Chilling-Mediated DNA Methylation Changes during Dormancy and Its Release Reveal the Importance of Epigenetic Regulation during Winter Dormancy in Apple (Malus x domestica Borkh.)

Epigenetic responses of trees to environmental stress in the context of climate change

In long-lived tree populations, when environmental change outpaces rates of evolutionary adaptation, plasticity in traits related to stress tolerance, dormancy, and dispersal may be vital for preventing extinction. While a population's genetic background partly determines its ability to adapt to a changing environment, so too do the many types of epigenetic modifications that occur within and among populations, which vary on timescales orders of magnitude faster than the emergence of new beneficial alleles. Consequently, phenotypic plasticity driven by epigenetic modification may be especially critical for sessile, long-lived organisms such as trees that must rely on this plasticity to keep pace with rapid anthropogenic environmental change. While studies have reported large effects of DNA methylation, histone modification, and non-coding RNAs on the expression of stress-tolerance genes and resulting phenotypic responses, little is known about the role of these effects in non-model plants and particularly in trees. Here, we review new findings in plant epigenetics with particular relevance to the ability of trees to adapt to or escape stressors associated with rapid climate change. Such findings include specific epigenetic influences over drought, heat, and salinity tolerance, as well as dormancy and dispersal traits. We also highlight promising findings concerning transgenerational inheritance of an epigenetic 'stress memory' in plants. As epigenetic information is becoming increasingly easy to obtain, we close by outlining ways in which ecologists can use epigenetic information better to inform population management and forecasting efforts. Understanding the molecular mechanisms behind phenotypic plasticity and stress memory in tree species offers a promising path towards a mechanistic understanding of trees' responses to climate change.

Unravelling the Epigenetic Code: DNA Methylation in Plants and Its Role in Stress Response

Environmental stress significantly affects plant growth, development, and survival. Plants respond to stressors such as temperature fluctuations, water scarcity, nutrient deficiencies, and pathogen attacks through intricate molecular and physiological adaptations. Epigenetic mechanisms are crucial in regulating gene expression in response to environmental stress. This review explores the current understanding of epigenetic modifications, including DNA methylation, and their roles in modulating gene expression patterns under environmental stress conditions. The dynamic nature of epigenetic modifications, their crosstalk with stress-responsive pathways, and their potential implications for plant adaptation and crop improvement are highlighted in the face of changing environmental conditions.

Molecular Mechanisms of Seasonal Gene Expression in Trees

In trees, the annual cycling of active and dormant states in buds is closely regulated by environmental factors, which are of primary significance to their productivity and survival. It has been found that the parallel or convergent evolution of molecular pathways that respond to day length or temperature can lead to the establishment of conserved periodic gene expression patterns. In recent years, it has been shown in many woody plants that change in annual rhythmic patterns of gene expression may underpin the adaptive evolution in forest trees. In this review, we summarize the progress on the molecular mechanisms of seasonal regulation on the processes of shoot growth, bud dormancy, and bud break in response to day length and temperature factors. We focus on seasonal expression patterns of genes involved in dormancy and their associated epigenetic modifications; the seasonal changes in the extent of modifications, such as DNA methylation, histone acetylation, and histone methylation, at dormancy-associated loci have been revealed for their actions on gene regulation. In addition, we provide an outlook on the direction of research on the annual cycle of tree growth under climate change.

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.

Exploring the crop epigenome: a comparison of DNA methylation profiling techniques

Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.

Small RNA and Degradome Sequencing in Floral Bud Reveal Roles of miRNAs in Dormancy Release of Chimonanthus praecox

Chimonanthus praecox (wintersweet) is highly valued ornamentally and economically. Floral bud dormancy is an important biological characteristic in the life cycle of wintersweet, and a certain period of chilling accumulation is necessary for breaking floral bud dormancy. Understanding the mechanism of floral bud dormancy release is essential for developing measures against the effects of global warming. miRNAs play important roles in low-temperature regulation of flower bud dormancy through mechanisms that are unclear. In this study, small RNA and degradome sequencing were performed for wintersweet floral buds in dormancy and break stages for the first time. Small RNA sequencing identified 862 known and 402 novel miRNAs; 23 differentially expressed miRNAs (10 known and 13 novel) were screened via comparative analysis of breaking and other dormant floral bud samples. Degradome sequencing identified 1707 target genes of 21 differentially expressed miRNAs. The annotations of the predicted target genes showed that these miRNAs were mainly involved in the regulation of phytohormone metabolism and signal transduction, epigenetic modification, transcription factors, amino acid metabolism, and stress response, etc., during the dormancy release of wintersweet floral buds. These data provide an important foundation for further research on the mechanism of floral bud dormancy in wintersweet.

From Floral Induction to Blooming: The Molecular Mysteries of Flowering in Woody Plants

Flowering is a pivotal developmental process in response to the environment and determines the start of a new life cycle in plants. Woody plants usually possess a long juvenile nonflowering phase followed by an adult phase with repeated flowering cycles. The molecular mechanism underlying flowering regulation in woody plants is believed to be much more complex than that in annual herbs. In this review, we briefly describe the successive but distinct flowering processes in perennial trees, namely the vegetative phase change, the floral transition, floral organogenesis, and final blooming, and summarize in detail the most recent advances in understanding how woody plants regulate flowering through dynamic gene expression. Notably, the florigen gene FLOWERING LOCUS T(FT) and its antagonistic gene TERMINAL FLOWER 1 (TFL1) seem to play a central role in various flowering transition events. Flower development in different taxa requires interactions between floral homeotic genes together with AGL6 conferring floral organ identity. Finally, we illustrate the issues and corresponding measures of flowering regulation investigation. It is of great benefit to the future study of flowering in perennial trees.

DNA Methylation in Plant Responses and Adaption to Abiotic Stresses

Due to their sessile state, plants are inevitably affected by and respond to the external environment. So far, plants have developed multiple adaptation and regulation strategies to abiotic stresses. One such system is epigenetic regulation, among which DNA methylation is one of the earliest and most studied regulatory mechanisms, which can regulate genome functioning and induce plant resistance and adaption to abiotic stresses. In this review, we outline the most recent findings on plant DNA methylation responses to drought, high temperature, cold, salt, and heavy metal stresses. In addition, we discuss stress memory regulated by DNA methylation, both in a transient way and the long-term memory that could pass to next generations. To sum up, the present review furnishes an updated account of DNA methylation in plant responses and adaptations to abiotic stresses.

Antioxidant Regulation and DNA Methylation Dynamics During Mikania micrantha Seed Germination Under Cold Stress

As a primary goal, adaptation to cold climate could expand an invasion range of exotic plants. Here, we aimed to explore the regulation strategy of M. micrantha seed development under cold stress through molecular physiology and multi-omics analysis. Significant increase of hydrogen peroxide, malondialdehyde, and electrolyte leakage observed under cold stress revealed that oxidative damage within M. micrantha seed cells was induced in the initial germination phase. Proteomic data underscored an activation of antioxidant activity to maintain redox homeostasis, with a cluster of antioxidant proteins identified. Genomic-wide transcriptome, in combination with time-series whole-genome bisulfite sequencing mining, elucidated that seven candidate genes, which were the target of DNA demethylation-dependent ROS scavenging, were possibly associated with an M. micrantha germ break. Progressive gain of CHH context DNA methylation identified in an early germination phrase suggested a role of a DNA methylation pathway, while an active DNA demethylation pathway was also initiated during late seed development, which was in line with the expression trend of methylation and demethylation-related genes verified through qRT-PCR. These data pointed out that cold-dependent DNA demethylation and an antioxidant regulatory were involved together in restoring seed germination. The expression level of total 441 genes presented an opposite trend to the methylation divergence, while the expression of total 395 genes was proved to be negatively associated with their methylation levels. These data provided new insights into molecular reprograming events during M. micrantha seed development.

The genome of low-chill Chinese plum 'Sanyueli' (Prunus salicina Lindl.) provides insights into the regulation of the chilling requirement of flower buds

Chinese plum (Prunus salicina Lindl.) is a stone fruit that belongs to the Prunus genus and plays an important role in the global production of plum. In this study, we report the genome sequence of the Chinese plum 'Sanyueli', which is known to have a low-chill requirement for flower bud break. The assembled genome size was 282.38 Mb, with a contig N50 of 1.37 Mb. Over 99% of the assembly was anchored to eight pseudochromosomes, with a scaffold N50 of 34.46Mb. A total of 29,708 protein-coding genes were predicted from the genome and 46.85% (132.32 Mb) of the genome was annotated as repetitive sequence. Bud dormancy is influenced by chilling requirement in plum and partly controlled by DORMANCY ASSOCIATED MADS-box (DAM) genes. Six tandemly arrayed PsDAM genes were identified in the assembled genome. Sequence analysis of PsDAM6 in 'Sanyueli' revealed the presence of large insertions in the intron and exon regions. Transcriptome analysis indicated that the expression of PsDAM6 in the dormant flower buds of 'Sanyueli' was significantly lower than that in the dormant flower buds of the high chill requiring 'Furongli' plum. In addition, the expression of PsDAM6 was repressed by chilling treatment. The genome sequence of 'Sanyueli' plum provides a valuable resource for elucidating the molecular mechanisms responsible for the regulation of chilling requirements, and it is also useful for the identification of the genes involved in the control of other important agronomic traits and molecular breeding in plum.

Insight Between the Epigenetics and Transcription Responding of Cotton Hypocotyl Cellular Elongation Under Salt-Alkaline Stress

Gossypium barbadense is a cultivated cotton not only known for producing superior fiber but also for its salt and alkaline resistance. Here, we used Whole Genome Bisulfite Sequencing (WGBS) technology to map the cytosine methylation of the whole genome of the G. barbadense hypocotyl at single base resolution. The methylation sequencing results showed that the mapping rates of the three samples were 75.32, 77.54, and 77.94%, respectively. In addition, the Bisulfite Sequence (BS) conversion rate was 99.78%. Approximately 71.03, 53.87, and 6.26% of the cytosine were methylated at CG, CHG, and CHH sequence contexts, respectively. A comprehensive analysis of DNA methylation and transcriptome data showed that the methylation level of the promoter region was a positive correlation in the CHH context. Saline-alkaline stress was related to the methylation changes of many genes, transcription factors (TFs) and transposable elements (TEs), respectively. We explored the regulatory mechanism of DNA methylation in response to salt and alkaline stress during cotton hypocotyl elongation. Our data shed light into the relationship of methylation regulation at the germination stage of G. barbadense hypocotyl cell elongation and salt-alkali treatment. The results of this research help understand the early growth regulation mechanism of G. barbadense in response to abiotic stress.

Characterization of evolutionarily distinct rice BAHD-Acyltransferases provides insight into their plausible role in rice susceptibility to Rhizoctonia solani

Plants produce diverse secondary metabolites in response to different environmental cues including pathogens. The modification of secondary metabolites, including acylation, modulates their biological activity, stability, transport, and localization. A plant-specific BAHD-acyltransferase (BAHD-AT) gene family members catalyze the acylation of secondary metabolites. Here we characterized the rice (Oryza sativa L.) BAHD-ATs at the genome-wide level and endeavor to define their plausible role in the tolerance against Rhizoctonia solani AG1-IA. We identified a total of 85 rice OsBAHD-AT genes and classified them into five canonical clades based on their phylogenetic relationship with characterized BAHD-ATs from other plant species. The time-course RNA sequencing (RNA-seq) analysis of OsBAHD-AT genes and qualitative real-time polymerase chain reaction (qRT-PCR) validation showed higher expression in sheath blight susceptible rice genotype. Furthermore, the DNA methylation analysis revealed higher hypomethylation of OsBAHD-AT genes that corresponds to their higher expression in susceptible rice genotype, indicating epigenetic regulation of OsBAHD-AT genes in response to R. solani AG1-IA inoculation. The results shown here indicate that BAHD-ATs may have a negative role in rice tolerance against R. solani AG1-IA possibly mediated through the brassinosteroid (BR) signaling pathway. Altogether, the present analysis suggests the putative functions of several OsBAHD-AT genes, which will provide a blueprint for their functional characterization and to understand the rice-R. solani AG1-IA interaction.

Plants' Epigenetic Mechanisms and Abiotic Stress

Plants are sessile organisms that need to adapt to constantly changing environmental conditions. Unpredictable climate change places plants under a variety of abiotic stresses. Studying the regulation of stress-responsive genes can help to understand plants’ ability to adapt to fluctuating environmental conditions. Changes in epigenetic marks such as histone modifications and DNA methylation are known to regulate gene expression by their dynamic variation in response to stimuli. This can then affect their phenotypic plasticity, which helps with the adaptation of plants to adverse conditions. Epigenetic marks may also provide a mechanistic basis for stress memory, which enables plants to respond more effectively and efficiently to recurring stress and prepare offspring for potential future stresses. Studying epigenetic changes in addition to genetic factors is important to better understand the molecular mechanisms underlying plant stress responses. This review summarizes the epigenetic mechanisms behind plant responses to some main abiotic stresses.

Bud endodormancy in deciduous fruit trees: advances and prospects

Bud endodormancy is a complex physiological process that is indispensable for the survival, growth, and development of deciduous perennial plants. The timely release of endodormancy is essential for flowering and fruit production of deciduous fruit trees. A better understanding of the mechanism of endodormancy will be of great help in the artificial regulation of endodormancy to cope with climate change and in creating new cultivars with different chilling requirements. Studies in poplar have clarified the mechanism of vegetative bud endodormancy, but the endodormancy of floral buds in fruit trees needs further study. In this review, we focus on the molecular regulation of endodormancy induction, maintenance and release in floral buds of deciduous fruit trees. We also describe recent advances in quantitative trait loci analysis of chilling requirements in fruit trees. We discuss phytohormones, epigenetic regulation, and the detailed molecular network controlling endodormancy, centered on SHORT VEGETATIVE PHASE (SVP) and Dormancy-associated MADS-box (DAM) genes during endodormancy maintenance and release. Combining previous studies and our observations, we propose a regulatory model for bud endodormancy and offer some perspectives for the future.

Transcriptomic and epigenomic remodeling occurs during vascular cambium periodicity in Populus tomentosa

Trees in temperate regions exhibit evident seasonal patterns, which play vital roles in their growth and development. The activity of cambial stem cells is the basis for regulating the quantity and quality of wood, which has received considerable attention. However, the underlying mechanisms of these processes have not been fully elucidated. Here we performed a comprehensive analysis of morphological observations, transcriptome profiles, the DNA methylome, and miRNAs of the cambium in Populus tomentosa during the transition from dormancy to activation. Anatomical analysis showed that the active cambial zone exhibited a significant increase in the width and number of cell layers compared with those of the dormant and reactivating cambium. Furthermore, we found that differentially expressed genes associated with vascular development were mainly involved in plant hormone signal transduction, cell division and expansion, and cell wall biosynthesis. In addition, we identified 235 known miRNAs and 125 novel miRNAs. Differentially expressed miRNAs and target genes showed stronger negative correlations than other miRNA/target pairs. Moreover, global methylation and transcription analysis revealed that CG gene body methylation was positively correlated with gene expression, whereas CHG exhibited the opposite trend in the downstream region. Most importantly, we observed that the number of CHH differentially methylated region (DMR) changes was the greatest during cambium periodicity. Intriguingly, the genes with hypomethylated CHH DMRs in the promoter were involved in plant hormone signal transduction, phenylpropanoid biosynthesis, and plant-pathogen interactions during vascular cambium development. These findings improve our systems-level understanding of the epigenomic diversity that exists in the annual growth cycle of trees.

Growing in time: exploring the molecular mechanisms of tree growth

Trees cover vast areas of the Earth's landmasses. They mitigate erosion, capture carbon dioxide, produce oxygen and support biodiversity, and also are a source of food, raw materials and energy for human populations. Understanding the growth cycles of trees is fundamental for many areas of research. Trees, like most other organisms, have evolved a circadian clock to synchronize their growth and development with the daily and seasonal cycles of the environment. These regular changes in light, daylength and temperature are perceived via a range of dedicated receptors and cause resetting of the circadian clock to local time. This allows anticipation of daily and seasonal fluctuations and enables trees to co-ordinate their metabolism and physiology to ensure vital processes occur at the optimal times. In this review, we explore the current state of knowledge concerning the regulation of growth and seasonal dormancy in trees, using information drawn from model systems such as Populus spp.

Sugarcane mosaic virus mediated changes in cytosine methylation pattern and differentially transcribed fragments in resistance-contrasting sugarcane genotypes

Sugarcane mosaic virus (SCMV) is the causal agent of sugarcane mosaic disease (SMD) in Brazil; it is mainly controlled by using resistant cultivars. Studies on the changes in sugarcane transcriptome provided the first insights about the molecular basis underlying the genetic resistance to SMD; nonetheless, epigenetic modifications such as cytosine methylation is also informative, considering its roles in gene expression regulation. In our previous study, differentially transcribed fragments (DTFs) were obtained using cDNA-amplified fragment length polymorphism by comparing mock- and SCMV-inoculated plants from two sugarcane cultivars with contrasting responses to SMD. In this study, the identification of unexplored DTFs was continued while the same leaf samples were used to evaluate SCMV-mediated changes in the cytosine methylation pattern by using methylation-sensitive amplification polymorphism. This analysis revealed minor changes in cytosine methylation in response to SCMV infection, but distinct changes between the cultivars with contrasting responses to SMD, with higher hypomethylation events 24 and 72 h post-inoculation in the resistant cultivar. The differentially methylated fragments (DMFs) aligned with transcripts, putative promoters, and genomic regions, with a preponderant distribution within CpG islands. The transcripts found were associated with plant immunity and other stress responses, epigenetic changes, and transposable elements. The DTFs aligned with transcripts assigned to stress responses, epigenetic changes, photosynthesis, lipid transport, and oxidoreductases, in which the transcriptional start site is located in proximity with CpG islands and tandem repeats. Real-time quantitative polymerase chain reaction results revealed significant upregulation in the resistant cultivar of aspartyl protease and VQ protein, respectively, selected from DMF and DTF alignments, suggesting their roles in genetic resistance to SMD and supporting the influence of cytosine methylation in gene expression. Thus, we identified new candidate genes for further validation and showed that the changes in cytosine methylation may regulate important mechanisms underlying the genetic resistance to SMD.

DNA demethylation is involved in the regulation of temperature-dependent anthocyanin accumulation in peach

Anthocyanin biosynthesis is induced by low temperatures in a number of plants. However, in peach (cv Zhonghuashoutao), anthocyanin accumulation was observed in fruit stored at 16°C but not at or below 12°C. Fruit stored at 16°C showed elevated transcript levels of genes encoding anthocyanin biosynthetic enzymes, the transport protein glutathione S-transferase and key transcription factors. Higher transcript levels of PpPAL1/2, PpC4H, Pp4CL4/5/8, PpF3H, PpF3'H, PpDFR1/2/3 and PpANS, as well as transcription factor gene PpbHLH3, were associated with lower methylation levels in the promoter of these genes. The DNA methylation level was further highly correlated with the expression of the DNA methyltransferase genes and DNA demethylase genes. The application of DNA methylation inhibitor 5-azacytidine induced anthocyanin accumulation in peach flesh, further implicating a critical role for DNA demethylation in regulating anthocyanin accumulation in peach flesh. Our data reveal that temperature-dependent DNA demethylation is a key factor to the post-harvest temperature-dependent anthocyanin accumulation in peach flesh.

Responsive changes of DNA methylation in wheat (Triticum aestivum) under water deficit

DNA methylation plays an important role in the growth and development of plant, and would change under different environments. In this study, 5-methyl cytosine (5mC) content and methylation level exhibited tissue specificity in genomic DNA of wheat seedling, and increased significantly in leaf along with the increase of water deficit, which was especially significant in leaf of wheat AK58. Full-methylation might dominate in genomic DNA of wheat seedling, the increase of full-methylation level under water deficit was significantly higher than that of hemi-methylation level. Under water deficit, DNA methylation of wheat seedling showed significant polymorphism, this polymorphism was always higher in root, especially was higher in root of wheat AK58. Further analysis appeared that changes of DNA methylation in wheat seedling took methylation as principle and demethylation as supplement under water deficit. Therefore, under water deficit, the degree, level and polymorphism of DNA methylation in wheat seedling showed tissue specificity and species specificity, and were higher in wheat AK58 compared with those of wheat XM13, perhaps wheat AK58 could more rapidly respond to water deficit by changes of DNA methylation, which would contribute to reveal molecular mechanism of wheat adapting to water deficit.

Characterization of DNA methylation variations during fruit development and ripening of Vitis vinifera (cv. 'Fujiminori')

The fruit is the most important economical organ in the grape; accordingly, to investigate the grapevine genomic methylation landscape and examine its functional significance during fruit development, we generated whole genome DNA methylation maps for various developmental stages in the fruit of grapevine. In this study, thirteen DNA methylation-related genes and their expression profiles were identified and analyzed. The methylation levels for mC, mCG, mCHG, and mCHH contexts in 65 days after flowering (65DAF) fruit (véraison stage) were higher than those in 40DAF (green stage) and 90DAF (mature stage) fruits. Relative to methylation in the mC context, methylation levels in the mCHH context were higher than those of mCG and mCHG. The DNA methylation level in the ncRNA regions was significantly higher than that in exon, gene, intron, and mRNA regions. The differentially methylated regions (DMRs) and differentially methylated promoters (DMPs) in 65DAF_vs_40DAF were both higher than those in 90DAF_vs_65DAF and 90DAF_vs_40DAF. Most DMRs (or DMPs) were involved in metabolic processes and cell processes, binding, and catalytic activity. These results indicated that DNA methylation represses gene expression during grape fruit development, and it broadens our understanding of the landscape and function of DNA methylation in grapevine genomes.

Dormant but Active: Chilling Accumulation Modulates the Epigenome and Transcriptome of Prunus avium During Bud Dormancy

Temperate deciduous fruit tree species like sweet cherry (Prunus avium) require long periods of low temperatures to trigger dormancy release and flowering. In addition to sequence-based genetic diversity, epigenetic variation may contribute to different chilling requirements among varieties. For the low chill variety 'Royal Dawn' and high chill variety 'Kordia', we studied the methylome of floral buds during chilling accumulation using MethylC-seq to identify differentially methylated regions (DMRs) during chilling hours (CH) accumulation, followed by transcriptome analysis to correlate changes in gene expression with DNA methylation. We found that during chilling accumulation, DNA methylation increased from 173 CH in 'Royal Dawn' and 443 CH in 'Kordia' and was mostly associated with the CHH context. In addition, transcriptional changes were observed from 443 CH in 'Kordia' with 1,210 differentially expressed genes, increasing to 4,292 genes at 1,295 CH. While 'Royal Dawn' showed approximately 5,000 genes differentially expressed at 348 CH and 516 CH, showing a reprogramming that was specific for each genotype. From conserved upregulated genes that overlapped with hypomethylated regions and downregulated genes that overlapped with hypermethylated regions in both varieties, we identified genes related to cold-sensing, cold-signaling, oxidation-reduction process, metabolism of phenylpropanoids and lipids, and a MADS-box SVP-like gene. As a complementary analysis, we used conserved and non-conserved DEGs that presented a negative correlation between DNA methylations and mRNA levels across all chilling conditions, obtaining Gene Ontology (GO) categories related to abiotic stress, metabolism, and oxidative stress. Altogether, this data indicates that changes in DNA methylation precedes transcript changes and may occur as an early response to low temperatures to increase the cold tolerance in the endodormancy period, contributing with the first methylome information about the effect of environmental cues over two different genotypes of sweet cherry.

From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy

Background

Bud dormancy is a crucial stage in perennial trees and allows survival over winter to ensure optimal flowering and fruit production. Recent work highlighted physiological and molecular events occurring during bud dormancy in trees. However, they usually examined bud development or bud dormancy in isolation. In this work, we aimed to further explore the global transcriptional changes happening throughout bud development and dormancy onset, progression and release.

Results

Using next-generation sequencing and modelling, we conducted an in-depth transcriptomic analysis for all stages of flower buds in several sweet cherry (Prunus avium L.) cultivars that are characterized for their contrasted dates of dormancy release. We find that buds in organogenesis, paradormancy, endodormancy and ecodormancy stages are defined by the expression of genes involved in specific pathways, and these are conserved between different sweet cherry cultivars. In particular, we found that DORMANCY ASSOCIATED MADS-box (DAM), floral identity and organogenesis genes are up-regulated during the pre-dormancy stages while endodormancy is characterized by a complex array of signalling pathways, including cold response genes, ABA and oxidation-reduction processes. After dormancy release, genes associated with global cell activity, division and differentiation are activated during ecodormancy and growth resumption. We then went a step beyond the global transcriptomic analysis and we developed a model based on the transcriptional profiles of just seven genes to accurately predict the main bud dormancy stages.

Conclusions

Overall, this study has allowed us to better understand the transcriptional changes occurring throughout the different phases of flower bud development, from bud formation in the summer to flowering in the following spring. Our work sets the stage for the development of fast and cost effective diagnostic tools to molecularly define the dormancy stages. Such integrative approaches will therefore be extremely useful for a better comprehension of complex phenological processes in many species.

Annual growth cycle observation, hybridization and forcing culture for improving the ornamental application of Paeonia lactiflora Pall. in the low-latitude regions

Expanding the southern range of herbaceous peony (Paeonia lactiflora Pall.) is a meaningful and worthwhile horticultural endeavor in the Northern Hemisphere. However, high temperatures in winter seriously hinder the bud dormancy release and flowering of peony in the more southern areas of subtropical and tropical regions. Resource introduction and hybridization can contribute to creating new cultivars with high adaptability in a warmer winter climate. In this study, three representative cultivars of P. lactiflora were screened for flowering capabilities and their annual growth cycles were observed to provide information needed for hybridization. Among these three cultivars, ‘Hang Baishao’ is the best adapted cultivar for southern growing regions and is unique in its ability to thrive in southern areas of N 30°00’. Pollen viability of ‘Hang Baishao’ was 55.60% based on five measuring methods, which makes it an excellent male parent in hybridization. Hybrid plants among these three cultivars grew well, but all of their flower buds aborted. Additionally, the ability of three growth regulators that advance the flowering of ‘Hang Baishao’ to promote an indoor cultivation strategy for improving peony application as a potted or cut-flower plant was tested. 5-azacytidine could impact the growth of ‘Hang Baishao’ and induce dwarfism and small flowers but not advance the flowering time. Gibberellin A₃ promoted the sprouting and growth significantly, but all plants eventually withered. Chilling at 0–4°C for four weeks and irrigation with 300 mg/L humic acid was the optimal combination used to hasten flowering and ensure flowering quality simultaneously. These results can lay the foundation for future studies on the chilling requirement trait, bud dormancy release and key functional gene exploration of herbaceous peony. Additionally, this study can also provide guidance for expanding the range of economically important plants with the winter dormancy trait to the low-latitude regions.

Apple whole genome sequences: recent advances and new prospects

In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for "what's next" focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.

Transcriptome Analysis Reveals Key Cold-Stress-Responsive Genes in Winter Rapeseed (Brassica rapa L.)

Low ambient air temperature limits the growth and selection of crops in cold regions, and cold tolerance is a survival strategy for overwintering plants in cold winters. Studies of differences in transcriptional levels of winter rapeseed (Brassica rapa L.) under cold stress can improve our understanding of transcript-mediated cold stress responses. In this study, two winter rapeseed varieties, Longyou-7 (cold-tolerant) and Lenox (cold-sensitive), were used to reveal morphological, physiological, and transcriptome levels after 24 h of cold stress, and 24 h at room temperature, to identify the mechanism of tolerance to cold stress. Compared to Lenox, Longyou-7 has a shorter growth period and greater belowground mass, and exhibits stronger physiological activity after cold stress. Subsequently, more complete genomic annotation was obtained by sequencing. A total of 10,251 and 10,972 differentially expressed genes (DEG) were identified in Longyou-7 and Lenox, respectively. Six terms closely related to cold stress were found by the Gene Ontology (GO) function annotation. Some of these terms had greater upregulated expression in Longyou-7, and the expression of these genes was verified by qRT-PCR. Most of these DEGs are involved in phenylpropanoid biosynthesis, plant hormone signal transduction, ribosome biogenesis, MAPK signaling pathway, basal transcription factors, and photosynthesis. Analysis of the genes involved in the peroxisome pathway revealed that Longyou-7 and Lenox may have different metabolic patterns. Some transcription factors may play an important role in winter rapeseed tolerance to cold stress, and Longyou-7 is slightly slower than Lenox. Our results provide a transcriptome database and candidate genes for further study of winter rapeseed cold stress.

Engineering Tree Seasonal Cycles of Growth Through Chromatin Modification

In temperate and boreal regions, perennial trees arrest cell division in their meristematic tissues during winter dormancy until environmental conditions become appropriate for their renewed growth. Release from the dormant state requires exposure to a period of chilling temperatures similar to the vernalization required for flowering in Arabidopsis. Over the past decade, genomic DNA (gDNA) methylation and transcriptome studies have revealed signatures of chromatin regulation during active growth and winter dormancy. To date, only a few chromatin modification genes, as candidate regulators of these developmental stages, have been functionally characterized in trees. In this work, we summarize the major findings of the chromatin-remodeling role during growth-dormancy cycles and we explore the transcriptional profiling of vegetative apical bud and stem tissues during dormancy. Finally, we discuss genetic strategies designed to improve the growth and quality of forest trees.

DNA Methylation Analysis of Dormancy Release in Almond (Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing

DNA methylation and histone post-translational modifications have been described as epigenetic regulation mechanisms involved in developmental transitions in plants, including seasonal changes in fruit trees. In species like almond (Prunus dulcis (Mill.) D.A: Webb), prolonged exposure to cold temperatures is required for dormancy release and flowering. Aiming to identify genomic regions with differential methylation states in response to chill accumulation, we carried out Illumina reduced-representation genome sequencing on bisulfite-treated DNA from floral buds. To do this, we analyzed almond genotypes with different chilling requirements and flowering times both before and after dormancy release for two consecutive years. The study was performed using epi-Genotyping by Sequencing (epi-GBS). A total of 7317 fragments were sequenced and the samples compared. Out of these fragments, 677 were identified as differentially methylated between the almond genotypes. Mapping these fragments using the Prunus persica (L.) Batsch v.2 genome as reference provided information about coding regions linked to early and late flowering methylation markers. Additionally, the methylation state of ten gene-coding sequences was found to be linked to the dormancy release process.

DNA Methylation Analysis of Dormancy Release in Almond (Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing

DNA methylation and histone post-translational modifications have been described as epigenetic regulation mechanisms involved in developmental transitions in plants, including seasonal changes in fruit trees. In species like almond (Prunus dulcis (Mill.) D.A: Webb), prolonged exposure to cold temperatures is required for dormancy release and flowering. Aiming to identify genomic regions with differential methylation states in response to chill accumulation, we carried out Illumina reduced-representation genome sequencing on bisulfite-treated DNA from floral buds. To do this, we analyzed almond genotypes with different chilling requirements and flowering times both before and after dormancy release for two consecutive years. The study was performed using epi-Genotyping by Sequencing (epi-GBS). A total of 7317 fragments were sequenced and the samples compared. Out of these fragments, 677 were identified as differentially methylated between the almond genotypes. Mapping these fragments using the Prunus persica (L.) Batsch v.2 genome as reference provided information about coding regions linked to early and late flowering methylation markers. Additionally, the methylation state of ten gene-coding sequences was found to be linked to the dormancy release process.

Seasonal Growth of Zygophyllum dumosum Boiss.: Summer Dormancy Is Associated with Loss of the Permissive Epigenetic Marker Dimethyl H3K4 and Extensive Reduction in Proteins Involved in Basic Cell Functions

Plants thriving in desert environments are suitable for studying mechanisms for plant survival under extreme seasonal climate variation. We studied epigenetic mechanisms underlying seasonal growth cycles in the desert plant Zygophyllum dumosum Boiss., which was previously shown to be deficient in repressive markers of di-methyl and tri-methyl H3K9 and their association with factors regulating basic cell functions. We showed a contingent association between rainfall and seasonal growth and the epigenetic marker of dimethyl H3K4, which disappears upon entry into the dry season and the acquisition of a dormant state. DNA methylation is not affected by a lack of H3K9 di-methyl and tri-methyl. Changes in methylation can occur between the wet and dry season. Proteome analysis of acid soluble fractions revealed an extensive reduction in ribosomal proteins and in proteins involved in chloroplasts and mitochondrial activities during the dry seasons concomitantly with up-regulation of molecular chaperone HSPs. Our results highlight mechanisms underlying Z. dumosum adaptation to seasonal climate variation. Particularly, summer dormancy is associated with a loss of the permissive epigenetic marker dimethyl H3K4, which might facilitate genome compaction concomitantly with a significant reduction in proteins involved in basic cell functions. HSP chaperones might safeguard the integrity of cell components.

Chilling-induced DNA Demethylation is associated with the cold tolerance of Hevea brasiliensis

BACKGROUND

Low temperature influences the development and latex production of rubber trees (Hevea brasiliensis) when extension to suboptimal high-latitude areas. The successful extension of Hevea brasiliensis cultivation to high-latitude areas has long believed to benefit from the breeding of cold-tolerant cultivars. A puzzling incongruity is the variation in cold tolerance among the cultivated clones despite their similar genetic make-up.

RESULTS

To investigate this, we first transferred cultivar Reyan 7-33-97 to short-term cold treatment, and showed that cold-related genes (such as HbICE1 and HbCBF2), cold-responsive (COR) genes, and DNA-methylation related genes (such as HbMET1) were induced by cold treatment. Furthermore, long-term cold treatment not only elevated the transcriptional activities of the HbICE1, HbCBF2, and HbMET, but also induced DNA demethylation of their promoters. Cold treatment increased the transcriptional activities of demethylation-related genes such as the HbDME, HbROS, and HbDML genes, but did not alter the promoter methylation status. Furthermore, the HbICE1 and HbMET promoters showed hypomethylation status in samples collected at the end of winter from 12 different cultivars grown in four geographical locations, but switched to hypermethylation status at the end of summer. Expression of COR was correlated with the low temperature. Given that little genetic diversity exists in the HbICE1 and HbMET promoters among different cultivars, the DNA demethylation induced by cold was highly correlated with low temperature, but not with the genetic backgrounds of cultivars.

CONCLUSION

Cold-induced epigenetic modification might play an important role in cold tolerance of H. brasiliensis.

Transcriptome Profiles Reveal the Crucial Roles of Hormone and Sugar in the Bud Dormancy of Prunus mume

Bud dormancy transition is a vital developmental process for perennial plant survival. The process is precisely regulated by diverse endogenous genetic factors and environmental cues, but the mechanisms are not yet fully understood. Prunus mume is an ideal crop for bud dormancy analysis because of its early spring-flowering characteristics and small sequenced genome. Here, we analyzed the transcriptome profiles at the three endodormancy stages and natural flush stage using RNA sequencing combined with phytohormone and sugar content measurements. Significant alterations in hormone contents and carbohydrate metabolism have been observed, and α-amylases, Glucan Hydrolase Family 17 and diphosphate-glycosyltransferase family might play crucial roles in the interactions between hormones and sugars. The following hypothetical model for understanding the molecular mechanism of bud dormancy in Prunus mume is proposed: low temperatures exposure induces the significant up-regulation of eight C-repeat binding factor genes, which directly promotes all six dormancy-associated MADS-box genes, resulting in dormancy establishment. The prolonged cold and/or subsequently increasing temperature then decreases the expression levels of these two gene families, which alleviates the inhibition of FLOWERING LOCUS T and reopens the growth-promoting pathway, resulting in dormancy release and the initiation of the bud break process.

Transcriptome profiling provides insights into dormancy release during cold storage of Lilium pumilum

Background

Bulbs of the ornamental flower Lilium pumilum enter a period of dormancy after flowering in spring, and require exposure to cold for a period of time in order to release dormancy. Previous studies focused mainly on anatomical, physiological and biochemical changes during dormancy release. There are no dormancy studies of the northern cold-hardy wild species of Lilium at the molecular level. This study observed bulb cell and starch granule ultrastructures during cold storage; and analysed the transcriptome using sequencing. The combination of morphological and transcriptomic methods provides valuable insights into dormancy release during cold storage of Lilium pumilum.

Results

Ultrastructural changes reflected dormancy release during cold storage of the bulbs. We compared gene expression levels among samples at 0 (S1 stage), 30 (S2 stage), 60 (S3 stage) and 90 (S4 stage) d of cold storage, with 0 d as the control. The data showed that some regulatory pathways such as carbohydrate metabolism and plant hormone signal transduction were activated to break dormancy. Some differentially expressed genes (DEGs) related to antioxidant activity, epigenetic modification and transcription factors were induced to respond to low temperature conditions. These genes constituted a complex regulatory mechanism of dormancy release.

Conclusions

Cytological data related to dormancy regulation was obtained through histomorphological observation; transcriptome sequencing provided comprehensive sequences and digital gene expression tag profiling (DGE) data, and bulb cell ultrastructural changes were closely related to DEGs. The novel Lilium pumilum genetic information from this study provides a reference for the regulation of dormancy by genetic engineering using molecular biology tools.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4536-x) contains supplementary material, which is available to authorized users.

Modulation of Dormancy and Growth Responses in Reproductive Buds of Temperate Trees

During autumn perennial trees cease growth and form structures called buds in order to protect meristems from the unfavorable environmental conditions, including low temperature and desiccation. In addition to increased tolerance to these abiotic stresses, reproductive buds modulate developmental programs leading to dormancy induction to avoid premature growth resumption, and flowering pathways. Stress tolerance, dormancy, and flowering processes are thus physically and temporarily restricted to a bud, and consequently forced to interact at the regulatory level. We review recent genomic, genetic, and molecular contributions to the knowledge of these three processes in trees, highlighting the role of epigenetic modifications, phytohormones, and common regulatory factors. Finally, we emphasize the utility of transcriptomic approaches for the identification of key structural and regulatory genes involved in bud processes, illustrated with our own experience using peach as a model.

Chromatin-associated regulation of sorbitol synthesis in flower buds of peach

PpeS6PDH gene is postulated to mediate sorbitol synthesis in flower buds of peach concomitantly with specific chromatin modifications. Perennial plants have evolved an adaptive mechanism involving protection of meristems within specialized structures named buds in order to survive low temperatures and water deprivation during winter. A seasonal period of dormancy further improves tolerance of buds to environmental stresses through specific mechanisms poorly known at the molecular level. We have shown that peach PpeS6PDH gene is down-regulated in flower buds after dormancy release, concomitantly with changes in the methylation level at specific lysine residues of histone H3 (H3K27 and H3K4) in the chromatin around the translation start site of the gene. PpeS6PDH encodes a NADPH-dependent sorbitol-6-phosphate dehydrogenase, the key enzyme for biosynthesis of sorbitol. Consistently, sorbitol accumulates in dormant buds showing higher PpeS6PDH expression. Moreover, PpeS6PDH gene expression is affected by cold and water deficit stress. Particularly, its expression is up-regulated by low temperature in buds and leaves, whereas desiccation treatment induces PpeS6PDH in buds and represses the gene in leaves. These data reveal the concurrent participation of chromatin modification mechanisms, transcriptional regulation of PpeS6PDH and sorbitol accumulation in flower buds of peach. In addition to its role as a major translocatable photosynthate in Rosaceae species, sorbitol is a widespread compatible solute and cryoprotectant, which suggests its participation in tolerance to environmental stresses in flower buds of peach.

Chilling Affects Phytohormone and Post-Embryonic Development Pathways during Bud Break and Fruit Set in Apple (Malus domestica Borkh.)

The availability of sufficient chilling during bud dormancy plays an important role in the subsequent yield and quality of apple fruit, whereas, insufficient chilling availability negatively impacts the apple production. The transcriptome profiling during bud dormancy release and initial fruit set under low and high chill conditions was performed using RNA-seq. The comparative high number of differentially expressed genes during bud break and fruit set under high chill condition indicates that chilling availability was associated with transcriptional reorganization. The comparative analysis reveals the differential expression of genes involved in phytohormone metabolism, particularly for Abscisic acid, gibberellic acid, ethylene, auxin and cytokinin. The expression of Dormancy Associated MADS-box, Flowering Locus C-like, Flowering Locus T-like and Terminal Flower 1-like genes was found to be modulated under differential chilling. The co-expression network analysis indentified two high chill specific modules that were found to be enriched for "post-embryonic development" GO terms. The network analysis also identified hub genes including Early flowering 7, RAF10, ZEP4 and F-box, which may be involved in regulating chilling-mediated dormancy release and fruit set. The results of transcriptome and co-expression network analysis indicate that chilling availability majorly regulates phytohormone-related pathways and post-embryonic development during bud break.

Global DNA Methylation Patterns Can Play a Role in Defining Terroir in Grapevine (Vitis vinifera cv. Shiraz)

Understanding how grapevines perceive and adapt to different environments will provide us with an insight into how to better manage crop quality. Mounting evidence suggests that epigenetic mechanisms are a key interface between the environment and the genotype that ultimately affect the plant's phenotype. Moreover, it is now widely accepted that epigenetic mechanisms are a source of useful variability during crop varietal selection that could affect crop performance. While the contribution of DNA methylation to plant performance has been extensively studied in other major crops, very little work has been done in grapevine. To study the genetic and epigenetic diversity across 22 vineyards planted with the cultivar Shiraz in six wine sub-regions of the Barossa, South Australia. Methylation sensitive amplified polymorphisms (MSAPs) were used to obtain global patterns of DNA methylation. The observed epigenetic profiles showed a high level of differentiation that grouped vineyards by their area of provenance despite the low genetic differentiation between vineyards and sub-regions. Pairwise epigenetic distances between vineyards indicate that the main contributor (23-24%) to the detected variability is associated to the distribution of the vineyards on the N-S axis. Analysis of the methylation profiles of vineyards pruned with the same system increased the positive correlation observed between geographic distance and epigenetic distance suggesting that pruning system affects inter-vineyard epigenetic differentiation. Finally, methylation sensitive genotyping by sequencing identified 3,598 differentially methylated genes in grapevine leaves that were assigned to 1,144 unique gene ontology terms of which 8.6% were associated with response to environmental stimulus. Our results suggest that DNA methylation differences between vineyards and sub-regions within The Barossa are influenced both by the geographic location and, to a lesser extent, by pruning system. Finally, we discuss how epigenetic variability can be used as a tool to understand and potentially modulate terroir in grapevine.

A Concise Review on Multi-Omics Data Integration for Terroir Analysis in Vitis vinifera

Vitis vinifera (grapevine) is one of the most important fruit crops, both for fresh consumption and wine and spirit production. The term terroir is frequently used in viticulture and the wine industry to relate wine sensory attributes to its geographic origin. Although, it can be cultivated in a wide range of environments, differences in growing conditions have a significant impact on fruit traits that ultimately affect wine quality. Understanding how fruit quality and yield are controlled at a molecular level in grapevine in response to environmental cues has been a major driver of research. Advances in the area of genomics, epigenomics, transcriptomics, proteomics and metabolomics, have significantly increased our knowledge on the abiotic regulation of yield and quality in many crop species, including V. vinifera. The integrated analysis of multiple 'omics' can give us the opportunity to better understand how plants modulate their response to different environments. However, 'omics' technologies provide a large amount of biological data and its interpretation is not always straightforward, especially when different 'omic' results are combined. Here we examine the current strategies used to integrate multi-omics, and how these have been used in V. vinifera. In addition, we also discuss the importance of including epigenomics data when integrating omics data as epigenetic mechanisms could play a major role as an intermediary between the environment and the genome.

Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)-A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes

Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare. However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop plants with large and complex genomes.

Rosaceae Fruit Development, Ripening and Post-harvest: An Epigenetic Perspective

Rosaceae is a family with an extraordinary spectrum of fruit types, including fleshy peach, apple, and strawberry that provide unique contributions to a healthy diet for consumers, and represent an excellent model for studying fruit patterning and development. In recent years, many efforts have been made to unravel regulatory mechanism underlying the hormonal, transcriptomic, proteomic and metabolomic changes occurring during Rosaceae fruit development. More recently, several studies on fleshy (tomato) and dry (Arabidopsis) fruit model have contributed to a better understanding of epigenetic mechanisms underlying important heritable crop traits, such as ripening and stress response. In this context and summing up the results obtained so far, this review aims to collect the available information on epigenetic mechanisms that may provide an additional level in gene transcription regulation, thus influencing and driving the entire Rosaceae fruit developmental process. The whole body of information suggests that Rosaceae fruit could become also a model for studying the epigenetic basis of economically important phenotypes, allowing for their more efficient exploitation in plant breeding.

Comprehensive Transcriptome Analyses Reveal Differential Gene Expression Profiles of Camellia sinensis Axillary Buds at Para-, Endo-, Ecodormancy, and Bud Flush Stages

Winter dormancy is an important biological feature for tea plant to survive cold winters, and it also affects the economic output of tea plant, one of the few woody plants in the world whose leaves are harvested and one of the few non-conifer evergreen species with characterized dormancies. To discover the bud dormancy regulation mechanism of tea plant in winter, we analyzed the global gene expression profiles of axillary buds at the paradormancy, endodormancy, ecodormancy, and bud flush stages by RNA-Seq analysis. In total, 16,125 differentially expressed genes (DEGs) were identified among the different measured conditions. Gene set enrichment analysis was performed on the DEGs identified from each dormancy transition. Enriched gene ontology terms, gene sets and transcription factors were mainly associated with epigenetic mechanisms, phytohormone signaling pathways, and callose-related cellular communication regulation. Furthermore, differentially expressed transcription factors as well as chromatin- and phytohormone-associated genes were identified. GI-, CAL-, SVP-, PHYB-, SFR6-, LHY-, ZTL-, PIF4/6-, ABI4-, EIN3-, ETR1-, CCA1-, PIN3-, CDK-, and CO-related gene sets were enriched. Based on sequence homology analysis, we summarized the key genes with significant expression differences in poplar and tea plant. The major molecular pathways involved in tea plant dormancy regulation are consistent with those of poplar to a certain extent; however, the gene expression patterns varied. This study provides the global transcriptome profiles of overwintering buds at different dormancy stages and is meaningful for improving the understanding of bud dormancy in tea plant.