MYB Transcription Factors and Its Regulation in Secondary Cell Wall Formation and Lignin Biosynthesis during Xylem Development

Functional analysis of AobHLH88 involved in anthocyanin synthesis using multi-omics data in Asparagus officinalis

Basic helix loop helix (bHLH) proteins play critical functions in various aspects of plant growth and development, especially in anthocyanin synthesis. Although the Asparagus genome has been sequenced, there is limited information on the bHLH gene family within this species. This study identifies 96 AobHLH transcription factor genes in the Asparagus genome. Chromosomal localization indicated 91 AobHLHs across nine chromosomes. Phylogenetic analysis categorized them into nine distinct subfamilies, each with specific motif characteristics. Synteny analysis showed that both dispersed duplication and whole-genome or segmental duplications contributed to the expansion of AobHLHs, identifying 19 orthologous pairs between Asparagus and Arabidopsis. Differential expression analysis indicated a notable increase in AobHLH10, AobHLH18, and AobHLH88 gene expression during anthocyanin synthesis, as shown in Asparagus RNA-seq data. Among them, AobHLH88 displayed the higher differential expression pattern in 'Purple Passion'. Subcellular localization analysis displayed that AobHLH88 was localized in the nucleus. Furthermore, overexpression of AobHLH88 in tobacco plants highlighted its significant role in enhancing anthocyanin accumulation in Asparagus spear color. Collectively, this in-depth identification and characterization of AobHLH gene family members establish a foundational resource for future investigations on the molecular mechanism involvement of bHLH genes in Asparagus.

PcMYB44 regulated host resistance to Botryosphaeria dothidea through activation of lignin biosynthesis and disease-resistance gene expression in pear

Pear ring rot disease, the pathogen of Botryosphaeria dothidea causes significant threat to the healthy development of the pear industry, therefore the exploration of disease-resistant gene resources is crucial for disease prevention and control. Members of the R2R3-MYB subfamily play important roles in regulating pathogen resistance in plants, however the gene function in regulating host resistance in pear remains unclear. In this study, the role of PcMYB44 were investigated in regulating host resistance disease in pear calli using both forward and reverse genetic approaches. Overexpression of PcMYB44 positively regulates the disease resistance, whereas knockout of PcMYB44 results in a phenotype with decreased resistance. Our results further demonstrated that PcMYB44 could directly affect lignin content and resistance to fungal diseases by regulating the PcmiR397-PcLACs module and lignin biosynthesis gene expression levels. Additionally, overexpressing PcMYB44 also elevated expression levels of key genes of JA/SA/ET pathway. The obtained results revealed that PcMYB44 regulated host resistance to ring rot disease through synergistic regulation the lignification and activating disease-resistance gene expression of JA/SA/ET defense pathways as a underlying secondary mechanism, which provide valuable genetic resources for molecular breeding for disease resistance.

PdGSTF1, PdGSTU3, and PdGSTU5 are essential for the accumulation of isosalipurposide and other pigments in peonies

Isosalipurposide (ISP) is a critical substance that gives peony its yellow phenotype; however, studies on its synthesis and transport in petals have not yet been conducted. During plant coloration, the transport of pigments is closely related to glutathione S-transferases (GSTs). To this end, we performed the metabolomic analysis of petals from three different developmental stages of Paeonia delavayi var. lutea and combined it with transcriptomic data to comprehensively characterize the GST gene family. We identified 42 GST genes from P. delavayi var. lutea through transcriptome data mining. Among these, the molecular docking results of PdGSTF1, PdGSTU3, and PdGSTU5 showed that they have the ability to bind multiple flavonoids. Virus-induced gene silencing (VIGS) experiments and overexpression experiments demonstrated that PdGSTF1, PdGSTU3, and PdGSTU5 can not only transport ISP but also transfer various pigments, including flavone glycosides, flavonol glycosides, and anthocyanin glycosides. Additionally, through yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays, PdMYB2 was identified as a protein interacting with PdGSTF1 and PdGSTU3, co-participating in the transport of flavonoids. Our research findings have elucidated the roles of key candidate PdGSTs in pigment transportation in P. delavayi var. lutea and uncovered their underlying molecular mechanisms.

MYB74 transcription factor guides de novo specification of epidermal cells in the abscission zone of Arabidopsis

The waxy cuticle layer is crucial for plant defence, growth and survival, and is produced by epidermal cells, which were thought to be specified only during embryogenesis. New surface cells are exposed during abscission, by which leaves, fruits, flowers and seeds are shed. Recent work has shown that nonepidermal residuum cells (RECs) can accumulate a protective cuticle layer after abscission, implying the potential de novo specification of epidermal cells by transdifferentiation. However, it remains unknown how this process occurs and what advantage this mechanism may offer over the other surface protection alternative, the wound healing pathways. Here we followed this transdifferentiation process with single-cell RNA sequencing analysis of RECs, showing that nonepidermal RECs transdifferentiate into epidermal cells through three distinct stages. During this vulnerable process, which involves a transient period when the protective layer is not yet formed, stress genes that protect the plant from environmental exposure are expressed before epidermis formation, ultimately facilitating cuticle development. We identify a central role for the transcription factor MYB74 in directing the transdifferentiation. In contrast to alternative protective mechanisms, our results suggest that de novo epidermal specification supports the subsequent growth of fruit at the abscission site. Altogether, we reveal a developmental programme by which plants use a transdifferentiation pathway to protect the plant while promoting growth.

SCPL48 regulates the vessel cell programmed cell death during xylem development in Arabidopsis thaliana

Secondary cell wall (SCW) deposition is tightly coordinated with programmed cell death (PCD) during xylem development and plays a crucial role in plant stress responses. In this study, we characterized a serine carboxypeptidase-like gene, SCPL48, which exhibits xylem cell-specific expression patterns in stem xylem during vascular development. The scpl48 plants exhibited reduced stem xylem cell numbers, particularly vessel cells, accompanied by delayed organelle degradation during PCD and increased secondary wall thickness in xylem vessel cells. In contrast, SCPL48 overexpression resulted in increased vessel cell abundance and accelerated degradation of vessel cell contents, suggesting its critical role in xylem vessel cell differentiation. Notably, SCPL48 expression was significantly up-regulated in response to ABA treatment and drought stress, with SCPL48 overexpression lines demonstrating enhanced drought resistance. Further molecular analyses revealed that SCPL48 was directly targeted and transcriptionally activated by key SCW regulators VND6, and MYB46. Furthermore, the expression of PCD-related protease genes, including XCP1, XSP1, RNS3, MC9, γVPE, and CEP1, showed compensatory changes in both scpl48 mutants and SCPL48 overexpression lines. Collectively, our findings demonstrate that SCPL48 functions as a key regulator in xylem vessel cell differentiation, PCD and drought stress responses.

Diverse roles of MYB transcription factors in plants

MYB transcription factors (TFs), one of the largest TF families in plants, are involved in various plant-specific processes as the central regulators, such as in phenylpropanoid metabolism, cell cycle, formation of root hair and trichome, phytohormones responses, reproductive growth and abiotic or biotic stress responses. Here we summarized multiple roles and explained the molecular mechanisms of MYB TFs in plant development and stress adaptation. The exploration of MYB TFs contributes to a better comprehension of molecular regulation in plant development and environmental adaptability.

CRISPR-Cas9-mediated deletions of FvMYB46 in Fragaria vesca reveal its role in regulation of fruit set and phenylpropanoid biosynthesis

The phenylpropanoid pathway, regulated by transcription factors of the MYB family, produces secondary metabolites that play important roles in fertilization and early phase of fruit development. The MYB46 transcription factor is a key regulator of secondary cell wall structure, lignin and flavonoid biosynthesis in many plants, but little is known about its activity in flowers and berries in F. vesca. For functional analysis of FvMYB46, we designed a CRISPR-Cas9 construct with an endogenous F. vesca-specific U6 promoter for efficient and specific expression of two gRNAs targeting the first exon of FvMYB46. This generated mutants with an in-frame 81-bp deletion of the first conserved MYB domain or an out-of-frame 82-bp deletion potentially knocking out gene function. In both types of mutant plants, pollen germination and fruit set were significantly reduced compared to wild type. Transcriptomic analysis of flowers revealed that FvMYB46 positively regulates the expression of genes involved in processes like xylan biosynthesis and metabolism, homeostasis of reactive oxygen species (ROS) and the phenylpropanoid pathway, including secondary cell wall biosynthesis and flavonoid biosynthesis. Genes regulating carbohydrate metabolism and signalling were also deregulated, suggesting that FvMYB46 might regulate the crosstalk between carbohydrate metabolism and phenylpropanoid biosynthesis. In the FvMYB46-mutant flowers, the flavanol and flavan-3-ol contents, especially epicatechin, quercetin-glucoside and kaempferol-3-coumaroylhexoside, were reduced, and we observed a local reduction in the lignin content in the anthers. Together, these results suggest that FvMYB46 controls fertility and efficient fruit set by regulating the cell wall structure, flavonoid biosynthesis, carbohydrate metabolism, and sugar and ROS signalling in flowers and early fruit development in F. vesca.

Mitigating Response of SlCSE06 Induced by 2-Ethylfuran to Botrytis cinerea Infection

Tomato (Solanum lycopersicum L.) is a major economic vegetable crop globally, yet it is prone to gray mold disease caused by Botrytis cinerea infection during cultivation. Caffeoyl shikimate esterase (CSE) is a crucial component of the lignin biosynthesis pathway, which significantly contributes to plant stress resistance. Therefore, investigating the expression patterns of SlCSE after Botrytis cinerea infection may offer a theoretical foundation for breeding resistant tomato varieties. In this study, 11 SlCSE family members were identified from the tomato genome using bioinformatics analyses. Public transcriptome databases and RT-qPCR experiments were used to analyze gene expression in tomato tissues, responses to Botrytis cinerea infection, and the temporal characteristics of the response to 2-ethylfuran treatment during infection. These experiments resulted in the identification of the key gene SlCSE06. Transgenic tomato lines that overexpressed SlCSE06 were constructed to examine their resistance levels to gray mold disease. Many SlCSE genes were upregulated when tomato fruit were infected with Botrytis cinerea during the ripening stage. Furthermore, 24 h after treatment with 2-ethylfuran, most SlCSE genes exhibited increased expression levels compared with the control group, but they exhibited significantly lower levels at other time points. Thus, 2-ethylfuran treatment may enhance the responsiveness of SlCSEs. Based on this research, SlCSE06 was identified as the key gene involved in the response to Botrytis cinerea infection. The SlCSE06-overexpressing (OE6) tomato plants exhibited a 197.94% increase in expression levels compared to the wild type (WT). Furthermore, the lignin content in OE6 was significantly higher than in WT, suggesting that the overexpression of SlCSE06 enhanced lignin formation in tomato plants. At 5 days post-inoculation with Botrytis cinerea, the lesion diameter in OE6 decreased by 31.88% relative to the WT, whereas the lignin content increased by 370.90%. Furthermore, the expression level of SlCSE06 was significantly upregulated, showing a 17.08-fold increase compared with the WT. These findings suggest that 2-ethylfuran enhances the activation of the critical tomato disease resistance gene SlCSE06 in response to gray mold stress, thereby promoting lignin deposition to mitigate further infection by Botrytis cinerea.

Insights into Molecular Mechanism of Secondary Xylem Rapid Growth in Salix psammophila

Salix psammophila C. Wang & C. Y. Yang is an important windbreak and sand-fixing shrub species in Northwest China, with excellent characteristics such as resistance to drought, wind, and sand. S. psammophila needs to be stubbed flat after several years of growth to continue to grow, otherwise, its growth rate will slow down and even begin to die. To understand the genetic regulatory mechanism of secondary growth in S. psammophila, cell structure and transcriptome analysis were performed on the secondary xylem and secondary phloem of stems. The results showed that the secondary xylem and the secondary phloem of S. psammophila were well developed at 1, 2, and 3-year-old stages, and the secondary growth changes mainly occurred in the secondary xylem at the 2 to 3-year-old stage, with a faster growth rate. The CSE2 and CSE1 genes that regulate CSE (caffeoyl shikimate esterase) have high sequence similarity (92% and 93%) with the CSE2 and CSE1 genes of the genus Populus, respectively, and regulate lignin biosynthesis. Notably, the expression levels of these two genes decreased in the secondary xylem of 3-year-old S. psammophila, indicating that the rapid growth of S. psammophila may be related to lignin biosynthesis. Weighted gene co-expression network analysis (WGCNA) was utilized to screen candidate TFs and genes involved in the secondary growth processes of S. psammophila, which were categorized into six co-expression modules. A total of 79 genes were selected from these co-expression modules, and co-expression network maps of the genes were constructed. The results indicate that the secondary growth of S. psammophila was regulated by a TF regulatory network. Interestingly, PLATZ TFs were involved in the rapid secondary growth and stress tolerance in S. psammophila. This hints that S. psammophila may promote secondary growth by increasing stress tolerance.

Transcriptomic analysis reveals potential roles of polyamine and proline metabolism in waterlogged peach roots inoculated with Funneliformis mosseae and Serendipita indica

Root-associated endophytic fungi can create symbiotic relationships with trees to enhance stress tolerance, but the underlying mechanisms, especially with regard to waterlogging tolerance, remain unclear. This study aimed to elucidate the effects of Funneliformis mosseae and Serendipita indica on the growth, root cross-section structure, and root transcriptional responses of peach under waterlogging stress, with a focus on polyamine and proline metabolism. Genes and transcription factors associated with secondary cell wall biosynthesis were selected, and their expression profiles were analyzed. Funneliformis mosseae significantly increased the height, stem diameter and leaf number of peach seedlings subjected to 2 weeks of waterlogging stress, whereas S. indica only significantly improved stem diameter. Both fungal species substantially increased root diameter, stele diameter, the number of late metaxylem inside the stele and late metaxylem diameter, thus improving aeration within inoculated roots under waterlogging stress. Transcriptomic analysis of waterlogged roots identified 5425 and 5646 differentially expressed genes following inoculation with F. mosseae and S. indica, respectively. The arginine and proline metabolism and arginine biosynthesis pathways were enriched following fungal inoculations. Both fungi reduced the conversion of glutamate and ornithine for proline synthesis. However, S. indica promoted peptide-to-proline conversion by up-regulating the expression of PIPs. Although both fungi promoted the expression of genes involved in arginine and ornithine synthesis pathway, only F. mosseae led to increased levels of arginine and ornithine. Additionally, F. mosseae promoted the accumulation of putrescine and maintained polyamine homeostasis by down-regulating PAO2 and SAMDC. Moreover, F. mosseae facilitated the metabolism of cadaverine. In conclusion, both F. mosseae and S. indica formed symbiotic relationships with peach plants, with F. mosseae primarily improving polyamine accumulation and S. indica predominantly facilitating proline accumulation for enhanced waterlogging resistance.

The DC1 domain protein Vacuoleless Gametophytes regulates stamen development in Arabidopsis

Vacuoleless Gametophytes (VLG) is a DC1 domain protein that was initially characterized as essential for early female and male gametophytes development in Arabidopsis. However, VLG expression was also detected in stamens, pistils and other sporophytic tissues, implying a broader role for this protein. As homozygous insertional VLG lines resulted unviable, we generated Arabidopsis amiRNA VLG knock-down plants to study the role of VLG in sporophyte development. The phenotypic characterization of VLG knock-down plants showed reduced seed set and indehiscent anthers with shorter filaments and stigma exsertion. Moreover, amiRNA VLG knock-down plants displayed unbroken stomia and septa, markedly reduced endothecium lignification, diminished ROS accumulation, and lower transcript levels of genes involved in jasmonic acid and lignin biosynthesis. The indehiscent phenotype was rescued by exogenous application of either jasmonic acid or H2O2. Altogether, our results suggest that VLG is involved in lignin and jasmonic acid biosynthesis pathways, and that proper levels of VLG are required in the process that leads to stomium breakage and anther dehiscence. Our findings shed light on the mechanisms underlying stamen development and provide new insights into the roles of a DC1 domain protein in plant reproduction.

MYB proteins: Versatile regulators of plant development, stress responses, and secondary metabolite biosynthetic pathways

MYB proteins are ubiquitous in nature, regulating key aspects of plant growth and development. Although MYB proteins are known for regulating genes involved in secondary metabolite biosynthesis, particularly phenylpropanoids, their roles in terpenoid, glucosinolate, and alkaloid biosynthesis remain less understood. This review explores the structural and functional differences between activator and repressor MYB proteins along with their roles in plant growth, development, stress responses, and secondary metabolite production. MYB proteins serve as central hubs in protein-protein interaction networks that regulate expression of numerous genes involved in the adaptation of plants to varying environmental conditions. Thus, we also highlight key interacting partners of MYB proteins and their roles in these adaptation mechanisms. We further discuss the mechanisms regulating MYB proteins, including autoregulation, epigenetics, and post-transcriptional and post-translational modifications. Overall, we propose MYB proteins as versatile regulators for improving plant traits, stress responses, and secondary metabolite production.

The miR172a-SNB module orchestrates both induced and adult-plant resistance to multiple diseases via MYB30-mediated lignin accumulation in rice

Plants mount induced resistance and adult-plant resistance against different pathogens throughout the whole growth period. Rice production faces threats from multiple major diseases, including rice blast, sheath blight, and bacterial leaf blight. Here, we report that the miR172a-SNB-MYB30 module regulates both induced and adult-plant resistance to these three major diseases via lignification in rice. Mechanistically, pathogen infections induce the expression of miR172a, which downregulates the transcription factor SNB to release its suppression of MYB30, leading to an increase in lignin biosynthesis and disease resistance throughout the whole growth period. Moreover, expression levels of miR172a and MYB30 gradually increase and are consistently correlated with lignin contents and disease resistance during rice development, reaching a peak at full maturity, whereas SNB RNA levels are negatively correlated with lignin contents and disease resistance, indicating the involvement of the miR172a-SNB-MYB30 module in adult-plant resistance. The functional domain of SNB protein and its binding sites in the MYB30 promoter are highly conserved among more than 4000 rice accessions, while abnormal expression of miR172a, SNB, or MYB30 compromises yield traits, suggesting artificial selection of the miR172a-SNB-MYB30 module during rice domestication. Taken together, these results reveal a novel role for a conserved miRNA-regulated module that contributes significantly to induced and adult-plant resistance against multiple pathogens by increasing lignin accumulation, deepening our understanding of broad-spectrum resistance and adult-plant resistance.

Transcription factor PdMYB118 in poplar regulates lignin deposition and xylem differentiation in addition to anthocyanin synthesis through suppressing the expression of PagKNAT2/6b gene

R2R3-MYB transcription factors function as the master regulators of the phenylpropanoid pathway in which both lignin and anthocyanin are produced. In poplar, R2R3-MYB transcription factor PdMYB118 positively regulates anthocyanin production to change leaf color. However, the molecular mechanism by which it controls different branches of the phenylpropanoid pathway still remains poorly understood. Here, we reported that in addition to anthocyanin synthesis, lignin deposition and xylem differentiation were regulated by PdMYB118 through inhibiting PagKNAT2/6b gene expression. The transgenic poplar plants overexpressing PdMYB118 accumulated more xylem, lignin and anthocyanin. Transcriptome and reverse transcription quantitative PCR analyses revealed that the expression of PagKNAT2/6b gene which inhibited lignin deposition and xylem differentiation was significantly down-regulated in transgenic poplar plants. Subsequent dual-luciferase reporter and yeast-one-hybrid assays demonstrated that PdMYB118 directly inhibited the transcription of PagKNAT2/6b by binding to the AC elements in its promoter region. Further experiments with transgenic poplar plants overexpressing PagKNAT2/6b demonstrated that overexpression of PagKNAT2/6b in the PdMYB118 overexpression background rescued lignin accumulation and xylem width to the same level of wild type plants. The findings in this work suggest that PdMYB118 is involved in the lignin deposition and xylem differentiation via modulating the expression of PagKNAT2/6b, and the PdMYB118- PagKNAT2/6b model can be used for the genetic breeding of new woody tree with high lignin production.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

PagHAM4a-PagSCL21 and PagHAM4b-PagTCP20 modules positively regulate cambial activity and its differentiation into secondary xylem in poplar

Stem secondary xylem produced by cambial division and differentiation is the main source of tree biomass. Secondary xylem formation involves a complex transcriptional regulatory network; however, the underlying mechanism is still being explored. Here, we report that PagHAM4a and PagHAM4b are positive regulators of cambial differentiation into secondary xylem in hybrid poplar (Populus alba × Populus glandulosa clone 84K). Overexpression of PagHAM4a and PagHAM4b enhanced cambial activity and increased the number of secondary xylem cells in the stems of poplar. By contrast, single or double mutations of PagHAM4a and PagHAM4b generated by CRISPR/Cas9 decreased cambial activity, leading to a significant reduction of secondary xylem. Neither overexpression nor mutation of the two genes affected the size of vessels and fibers in xylem. Both PagHAM4a- and PagHAM4b-regulated gene networks were mainly centered at the stage when cambium had just initiated secondary growth, but the molecular networks regulated by the two genes were distinct. Further analysis revealed that PagSCL21 and PagTCP20 are direct targets of PagHAM4a and PagHAM4b, respectively, and their overexpression also promoted cambial differentiation into secondary xylem. Taken together, we identified two novel key regulatory modules in poplar, PagHAM4a-PagSCL21 and PagHAM4b-PagTCP20, which provide new insights into the mechanism of secondary xylem formation in trees.

Lignin lite: Boosting plant power through selective downregulation

This article explores the dual benefits of reducing lignin content in plants, which streamlines biofuel production while maintaining robust defence mechanisms. It discusses how plants compensate for lower lignin levels through alternative defence strategies, recent biotechnological advances in lignin modification, and the implications for agriculture and industry.

Enhancing aphid resistance in horticultural crops: a breeding prospective

Increasing agricultural losses caused by insect infestations are a significant problem, so it is important to generate pest-resistant crop varieties to address this issue. Several reviews have examined aphid-plant interactions from an entomological perspective. However, few have specifically focused on plant resistance mechanisms to aphids and their applications in breeding for aphid resistance. In this review, we first outline the types of resistance to aphids in plants, namely antixenosis, tolerance (cell wall lignification, resistance proteins), and antibiosis, and we discuss strategies based on each of these resistance mechanisms to generate plant varieties with improved resistance. We then outline research on the complex interactions amongst plants, viruses, and aphids, and discuss how aspects of these interactions can be exploited to improve aphid resistance. A deeper understanding of the epigenetic mechanisms related to induced resistance, i.e. the phenomenon where plants become more resistant to a stress they have encountered previously, may allow for its exploitation in breeding for aphid resistance. Wild relatives of crop plants serve as important sources of resistance traits. Genes related to these traits can be introduced into cultivated crop varieties by breeding or genetic modification, and de novo domestication of wild varieties can be used to exploit multiple excellent characteristics, including aphid resistance. Finally, we discuss the use of molecular design breeding, genomic data, and gene editing to generate new aphid-resistant, high-quality crop varieties.

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.

Leveraging transcriptomics-based approaches to enhance genomic prediction: integrating SNPs and gene networks for cotton fibre quality improvement

Cultivated cotton plants are the world's largest source of natural fibre, where yield and quality are key traits for this renewable and biodegradable commodity. The Gossypium hirsutum cotton genome contains ~80K protein-coding genes, making precision breeding of complex traits a challenge. This study tested approaches to improving the genomic prediction (GP) accuracy of valuable cotton fibre traits to help accelerate precision breeding. With a biology-informed basis, a novel approach was tested for improving GP for key cotton fibre traits with transcriptomics of key time points during fibre development, namely, fibre cells undergoing primary, transition, and secondary wall development. Three test approaches included weighting of SNPs in DE genes overall, in target DE gene lists informed by gene annotation, and in a novel approach of gene co-expression network (GCN) clusters created with partial correlation and information theory (PCIT) as the prior information in GP models. The GCN clusters were nucleated with known genes for fibre biomechanics, i.e., fasciclin-like arabinogalactan proteins, and cluster size effects were evaluated. The most promising improvements in GP accuracy were achieved by using GCN clusters for cotton fibre elongation by 4.6%, and strength by 4.7%, where cluster sizes of two and three neighbours proved most effective. Furthermore, the improvements in GP were due to only a small number of SNPs, in the order of 30 per trait using the GCN cluster approach. Non-trait-specific biological time points, and genes, were found to have neutral effects, or even reduced GP accuracy for certain traits. As the GCN clusters were generated based on known genes for fibre biomechanics, additional candidate genes were identified for fibre elongation and strength. These results demonstrate that GCN clusters make a specific and unique contribution in improving the GP of cotton fibre traits. The findings also indicate that there is room for incorporating biology-based GCNs into GP models of genomic selection pipelines for cotton breeding to help improve precision breeding of target traits. The PCIT-GCN cluster approach may also hold potential application in other crops and trees for enhancing breeding of complex traits.

Lignin biosynthesis pathway repressors in gymnosperms: differential repressor domains as compared to angiosperms

Lignin is a polyphenolic polymer present in the cell walls of specialized plant cell types in vascular plants that provides structural support and plays a major role in plant protection. The lignin biosynthesis pathway is regulated by transcription factors from the MYB (myeloblastosis) family. While several MYB members positively regulate lignin synthesis, only a few negatively regulate lignin synthesis. These lignin suppressors are well characterized in model plant species; however, their role has not been fully explored in gymnosperms. Lignin forms one of the major hurdles for the forest-based industry e.g. paper, pulp, and biofuel production. Therefore, the detailed mechanisms involved in the regulation of lignin synthesis are valuable, especially in conifers that form the major source of softwood for timber and paper production. In this review, the potential and differential domains present in the MYB suppressors in gymnosperms are discussed, along with their phylogenetic analysis. Sequence analysis revealed that the N-terminal regions of the MYB suppressor members were found to be conserved among the gymnosperms and angiosperms containing the R2, R3, and bHLH domains, while the C-terminal regions were found to be highly variable. The typical repressor motifs like the LxLxL-type EAR motif and the TLLLFR motif were absent from the C-terminal regions of MYB suppressors from most gymnosperms. However, although the gymnosperms lacked the characteristic repressor domains, a R2R3-type MYB member from Ginkgo was reported to repress the lignin biosynthetic pathway. It is proposed that gymnosperms possess unique kinds of repressors that need further functional validation.

A Spatiotemporal Transcriptome Reveals Stalk Development in Pearl Millet

Pearl millet is a major cereal crop that feeds more than 90 million people worldwide in arid and semi-arid regions. The stalk phenotypes of Poaceous grasses are critical for their productivity and stress tolerance; however, the molecular mechanisms governing stalk development in pearl millet remain to be deciphered. In this study, we spatiotemporally measured 19 transcriptomes for stalk internodes of four different early developmental stages. Data analysis of the transcriptomes defined four developmental zones on the stalks and identified 12 specific gene sets with specific expression patterns across the zones. Using weighted gene co-expression network analysis (WGCNA), we found that two co-expression modules together with candidate genes were involved in stalk elongation and the thickening of pearl millet. Among the elongation-related candidate genes, we established by SELEX that a MYB-family transcription factor PMF7G02448 can bind to the promoters of three cell wall synthases genes (CesAs). In summary, these findings provide insights into stalk development and offer potential targets for future genetic improvement in pearl millet.

Mining Candidate Genes for Leaf Angle in Brassica napus L. by Combining QTL Mapping and RNA Sequencing Analysis

Leaf angle (LA) is an important trait of plant architecture, and individuals with narrow LA can better capture canopy light under high-density planting, which is beneficial for increasing the overall yield per unit area. To study the genetic basis and molecular regulation mechanism of leaf angle in rapeseed, we carried out a series of experiments. Quantitative trait loci (QTL) mapping was performed using the RIL population, and seven QTLs were identified. Transcriptome analysis showed that the cell wall formation/biogenesis processes and biosynthesis/metabolism of cell wall components were the most enrichment classes. Most differentially expressed genes (DEGs) involved in the synthesis of lignin, xylan, and cellulose showed down-regulated expression in narrow leaf material. Microscopic analysis suggested that the cell size affected by the cell wall in the junction area of the stem and petiole was the main factor in leaf petiole angle (LPA) differences. Combining QTL mapping and RNA sequencing, five promising candidate genes BnaA01G0125600ZS, BnaA01G0135700ZS, BnaA01G0154600ZS, BnaA10G0154200ZS, and BnaC03G0294200ZS were identified in rapeseed, and most of them were involved in cell wall biogenesis and the synthesis/metabolism of cell wall components. The results of QTL, transcriptome analysis, and cytological analysis were highly consistent, collectively revealing that genes related to cell wall function played a crucial role in regulating the LA trait in rapeseed. The study provides further insights into LA traits, and the discovery of new QTLs and candidate genes is highly beneficial for genetic improvement.

Stem lodging Resistance-1 controls stem strength by positively regulating the biosynthesis of cell wall components in Capsicum annuum L

Lodging presents a significant challenge in cultivating high-yield crops with extensive above-ground biomass, yet the molecular mechanisms underlying this phenomenon in the Solanaceae family remain largely unexplored. In this study, we identified a gene, CaSLR1 (Capsicum annuum Stem Lodging Resistance 1), which encodes a MYELOBLASTOSIS (MYB) family transcription factor, from a lodging-affected C. annuum EMS mutant. The suppression of CaSLR1 expression in pepper led to notable stem lodging, reduced thickness of the secondary cell wall, and decreased stem strength. A similar phenotype was observed in tomato with the knockdown of SlMYB61, the orthologous gene to CaSLR1. Further investigations demonstrated that CaNAC6, a gene involved in secondary cell wall (SCW) formation, is co-expressed with CaSLR1 and acts as a positive regulator of its expression, as confirmed through yeast one-hybrid, dual-luciferase reporter assays, and electrophoretic mobility shift assays. These findings elucidate the CaNAC6-CaSLR1 module that contributes to lodging resistance, emphasizing the critical role of CaSLR1 in the lodging resistance regulatory network.

The RALF2-FERONIA-MYB63 module orchestrates growth and defense in tomato roots

Plant secreted peptides RAPID ALKALINISATION FACTORs (RALFs), which act through the receptor FERONIA (FER), play important roles in plant growth. However, it remains unclear whether and how RALF-FER contributes to the trade-off of plant growth-defense. Here, we used a variety of techniques such as CRISPR/Cas9, protein-protein interaction and transcriptional regulation methods to investigate the role of RALF2 and its receptor FER in regulating lignin deposition, root growth, and defense against Fusarium oxysporum f. sp. lycopersici (Fol) in tomato (Solanum lycopersicum). The ralf2 and fer mutants show reduced primary root length, elevated lignin accumulation, and enhanced resistance against Fol than the wild-type. FER interacts with and phosphorylates MYB63 to promote its degradation. MYB63 serves as an activator of lignin deposition by regulating the transcription of dirigent protein gene DIR19. Mutation of DIR19 suppresses lignin accumulation, and reverses the short root phenotype and Fol resistance in ralf2 or fer mutant. Collectively, our results demonstrate that the RALF2-FER-MYB63 module fine-tunes root growth and resistance against Fol through regulating the deposition of lignin in tomato roots. The study sheds new light on how plants maintain the growth-defense balance via RALF-FER.

VdP5CDH is involved in melanin formation, stress resistance and play a regulatory role in virulence of Verticillium dahliae

Introduction

Verticillium dahliae, a soil-borne fungal pathogen, can cause cotton Verticillium wilt. In this study, VdP5CDH, the member of the ALDH_F4-17 family of carboxylate dehydrogenases, was identified in the genome of V. dahliae and investigated function in regulating virulence by generating gene deletion mutants and complementary mutants.

Methods

Homologous recombination method was used to construct mutants, transcriptome sequencing revealed gene-related metabolic pathways, and disease degree of cotton was observed through pathogen infection experiments.

Results

The conidial surface of VdP5CDH deletion strains was dented and shriveled, and the number of conidial spores increased. Compared with the wild-type (WT), the mycelial diameter of deletion mutants increased by 10.59%-11.16%, the mycelial growth showed irregular branching patterns, and misaligned arrangement. Although capable of penetrating cellophane, deletion mutants were unable to produce melanin. VdP5CDH was mainly associated with glucose metabolism, nitrogen metabolism, ABC transporter activity as well as various amino acid metabolic processes. After gene knockout, raffinose and pectin were used as the main carbon sources to promote the growth of strains and the growth rate of deletion strains in the medium containing raffinose was higher than that of WT. Consequently, the deletion mutant strains decreased utilization efficiency with which they utilized various nitrogen sources. The deletion mutants maintain responsiveness to osmotic stress and oxidative stress stimuli. Additionally, compared to WT strains, the deletion mutant strains exhibited differences in culture temperature tolerance, UV exposure response, and fungicide sensitivity. After cotton was infected with deletion strains conidial suspension, its disease index increased dramatically, while it gradually decreased after spraying with 2 mM glutamate in batches. With the increase of spraying times, the effect was more significant, and the disease index decreased by 18.95%-19.66% at 26 dpi.

Discussion

These results indicated that VdP5CDH regulates the pathogenicity of fungi and controls mycelia growth, melanin formation, conidia morphology, abiotic stress resistance, and the expression of infecting structure-related genes.

Expression profile analysis of cotton fiber secondary cell wall thickening stage

To determine the genes associated with the fiber strength trait in cotton, three different cotton cultivars were selected: Sea Island cotton (Xinhai 32, with hyper-long fibers labeled as HL), and upland cotton (17-24, with long fibers labeled as L, and 62-33, with short fibers labeled as S). These cultivars were chosen to assess fiber samples with varying qualities. RNA-seq technology was used to analyze the expression profiles of cotton fibers at the secondary cell wall (SCW) thickening stage (20, 25, and 30 days post-anthesis (DPA)). The results showed that a large number of differentially expressed genes (DEGs) were obtained from the three assessed cotton cultivars at different stages of SCW development. For instance, at 20 DPA, Sea Island cotton (HL) had 6,215 and 5,364 DEGs compared to upland cotton 17-24 (L) and 62-33 (S), respectively. Meanwhile, there were 1,236 DEGs between two upland cotton cultivars, 17-24 (L) and 62-33 (S). Gene Ontology (GO) term enrichment identified 42 functions, including 20 biological processes, 11 cellular components, and 11 molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified several pathways involved in SCW synthesis and thickening, such as glycolysis/gluconeogenesis, galactose metabolism, propanoate metabolism, biosynthesis of unsaturated fatty acids pathway, valine, leucine and isoleucine degradation, fatty acid elongation pathways, and plant hormone signal transduction. Through the identification of shared DEGs, 46 DEGs were found to exhibit considerable expressional differences at different fiber stages from the three cotton cultivars. These shared DEGs have functions including REDOX enzymes, binding proteins, hydrolases (such as GDSL thioesterase), transferases, metalloproteins (cytochromatin-like genes), kinases, carbohydrates, and transcription factors (MYB and WRKY). Therefore, RT-qPCR was performed to verify the expression levels of nine of the 46 identified DEGs, an approach which demonstrated the reliability of RNA-seq data. Our results provided valuable molecular resources for clarifying the cell biology of SCW biosynthesis during fiber development in cotton.

Xylem cell size regulation is a key adaptive response to water deficit in Eucalyptus grandis

Future climatic scenarios forecast increasingly frequent droughts that will pose substantial consequences on tree mortality. In light of this, drought-tolerant eucalypts have been propagated; however, the severity of these conditions will invoke adaptive responses, impacting the commercially valuable wood properties. To determine what mechanisms govern the wood anatomical adaptive response, highly controlled drought experiments were conducted in Eucalyptus grandis W. Hill ex Maiden, with the tree physiology and transcriptome closely monitored. In response to water deficit, E. grandis displays an isohydric stomatal response to conserve water and enable stem growth to continue, albeit at a reduced rate. Maintaining gaseous exchange is likely a critical short-term response that drives the formation of hydraulically safer xylem. For instance, the development of significantly smaller fibers and vessels was found to increase cellular density, thereby promoting drought tolerance through improved functional redundancy, as well as implosion and cavitation resistance. The transcriptome was explored to identify the molecular mechanisms responsible for controlling xylem cell size during prolonged water deficit. Downregulation of genes associated with cell wall remodeling and the biosynthesis of cellulose, hemicellulose and pectin appeared to coincide with a reduction in cellular enlargement during drought. Furthermore, transcript levels of NAC and MYB transcription factors, vital for cell wall component biosynthesis, were reduced, while those linked to lignification increased. The upregulation of EgCAD and various peroxidases under water deficit did not correlate with an increased lignin composition. However, with the elevated cellular density, a higher lignin content per xylem cross-sectional area was observed, potentially enhancing hydraulic safety. These results support the requirement for higher density, drought-adapted wood as a long-term adaptive response in E. grandis, which is largely influenced by the isohydric stomatal response coupled with cellular expansion-related molecular processes.

Lysine 2-hydroxyisobutyrylation proteomics analyses reveal the regulatory mechanism of CaMYB61-CaAFR1 module in regulating stem development in Capsicum annuum L

Plant stems constitute the most abundant renewable resource on earth. The function of lysine (K)-2-hydroxyisobutyrylation (Khib), a novel post-translational modification (PTM), has not yet been elucidated in plant stem development. Here, by assessing typical pepper genotypes with straight stem (SS) and prostrate stem (PS), we report the first large-scale proteomics analysis for protein Khib to date. Khib-modifications influenced central metabolic processes involved in stem development, such as glycolysis/gluconeogenesis and protein translation. The high Khib level regulated gene expression and protein accumulation associated with cell wall formation in the pepper stem. Specially, we found that CaMYB61 knockdown lines that exhibited prostrate stem phenotypes had high Khib levels. Most histone deacetylases (HDACs, e.g., switch-independent 3 associated polypeptide function related 1, AFR1) potentially function as the "erasing enzymes" involved in reversing Khib level. CaMYB61 positively regulated CaAFR1 expression to erase Khib and promote cellulose and hemicellulose accumulation in the stem. Therefore, we propose a bidirectional regulation hypothesis of "Khib modifications" and "Khib erasing" in stem development, and reveal a novel epigenetic regulatory network in which the CaMYB61-CaAFR1 molecular module participating in the regulation of Khib levels and biosynthesis of cellulose and hemicellulose for the first time.

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.

Cloning and functional mechanism of the dwarf gene gba affecting stem elongation and cellulose biosynthesis in jute (Corchorus olitorius)

Plant height (PH) is an important factor affecting bast fiber yield in jute. Here, we report the mechanism of dwarfism in the 'Guangbaai' (gba) of jute. The mutant gba had shorter internode length and cell length compared to the standard cultivar 'TaiZi 4' (TZ4). Exogenous GA3 treatment indicated that gba is a GA-insensitive dwarf mutant. Quantitative trait locus (QTL) analysis of three PH-related traits via a high-density genetic linkage map according to re-seq showed that a total of 25 QTLs were identified, including 13 QTLs for PH, with phenotypic variation explained ranging from 2.42 to 74.16%. Notably, the functional mechanism of the candidate gene CoGID1a, the gibberellic acid receptor, of the major locus qPHIL5 was evaluated by transgenic analysis and virus-induced gene silencing. A dwarf phenotype-related single nucleotide mutation in CoGID1a was identified in gba, which was also unique to the dwarf phenotype of gba among 57 cultivars. Cogid1a was unable to interact with the growth-repressor DELLA even in the presence of highly accumulated gibberellins in gba. Differentially expressed genes between transcriptomes of gba and TZ4 after GA3 treatment indicated up-regulation of genes involved in gibberellin and cellulose synthesis in gba. Interestingly, it was found that up-regulation of CoMYB46, a key transcription factor in the secondary cell wall, by the highly accumulated gibberellins in gba promoted the expression of cellulose synthase genes CoCesA4 and CoCesA7. These findings provide valuable insights into fiber development affected by endogenous gibberellin accumulation in plants.

Modifying lignin: A promising strategy for plant disease control

Lignin is a complex polymer found in the cell walls of plants, providing structural support and protection against pathogens. By modifying lignin composition and structure, scientists aim to optimize plant defense responses and increase resistance to pathogens. This can be achieved through various genetic engineering techniques which involve manipulating the genes responsible for lignin synthesis. By either up regulating or down regulating specific genes, researchers can alter the lignin content, composition, or distribution in plant tissues. Reducing lignin content in specific tissues like leaves can improve the effectiveness of defense mechanisms by allowing for better penetration of antimicrobial compounds. Overall, Lignin modification through techniques has shown promising results in enhancing various plants resistance against pathogens. Furthermore, lignin modification can have additional benefits beyond pathogen resistance. It can improve biomass processing for biofuel production by reducing lignin recalcitrance, making the extraction of sugars from cellulose more efficient. The complexity of lignin biosynthesis and its interactions with other plant components make it a challenging target for modification. Additionally, the potential environmental impact and regulatory considerations associated with genetically modified organisms (GMOs) require careful evaluation. Ongoing research aims to further optimize this approach and develop sustainable solutions for crop protection.

GhMYB52 Like: A Key Factor That Enhances Lint Yield by Negatively Regulating the Lignin Biosynthesis Pathway in Fibers of Upland Cotton (Gossypium hirsutum L.)

In the context of sustainable agriculture and biomaterial development, understanding and enhancing plant secondary cell wall formation are crucial for improving crop fiber quality and biomass conversion efficiency. This is especially critical for economically important crops like upland cotton (Gossypium hirsutum L.), for which fiber quality and its processing properties are essential. Through comprehensive genome-wide screening and analysis of expression patterns, we identified a particularly high expression of an R2R3 MYB transcription factor, GhMYB52 Like, in the development of the secondary cell wall in cotton fiber cells. Utilizing gene-editing technology to generate a loss-of-function mutant to clarify the role of GhMYB52 Like, we revealed that GhMYB52 Like does not directly contribute to cellulose synthesis in cotton fibers but instead represses a subset of lignin biosynthesis genes, establishing it as a lignin biosynthesis inhibitor. Concurrently, a substantial decrease in the lint index, a critical measure of cotton yield, was noted in parallel with an elevation in lignin levels. This study not only deepens our understanding of the molecular mechanisms underlying cotton fiber development but also offers new perspectives for the molecular improvement of other economically important crops and the enhancement of biomass energy utilization.

CsREV-CsTCP4-CsVND7 module shapes xylem patterns differentially between stem and leaf to enhance tea plant tolerance to drought

Cultivating drought-tolerant tea varieties enhances both yield and quality of tea plants in northern China. However, the mechanisms underlying their drought tolerance remain largely unknown. Here we identified a key regulator called CsREV, which differentially regulates xylem patterns between leaves and stems, thereby conferring drought tolerance in tea plants. When drought occurs, upregulation of CsREV activates the CsVND7a-dependent xylem vessel differentiation. However, when drought persists, the vessel differentiation is hindered as CsVND7a is downregulated by CsTCP4a. This, combined with the CsREV-promoted secondary-cell-wall thickness of xylem vessel, leads to the enhanced curling of leaves, a characteristic closely associated with plant drought tolerance. Notably, this inhibitory effect of CsTCP4a on CsVND7a expression is absent in stems, allowing stem xylem vessels to continuously differentiate. Overall, the CsREV-CsTCP4-CsVND7 module is differentially utilized to shape the xylem patterns in leaves and stems, potentially balancing water transportation and utilization to improve tea plant drought tolerance.

Strong culm: a crucial trait for developing next-generation climate-resilient rice lines

Lodging, a phenomenon characterized by the bending or breaking of rice plants, poses substantial constraints on productivity, particularly during the harvesting phase in regions susceptible to strong winds. The rice strong culm trait is influenced by the intricate interplay of genetic, physiological, epigenetic, and environmental factors. Stem architecture, encompassing morphological and anatomical attributes, alongside the composition of both structural and non-structural carbohydrates, emerges as a critical determinant of lodging resistance. The adaptive response of the rice culm to various biotic and abiotic environmental factors further modulates the propensity for lodging. Advancements in next-generation sequencing technologies have expedited the genetic dissection of lodging resistance, enabling the identification of pertinent genes, quantitative trait loci, and novel alleles. Concurrently, contemporary breeding strategies, ranging from biparental approaches to more sophisticated methods such as multi-parent-based breeding, gene pyramiding, genomic selection, genome-wide association studies, and haplotype-based breeding, offer perspectives on the genetic underpinnings of culm strength. This review comprehensively delves into physiological attributes, culm histology, epigenetic determinants, and gene expression profiles associated with lodging resistance, with a specialized focus on leveraging next-generation sequencing for candidate gene discovery.

Comparative transcriptional analysis of Persea americana MYB, WRKY and AP2/ERF transcription factors following Phytophthora cinnamomi infection

Plant cells undergo extensive transcriptional reprogramming following pathogen infection, with these reprogramming patterns becoming more complex when pathogens, such as hemibiotrophs, exhibit different lifestyles. These transcriptional changes are often orchestrated by MYB, WRKY and AP2/ERF transcription factors (TFs), which modulate both growth and defence-related gene expression. Transcriptional analysis of defence-related genes in avocado (Persea americana) infected with Phytophthora cinnamomi indicated differential immune response activation when comparing a partially resistant and susceptible rootstock. This study identified 226 MYB, 82 WRKY, and 174 AP2/ERF TF-encoding genes in avocado, using a genome-wide approach. Phylogenetic analysis revealed substantial sequence conservation within TF groups underscoring their functional significance. RNA-sequencing analysis in a partially resistant and susceptible avocado rootstock infected with P. cinnamomi was indicative of an immune response switch occurring in either rootstock after 24 and 6 h post-inoculation, respectively. Different clusters of co-expressed TF genes were observed at these times, suggesting the activation of necrotroph-related immune responses at varying intervals between the two rootstocks. This study aids our understanding of avocado immune response activation following P. cinnamomi infection, and the role of the TFs therein, elucidating the transcriptional reprogramming disparities between partially resistant and susceptible rootstocks.

Comparative transcriptome analysis reveals the adaptive mechanisms of halophyte Suaeda dendroides encountering high saline environment

Suaeda dendroides, a succulent euhalophyte of the Chenopodiaceae family, intermittently spread around northern Xinjiang, China, has the ability to grow and develop in saline and alkali environments. The objective of this study was therefore to investigate the underlying molecular mechanisms of S. dendroides response to high salt conditions. 27 sequencing libraries prepared from low salt (200 mM NaCl) and high salt (800 mM NaCl) treated plants at 5 different stages were sequenced using Illumina Hiseq 2000. A total of 133,107 unigenes were obtained, of which 4,758 were DEGs. The number of DEGs in the high salt group (3,189) was more than the low salt treatment group (733) compared with the control. GO and KEGG analysis of the DEGs at different time points of the high salt treatment group showed that the genes related to cell wall biosynthesis and modification, plant hormone signal transduction, ion homeostasis, organic osmolyte accumulation, and reactive oxygen species (ROS) detoxification were significantly expressed, which indicated that these could be the main mechanisms of S. dendroides acclimate to high salt stress. The study provides a new perspective for understanding the molecular mechanisms of halophytes adapting to high salinity. It also provides a basis for future investigations of key salt-responsive genes in S. dendroides.

Deciphering the intricate hierarchical gene regulatory network: unraveling multi-level regulation and modifications driving secondary cell wall formation

Wood quality is predominantly determined by the amount and the composition of secondary cell walls (SCWs). Consequently, unraveling the molecular regulatory mechanisms governing SCW formation is of paramount importance for genetic engineering aimed at enhancing wood properties. Although SCW formation is known to be governed by a hierarchical gene regulatory network (HGRN), our understanding of how a HGRN operates and regulates the formation of heterogeneous SCWs for plant development and adaption to ever-changing environment remains limited. In this review, we examined the HGRNs governing SCW formation and highlighted the significant key differences between herbaceous Arabidopsis and woody plant poplar. We clarified many confusions in existing literatures regarding the HGRNs and their orthologous gene names and functions. Additionally, we revealed many network motifs including feed-forward loops, feed-back loops, and negative and positive autoregulation in the HGRNs. We also conducted a thorough review of post-transcriptional and post-translational aspects, protein-protein interactions, and epigenetic modifications of the HGRNs. Furthermore, we summarized how the HGRNs respond to environmental factors and cues, influencing SCW biosynthesis through regulatory cascades, including many regulatory chains, wiring regulations, and network motifs. Finally, we highlighted the future research directions for gaining a further understanding of molecular regulatory mechanisms underlying SCW formation.

Trees need closure too: Wound-induced secondary vascular tissue regeneration

Trees play a pivotal role in terrestrial ecosystems as well as being an important natural resource. These attributes are primarily associated with the capacity of trees to continuously produce woody tissue from the vascular cambium, a ring of stem cells located just beneath the bark. Long-lived trees are exposed to a myriad of biological and environmental stresses that may result in wounding, leading to a loss of bark and the underlying vascular cambium. This affects both wood formation and the quality of timber arising from the tree. In addition, the exposed wound site is a potential entry point for pathogens that cause disease. In response to wounding, trees have the capacity to regenerate lost or damaged tissues at this site. Investigating gene expression changes associated with different stages of wound healing reveals complex and dynamic changes in the activity of transcription factors, signalling pathways and hormone responses. In this review we summarise these data and discuss how they relate to our current understanding of vascular cambium formation and xylem differentiation during secondary growth. Based on this analysis, a model for wound healing that provides the conceptual foundations for future studies aimed at understanding this intriguing process is proposed.

Jasmonate activates secondary cell wall biosynthesis through MYC2-MYB46 module

Formation of secondary cell wall (SCW) is tightly regulated spatiotemporally by various developmental and environmental signals. Successful fine-tuning of the trade-off between SCW biosynthesis and stress responses requires a better understanding of how plant growth is regulated under environmental stress conditions. However, the current understanding of the interplay between environmental signaling and SCW formation is limited. The lipid-derived plant hormone jasmonate (JA) and its derivatives are important signaling components involved in various physiological processes including plant growth, development, and abiotic/biotic stress responses. Recent studies suggest that JA is involved in SCW formation but the signaling pathway has not been studied for how JA regulates SCW formation. We tested this hypothesis using the transcription factor MYB46, a master switch for SCW biosynthesis, and JA treatments. Both the transcript and protein levels of MYB46, a master switch for SCW formation, were significantly increased by JA treatment, resulting in the upregulation of SCW biosynthesis. We then show that this JA-induced upregulation of MYB46 is mediated by MYC2, a central regulator of JA signaling, which binds to the promoter of MYB46. We conclude that this MYC2-MYB46 module is a key component of the plant response to JA in SCW formation.

PtoMYB031, the R2R3 MYB transcription factor involved in secondary cell wall biosynthesis in poplar

Introduction

The biosynthesis of the secondary cell wall (SCW) is orchestrated by an intricate hierarchical transcriptional regulatory network. This network is initiated by first-layer master switches, SCW-NAC transcription factors, which in turn activate the second-layer master switches MYBs. These switches play a crucial role in regulating xylem specification and differentiation during SCW formation. However, the roles of most MYBs in woody plants are yet to be fully understood.

Methods

In this study, we identified and isolated the R2R3-MYB transcription factor, PtoMYB031, from Populus tomentosa. We explored its expression, mainly in xylem tissues, and its role as a transcriptional repressor in the nucleus. We used overexpression and RNA interference techniques in poplar, along with Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays, to analyze the regulatory effects of PtoMYB031.

Results

Overexpression of PtoMYB031 in poplar significantly reduced lignin, cellulose, and hemicellulose content, and inhibited vascular development in stems, resulting in decreased SCW thickness in xylem tissues. Gene expression analysis showed that structural genes involved in SCW biosynthesis were downregulated in PtoMYB031-OE lines. Conversely, RNA interference of PtoMYB031 increased these compounds. Additionally, PtoMYB031 was found to recruit the repressor PtoZAT11, forming a transcriptional inhibition complex.

Discussion

Our findings provide new insights into how PtoMYB031, through its interaction with PtoZAT11, forms a complex that can suppress the expression of key regulatory genes, PtoWND1A and PtoWND2B, in SCW biosynthesis. This study enhances our understanding of the transcriptional regulation involved in SCW formation in poplar, highlighting the significant role of PtoMYB031.

Characterization key genes of Arabidopsis seedlings in response to β-caryophyllene, eugenol using combined transcriptome and WGCN analysis

Weeds present a significant challenge to high crop yield and quality. In our study, we investigated the phytotoxic activity of β-caryophyllene (BCP) and eugenol, which are natural allelopathic chemical compounds, on Arabidopsis seedlings. We found that these compounds inhibited the growth of Arabidopsis thaliana plants. When either BCP or eugenol was applied, it led to decrease in the content of cell wall components such as lignin, cellulose, hemicellulose, and pectin; and increase in the levels of endogenous hormones like ETH, ABA, SA, and JA in the seedlings. Through transcriptome profiling, we identified 7181 differentially expressed genes (DEGs) in the roots and shoots that were induced by BCP or eugenol. The genes involved in the synthesis of lignin, cellulose, hemicellulose, and pectin were down-regulated, whereas genes related to synthesis and signal transduction of ABA, ETH, SA, and JA were up-regulated. However, genes related to IAA synthesis and signal transduction were found to be down-regulated. Furthermore, we characterized 24 hub genes using Weighted Correlation Network Analysis (WGCNA). Among them, the identified 16 genes in response to BCP was primarily associated with hypoxia stress, while 8 genes induced by eugenol were linked to inhibition of cell division. Our results suggested that BCP and eugenol had ability to target multiple genes to inhibit growth and development of Arabidopsis plants. Therefore, they can serve as excellent candidates for natural biological herbicides.

Integrated Comparative Transcriptome and Weighted Gene Co-Expression Network Analysis Provide Valuable Insights into the Mechanisms of Pinhead Initiation in Chinese Caterpillar Mushroom Ophiocordyceps sinensis (Ascomycota)

The initiation and formation of the "pinhead" is the key node in growth process of Ophiocordyceps sinensis (Chinese Cordyceps). The research on the mechanism of changes in this growth stage is the basis for realizing the industrialization of its artificial cultivation. Clarifying the mechanisms of pinhead initiation is essential for its further application. Here, we performed a comprehensive transcriptome analysis of pinhead initiation process in O. sinensis. Comparative transcriptome analysis revealed remarkable variation in gene expression and enriched pathways at different pinhead initiation stages. Gene co-expression network analysis by WGCNA identified 4 modules highly relevant to different pinhead initiation stages, and 23 hub genes. The biological function analysis and hub gene annotation of these identified modules demonstrated that transmembrane transport and nucleotide excision repair were the topmost enriched in pre-pinhead initiation stage, carbohydrate metabolism and protein glycosylation were specially enriched in pinhead initiation stage, nucleotide binding and DNA metabolic process were over-represented after pinhead stage. These key regulators are mainly involved in carbohydrate metabolism, synthesis of proteins and nucleic acids. This work excavated the candidate pathways and hub genes related to the pinhead initiation stage, which will serve as a reference for realizing the industrialization of artificial cultivation in O. sinensis.

Comparative analysis of the carrot miRNAome in response to salt stress

Soil salinity adversely affects the yield and quality of crops, including carrot. During salt stress, plant growth and development are impaired by restricted water uptake and ion cytotoxicity, leading to nutrient imbalance and oxidative burst. However, the molecular mechanisms of the carrot plant response to salt stress remain unclear. The occurrence and expression of miRNAs that are potentially involved in the regulation of carrot tolerance to salinity stress were investigated. The results of small RNA sequencing revealed that salt-sensitive (DH1) and salt-tolerant (DLBA) carrot varieties had different miRNA expression profiles. A total of 95 miRNAs were identified, including 71 novel miRNAs, of which 30 and 23 were unique to DH1 and DLBA, respectively. The comparison of NGS and qPCR results allowed identification of two conserved and five novel miRNA involved in carrot response to salt stress, and which differentiated the salt-tolerant and salt-sensitive varieties. Degradome analysis supported by in silico-based predictions and followed by expression analysis of exemplary target genes pointed at genes related to proline, glutathione, and glutamate metabolism pathways as potential miRNA targets involved in salt tolerance, and indicated that the regulation of osmoprotection and antioxidant protection, earlier identified as being more efficient in the tolerant variety, may be controlled by miRNAs. Furthermore, potential miRNA target genes involved in chloroplast protection, signal transduction and the synthesis and modification of cell wall components were indicated in plants growing in saline soil.

The Characterization of R2R3-MYB Genes in Ammopiptanthus nanus Uncovers That the miR858-AnaMYB87 Module Mediates the Accumulation of Anthocyanin under Osmotic Stress

R2R3-MYB transcription factors (TFs) participate in the modulation of plant development, secondary metabolism, and responses to environmental stresses. Ammopiptanthus nanus, a leguminous dryland shrub, tolerates a high degree of environmental stress, including drought and low-temperature stress. The systematic identification, structural analysis, evolutionary analysis, and gene profiling of R2R3-MYB TFs under cold and osmotic stress in A. nanus were performed. Up to 137 R2R3-MYB TFs were identified and clustered into nine clades, with most A. nanus R2R3-MYB members belonging to clade VIII. Tandem and segmental duplication events drove the expansion of the A. nanus R2R3-MYB family. Expression profiling revealed that multiple R2R3-MYB genes significantly changed under osmotic and cold stress conditions. MiR858 and miR159 targeted 88 R2R3-MYB genes. AnaMYB87, an miR858-targeted clade VIII R2R3-MYB TF, was up-regulated under both osmotic and cold stress. A transient expression assay in apples showed that the overexpression of AnaMYB87 promoted anthocyanin accumulation. A luciferase reporter assay in tobacco demonstrated that AnaMYB87 positively affected the transactivation of the dihydroflavonol reductase gene, indicating that the miR858-MYB87 module mediates anthocyanin accumulation under osmotic stress by regulating the dihydroflavonol reductase gene in A. nanus. This study provides new data to understand the roles of R2R3-MYB in plant stress responses.

Transcriptome and miRNAs Profiles Reveal Regulatory Network and Key Regulators of Secondary Xylem Formation in "84K" Poplar

Secondary xylem produced by stem secondary growth is the main source of tree biomass and possesses great economic and ecological value in papermaking, construction, biofuels, and the global carbon cycle. The secondary xylem formation is a complex developmental process, and the underlying regulatory networks and potential mechanisms are still under exploration. In this study, using hybrid poplar (Populus alba × Populus glandulosa clone 84K) as a model system, we first ascertained three representative stages of stem secondary growth and then investigated the regulatory network of secondary xylem formation by joint analysis of transcriptome and miRNAs. Notably, 7507 differentially expressed genes (DEGs) and 55 differentially expressed miRNAs (DEMs) were identified from stage 1 without initiating secondary growth to stage 2 with just initiating secondary growth, which was much more than those identified from stage 2 to stage 3 with obvious secondary growth. DEGs encoding transcription factors and lignin biosynthetic enzymes and those associated with plant hormones were found to participate in the secondary xylem formation. MiRNA-target analysis revealed that a total of 85 DEMs were predicted to have 2948 putative targets. Among them, PagmiR396d-PagGRFs, PagmiR395c-PagGA2ox1/PagLHW/PagSULTR2/PagPolyubiquitin 1, PagmiR482d-PagLAC4, PagmiR167e-PagbHLH62, and PagmiR167f/g/h-PagbHLH110 modules were involved in the regulating cambial activity and its differentiation into secondary xylem, cell expansion, secondary cell wall deposition, and programmed cell death. Our results give new insights into the regulatory network and mechanism of secondary xylem formation.

Transcriptional Landscape of Cotton Roots in Response to Salt Stress at Single-cell Resolution

Increasing soil salinization has led to severe losses of plant yield and quality. Thus, it is urgent to investigate the molecular mechanism of the salt stress response. In this study, we took systematically analyzed cotton root response to salt stress by single-cell transcriptomics technology; 56,281 high-quality cells were totally obtained from 5-days-old lateral root tips of Gossypium arboreum under natural growth and different salt-treatment conditions. Ten cell types with an array of novel marker genes were synthetically identified and confirmed with in situ RNA hybridization, and some specific-type cells of pesudotime analysis also pointed out their potential differentiation trajectory. The prominent changes of cell numbers responding to salt stress were observed on outer epidermal and inner endodermic cells, which were significantly enriched in response to stress, amide biosynthetic process, glutathione metabolism, and glycolysis/gluconeogenesis. Other functional aggregations were concentrated on plant-type primary cell wall biogenesis, defense response, phenylpropanoid biosynthesis and metabolic pathways by analyzing the abundant differentially expressed genes (DEGs) identified from multiple comparisons. Some candidate DEGs related with transcription factors and plant hormones responding to salt stress were also identified, of which the function of Ga03G2153, an annotated auxin-responsive GH3.6, was confirmed by using virus-induced gene silencing (VIGS). The GaGH3.6-silenced plants presented severe stress-susceptive phenotype, and suffered more serious oxidative damages by detecting some physiological and biochemical indexes, indicating that GaGH3.6 might participate in salt tolerance in cotton through regulating oxidation-reduction process. For the first time, a transcriptional atlas of cotton roots under salt stress were characterized at a single-cell resolution, which explored the cellular heterogeneityand differentiation trajectory, providing valuable insights into the molecular mechanism underlying stress tolerance in plants.

Genes expression profiles in vascular cambium of Eucalyptus urophylla × Eucalyptus grandis at different ages

BACKGROUND

Wood is a secondary xylem generated by vascular cambium. Vascular cambium activities mainly include cambium proliferation and vascular tissue formation through secondary growth, thereby producing new secondary phloem inward and secondary xylem outward and leading to continuous tree thickening and wood formation. Wood formation is a complex biological process, which is strictly regulated by multiple genes. Therefore, molecular level research on the vascular cambium of different tree ages can lead to the identification of both key and related genes involved in wood formation and further explain the molecular regulation mechanism of wood formation.

RESULTS

In the present study, RNA-Seq and Pac-Bio Iso-Seq were used for profiling gene expression changes in Eucalyptus urophylla × Eucalyptus grandis (E. urograndis) vascular cambium at four different ages. A total of 59,770 non-redundant transcripts and 1892 differentially expressed genes (DEGs) were identified. The expression trends of the DEGs related to cell division and differentiation, cell wall biosynthesis, phytohormone, and transcription factors were analyzed. The DEGs encoding expansin, kinesin, cycline, PAL, GRP9, KNOX, C2C2-dof, REV, etc., were highly expressed in E. urograndis at three years old, leading to positive effects on growth and development. Moreover, some gene family members, such as NAC, MYB, HD-ZIP III, RPK, and RAP, play different regulatory roles in wood formation because of their sophisticated transcriptional network and function redundantly.

CONCLUSIONS

These candidate genes are a potential resource to further study wood formation, especially in fast-growing and adaptable eucalyptus. The results may also serve as a basis for further research to unravel the molecular mechanism underlying wood formation.

Anatomical and Transcriptome Analyses of Moso Bamboo Culm Neck Growth: Unveiling Key Insights

The Moso bamboo culm neck, connected with the rhizome and the shoot bud, is an important hub for connecting and transporting the aboveground and belowground systems of bamboo for the shoot bud development and rapid growth. Our previous study revealed that the culm neck generally undergoes six different developmental stages (CNS1-CNS6), according to the primary thickening growth of the underground shoot bud. However, the molecular mechanism of the culm neck development remains unknown. The present study focused on the developmental process of the CNS3-CNS5 stages, representing the early, middle, and late elongation stages, respectively. These stages are densely packed with vascular tissues and consist of epidermis, hypodermis, cortex, and ground tissue. Unlike the hollow structure of the culms, the culm necks are solid structures. As the culm neck continues to grow, the lignin deposition increases noticeably, contributing to its progressive strengthening. For the transcriptome analysis, a total of 161,160 transcripts with an average length of 2373 were obtained from these stages using both PacBio and Illumina sequencing. A total of 92.2% of the reads mapped to the Moso bamboo reference genome. Further analysis identified a total of 5524 novel genes and revealed a dynamic transcriptome. Secondary-metabolism- and transport-related genes were upregulated particularly with the growth of the culm neck. Further analysis revealed the molecular processes of lignin accumulation in the culm neck, which include differentially expressed genes (DEGs) related to cell wall loosening and remodeling and secondary metabolism. Moreover, the upregulations of transcription factors such as MYBH and RSM in the MYB family play crucial roles during critical transitions in the culm neck development, such as changes in the angle between the rhizome and the culm neck. Our new findings provide essential insights into the cellular roadmaps, transcriptional networks, and key genes involved in the culm neck development.

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.