Transcriptome-based identification of genes revealed differential expression profiles and lignin accumulation during root development in cultivated and wild carrots

Effects of leaf and stem maturation on nutritional value in Megathyrsus maximus

BACKGROUND

Megathyrsus maximus is a forage grass native to Africa but widely cultivated in tropical and subtropical regions of the world where it is part of the grazing food chain. This study aimed to evaluate five M. maximus genotypes for the effect of maturity on their morpho-agronomic traits, nutritional composition and digestibility, and to correlate their leaf blade and stem anatomy with their nutritional value.

RESULTS

The proportion of sclerenchyma tissues increased as maturity was reached, while lignin accumulation was differentiated between genotypes. Gatton Panic, Green Panic and Mutale genotypes maintained their acid detergent lignin (ADL) values for leaf blades in the three cuts evaluated. In sacco ruminal dry matter disappearance was lower in Green Panic genotype at the vegetative stage for stems, but not for leaf blades. Significant positive correlations were found between dry matter disappearance and mesophyll tissues, and the latter were negatively correlated with neutral detergent fiber (NDF) and ADL.

CONCLUSION

Our results strongly indicate that cutting age and genotype affected the nutritional value of M. maximus leaf blades and stems, with a more pronounced loss of quality in stems than in leaf blades. We recommend increasing the frequency of grazing at early stage or anticipating the stage of stem elongation in Green Panic to produce forage with better nutritional value. © 2023 Society of Chemical Industry.

Combined metabolome and transcriptome analysis reveals a critical role of lignin biosynthesis and lignification in stem-like pneumatophore development of the mangrove Avicennia marina

MAIN CONCLUSION

Transcriptional and metabolic regulation of lignin biosynthesis and lignification plays crucial roles in Avicennia marina pneumatophore development, facilitating its adaptation to coastal habitats. Avicennia marina is a pioneer mangrove species in coastal wetland. To cope with the periodic intertidal flooding and hypoxia environment, this species has developed a complex and extensive root system, with its most unique feature being a pneumatophore with a distinct above- and below-ground morphology and vascular structure. However, the characteristics of pneumatophore lignification remain unknown. Studies comparing the anatomy among above-ground pneumatophore, below-ground pneumatophore, and feeding root have suggested that vascular structure development in the pneumatophore is more like the development of a stem than of a root. Metabolome and transcriptome analysis illustrated that the accumulation of syringyl (S) and guaiacyl (G) units in the pneumatophore plays a critical role in lignification of the stem-like structure. Fourteen differentially accumulated metabolites (DAMs) and 10 differentially expressed genes involved in the lignin biosynthesis pathway were targeted. To identify genes significantly associated with lignification, we analyzed the correlation between 14 genes and 8 metabolites and further built a co-expression network between 10 transcription factors (TFs), including 5 for each of MYB and NAC, and 23 enzyme-coding genes involved in lignin biosynthesis. 4-Coumarate-CoA ligase, shikimate/quinate hydroxycinnamoyl transferase, cinnamyl alcohol dehydrogenase, caffeic acid 3-O-methyltransferase, phenylalanine ammonia-lyase, and peroxidase were identified to be strongly correlated with these TFs. Finally, we examined 9 key candidate genes through quantitative real-time PCR to validate the reliability of transcriptome data. Together, our metabolome and transcriptome findings reveal that lignin biosynthesis and lignification regulate pneumatophore development in the mangrove species A. marina and facilitate its adaptation to coastal habitats.

Genome-wide analysis of the cellulose toolbox of Primulina eburnea, a calcium-rich vegetable

BACKGROUND

Human-guided crop domestication has lasted for more than 10,000 years. In terms of the domestication and breeding of vegetables, cellulose content in edible tissues is one of the most important traits. Primulina eburnea is a recently developed calcium-rich vegetable with a high soluble and bioavailable calcium content in its leaves. However, the high cellulose content in the leaves hampers the taste, and no research has been reported on the genetic basis of cellulose biosynthesis in this calcium-rich vegetable.

RESULTS

We identified 36 cellulose biosynthesis-involved genes belonging to eight gene families in the P. eburnea genome. The cellulose accumulated decreasingly throughout leaf development. Nineteen genes were considered core genes in cellulose biosynthesis, which were highly expressed in buds but lowly expressed in mature leaves. In the nitrogen fertilization experiment, exogenous nitrogen decreased the cellulose content in the buds. The expressing pattern of 14 genes were consistent with phenotypic variation in the nitrogen fertilization experiment, and thus they were proposed as cellulose toolbox genes.

CONCLUSIONS

The present study provides a strong basis for the subsequent functional research of cellulose biosynthesis-involved genes in P. eburnea, and provides a reference for breeding and/or engineering this calcium-rich vegetable with decreased leaf cellulose content to improve the taste.

Exogenous methyl jasmonate and cytokinin antagonistically regulate lignin biosynthesis by mediating CsHCT expression in Camellia sinensis

Tea plant, an important beverage crop, is cultivated worldwide. Lignification can improve the hardness of tea plant, which is of great significance for tea quality. Jasmonates (JAs) and cytokinin are plant hormones that control processes of plant development and secondary metabolite accumulation. Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HCT) is primarily involved in lignin biosynthesis. The effects of exogenous application of JAs and cytokinin on lignin biosynthesis and related HCT gene expression profiles in tea plants are still unclear. In order to investigate the effects of exogenous JAs and cytokinin on lignin accumulation, anatomical structures, and CsHCT gene profiles in tea plants, we treated tea plants with methyl jasmonate (MeJA) and cytokinin (6-BA). MeJA and 6-BA treatments triggered the lignification at 6 and 12 d in tea leaves. The combined treatment resulted in an increase in lignin content at 6 d, which was 1.32 times of that at 0 d for 'Mengshan 9.' The CsHCTs in clade 2 (CsHCT5, CsHCT6, CsHCT7, and CsHCT8) were mainly expressed in leaves. We found that exogenous MeJA and cytokinin might be able to antagonistically regulate tea plant lignin accumulation through the mediation of CsHCT expression. This study revealed that HCTs play potential important roles involved in lignin biosynthesis of tea plant development and hormonal stimuli.

Integrated metabolome, transcriptome analysis, and multi-flux full-length sequencing offer novel insights into the function of lignin biosynthesis as a Sesuvium portulacastrum response to salt stress

Sesuvium portulacastrum is a typical halophyte. However, few studies have investigated its salt-tolerant molecular mechanism. In this study, metabolome, transcriptome, and multi-flux full-length sequencing analysis were conducted to investigate the significantly different metabolites (SDMs) and differentially expressed genes (DEGs) of S. portulacastrum samples under salinity. The complete-length transcriptome of S. portulacastrum was developed, which contained 39,659 non-redundant unigenes. RNA-seq results showed that 52 DEGs involved in lignin biosynthesis may be responsible for S. portulacastrum salt tolerance. Furthermore, 130 SDMs were identified, and the salt response could be attributed to the p-coumaryl alcohol-rich in lignin biosynthesis. The co-expression network that was constructed after comparing the different salt treatment processes showed that the p-Coumaryl alcohol was linked to 30 DEGs. Herein, 8 structures genes, i.e., Sp4CL, SpCAD, SpCCR, SpCOMT, SpF5H, SpCYP73A, SpCCoAOMT, and SpC3'H were identified as significant factors in regulating lignin biosynthesis. Further investigation revealed that 64 putative transcription factors (TFs) may interact with the promoters of the above-mentioned genes. Together, the data revealed a potential regulatory network comprising important genes, putative TFs, and metabolites involved in the lignin biosynthesis of S. portulacastrum roots under salt stress, which could serve as a rich useful genetic resource for breeding excellent salt-tolerant plants.

OsGLP participates in the regulation of lignin synthesis and deposition in rice against copper and cadmium toxicity

Copper (Cu) and cadmium (Cd) are common heavy metal pollutants. When Cd and excessive Cu accumulate in plants, plant growth is reduced. Our previous study showed that Germin-like proteins (GLPs), which exist in tandem on chromosomes, are a class of soluble glycoproteins that respond to Cu stress. In this study, hydroponic cultures were carried out to investigate the effect of GLP on Cd and Cu tolerance and accumulation in rice. The results showed that knockout of a single OsGLP8-2 gene or ten OsGLP genes (OsGLP8-2 to OsGLP8-11) resulted in a similar sensitivity to Cd and Cu toxicity. When subjected to Cu and Cd stress, the glp8-2 and glp8-(2-11) mutants displayed a more sensitive phenotype based on the plant height, root length, and dry biomass of the rice seedlings. Correspondingly, Cu and Cd concentrations in the glp8-2 and glp8-(2-11) mutants were significantly higher than those in the wild-type (WT) and OsGLP8-2-overexpressing line. However, Cu and Cd accumulation in the cell wall was the opposite. Furthermore, we determined lignin accumulation. The overexpressing-OsGLP8-2 line had a higher lignin accumulation in the shoot and root cell walls than those of the WT, glp8-2, and glp8-(2-11). The expression of lignin synthesis genes in the OsGLP8-2-overexpressing line was significantly higher than that in the WT, glp8-2, and glp8-(2-11). The SOD activity of OsGLP8-2, Diaminobe-nzidine (DAB), propidium iodide (PI) staining, and Malondialdehyde (MDA) content determination suggested that OsGLP8-2 is involved in heavy metal-induced antioxidant defense in rice. Our findings clearly suggest that OsGLPs participate in responses to heavy metal stress by lignin deposition and antioxidant defense capacity in rice, and OsGLP8-2 may play a major role in the tandem repeat gene clusters of chromosome 8 under heavy metal stress conditions.

The regulation of plant lignin biosynthesis under boron deficiency conditions

Boron (B) is a required micronutrient that is crucial for the growth and development of vascular plants. A deficiency in B is generally regarded as a limiting factor affecting agricultural production in many parts of the world. Boron is involved in the metabolism of plant lignin and additionally, B deficiency can lead to the excessive accumulation of lignin in plant leaves/roots, resulting in corking symptoms and inhibited growth. However, the effect of B on lignin biosynthesis is not as well characterized as the specific function of B in the cell wall. In this article, recent studies on the regulation of lignin biosynthesis in plants under low-B stress conditions are reviewed. Moreover, the following possible mechanisms underlying the lignin synthesis promoted by B deficiency are discussed: (1) the accumulation of phenolic substances during B deficiency directly enhances lignin synthesis; (2) excess H₂ O₂ has a dual function to the enhancement of lignin under boron deficiency conditions, serving as a substrate and a signaling molecule; and (3) B deficiency regulates lignin synthesis through the expression of genes encoding transcription factors such as MYBs. Finally, future studies regarding physiology, molecules, and transcriptional regulation may reveal the mechanism(s) mediating the relationship between lignin synthesis and B deficiency. This review provides new insights and important references for future research and the enhancement of plant B nutrition.

Transcriptomic Insights Into Root Development and Overwintering Transcriptional Memory of Brassica rapa L. Grown in the Field

As the only overwintering oil crop in the north area of China, living through winter is the primary feature of winter rapeseed. Roots are the only survival organ during prolonged cold exposure during winter to guarantee flowering in spring. However, little is known about its root development and overwintering memory mechanism. In this study, root collar tissues (including the shoot apical meristem) of three winter rapeseed varieties with different cold resistance, i.e., Longyou-7 (strong cold tolerance), Tianyou-4 (middle cold tolerance), and Lenox (cold-sensitive), were sampled in the pre-winter period (S1), overwintering periods (S2-S5), and re-greening stage (S6), and were used to identify the root development and overwintering memory mechanisms and seek candidate overwintering memory genes by measuring root collar diameter and RNA sequencing. The results showed that the S1-S2 stages were the significant developmental stages of the roots as root collar diameter increased slowly in the S3-S5 stages, and the roots developed fast in the strong cold resistance variety than in the weak cold resistance variety. Subsequently, the RNA-seq analysis revealed that a total of 37,905, 45,102, and 39,276 differentially expressed genes (DEGs), compared to the S1 stage, were identified in Longyou-7, Tianyou-4, and Lenox, respectively. The function enrichment analysis showed that most of the DEGs are significantly involved in phenylpropanoid biosynthesis, plant hormone signal transduction, MAPK signaling pathway, starch and sucrose metabolism, photosynthesis, amino sugar and nucleotide sugar metabolism, and spliceosome, ribosome, proteasome, and protein processing in endoplasmic reticulum pathways. Furthermore, the phenylpropanoid biosynthesis and plant hormone signal transduction pathways were related to the difference in root development of the three varieties, DEGs involved in photosynthesis and carbohydrate metabolism processes may participate in overwintering memory of Longyou-7 and Tianyou-4, and the spliceosome pathway may contribute to the super winter resistance of Longyou-7. The transcription factor enrichment analysis showed that the WRKY family made up the majority in different stages and may play an important regulatory role in root development and overwintering memory. These results provide a comprehensive insight into winter rapeseed's complex overwintering memory mechanisms. The identified candidate overwintering memory genes may also serve as important genetic resources for breeding to further improve the cold resistance of winter rapeseed.

Enzyme Activities in the Lignin Metabolism of Chinese Olive (Canarium album) with Different Flesh Characteristics

Lignin is crucial to the formation of fruit texture quality. Here, we aimed to explore the relationship between lignin metabolism and fruit texture by investigating the lignin content, total phenols and their related enzyme activities among three Chinese olive (Canarium album (Lour.) Raeusch) genotypes. Our results showed that lignin deposition moved from the exocarp to the flesh in Chinese olive fruit. The lignin, total phenols and enzyme activities were all different between the three Chinese olive cultivars at each developmental stage. The lignin content was positively correlated with the PAL, 4CL and POD activities. These results demonstrated that lignin metabolism was regulated through the related enzyme activities. Therefore, our findings may provide insight to facilitate further improvement in fruit texture quality in Chinese olive.

Roles of Abscisic Acid and Gibberellins in Stem/Root Tuber Development

Root and tuber crops are of great importance. They not only contribute to feeding the population but also provide raw material for medicine and small-scale industries. The yield of the root and tuber crops is subject to the development of stem/root tubers, which involves the initiation, expansion, and maturation of storage organs. The formation of the storage organ is a highly intricate process, regulated by multiple phytohormones. Gibberellins (GAs) and abscisic acid (ABA), as antagonists, are essential regulators during stem/root tuber development. This review summarizes the current knowledge of the roles of GA and ABA during stem/root tuber development in various tuber crops.

Origin, evolution, breeding, and omics of Apiaceae: a family of vegetables and medicinal plants

Many of the world's most important vegetables and medicinal crops, including carrot, celery, coriander, fennel, and cumin, belong to the Apiaceae family. In this review, we summarize the complex origins of Apiaceae and the current state of research on the family, including traditional and molecular breeding practices, bioactive compounds, medicinal applications, nanotechnology, and omics research. Numerous molecular markers, regulatory factors, and functional genes have been discovered, studied, and applied to improve vegetable and medicinal crops in Apiaceae. In addition, current trends in Apiaceae application and research are also briefly described, including mining new functional genes and metabolites using omics research, identifying new genetic variants associated with important agronomic traits by population genetics analysis and GWAS, applying genetic transformation, the CRISPR-Cas9 gene editing system, and nanotechnology. This review provides a reference for basic and applied research on Apiaceae vegetable and medicinal plants.

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.

Symbiotic responses of Lotus japonicus to two isogenic lines of a mycorrhizal fungus differing in the presence/absence of an endobacterium

As other arbuscular mycorrhizal fungi, Gigaspora margarita contains unculturable endobacteria in its cytoplasm. A cured fungal line has been obtained and showed it was capable of establishing a successful mycorrhizal colonization. However, previous OMICs and physiological analyses have demonstrated that the cured fungus is impaired in some functions during the pre-symbiotic phase, leading to a lower respiration activity, lower ATP, and antioxidant production. Here, by combining deep dual-mRNA sequencing and proteomics applied to Lotus japonicus roots colonized by the fungal line with bacteria (B+) and by the cured line (B-), we tested the hypothesis that L. japonicus (i) activates its symbiotic pathways irrespective of the presence or absence of the endobacterium, but (ii) perceives the two fungal lines as different physiological entities. Morphological observations confirmed the absence of clear endobacteria-dependent changes in the mycorrhizal phenotype of L. japonicus, while transcript and proteomic datasets revealed activation of the most important symbiotic pathways. They included the iconic nutrient transport and some less-investigated pathways, such as phenylpropanoid biosynthesis. However, significant differences between the mycorrhizal B+/B- plants emerged in the respiratory pathways and lipid biosynthesis. In both cases, the roots colonized by the cured line revealed a reduced capacity to activate genes involved in antioxidant metabolism, as well as the early biosynthetic steps of the symbiotic lipids, which are directed towards the fungus. Similar to its pre-symbiotic phase, the intraradical fungus revealed transcripts related to mitochondrial activity, which were downregulated in the cured line, as well as perturbation in lipid biosynthesis.

Characterisation of the class III peroxidase gene family in carrot taproots and its role in anthocyanin and lignin accumulation

Plant class III peroxidases (CIII Prxs) are involved in numerous essential plant life processes, such as plant development and differentiation, lignification and seed germination, and defence against pathogens. However, there is limited information about the structure-function relationships of Prxs in carrots. This study identified 75 carrot peroxidases (DcPrxs) and classified them into seven subgroups based on phylogenetic analysis. Gene structure analysis revealed that these DcPrxs had between one and eight introns, while conserved motif analysis showed a typical motif composition and arrangement for CIII Prx. In addition, eighteen tandem duplication events, but only eight segmental duplications, were identified among these DcPrxs, indicating that tandem duplication was the main contributor to the expansion of this gene family. Histochemical analyses showed that lignin was mainly localised in the cell walls of xylem, and Prx activity was determined in the epidermal region of taproots. The xylem always showed higher lignin concentration and lower Prx activity compared to the phloem in the taproots of both carrot cultivars. Combining these observations with RNA sequencing, some Prx genes were identified as candidate genes related to lignification and pigmentation. Three peroxidases (DcPrx30, DcPrx32, DcPrx62) were upregulated in the phloem of both genotypes. Carrot taproots are an attractive resource for natural food colourants and this study elucidated genome-wide insights of Prx for the first time, developing hypotheses concerning their involvement with lignin and anthocyanin in purple carrots. The findings provide an essential foundation for further studies of Prx genes in carrot, especially on pigmentation and lignification mechanisms.

Contrasting adaptive responses to cope with drought stress and recovery in Cenchrus ciliaris L. and their implications for tissue lignification

Cenchrus ciliaris L. is a widely used species for cattle feed in arid and semi-arid regions due to good forage value and known tolerance to drought conditions. Here, we provide insights to adaptive responses of two contrasting genotypes of C. ciliaris (drought-tolerant "RN51" and drought-sensitive "RN1") to face drought stress and recovery conditions and the implications for tissue lignification. Drought stress caused a reversible decrease in the leaf water relationship and damage to photosystem II, leading to an increased generation of reactive oxygen species and lipid peroxidation. Plants of RN51 exhibited a pronounced increase of antioxidant enzymatic activities. Unlike the drought-sensitive genotype, RN51 exhibited further development of lignified tissues and bulliform cells and had the greatest thickness of the adaxial epidermis. Drought stress led to the rapid activation of the expression of lignin biosynthesis pathway-related enzymes. The transcript level of the caffeoyl-CoA O-methyltransferase gene decreased in RN1, whereas cinnamoyl-CoA reductase transcripts were increased in RN51. After rewatering, the tolerant genotype recovered more rapidly than RN1. Even though the two genotypes survived when they were exposed to drought stress, RN1 showed the highest reduction in growth parameters, and this reduction was sustained during rewatering. The results indicated that the capacity to regulate lipid peroxidation and mitigate oxidative damage could be one of the mechanisms included in tolerance to drought stress. In addition, the development of foliar characteristics, like thickness of the adaxial epidermis, well-developed bulliform cells, and intensive lignified tissues, are considered anatomical adaptive strategies for drought tolerance in C. ciliaris.

Changes in phenotype and gene expression under lead stress revealed key genetic responses to lead tolerance in Medicago sativa L

Lead (Pb) is a serious heavy metal soil pollutant. It can be absorbed and accumulated by plant roots and impact plant growth. Medicago sativa L. (alfalfa) is a low-input forage and potential bioenergy crop, and improving its yield and quality has always been a focus of the alfalfa breeding industry. Little is known about the mechanism by which alfalfa responds to Pb stress at the molecular level. In this study, three alfalfa genotypes (a lead-resistant type (LR), a lead-sensitive type (LS) and an intermediate type (IN)) with contrasting abilities to resist lead were exposed to different durations of Pb treatment. Next-generation sequencing (NGS)-based RNA-seq technology was employed to characterize the root transcriptomes of three genotypes of alfalfa and identify differentially expressed genes (DEGs) during Pb stress. Genotypes LR and LS displayed different mechanisms of tolerance. In LR, the accumulation of more resistant substances was induced by the upregulation of sucrose synthase, glucan endo-1,3-beta-glucosidase, beta-amylase 3, probable trehalose-phosphate phosphatase J, 6-phosphofructo-2-kinase delta-1-pyrroline-5-carboxylate synthase (P5CS) and δ-ornithine aminotransferase (δ-OAT). In addition, flavin monooxygenase (YUCCA), 4-coumarate:CoA ligase-like protein (4CL), cinnamoyl-CoA reductase-like protein (CCR), ferulate 5-hydroxylase (F5H) and caffeic acid O-methyltransferase (COMT) were upregulated, leading to root development in a short time under Pb stress. Further study of the expression levels of metal transport-related genes, such as NRAMP (metal transporter), MATE (multidrug and toxin extrusion), HIPPs (heavy metal-associated isoprenylated plant proteins), MTP (metal tolerance protein), and ABC transporter, suggested that these genes were differentially expressed after lead treatment in the three alfalfa genotypes. Our research provides useful information for further studies on the molecular mechanism of Pb resistance in Medicago sativa L.

Exogenous melatonin positively regulates lignin biosynthesis in Camellia sinensis

Melatonin (MT) is a bioactive molecule that can regulate various developmental processes. Changes in lignin content play important roles in plant growth and development. Herein, quantitative analysis and histochemical staining showed that lignin content significantly increased over time, and melatonin treatment triggered the lignification at 8 and 16 d in tea leaves. The POD activity participated in lignin formation had also been significantly improved. The effect of melatonin on the increase of lignin content was attenuation over time. Sequencing results based on transcriptome at 8 and 16 d showed that 5273 and 3019 differentially expressed genes (DEGs) were identified in CK1 vs. MT1 and CK2 vs. MT2, respectively. A total of 67 DEGs were annotated to lignin biosynthesis, and 38 and 9 genes were significantly up-regulated under melatonin treatment, respectively. Some transcription factor genes such as MYB were also identified among the two pairwise comparisons, which might relate to lignin metabolism. Melatonin increased the degree of lignification in tea leaves by modifying the enzyme genes expression involved in lignin synthesis pathway. These results provide a reference for further study on the molecular mechanism of the dynamic changes of lignin content induced by melatonin treatment in tea plants.

Lignin provides mechanical support to herbaceous peony (Paeonia lactiflora Pall.) stems

Stem bending caused by mechanical failure is a major constraint for high-quality herbaceous peony (Paeonia lactiflora Pall.) cut flowers, but little is known about the underlying factors. In this study, two P. lactiflora cultivars, Xixia Yingxue (bending) and Hong Feng (upright), were used to investigate differences in stem bending. The results showed that the stem mechanical strength of Hong Feng was significantly higher than that of Xixia Yingxue, and the thickening of the secondary cell wall and the number of thickened secondary cell wall layers in Hong Feng were significantly higher than those in Xixia Yingxue. Moreover, compared with Xixia Yingxue, Hong Feng showed greater lignification of the cell wall and lignin deposition in the cell walls of the sclerenchyma, vascular bundle sheath and duct. All three types of lignin monomers were detected. The S-lignin, G-lignin, and total lignin contents and the activities of several lignin biosynthesis-related enzymes were higher in Hong Feng than in the other cultivar, and the S-lignin content was closely correlated with stem mechanical strength. In addition, 113,974 full-length isoforms with an average read length of 2106 bp were obtained from the full-length transcriptome of P. lactiflora stems, and differential expression analysis was performed based on the comparative transcriptomes of these two cultivars. Ten lignin biosynthesis-related genes, including 26 members that were closely associated with lignin content, were identified, and multiple upregulated and downregulated transcription factors were found to positively or negatively regulate lignin biosynthesis. Consequently, lignin was shown to provide mechanical support to P. lactiflora stems, providing useful information for understanding the formation of P. lactiflora stem strength.

Effects of shading on lignin biosynthesis in the leaf of tea plant (Camellia sinensis (L.) O. Kuntze)

Shading can effectively reduce photoinhibition and improve the quality of tea. Lignin is one of the most important secondary metabolites that play vital functions in plant growth and development. However, little is known about the relationship between shading and xylogenesis in tea plant. To investigate the effects of shading on lignin accumulation in tea plants, 'Longjing 43' was treated with no shading (S0), 40% (S1) and 80% (S2) shading treatments, respectively. The leaf area and lignin content of tea plant leaves decreased under shading treatments (especially S2). The anatomical characteristics showed that lignin is mainly distributed in the xylem of tea leaves. Promoter analysis indicated that the genes involved in lignin pathway contain several light recognition elements. The transcript abundances of 12 lignin-associated genes were altered under shading treatments. Correlation analysis indicated that most genes showed strong positive correlation with lignin content, and CsPAL, Cs4CL, CsF5H, and CsLAC exhibited significant positively correlation under 40% and 80% shading treatments. The results showed that shading may have an important effect on lignin accumulation in tea leaves. This work will potentially helpful to understand the regulation mechanism of lignin pathway under shading treatment, and provide reference for reducing lignin content and improving tea quality through shading treatment in field operation.

DcMYB113, a root-specific R2R3-MYB, conditions anthocyanin biosynthesis and modification in carrot

Purple carrots, the original domesticated carrots, accumulate highly glycosylated and acylated anthocyanins in root and/or petiole. Previously, a quantitative trait locus (QTL) for root-specific anthocyanin pigmentation was genetically mapped to chromosome 3 of carrot. In this study, an R2R3-MYB gene, namely DcMYB113, was identified within this QTL region. DcMYB113 expressed in the root of 'Purple haze', a carrot cultivar with purple root and nonpurple petiole, but not in the roots of two carrot cultivars with a purple root and petiole (Deep purple and Cosmic purple) and orange carrot 'Kurodagosun', which appeared to be caused by variation in the promoter region. The function of DcMYB113 from 'Purple haze' was verified by transformation in 'Cosmic purple' and 'Kurodagosun', resulting in anthocyanin biosynthesis. Transgenic 'Kurodagosun' carrying DcMYB113 driven by the CaMV 35S promoter had a purple root and petiole, while transgenic 'Kurodagosun' expressing DcMYB113 driven by its own promoter had a purple root and nonpurple petiole, suggesting that root-specific expression of DcMYB113 was determined by its promoter. DcMYB113 could activate the expression of DcbHLH3 and structural genes related to anthocyanin biosynthesis. DcUCGXT1 and DcSAT1, which were confirmed to be responsible for anthocyanins glycosylation and acylation, respectively, were also activated by DcMYB113. The WGCNA identified several genes co-expressed with anthocyanin biosynthesis and the results indicated that DcMYB113 may regulate anthocyanin transport. Our findings provide insight into the molecular mechanism underlying root-specific anthocyanin biosynthesis and further modification in carrot and even other root crops.

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

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

Elevated gibberellin altered morphology, anatomical structure, and transcriptional regulatory networks of hormones in celery leaves

Gibberellins (GAs), as one of the important hormones in regulating the growth and development of higher plants, can significantly promote cell elongation and expansion. Celery is a widely grown leafy vegetable crop with rich nutritional value. However, the effect of gibberellins on celery leaves is unclear. In this paper, the celery variety "Jinnan Shiqin" plants were treated with gibberellic acid (GA₃) and paclobutrazol (PBZ, a gibberellin inhibitor). Our results showed that GA₃ treatment promoted the growth of celery leaves and caused lignification of celery leaf tissue. In addition, the transcript levels of genes associated with gibberellins, auxin, cytokinins, ethylene, jasmonic acid, abscisic acid, and brassinolide were altered in response to increased or decreased exogenous gibberellins or inhibitor. GA₃ may regulate celery growth by interacting with other hormones through crosstalk mechanisms. This study provided a reference for further study of the regulation mechanism of gibberellins metabolism, and exerted effects on understanding the role of gibberellins in the growth and development of celery.

Elevated gibberellin enhances lignin accumulation in celery (Apium graveolens L.) leaves

Gibberellin (GA) is a phytohormone of a biguanide compound that plays an important role throughout the life cycle of a plant. Lignin, a phenylalanine-derived aromatic polymer, can enhance the water transport function and structural resistance of cell walls. This function is also the core on biology of higher terrestrial plants. An appropriate lignin level is important to the quality of leafy vegetables, such as celery. The relationship between gibberellin levels and the occurrence of lignification has not been reported in celery. In this study, the leaf blades and petioles of celery cultivars 'Liuhe Huangxinqin' and 'Jinnan Shiqin' were used as materials, and different concentrations of exogenous gibberellin were applied to analyze the growth and lignin distribution of leaf blades and petioles. It was found that gibberellin treatment could influence the lignin content in celery leaves. Autofluorescence analysis under ultraviolet (UV) excitation showed that gibberellin treatment caused lignification of celery leaf tissue. The expression profiles of 12 genes related to lignin synthesis changed with the increase of gibberellin concentration. Our results showed that gibberellin played a significant role in the accumulation of lignin in the development of celery leaves. This provides a basis for further study on the regulation of lignin metabolism in plants and exerts a vital part in the application of plant growth regulators to production.

Identification of genes revealed differential expression profiles and lignin accumulation during leaf and stem development in tea plant (Camellia sinensis (L.) O. Kuntze)

Lignin is a complex aromatic heteropolymer that plays essential roles in mechanical support, water transport, and response to biotic and abiotic stresses. The tea plant is a leaf-type beverage crop, which serves as a resource for non-alcoholic beverage tea. The content and distribution of lignin in tea plant leaves seriously affect the quality of tea. However, the biosynthetic pathways of lignin remain to be characterized in the tea plant. In the present study, lignin accumulation was investigated in tea plant leaves and stems at three developmental stages. The lignin content continuously increased during leaf and stem development in both tea plant cultivars 'Fudingdabai' and 'Suchazao.' The lignin distribution and anatomical characteristics of the tea plant leaves coincided with lignin accumulation and showed that lignin is mainly distributed in the epidermis, xylem, and vascular bundle sheath. 'Suchazao' exhibits a low lignin content and lacks a vascular bundle sheath. Twelve genes encoding the enzymes involved in the lignin biosynthesis of tea plant were identified and included CsPAL, CsC4H, Cs4CL, CsHCT, CsC3H, CsCCoAOMT, CsCCR, CsCAD, CsF5H, CsCOMT, CsPER, and CsLAC. The expression profiling of lignin biosynthesis-related genes and analysis of lignin accumulation may help elaborate the regulatory mechanisms of lignin biosynthesis in tea plant.

Biosynthesis of methyleugenol and methylisoeugenol in Daucus carota leaves: Characterization of eugenol/isoeugenol synthase and O-Methyltransferase

Carrot (Daucus carota subsp. sativus) is a widely cultivated root vegetable of high economic importance. The aroma of carrot roots and aboveground organs is mainly defined by terpenes. We found that leaves of orange carrot cultivar also produce considerable amounts of the phenylpropenes methyleugenol and methylisoeugenol. Notably, methyleugenol is most abundant in young leaves, while methylisoeugenol is the dominant phenylpropene in mature leaf tissue. The goal of the present study was to shed light on the biochemistry and molecular biology of these compounds' biosynthesis and accumulation. Using the available genomic and transcriptomic data, we isolated a cDNA encoding eugenol/isoeugenol synthase (DcE(I)GS1), an NADPH-dependent enzyme that converts coniferyl acetate to eugenol. This enzyme exhibits dual product specificity and yields propenylphenol isoeugenol alongside allylphenol eugenol. Furthermore, we identified a cDNA encoding S-adenosyl-L-methionine:eugenol/isoeugenol O-methyltransferase 1 (DcE(I)OMT1) that produces methyleugenol and methylisoeugenol via methylation of the para-OH-group of their respective precursors. Both DcE(I)GS1 and DcE(I)OMT1 were expressed in seeds, roots, young and mature leaves, and the DcE(I)OMT1 transcript levels were the highest in leaves. The DcE(I)GS1 protein is 67% identical to anise t-anol/isoeugenol synthase and displays an apparent K_m of 247 μM for coniferyl acetate. The catalytic efficiency of DcEOMT1 with eugenol is more than five-fold higher than that with isoeugenol, with K_m values of 40 μM for eugenol, and of 115 μM for isoeugenol. This work expands the current knowledge of the enzymes involved in phenylpropene biosynthesis and would enable studies into structural elements defining the regioselectivity of phenylpropene synthases.

Hypoxia enhances lignification and affects the anatomical structure in hydroponic cultivation of carrot taproot

Hypoxia enhances lignification of carrot root. Hypoxia stress was thought to be one of the major abiotic stresses that inhibiting the growth and development of higher plants. The genes encoding the plant alcohol dehydrogenase (ADH-P) were induced when suffering hypoxia. To investigate the impact of hypoxia on the carrot root growth, carrot plants were cultivated in the hydroponics with or without aeration. Morphological characteristics, anatomical structure, lignin content, and the expression profiles of DcADH-P genes and lignin biosynthesis-related genes were measured. Six DcADH-P genes were identified from the carrot genome. The expression profiles of only three (DcADH-P1, DcADH-P2, and DcADH-P3) genes could be detected and the other three (DcADH-P4, DcADH-P5, and DcADH-P6) could not be detected when carrot cultivated in the solution without aeration. In addition, carrot roots had more lignin content, aerenchyma and less fresh weight when cultivated in the solution without aeration. These results suggested that hypoxia could enhance the lignification and affect anatomical structure of the carrot root. However, the expression levels of the genes related to lignin biosynthesis were down-regulated under the hypoxia. The enhancement of lignification may be the consequence of the structure changes in the carrot root. Our work was potentially helpful for studying the effect of hypoxia on carrot growth and may provide useful information for carrot hydroponics.

Elevated CO2 induces alteration in lignin accumulation in celery (Apium graveolens L.)

Carbon dioxide (CO₂) is an important regulator of plant growth and development, and its proportion in the atmosphere continues to rise now. Lignin is one of the major secondary products in plants with vital biological functions. However, the relationship between CO₂ level and xylogenesis in celery is still unknown. In order to investigate the effects of increasing CO₂ concentration on lignin accumulation in celery, 'Jinnanshiqin' were exposed to two CO₂ applications, 400 (e₀) and 1000 μmol mol^-1 (e₁), respectively. Plant morphology and lignin distribution in celery plants treated with elevated CO₂ did not change significantly. There was an upward trend on lignin content in celery leaves, and the transcript abundance of 12 genes involved in lignin metabolism has altered in response to elevated CO₂. The effects of high level of CO₂ on different tissues were different. Our works confirmed that CO₂ may play an important role in lignin accumulation in celery leaves. The current study will offer new evidence to understand the regulation mechanism of lignin biosynthesis under elevated CO₂ and provide a reference to improve celery quality by adjusting the growth environment.

Comparative transcriptomics reveals shared gene expression changes during independent evolutionary origins of stem and hypocotyl/root tubers in Brassica (Brassicaceae)

Plant succulence provides a classic example of evolutionary convergence in over 40 plant families. If evolutionary parallelism is in fact responsible for separate evolutionary origins of expanded storage tissues in stems, hypocotyls, and roots, we expect similar gene expression profiles in stem and hypocotyl / root tubers. We analyzed RNA-Seq transcript abundance patterns in stem and hypocotyl / root tubers of the Brassica crops kohlrabi (B. oleracea) and turnip (B. rapa) and compared their transcript expression profiles to those in the conspecific thin-stemmed and thin-rooted crops flowering kale and pak choi, respectively. Across these four cultivars, 38,192 expressed gene loci were identified. Of the 3,709 differentially-expressed genes (DEGs) in the turnip: pak choi comparison and the 6,521 DEGs in the kohlrabi: kale comparison, turnips and kohlrabies share a statistically disproportionate overlap of 841 DEG homologs in their tubers (p value < 1e-10). This overlapping set is statistically enriched in biochemical functions that are also associated with tuber induction in potatoes and sweet potatoes: sucrose metabolism, lipoxygenases, auxin metabolism, and meristem development. These shared expression profiles in tuberous stems and root / hypocotyls in Brassica suggest parallel employment of shared molecular genetic pathways during the evolution of tubers in stems, hypocotyls and roots of Brassica crops and more widely in other tuberous plants as well.

The root transcriptome of Achyranthes bidentata and the identification of the genes involved in the replanting benefit

The transcriptome profiling in replanting roots revealed that expression pattern changes of key genes promoted important metabolism pathways, antioxidant and pathogen defense systems, adjusted phytohormone signaling and inhibited lignin biosynthesis. The yield of the medicinal plant Achyranthes bidentata could be significantly increased when replanted into a field cultivated previously for the same crop, but the biological basis of this so-called "replanting benefit" is unknown. Here, the RNA-seq technique was used to identify candidate genes responsible for the benefit. The analysis of RNA-seq libraries prepared from mRNA extracted from the roots of first year planting (normal growth, NG) and second year replanting (consecutive monoculture, CM) yielded about 40.22 GB sequencing data. After de novo assembly, 87,256 unigenes were generated with an average length of 1060 bp. Among these unigenes, 55,604 were annotated with public databases, and 52,346 encoding sequences and 2881 transcription factors were identified. A contrast between the NG and CM libraries resulted in a set of 3899 differentially transcribed genes (DTGs). The DTGs related to the replanting benefit and their expression profiles were further analyzed by bioinformatics and qRT-PCR approaches. The major differences between the NG and CM transcriptomes included genes encoding products involved in glycolysis/gluconeogenesis, glutathione metabolism and antioxidant defense, in aspects of the plant/pathogen interaction, phytohormone signaling and phenylpropanoid biosynthesis. The indication was that replanting material enjoyed a stronger level of defense systems, a balance regulation of hormone signals and a suppression of lignin formation, thereby promoting root growth and development. The study provides considerable significant insights for a better understanding of the molecular mechanism of the replanting benefit and suggests their possible application in developing methods to reinforce the effects in medicinal plants.

Maturation-related changes of carrot lignins

BACKGROUND

Lignified cell walls are important factors for textural and physiological properties of plant-based foods. However, carrot lignins and their modifications during maturation are poorly described. The objective of this study was to describe carrot lignins in detail and to study lignin structural alterations at later stages of maturity.

RESULTS

Klason and acetyl bromide soluble lignin contents of insoluble fibers of carrots harvested at different times (26, 29 and 35 weeks after seeding) ranged between 46.38 and 62.68 g kg^-1 and between 19.79 and 28.08 g kg^-1 , respectively. As determined by both 2D-nuclear magnetic resonance and the derivatization followed by reductive cleavage method, coniferyl alcohol heavily dominated the traditional monolignol composition in carrot lignins, independently of harvest times. By using 2D-nuclear magnetic resonance experiments on isolated lignins, p-hydroxybenzoate was identified as a less common lignin constituent, attached to lignin γ-hydroxyl groups and being increasingly incorporated with maturation. β-Aryl ethers, phenylcoumaran, resinol and dibenzodioxocin structures were identified as lignin interunit linkages, largely independent of harvest times and with β-aryl ethers being expectedly dominant.

CONCLUSION

Carrots contain guaiacyl-rich lignins that incorporate increasing amounts of p-hydroxybenzoate with maturation. All other lignin characteristics appear to be widely independent of harvest times. © 2017 Society of Chemical Industry.

Identification of critical genes associated with lignin biosynthesis in radish (Raphanus sativus L.) by de novo transcriptome sequencing

Radish is an important root vegetable crop with high nutritional, economic, and medicinal value. Lignin is an important secondary metabolite possessing a great effect on plant growth and product quality. To date, lignin biosynthesis-related genes have been identified in some important plant species. However, little information on characterization of critical genes involved in plant lignin biosynthesis is available in radish. In this study, a total of 71,148 transcripts sequences were obtained from radish root, of which 66 assembled unigenes and ten candidate genes were identified to be involved in lignin monolignol biosynthesis. Full-length cDNA sequences of seven randomly selected genes were isolated and sequenced from radish root, and the assembled unigenes covered more than 80% of their corresponding cDNA sequences. Moreover, the lignin content gradually accumulated in leaf during the developmental stages, and it increased from pre-cortex to cortex splitting stage, followed by a decrease at thickening stage and then increased at mature stage in root. RT-qPCR analysis revealed that all these genes except RsF5H exhibited relatively low expression level in root at thickening stage. The expression profiles of Rs4CL5, RsCCoAOMT1, and RsCOMT genes were consistent with the changes of root lignin content, implying that these candidate genes may play important roles in lignin formation in radish root. These findings would provide valuable information for identification of lignin biosynthesis-related genes and facilitate dissection of molecular mechanism underlying lignin biosynthesis in radish and other root vegetable crops.