Roles of lignin biosynthesis and regulatory genes in plant development

Gibberellin regulates the synthesis of stone cells in 'Nanguo' pear via the PuMYB91-PuERF023 module

Stone cells are one of the limiting factors affecting pear fruit quality and commodity value. The formation of stone cell is highly correlated with lignin deposition. However, the molecular mechanism of stone cell formation and regulation is still unclear. Here, we observed that exogenous application of GA significantly inhibited the formation of stone cells and also decreased the content of lignin in 'Nanguo' (Pyrus ussuriensis) pear fruits. The key gene PuPRX73 involved in the lignin synthesis pathway was further identified using RT-PCR, and GA-treatment significantly inhibited the expression of PuPRX73. Overexpression or silencing of PuPRX73 in pear fruits significantly increases or decreases the content of stone cells and lignin. We identified the transcription factors PuMYB91 and PuERF023 using mRNA-seq and their expression was significantly decreased after GA-treatment. Transient overexpression of PuMYB91 and PuERF023 promotes lignin and stone cells content in pear fruits, while silencing of PuMYB91 and PuERF023 led to the opposite results and inhibited the expression of PuPRX73. Yeast one-hybrid (Y1H) and GUS activity analysis revealed that PuMYB91 and PuERF023 directly bind and activate the PuPRX73 promoter, and co-transfection of PuMYB91 and PuERF023 in Nicotiana benthamiana leaves further promoted the promoter activity of PuPRX73. Furthermore, we found that PuMYB91 interacted with PuERF023 in vitro by using Yeast two-hybrid assays (Y2H). In conclusion, our results revealed that exogenous GA-treatment inhibits stone cell production by suppressing the expression of PuMYB91 and PuERF023 in pear fruits.

From fibers to flowering to metabolites: unlocking hemp (Cannabis sativa) potential with the guidance of novel discoveries and tools

Cannabis sativa L. is an ancient crop, but its agricultural adoption has been interrupted to prevent the use of marijuana as a psychoactive drug. Nevertheless, hemp-the C. sativa type with low concentrations of intoxicating Δ9-tetrahydrocannabinoid-is experiencing a resurgence in interest due to loosened cultivation restrictions and its potential as a multipurpose bio-based crop. Hemp has valuable applications, including production of medicines from its non-intoxicating cannabinoids, food, medical, and industrial uses of its seed oil rich in polyunsaturated fatty acids, and production of fibers for textiles and industry from its stems. Recently, several hemp genomic and genetic resources have been developed, allowing significant expansion of our knowledge of major hemp traits, such as synthesis of cannabinoids, oil, and fibers, and regulation of flowering and sex determination. Still, hemp is an underimproved crop, and its development will depend on the ability to expand and collectively use the novel resources arising from fast advancements in bioinformatics and plant phenotyping. This review discusses current genetic and genomic knowledge of the most important hemp traits, and provides a perspective on how to further expand such knowledge and tackle hemp improvement with the most up-to-date tools for plant and hemp research.

A glutathione S-transferase regulates lignin biosynthesis and enhances salt tolerance in tomato

Salt stress adversely affects the growth and yield of crops. Glutathione S-transferases (GSTs) are involved in plant growth and responses to biotic and abiotic stresses. In this study, 400 mm NaCl stress significantly induced the expression of Glutathione S-transferase U43 (SlGSTU43) in the roots of the wild-type tomato (Solanum lycopersicum L.) plants. Overexpressing SlGSTU43 enhanced the ability of scavenging reactive oxygen species in tomato leaves and roots under NaCl stress, while SlGSTU43 knock-out mutants showed the opposite performance. RNA sequencing analysis revealed that overexpressing SlGSTU43 affected the expression of genes related to lignin biosynthesis. We demonstrated that SlGSTU43 can regulate the lignin content in tomato through its interaction with SlCOMT2, a key enzyme involved in lignin biosynthesis, and promote the growth of tomato plants under NaCl stress. In addition, SlMYB71 and SlWRKY8 interact each other, and can directly bind to the promoter of SlGSTU43 to transcriptionally activate its expression separately or in combination. When SlMYB71 and SlWRKY8 were silenced in tomato plants individually or collectively, the plants were sensitive to NaCl stress, and their GST activities and lignin contents decreased. Our research indicates that SlGSTU43 can enhance salt stress tolerance in tomato by regulating lignin biosynthesis, which is regulated by interacting with SlCOMT2, as well as SlMYB71 and SlWRKY8. This finding broadens our understanding of GST functions.

Regulation of lignin biosynthesis by GhCAD37 affects fiber quality and anther vitality in upland cotton

Cotton stands as a pillar in the textile industry due to its superior natural fibers. Lignin, a complex polymer synthesized from phenylalanine and deposited in mature cotton fibers, is believed to be essential for fiber quality, although the precise effects remain largely unclear. In this study, we characterized two ubiquitously expressed cinnamyl alcohol dehydrogenases (CAD), GhCAD37A and GhCAD37D (GhCAD37A/D), in Gossypium hirsutum. GhCAD37A/D possess CAD enzymatic activities, to catalyze the generation of monolignol products during lignin biosynthesis. Analysis of transgenic cotton knockout and overexpressing plants revealed that GhCAD37A/D are important regulators of fiber quality, positively impacting breaking strength but negatively affecting fiber length and elongation percentage by modulating lignin biosynthesis in fiber cells. Moreover, GhCAD37A/D are shown to modulate anther vitality and affect stem lodging trait in cotton by influencing lignin biosynthesis in the vascular bundles of anther and stem, respectively. Additionally, our study revealed that Ghcad37A/D knockout plants displayed red stem xylem, likely due to the overaccumulation of aldehyde intermediates in the phenylpropanoid metabolism pathway, as indicated by metabolomics analysis. Thus, our work illustrates that GhCAD37A/D are two important enzymes of lignin biosynthesis in different cotton organs, influencing fiber quality, anther vitality, and stem lodging.

Unveiling Key Genes and Unique Transcription Factors Involved in Secondary Cell Wall Formation in Pinus taeda

Pinus taeda is a key timber species, and extensive research has been conducted on its wood formation. However, a comprehensive investigation into the biosynthetic pathways of lignin, cellulose, and hemicellulose in P. taeda is lacking, resulting in an incomplete understanding of secondary cell wall (SCW) formation in this species. In this study, we systematically analyzed transcriptomic data from previously published sources and constructed detailed pathways for lignin, cellulose, and hemicellulose biosynthesis. We identified 188 lignin-related genes and 78 genes associated with cellulose and hemicellulose biosynthesis. An RT-qPCR highlighted 15 key lignin biosynthesis genes and 13 crucial genes for cellulose and hemicellulose biosynthesis. A STEM analysis showed that most essential enzyme-coding genes clustered into Profile 14, suggesting their significant role in SCW formation. Additionally, we identified seven NAC and six MYB transcription factors (TFs) from atypical evolutionary clades, with distinct expression patterns from those of the previously characterized NAC and MYB genes, indicating potentially unique functions in SCW formation. This research provides the first comprehensive overview of lignin, cellulose, and hemicellulose biosynthetic genes in P. taeda and underscores the importance of non-canonical NAC and MYB TFs, laying a genetic foundation for future studies on SCW regulatory mechanisms.

Sweetpotato sucrose transporter IbSUT1 alters storage roots formation by regulating sucrose transport and lignin biosynthesis

The formation and development of storage roots is the most important physiological process in sweetpotato production. Sucrose transporters (SUTs) regulate sucrose transport from source to sink organs and play important roles in growth and development of plants. However, whether SUTs involved in sweetpotato storage roots formation is so far unknown. In this study, we show that IbSUT1, a SUT, is localized to the plasma membrane. Overexpression of IbSUT1 in sweetpotato promotes the sucrose efflux rate from leaves, leading to increased sucrose levels in roots, thus induces lignin deposition in the stele, which inhibits the storage roots formation and compromises the yield. Heterologous expression of IbSUT1 in Arabidopsis significantly increases the sucrose accumulation and promotes lignification in the inflorescence stems. RNA-seq and biochemical analysis further demonstrated that IbMYB1 negatively regulates the expression of IbSUT1. Overexpression of IbMYB1 in Arabidopsis reduces the sucrose accumulation and lignification degree in the inflorescence stems. Moreover, co-overexpression of IbMYB1 and IbSUT1 restores the phenotype of lignin over-deposition in Arabidopsis. Collectively, our results reveal that IbSUT1 regulates source-sink sucrose transport and participates in the formation of sweetpotato storage roots and highlight the potential application of IbSUT1 in improving sweetpotato yield in the future.

Influence of Natural Dentin Biomodification Agent on Push-Out Bond Strength and Nanoleakage of Self-Adhesive Resin Cement Luting of Glass-Fiber Posts

OBJECTIVE

To evaluate the plant-derived compound lignin (LIG) as a pretreatment of intraradicular dentin in combination with EDTA on push-out bond strength (PBS) and nanoleakage of the glass fiber posts (GFPs) cemented using adhesive resin cement.

MATERIAL AND METHODS

Twenty-eight human incisor roots were prepared for GFP cementation and divided based on dentin pretreatment: (1) CONTROL: no pretreatment, (2) EDTA: 17% EDTA for 3 min, (3) EDTA-LIG: 17% EDTA and 2% lignin for 3 min, (4) EDTA-PAC: 17% EDTA and 2% lignin for 3 min. The GFPs were cemented using the self-adhesive resin cement Multilink Speed. The roots (n = 7) were sectioned into 1 mm-thick discs and subjected to PBS testing after 1 week or 6 months. Nanoleakage was analyzed by SEM. Statistical analysis was performed using two-factor ANOVA and Tukey's test (p < 0.05).

RESULTS

Higher PBS was identified for the CONTROL group (p < 0.001). After 6 months, the EDTA-LIG maintained the bond strength with a predominance of mixed failures, while the EDTA-PAC, EDTA, and CONTROL groups showed reduction of bond strength, with a predominance of adhesive failures along with severe silver infiltration in the interface.

CONCLUSION

LIG associated with EDTA as a pretreatment for intraradicular dentin shows significant potential for attaining stable bond strength and interfacial integrity of self-adhesive resin cement to intraradicular dentin.

Herbicidal Sorbicillinoid Analogs Cause Lignin Accumulation in Aspergillus aculeatus TE-65L

Five new sorbicillinoid derivatives, including (±)-aspersorbicillin A [(±)-1], a pair of enantiomers at C-9, and aspersorbicillins B-D (2-4), together with two known analogs (5 and 6) were isolated from the endophytic fungus Aspergillus aculeatus TE-65L. Their structures including absolute configurations were determined by detailed spectroscopic analyses and electronic circular dichroism calculations. The herbicidal activity of sorbicillinoids on the germ and radicle elongation of various weed types was reported for the first time. Compound 1 displayed significant herbicidal activity against Eleusine indica germ elongation (IC50 = 28.8 μg/mL), while compound 6 inhibited radicle elongation (IC50 = 25.6 μg/mL). Both were stronger than those of glyphosate (66.2 and 30.9 μg/mL, respectively). Further transcriptomic and LC-MS/MS metabolomic analysis indicated that 6 induced the transcriptional expressions of genes related to the lignin biosynthetic pathway, resulting in lignin accumulation. Transmission electron microscopy confirmed the cell wall thickening of seeds treated with 6, suggesting weed growth inhibition. This study reveals new lead compounds for fabricating natural herbicides and expands the agricultural use of sorbicillinoid analogs.

Polystyrene nanoplastics induce cell type-dependent secondary wall reinforcement in rice (Oryza sativa) roots and reduce root hydraulic conductivity

Nanoplastics (NPs) have been demonstrated the ability to penetrate plant roots and cause stress. However, the extent of NPs penetration into various root tissues and the corresponding plant defense mechanisms remain unclear. This study examined the penetration and accumulation patterns of polystyrene nanoplastics (PS-NPs) in different cell types within rice roots, and explored how the roots quickly modify their cell wall structure in response. The findings showed that fully developed sclerenchyma cells in rice roots effectively prevented the invasion of PS-NPs. Meanwhile, PS-NPs triggered the accumulation of lignin and suberin in specific cells such as the exodermis, sclerenchyma, and xylem vessels. PS-NPs at a concentration of 50 mg L-1 increased cell wall thickness by 18.6 %, 21.1 %, and 22.4 % in epidermis, exodermis, and sclerenchyma cells, respectively, and decreased root hydraulic conductivity by 14.8 %. qPCR analysis revealed that PS-NPs influenced the cell wall synthesis pathway, promoting the deposition of lignin and suberin monomers on the secondary wall through the up-regulation of genes such as OsLAC and OsABCG. These results demonstrate that PS-NPs can induce cell type-specific strengthening of secondary walls and barrier formation in rice roots, suggesting the potential role of plant secondary wall development in mitigating NPs contamination risks in crops.

Identification of the Key Gene DfCCoAOMT1 through Comparative Analysis of Lignification in Dendrocalamus farinosus XK4 and ZPX Bamboo Shoots during Cold Storage

Dendrocalamus farinosus bamboo shoots, a species with rich nutritional value, are important in Southwest China. Lignin is an important factor affecting the postharvest flavor quality of bamboo shoots; however, the underlying mechanism of lignin deposition in D. farinosus bamboo shoots during cold storage is still not fully understood. In this study, the mutant D. farinosus XK4 with low lignin content at 3.11% and the cultivated variety ZPX at 4.47% were used as experimental materials. The lignin content of D. farinosus XK4 and ZPX, as well as the gene expression differences between them, were compared and analyzed during cold storage using transcriptomic and physiological methods. Our analysis revealed several key genes and found that D. farinosus CCoAOMT1 plays a key role in the regulatory network of bamboo shoots during cold storage. Tobacco heterologous transformation experiments demonstrated that overexpression of DfCCoAOMT1 significantly increases lignin content. This study provides a novel foundation for future research aimed at improving the postharvest quality and flavor of D. farinosus bamboo shoots through targeted genetic manipulation during cold storage.

A Combined Metabolome and Transcriptome Reveals the Lignin Metabolic Pathway during the Developmental Stages of Peel Coloration in the 'Xinyu' Pear

Sand pear is the main cultivated pear species in China, and brown peel is a unique feature of sand pear. The formation of brown peel is related to the activity of the cork layer, of which lignin is an important component. The formation of brown peel is intimately associated with the biosynthesis and accumulation of lignin; however, the regulatory mechanism of lignin biosynthesis in pear peel remains unclear. In this study, we used a newly bred sand pear cultivar 'Xinyu' as the material to investigate the biosynthesis and accumulation of lignin at nine developmental stages using metabolomic and transcriptomic methods. Our results showed that the 30 days after flowering (DAF) to 50DAF were the key periods of lignin accumulation according to data analysis from the assays of lignin measurement, scanning electron microscope (SEM) observation, metabolomics, and transcriptomics. Through weighted gene co-expression network analysis (WGCNA), positively correlated modules with lignin were identified. A total of nine difference lignin components were identified and 148 differentially expressed genes (DEGs), including 10 structural genes (PAL1, C4H, two 4CL genes, HCT, CSE, two COMT genes, and two CCR genes) and MYB, NAC, ERF, and TCP transcription factor genes were involved in lignin metabolism. An analysis of RT-qPCR confirmed that these DEGs were involved in the biosynthesis and regulation of lignin. These findings further help us understand the mechanisms of lignin biosynthesis and provide a theoretical basis for peel color control and quality improvement in pear breeding and cultivation.

Mechanistic analysis of the hardening process of the thorns on stems of Bougainvillea glabra "Elizabeth Angus"

Introduction: Bougainvillea glabra "Elizabeth Angus" is a thorny woody vine or shrub. However, the hard thorns are considered a deficiency in its ornamental value. Methods: To find the genes and pathways related to the hardening process of the thorns on the stems of B. glabra, the eukaryotic unreferenced transcriptome sequencing analysis was conducted to explore the 3 stages of the thorn-hardening process. Total RNA was extracted from thorns and stems, and transcriptome libraries were constructed and sequenced using unreferenced Illumina sequencing. Results: Gene function annotation was performed using various databases, resulting in 8937 co-annotated genes. The density distribution of Fragments Per Kilobase of transcript per Million mapped reads (FPKM) depicted the overall gene expression patterns. The study found that stage 2 as the period of highest gene expression activity during the thorns hardening process in B. glabra. Differential expression analysis revealed that during thorn-hardening, 1045 genes up-regulated and 391 genes down-regulated significantly in thorns at stage 2 compared to stage 1 (early stage of thorns formation). Meanwhile, 938 genes up-regulated and 784 genes down-regulated significantly in stems. At stage 3, as thorns became harder, 63 genes exhibited notable expression increase and 98 genes' expression decreased obviously within thorns, and 46 genes up-regulated and 29 genes down-regulated in stems, compared to stage 2. Phenylpropanoid biosynthesis was the key step in the hardening process of the thorns of B. glabra. The formation and hardening of thorns on the stem of B. glabra was a process in which lignin gradually accumulated in the thorns, and several genes were involved in this process. They include PAL (EC:4.3.1.24), CYP73A (EC:1.14.14.91), 4CL (EC:6.2.1.12), CCR (EC:1.2.1.44), CAD (EC:1.1.1.195) and POX (EC:1.11.1.7). Discussion: This transcriptome analysis offers insights into the molecular mechanisms underlying thorns development in this plant species.

Metabolic engineering of Oryza sativa for lignin augmentation and structural simplification

The sustainable production and utilization of lignocellulose biomass are indispensable for establishing sustainable societies. Trees and large-sized grasses are the major sources of lignocellulose biomass, while large-sized grasses greatly surpass trees in terms of lignocellulose biomass productivity. With an overall aim to improve lignocellulose usability, it is important to increase the lignin content and simplify lignin structures in biomass plants via lignin metabolic engineering. Rice (Oryza sativa) is not only a representative and important grass crop, but also is a model for large-sized grasses in biotechnology. This review outlines progress in lignin metabolic engineering in grasses, mainly rice, including characterization of the lignocellulose properties, the augmentation of lignin content and the simplification of lignin structures. These findings have broad applicability for the metabolic engineering of lignin in large-sized grass biomass plants.

Dissection of transcriptional events in graft incompatible reactions of "Bearss" lemon (Citrus limon) and "Valencia" sweet orange (C. sinensis) on a novel citrandarin (C. reticulata × Poncirus trifoliata) rootstock

Citrus is commercially propagated via grafting, which ensures trees have consistent fruit traits combined with favorable traits from the rootstock such as soil adaptability, vigor, and resistance to soil pathogens. Graft incompatibility can occur when the scion and rootstock are not able to form a permanent, healthy union. Understanding and preventing graft incompatibility is of great importance in the breeding of new fruit cultivars and in the choice of scion and rootstock by growers. The rootstock US-1283, a citrandarin generated from a cross of "Ninkat" mandarin (Citrus reticulata) and "Gotha Road" #6 trifoliate orange (Poncirus trifoliata), was released after years of field evaluation because of its superior productivity and good fruit quality on "Hamlin" sweet orange (C. sinensis) under Florida's growing conditions. Subsequently, it was observed that trees of "Bearss" lemon (C. limon) and "Valencia" sweet orange (C. sinensis) grafted onto US-1283 exhibited unhealthy growth near the graft union. The incompatibility manifested as stem grooving and necrosis underneath the bark on the rootstock side of the graft. Another citrandarin rootstock, US-812 (C. reticulata "Sunki" × P. trifoliata "Benecke"), is fully graft compatible with the same scions. Transcriptome analysis was performed on the vascular tissues above and below the graft union of US-812 and US-1283 graft combinations with "Bearss" and "Valencia" to identify expression networks associated with incompatibility and help understand the processes and potential causes of incompatibility. Transcriptional reprogramming was stronger in the incompatible rootstock than in the grafted scions. Differentially expressed genes (DEGs) in US-1283, but not the scions, were associated with oxidative stress and plant defense, among others, similar to a pathogen-induced immune response localized to the rootstock; however, no pathogen infection was detected. Therefore, it is hypothesized that this response could have been triggered by signaling miscommunications between rootstock and scion either through (1) unknown molecules from the scion that were perceived as danger signals by the rootstock, (2) missing signals from the scion or missing receptors in the rootstock necessary for the formation of a healthy graft union, (3) the overall perception of the scion by the rootstock as non-self, or (4) a combination of the above.

Integrated Multi-Omics Analysis to Reveal the Molecular Mechanisms of Inflorescence Elongation in Medicago sativa

The morphological architecture of inflorescence influences seed production. The regulatory mechanisms underlying alfalfa (Medicago sativa) inflorescence elongation remain unclear. Therefore, in this study, we conducted a comparative analysis of the transcriptome, proteome, and metabolome of two extreme materials at three developmental stages to explore the mechanisms underlying inflorescence elongation in alfalfa. We observed the developmental processes of long and short inflorescences and found that the elongation capacity of alfalfa with long inflorescence was stronger than that of alfalfa with short inflorescences. Furthermore, integrative analysis of the transcriptome and proteome indicated that the phenylpropanoid biosynthesis pathway was closely correlated with the structural formation of the inflorescence. Additionally, we identified key genes and proteins associated with lignin biosynthesis based on the differential expressed genes and proteins (DEGs and DEPs) involved in phenylpropanoid biosynthesis. Moreover, targeted hormone metabolome analysis revealed that IAA, GA, and CK play an important role in the peduncle elongation of alfalfa inflorescences. Based on omics analysis, we detected key genes and proteins related to plant hormone biosynthesis and signal transduction. From the WGCNA and WPCNA results, we furthermore screened 28 candidate genes and six key proteins that were correlated with lignin biosynthesis, plant hormone biosynthesis, and signaling pathways. In addition, 19 crucial transcription factors were discovered using correlation analysis that might play a role in regulating candidate genes. This study provides insight into the molecular mechanism of inflorescence elongation in alfalfa and establishes a theoretical foundation for improving alfalfa seed production.

The OsDIR55 gene increases salt tolerance by altering the root diffusion barrier

The increased soil salinity is becoming a major challenge to produce more crops and feed the growing population of the world. In this study, we demonstrated that overexpression of OsDIR55 gene enhances rice salt tolerance by altering the root diffusion barrier. OsDIR55 is broadly expressed in all examined tissues and organs with the maximum expression levels at lignified regions in rice roots. Salt stress upregulates the expression of OsDIR55 gene in an abscisic acid (ABA)-dependent manner. Loss-function and overexpression of OsDIR55 compromised and improved the development of CS and root diffusion barrier, manifested with the decreased and increased width of CS, respectively, and ultimately affected the permeability of the apoplastic diffusion barrier in roots. OsDIR55 deficiency resulted in Na+ accumulation, ionic imbalance, and growth arrest, whereas overexpression of OsDIR55 enhances salinity tolerance and provides an overall benefit to plant growth and yield potential. Collectively, we propose that OsDIR55 is crucial for ions balance control and salt stress tolerance through regulating lignification-mediated root barrier modifications in rice.

Maize requires arogenate dehydratase 2 for resistance to Ustilago maydis and plant development

Maize (Zea mays) smut is a common biotrophic fungal disease caused by Ustilago maydis and leads to low maize yield. Maize resistance to U. maydis is a quantitative trait. However, the molecular mechanism underlying the resistance of maize to U. maydis is poorly understood. Here, we reported that a maize mutant caused by a single gene mutation exhibited defects in both fungal resistance and plant development. maize mutant highly susceptible to U. maydis (mmsu) with a dwarf phenotype forms tumors in the ear. A map-based cloning and allelism test demonstrated that 1 gene encoding a putative arogenate dehydratase/prephenate dehydratase (ADT/PDT) is responsible for the phenotypes of the mmsu and was designated as ZmADT2. Combined transcriptomic and metabolomic analyses revealed that mmsu had substantial differences in multiple metabolic pathways in response to U. maydis infection compared with the wild type. Disruption of ZmADT2 caused damage to the chloroplast ultrastructure and function, metabolic flux redirection, and reduced the amounts of salicylic acid (SA) and lignin, leading to susceptibility to U. maydis and dwarf phenotype. These results suggested that ZmADT2 is required for maintaining metabolic flux, as well as resistance to U. maydis and plant development in maize. Meanwhile, our findings provided insights into the maize response mechanism to U. maydis infection.

The DEP1 Mutation Improves Stem Lodging Resistance and Biomass Saccharification by Affecting Cell Wall Biosynthesis in Rice

BACKGROUND

Plant cell walls have evolved precise plasticity in response to environmental stimuli. The plant heterotrimeric G protein complexes could sense and transmit extracellular signals to intracellular signaling systems, and activate a series of downstream responses. dep1 (Dense and Erect Panicles 1), the gain-of-function mutation of DEP1 encoding a G protein γ subunit, confers rice multiple improved agronomic traits. However, the effects of DEP1 on cell wall biosynthesis and wall-related agronomic traits remain largely unknown.

RESULTS

In this study, we showed that the DEP1 mutation affects cell wall biosynthesis, leading to improved lodging resistance and biomass saccharification. The DEP1 is ubiquitously expressed with a relatively higher expression level in tissues rich in cell walls. The CRISPR/Cas9 editing mutants of DEP1 (dep1-cs) displayed a significant enhancement in stem mechanical properties relative to the wild-type, leading to a substantial improvement in lodging resistance. Cell wall analyses showed that the DEP1 mutation increased the contents of cellulose, hemicelluloses, and pectin, and reduced lignin content and cellulose crystallinity (CrI). Additionally, the dep1-cs seedlings exhibited higher sensitivity to cellulose biosynthesis inhibitors, 2,6-Dichlorobenzonitrile (DCB) and isoxaben, compared with the wild-type, confirming the role of DEP1 in cellulose deposition. Moreover, the DEP1 mutation-mediated alterations of cell walls lead to increased enzymatic saccharification of biomass after the alkali pretreatment. Furthermore, the comparative transcriptome analysis revealed that the DEP1 mutation substantially altered expression of genes involved in carbohydrate metabolism, and cell wall biosynthesis.

CONCLUSIONS

Our findings revealed the roles of DEP1 in cell wall biosynthesis, lodging resistance, and biomass saccharification in rice and suggested genetic modification of DEP1 as a potential strategy to develop energy rice varieties with high lodging resistance.

Disease resistance features of the executor R gene Xa7 reveal novel insights into the interaction between rice and Xanthomonas oryzae pv. oryzae

Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a widespread and destructive disease in rice production. Previously, we cloned an executor R gene, Xa7, which confers durable and broad-spectrum resistance to BB. Here, we further confirmed that the transcription activator-like effector (TALE) AvrXa7 in Xoo strains could directly bind to the effector-binding element (EBE) in the promoter of the Xa7 gene. Other executor R genes (Xa7, Xa10, Xa23, and Xa27) driven by the promoter of the Xa7 gene could be activated by AvrXa7 and trigger the hypersensitive response (HR) in tobacco leaves. When the expression of the Xa23 gene was driven by the Xa7 promoter, the transgenic rice plants displayed a similar resistance spectrum as the Xa7 gene, demonstrating that the disease resistance characteristics of executor R genes are mainly determined by their induction patterns. Xa7 gene is induced locally by Xoo in the infected leaves, and its induction not only inhibited the growth of incompatible strains but also enhanced the resistance of rice plants to compatible strains, which overcame the shortcomings of its race-specific resistance. Transcriptome analysis of the Xa7 gene constitutive expression in rice plants displayed that Xa7-mediated disease resistance was related to the biosynthesis of lignin and thus enhanced resistance to Xoo. Overall, our results provided novel insights and important resources for further clarifying the molecular mechanisms of the executor R genes.

Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution

Nypa fruticans (Wurmb), a mangrove palm species with origins dating back to the Late Cretaceous period, is a unique species for investigating long-term adaptation strategies to intertidal environments and the early evolution of palms. Here, we present a chromosome-level genome sequence and assembly for N. fruticans. We integrated the genomes of N. fruticans and other palm family members for a comparative genomic analysis, which confirmed that the common ancestor of all palms experienced a whole-genome duplication event around 89 million years ago, shaping the distinctive characteristics observed in this clade. We also inferred a low mutation rate for the N. fruticans genome, which underwent strong purifying selection and evolved slowly, thus contributing to its stability over a long evolutionary period. Moreover, ancient duplicates were preferentially retained, with critical genes having experienced positive selection, enhancing waterlogging tolerance in N. fruticans. Furthermore, we discovered that the pseudogenization of Early Methionine-labelled 1 (EM1) and EM6 in N. fruticans underly its crypto-vivipary characteristics, reflecting its intertidal adaptation. Our study provides valuable genomic insights into the evolutionary history, genome stability, and adaptive evolution of the mangrove palm. Our results also shed light on the long-term adaptation of this species and contribute to our understanding of the evolutionary dynamics in the palm family.

Lignin reduction in sugarcane by performing CRISPR/Cas9 site-direct mutation of SoLIM transcription factor

Genetic engineering of plant cell walls is limited for reducing lignocellulose recalcitrance, so mild and/or green-like pretreatment is still required for sequential enzymatic saccharification. Here, we report a method to reduce lignin content in sugarcane stalks using the CRISPR/Cas 9 technique. Three target sequences of SoLIM were designed and fused to pRGEB32. The cassette constructs were introduced into sugarcane calli cv. KK3 through Agrobacterium-mediated transformation. We produced one base substitution and one insertion line for the 1st target site; two insertions, one deletion, and one base substitution for the 2nd target site; and one base substitution and insertion for the 3rd target site. qRT-PCR analysis of SoLIM, SoPAL, SoC4H, and SoCAD showeded that downregulation of SoLIM by single nucleotide insertions or deletions reduced the expression of SoPAL, SoC4H, and SoCAD. Consequently, the edited lines contained 9.74 to 51.46% less lignin content compared to that in the wild-type plants. The syringyl/guaiacyl (S/G) ratio of the edited lines ranged between 0.23 and 0.49, while the wild-type was 0.22. The histochemical evaluation and scanning electron microscopy of the cell walls supported this observation. A low lignin content sugarcane will provide a better feedstock for second-generation bioethanol production.

The Physiological Basis of Alfalfa Plant Height Establishment

Plant height plays an important role in crop yield, product quality, and cultivation management. However, the physiological mechanisms that regulate the establishment of plant height in alfalfa plants remain unclear. Herein, we measured plant height traits, leaf characteristics, photosynthetic physiology, cell wall composition, and endogenous hormone contents of tall- and short-stalked alfalfa materials at different reproductive periods. We analyzed the physiology responsible for differences in plant height. The results demonstrated that the number of internodes in tall- and short-stalked alfalfa materials tended to converge with the advancement of the fertility period. Meanwhile, the average internode length (IL) of tall-stalked materials was significantly higher than that of short-stalked materials at different fertility periods, with internode length identified as the main trait determining the differences in alfalfa plant height. Leaf characteristics, which are closely related to photosynthetic capacity, are crucial energy sources supporting the expression of plant height traits, and we found that an increase in the number of leaves contributed to a proportional increase in plant height. Additionally, a significant positive correlation was observed between plant height and leaf dry weight per plant during the branching and early flowering stages of alfalfa. The leaves of alfalfa affect plant height through photosynthesis, with the budding stage identified as the key period for efficient light energy utilization. Plant height at the budding stage showed a significant positive correlation with soluble sugar (SS) content and a significant negative correlation with intercellular CO2 concentration. Moreover, we found that alfalfa plant height was significantly correlated with the contents of indole-3-acetic acid in stem tips (SIAA), gibberellin A3 in leaves (LGA3), zeatin in stem tips (SZT), and abscisic acid in leaves (LABA). Further investigation revealed that SS, SIAA, and LGA3 contents were important physiological indicators affecting alfalfa plant height. This study provides a theoretical basis for understanding the formation of alfalfa plant height traits and for genetic improvement studies.

Characterization of sugarcane mutants developed through gamma irradiations for their lignin content and caffeic acid-O-methyl transferase (COMT) gene mutations

PURPOSE

Bagasse, the residue left after extracting juice from sugarcane stalks, is rich in lignocellulosic biomass. The lignin present in this plant biomass is the key factor that hinders the efficient extraction of ethanol from the bagasse. In the current study, γ-irradiated sugarcane mutants were evaluated for variation in lignin content and its corresponding caffeic acid-O-methyl transferase (COMT) gene.

MATERIALS AND METHODS

The acetyl bromide method was used to estimate lignin content in sugarcane mutants. PCR-based cloning of the COMT gene was performed in low lignin mutants as well as control plants in E. coli (strain DH5α) to understand the mechanism of variation at the molecular level. The Sanger sequencing for cloned gene was performed to check variation in gene sequence.

RESULTS

In comparison to the control (21.5%), the mutant plants' lignin content ranged from 13 to 28%. The Sanger sequencing revealed approximately the same length of the gene from mutants as well as a control plant. In comparison to the reference gene, the mutated gene showed SNPs and indels in different regions, which may have an impact on lignin content.

CONCLUSIONS

Therefore, γ-irradiated mutagenesis is an acceptable approach to develop novel mutants of sugarcane with low lignin content to enhance bioethanol production from waste material using bioprocess technology.

Genome-wide family prediction unveils molecular mechanisms underlying the regulation of agronomic traits in Urochloa ruziziensis

Tropical forage grasses, particularly those belonging to the Urochloa genus, play a crucial role in cattle production and serve as the main food source for animals in tropical and subtropical regions. The majority of these species are apomictic and tetraploid, highlighting the significance of U. ruziziensis, a sexual diploid species that can be tetraploidized for use in interspecific crosses with apomictic species. As a means to support breeding programs, our study investigates the feasibility of genome-wide family prediction in U. ruziziensis families to predict agronomic traits. Fifty half-sibling families were assessed for green matter yield, dry matter yield, regrowth capacity, leaf dry matter, and stem dry matter across different clippings established in contrasting seasons with varying available water capacity. Genotyping was performed using a genotyping-by-sequencing approach based on DNA samples from family pools. In addition to conventional genomic prediction methods, machine learning and feature selection algorithms were employed to reduce the necessary number of markers for prediction and enhance predictive accuracy across phenotypes. To explore the regulation of agronomic traits, our study evaluated the significance of selected markers for prediction using a tree-based approach, potentially linking these regions to quantitative trait loci (QTLs). In a multiomic approach, genes from the species transcriptome were mapped and correlated to those markers. A gene coexpression network was modeled with gene expression estimates from a diverse set of U. ruziziensis genotypes, enabling a comprehensive investigation of molecular mechanisms associated with these regions. The heritabilities of the evaluated traits ranged from 0.44 to 0.92. A total of 28,106 filtered SNPs were used to predict phenotypic measurements, achieving a mean predictive ability of 0.762. By employing feature selection techniques, we could reduce the dimensionality of SNP datasets, revealing potential genotype-phenotype associations. The functional annotation of genes near these markers revealed associations with auxin transport and biosynthesis of lignin, flavonol, and folic acid. Further exploration with the gene coexpression network uncovered associations with DNA metabolism, stress response, and circadian rhythm. These genes and regions represent important targets for expanding our understanding of the metabolic regulation of agronomic traits and offer valuable insights applicable to species breeding. Our work represents an innovative contribution to molecular breeding techniques for tropical forages, presenting a viable marker-assisted breeding approach and identifying target regions for future molecular studies on these agronomic traits.

Integrated transcriptomic and proteomic analyses of two sugarcane (Saccharum officinarum Linn.) varieties differing in their lodging tolerance

BACKGROUND

Lodging seriously affects sugarcane stem growth and sugar accumulation, reduces sugarcane yield and sucrose content, and impedes mechanization. However, the molecular mechanisms underlying sugarcane lodging tolerance remain unclear. In this study, comprehensive transcriptomic and proteomic analyses were performed to explore the differential genetic regulatory mechanisms between upright (GT42) and lodged (GF98-296) sugarcane varieties.

RESULTS

The stain test showed that GT42 had more lignin and vascular bundles in the stem than GF98-296. The gene expression analysis revealed that the genes that were differentially expressed between the two varieties were mainly involved in the phenylpropanoid pathway at the growth stage. The protein expression analysis indicated that the proteins that were differentially expressed between the two varieties were related to the synthesis of secondary metabolites, the process of endocytosis, and the formation of aminoacyl-tRNA. Time-series analysis revealed variations in differential gene expression patterns between the two varieties, whereas significant protein expression trends in the two varieties were largely consistent, except for one profile. The expression of CYP84A, 4CL, and CAD from the key phenylpropanoid biosynthetic pathway was enhanced in GT42 at stage 2 but suppressed in GF98-296 at the growth stage. Furthermore, the expression of SDT1 in the nicotinate and nicotinamide metabolism was enhanced in GT42 cells but suppressed in GF98-296 cells at the growth stage.

CONCLUSION

Our findings provide reference data for mining lodging tolerance-related genes that are expected to facilitate the selective breeding of sugarcane varieties with excellent lodging tolerance.

Functional investigation of five R2R3-MYB transcription factors associated with wood development in Eucalyptus using DAP-seq-ML

A multi-tiered transcriptional network regulates xylem differentiation and secondary cell wall (SCW) formation in plants, with evidence of both conserved and lineage-specific SCW network architecture. We aimed to elucidate the roles of selected R2R3-MYB transcription factors (TFs) linked to Eucalyptus wood formation by identifying genome-wide TF binding sites and direct target genes through an improved DAP-seq protocol combined with machine learning for target gene assignment (DAP-seq-ML). We applied this to five TFs including a well-studied SCW master regulator (EgrMYB2; homolog of AtMYB83), a repressor of lignification (EgrMYB1; homolog of AtMYB4), a TF affecting SCW thickness and vessel density (EgrMYB137; homolog of PtrMYB074) and two TFs with unclear roles in SCW regulation (EgrMYB135 and EgrMYB122). Each DAP-seq TF peak set (average 12,613 peaks) was enriched for canonical R2R3-MYB binding motifs. To improve the reliability of target gene assignment to peaks, a random forest classifier was developed from Arabidopsis DAP-seq, RNA-seq, chromatin, and conserved noncoding sequence data which demonstrated significantly higher precision and recall to the baseline method of assigning genes to proximal peaks. EgrMYB1, EgrMYB2 and EgrMYB137 predicted targets showed clear enrichment for SCW-related biological processes. As validation, EgrMYB137 overexpression in transgenic Eucalyptus hairy roots increased xylem lignification, while its dominant repression in transgenic Arabidopsis and Populus reduced xylem lignification, stunted growth, and caused downregulation of SCW genes. EgrMYB137 targets overlapped significantly with those of EgrMYB2, suggesting partial functional redundancy. Our results show that DAP-seq-ML identified biologically relevant R2R3-MYB targets supported by the finding that EgrMYB137 promotes SCW lignification in planta.

Histology, physiology, and transcriptomic and metabolomic profiling reveal the developmental dynamics of annual shoots in tree peonies (Paeonia suffruticosa Andr.)

The development of tree peony annual shoots is characterized by "withering", which is related to whether there are bud points in the leaf axillaries of annual shoots. However, the mechanism of "withering" in tree peony is still unclear. In this study, Paeonia ostii 'Fengdan' and P. suffruticosa 'Luoyanghong' were used to investigate dynamic changes of annual shoots through anatomy, physiology, transcriptome, and metabolome. The results demonstrated that the developmental dynamics of annual shoots of the two cultivars were comparable. The withering degree of P. suffruticosa 'Luoyanghong' was higher than that of P. ostii 'Fengdan', and their upper internodes of annual flowering shoots had a lower degree of lignin deposition, cellulose, C/N ratio, showing no obvious sclerenchyma, than the bottom ones and the whole internodes of vegetative shoot, which resulted in the "withering" of upper internodes. A total of 36 phytohormone metabolites were detected, of which 33 and 31 were detected in P. ostii 'Fengdan' and P. suffruticosa 'Luoyanghong', respectively. In addition, 302 and 240 differentially expressed genes related to lignin biosynthesis, carbon and nitrogen metabolism, plant hormone signal transduction, and zeatin biosynthesis were screened from the two cultivars. Furtherly, 36 structural genes and 40 transcription factors associated with the development of annual shoots were highly co-expressed, and eight hub genes involved in this developmental process were identified. Consequently, this study explained the developmental dynamic on the varied annual shoots through multi-omics, providing a theoretical foundation for germplasm innovation and the mechanized harvesting of tree peony annual shoots.

The ARF2-MYB6 module mediates auxin-regulated petal expansion in rose

In cut rose (Rosa hybrida), the flower-opening process is closely associated with vase life. Auxin induces the expression of transcription factor genes that function in petal growth via cell expansion. However, the molecular mechanisms underlying the auxin effect during flower opening are not well understood. Here, we identified the auxin-inducible transcription factor gene RhMYB6, whose expression level is high during the early stages of flower opening. Silencing of RhMYB6 delayed flower opening by controlling petal cell expansion through down-regulation of cell expansion-related genes. Furthermore, we demonstrated that the auxin response factor RhARF2 directly interacts with the promoter of RhMYB6 and represses its transcription. Silencing of RhARF2 resulted in larger petal size and delayed petal movement. We also showed that the expression of genes related to ethylene and petal movement showed substantial differences in RhARF2-silenced petals. Our results indicate that auxin-regulated RhARF2 is a critical player that controls flower opening by governing RhMYB6 expression and mediating the crosstalk between auxin and ethylene signaling.

Uncovering mechanisms governing stem growth in peanut (Arachis hypogaea L.) with varying plant heights through integrated transcriptome and metabolomics analyses

The mechanisms responsible for stem growth in peanut (Arachis hypogaea L.) cultivars with varying plant heights remain unclear, despite the significant impact of plant height on peanut yield. Therefore, this study aimed to investigate the underlying mechanisms of peanut stem growth using phenotypic, physiological, transcriptomic, and metabolomic analyses. The findings revealed that the tallest cultivar, HY33, exhibited the highest rate of stem growth and accumulated the most stem dry matter, followed by the intermediate cultivar, SH108, while the dwarf cultivar, Df216, displayed the lowest values. Furthermore, SH108 exhibited a higher harvest index, as well as superior pod and kernel yields compared to both HY33 and Df216. Transcriptome and metabolome analyses identified differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) associated with phenylpropanoid and flavonoid biosynthesis. Notably, downregulated DEGs in Df216/HY33 and Df216/SH108 included phenylalanine ammonia-lyase (PAL), caffeoyl-CoA O-methyltransferase (COMT), and ferulate-5-hydroxylase (F5H), while downregulated DEMs included p-coumaryl alcohol, chlorogenic acid, and L-epicatechin. Compared to HY33, the reduced activities of PAL, COMT, and F5H resulted in a decreased stem lignin content in Df216. Additionally, downregulated DEGs involved in gibberellin (GA) and brassinosteroid (BR) biosynthesis were identified in Df216/HY33, which contributed to the lowest levels of GA1, GA3, and BR contents in Df216. The results suggest that the dwarf phenotype arises from impaired GA and BR biosynthesis and signaling, resulting in a slower stem growth rate and reduced lignin accumulation.

Integrated transcriptomic and metabolomic analysis reveals the effects of polyploidization on the lignin content and metabolic pathway in Eucalyptus

BACKGROUND

Lignin is a major restriction factor for the industrial production of biomass resources, such as pulp and bioenergy. Eucalyptus is one of the most important sources of pulp and bioenergy. After polyploidization, the lignin content of forest trees is generally reduced, which is considered a beneficial genetic improvement. However, the differences in the lignin content between triploid and diploid Eucalyptus and the underlying regulatory mechanism are still unclear.

RESULTS

We conducted a comprehensive analysis at the phenotypic, transcriptional and metabolite levels between Eucalyptus urophylla triploids and diploids to reveal the effects of polyploidization on the lignin content and lignin metabolic pathway. The results showed that the lignin content of Eucalyptus urophylla triploid stems was significantly lower than that of diploids. Lignin-related metabolites were differentially accumulated between triploids and diploids, among which coniferaldehyde, p-coumaryl alcohol, sinapaldehyde and coniferyl alcohol had significant positive correlations with lignin content, indicating that they might be primarily contributing metabolites. Most lignin biosynthetic genes were significantly downregulated, among which 11 genes were significantly positively correlated with the lignin content and above metabolites. Furthermore, we constructed a co-expression network between lignin biosynthetic genes and transcription factors based on weighted gene co-expression network analysis. The network identified some putative orthologues of secondary cell wall (SCW)-related transcription factors, among which MYB52, MYB42, NAC076, and LBD15 were significantly downregulated in Eucalyptus urophylla triploids. In addition, potential important transcription factors, including HSL1, BEE3, HHO3, and NAC046, also had high degrees of connectivity and high edge weights with lignin biosynthetic genes, indicating that they might also be involved in the variation of lignin accumulation between triploid and diploid Eucalyptus urophylla.

CONCLUSIONS

The results demonstrated that some lignin-related metabolites, lignin biosynthetic genes and transcription factors in Eucalyptus urophylla triploids may be relatively sensitive in response to the polyploidization effect, significantly changing their expression levels, which ultimately correlated with the varied lignin content. The analysis of the underlying formation mechanism could provide beneficial information for the development and utilization of polyploid biomass resources, which will be also valuable for genetic improvement in other bioenergy plants.

Novel insight into functions of ascorbate peroxidase in higher plants: More than a simple antioxidant enzyme

As plants are sessile organisms, they are inevitably exposed to a variety of environmental stimuli that trigger rapid changes in the generation and disposal of reactive oxygen species such as hydrogen peroxide (H₂O₂). A major H₂O₂ scavenging system in plant cells is the ascorbate-glutathione cycle, in which ascorbate peroxidase (APX) catalyzes the conversion of H₂O₂ into water employing ascorbate as specific electron donor. In higher plants, distinct APX isoforms can occur in multiple subcellular compartments, including chloroplasts, mitochondria, and peroxisomes and the cytosol, to modulate organellar and cellular levels of H₂O₂. It is well established that APX plays crucial roles in protecting plant cells against diverse environmental stresses, as well as in plant growth and development. Apart from ascorbate, recently, APXs have been found to have a broader substrate specificity and possess chaperone activity, hence participating various biological processes. In this review, we describe the antioxidant properties of APXs and highlight their novel roles beyond 'ascorbate peroxidases'.

OsPEX1, an extensin-like protein, negatively regulates root growth in a gibberellin-mediated manner in rice

Leucine-rich repeat extensins (LRXs) are required for plant growth and development through affecting cell growth and cell wall formation. LRX gene family can be classified into two categories: predominantly vegetative-expressed LRX and reproductive-expressed PEX. In contrast to the tissue specificity of Arabidopsis PEX genes in reproductive organs, rice OsPEX1 is also highly expressed in roots in addition to reproductive tissue. However, whether and how OsPEX1 affects root growth is unclear. Here, we found that overexpression of OsPEX1 retarded root growth by reducing cell elongation likely caused by an increase of lignin deposition, whereas knockdown of OsPEX1 had an opposite effect on root growth, indicating that OsPEX1 negatively regulated root growth in rice. Further investigation uncovered the existence of a feedback loop between OsPEX1 expression level and GA biosynthesis for proper root growth. This was supported by the facts that exogenous GA₃ application downregulated transcript levels of OsPEX1 and lignin-related genes and rescued the root developmental defects of the OsPEX1 overexpression mutant, whereas OsPEX1 overexpression reduced GA level and the expression of GA biosynthesis genes. Moreover, OsPEX1 and GA showed antagonistic action on the lignin biosynthesis in root. OsPEX1 overexpression upregulated transcript levels of lignin-related genes, whereas exogenous GA₃ application downregulated their expression. Taken together, this study reveals a possible molecular pathway of OsPEX1mediated regulation of root growth through coordinate modulation of lignin deposition via a negative feedback regulation between OsPEX1 expression and GA biosynthesis.

Alternative Splicing of NAC Transcription Factor Gene CmNST1 Is Associated with Naked Seed Mutation in Pumpkin, Cucurbita moschata

In pumpkin (Cucurbita moschata), the naked or hull-less seed phenotype has great benefits for breeding this crop for oil or snack use. We previously identified a naked seed mutant in this crop. In this study, we report genetic mapping, identification, and characterization of a candidate gene for this mutation. We showed that the naked seed phenotype is controlled by a single recessive gene (N). The bulked segregant analysis identified a 2.4 Mb region on Chromosome 17 with 15 predicted genes. Multiple lines of evidence suggested that CmoCh17G004790 is the most probable candidate gene for the N locus which encodes a NAC transcription factor WALL THICKENING PROMOTING FACTOR 1 (CmNST1). No nucleotide polymorphism or structural variation was found in the genomic DNA sequences of CmNST1 between the mutant and the wildtype inbred line (hulled seed). However, the cDNA sequence cloned from developing seed coat samples of the naked seed mutant was 112 bp shorter than that from the wildtype which is due to seed coat-specific alternative splicing in the second exon of the mutant CmNST1 transcript. The expression level of CmNST1 in the developing seed coat was higher in the mutant than in the wildtype during early seed coat development which was reversed later. Transcriptomic profiling with RNA-Seq at different stages of seed development in the mutant and wildtype revealed a critical role of CmNST1 as a master regulator for the lignin biosynthesis pathway during seed coat development while other NAC and MYB transcription factors were also involved in forming a regulatory network for the building of secondary cell walls. This work provides a novel mechanism for the well-characterized NST1 transcription factor gene in regulating secondary cell wall development. The cloned gene also provides a useful tool for marker-assisted breeding of hull-less C. moschata varieties.

Homeobox transcription factors OsZHD1 and OsZHD2 induce inflorescence meristem activity at floral transition in rice

Floral transition starts in the leaves when florigens respond to various environmental and developmental factors. Among several regulatory genes that are preferentially expressed in the inflorescence meristem during the floral transition, this study examines the homeobox genes OsZHD1 and OsZHD2 for their roles in regulating this transition. Although single mutations in these genes did not result in visible phenotype changes, double mutations in these genes delayed flowering. Florigen expression was not altered in the double mutants, indicating that the delay was due to a defect in florigen signaling. Morphological analysis of shoot apical meristem at the early developmental stage indicated that inflorescence meristem development was significantly delayed in the double mutants. Overexpression of ZHD2 causes early flowering because of downstream signals after the generation of florigens. Expression levels of the auxin biosynthesis genes were reduced in the mutants and the addition of indole-3-acetic acid recovered the defect in the mutants, suggesting that these homeobox genes play a role in auxin biosynthesis. A rice florigen, RICE FLOWERING LOCUS T 1, binds to the promoter regions of homeobox genes. These results indicate that florigens stimulate the expression of homeobox genes, enhancing inflorescence development in the shoot apex.

SCL14 Inhibits the Functions of the NAC043-MYB61 Signaling Cascade to Reduce the Lignin Content in Autotetraploid Populus hopeiensis

Whole-genome duplication often results in a reduction in the lignin content in autopolyploid plants compared with their diploid counterparts. However, the regulatory mechanism underlying variation in the lignin content in autopolyploid plants remains unclear. Here, we characterize the molecular regulatory mechanism underlying variation in the lignin content after the doubling of homologous chromosomes in Populus hopeiensis. The results showed that the lignin content of autotetraploid stems was significantly lower than that of its isogenic diploid progenitor throughout development. Thirty-six differentially expressed genes involved in lignin biosynthesis were identified and characterized by RNA sequencing analysis. The expression of lignin monomer synthase genes, such as PAL, COMT, HCT, and POD, was significantly down-regulated in tetraploids compared with diploids. Moreover, 32 transcription factors, including MYB61, NAC043, and SCL14, were found to be involved in the regulatory network of lignin biosynthesis through weighted gene co-expression network analysis. We inferred that SCL14, a key repressor encoding the DELLA protein GAI in the gibberellin (GA) signaling pathway, might inhibit the NAC043-MYB61 signaling functions cascade in lignin biosynthesis, which results in a reduction in the lignin content. Our findings reveal a conserved mechanism in which GA regulates lignin synthesis after whole-genome duplication; these results have implications for manipulating lignin production.

Sweet potato NAC transcription factor NAC43 negatively regulates plant growth by causing leaf curling and reducing photosynthetic efficiency

Leaves comprise one of the most important organs for plant growth and development. Although there have been some reports on leaf development and the establishment of leaf polarity, their regulatory mechanisms are not very clear. In this study, we isolated a NAC (NAM, ATAF, and CUC) transcription factor (TF), i.e., IbNAC43, from Ipomoea trifida, which is a wild ancestor of sweet potato. This TF was highly expressed in the leaves and encoded a nuclear localization protein. The overexpression of IbNAC43 caused leaf curling and inhibited the growth and development of transgenic sweet potato plants. The chlorophyll content and photosynthetic rate in transgenic sweet potato plants were significantly lower than those in wild-type (WT) plants. Scanning electron microscopy (SEM) and paraffin sections showed that the ratio of cells in the upper and lower epidermis of the transgenic plant leaves was unbalanced; moreover, the abaxial epidermal cells were irregular and uneven in transgenic plants. In addition, the xylem of transgenic plants was more developed than that of WT plants, while their lignin and cellulose contents were significantly higher than those of WT. Quantitative real-time PCR (qRT-PCR) analysis showed that the overexpression of IbNAC43 upregulated the genes involved in leaf polarity development and lignin biosynthesis in transgenic plants. Moreover, it was found that IbNAC43 could directly activate the expression of the leaf adaxial polarity-related genes IbREV and IbAS1 by binding to their promoters. These results indicate that IbNAC43 might play a critical role in plant growth by affecting the establishment of leaf adaxial polarity. This study provides new insights regarding leaf development.

Silicon Nanodots Increase Plant Resistance against Herbivores by Simultaneously Activating Physical and Chemical Defenses

Nanosilicon applications have been shown to increase plant defenses against both abiotic and biotic stresses. Silicon quantum nanodots (Si NDs), a form of nanosilicon, possess excellent biological and physiochemical properties (e.g., minimal size, high water solubility, stability, and biocompatibility), potentially making them more efficient in regulating plant responses to stress than other forms of silicon. However, to date, we still lack mechanistic evidence for how soil-applied Si NDs alter the regulation of plant physical and chemical defenses against insect herbivores. To address this gap, we compared the effect of fluorescent amine-functionalized Si NDs (5 nm) and the conventional fertilizer sodium silicate on maize (Zea mays L.) physical and chemical defenses against the oriental armyworm (Mythimna separata, Walker) caterpillars. We found that 50 mg/kg Si NDs and sodium silicate additions inhibited the growth of caterpillars the most (35.7% and 22.8%, respectively) as compared to other application doses (0, 10, and 150 mg/kg). Both Si NDs and silicate addition activated biosynthesis genes responsible for chemical (benzoxazinoids) and physical (lignin) defense production. Moreover, Si NDs upregulated the gene expression of antioxidant enzymes (SOD, CAT, and POD) and promoted the antioxidant metabolism (flavonoids) in maize leaves under M. separata attack. Finally, we show that, under field conditions, Si ND addition increased maize cob weight (28.7%), cob grain weight (40.8%), and 100-grain weight (26.5%) as compared to the control, and more so than the conventional silicon fertilizer. Altogether, our findings highlight the potential for Si NDs to be used as an effective and ecofriendly crop protection strategy in agroecosystems.

Lignin Biosynthesis in Postharvest Water Bamboo (Zizania latifolia) Shoots during Cold Storage Is Regulated by RBOH-Mediated Reactive Oxygen Species Signaling

Lignification is a major cause of senescence in fresh shoots of water bamboo (Zizania latifolia), which is a popular vegetable in southeast Asia; however, its physiological and molecular mechanisms is less understood. In the present study, lignin content and transcriptome change in postharvested water bamboo shoots under cold storage were investigated. We found that lignin significantly accumulated in the epidermis of the shoots with the increase of firmness. In the cold storage shoots, the major up-regulated genes were involved in phenylpropanoid biosynthesis, plant-pathogen interactions, and starch and sucrose metabolism. The lignin biosynthesis genes PAL, 4CL, C4H, CCoAOMT, CCR, F5H, CAD, and POD family were up-regulated during cold storage, while HCT and C3H were down-regulated. The MAPK signaling pathway was also up-regulated and respiratory burst oxidase homologue (RBOH) genes were strongly up-regulated. Therefore, we investigated the RBOH gene family and their expression profile in water bamboo shoots. The results indicated that 10 ZlRBOHs were up-regulated in cold storage shoots. Diphenyleneiodonium chloride (DPI), an inhibitor of RBOH oxidase, significantly inhibited the expression of genes involved in lignin deposition and biosynthesis, while H2O2 enhanced these processes. These results suggest that lignification of water bamboo shoots is regulated by RBOH-mediated ROS signaling.

Metabolite profiling and transcriptome analyses provide insight into the regulatory network of graft incompatibility in litchi

Litchi is an important commercial fruit crop widely grown in the world. Graft incompatibility between rootstocks and scions is a major constraint for large-scale cultivation of litchi orchards, popularization of new and excellent litchi varieties, and associated industrial development. Further, the genetic mechanism of graft incompatibility is still unclear in litchi. To reduce the incompatibility problems, this study investigated metabolic and transcriptomic differences between graft compatible and incompatible rootstock-scion combinations of litchi. The result of metabolomics analysis showed that incompatible rootstock-scion interaction modified the profiles of several metabolic substances. However, various compounds of flavonoids, phenolic acids, and lignin predominantly exhibited significantly altered abundance in graft incompatible combinations. Transcriptome analysis identified that graft incompatibility induces dynamic gene differences. The majority of these differentially expressed genes were enriched in biosynthetic pathways of phenylpropanoids. The differential expressions of genes in these pathways could be linked to the differential abundance levels of flavonoids, phenolic acids, and lignin compounds. Integrated metabolomic and transcriptomic analyses revealed a strong relationship between differential genes and differential metabolites identified in this study. In addition, identified hub genes and metabolites were closely associated with graft incompatibility of litchi. This study characterized the abundance of metabolites and genes in graft incompatible combinations and further discussed the genetic mechanism of graft incompatibility in litchi. Our results provide a platform to dissect the molecular mechanisms of graft incompatibility in the litchi fruit.

Caffeoyl-CoA 3-O-methyltransferase gene family in jute: Genome-wide identification, evolutionary progression and transcript profiling under different quandaries

Jute (Corchorus sp.), is a versatile, naturally occurring, biodegradable material that holds the promising possibility of diminishing the extensive use of plastic bags. One of the major components of the cell wall, lignin plays both positive and negative roles in fiber fineness and quality. Although it gives mechanical strength to plants, an excess amount of it is responsible for the diminution of fiber quality. Among various gene families involved in the lignin biosynthesis, Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) is the most significant and has remained mostly unexplored. In this study, an extensive in-silico characterization of the CCoAOMT gene family was carried out in two jute species (C. capsularis L. and C. olitoroius L.) by analyzing their structural, functional, molecular and evolutionary characteristics. A total of 6 CCoAOMT gene members were identified in each of the two species using published reference genomes. These two jute species showed high syntenic conservation and the identified CCoAOMT genes formed four clusters in the phylogenetic tree. Histochemical assay of lignin in both jute species could shed light on the deposition pattern in stems and how it changes in response to abiotic stresses. Furthermore, expression profiling using qPCR showed considerable alteration of CCoAOMT transcripts under various abiotic stresses and hormonal treatment. This study will lay a base for further analysis and exploration of target candidates for overexpression of gene silencing using modern biotechnological techniques to enhance the quality of this economically important fiber crop.

Reduced Expression of PRX2/ATPRX1, PRX8, PRX35, and PRX73 Affects Cell Elongation, Vegetative Growth, and Vasculature Structures in Arabidopsis thaliana

Class III peroxidases (PRXs) are involved in a broad spectrum of physiological and developmental processes throughout the life cycle of plants. However, the specific function of each PRX member in the family remains largely unknown. In this study, we selected four class III peroxidase genes (PRX2/ATPRX1, PRX8, PRX35, and PRX73) from a previous genome-wide transcriptome analysis, and performed phenotypic and morphological analyses, including histochemical staining, in PRX2RNAi, PRX8RNAi, PRX35RNAi, and PRX73RNAi plants. The reduced mRNA levels of corresponding PRX genes in PRX2RNAi, PRX8RNAi, PRX35RNAi, and PRX73RNAi seedlings resulted in elongated hypocotyls and roots, and slightly faster vegetative growth. To investigate internal structural changes in the vasculature, we performed histochemical staining, which revealed alterations in cell wall structures in the main vasculature of hypocotyls, stems, and roots of each PRXRNAi plant compared to wild-type (Col-0) plants. Furthermore, we found that PRX35RNAi plants displayed the decrease in the cell wall in vascular regions, which are involved in downregulation of lignin biosynthesis and biosynthesis-regulated genes' expression. Taken together, these results indicated that the reduced expression levels of PRX2/ATPRX1, PRX8, PRX35, and PRX73 affected hypocotyl and root elongation, vegetative growth, and the vasculature structures in hypocotyl, stem, and root tissues, suggesting that the four class III PRX genes play roles in plant developmental processes.

Climate-responsive DNA methylation is involved in the biosynthesis of lignin in birch

Lignin is one of the most important secondary metabolites and essential to the formation of cell walls. Changes in lignin biosynthesis have been reported to be associated with environmental variations and can influence plant fitness and their adaptation to abiotic stresses. However, the molecular mechanisms underlying this association remain unclear. In this study, we evaluated the relations between the lignin biosynthesis and environmental factors and explored the role of epigenetic modification (DNA methylation) in contributing to these relations if any in natural birch. Significantly negative correlations were observed between the lignin content and temperature ranges. Analyzing the transcriptomes of birches in two habitats with different temperature ranges showed that the expressions of genes and transcription factors (TFs) involving lignin biosynthesis were significantly reduced at higher temperature ranges. Whole-genome bisulfite sequencing revealed that promoter DNA methylation of two NAC-domain TFs, BpNST1/2 and BpSND1, may be involved in the inhibition of these gene expressions, and thereby reduced the content of lignin. Based on these results we proposed a DNA methylation-mediated lignin biosynthesis model which responds to environmental factors. Overall, this study suggests the possibility of environmental signals to induce epigenetic variations that result in changes in lignin content, which can aid to develop resilient plants to combat ongoing climate changes or to manipulate secondary metabolite biosynthesis for agricultural, medicinal, or industrial values.

Proteomic Analysis of the Inflorescence Stem Mechanical Strength Difference in Herbaceous Peonies (Paeonia lactiflora Pall.)

The herbaceous peony (Paeonia lactiflora Pall.) is a traditional rare flower in China, and production of its cut flowers has developed gradually in many places of the world. However, the inflorescence stems of some P. lactiflora cultivars have such low mechanical strength that the cut flower production was severely restricted. To better understand the causes of this problem from a protein expression level, two P. lactiflora cultivars with different inflorescence stem mechanical strengths were analyzed by two-dimensional electrophoresis and MALDI-TOF/MS. More than 1700 clear protein spots were detected, 53 of which varied significantly. Moreover, 23 of the differentially expressed proteins were identified and confirmed and are involved in various biological processes such as metabolism, protein biosynthesis and transport, signal transduction, and defensive response. Especially, cinnamyl alcohol dehydrogenase (CAD) and xyloglucan endotransglucosylase/hydrolase (XTH) were strongly connected to the inflorescence stem mechanical strength in P. lactiflora.

Unveiling the genetic architecture for lodging resistance in rice (Oryza sativa. L) by genome-wide association analyses

Lodging is one of the major abiotic stresses, affecting the total crop yield and quality. The improved lodging resistance and its component traits potentially reduce the yield losses. The section modulus (SM), bending moment at breaking (M), pushing resistance (PR), and coefficient of lodging resistance (cLr) are the key elements to estimate the lodging resistance. Understanding the genetic architecture of lodging resistance-related traits will help to improve the culm strength and overall yield potential. In this study, a natural population of 795 globally diverse genotypes was further divided into two (indica and japonica) subpopulations and was used to evaluate the lodging resistance and culm strength-related traits. Significant diversity was observed among the studied traits. We carried out the genome-wide association evaluation of four lodging resistance traits with 3.3 million deep resolution single-nucleotide polymorphic (SNP) markers. The general linear model (GLM) and compressed mixed linear model (MLM) were used for the whole population and two subpopulation genome-wide association studies (GWAS), and a 1000-time permutation test was performed to remove the false positives. A total of 375 nonredundant QTLs were observed for four culm strength traits on 12 chromosomes of the rice genome. Then, 33 pleiotropic loci governing more than one trait were mined. A total of 4031 annotated genes were detected within the candidate genomic region of 33 pleiotropic loci. The functional annotations and metabolic pathway enrichment analysis showed cellular localization and transmembrane transport as the top gene ontological terms. The in silico and in vitro expression analyses were conducted to validate the three candidate genes in a pleiotropic QTL on chromosome 7. It validated OsFBA2 as a candidate gene to contribute to lodging resistance in rice. The haplotype analysis for the candidate gene revealed a significant functional variation in the promoter region. Validation and introgression of alleles that are beneficial to induce culm strength may be used in rice breeding for lodging resistance.

Analyzing lignin biosynthesis pathways in rattan using improved co-expression networks of NACs and MYBs

BACKGROUND

The rattan is a valuable plant resource with multiple applications in tropical forests. Calamus simplicifolius and Daemonorops jenkinsiana are the two most representative rattan species, supplying over 95% of the raw materials for the rattan industry. Hence, the wood properties of both rattans have always attracted researchers' attention.

RESULTS

We re-annotated the genomes, obtained 81 RNA-Seq datasets, and developed an improved pipeline to increase the reliability of co-expression networks of both rattans. Based on the data and pipeline, co-expression relationships were detected in 11 NACs, 49 MYBs, and 86 lignin biosynthesis genes in C. simplicifolius and four NACs, 59 MYBs, and 76 lignin biosynthesis genes in D. jenkinsiana, respectively. Among these co-expression pairs, several genes had a close relationship to the development of wood properties. Additionally, we detected the enzyme gene on the lignin biosynthesis pathway was regulated by either NAC or MYB, while LACCASES was regulated by both NAC and MYB. For D. jenkinsiana, the lignin biosynthesis regulatory network was characterized by positive regulation, and MYB possible negatively regulate non-expressed lignin biosynthesis genes in stem tissues. For C. simplicifolius, NAC may positively regulate highly expressed genes and negatively regulate non-expressed lignin biosynthesis genes in stem tissues. Furthermore, we established core regulatory networks of NAC and MYB for both rattans.

CONCLUSIONS

This work improved the accuracy of rattan gene annotation by integrating an efficient co-expression network analysis pipeline, enhancing gene coverage and accuracy of the constructed network, and facilitating an understanding of co-expression relationships among NAC, MYB, and lignin biosynthesis genes in rattan and other plants.

The MicroRNA397a-LACCASE17 module regulates lignin biosynthesis in Medicago ruthenica (L.)

Mechanical strength is essential for the upright growth habit, which is one of the most important characteristics of terrestrial plants. Lignin, a phenylpropanoid-derived polymer mainly present in secondary cell walls plays critical role in providing mechanical support. Here, we report that the prostrate-stem cultivar of the legume forage Medicago ruthenica cultivar 'Mengnong No. 1' shows compromised mechanical strength compared with the erect-stem cultivar 'Zhilixing'. The erect-stem cultivar, 'Zhilixing' has significantly higher lignin content, leading to higher mechanical strength than the prostrate-stem cultivar. The low abundance of miRNA397a in the Zhiixing cultivar causes reduced cleavage of MrLAC17 transcript, which results in enhanced expression level of MrLAC17 compared to that in the prostrate-stem cultivar Mengnong No. 1. Complementation of the Arabidopsis lac4 lac17 double mutants with MrLAC17 restored the lignin content to wild-type levels, confirming that MrLAC17 perform an exchangeable role with Arabidopsis laccases. LAC17-mediated lignin polymerization is therefore increased in the 'Zhilixing', causing the erect stem phenotype. Our data reveal the importance of the miR397a in the lignin biosynthesis and suggest a strategy for molecular breeding targeting plant architecture in legume forage.

Identification of single major QTL and candidate gene(s) governing hull-less seed trait in pumpkin

The hull-less pumpkin (Cucurbita pepo) seed does not require de-hulling before use for human consumption, as a result highly preferred by the oil, nut, and baking industries. In hull-less seeds, a single recessive gene is responsible for the absence of outer thick seed coat layers; however, the genomic region and gene(s) controlling the trait are unclear to date. In this study, four crosses attempted to derive F₂ and backcross populations confirmed the single recessive gene inheritance of hull-less seed trait in populations adapted to the sub-tropical climate. The candidate genomic region for hull-less seed trait was identified through the BSA-QTLseq approach using bulks of F_2:3 progenies from a cross of HP111 (hulled) and HLP36 (hull-less). A novel genomic region on chromosome 12 ranging from 1.80 to 3.86 Mb was associated with the hull-less seed trait. The re-sequencing data identified a total of 396 SNPs within this region and eight were successfully converted into polymorphic KASP assays. The genotyping of segregating F₂ (n = 160) with polymorphic KASP assays resulted in a 40.3 cM partial linkage map and identified Cp_3430407 (10 cM) and Cp_3498687 (16.1 cM) as flanking markers for hull-less locus (Cphl-1). These flanking markers correspond to the 68.28 kb region in the reference genome, and the marker, Cp_3430407 successfully predicted the genotype in 93.33% of the C. pepo hull-less germplasm lines, thus can be used for marker-assisted selection in parents polymorphic for the hull-less seed trait. The Cphl-1-linked genomic region (2.06 Mb) encompasses a total of 182 genes, including secondary cell wall and lignin biosynthesis-related transcriptional factors viz., "NAC" (Cp4.1LG12g04350) and "MYB" (Cp4.1LG12g03120). These genes were differentially expressed in the seeds of hulled and hull-less genotypes, and therefore could be the potential candidate genes governing the hull-less seed trait in pumpkin.

Single-walled carbon nanotubes promotes wood formation in Populus davidiana × P.bolleana

Abundant studies have revealed that single-walled carbon nanotubes (SWCNTs) regulate plant growth. However, whether or how SWCNTs influence plant wood formation remains largely unknown. In this report, we found that SWCNTs had positive effects on poplar growth, as reflected by significantly increased plant height, leaf size, and fresh and dry weight. Transmission electron microscopy (TEM) images showed that the SWCNTs were absorbed in the exposed poplar root cells. A relatively higher content of cellulose and lignin was observed in the SWCNTs-treated poplar stems than in those of the control plants. It also showed darker phloroglucinol staining in the stems of exposed plants than that in control plants. Further analysis showed that the activities of key enzymes related to cellulose synthesis (cellulose synthase, CesA) and lignin biosynthesis (phenylalanine ammonia-lyase, PAL; cinnamate 4-hydroxylase, C4H; 4-coumarate:CoA ligase, 4CL; cinnamyl alcohol dehydrogenase, CAD) increased significantly after SWCNTs treatment. Consistent with the change trend of enzyme activity, the relative expression levels of a few lignin- and cellulose-related genes were activated by SWCNTs. Taken together, we proposed that SWCNTs have positive effects on poplar wood formation by modifying the expression of enzymes involved in the cellulose and lignin synthesis pathways. Our data suggest the modifications of wood formation through SWCNTs application could be a useful strategy for improvement of wood bioengineering.

Characteristics and candidate genes associated with excellent stalk strength in maize (Zea mays L.)

Lodging is a major problem in maize production, which seriously affects yield and hinders mechanized harvesting. Improving stalk strength is an effective way to improve lodging. The maize inbred line Jing2416 (J2416) was an elite germplasm in maize breeding which had strong stalk mechanical strength. To explore the characteristics its stalk strength, we conducted physiological, metabolic and transcriptomic analyses of J2416 and its parents Jing24 (J24) and 5237. At the kernel dent stage, the stalk rind penetrometer strength of J2416 was significantly higher than those of its two parents in multiple environments. The rind thickness, sclerenchyma tissue thickness, and cellulose, hemicellulose, and lignin contents of J2416 were significantly higher than those of its parents. Based on the significant differences between J2416 and 5237, we detected metabolites and gene transcripts showing differences in abundance between these two materials. A total of 212 (68.60%) metabolites and 2287 (43.34%) genes were up-regulated in J2416 compared with 5237. The phenylpropanoid and glycan synthesis/metabolism pathways were enriched in metabolites and genes that were up-regulated in J2416. Twenty-eight of the up-regulated genes in J2416 were involved in lignin, cellulose, and hemicellulose synthesis pathways. These analyses have revealed important physiological characteristics and candidate genes that will be useful for research and breeding of inbred lines with excellent stalk strength.

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.