Changes in histone H3 and H4 multi-acetylation during natural and forced dormancy break in potato tubers

Genome-wide analysis of non-coding RNA reveals the role of a novel miR319c for tuber dormancy release process in potato

Tuber dormancy and sprouting are significant for potato cultivation, storage, and processing. Although the substantial role of microRNAs (miRNAs) in some biological processes has been recognized, the critical role of miRNA in breaking potato tuber dormancy is not well understood to date. In this investigation, we expand research on miRNA-mediated gene regulation in tuber dormancy release. In this work, 204 known and 192 novel miRNAs were identified. One hundred thirty-six differentially expressed miRNAs (DE-miRNAs) were also screened out, of which 56 DE-miRNAs were regulated by temperature during tuber dormancy release. Additionally, degradome sequencing revealed that 821 target genes for 202 miRNAs were discovered. Among them, 63 target genes and 48 miRNAs were predicted to be involved in plant hormone signaling pathways. This study used degradome sequencing, tobacco cotransformation system, and β-glucuronidase (GUS) staining technology to confirm that stu-miR319c can target StTCP26 and StTCP27 and effectively suppress their expression. The transgenic approach exhibited that stu-miR319c overexpressed tubers sprouted in advance, while silent expression of stu-miR319c showed delayed sprouting. Treatment of wild-type tubers with exogenous MeJA revealed that 1 mg/L MeJA significantly broke dormancy and enhanced potato sprouting ability. Furthermore, transgenic tubers revealed variance in jasmonic acid (JA) content and relative expression of genes associated with the JA synthesis pathway, including StAOC, StLOX2, and StLOX4, suggesting that the miR319c may participate in the JA pathway to regulate tuber dormancy release. In summary, our research offers evidence that miRNA regulates potato dormancy release and supports the idea that stu-miR319c is a unique epigenetic regulator for dormancy-sprouting transition in potatoes.

Analysis of Stress Response Genes in Microtuberization of Potato Solanum tuberosum L.: Contributions to Osmotic and Combined Abiotic Stress Tolerance

Wild Solanum species have contributed many introgressed genes during domestication into current cultivated potatoes, enhancing their biotic and abiotic stress resistance and facilitating global expansion. Abiotic stress negatively impacts potato physiology and productivity. Understanding the molecular mechanisms regulating tuber development may help solve this global problem. We made a transcriptomic analysis of potato microtuberization under darkness, cytokinins, and osmotic stress conditions. A protein-protein interaction (PPI) network analysis identified 404 genes with high confidence. These genes were involved in important processes like oxidative stress, carbon metabolism, sterol biosynthesis, starch and sucrose metabolism, fatty acid biosynthesis, and nucleosome assembly. From this network, we selected nine ancestral genes along with eight additional stress-related genes. We used qPCR to analyze the expression of the selected genes under osmotic, heat-osmotic, cold-osmotic, salt-osmotic, and combined-stress conditions. The principal component analysis (PCA) revealed that 60.61% of the genes analyzed were associated with osmotic, cold-osmotic, and heat-osmotic stress. Seven out of ten introgression/domestication genes showed the highest variance in the analysis. The genes H3.2 and GAPCP1 were involved in osmotic, cold-osmotic, and heat-osmotic stress. Under combined-all stress, TPI and RPL4 were significant, while in salt-osmotic stress conditions, ENO1, HSP70-8, and PER were significant. This indicates the importance of ancestral genes for potato survival during evolution. The targeted manipulation of these genes could improve combined-stress tolerance in potatoes, providing a genetic basis for enhancing crop resilience.

Similar chilling response of dormant buds in potato tuber and woody perennials

Bud dormancy is a survival strategy that plants have developed in their native habitats. It helps them endure harsh seasonal changes by temporarily halting growth and activity until conditions become more favorable. Research has primarily focused on bud dormancy in tree species and the ability to halt growth in vegetative tissues, particularly in meristems. Various plant species, such as potato, have developed specialized storage organs, enabling them to become dormant during their yearly growth cycle. Deciduous trees and potato tubers exhibit a similar type of bud endodormancy, where the bud meristem will not initiate growth, even under favorable environmental conditions. Chilling accumulation activates C-repeat/dehydration responsive element binding (DREB) factors (CBFs) transcription factors that modify the expression of dormancy-associated genes. Chilling conditions shorten the duration of endodormancy by influencing plant hormones and sugar metabolism, which affect the timing and rate of bud growth. Sugar metabolism and signaling pathways can interact with abscisic acid, affecting the symplastic connection of dormant buds. This review explores how chilling affects endodormancy duration and explores the similarity of the chilling response of dormant buds in potato tubers and woody perennials.

Physiological and molecular mechanisms associated with potato tuber dormancy

Tuber dormancy is an important physiological trait that impacts post-harvest storage and end-use qualities of potatoes. Overall, dormancy regulation of potato tubers is a complex process driven by genetic as well as environmental factors. Elucidation of the molecular and physiological mechanisms that influence different dormancy stages of tubers has wider potato breeding and industry-relevant implications. Therefore, the primary objective of this review is to present current knowledge of the diversity in tuber dormancy traits among wild relatives of potatoes and discuss how genetic and epigenetic factors contribute to tuber dormancy. Advancements in understanding of key physiological mechanisms involved in tuber dormancy regulation, such as apical dominance, phytohormone metabolism, and oxidative stress responses, are also discussed. This review highlights the impacts of common sprout suppressors on the molecular and physiological mechanisms associated with tuber dormancy and other storage qualities. Collectively, the literature suggests that significant changes in expression of genes associated with the cell cycle, phytohormone metabolism, and oxidative stress response influence initiation, maintenance, and termination of dormancy in potato tubers. Commercial sprout suppressors mainly alter the expression of genes associated with the cell cycle and stress responses and suppress sprout growth rather than prolonging tuber dormancy.

Emerging into the world: regulation and control of dormancy and sprouting in geophytes

Geophytic plants synchronize growth and quiescence with the external environment to survive and thrive under changing seasons. Together with seasonal growth adaptation, dormancy and sprouting are critical factors determining crop yield and market supply, as various geophytes also serve as major food, floriculture, and ornamental crops. Dormancy in such crops determines crop availability in the market, as most of them are consumed during the dormant stage. On the other hand, uniform/maximal sprouting is crucial for maximum yield. Thus, dormancy and sprouting regulation have great economic importance. Dormancy-sprouting cycles in geophytes are regulated by genetic, exogenous (environmental), and endogenous (genetic, metabolic, hormonal, etc.) factors. Comparatively, the temperature is more dominant in regulating dormancy and sprouting in geophytes, unlike above-ground tissues, where both photoperiod and temperature control are involved. Despite huge economic importance, studies concerning the regulation of dormancy and sprouting are scarce in the majority of geophytes. To date, only a few molecular factors involved in the process have been suggested. Recently, omics studies on molecular and metabolic factors involved in dormancy and growth regulation of underground vegetative tissues have provided more insight into the mechanism. Here, we discuss current knowledge of the environmental and molecular regulation and control of dormancy and sprouting in geophytes, and discuss challenges/questions that need to be addressed in the future for crop improvement.

Comprehensive Proteome and Acetylome Analysis of Needle Senescence in Larix gmelinii

Leaf senescence is essential for the growth and development of deciduous trees in the next season. Larix gmelinii, a deciduous coniferous tree, exhibits its most distinctive feature by turning yellow in the autumn and eventually shedding its leaves, resulting in significant changes in its appearance during the fall. Lysine acetylation plays an important role in diverse cellular processes; however, limited knowledge is available regarding acetylations in the needle senescence of L. gmelinii. In this study, the proteomics and acetylated modification omics of two phenotypic leaves, yellow and green (senescent and non-senescent) needles, were analyzed before autumn defoliation. In total, 5022 proteins and 4469 unique acetylation sites in 2414 lysine acylated proteins were identified, and this resulted in the discovery of 1335 differentially expressed proteins (DEPs) and 605 differentially expressed acetylated proteins (DAPs) in yellow versus green needles. There are significant differences between the proteome and acetylome; only 269 proteins were found to be DEP and DAP, of which 136 proteins were consistently expressed in both the DEP and DAP, 91 proteins were upregulated, and 45 proteins were down-regulated. The DEPs participate in the metabolism of starch and sucrose, while the DAPs are involved in glycolysis and the tricarboxylic acid cycle. Among them, DEPs underwent significant changes in glycolysis and citric acid cycling. Most of the enzymes involved in glycolysis and the citrate cycle were acetylated. DAPs were down-regulated in glycolysis and up-regulated in the citrate cycle. In all, the results of this study reveal the important role of lysine acetylation in the senescence of L. gmelinii needles and provide a new perspective for understanding the molecular mechanism of leaf senescence and tree seasonal growth.

Advances in the Modulation of Potato Tuber Dormancy and Sprouting

The post-harvest phase of potato tuber dormancy and sprouting are essential in determining the economic value. The intricate transition from dormancy to active growth is influenced by multiple factors, including environmental factors, carbohydrate metabolism, and hormonal regulation. Well-established environmental factors such as temperature, humidity, and light play pivotal roles in these processes. However, recent research has expanded our understanding to encompass other novel influences such as magnetic fields, cold plasma treatment, and UV-C irradiation. Hormones like abscisic acid (ABA), gibberellic acid (GA), cytokinins (CK), auxin, and ethylene (ETH) act as crucial messengers, while brassinosteroids (BRs) have emerged as key modulators of potato tuber sprouting. In addition, jasmonates (JAs), strigolactones (SLs), and salicylic acid (SA) also regulate potato dormancy and sprouting. This review article delves into the intricate study of potato dormancy and sprouting, emphasizing the impact of environmental conditions, carbohydrate metabolism, and hormonal regulation. It explores how various environmental factors affect dormancy and sprouting processes. Additionally, it highlights the role of carbohydrates in potato tuber sprouting and the intricate hormonal interplay, particularly the role of BRs. This review underscores the complexity of these interactions and their importance in optimizing potato dormancy and sprouting for agricultural practices.

Genome-wide identification and expression analysis reveal the role of histone methyltransferase and demethylase genes in heat stress response in potato (Solanum tuberosum L.)

BACKGROUND

Potato (Solanum tuberosum L.), the third most important non-cereal crop, is sensitive to high temperature. Histone modifications have been known to regulate various abiotic stress responses. However, the role of histone methyltransferases and demethylases remain unexplored in potato under heat stress.

METHODS

Potato genome database was used for genome-wide analysis of StPRMT and StHDMA gene families, which were further characterized by analyzing gene structure, conserved motif, domain organization, sub-cellular localization, promoter region and phylogenetic relationships. Additionally, expression profiling under high-temperature stress in leaf and stolon tissue of heat contrasting potato genotypes was done to study their role in response to high temperature stress.

RESULTS

The genome-wide analysis led to identification of nine StPRMT and eleven StHDMA genes. Structural analysis, including conserved motifs, exon/intron structure and phylogenetic relationships classified StPRMT and StHDMA gene families into two classes viz. Class I and Class II. A variety of cis-regulatory elements were explored in the promoter region associated with light, developmental, hormonal and stress responses. Prediction of sub-cellular localization of StPRMT proteins revealed their occurrence in nucleus and cytoplasm, whereas StHDMA proteins were observed in different sub-cellular compartments. Furthermore, expression profiling of StPRMT and StHDMA gene family members revealed genes responding to heat stress. Heat-inducible expression of StPRMT1, StPRMT3, StPRMT4 and StPRMT5 in leaf and stolon tissues of HS and HT cultivar indicated them as probable candidates for enhancing thermotolerance in potato. However, StHDMAs responded dynamically in leaf and stolon tissue of heat contrasting genotypes under high temperature.

CONCLUSION

The current study presents a detailed analysis of histone modifiers in potato and indicates their role as an important epigenetic regulators modulating heat tolerance.

GENERAL SIGNIFICANCE

Understanding epigenetic mechanisms underlying heat tolerance in potato will contribute towards breeding of thermotolerant potato varieties.

Multi-Omic Analysis Reveals the Molecular Mechanism of UV-B Stress Resistance in Acetylated RcMYB44 in Rhododendron chrysanthum

Ultraviolet-B (UV-B) radiation is a significant environmental factor influencing the growth and development of plants. MYBs play an essential role in the processes of plant responses to abiotic stresses. In the last few years, the development of transcriptome and acetylated proteome technologies have resulted in further and more reliable data for understanding the UV-B response mechanism in plants. In this research, the transcriptome and acetylated proteome were used to analyze Rhododendron chrysanthum Pall. (R. chrysanthum) leaves under UV-B stress. In total, 2348 differentially expressed genes (DEGs) and 685 differentially expressed acetylated proteins (DAPs) were found. The transcriptome analysis revealed 232 MYB TFs; we analyzed the transcriptome together with the acetylated proteome, and screened 4 MYB TFs. Among them, only RcMYB44 had a complete MYB structural domain. To investigate the role of RcMYB44 under UV-B stress, a homology tree was constructed between RcMYB44 and Arabidopsis MYBs, and it was determined that RcMYB44 shares the same function with ATMYB44. We further constructed the hormone signaling pathway involved in RcMYB44, revealing the molecular mechanism of resistance to UV-B stress in R. chrysanthum. Finally, by comparing the transcriptome and the proteome, it was found that the expression levels of proteins and genes were inconsistent, which is related to post-translational modifications of proteins. In conclusion, RcMYB44 of R. chrysanthum is involved in mediating the growth hormone, salicylic acid, jasmonic acid, and abscisic acid signaling pathways to resist UV-B stress.

Deciphering the Atlas of Post-Translational Modification in Sugarcane

In plants, lysine acetylation (Kac), 2-hydroxyisobutyrylation (Khib), and lysine lactylation (Kla), the three new types of post-translational modification (PTM), play very important roles in growth, development, and resistance to adverse environmental stresses. Herein, we report the first global acetylome, 2-hydroxyisobutyrylome, and lactylome in sugarcane. A total of 8573 Kac, 4637 Khib, and 215 Kla sites across 3903, 1507, and 139 modified proteins were identified. Besides, homology analyses revealed the Kac, Khib, and Kla sites on histones were conserved between sugarcane and rice or poplar. Functional annotations demonstrated that the Kac, Khib, and Kla proteins were mainly involved in energy metabolism. In addition, a number of modified transcription factors and stress-related proteins, which were constitutively expressed in different tissues of sugarcane and induced by drought, cold or Sporisorium scitamineum stress, were identified. Finally, a proposed working mode on how PTM functions in sugarcane was depicted. We thus concluded that PTM should play a role in sugarcane growth, development, and response to biotic and abiotic stresses, but the mechanisms require further investigation. The present study provided the all-new comprehensive profile of proteins Kac, Khib, and Kla and a new perspective to understand the molecular mechanisms of protein PTMs in sugarcane.

Global DNA methylation and cellular 5-methylcytosine and H4 acetylated patterns in primary and secondary dormant seeds of Capsella bursa-pastoris (L.) Medik. (shepherd's purse)

Despite the importance of dormancy and dormancy cycling for plants' fitness and life cycle phenology, a comprehensive characterization of the global and cellular epigenetic patterns across space and time in different seed dormancy states is lacking. Using Capsella bursa-pastoris (L.) Medik. (shepherd's purse) seeds with primary and secondary dormancy, we investigated the dynamics of global genomic DNA methylation and explored the spatio-temporal distribution of 5-methylcytosine (5-mC) and histone H4 acetylated (H4Ac) epigenetic marks. Seeds were imbibed at 30 °C in a light regime to maintain primary dormancy, or in darkness to induce secondary dormancy. An ELISA-based method was used to quantify DNA methylation, in relation to total genomic cytosines. Immunolocalization of 5-mC and H4Ac within whole seeds (i.e., including testa) was assessed with reference to embryo anatomy. Global DNA methylation levels were highest in prolonged (14 days) imbibed primary dormant seeds, with more 5-mC marked nuclei present only in specific parts of the seed (e.g., SAM and cotyledons). In secondary dormant seeds, global methylation levels and 5-mC signal where higher at 3 and 7 days than 1 or 14 days. With respect to acetylation, seeds had fewer H4Ac marked nuclei (e.g., SAM) in deeper dormant states, for both types of dormancy. However, the RAM still showed signal after 14 days of imbibition under dormancy-inducing conditions, suggesting a central role for the radicle/RAM in the response to perceived ambient changes and the adjustment of the seed dormancy state. Thus, we show that seed dormancy involves extensive cellular remodeling of DNA methylation and H4 acetylation.

Advances in proteome-wide analysis of plant lysine acetylation

Lysine acetylation (LysAc) is a conserved and important post-translational modification (PTM) that plays a key role in plant physiological and metabolic processes. Based on advances in Lys-acetylated protein immunoenrichment and mass-spectrometric technology, LysAc proteomics studies have been performed in many species. Such studies have made substantial contributions to our understanding of plant LysAc, revealing that Lys-acetylated histones and nonhistones are involved in a broad spectrum of plant cellular processes. Here, we present an extensive overview of recent research on plant Lys-acetylproteomes. We provide in-depth insights into the characteristics of plant LysAc modifications and the mechanisms by which LysAc participates in cellular processes and regulates metabolism and physiology during plant growth and development. First, we summarize the characteristics of LysAc, including the properties of Lys-acetylated sites, the motifs that flank Lys-acetylated lysines, and the dynamic alterations in LysAc among different tissues and developmental stages. We also outline a map of Lys-acetylated proteins in the Calvin-Benson cycle and central carbon metabolism-related pathways. We then introduce some examples of the regulation of plant growth, development, and biotic and abiotic stress responses by LysAc. We discuss the interaction between LysAc and Nα-terminal acetylation and the crosstalk between LysAc and other PTMs, including phosphorylation and succinylation. Finally, we propose recommendations for future studies in the field. We conclude that LysAc of proteins plays an important role in the regulation of the plant life cycle.

ABA and Bud Dormancy in Perennials: Current Knowledge and Future Perspective

Bud dormancy is an evolved trait that confers adaptation to harsh environments, and affects flower differentiation, crop yield and vegetative growth in perennials. ABA is a stress hormone and a major regulator of dormancy. Although the physiology of bud dormancy is complex, several advancements have been achieved in this field recently by using genetics, omics and bioinformatics methods. Here, we review the current knowledge on the role of ABA and environmental signals, as well as the interplay of other hormones and sucrose, in the regulation of this process. We also discuss emerging potential mechanisms in this physiological process, including epigenetic regulation.

Phytohormones: plant switchers in developmental and growth stages in potato

BACKGROUND

Potato is one of the most important food crops worldwide, contributing key nutrients to the human diet. Plant hormones act as vital switchers in the regulation of various aspects of developmental and growth stages in potato. Due to the broad impacts of hormones on many developmental processes, their role in potato growth and developmental stages has been investigated. This review presents a description of hormonal basic pathways, various interconnections between hormonal network and reciprocal relationships, and clarification of molecular events underlying potato growth. In the last decade, new findings have emerged regarding their function during sprout development, vegetative growth, tuber initiation, tuber development, and maturation in potato. Hormones can control the regulation of various aspects of growth and development in potato, either individually or in combination with other hormones. The molecular characterization of interplay between cytokinins (CKs), abscisic acid (ABA), and auxin and/or gibberellins (GAs) during tuber formation requires further undertaking. Recently, new evidences regarding the relative functions of hormones during various stages and an intricate network of several hormones controlling potato tuber formation are emerging. Although some aspects of their functions are widely covered, remarkable breaks in our knowledge and insights yet exist in the regulation of hormonal networks and their interactions during different stages of growth and various aspects of tuber formation.

SHORT CONCLUSION

The present review focuses on the relative roles of hormones during various developmental stages with a view to recognize their mechanisms of function in potato tuber development. For better insight, relevant evidences available on hormonal interaction during tuber development in other species are also described. We predict that the present review highlights some of the conceptual developments in the interplay of hormones and their associated downstream events influencing tuber formation.

Poplar acetylome profiling reveals lysine acetylation dynamics in seasonal bud dormancy release

For perennials in boreal and temperate ecosystems, bud dormancy is crucial for survival in harsh winter. Dormancy is released by prolonged exposure to low temperatures and is followed by reactive growth in the spring. Lysine acetylation (Kac) is one of the major post-translational modifications (PTMs) that are involved in plant response to environmental signals. However, little information is available on the effects of Kac modification on bud dormancy release. Here, we report the dynamics of lysine acetylome in hybrid poplar (Populus tremula × Populus alba) dormant buds. A total of 7,594 acetyl-sites from 3,281 acetyl-proteins were identified, representing a large dataset of lysine acetylome in plants. Of them, 229 proteins were differentially acetylated during bud dormancy release and were mainly involved in the primary metabolic pathways. Site-directed mutagenesis enzymatic assays showed that Kac strongly modified the activities of two key enzymes of primary metabolism, pyruvate dehydrogenase (PDH) and isocitrate dehydrogenase (IDH). We thus propose that Kac of enzymes could be an important strategy for reconfiguration of metabolic processes during bud dormancy release. In all, our results reveal the importance of Kac in bud dormancy release and provide a new perspective to understand the molecular mechanisms of seasonal growth of trees.

Morphological, anatomical and DNA methylation changes of tree peony buds during chilling induced dormancy release

Bud endodormancy in tree peony is a growth cessation-like state, and sufficient chilling perception is necessary to break it. In this study, 120 plants were subjected to 0-4 °C climate chamber for 0-28 d with a weekly interval, morphology and structure changes of buds were studied with a scanning electron microscope (SEM) and paraffin sections during the dormancy process. Dormancy status was evaluated after being transferred to greenhouse for 30 d. Results showed that the diameter of the buds gradually expanded, along with continuous elongation of sepals, petals, stamens and carpels in the chilling accumulation process. Notably, dormancy release was marked with the establishment of xylem vessels in lateral vein of the petal. Meanwhile, DNA methylation was detected by HPLC and immunochemical technology, aimed to illuminate the role of DNA methylation in the dormancy release, we found that 5 mC level fell from 39.4% to 24.2% after exposed to 28 d chilling. These results were consistent with the immunochemical analysis, and inversely related to the sprouting rate after being moved to greenhouse for 30 d. Exogenous application of 5azaC (5-azacytidine) decreased DNA methylation level, accompanied by an improved bud sprouting capacity, while the effect of SAM (S-adenosylmethionine) was the opposite. In summary, prolonged chilling was accompanied by further differentiation and development of the compound bud, which resulted in DNA hypomethylation and promoted dormancy release in tree peony.

MADS-Box Genes Are Key Components of Genetic Regulatory Networks Involved in Abiotic Stress and Plastic Developmental Responses in Plants

Plants, as sessile organisms, adapt to different stressful conditions, such as drought, salinity, extreme temperatures, and nutrient deficiency, via plastic developmental and growth responses. Depending on the intensity and the developmental phase in which it is imposed, a stress condition may lead to a broad range of responses at the morphological, physiological, biochemical, and molecular levels. Transcription factors are key components of regulatory networks that integrate environmental cues and concert responses at the cellular level, including those that imply a stressful condition. Despite the fact that several studies have started to identify various members of the MADS-box gene family as important molecular components involved in different types of stress responses, we still lack an integrated view of their role in these processes. In this review, we analyze the function and regulation of MADS-box gene family members in response to drought, salt, cold, heat, and oxidative stress conditions in different developmental processes of several plants. In addition, we suggest that MADS-box genes are key components of gene regulatory networks involved in plant responses to stress and plant developmental plasticity in response to seasonal changes in environmental conditions.

On the language and physiology of dormancy and quiescence in plants

The language of dormancy is rich and poetic, as researchers spanning disciplines and decades have attempted to understand the spell that entranced 'Sleeping Beauty', and how she was gently awoken. The misleading use of 'dormancy', applied to annual axillary buds, for example, has confounded progress. Language is increasingly important as genetic and genomic approaches become more accessible to species of agricultural and ecological importance. Here we examine how terminology has been applied to different eco-physiological states in plants, and with pertinent reference to quiescent states described in other domains of life, in order to place plant quiescence and dormancy in a more complete context than previously described. The physiological consensus defines latency or quiescence as opportunistic avoidance states, where growth resumes in favourable conditions. In contrast, the dormant state in higher plants is entrained in the life history of the organism. Competence to resume growth requires quantitative and specific conditioning. This definition applies only to the embryo of seeds and specialized meristems in higher plants; however, mechanistic control of dormancy extends to mobile signals from peripheral tissues and organs, such as the endosperm of seed or subtending leaf of buds. The distinction between dormancy, quiescence, and stress-hardiness remains poorly delineated, most particularly in buds of winter perennials, which comprise multiple meristems of differing organogenic states. Studies in seeds have shown that dormancy is not a monogenic trait, and limited study has thus far failed to canalize dormancy as seen in seeds and buds. We argue that a common language, based on physiology, is central to enable further dissection of the quiescent and dormant states in plants. We direct the topic largely to woody species showing a single cycle of growth and reproduction per year, as these bear the majority of global timber, fruit, and nut production, as well being of great ecological value. However, for context and hypotheses, we draw on knowledge from annuals and other specialized plant conditions, from a perspective of the major physical, metabolic, and molecular cues that regulate cellular activity.

Transcriptomic analysis of the underground renewal buds during dormancy transition and release in 'Hangbaishao' peony (Paeonia lactiflora)

Paeonia lactiflora is one of the most famous species of herbaceous peonies with gorgeous flowers. Bud dormancy is a crucial developmental process that allows P. lactiflora to survive unfavorable environmental conditions. However, little information is available on the molecular mechanism of the bud dormancy in P. lactiflora. We performed de novo transcriptome sequencing using the Illumina RNA sequencing platform for the underground renewal buds of P. lactiflora 'Hangbaishao' to study the molecular mechanism underlying its bud dormancy transition (the period from endodormancy to ecodormancy) and release (the period from ecodormancy to bud elongation and sprouting). Approximately 300 million high-quality clean reads were generated and assembled into 207,827 (mean length = 828 bp) and 51,481 (mean length = 1250 bp) unigenes using two assembly methods named "Trinity" and "Trinity+PRICE", respectively. Based on the data obtained by the latter method, 32,316 unigenes were annotated by BLAST against various databases. Approximately 1,251 putative transcription factors were obtained, of which the largest number of unique transcripts belonged to the basic helix-loop-helix protein (bHLH) transcription factor family, and five of the top ten highly expressed transcripts were annotated as dehydrin (DHN). A total of 17,705 simple sequence repeat (SSR) motifs distributed in 13,797 sequences were obtained. The budbreak morphology, levels of indole-3-acetic acid (IAA) and abscisic acid (ABA), and activities of guaiacol peroxidase (POD) and catalase (CAT) were observed. The expression of 20 interested unigenes, which annotated as DHN, heat shock protein (HSP), histone, late elongated hypocotyl (LHY), and phytochrome (PHY), and so on, were also analyzed. These studies were based on morphological, physiological, biochemical, and molecular levels and provide comprehensive insight into the mechanism of dormancy transition and release in P. lactiflora. Transcriptome dataset can be highly valuable for future investigation on gene expression networks in P. lactiflora as well as research on dormancy in other non-model perennial horticultural crops of commercial significance.

Proteomic changes during tuber dormancy release process revealed by iTRAQ quantitative proteomics in potato

Given that limited information is available with regard to tuber dormancy release related proteome, we conducted proteome analysis of tuber dormancy release process at dormant tuber (DT), dormancy release tuber (DRT) and sprouting tuber (ST) using the iTRAQ technology. A total of 1,752 proteins were identified. Among them, a subset of 316 proteins was screened as significant up- (137) and down regulated (179) between DT vs DRT. A subset of 120 proteins experienced significant up- (40) or down-regulation (80) between DRT vs ST. The differentially expressed proteins were grouped into 11 functional categories. Proteins enriched in functional categories of major carbohydrate (CHO) metabolism, glycolysis, fermentation, amino acid metabolism, protein and transport were highly up-regulated, while functional categories of photosynthesis and RNA were down-regulated between DT vs DRT. Proteins enriched in functional groups of protein, cell wall, lipid metabolism, miscellaneous, and signaling were strongly up-regulated, while functional categories of photosynthesis, hormone metabolism and protein were down-regulated between DRT vs ST. Consistent with previous documented differentially expressed genes, most of differentially expressed proteins were also identified between DT and DRT, indicating the metabolism shift from growth suspension to growth activation as tubers dormancy breaking. The changes in protein profiles showed lower concordance with corresponding alterations in transcript levels, indicating possible transcriptional and posttranscriptional regulation. Furthermore, the possible mechanism of tuber dormancy release was discussed in relation to what was known in transcripts change and other plant models from carbohydrate metabolism, protein metabolism, stress response, redox regulation, transcription regulation, DNA metabolism, amino acid metabolism, development, signaling as well as hormone metabolism.

Treatment of potato tubers with the synthetic cytokinin 1-(α-ethylbenzyl)-3-nitroguanidine results in rapid termination of endodormancy and induction of transcripts associated with cell proliferation and growth

Perennial plants undergo repression of meristematic activity in a process called dormancy. Dormancy is a complex metabolic process with implications for plant breeding and crop yield. Endodormancy, a specific subclass of dormancy, is characteristic of internal physiological mechanisms resulting in growth suppression. In this study, we examine transcriptional changes associated with the natural cessation of endodormancy in potato tuber meristems and in endodormant tubers treated with the cytokinin analog 1-(α-ethylbenzyl)-3-niroguanidine (NG), which terminates dormancy. RNA-sequencing was used to examine transcriptome changes between endodormant and non-dormant meristems from four different harvest years. A total of 35,091 transcripts were detected with 2132 differentially expressed between endodormant and non-dormant tuber meristems. Endodormant potato tubers were treated with the synthetic cytokinin NG and transcriptome changes analyzed using RNA-seq after 1, 4, and 7 days following NG exposure. A comparison of natural cessation of dormancy and NG-treated tubers demonstrated that by 4 days after NG exposure, potato meristems exhibited transcriptional profiles similar to the non-dormant state with elevated expression of multiple histones, a variety of cyclins, and other genes associated with proliferation and cellular replication. Three homologues encoding for CYCD3 exhibited elevated expression in both non-dormant and NG-treated potato tissues. These results suggest that NG terminates dormancy and induces expression cell cycle-associated transcripts within 4 days of treatment.

Changes in histone methylation and acetylation during microspore reprogramming to embryogenesis occur concomitantly with Bn HKMT and Bn HAT expression and are associated with cell totipotency, proliferation, and differentiation in Brassica napus

In response to stress treatments, microspores can be reprogrammed to become totipotent cells that follow an embryogenic pathway producing haploid and double-haploid embryos which are important biotechnological tools in plant breeding. Recent studies have revealed the involvement of DNA methylation in regulating this process, but no information is available on the role of histone modifications in microspore embryogenesis. Histone modifications are major epigenetic marks controlling gene expression during plant development and in response to environmental changes. Lysine methylation of histones, accomplished by histone lysine methyltransferases (HKMTs), can occur on different lysine residues, with histone H3K9 methylation being mainly associated with transcriptionally silenced regions. In contrast, histone H3 and H4 acetylation is carried out by histone acetyltransferases (HATs) and is associated with actively transcribed genes. In this work, we analyzed 3 different histone epigenetic marks: dimethylation of H3K9 (H3K9me2) and acetylation of H3 and H4 (H3Ac and H4Ac) during microspore embryogenesis in Brassica napus by Western blot and immunofluorescence assays. The expression patterns of histone methyltransferase BnHKMT and histone acetyltransferase BnHAT genes have also been analyzed by qPCR. Our results revealed different spatial and temporal distribution patterns for methylated and acetylated histone variants during microspore embryogenesis and their similarity with the expression profiles of BnHKMT and BnHAT, respectively. The data presented suggest the participation of H3K9me2 and HKMT in embryo cell differentiation and heterochromatinization events, whereas H3Ac, H4Ac, and HAT would be involved in transcriptional activation, totipotency, and proliferation events during cell reprogramming and embryo development.

Regulation of potato tuber sprouting

Following tuber induction, potato tubers undergo a period of dormancy during which visible bud growth is inhibited. The length of the dormancy period is under environmental, physiological and hormonal control. Sucrose availability is one prerequisite for bud break. In the absence of sucrose, no bud break occurs. Thus, sucrose is likely to serve as nutrient and signal molecule at the same time. The mode of sucrose sensing is only vaguely understood, but most likely involves trehalose-6-phosphate and SnRK1 signalling networks. This conclusion is supported by the observation that ectopically manipulation of trehalose-6-phosphate levels influences the length of the dormancy period. Once physiological competence is achieved, sprouting is controlled by the level of phytohormones. Two phytohormones, ABA and ethylene, are supposed to suppress tuber sprouting; however, the exact role of ethylene remains to be elucidated. Cytokinins and gibberellins are required for bud break and sprout growth, respectively. The fifth classical phytohormone, auxin, seems to play a role in vascular development. During the dormancy period, buds are symplastically isolated, which changes during bud break. In parallel to the establishment of symplastic connectivity, vascular tissue develops below the growing bud most likely to support the outgrowing sprout with assimilates mobilised in parenchyma cells. Sprouting leads to major quality losses of stored potato tubers. Therefore, control of tuber sprouting is a major objective in potato breeding. Although comparative transcriptome analysis revealed a large number of genes differentially expressed in growing versus dormant buds, no master-regulator of potato tuber sprouting has been identified so far.

Transcriptome analysis of Japanese pear (Pyrus pyrifolia Nakai) flower buds transitioning through endodormancy

The transcriptomes of endodormant and ecodormant Japanese pear (Pyrus pyrifolia Nakai 'Kosui') flower buds were analyzed using RNA-seq technology and compared. Among de novo assembly of 114,191 unigenes, 76,995 unigenes were successfully annotated by BLAST searches against various databases. Gene Ontology (GO) enrichment analysis revealed that oxidoreductases were enriched in the molecular function category, a result consistent with previous observations of notable changes in hydrogen peroxide concentration during endodormancy release. In the GO categories related to biological process, the abundance of DNA methylation-related gene transcripts also significantly changed during endodormancy release, indicating the involvement of epigenetic regulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis also showed the changes in transcript abundance of genes involved in the metabolism of various phytohormones. Genes for both ABA and gibberellin biosynthesis were down-regulated, whereas the genes encoding their degradation enzymes were up-regulated during endodormancy release. In the ethylene pathway, 1-aminocyclopropane-1-carboxylate synthase (ACS), a gene encoding the rate-limiting enzyme for ethylene biosynthesis, was induced towards endodormancy release. All of these results indicated the involvement of phytohormones in endodormancy release. Furthermore, the expression of dormancy-associated MADS-box (DAM) genes was down-regulated concomitant with endodormancy release, although changes in the abundance of these gene transcripts were not as significant as those identified by transcriptome analysis. Consequently, characterization of the Japanese pear transcriptome during the transition from endormancy to ecodormancy will provide researchers with useful information for data mining and will facilitate further experiments on endodormancy especially in rosaceae fruit trees.

Loss of nuclear flavanols during drought periods in Taxus baccata

Normally, needles of Taxus baccata during the growth period prominently stain blue for nuclear flavanols with the histochemical DMACA procedure. However, under excess heat and drought conditions, nuclear flavanols of current-year needles decline to zero. Nevertheless, greenish-yellow-coloured flavonols (quercetin derivatives) were still observed in nuclei. All of these yellow nuclei were in a silenced state and without mitosis. This link between drought and loss of nuclear flavanols was found in 3 years, 2003, 2007 and 2010. In 2007, exceptional drought occurred in early spring, interrupted by short rains. This, in turn, led to flushing of new sprouts, a characteristic feature in which nuclei were overloaded with flavanols. By the end of three drought periods, all nuclei developed blue-coloured nuclear flavanols. The flavanols seem to be associated with the histone proteins of chromatin. The oxidative degradation of catechin in Tris buffer (pH 8.0) containing MgCl2 was studied in the presence of the H4-core fragment TYTEHAKRKTVTAMD, modified according to the epigenetic histone code. The results show that catechin degradation can be significantly inhibited by the non-modified peptides and the methylated peptides (methylation at both lysine residues). The acetylated and formylated peptides do not show this behaviour. These observations indicate that flavanol association at chromosomes appears to be regulated by the epigenetic histone code.

Epigenetics, the role of DNA methylation in tree development

During development of multicellular organisms, cells become differentiated by modulating different programs of gene expression. Cells have their own epigenetic signature which reflects genotype, developmental history, and environmental influences, and it is ultimately reflected in the phenotype of the cells and the organism. However, in normal development or disease situations, such as adaptation to climate change or during in vitro culture, some cells undergo major epigenetic reprogramming involving the removal of epigenetic marks in the nuclei followed by the establishment of a different new set of marks. Compared with animal cells, biotech-mediated achievements are reduced in plants despite the presence of cell polypotency. In forestry, any sustainable developments using biotech tools remain restricted to the lab, without progressing to the field for application. Such barriers in the translation between development and implementation need to be addressed by organizations that have the power to integrate these two fields. However, a lack of understanding of gene regulation is also to blame for this barrier. In recent years, great progress has been made in unraveling the control of gene expression. These advances are discussed in this chapter, including the possibility of applying this knowledge in forestry practice.

Dehydration and vernalization treatments identify overlapping molecular networks impacting endodormancy maintenance in leafy spurge crown buds

Leafy spurge (Euphorbia esula L.) is a herbaceous perennial weed that reproduces vegetatively from an abundance of underground adventitious buds (UABs), which undergo well-defined phases of seasonal dormancy (para-, endo-, and ecodormancy). In this study, the effects of dehydration stress on vegetative growth and flowering potential from endodormant UABs of leafy spurge was monitored. Further, microarray analysis was used to identify critical signaling pathways of transcriptome profiles associated with endodormancy maintenance in UABs. Surprisingly, only 3-day of dehydration stress is required to break the endodormant phase in UABs; however, the dehydration-stress treatment did not induce flowering. Previous studies have shown that prolonged cold treatment of UABs breaks endodormancy and induces a vernalization response leading to flowering. Thus, in this study, comparing transcriptome data from UABs exposed to short-term dehydration and vernalization provided a unique approach to identify overlapping molecular mechanisms involved in endodormancy maintenance and floral competence. Analysis of transcriptome data associated with breaking endodormancy by both environmental treatments identified LEC1, PHOTOSYSTEM I RC, and brassinosteroids as common central hubs of upregulated genes, while DREB1A, CBF2, GPA1, MYC2, bHLH, BZIP, and flavonoids were identified as common central hubs of downregulated genes. The majority of over-represented gene sets common to breaking endodormancy by dehydration stress and vernalization were downregulated and included pathways involved in hormone signaling, chromatin modification, and circadian rhythm. Additionally, the over-represented gene sets highlighted pathways involved in starch and sugar degradation and biogenesis of carbon skeletons, suggesting a high metabolic activity is necessary during the endodormant phase. The data presented in this study helped to refine our previous model for dormancy regulation.

Dormancy cycling at the shoot apical meristem: transitioning between self-organization and self-arrest

To survive winter deciduous perennials of the temperate zones cease growth and acquire a cold-acclimated state. Timing of these events is guided by sensory systems in the leaves that register critical alterations in photoperiod. Growth cessation on its own is not sufficient to develop adequate freezing tolerance, which requires entry of the shoot apical meristem (SAM) into dormancy. To fully appreciate perennial dormancy as a precondition for cold acclimation it is necessary to assess how it is brought about in a timely fashion, what the nature of it is, and how it is released. Short day (SD) exposure results in growth cessation, bud set, dormancy establishment at the SAM, and a moderate to high level of freezing tolerance. Subsequent chilling releases the SAM from dormancy and enhances freezing tolerance further. Recent investigations indicate that dormancy is a state of self-arrest that is brought about by an enzyme-based system which disrupts the intrinsic signal network of the SAM. Release from this state requires a complimentary enzyme-based system that is preformed during SD and mobilized by chilling. These findings are in agreement with the paradigm of dormancy cycling, which defines the seasonal alternations at the SAM as transitions between states of self-organization and self-arrest. The success of this survival strategy is based on the adequate scheduling of a complex array of events. The appreciation is growing that this involves signal cascades that are, mutatis mutandis, also recruited in floral evocation in many annuals, including Arabidopsis. A heuristic model is presented of dormancy cycling at the SAM, which depicts crucial molecular and cellular events that drive the cycle.

Acetylated H4 histone and genomic DNA methylation patterns during bud set and bud burst in Castanea sativa

The relationships between genomic DNA cytosine methylation, histone H4 acetylation and bud dormancy in Castanea sativa are described. Acetylated H4 histone and genomic DNA methylation patterns showed opposite abundance patterns during bud set and bud burst. Increased and decreased methylation levels in the apical buds coincided with bud set and bud burst, respectively. Intermediate axillary buds were characterized by constant levels of DNA methylation during burst of apical buds and reduced fluctuation in DNA methylation throughout the year, which coincided with the absence of macro-morphological changes. Furthermore, acetylated histone H4 (AcH4) levels from apical buds were higher during bud burst than during bud set, as was demonstrated by immunodetection. Results were validated with three additional C. sativa provenances. Thus, global DNA methylation and AcH4 levels showed opposite patterns and coincided with changes in bud dormancy in C. sativa.

Transcriptome analysis identifies novel responses and potential regulatory genes involved in seasonal dormancy transitions of leafy spurge (Euphorbia esula L.)

BACKGROUND

Dormancy of buds is a critical developmental process that allows perennial plants to survive extreme seasonal variations in climate. Dormancy transitions in underground crown buds of the model herbaceous perennial weed leafy spurge were investigated using a 23 K element cDNA microarray. These data represent the first large-scale transcriptome analysis of dormancy in underground buds of an herbaceous perennial species. Crown buds collected monthly from August through December, over a five year period, were used to monitor the changes in the transcriptome during dormancy transitions.

RESULTS

Nearly 1,000 genes were differentially-expressed through seasonal dormancy transitions. Expected patterns of gene expression were observed for previously characterized genes and physiological processes indicated that resolution in our analysis was sufficient for identifying shifts in global gene expression.

CONCLUSION

Gene ontology of differentially-expressed genes suggests dormancy transitions require specific alterations in transport functions (including induction of a series of mitochondrial substrate carriers, and sugar transporters), ethylene, jasmonic acid, auxin, gibberellic acid, and abscisic acid responses, and responses to stress (primarily oxidative and cold/drought). Comparison to other dormancy microarray studies indicated that nearly half of the genes identified in our study were also differentially expressed in at least two other plant species during dormancy transitions. This comparison allowed us to identify a particular MADS-box transcription factor related to the DORMANCY ASSOCIATED MADS-BOX genes from peach and hypothesize that it may play a direct role in dormancy induction and maintenance through regulation of FLOWERING LOCUS T.

Dormancy in potato tuber meristems: chemically induced cessation in dormancy matches the natural process based on transcript profiles

Meristem dormancy in perennial plants is a developmental process that results in repression of metabolism and growth. The cessation of dormancy results in rapid growth and should be associated with the production of nascent transcripts that encode for gene products controlling for cell division and growth. Dormancy cessation was allowed to progress normally or was chemically induced using bromoethane (BE), and microarray analysis was used to demonstrate changes in specific transcripts in response to dormancy cessation before a significant increase in cell division. Comparison of normal dormancy cessation to BE-induced dormancy cessation revealed a commonality in both up and downregulated transcripts. Many transcripts that decrease as dormancy terminates are inducible by abscisic acid particularly in the conserved BURP domain proteins, which include the RD22 class of proteins and in the storage protein patatin. Transcripts that are associated with an increase in expression encoded for proteins in the oxoglutarate-dependent oxygenase family. We conclude that BE-induced cessation of dormancy initiates transcript profiles similar to the natural processes that control dormancy.

Plant dormancy in the perennial context

A key feature of the perennial life style in plants is the ability to cease meristem activity and to establish a dormant state in which the meristem is rendered insensitive to growth-promoting signals for some time before it is released and can resume growth. The seasonal cycling between growth and dormancy has received little attention despite its importance for perennial behaviour. In this review, we reconsider seasonal cycles of growth and dormancy in view of a new definition of dormancy as a state within the meristem, together with recent exciting developments in the study of perennials, particularly the identification of common signalling intermediates between flowering time and growth cessation in trees.

The absence of histone H2B monoubiquitination in the Arabidopsis hub1 (rdo4) mutant reveals a role for chromatin remodeling in seed dormancy

Seed dormancy is defined as the failure of a viable seed to germinate under favorable conditions. Besides playing an adaptive role in nature by optimizing germination to the most suitable time, a tight control of dormancy is important in crop plants. Extensive genetic and physiological studies have identified the involvement of several factors, but the molecular mechanisms underlying this process are still largely unknown. We cloned the HISTONE MONOUBIQUITINATION1 (HUB1) gene, of which the mutant (previously identified as reduced dormancy4) has reduced seed dormancy and several pleiotropic phenotypes. HUB1 encodes a C3HC4 RING finger protein. The Arabidopsis thaliana genome contains one HUB1 homolog, which we named HUB2. The hub2 mutant also has reduced seed dormancy and is not redundant with hub1. Homologs of HUB1 and HUB2 in other species are required for histone H2B monoubiquitination. In agreement with this, the ubiquitinated form of histone H2B could not be detected in the hub1 and hub2 mutants. In yeast and human cells, histone H2B monoubiquitination is associated with actively transcribed genes. The hub1 mutant showed altered expression levels for several dormancy-related genes. We propose a role for chromatin remodeling in seed dormancy by H2B monoubiquitination through HUB1 and HUB2.

Biochemical limitations to high-level expression of humanized monoclonal antibodies in transgenic maize seed endosperm

Transgenic plants are potentially valuable systems for the large scale manufacture of therapeutic proteins. To improve this technology, determining the importance of transgene transcript levels on protein accumulation in sink tissues during their development is crucial. In transgenic maize (Zea mays L.) plants expressing humanized monoclonal antibodies (mAbs) in their seed endosperm, steady-state kappa light chain (LC) and gamma heavy chain (HC) mRNA levels were quantified during development and compared to the levels of fully-assembled mAb protein present at seed maturity. RNA blots and non-reducing SDS-PAGE western immunoblots revealed that steady-state LC and HC mRNA and protein levels were undetectable at 10 days after pollination (DAP) but increased quickly thereafter in three transgenic events expressing different mAb molecules. Similar to gamma-zein mRNA, LC and HC messages were highly abundant between 15 and 25 DAP. Quantitative RNA blots and western immunoblots showed that steady-state LC transcript levels during development correlated extremely closely with protein levels in mature seed (r(2)=0.99). For HC, this correlation was not as strong (r(2)=0.85). Consistent with this finding, concomitantly increasing the zygosity levels of the LC and HC transgenes enhanced mAb concentration in mature seed, in contrast to increasing the copy number of the transgene insert, which did not correlate with high seed mAb levels. The results indicate that high-level expression of fully-assembled mAb protein in maize endosperm was favored by high LC and HC mRNA levels and was largely limited by HC protein concentration.

Chromatin remodeling in plant cell culture: patterns of DNA methylation and histone H3 and H4 acetylation vary during growth of asynchronous potato cell suspensions

Changes in DNA cytosine methylation and core histone multi-acetylation were determined in cell suspension cultures of potato (Solanum tuberosum L. cv. Russet Burbank) during 15 days of in vitro culture. Cell subculture induced a transient 33% decrease in genome-wide 5-methylcytosine (5mC) content and a transient threefold increase in transcription rates that were most evident at 6 and 9 days after subculture, respectively. In contrast to the global reduction in 5mC content, subculture resulted in a transient twofold increase in 5mC levels within 5'-CCGG-3' sequences and no detectable change in 5'-CG-3' methylation. Multi-acetylation of histones H3.1, H3.2 and H4 rose 2-, 1.5- and 3-fold by 9, 9 and 12 days after subculture, respectively. All observed epigenetic changes were reset during aging of cell cultures. Inclusion of the histone deacetylase inhibitor trichostatin A (TSA) and/or the cytosine methylation inhibitor 5-azacytidine (5AC) in culture sequentially decreased genome-wide 5mC levels by approximately 25% at day 9, then decreased 5'-mCmCGG-3' by 30-50% and increased H3 and H4 multi-acetylation by 30-60% at day 15, compared to controls. Treatment with 5AC or TSA alone or in combination had no effect on RNA synthesis at day 9. At day 15, 5AC treatment remained ineffective, while de novo RNA synthesis was approximately twofold higher in cells grown in both inhibitors or in TSA alone. Collectively, these results demonstrate that in potato suspension cultures, rapid, reversible changes in 5mC levels precede regulatory post-translational acetylation of core histones, and suggest that interactions between these epigenetic processes appear to be necessary to power transcription and growth induction in potato cells.