S-adenosylmethionine synthetase-like protein (SAMSL) and increased the delivery of SAMSL outside the cells. The functional impairment of OsEXO70H3 and SAMSL reduced the lignin content and the planthopper resistance level of rice plants. Our results suggest that OsEXO70H3 may recruit SAMSL and help its excretion to the apoplast where it may be involved in lignin deposition in cell walls, thus contributing to rice resistance to planthoppers.

Changes in xylem morphology and activity of defense-related enzymes are associated with bean resistance during Fusarium oxysporum colonization

Genetic resistance is the main strategy to control Fusarium wilt in common bean. Despite this, few studies have focused on defense mechanisms involved in bean resistance to Fusarium oxysporum f. sp. phaseoli (Fop). Thus, the present study aimed to investigate the changes in xylem morphology and involvement of phenylpropanoid compounds and their biosynthetic enzymes in bean resistance against Fop. Uirapuru and UFSC-01 genotypes characterized, respectively, as susceptible and resistant were used. In roots and hypocotyls, guaiacol peroxidase (GPX), phenylalanine ammonia-lyase (PAL), and polyphenol oxidase (PPO) activities were determined at 0, 1, 2, 3, 4, 5, and 6 days after inoculation (dai), and flavonoids, total phenolics, and lignin content were quantified at 0, 3, and 6 dai. Cross sections of taproots and hypocotyls were examined under epifluorescence (at 1, 3, and 6 dai) and transmission electron (at 6 dai) microscopic to analyze the morphology of xylem cell walls. Overall, there was an increase in the activity of all studied enzymes in resistant bean plants, mainly during advanced colonization stages. Modifications in xylem morphology were more intense in roots of resistant genotype resulting in an increase of occluded cells, organelles, and cell wall strengthening. This study provides evidence that bean resistance is associated with increased phenylpropanoid enzymatic activity and cell wall reinforcement of some xylem cells.

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.

Insights into the Molecular Regulation of Lignin Content in Triploid Poplar Leaves

After polyploidization, plants usually undergo some morphological and physiological changes, including the lignin content of polyploids usually becoming lower than that of diploids. However, the regulatory mechanism of the variation of lignin content in polyploid plants remains unclear. Therefore, in this research, we used full-sib poplar triploids and diploids to explore the molecular regulatory basis of lignin content in poplar triploid leaves through the determination of lignin content, the observation of xylem cells, and transcriptome sequencing. The results showed that the lignin content of triploid leaves was significantly lower than that of diploid leaves. The xylem cells of triploid leaves were significantly larger than those of diploids. Transcriptome sequencing data show that most lignin biosynthesis genes were significantly downregulated, and genes related to cell growth were mostly upregulated in triploid leaves compared with diploid leaves. In addition, co-expression network analysis showed that several transcription factors might be involved in the regulation of lignin biosynthesis. Consequently, the altered expression of genes related to lignin might lead to the reduced lignin content in triploids. These results provide a theoretical basis for further exploring the molecular mechanism of the variation of polyploid lignin content and the utilization of polyploid lignocellulosic resources.

Integrated Degradome and Srna Sequencing Revealed miRNA-mRNA Regulatory Networks between the Phloem and Developing Xylem of Poplar

Lignin and cellulose are the most abundant natural organic polymers in nature. MiRNAs are a class of regulatory RNAs discovered in mammals, plants, viruses, and bacteria. Studies have shown that miRNAs play a role in lignin and cellulose biosynthesis by targeting key enzymes. However, the specific miRNAs functioning in the phloem and developing xylem of Populus deltoides are still unknown. In this study, a total of 134 miRNAs were identified via high-throughput small RNA sequencing, including 132 known and two novel miRNAs, six of which were only expressed in the phloem. A total of 58 differentially expressed miRNAs (DEmiRNAs) were identified between the developing xylem and the phloem. Among these miRNAs, 21 were significantly upregulated in the developing xylem in contrast to the phloem and 37 were significantly downregulated. A total of 2431 target genes of 134 miRNAs were obtained via high-throughput degradome sequencing. Most target genes of these miRNAs were transcription factors, including AP2, ARF, bHLH, bZIP, GRAS, GRF, MYB, NAC, TCP, and WRKY genes. Furthermore, 13 and nine miRNAs were involved in lignin and cellulose biosynthesis, respectively, and we validated the miRNAs via qRT-PCR. Our study explores these miRNAs and their regulatory networks in the phloem and developing xylem of P.deltoides and provides new insight into wood formation.

Cross-species transcriptomes reveal species-specific and shared molecular adaptations for plants development on iron-rich rocky outcrops soils

Background

Canga is the Brazilian term for the savanna-like vegetation harboring several endemic species on iron-rich rocky outcrops, usually considered for mining activities. Parkia platycephala Benth. and Stryphnodendron pulcherrimum (Willd.) Hochr. naturally occur in the cangas of Serra dos Carajás (eastern Amazonia, Brazil) and the surrounding forest, indicating high phenotypic plasticity. The morphological and physiological mechanisms of the plants’ establishment in the canga environment are well studied, but the molecular adaptative responses are still unknown. To understand these adaptative responses, we aimed to identify molecular mechanisms that allow the establishment of these plants in the canga environment.

Results

Plants were grown in canga and forest substrates collected in the Carajás Mineral Province. RNA was extracted from pooled leaf tissue, and RNA-seq paired-end reads were assembled into representative transcriptomes for P. platycephala and S. pulcherrimum containing 31,728 and 31,311 primary transcripts, respectively. We identified both species-specific and core molecular responses in plants grown in the canga substrate using differential expression analyses. In the species-specific analysis, we identified 1,112 and 838 differentially expressed genes for P. platycephala and S. pulcherrimum, respectively. Enrichment analyses showed that unique biological processes and metabolic pathways were affected for each species. Comparative differential expression analysis was based on shared single-copy orthologs. The overall pattern of ortholog expression was species-specific. Even so, we identified almost 300 altered genes between plants in canga and forest substrates with conserved responses in the two species. The genes were functionally associated with the response to light stimulus and the circadian rhythm pathway.

Conclusions

Plants possess species-specific adaptative responses to cope with the substrates. Our results also suggest that plants adapted to both canga and forest environments can adjust the circadian rhythm in a substrate-dependent manner. The circadian clock gene modulation might be a central mechanism regulating the plants’ development in the canga substrate in the studied legume species. The mechanism may be shared as a common mechanism to abiotic stress compensation in other native species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08449-0.

New Insights into Green Protocols for Oxidative Depolymerization of Lignin and Lignin Model Compounds

Oxidative depolymerization of lignin is a hot topic in the field of biomass valorization. The most recent and green procedures have been herein detailed. Photochemical and electrochemical approaches are reviewed highlighting the pros and cons of each method. Mechanochemistry activated strategies are able to combine oxidation and depolymerization in the deconstruction of lignin. Homogenous and heterogeneous catalytic systems are exemplified stressing the green aspects associated with both the procedures. Solvent-free approaches as well as those carried out in alternative media are listed. Finally, the few examples of selenium catalyzed lignin valorization reported so far are cited.

Novel miRNA-SSRs for Improving Seed Hardness Trait of Pomegranate (Punica granatum L.)

Present research discovered novel miRNA-SSRs for seed type trait from 761 potential precursor miRNA sequences of pomegranate. SSR mining and BLASTx of the unique sequences identified 69 non-coding pre-miRNA sequences, which were then searched for BLASTn homology against Dabenzi genome. Sixty three true pri-miRNA contigs encoding 213 pre-miRNAs were predicted. Analysis of the resulting sequences enabled discovery of SSRs within pri-miRNA (227) and pre-miRNA sequences (79). A total of 132 miRNA-SSRs were developed for seed type trait from 63 true pri-miRNAs, of which 46 were specific to pre-miRNAs. Through ePCR, 123 primers were validated and mapped on eight Tunisia chromosomes. Further, 80 SSRs producing specific amplicons were ePCR-confirmed on multiple genomes i.e. Dabenzi, Taishanhong, AG2017 and Tunisia, yielding a set of 63 polymorphic SSRs (polymorphism information content ≥0.5). Of these, 32 miRNA-SSRs revealed higher polymorphism level (89.29%) when assayed on six pomegranate genotypes. Furthermore, target prediction and network analysis suggested a possible association of miRNA-SSRs i.e. miRNA_SH_SSR69, miRNA_SH_SSR36, miRNA_SH_SSR103, miRNA_SH_SSR35 and miRNA_SH_SSR53 with seed type trait. These miRNA-SSRs would serve as important genomic resource for rapid and targeted improvement of seed type trait of pomegranate.

Transcriptomic and Metabolic Profiling Reveals a Lignin Metabolism Network Involved in Mesocotyl Elongation during Maize Seed Germination

Lignin is an important factor affecting agricultural traits. The mechanism of lignin metabolism in maize (Zea mays) mesocotyl elongation was investigated during seed germination. Maize seeds were treated with 24-epibrassinolide (EBR) and brassinazole stimulation under 3 and 20 cm deep-seeding stress. Mesocotyl transcriptome sequencing together with targeted metabolomics analysis and physiological measurements were employed in two contrasting genotypes. Our results revealed differentially expressed genes (DEGs) were significantly enriched in phenylpropanoid biosynthesis, plant hormone signal transduction, flavonoid biosynthesis, and alpha-linolenic acid metabolism. There were 153 DEGs for lignin biosynthesis pathway, 70 DEGs for peroxisome pathway, and 325 differentially expressed transcription factors (TFs) of MYB, NAC, WRKY, and LIM were identified in all comparisons, and highly interconnected network maps were generated among multiple TFs (MYB and WRKY) and DEGs for lignin biosynthesis and peroxisome biogenesis. This caused p-coumaraldehyde, p-coumaryl alcohol, and sinapaldehyde down-accumulation, however, caffeyl aldehyde and caffeyl alcohol up-accumulation. The sum/ratios of H-, S-, and G-lignin monomers was also altered, which decreased total lignin formation and accumulation, resulting in cell wall rigidity decreasing. As a result, a significant elongation of maize mesocotyl was detected under deep-seeding stress and EBR signaling. These findings provide information on the molecular mechanisms controlling maize seedling emergence under deep-seeding stress and will aid in the breeding of deep-seeding maize cultivars.

Improved Growth Performance of Elaeis guineensis Jacq. Through the Applications of Arbuscular Mycorrhizal (AM) Fungi and Endophytic Bacteria

Agrochemical application in the oil palm industry has been estimated to be the largest component amounting to almost 30% of the operational costing. Therefore, there is a huge pressure in the oil palm cultivation to exercise sustainable practices, preferably using cheaper alternatives such as biofertilizers and organic substrates. This study investigates the effect of arbuscular mycorrhizal (AM) fungi and endophytic bacteria applied independently and in combination on oil palm growth and nutrient uptake. Greenhouse and field studies were conducted with plant responses assessed through growth parameters. Greenhouse plants were significantly stimulated by AM fungi, Rhizophagus intraradices UT126 (M1), through single microbe application. An increase of 36% in leaf area was noted in M1 plants while the calcium (Ca) uptake in leaves increased by 11%. There was no significant improvement in overall nitrogen, phosphate, and potassium (NPK) uptake but a significant improvement of Ca measurement in greenhouse and field was observed in the leaves. The predicted synergism between mixed inocula of M1 and R. clarus BR152B (M2) on vegetative growth was not observed, suggesting the probability of interspecies incompatibility that requires further investigation. Growth readings in plants treated with the combination of M1-M2 and Pseudomonas aeruginosa UPMP3 in the field were highest without a significant difference as compared to single application of M1. The difference in readings for field and greenhouse may have been influenced by other external factors such as soil type, rhizospheric microbial community, and climate, and therefore requires further elucidation. These findings suggest R. intraradices UT126 as a promising biostimulant candidate in sustainable agronomic practices especially in the nursery practices.

Comparative Metabolomic Profiling of Compatible and Incompatible Interactions Between Potato and Phytophthora infestans

Late blight is one of the main biological stresses limiting the potato yield; however, the biochemical mechanisms underlying the infection process of Phytophthora infestans remain unrevealed. In this study, the late blight-resistant potato cultivar Ziyun No.1 (R) and the susceptible cultivar Favorita (S) were inoculated with P. infestans. Untargeted metabolomics was used to study the changes of metabolites in the compatible and incompatible interactions of the two cultivars and the pathogen at 0, 48, and 96 h postinoculation (hpi). A total of 819 metabolites were identified, and the metabolic differences mainly emerged after 48 hpi. There were 198 and 115 differentially expressed metabolites (DEMs) in the compatible and incompatible interactions. These included 147 and 100 upregulated metabolites during the compatible and incompatible interactions, respectively. Among them, 73 metabolites were identified as the P. infestans-responsive DEMs. Furthermore, the comparisons between the two cultivars identified 57 resistance-related metabolites. Resistant potato cultivar had higher levels of salicylic acid and several upstream phenylpropanoid biosynthesis metabolites, triterpenoids, and hydroxycinnamic acids and their derivatives, such as sakuranetin, ferulic acid, ganoderic acid Mi, lucidenic acid D2, and caffeoylmalic acid. These metabolites play crucial roles in cell wall thickening and have antibacterial and antifungal activities. This study reports the time-course metabolomic responses of potatoes to P. infestans. The findings reveal the responses involved in the compatible and incompatible interactions of potatoes and P. infestans.

Rerouting of the lignin biosynthetic pathway by inhibition of cytosolic shikimate recycling in transgenic hybrid aspen

Lignin is a phenolic polymer deposited in the plant cell wall, and is mainly polymerized from three canonical monomers (monolignols), i.e. p-coumaryl, coniferyl and sinapyl alcohols. After polymerization, these alcohols form different lignin substructures. In dicotyledons, monolignols are biosynthesized from phenylalanine, an aromatic amino acid. Shikimate acts at two positions in the route to the lignin building blocks. It is part of the shikimate pathway that provides the precursor for the biosynthesis of phenylalanine, and is involved in the transesterification of p-coumaroyl-CoA to p-coumaroyl shikimate, one of the key steps in the biosynthesis of coniferyl and sinapyl alcohols. The shikimate residue in p-coumaroyl shikimate is released in later steps, and the resulting shikimate becomes available again for the biosynthesis of new p-coumaroyl shikimate molecules. In this study, we inhibited cytosolic shikimate recycling in transgenic hybrid aspen by accelerated phosphorylation of shikimate in the cytosol through expression of a bacterial shikimate kinase (SK). This expression elicited an increase in p-hydroxyphenyl units of lignin and, by contrast, a decrease in guaiacyl and syringyl units. Transgenic plants with high SK activity produced a lignin content comparable to that in wild-type plants, and had an increased processability via enzymatic saccharification. Although expression of many genes was altered in the transgenic plants, elevated SK activity did not exert a significant effect on the expression of the majority of genes responsible for lignin biosynthesis. The present results indicate that cytosolic shikimate recycling is crucial to the monomeric composition of lignin rather than for lignin content.

Transcriptional activation of rice CINNAMOYL-CoA REDUCTASE 10 by OsNAC5, contributes to drought tolerance by modulating lignin accumulation in roots

Drought is a common abiotic stress for terrestrial plants and often affects crop development and yield. Recent studies have suggested that lignin plays a crucial role in plant drought tolerance; however, the underlying molecular mechanisms are still largely unknown. Here, we report that the rice (Oryza sativa) gene CINNAMOYL-CoA REDUCTASE 10 (OsCCR10) is directly activated by the OsNAC5 transcription factor, which mediates drought tolerance through regulating lignin accumulation. CCR is the first committed enzyme in the monolignol synthesis pathway, and the expression of 26 CCR genes was observed to be induced in rice roots under drought. Subcellular localisation assays revealed that OsCCR10 is a catalytically active enzyme that is localised in the cytoplasm. The OsCCR10 transcript levels were found to increase in response to abiotic stresses, such as drought, high salinity, and abscisic acid (ABA), and transcripts were detected in roots at all developmental stages. In vitro enzyme activity and in vivo lignin composition assay suggested that OsCCR10 is involved in H- and G-lignin biosynthesis. Transgenic rice plants overexpressing OsCCR10 showed improved drought tolerance at the vegetative stages of growth, as well as higher photosynthetic efficiency, lower water loss rates, and higher lignin content in roots compared to non-transgenic (NT) controls. In contrast, CRISPR/Cas9-mediated OsCCR10 knock-out mutants exhibited reduced lignin accumulation in roots and less drought tolerance. Notably, transgenic rice plants with root-preferential overexpression of OsCCR10 exhibited higher grain yield than NT controls plants under field drought conditions, indicating that lignin biosynthesis mediated by OsCCR10 contributes to drought tolerance.

Assessment of membrane stability, central nervous system depressant, and gut motility effects of Lablab purpureus seeds

Introduction: Lablab purpureus, under the family of Fabaceae, is a plant with various pharmacological activities. The present study was aimed to investigate the phytoconstituents, membrane stabilizing activity, central nervous system (CNS) depressant potential, and gastrointestinal (GI) motility of the methanol extract of L. purpureus seeds (MELPS).Methods: The methanol plant extract was screened for different phytochemical groups. Mice were classified into four groups for in vivo activities. Group-I was designated as negative control and received distilled water (10 mL/kg body weight); group-II served as positive control and received diazepam (1 mg/kg body weight). Group-III and group-IV both were experimental groups and received plant extract at 200 and 400 mg/kg body weight, respectively.Results: Alkaloids, carbohydrates, saponins, glycosides, tannins, phenols, flavonoids, and proteins were found after phytochemical analysis. On hypotonic solution-induced hemolysis of erythrocyte membrane, MELPS9 (9 mg/mL) resulted in the highest percentage of inhibition (60.51 ± 0.889), and on heat-induced hemolysis, MELPS9 (9 mg/mL) resulted in the highest percentage of inhibition (33.97 ± 0.21). In the case of the CNS depressant potential experiment, mice that received a sample at a dose of 400 mg/kg body weight showed the highest result (54.40 ± 4.51) compared with the positive control (14.2 ± 3.70) (P < 0.001). Similarly, 400 mg/kg dose sample exhibited the highest percentage of inhibition (60.51 ± 0.889) of hemolysis and GI motility (22.26%).Conclusion: It can be concluded that the MELPS has potential membrane stability, CNS depressant, and antimotility effects.

The Effect of Bio-Synthesized Silver Nanoparticles on Germination, Early Seedling Development, and Metabolome of Wheat (Triticum aestivum L.)

Changes in the metabolome of germinating seeds and seedlings caused by metal nanoparticles are poorly understood. In the present study, the effects of bio-synthesized silver nanoparticles ((Bio)Ag NPs) on grains germination, early seedlings development, and metabolic profiles of roots, coleoptile, and endosperm of wheat were analyzed. Grains germinated well in (Bio)Ag NPs suspensions at the concentration in the range 10–40 mg/L. However, the growth of coleoptile was inhibited by 25%, regardless of (Bio)Ag NPs concentration tested, whereas the growth of roots gradually slowed down along with the increasing concentration of (Bio)Ag NPs. The deleterious effect of Ag NPs on roots was manifested by their shortening, thickening, browning of roots tips, epidermal cell death, progression from apical meristem up to root hairs zone, and the inhibition of root hair development. (Bio)Ag NPs stimulated ROS production in roots and affected the metabolic profiles of all tissues. Roots accumulated sucrose, maltose, 1-kestose, phosphoric acid, and some amino acids (i.e., proline, aspartate/asparagine, hydroxyproline, and branched-chain amino acids). In coleoptile and endosperm, contrary to roots, the concentration of most metabolites decreased. Moreover, coleoptile accumulated galactose. Changes in the concentration of polar metabolites in seedlings revealed the affection of primary metabolism, disturbances in the mobilization of storage materials, and a translocation of sugars and amino acids from the endosperm to growing seedlings.

Gene expression analysis during the fruit development in dehiscent and indehiscent Bixa orellana L. accessions

Fruit morphology and dehiscence-related genes were analyzed in dehiscent N4P and dehiscent P12 Bixa orellana accessions. Fruit architecture (exocarp and pericarp cells, trichomes, vascular bundles, vesicles, and bixin cells) documented by Scanning electron microscopy (SEM) morphology, blue toluidine stain, and phloroglucinol and hydrochloric acid (PHCL) stain was similar in both accessions. Although, the dehiscent zone (DZ) was higher in the indehiscent P12 B. orellana accession, lignification values, obtained by phloroglucinol and hydrochloric acid stain, within the DZ remain was similar in both variants being lower at 34 days after floral anthesis in the dehiscent N4P B. orellana accession. Dehiscence-related genes APETALA (AP2), SHATTERPROOF (SHP), and SPATULA (SPT) were identified on the reported B. orellana transcriptome (SRX1117606). Real-time quantitative polymerase chain reaction primers build by using these genes allow observing a differential expression during six fruit development stages. In both B. orellana accessions, the AP2 transcripts have a reduced expression, whereas the SHP transcripts were significantly higher during the first two days and ten days of development. SPT transcripts show an expression differential between both accessions being significantly higher in the dehiscent N4P, peaking with 9.66% at 42 days after floral anthesis (DAFA) of development. SPT transcription profile suggested that this gene has an important role during the fruit opening in the dehiscent N4P B. orellana accession.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01180-w.

Biochar and/or Compost to Enhance Nursery-Produced Seedling Performance: A Potential Tool for Forest Restoration Programs

Today, the use of nursery-produced seedlings is the most widely adopted method in forest restoration processes. To ensure and enhance the performance of transplanting seedlings into a specific area, soil amendments are often used due to their ability to improve soil physicochemical properties and, in turn, plant growth and development. The aim of the present study was to evaluate Populus euramericana growth and development on a growing substrate added with biochar and compost, both alone and in combination. To accomplish this aim, a pot experiment was performed to test biochar and/or compost effects on growing substrate physicochemical characteristics, plant morpho-physiological traits, and plant phenology. The results showed that biochar and/or compost improved growing substrate properties by increasing electrical conductivity, cation exchange capacity, and nutrient concentrations. On the one hand, these ameliorations accelerated poplar growth and development. On the other hand, amendments did not have positive effects on some plant morphological traits, although compost alone increased plant height, and very fine and fine root length. The combined use of biochar and compost did not show any synergistic or cumulative beneficial effects and led to a reduction in plant growth and development. In conclusion, compost alone seems to be the best solution in both ameliorating substrate characteristics and increasing plant growth, highlighting the great potential for its proper and effective application in large-scale forest restoration strategies.

Defense response changes in roots of oil palm (Elaeis guineensis Jacq.) seedlings after internal symptoms of Ganoderma boninense Pat. infection

BACKGROUND

The development of basal stem rot (BSR) disease in oil palm is associated with lignin during vegetative growth and salicylic acid (SA) biosynthesis. The increase in the lignin content, SA accumulation, growth, and root biomass could indicate the resistance of oil palm seedlings to BSR disease. Therefore, although there are many studies on the interactions between the Ganoderma boninense and oil palm, research on evaluation of physiological processes, biochemistry, and molecules occurring during early internal symptoms of BSR in roots of oil palm (Elaeis guineensis Jacq.) are essential.

RESULTS

Ganoderma boninense inoculation indicated that C01, C02, and C05 seedlings were susceptible, while the other three seedlings, C03, C07, and C08, were resistant based on Ganoderma Disease Index (GDI). Infection by G. boninense in the most susceptible seedlings C05 reduced fresh weight of roots (FW) by 9.0%, and lignin content by 10.9%. The most resistant seedlings C08 were reduced by only 8.4%, and 0.2% regarding their fresh weight and lignin content, respectively. BSR disease induced SA accumulation in the most susceptible C08 and decreased peroxidase (PRX) enzyme (EC 1.11.1.7) activities in root tissues of oil palm seedlings except C07 and C08 where PRX activities remained high in the 4 months after planting. Infection with G. boninense also increased glutathione S-transferase U19-like (EgGSTU19) gene expression in the root tissues of susceptible seedlings, while laccase-24 (EgLCC24) gene expression was associated with resistance against BSR disease. Based on the relative expression of twelve genes, two genes are categorized as receptors (EgWAKL5, EgMIK1), two genes as biosynthesis signal transduction compound (EgOPR5, EgACO1), five genes as defense responses (EgROMT, EgSOT12, EgLCC24, EgGLT3, EgGSTU19), and one gene as trans-resveratrol di-O-methyltransferase-like (EgRNaseIII) predicted related to BSR infection. While two other genes remain unknown (EgUnk1, EgUnk2).

CONCLUSIONS

Ganoderma infection-induced SA accumulation and lignification in resistant accessions promote the seedlings root biomass. Oil palm seedlings have a synergistic physical, biochemical, and molecular defense mechanism to the BSR disease. The utilization of nucleotide-based molecular markers using EgLCC24 gene is able to detect resistant oil palm seedlings to G. boninense.

RNA-Seq Reveals Differentially Expressed Genes Associated with High Fiber Quality in Abaca (Musa textilis Nee)

Despite the importance of and current demand for abaca (Musa textilis Nee) fiber, there has been limited study that capitalizes on RNA-seq to identify candidate genes associated with high fiber quality and bunchy top virus (AbBTV) resistance. Three varieties (Abuab, Inosa, and Tangongon), one wild banana variety (Musa balbisiana Colla) Pacol, and two developed backcrosses (Abuab × Pacol BC₂ and BC₃) were grown at the Institute of Plant Breeding (IPB), Laguna, Philippines. The pseudostems of 3-month-old suckers of each genotype were sampled for RNA-seq. Datasets were analyzed for differential expression (DE) implementing various model frameworks, including pairwise, genotypic and non-DE models. Results indicate that Abuab and BC₃ induce the highest proportion (70%) of abaca-specific genes. Gene ontology (GO) enrichment analysis showed several genes associated with cellulose synthase activity, callose synthase, ß-glucosidase activity, glucan biosynthetic process, etc. KEGG pathway analysis showed several genes encoding for enzymes involved in the lignin biosynthetic pathway. Analysis using genotypic DE (GDE) between abaca bunchy top virus (AbBTV)-resistant and -susceptible groups revealed genes such as pathogenesis-related protein and NBS-LRR. As the genotypes were not infected with the pathogen, these genes are yet to be confirmed for their roles in disease resistance and are an interesting subject for further investigation.

Antifungal Potential of Green Synthesized Magnetite Nanoparticles Black Coffee-Magnetite Nanoparticles Against Wilt Infection by Ameliorating Enzymatic Activity and Gene Expression in Solanum lycopersicum L

Tomato plants are prone to various biotic and abiotic stresses. Fusarium wilt is one of the most devasting diseases of tomatoes caused by Fusarium oxysporum f. sp. lycopersici, causing high yield and economic losses annually. Magnetite nanoparticles (Fe3O4 NPs) are one of the potent candidates to inhibit fungal infection by improving plant growth parameters. Spinach has been used as a starting material to synthesize green-synthesized iron oxide nanoparticles (IONPs). Various extracts, i.e., pomegranate juice, white vinegar, pomegranate peel, black coffee (BC), aloe vera peel, and aspirin, had been used as reducing/stabilizing agents to tune the properties of the Fe3O4 NPs. After utilizing spinach as a precursor and BC as a reducing agent, the X-ray diffraction (XRD) pattern showed cubic magnetite (Fe3O4) phase. Spherical-shaped nanoparticles (∼20 nm) with superparamagnetic nature indicated by scanning electron microscopy (SEM) monographs, whereas energy-dispersive X-ray gives good elemental composition in Fe3O4 NPs. A characteristic band of Fe-O at ∼ 561 cm-1 was exhibited by the Fourier transform infrared (FTIR) spectrum. X-ray photoelectron spectroscopy (XPS) results confirmed the binding energies of Fe 2p3/2 (∼710.9 eV) and Fe 2p1/2 (∼724.5 eV) while, Raman bands at ∼310 cm-1 (T2 g ), ∼550 cm-1 (T2 g ), and 670 cm-1 (A1 g ) indicated the formation of Fe3O4 NPs synthesized using BC extract. The in vitro activity of BC-Fe3O4 NPs significantly inhibited the mycelial growth of F. oxysporum both at the third and seventh day after incubation, in a dose-dependent manner. In vivo studies also exhibited a substantial reduction in disease severity and incidence by improving plant growth parameters after treatment with different concentrations of BC-Fe3O4 NPs. The increasing tendency in enzymatic activities had been measured after treatment with different concentrations of NPs both in roots and shoot of tomato plants as compared to the control. Correspondingly, the upregulation of PR-proteins and defense genes are in line with the results of the enzymatic activities. The outcome of the present findings suggests that Fe3O4 NPs has the potential to control wilt infection by enhancing plant growth. Hence, Fe3O4 NPs, being non-phytotoxic, have impending scope in the agriculture sector to attain higher yield by managing plant diseases.

Genome-wide association study for lignocellulosic compounds and fermentable sugar in rice straw

Cellulose and lignin are the two main components of secondary plant cell walls with substantial impact on stalk in the field and on straw during industrial processing. The amount of fermentable sugar that can be accessed is another important parameter affecting various industrial applications. In the present study, genetic variability of rice (Oryza sativa L.) genotypes for cellulose, lignin, and fermentable sugars contents was analyzed in rice straw. A genome-wide association study of 33,484 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) >0.05 was performed. The genome-wide association study identified seven, three, and three genomic regions to be significantly associated with cellulose, lignin, and fermentable sugar contents, respectively. Candidate genes in the associated genomic regions were enzymes mainly involved in cell wall metabolism. Novel SNP markers associated with cellulose were tagged to GH16, peroxidase, GT6, GT8, and CSLD2. For lignin content, Villin protein, OsWAK1/50/52/53, and GH16 were identified. For fermentable sugar content, UTP-glucose-1-phosphate uridylyltransferase, BRASSINOSTEROID INSENSITIVE 1, and receptor-like protein kinase 5 were found. The results of this study should improve our understanding of the genetic basis of the factors that might be involved in biosynthesis, turnover, and modification of major cell wall components and saccharides in rice straw.

White rot fungal impact on the evolution of simple phenols during decay of silver fir wood by UHPLC-HQOMS

INTRODUCTION

Silver fir (Abies alba Mill.) is one of the most valuable conifer wood species in Europe. Among the main opportunistic pathogens that cause root and butt rot on silver fir are Armillaria ostoyae and Heterobasidion abietinum. Due to the different enzymatic pools of these wood-decay fungi, different strategies in metabolizing the phenols were available.

OBJECTIVE

This work explores the changes in phenolic compounds during silver fir wood degradation.

METHODOLOGY

Phenols were analyzed before and after fungus inoculation in silver fir macerated wood after 2, 4 and 6 months. All samples were analyzed using high-performance liquid chromatography coupled to a hybrid quadrupole-orbitrap mass spectrometer.

RESULTS

Thirteen compounds, including simple phenols, alkylphenyl alcohols, hydroxybenzoketones, hydroxycinnamaldehydes, hydroxybenzaldehydes, hydroxyphenylacetic acids, hydroxycinnamic acids, hydroxybenzoic acids and hydroxycoumarins, were detected. Pyrocatechol, coniferyl alcohol, acetovanillone, vanillin, benzoic acid, 4-hydroxybenzoic acid and vanillic acid contents decreased during the degradation process. Methyl vanillate, ferulic acid and p-coumaric were initially produced and then degraded. Scopoletin was accumulated. Pyrocatechol, acetovanillone and methyl vanillate were found for the first time in both degrading and non-degrading wood of silver fir.

CONCLUSIONS

Despite differences in the enzymatic pool, both fungi caused a significant decrease in the amounts of phenolic compounds with the accumulation of the only scopoletin. Principal component analysis revealed an initial differentiation between the degradation activity of the two fungal species during degradation, but similar phenolic contents at the end of wood degradation.

Genome-Wide Expression Analysis of Root Tips in Contrasting Rice Genotypes Revealed Novel Candidate Genes for Water Stress Adaptation

Root system architecture (RSA) is an important agronomic trait with vital roles in plant productivity under water stress conditions. A deep and branched root system may help plants to avoid water stress by enabling them to acquire more water and nutrient resources. Nevertheless, our knowledge of the genetics and molecular control mechanisms of RSA is still relatively limited. In this study, we analyzed the transcriptome response of root tips to water stress in two well-known genotypes of rice: IR64, a high-yielding lowland genotype, which represents a drought-susceptible and shallow-rooting genotype; and Azucena, a traditional, upland, drought-tolerant and deep-rooting genotype. We collected samples from three zones (Z) of root tip: two consecutive 5 mm sections (Z1 and Z2) and the following next 10 mm section (Z3), which mainly includes meristematic and maturation regions. Our results showed that Z1 of Azucena was enriched for genes involved in cell cycle and division and root growth and development whereas in IR64 root, responses to oxidative stress were strongly enriched. While the expansion of the lateral root system was used as a strategy by both genotypes when facing water shortage, it was more pronounced in Azucena. Our results also suggested that by enhancing meristematic cell wall thickening for insulation purposes as a means of confronting stress, the sensitive IR64 genotype may have reduced its capacity for root elongation to extract water from deeper layers of the soil. Furthermore, several members of gene families such as NAC, AP2/ERF, AUX/IAA, EXPANSIN, WRKY, and MYB emerged as main players in RSA and drought adaptation. We also found that HSP and HSF gene families participated in oxidative stress inhibition in IR64 root tip. Meta-quantitative trait loci (QTL) analysis revealed that 288 differentially expressed genes were colocalized with RSA QTLs previously reported under drought and normal conditions. This finding warrants further research into their possible roles in drought adaptation. Overall, our analyses presented several major molecular differences between Azucena and IR64, which may partly explain their differential root growth responses to water stress. It appears that Azucena avoided water stress through enhancing growth and root exploration to access water, whereas IR64 might mainly rely on cell insulation to maintain water and antioxidant system to withstand stress. We identified a large number of novel RSA and drought associated candidate genes, which should encourage further exploration of their potential to enhance drought adaptation in rice.

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.

Characterization and Interaction Analysis of the Secondary Cell Wall Synthesis-Related Transcription Factor PmMYB7 in Pinus massoniana Lamb

In vascular plants, the importance of R2R3-myeloblastosis (R2R3-MYB) transcription factors (TFs) in the formation of secondary cell walls (SCWs) has long been a controversial topic due to the lack of empirical evidence of an association between TFs and downstream target genes. Here, we found that the transcription factor PmMYB7, which belongs to the R2R3-MYB subfamily, is involved in lignin biosynthesis in Pinus massoniana. PmMYB7 was highly expressed in lignified tissues and upon abiotic stress. As a bait carrier, the PmMYB7 protein had no toxicity or autoactivation in the nucleus. Forty-seven proteins were screened from the P. massoniana yeast library. These proteins were predicted to be mainly involved in resistance, abiotic stress, cell wall biosynthesis, and cell development. We found that the PmMYB7 protein interacted with caffeoyl CoA 3-O-methyltransferase-2 (PmCCoAOMT2)—which is involved in lignin biosynthesis—but not with beta-1, 2-xylosyltransferase (PmXYXT1) yeast two-hybrid (Y2H) studies. Our in vivo coimmunoprecipitation (Co-IP) assay further showed that the PmMYB7 and PmCCoAOMT2 proteins could interact. Therefore, we concluded that PmMYB7 is an upstream TF that can interact with PmCCoAOMT2 in plant cells. These findings lay a foundation for further research on the function of PmMYB7, lignin biosynthesis and molecular breeding in P. massoniana.

Evaluation of Cell Wall Chemistry of Della and Its Mutant Sweet Sorghum Stalks

The cell wall compositional (lignin and polysaccharides) variation of two sweet sorghum varieties, Della (D) and its variant REDforGREEN (RG), was evaluated at internodes (IN) and nodes (N) using high-performance liquid chromatography (HPLC), pyrolysis-gas chromatography-mass spectrometry (Py-GCMS), X-ray diffraction (XRD), and two-dimensional (2D) ¹H-¹³C nuclear magnetic resonance (NMR). The stalks were grown in 2018 (D1 and RG1) and 2019 (D2 and RG2) seasons. In RG1, Klason lignin reductions by 16-44 and 2-26% were detected in IN and N, respectively. The analyses also revealed that lignin from the sorghum stalks was enriched in guaiacyl units and the syringyl/guaiacyl ratio was increased in RG1 and RG2, respectively, by 96% and more than 2-fold at IN and 61 and 23% at N. The glucan content was reduced by 23-27% for RG1 and by 17-22% for RG2 at internodes. Structural variations due to changes in both cellulose- and hemicellulose-based sugars were detected. The nonacylated and γ-acylated β-O-4 linkages were the main interunit linkages detected in lignin. These results indicate compositional variation of stalks due to the RG variation, and the growing season could influence their mechanical and lodging behavior.

Comparative cytology combined with transcriptomic and metabolomic analyses of Solanum nigrum L. in response to Cd toxicity

Cadmium (Cd) triggers molecular alterations in plants, perturbs metabolites and damages plant growth. Therefore, understanding the molecular mechanism underlying the Cd tolerance in plants is necessary for assessing the persistent environmental impact of Cd. In this study, Solanum nigrum was selected as the test plant to investigate changes in biomass, Cd translocation, cell ultrastructure, metabolites and genes under hydroponic conditions. The results showed that the plant biomass was significantly decreased under Cd stress, and the plant has a stronger Cd transport capability. Transmission electron microscopy revealed that increased Cd concentration gradually damaged the plant organs (roots, stems and leaves) cell ultrastructure, as evidenced by swollen chloroplasts and deformed cell walls. Additionally, metabolomics analyses revealed that Cd stress mainly affected seven metabolism pathways, including 19 differentially expressed metabolites (DEMs). Moreover, 3908 common differentially expressed genes (DEGs, 1049 upregulated and 2859 downregulated) were identified via RNA-seq among five Cd treatments. Meanwhile, conjoint analysis found several DEGs and DEMs, including laccase, peroxidase, D-fructose, and cellobiose etc., are associated with cell wall biosynthesis, implying the cell wall biosynthesis pathway plays a critical role in Cd detoxification. Our comprehensive investigation using multiple approaches provides a molecular-scale perspective on plant response to Cd stress.

Profiling the cell walls of seagrasses from A (Amphibolis) to Z (Zostera)

BACKGROUND

The polyphyletic group of seagrasses shows an evolutionary history from early monocotyledonous land plants to the marine environment. Seagrasses form important coastal ecosystems worldwide and large amounts of seagrass detritus washed on beaches might also be valuable bioeconomical resources. Despite this importance and potential, little is known about adaptation of these angiosperms to the marine environment and their cell walls.

RESULTS

We investigated polysaccharide composition of nine seagrass species from the Mediterranean, Red Sea and eastern Indian Ocean. Sequential extraction revealed a similar seagrass cell wall polysaccharide composition to terrestrial angiosperms: arabinogalactans, pectins and different hemicelluloses, especially xylans and/or xyloglucans. However, the pectic fractions were characterized by the monosaccharide apiose, suggesting unusual apiogalacturonans are a common feature of seagrass cell walls. Detailed analyses of four representative species identified differences between organs and species in their constituent monosaccharide composition and lignin content and structure. Rhizomes were richer in glucosyl units compared to leaves and roots. Enhalus had high apiosyl and arabinosyl abundance, while two Australian species of Amphibolis and Posidonia, were characterized by high amounts of xylosyl residues. Interestingly, the latter two species contained appreciable amounts of lignin, especially in roots and rhizomes whereas Zostera and Enhalus were lignin-free. Lignin structure in Amphibolis was characterized by a higher syringyl content compared to that of Posidonia.

CONCLUSIONS

Our investigations give a first comprehensive overview on cell wall composition across seagrass families, which will help understanding adaptation to a marine environment in the evolutionary context and evaluating the potential of seagrass in biorefinery incentives.

How salt stress-responsive proteins regulate plant adaptation to saline conditions

An overview is presented of recent advances in our knowledge of candidate proteins that regulate various physiological and biochemical processes underpinning plant adaptation to saline conditions. Salt stress is one of the environmental constraints that restrict plant distribution, growth and yield in many parts of the world. Increased world population surely elevates food demands all over the globe, which anticipates to add a great challenge to humanity. These concerns have necessitated the scientists to understand and unmask the puzzle of plant salt tolerance mechanisms in order to utilize various strategies to develop salt tolerant crop plants. Salt tolerance is a complex trait involving alterations in physiological, biochemical, and molecular processes. These alterations are a result of genomic and proteomic complement readjustments that lead to tolerance mechanisms. Proteomics is a crucial molecular tool that indicates proteins expressed by the genome, and also identifies the functions of proteins accumulated in response to salt stress. Recently, proteomic studies have shed more light on a range of promising candidate proteins that regulate various processes rendering salt tolerance to plants. These proteins have been shown to be involved in photosynthesis and energy metabolism, ion homeostasis, gene transcription and protein biosynthesis, compatible solute production, hormone modulation, cell wall structure modification, cellular detoxification, membrane stabilization, and signal transduction. These candidate salt responsive proteins can be therefore used in biotechnological approaches to improve tolerance of crop plants to salt conditions. In this review, we provided comprehensive updated information on the proteomic data of plants/genotypes contrasting in salt tolerance in response to salt stress. The roles of salt responsive proteins that are potential determinants for plant salt adaptation are discussed. The relationship between changes in proteome composition and abundance, and alterations observed in physiological and biochemical features associated with salt tolerance are also addressed.

Proteomic Studies of Roots in Hypoxia-Sensitive and -Tolerant Tomato Accessions Reveal Candidate Proteins Associated with Stress Priming

Tomato (Solanum lycopersicum L.) is a vegetable frequently exposed to hypoxia stress induced either by being submerged, flooded or provided with limited oxygen in hydroponic cultivation systems. The purpose of the study was to establish the metabolic mechanisms responsible for overcoming hypoxia in two tomato accessions with different tolerance to this stress, selected based on morphological and physiological parameters. For this purpose, 3-week-old plants (plants at the juvenile stage) of waterlogging-tolerant (WL-T), i.e., POL 7/15, and waterlogging-sensitive (WL-S), i.e., PZ 215, accessions were exposed to hypoxia stress (waterlogging) for 7 days, then the plants were allowed to recover for 14 days, after which another 7 days of hypoxia treatment was applied. Root samples were collected at the end of each time-point and 2D-DIGE with MALDI TOF/TOF, and expression analyses of gene and protein-encoded alcohol dehydrogenase (ADH2) and immunolabelling of ADH were conducted. After collating the obtained results, the different responses to hypoxia stress in the selected tomato accessions were observed. Both the WL-S and WL-T tomato accessions revealed a high amount of ADH2, which indicates an intensive alcohol fermentation pathway during the first exposure to hypoxia. In comparison to the tolerant one, the expression of the adh2 gene was about two times higher for the sensitive tomato. Immunohistochemical analysis confirmed the presence of ADH in the parenchyma cells of the cortex and vascular tissue. During the second hypoxia stress, the sensitive accession showed a decreased accumulation of ADH protein and similar expression of the adh2 gene in comparison to the tolerant accession. Additionally, the proteome showed a greater protein abundance of glyceraldehyde-3-phosphate dehydrogenase in primed WL-S tomato. This could suggest that the sensitive tomato overcomes the oxygen limitation and adapts by reducing alcohol fermentation, which is toxic to plants because of the production of ethanol, and by enhancing glycolysis. Proteins detected in abundance in the sensitive accession are proposed as crucial factors for hypoxia stress priming and their function in hypoxia tolerance is discussed.

Integrated Metabolomics and Transcriptome Analyses Unveil Pathways Involved in Sugar Content and Rind Color of Two Sugarcane Varieties

Metabolic composition can have potential impact on several vital agronomic traits, and metabolomics, which represents the bioactive compounds in plant tissues, is widely considered as a powerful approach for linking phenotype-genotype interactions. However, metabolites related to cane traits such as sugar content, rind color, and texture differences in different sugarcane cultivars using metabolome integrated with transcriptome remain largely inconclusive. In this study, metabolome integrated with transcriptome analyses were performed to identify and quantify metabolites composition, and have better insight into the molecular mechanisms underpinning the different cane traits, namely, brix, rind color, and textures in the stems (S) and leaves (L) of sugarcane varieties FN41 and 165402. We also identified metabolites and associated genes in the phenylpropanoid and flavonoid biosynthesis pathways, starch and sucrose metabolism. A total of 512 metabolites from 11 classes, with the vast majority (122) belonging to flavonoids were identified. Moreover, the relatively high amount of D-fructose 6-p, D-glucose6-p and glucose1-p detected in FN41L may have been transported and distributed by source and sink of the cane, and a majority of them reached the stem of sugarcane FN41L, thereby promoting the high accumulation of sugar in FN41S. Observations also revealed that genes such as C4H, CHS, F3H, F3'H, DFR, and FG2 in phenylpropanoid and flavonoid biosynthesis pathways were the major factors impacting the rind color and contrasting texture of FN41 and 165204. Further analysis revealed that weighted gene co-expression network analysis (WGCNA) hub genes and six transcription factors, namely, Tify and NAC, MYB-related, C2C2-Dof, WRKY, and bHLH play a key role in phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, starch and sucrose metabolism. Additionally, metabolites such as L-phenylalanine, tyrosine, sinapaldehyde, pinobanksin, kaempferin, and nictoflorin were the potential drivers of phenotypic differences. Our finding also demonstrated that genes and metabolites in the starch and sucrose metabolism had a significant effect on cane sugar content. Overall, this study provided valuable insight into the molecular mechanisms underpinning high sugar accumulation and rind color in sugarcane, which we believe is important for future sugarcane breeding programs and the selection of high biomass varieties.

PuC3H35 confers drought tolerance by enhancing lignin and proanthocyanidin biosynthesis in the roots of Populus ussuriensis

Since the roots are the very organ where plants first sense and respond drought stress, it is of great importance to better understand root responses to drought. Yet the underlying molecular mechanisms governing root responses to drought stress have been poorly understood. Here, we identified and functionally characterized a CCCH type transcription factor, PuC3H35, and its targets, anthocyanin reductase (PuANR) and early Arabidopsis aluminum induced1 (PuEARLI1), which are involved in mediating proanthocyanidin (PA) and lignin biosynthesis in response to drought stress in Populus ussuriensis root. PuC3H35 was root-specifically induced upon drought stress. Overexpressing PuC3H35 promoted PA and lignin biosynthesis and vascular tissue development, resulting in enhanced tolerance to drought stress by the means of anti-oxidation and mechanical supporting. We further demonstrated that PuC3H35 directly bound to the promoters of PuANR and PuEARLI1 and overexpressing PuANR or PuEARLI1 increased root PA or lignin levels, respectively, under drought stress. Taken together, these results revealed a novel regulatory pathway for drought tolerance, in which PuC3H35 mediated PA and lignin biosynthesis by collaboratively regulating 'PuC3H35-PuANR-PA' and 'PuC3H35-PuEARLI1-PuCCRs-lignin' modules in poplar roots.

Integrative small RNA and transcriptome analysis provides insight into key role of miR408 towards drought tolerance response in cowpea

Drought stress response studies and overexpression of vun-miR408 proved it to be essential for abiotic stress tolerance in cowpea. Small RNA and transcriptome sequencing of an elite high-yielding drought-tolerant Indian cowpea cultivar, Pusa Komal revealed a differential expression of 198 highly conserved, 21 legume-specific, 14 less-conserved, and 10 novel drought-responsive microRNAs (miRNAs) along with 3391 (up-regulated) and 3799 (down-regulated) genes, respectively, in the leaf and root libraries. Among the differentially expressed miRNAs, vun-miR408-3p, showed an up-regulation of 3.53-log₂-fold change under drought stress. Furthermore, laccase 12 (LAC 12) was identified as the potential target of vun-miR408-3p using 5' RNA ligase-mediated rapid amplification of cDNA ends. The stable transgenic cowpea lines overexpressing artificial vun-miR408-3p (OX-amiR408) displayed enhanced drought and salinity tolerance as compared to the wild-type plants. An average increase of 30.17% in chlorophyll, 26.57% in proline, and 27.62% in relative water content along with lesser cellular H₂O₂ level was observed in the transgenic lines in comparison with the wild-type plants under drought stress. Additionally, the scanning electron microscopic study revealed a decrease in the stomatal aperture and an increase in the trichome density in the transgenic lines. The expression levels of laccase 3 and laccase 12, the potential targets of miR408, related to lipid catabolic processes showed a significant reduction in the wild-type plants under drought stress and the transgenic lines, indicating the regulation of lignin content as a plausibly essential trait related to the drought tolerance in cowpea. Taken together, this study primarily focused on identification of drought-responsive miRNAs and genes in cowpea, and functional validation of role of miR408 towards drought stress response in cowpea.

Phytotoxic effects of plastic pollution in crops: what is the size of the problem?

Plastic pollution is one of the most impactful human interferences in our planet. Fragmentation of plastic leads to nano- and microplastics (NP/MP) formation, which accumulate in agricultural lands, representing an increasing risk for crop production and food safety. It has been shown that MP promote damage in plant tissues by several direct and indirect ways, and that NP can enter the tissues/cells and accumulate in edible organs. Investigation of the phytotoxic effects of NP/MP in plants started only in 2016, with most of the studies performed with crops. Since contradictory results are often observed, it is important to review the literature in order to identify robust effects and their possible mechanisms. In this review, we discuss the potential of NP/MP in damaging crop species, with focus on the physiological changes described in the literature. We also performed scientometrics analyses on research papers in this field during 2016-2021, to reveal the research situation of phytotoxic effects of plastic pollution in crops. Our review is as a starting point to help identify gaps and future directions in this important, emerging field.

Genome-Wide Identification and Characterization of Caffeic Acid O-Methyltransferase Gene Family in Soybean

Soybean is one of the most important legumes, providing high-quality protein for humans. The caffeic acid O-methyltransferase (COMT) gene has previously been demonstrated to be a critical gene that regulates lignin production in plant cell walls and plays an important function in plant growth and development. However, the COMT gene family has not been studied in soybeans. In this study, 55 COMT family genes in soybean were identified by phylogenetic analysis and divided into two groups, I and II. The analysis of conserved domains showed that all GmCOMTs genes contained Methyltransferase-2 domains. Further prediction of cis-acting elements showed that GmCOMTs genes were associated with growth, light, stress, and hormonal responses. Eventually, based on the genomic data of soybean under different stresses, the results showed that the expression of GmCOMTs genes was different under different stresses, such as salt and drought stress. This study has identified and characterized the COMT gene family in soybean, which provides an important theoretical basis for further research on the biological functions of COMT genes and promotes revealing the role of GmCOMTs genes under stress resistance.

Ammonia–Nitrate Mixture Dominated by NH4+–N Promoted Growth, Photosynthesis and Nutrient Accumulation in Pecan (Carya illinoinensis)

Although ammonia–nitrogen (NH4+–N) and nitrate–nitrogen (NO3−–N) are the two main forms of N absorbed and utilized by plants, the preferences of plants for these forms are still unclear. In this study, we analyzed the growth, photosynthesis, and nutrients of pecan under different NH4+:NO3− ratios (0/0, 0/100, 25/75, 50/50, 75/25, 100/0) by indoor aerosol incubation. The results showed that additions of different N forms promoted the growth and development of pecan seedlings. When NO3−–N was used as the sole N source, it significantly promoted the ground diameter growth of pecan and increased the leaf pigment content and photosynthetic rate. The NH4+:NO3− ratio of 75:25 and NH4+–N as the sole N source significantly increased the soluble sugars in stems and roots, starch in leaves, stems and roots, soluble protein in leaves and stems, and soluble phenols in stems and roots. Additionally, the NH4+:NO3− ratio of 75:25 increased plant height, leaf number, root soluble protein, and leaf soluble phenol contents. In conclusion, regarding the physiological aspects of pecan growth, pecans are more inclined to use NH4+–N. Considering that the NH4+–N as the only N source may lead to nutrient imbalance or even toxicity, the NH4+:NO3− ratio of 75:25 was most favorable for the growth and development of pecan seedlings.

qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)

BACKGROUND

Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of intuitive tools to browse and analyze the resulting large-scale genetic and genomic datasets remain a significant challenge. Furthermore, these integrative genomics approaches require innovative methods to dissect the flow and interconnectedness of biological information underlying complex trait variation. The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus. Since the Eucalyptus Genome Integrative Explorer (EucGenIE) is integrated within PlantGenIE, it shares genome and expression analysis tools previously implemented within the various subdomains (ConGenIE, PopGenIE and AtGenIE). Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking.

RESULTS

We have developed qtlXplorer ( https://eucgenie.org/QTLXplorer ) for visualizing and exploring systems genetics data from genome-wide association studies including quantitative trait loci (QTLs) and expression-based QTL (eQTL) associations. This module allows users to, for example, find co-located QTLs and eQTLs using an interactive version of Circos, or explore underlying genes using JBrowse. It provides users with a means to build systems genetics models and generate hypotheses from large-scale population genomics data. We also substantially upgraded the EucGenIE resource and show how it enables users to combine genomics and systems genetics approaches to discover candidate genes involved in biotic stress responses and wood formation by focusing on two multigene families, laccases and peroxidases.

CONCLUSIONS

qtlXplorer adds a new dimension, population genomics, to the EucGenIE and PlantGenIE environment. The resource will be of interest to researchers and molecular breeders working in Eucalyptus and other woody plant species. It provides an example of how systems genetics data can be integrated with functional genetics data to provide biological insight and formulate hypotheses. Importantly, integration within PlantGenIE enables novel comparative genomics analyses to be performed from population-scale data.

The SlHB8 Acts as a Negative Regulator in Stem Development and Lignin Biosynthesis

The stem is an important organ in supporting plant body, transporting nutrients and communicating signals for plant growing. However, studies on the regulation of stem development in tomato are rather limited. In our study, we demonstrated that SlHB8 negatively regulated tomato stem development. SlHB8 belongs to homeo domain-leucine zipper Class III gene family transcription factors and expressed in all the organs examined including root, stem, leaves, flower, and fruit. Among these tissues, SlHB8 showed stable high expression level during tomato stem development. Overexpression of SlHB8 gene decreased stem diameter with inhibited xylem width and xylem cell layers, while loss of function of SlHB8gene increased the stem diameter and xylem width. The contents of lignin were decreased both in leaves and stems of SlHB8 overexpression plants. RNA-seq analysis on the stems of wild type and SlHB8 transgenic plants showed that the 116 DEGs (differential expressed genes) with reversible expression profiles in SlHB8-ox and SlHB8-cr plants were significantly enriched in the phenylpropanoid biosynthesis pathway and plant-pathogen pathway which were related to lignin biosynthesis and disease resistance. Meanwhile, the key genes involved in the lignin biosynthesis pathway such as SlCCR (cinnamoyl-CoA reductase), SlCYP73A14/C4H (cinnamate 4-hydroxylase), SlC3H (coumarate 3-hydroxylase) and SlCAD (cinnamoyl alcohol dehydrogenase) were down-regulated in both stem and leaves of SlHB8 overexpression plants, indicating a negative regulatory role of SlHB8 in the lignin biosynthesis and stem development.

Challenges of Biomass Utilization for Bioenergy in a Climate Change Scenario

The climate changes expected for the next decades will expose plants to increasing occurrences of combined abiotic stresses, including drought, higher temperatures, and elevated CO2 atmospheric concentrations. These abiotic stresses have significant consequences on photosynthesis and other plants' physiological processes and can lead to tolerance mechanisms that impact metabolism dynamics and limit plant productivity. Furthermore, due to the high carbohydrate content on the cell wall, plants represent a an essential source of lignocellulosic biomass for biofuels production. Thus, it is necessary to estimate their potential as feedstock for renewable energy production in future climate conditions since the synthesis of cell wall components seems to be affected by abiotic stresses. This review provides a brief overview of plant responses and the tolerance mechanisms applied in climate change scenarios that could impact its use as lignocellulosic biomass for bioenergy purposes. Important steps of biofuel production, which might influence the effects of climate change, besides biomass pretreatments and enzymatic biochemical conversions, are also discussed. We believe that this study may improve our understanding of the plant biological adaptations to combined abiotic stress and assist in the decision-making for selecting key agronomic crops that can be efficiently adapted to climate changes and applied in bioenergy production.

Lignin degradation by microorganisms: A review

Lignin is an abundant plant-based biopolymer that has found applications in a variety of industries from construction to bioethanol production. This recalcitrant branched polymer is naturally degraded by many different species of microorganisms, including fungi and bacteria. These microbial lignin degradation mechanisms provide a host of possibilities to overcome the challenges of using harmful chemicals to degrade lignin biowaste in many industries. The classes and mechanisms of different microbial lignin degradation options available in nature form the primary focus of the present review. This review first discusses the chemical building blocks of lignin and the industrial sources and applications of this multifaceted polymer. The review further places emphasis on the degradation of lignin by natural means, discussing in detail the lignin degradation activities of various fungal and bacterial species. The lignin-degrading enzymes produced by various microbial species, specifically white-rot fungi, brown-rot fungi, and bacteria, are described. In the end, possible directions for future lignin biodegradation applications and research investigations have been provided.

Synergistic effect of lignin and ethylene glycol crosslinked epoxy resin on enhancing thermal, mechanical and shape memory performance

Lignosulfonate (LS) was successfully introduced into the epoxy resin matrix with the aid of ethylene glycol (EG) dissolution. Both the rigid LS and soft EG segments were linked into the cross-linked network structure of epoxy resin via esterification of hydroxyl groups in LS and EG molecules with anhydride. The ultimate properties of cured samples were adjusted effectively by changing the proportion of LS and EG components. Curing reaction and kinetics were analyzed, by which the optimal curing process parameters were determined. Although thermal stability of LS itself was relatively lower than that of neat epoxy, the thermal performance was significantly enhanced for the modified sample of epoxy/LS0.5-EG0.5. At the same time, the flexural strength, flexural modulus and impact strength were found to be increased by 23.1, 35.7 and 15.1% respectively compared with the neat epoxy. In addition, the excellent shape memory behavior and improved mechanical stability with LS addition were exhibited by the cured LS-EG modified specimens. This work reveals that lignin can be used as an efficient functional additive to regulate thermal, mechanical and shape memory properties of epoxy resin.

Evaluation of high salinity tolerance in Pongamia pinnata (L.) Pierre by a systematic analysis of hormone-metabolic network

Salinity stress results in significant losses in plant productivity and loss of cultivable lands. Although Pongamia pinnata is reported to be a salt-tolerant semiarid biofuel tree, the adaptive mechanisms to saline environments are elusive. Despite a reduction in carbon exchange rate (CER), the unchanged relative water content provides no visible salinity induced symptoms in leaves of hydroponic cultivated Pongamia seedlings for 8 days. Our Na⁺ -specific fluorescence results demonstrated that there was an effective apoplastic sodium sequestration in the roots. Salinity stress significantly increased zeatin (~5.5-fold), and jasmonic acid (~3.8-fold) levels in leaves while zeatin (~2.5-fold) content increased in leaves as well as in roots of salt-treated plants. Metabolite analysis suggested that osmolytes such as myo-inositol and mannitol were enhanced by ~12-fold in leaves and roots of salt-treated plants. Additionally, leaves of Pongamia showed a significant enhancement in carbohydrate content, while fatty acids were accumulated in roots under salt stress condition. At the molecular level, salt stress enhanced the expression of genes related to transporters, including the Salt Overly Sensitive 2 gene (SOS2), SOS3, vacuolar-cation/proton exchanger, and vacuolar-proton/ATPase exclusively in leaves, whereas the Sodium Proton Exchanger1 (NHX1), Cation Calcium Exchanger (CCX), and Cyclic Nucleotide Gated Channel 5 (CNGC5) were up-regulated in roots. Antioxidant gene expression analysis clearly demonstrated that peroxidase levels were significantly enhanced by ~10-fold in leaves, while Catalase and Fe-superoxide Dismutase (Fe-SOD) genes were increased in roots under salt stress. The correlation interaction studies between phytohormones and metabolites revealed new insights into the molecular and metabolic adaptations that confer salinity tolerance to Pongamia.