Integrated methylome and transcriptome analysis unravel the cold tolerance mechanism in winter rapeseed(Brassica napus L.)

BnaHSFA2, a heat shock transcription factor interacting with HSP70 and MPK11, enhances freezing tolerance in transgenic rapeseed

Heat shock transcription factors (Hsfs) play important roles in plant developmental regulations and various abiotic stress responses. However, their evolutionary mechanism of freezing tolerance remains poorly understood. In our previous transcriptomics study based on DNA methylation sequencing, the BnaHsfA2 was found to be significantly accumulated in winter rapeseed (Brassica rapa L.) under freezing stress, and the expression levels of BnaHsfA2 showed a gradual increasing trend over three years. In this study, BnaHsfA2 was isolated and characterized. Its' encoding protein has a relatively high phylogenetic relationship with the AtHsfA2; Subcellular localization results indicated that BnaHsfA2 was a nuclear protein; BnaHsfA2 exhibited higher expression levels in mature seed coats and seeds, seedling leaves, flowering filaments as well as anthers. The transcription level of BnaHsfA2 in leaves of rapeseed seedling was significantly increased at -4 °C stress for 12h and 24h. BnaHsfA2 promoter has many stress-responsive cis-regulatory elements. β-glucuronidase (GUS) staining assays indicated that the BnaHsfA2 promoter was induced under freezing stress, and it's 5'-deletion fragment from 465 to 1284 was essential for the transcriptional expression in response to freezing stress. The BnaHsfA2-transgenic rapeseed lines showed greater freezing resistance in comparison with the wild type (WT); the BnaHsfA2 overexpression lines showed increased antioxidant enzyme activities, decreased level of lipid peroxidation and reactive oxygen species (ROS) accumulation compared to the WT. Finally, yeast two-hybrid assay demonstrated that BnaHsfA2 interacted with rapeseed mitogen-activated protein kinase 11 (BnaMPK11) and heat shock factor-binding protein (BnaHsp70). The study will pave the way for further understanding the regulatory networks of BnaHsfA2 in plants under abiotic stress.

Epigenetic control of plant abiotic stress responses

On top of genetic information, organisms have evolved complex and sophisticated epigenetic regulation to adjust gene expression in response to developmental and environmental signals. Key epigenetic mechanisms include DNA methylation, histone modifications and variants, chromatin remodeling, and chemical modifications of RNAs. Epigenetic control of environmental responses is particularly important for plants, which are sessile and unable to move away from adverse environments. Besides enabling plants to rapidly respond to environmental stresses, some stress-induced epigenetic changes can be maintained, providing plants with a pre-adapted state to recurring stresses. Understanding these epigenetic mechanisms offers valuable insights for developing crop varieties with enhanced stress tolerance. Here, we focus on abiotic stresses and summarize recent progress in characterizing stress-induced epigenetic changes and their regulatory mechanisms and roles in plant abiotic stress resistance.

The strigolactones-mediated DNA demethylation activates the phosphoinositide pathway in response to salt stress

Salt stress severely affects the growth and development of tomato. Strigolactones (SLs) and DNA methylation have been shown to be involved in the growth and development and response to salt stress in tomato. However, the regulation of SLs on DNA methylation in tomato under salt stress remains unclear. In this study, the interaction between SLs and DNA methylation inhibitors 5-azacytidine (5-azaC) alleviate salt stress damage by increasing the plant height, stem diameter, leaf area, and root length of tomato, as well as enhancing the biosynthesis of chlorophyll, carotenoid and flavonoid. The transcriptome and genome-wide methylation analysis between NaCl and NaCl + GR24 treatment show that plant-pathogen interaction, MAPK signaling pathway, plant hormone signal transduction and phosphatidylinositol signaling system may be means for SLs in response to salt stress. Among, SLs strikingly up-regulate the pivotal genes related to phosphatidylinositol signaling system, and reduce CHG methylation level in promoter and body region of these genes under salt stress, implying that SLs mediated-demethylation may promote gene expression. The determination results of relevant metabolites and gene expression levels in the phosphatidylinositol signaling system suggest that PIP2, DAG, IP3, and PA are raised by co-treatment of SLs and 5-azaC under salt stress relative to NaCl + 5-azaC treatment. The same response pattern is also presented in the SlPLC2, SlNPC1, SlPLD-Z, SlPLD-B, SlDGK1, SlDGK5, SlDGK7 and SlPIP5K9 genes. These results strongly indicate that phosphatidylinositol signaling system response to salt stress is related to the SLs mediated-demethylation, and provide a potential means for defenses salt stress in tomato.

Induction and Transcriptome Analysis of Callus Tissue from Endosperm of Makapuno Coconut

The makapuno coconut endosperm is distinguished by its soft and irregular texture, in contrast to the solid endosperm of regular coconuts. To establish a scientific foundation for studying makapuno coconuts, callus was induced from makapuno endosperm using a combination of plant growth regulators. The induction was successful, and the resulting callus was subsequently subcultured for further study. Transcriptome sequencing of the makapuno callus identified 429 differentially expressed genes (DEGs), with 273 upregulated and 156 downregulated, compared to callus derived from regular coconut endosperm. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that these DEGs were involved in key metabolic pathways, including fructose and mannose metabolism, carbon fixation in photosynthetic organisms, galactose metabolism, and amino sugar and nucleotide sugar metabolism. Furthermore, lipid content analysis of the makapuno callus revealed a significantly higher total lipid level compared to regular callus, with notable differences in the levels of specific fatty acids, such as myristic acid, palmitic acid, and linoleic acid. This study establishes a novel platform for molecular biological research on makapuno coconuts and provides valuable insights into the molecular mechanisms underlying the formation of makapuno callus tissue. The findings also lay the groundwork for future research aimed at elucidating the unique properties of makapuno endosperm and exploring its potential applications.

Dynamic DNA methylation modifications in the cold stress response of cassava

Cassava, a crucial tropical crop, faces challenges from cold stress, necessitating an exploration of its molecular response. Here, we investigated the role of DNA methylation in moderating the response to moderate cold stress (10 °C) in cassava. Using whole-genome bisulfite sequencing, we examined DNA methylation patterns in leaf blades and petioles under control conditions, 5 h, and 48 h of cold stress. Tissue-specific responses were observed, with leaf blades exhibiting subtle changes, while petioles displayed a pronounced decrease in methylation levels under cold stress. We identified cold stress-induced differentially methylated regions (DMRs) that demonstrated both tissue and treatment specificity. Importantly, these DMRs were enriched in genes with altered expression, implying functional relevance. The cold-response transcription factor ERF105 associated with DMRs emerged as a significant and conserved regulator across tissues and treatments. Furthermore, we investigated DNA methylation dynamics in transposable elements, emphasizing the sensitivity of MITEs with bHLH binding motifs to cold stress. These findings provide insights into the epigenetic regulation of response to cold stress in cassava, contributing to an understanding of the molecular mechanisms underlying stress adaptation in this tropical plant.

DNA methylation-mediated ROS production contributes to seed abortion in litchi

Although there is increasing evidence suggesting that DNA methylation regulates seed development, the underlying mechanisms remain poorly understood. Therefore, we aimed to shed light on this by conducting whole-genome bisulfite sequencing using seeds from the large-seeded cultivar 'HZ' and the abortive-seeded cultivar 'NMC'. Our analysis revealed that the 'HZ' seeds exhibited a hypermethylation level compared to the 'NMC' seeds. Furthermore, we found that the genes associated with differentially methylated regions (DMRs) and differentially expressed genes (DEGs) were mainly enriched in the reactive oxygen species (ROS) metabolic pathway. To investigate this further, we conducted nitroblue tetrazolium (NBT) and 2,7-Dichlorodihydrofluorescein (DCF) staining, which demonstrated a significantly higher amount of ROS in the 'NMC' seeds compared to the 'HZ' seeds. Moreover, we identified that the gene LcGPX6, involved in ROS scavenging, exhibited hypermethylation levels and parallelly lower expression levels in 'NMC' seeds compared to 'HZ' seeds. Interestingly, the ectopic expression of LcGPX6 in Arabidopsis enhanced ROS scavenging and resulted in lower seed production. Together, we suggest that DNA methylation-mediated ROS production plays a significant role in seed development in litchi, during which hypermethylation levels of LcGPX6 might repress its expression, resulting in the accumulation of excessive ROS and ultimately leading to seed abortion.

Integrated analysis of transcriptome and metabolome reveals insights for low-temperature germination in hybrid rapeseeds (Brassica napus L.)

Rapeseed (Brassica napus L.) is an important oil-producing crop in China. However, cold stress in winter can adversely affect rapeseed germination and subsequently result in poor seed yield at the mature stage. Studies of differences in the transcriptional and metabolic levels of rapeseed under cold stress can improve our understanding of low-temperature germination (LTG). The current study aimed to identify the cold stress-responsive genes, metabolites, and metabolic pathways based on a combined transcriptome and metabolome analysis to understand the difference of LTG and tolerance mechanisms in the cold-tolerant (Yueyou1301, YY1301) and cold-normal (Fengyou737, FY737) rapeseed varieties. Compared to FY737, YY1301 had a higher germination rate, indole acetic acid (IAA) and gibberellic acid (GA)/(abscisic acid) ABA levels at 7.5 °C. A total of 951 differentially expressed genes (DEGs) and 86 differentially accumulated metabolites (DAMs) were identified in two rapeseed varieties. Conjoint analysis revealed 12 DAMs and 5 DEGs that were strongly correlated in inducing rapeseed LTG, which were mainly related to carbohydrate and amino acid metabolism, specifically the pathway of glutathione metabolism and starch and sucrose metabolism. These results suggest that the DAMs and DEGs involved in crucial biological pathways may regulate the LTG of rapeseed. It increases the understanding of the molecular mechanisms underlying the adaptation of rapeseed to LTG.

Exploring the Role of TaPLC1-2B in Heat Tolerance at Seedling and Adult Stages of Wheat through Transcriptome Analysis

Heat stress is a major abiotic stress that can cause serious losses of a crop. Our previous work identified a gene involved in heat stress tolerance in wheat, TaPLC1-2B. To further investigate its mechanisms, in the present study, TaPLC1-2B RNAi-silenced transgenic wheat and the wild type were comparatively analyzed at both the seedling and adult stages, with or without heat stress, using transcriptome sequencing. A total of 15,549 differentially expressed genes (DEGs) were identified at the adult stage and 20,535 DEGs were detected at the seedling stage. After heat stress, an enrichment of pathways such as phytohormones and mitogen-activated protein kinase signaling was mainly found in the seedling stage, and pathways related to metabolism, glycerophospholipid metabolism, circadian rhythms, and ABC transporter were enriched in the adult stage. Auxin and abscisic acid were downregulated in the seedling stage and vice versa in the adult stage; and the MYB, WRKY, and no apical meristem gene families were downregulated in the seedling stage in response to heat stress and upregulated in the adult stage in response to heat stress. This study deepens our understanding of the mechanisms of TaPLC1-2B in regard to heat stress in wheat at the seedling and adult stages.

Integration of Metabolome and Transcriptome Reveals the Major Metabolic Pathways and Potential Biomarkers in Response to Freeze-Stress Regulation in Apple (Malus domestica)

Freezing stress is the main factor affecting the normal growth and distribution of plants. The safe overwintering of a perennial deciduous plant is a crucial link to ensuring its survival and yield. However, little is known about the molecular mechanism of its gene regulation metabolites as related to its freeze-tolerance. In order to enhance our comprehension of freeze-tolerance metabolites and gene expression in dormant apple trees, we examined the metabolic and transcriptomic differences between 'Ralls' and 'Fuji', two apple varieties with varying degrees of resistance to freezing. The results of the freezing treatment showed that 'Ralls' had stronger freeze-tolerance than 'Fuji'. We identified 302, 334, and 267 up-regulated differentially accumulated metabolites (DAMs) and 408, 387, and 497 down-regulated DAMs between 'Ralls' and 'Fuji' under -10, -15, and -20 °C treatment, respectively. A total of 359 shared metabolites were obtained in the upward trend modules, of which 62 metabolites were associated with 89 pathways. The number of up-regulated genes accounted for 50.2%, 45.6%, and 43.2% of the total number of differentially expressed genes (DEGs), respectively, at -10, -15, and -20 °C. Through combined transcriptome and metabolome analysis, we identified 12 pathways that included 16 DAMs and 65 DEGs. Meanwhile, we found that 20 DEGs were identified in the phenylpropanoid biosynthesis pathway and its related pathways, involving the metabolism of p-Coumaroyl-CoA, 7, 4'-Dihydroxyflavone, and scolymoside. These discoveries advance our comprehension of the molecular mechanism underlying apple freeze-tolerance and provide genetic material for breeding apple cultivars with enhanced freeze-tolerance.