Genome-wide analyses of four major histone modifications in Arabidopsis hybrids at the germinating seed stage

Symphonies of Growth: Unveiling the Impact of Sound Waves on Plant Physiology and Productivity

The application of sound wave technology to different plant species has revealed that variations in the Hz, sound pressure intensity, treatment duration, and type of setup of the sound source significantly impact the plant performance. A study conducted on cotton plants treated with Plant Acoustic Frequency Technology (PAFT) highlighted improvements across various growth metrics. In particular, the treated samples showed increases in the height, size of the fourth expanded leaf from the final one, count of branches carrying bolls, quantity of bolls, and weight of individual bolls. Another study showed how the impact of a 4 kHz sound stimulus positively promoted plant drought tolerance. In other cases, such as in transgenic rice plants, GUS expression was upregulated at 250 Hz but downregulated at 50 Hz. In the same way, sound frequencies have been found to enhance the osmotic potential, with the highest observed in samples treated with frequencies of 0.5 and 0.8 kHz compared to the control. Furthermore, a sound treatment with a frequency of 0.4 kHz and a sound pressure level (SPL) of 106 dB significantly increased the paddy rice germination index, as evidenced by an increase in the stem height and relative fresh weight. This paper presents a complete, rationalized and updated review of the literature on the effects of sound waves on the physiology and growth parameters of sound-treated plants.

Mechanisms of Plant Epigenetic Regulation in Response to Plant Stress: Recent Discoveries and Implications

Plant stress is a significant challenge that affects the development, growth, and productivity of plants and causes an adverse environmental condition that disrupts normal physiological processes and hampers plant survival. Epigenetic regulation is a crucial mechanism for plants to respond and adapt to stress. Several studies have investigated the role of DNA methylation (DM), non-coding RNAs, and histone modifications in plant stress responses. However, there are various limitations or challenges in translating the research findings into practical applications. Hence, this review delves into the recent recovery, implications, and applications of epigenetic regulation in response to plant stress. To better understand plant epigenetic regulation under stress, we reviewed recent studies published in the last 5-10 years that made significant contributions, and we analyzed the novel techniques and technologies that have advanced the field, such as next-generation sequencing and genome-wide profiling of epigenetic modifications. We emphasized the breakthrough findings that have uncovered specific genes or pathways and the potential implications of understanding plant epigenetic regulation in response to stress for agriculture, crop improvement, and environmental sustainability. Finally, we concluded that plant epigenetic regulation in response to stress holds immense significance in agriculture, and understanding its mechanisms in stress tolerance can revolutionize crop breeding and genetic engineering strategies, leading to the evolution of stress-tolerant crops and ensuring sustainable food production in the face of climate change and other environmental challenges. Future research in this field will continue to unveil the intricacies of epigenetic regulation and its potential applications in crop improvement.

Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrid

Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops.

Sorghum root epigenetic landscape during limiting phosphorus conditions

Efficient acquisition and use of available phosphorus from the soil is crucial for plant growth, development, and yield. With an ever-increasing acreage of croplands with suboptimal available soil phosphorus, genetic improvement of sorghum germplasm for enhanced phosphorus acquisition from soil is crucial to increasing agricultural output and reducing inputs, while confronted with a growing world population and uncertain climate. Sorghum bicolor is a globally important commodity for food, fodder, and forage. Known for robust tolerance to heat, drought, and other abiotic stresses, its capacity for optimal phosphorus use efficiency (PUE) is still being investigated for optimized root system architectures (RSA). Whilst a few RSA-influencing genes have been identified in sorghum and other grasses, the epigenetic impact on expression and tissue-specific activation of candidate PUE genes remains elusive. Here, we present transcriptomic, epigenetic, and regulatory network profiling of RSA modulation in the BTx623 sorghum background in response to limiting phosphorus (LP) conditions. We show that during LP, sorghum RSA is remodeled to increase root length and surface area, likely enhancing its ability to acquire P. Global DNA 5-methylcytosine and H3K4 and H3K27 trimethylation levels decrease in response to LP, while H3K4me3 peaks and DNA hypomethylated regions contain recognition motifs of numerous developmental and nutrient responsive transcription factors that display disparate expression patterns between different root tissues (primary root apex, elongation zone, and lateral root apex).

OUP accepted manuscript

Interspecific hybridization is often seen as a genomic stress that may lead to new gene expression patterns and deregulation of transposable elements (TEs). The understanding of expression changes in hybrids compared with parental species is essential to disentangle their putative role in speciation processes. However, to date we ignore the detailed mechanisms involved in genomic deregulation in hybrids. We studied the ovarian transcriptome and epigenome of the Drosophila buzzatii and Drosophila koepferae species together with their F₁ hybrid females. We found a trend toward underexpression of genes and TE families in hybrids. The epigenome in hybrids was highly similar to the parental epigenomes and showed intermediate histone enrichments between parental species in most cases. Differential gene expression in hybrids was often associated only with changes in H3K4me3 enrichments, whereas differential TE family expression in hybrids may be associated with changes in H3K4me3, H3K9me3, or H3K27me3 enrichments. We identified specific genes and TE families, which their differential expression in comparison with the parental species was explained by their differential chromatin mark combination enrichment. Finally, cis–trans compensatory regulation could also contribute in some way to the hybrid deregulation. This work provides the first study of histone content in Drosophila interspecific hybrids and their effect on gene and TE expression deregulation.

AGL15 Controls the Embryogenic Reprogramming of Somatic Cells in Arabidopsis through the Histone Acetylation-Mediated Repression of the miRNA Biogenesis Genes

The embryogenic transition of somatic cells requires an extensive reprogramming of the cell transcriptome. Relevantly, the extensive modulation of the genes that have a regulatory function, in particular the genes encoding the transcription factors (TFs) and miRNAs, have been indicated as controlling somatic embryogenesis (SE) that is induced in vitro in the somatic cells of plants. Identifying the regulatory relationships between the TFs and miRNAs during SE induction is of central importance for understanding the complex regulatory interplay that fine-tunes a cell transcriptome during the embryogenic transition. Hence, here, we analysed the regulatory relationships between AGL15 (AGAMOUS-LIKE 15) TF and miR156 in an embryogenic culture of Arabidopsis. Both AGL15 and miR156 control SE induction and AGL15 has been reported to target the MIR156 genes in planta. The results showed that AGL15 contributes to the regulation of miR156 in an embryogenic culture at two levels that involve the activation of the MIR156 transcription and the containment of the abundance of mature miR156 by repressing the miRNA biogenesis genes DCL1 (DICER-LIKE1), SERRATE and HEN1 (HUA-ENHANCER1). To repress the miRNA biogenesis genes AGL15 seems to co-operate with the TOPLESS co-repressors (TPL and TPR1-4), which are components of the SIN3/HDAC silencing complex. The impact of TSA (trichostatin A), an inhibitor of the HDAC histone deacetylases, on the expression of the miRNA biogenesis genes together with the ChIP results implies that histone deacetylation is involved in the AGL15-mediated repression of miRNA processing. The results indicate that HDAC6 and HDAC19 histone deacetylases might co-operate with AGL15 in silencing the complex that controls the abundance of miR156 during embryogenic induction. This study provides new evidence about the histone acetylation-mediated control of the miRNA pathways during the embryogenic reprogramming of plant somatic cells and the essential role of AGL15 in this regulatory mechanism.

Whole-genome landscape of H3K4me3, H3K36me3 and H3K9ac and their association with gene expression during Paulownia witches' broom disease infection and recovery processes

Histone methylation and acetylation participate in the modulation of gene expression. Here, chromatin immunoprecipitation sequencing (ChIP-Seq) was used to determine genome-wide patterns of three histone modifications, H3K4me3, H3K36me3, and H3K9ac (associated with actively expressed genes) and their associations with gene expression in Paulownia fortunei following phytoplasma infection and recovery from Paulownia witches' broom (PaWB) disease after methyl methane sulfonate treatment. The three histone marks were preferentially deposited in genic regions, especially downstream of transcription start sites, and were highly concurrent with gene expression. Genes with all three histone marks exhibited the highest expression levels. Based on the comparison scheme, we detected 365, 2244, and 752 PaWB-associated genes with H3K4me3, H3K36me3, and H3K9ac marks, separately. KEGG pathway analysis showed that these genes were involved in plant-pathogen interaction, plant hormone signal transduction, and starch and sucrose metabolism. A small proportion of differentially modified genes showed changes in expression in response to phytoplasma infection, including genes involved in calcium ion signal transduction, abscisic acid signal transduction, and ethylene biosynthesis. This comprehensive analysis of genome-wide histone modifications and gene expression in Paulownia following phytoplasma infection provides new insights into the epigenetic responses to phytoplasma infection and will be useful for further studies on epigenetic regulation mechanisms in plants under biotic stress.

The histone modification H3 lysine 27 tri-methylation has conserved gene regulatory roles in the triplicated genome of Brassica rapa L

Brassica rapa L. is an important vegetable and oilseed crop. We investigated the distribution of the histone mark tri-methylation of H3K27 (H3K27me3) in B. rapa and its role in the control of gene expression at two stages of development (2-day cotyledons and 14-day leaves) and among paralogs in the triplicated genome. H3K27me3 has a similar distribution in two inbred lines, while there was variation of H3K27me3 sites between tissues. Sites that are specific to 2-day cotyledons have increased transcriptional activity, and low levels of H3K27me3 in the gene body region. In 14-day leaves, levels of H3K27me3 were associated with decreased gene expression. In the triplicated genome, H3K27me3 is associated with paralogs that have tissue-specific expression. Even though B. rapa and Arabidopsis thaliana are not closely related within the Brassicaceae, there is conservation of H3K27me3-marked sites in the two species. Both B. rapa and A. thaliana require vernalization for floral initiation with FLC being the major controlling locus. In all four BrFLC paralogs, low-temperature treatment increases H3K27me3 at the proximal nucleation site reducing BrFLC expression. Following return to normal temperature growth conditions, H3K27me3 spreads along all four BrFLC paralogs providing stable repression of the gene.

Heterosis Breeding in Eggplant (Solanum melongena L.): Gains and Provocations

Heterosis (or hybrid vigor) results in a hybrid’s phenotypic superiority over its founder parents for quantitative and qualitative traits. Hybrid vigor is defined by mechanisms such as dominant complementation, over-dominance, and epistasis. Eggplant (Solanum melongena L.) is an essential vegetable crop and a good source of dietary minerals, vitamins, and anthocyanins, with a high oxygen radical absorbance capacity and low caloric value. Given the economic and nutritional significance of eggplants, breeding efforts focus on developing high-yielding varieties—mostly F₁ hybrids—with important traits. Studies indicate the successful exploitation of heterosis in the eggplant for a considerable improvement with respect to quantitative traits. In this direction, estimating heterosis for yield-related traits could well be useful for examining the most beneficial hybrid mix with the exploitation of top-quality hybrid. This review examines the current perception of the breeding and molecular aspects of heterosis in eggplants and cites several studies describing the mechanisms. Rendering and combining recent genomics, epigenetic, proteomic, and metabolomics studies present new prospects towards the understanding of the regulatory events of heterosis involved in the evolution and the domestication of the eggplant ideotype.

Genome-wide analysis of three histone marks and gene expression in Paulownia fortunei with phytoplasma infection

BACKGROUND

Paulownia withes'-broom (PaWB) disease caused by phytoplasma is a serious infectious disease for Paulownia. However, the underlying molecular pathogenesis is not fully understood. Recent studies have demonstrated that histone modifications could play a role in plant defense responses to pathogens. But there is still no available genome-wide histone modification data in non-model ligneous species infected with phytoplasma.

RESULTS

Here, we provided the first genome-wide profiles of three histone marks (H3K4me3, H3K36me3 and H3K9ac) in Paulownia fortunei under phytoplasma stress by using chromatin immunoprecipitation sequencing (ChIP-Seq). We found that H3K4me3, H3K36me3 and H3K9ac were mainly enriched in the genic regions in P. fortunei with (PFI) and without (PF) phytoplasma infection. ChIP-Seq analysis revealed 1738, 986, and 2577 genes were differentially modified by H3K4me3, H3K36me3 and H3K9ac marks in PFI under phytoplasma infection, respectively. The functional analysis of these genes suggested that most of them were mainly involved in metabolic pathways, biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, plant-pathogen interaction and plant hormone signal transduction. In addition, the combinational analysis of ChIP-Seq and RNA-Seq showed that differential histone methylation and acetylation only affected a small subset of phytoplasma-responsive genes.

CONCLUSIONS

Taken together, this is the first report of integrated analysis of histone modifications and gene expression involved in Paulownia-phytoplasma interaction. Our results will provide the valuable resources for the mechanism studies of gene regulation in non-model plants upon pathogens attack.

Extensive allele-level remodeling of histone methylation modification in reciprocal F1 hybrids of rice subspecies

Epigenetic mechanisms play a major role in heterosis, partly as a result of the remodeling of epigenetic modifications in F₁ hybrids. Based on chromatin immunoprecipitation-sequencing (ChIP-Seq) analyses, we show that at the allele level extensive histone methylation remodeling occurred for a subset of genomic loci in reciprocal F₁ hybrids of Oryza sativa (rice) cultivars Nipponbare and 93-11, representing the two subspecies japonica and indica. Globally, the allele modification-altered loci in leaf or root of the reciprocal F₁ hybrids involved ˜12-43% or more of the genomic regions carrying either of two typical histone methylation markers, H3K4me3 (>21 000 genomic regions) and H3K27me3 (>11 000 genomic regions). Nevertheless, at the total modification level, the majority (from ˜43 to >90%) of the modification-altered alleles lay within the range of parental additivity in the hybrids because of concerted alteration in opposite directions, consistent with an overall attenuation of allelic differences in the modifications. Importantly, of the genomic regions that did show non-additivity in total modification level by either marker in the two tissues of hybrids, >80% manifested transgressivity, which involved genes enriched in specific functional categories. Extensive allele-level alteration of H3K4me3 alone was positively correlated with genome-wide changes in allele-level gene expression, whereas at the total level, both H3K4me3 and H3K27me3 remodeling, although affecting just a small number of genes, contributes to the overall non-additive gene expression to variable extents, depending on tissue/marker combinations. Our results emphasize the importance of allele-level analysis in hybrids to assess the remodeling of epigenetic modifications and their relation to changes in gene expression.

Seed Biology Updates - Highlights and New Discoveries in Seed Dormancy and Germination Research

An understanding of the biology of seeds has been greatly advanced in recent years. The progresses, particularly in the field of seed dormancy and germination research, have been made at a remarkable speed. Some of the possible epigenetic mechanisms, including an involvement of non-coding RNA, which were predicted for DELAY OF GERMINATION1 just a few years ago, have now been demonstrated with strong molecular and genetic evidence. Imprinting, or parent-of-origin-specific gene silencing/expression, which was characterized particularly for developing seeds, was also found in imbibed seeds and suggested for dormancy mechanisms. Hormone biology in seeds, which is the most advanced and almost a traditional area of seed research, also presents a new dimension. Upstream regulators of hormone metabolism and hormone transporters, such as abscisic acid and gibberellin influx/efflux carriers, have been identified. Characterization of the novel posttranslational modification pathways, including the N-end rule and S-nitrosylation pathways, which play a critical role in turnover of the major hormone signal transduction proteins, also expanded our knowledge about the complexity of hormone signaling in seeds. These progresses made at the molecular level are significant steps toward a better understanding of how seeds translate soil and other environmental signals into their internal hormone biology and make an important decision to stay dormant or commence with germination.