Identification of DNA Methylation and Transcriptomic Profiles Associated With Fruit Mealiness in Prunus persica (L.) Batsch

Developmental processes in the Rosaceae through the lens of DNA and RNA methylation

MAIN CONCLUSION

This review discusses the DNA and RNA methylation pathways and their biological roles in Rosaceae developmental processes relevant for breeding and production. The Rosaceae is a plant family of great importance for human nutrition and health. Many traits and developmental processes of the Rosaceae are influenced by epigenetic methylation, functions of which are now being unravelled in several important species of this family. Methylation of DNA at the 5th position of cytosine (5mC) is a well-established epigenetic mark that affects important cellular processes such as gene expression and genome stability and is involved in a wide range of plant biological functions. Further to this, recent technological advances have uncovered other naturally occurring chemical modifications of DNA and RNA as additional layers of regulatory epigenetic information in plants. In this review we give a comprehensive summary of plant 5-methylcytosine DNA methylation mechanisms and review their components identified in species of the Rosaceae family. We detail and discuss the role of 5mC DNA methylation dynamics in Rosaceae developmental processes, including phase transition, bud development, bud dormancy, plant architecture, plant regeneration, fruit development, ripening and senescence. We then review recent advances in understanding the newly identified nucleic acid modifications, N6-adenosine methylation of DNA (6mA) and RNA (m6A) as additional epigenetic mechanisms. We summarise identified components of adenosine methylation pathways in the Rosaceae and discuss the emerging roles of this modification in plant development including recent findings in Rosaceous species. Integrating epigenetic aspects of plant development with plant genetics and physiology is crucial for understanding biological processes in Rosaceous plants.

Almond Grafting for Plum Pox Virus Resistance Triggers Significant Transcriptomic and Epigenetic Shifts in Peaches

Sharka disease, caused by the plum pox virus (PPV), negatively impacts stone fruit production, resulting in economic losses. It has been demonstrated that grafting the almond (Prunus dulcis (Miller) D.A. Webb) variety 'Garrigues' into susceptible peach (Prunus persica (L.) Batsch) rootstocks can result in PPV resistance. The molecular circuits related to grafting in Prunus species, however, have not been fully investigated. In this study, susceptible peach rootstocks 'GF305' were either heterografted with 'Garrigues' almond or homografted with the same cultivar. Peach samples were collected at two stages of scion development, with ungrafted plants utilized as controls. Profiles of transcripts, small RNAs (sRNAs), and DNA methylation were obtained and analyzed on a genome-wide scale. Homografting and heterografting significantly altered the transcriptome and methylome of peach rootstocks, with these modifications being more pronounced during the early stages of scion development. The profiles of sRNAs were significantly more impacted when almonds were used as a scion as opposed to peaches, likely due to the transmission of PPV-unrelated viral sequences. Gene expression differences resulting from DNA methylation alterations are more thoroughly documented at the promoter sequences of genes than within their bodies. This study suggests that the 'Garrigues' almond variety triggers a complex defense response in the peach rootstock, potentially involving the interplay of epigenetic modifications and small RNA-mediated priming of antiviral defenses, which ultimately may contribute to PPV resistance.

Single-Base Methylome Analysis of Sweet Cherry (Prunus avium L.) on Dwarfing Rootstocks Reveals Epigenomic Differences Associated with Scion Dwarfing Conferred by Grafting

Plant grafting using dwarfing rootstocks is one of the important cultivation measures in the sweet cherry (Prunus avium) industry. In this work, we aimed to explore the effects of the dwarfing rootstock "Pd1" (Prunus tomentosa) on sweet cherry 'Shuguang2' scions by performing morphological observations using the paraffin slice technique, detecting GA (gibberellin) and IAA (auxin) contents using UPLC-QTRAP-MS (ultra-performance liquid chromatography coupled with a hybrid triple quadrupole-linear ion trap mass spectrometer), and implementing integration analyses of the epigenome and transcriptome using whole-genome bisulfite sequencing and transcriptome sequencing. Anatomical analysis indicated that the cell division ability of the SAM (shoot apical meristem) in dwarfing plants was reduced. Pd1 rootstock significantly decreased the levels of GAs and IAA in sweet cherry scions. Methylome analysis showed that the sweet cherry genome presented 15.2~18.6%, 59.88~61.55%, 28.09~33.78%, and 2.99~5.28% methylation at total C, CG, CHG, and CHH sites, respectively. Shoot tips from dwarfing plants exhibited a hypermethylated pattern mostly due to increased CHH methylation, while leaves exhibited a hypomethylated pattern. According to GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, DMGs (differentially methylated genes) and DEGs (differentially expressed genes) were enriched in hormone-related GO terms and KEGG pathways. Global correlation analysis between methylation and transcription revealed that mCpG in the gene body region enhanced gene expression and mCHH in the region near the TSS (transcription start site) was positively correlated with gene expression. Next, we found some hormone-related genes and TFs with significant changes in methylation and transcription, including SAURs, ARF, GA2ox, ABS1, bZIP, MYB, and NAC. This study presents a methylome map of the sweet cherry genome, revealed widespread DNA methylation alterations in scions caused by dwarfing rootstock, and obtained abundant genes with methylation and transcription alterations that are potentially involved in rootstock-induced growth changes in sweet cherry scions. Our findings can lay a good basis for further epigenetic studies on sweet cherry dwarfing and provide valuable new insight into understanding rootstock-scion interactions.

Inference of the genetic basis of fruit texture in highbush blueberries using genome-wide association analyses

The global production and consumption of blueberry (Vaccinium spp.), a specialty crop known for its abundant bioactive and antioxidant compounds, has more than doubled over the last decade. To hold this momentum, plant breeders have begun to use quantitative genetics and molecular breeding to guide their decisions and select new cultivars that are improved for fruit quality. In this study, we leveraged our inferences on the genetic basis of fruit texture and chemical components by surveying large breeding populations from northern highbush blueberries (NHBs) and southern highbush blueberries (SHBs), the two dominant cultivated blueberries. After evaluating 1065 NHB genotypes planted at the Oregon State University, and 992 SHB genotypes maintained at the University of Florida for 17 texture-related traits, evaluated over multiple years, our contributions consist of the following: (i) we drew attention to differences between NHB and SHB materials and showed that both blueberry types can be differentiated using texture traits; (ii) we computed genetic parameters and shed light on the genetic architecture of important texture attributes, indicating that most traits had a complex nature with low to moderate heritability; (iii) using molecular breeding, we emphasized that prediction could be performed across populations; and finally (iv) the genomic association analyses pinpointed some genomic regions harboring potential candidate genes for texture that could be used for further validation studies. Altogether, the methods and approaches used here can guide future breeding efforts focused on maximizing texture improvements in blueberries.

Dissecting postharvest chilling injuries in pome and stone fruit through integrated omics

Lowering the storage temperature is an effective method to extend the postharvest and shelf life of fruits. Nevertheless, this technique often leads to physiological disorders, commonly known as chilling injuries. Apples and pears are susceptible to chilling injuries, among which superficial scald is the most economically relevant. Superficial scald is due to necrotic lesions of the first layers of hypodermis manifested through skin browning. In peaches and nectarines, chilling injuries are characterized by internal symptoms, such as mealiness. Fruits with these aesthetic or compositional/structural defects are not suitable for fresh consumption. Genetic variation is a key factor in determining fruit susceptibility to chilling injuries; however, physiological, or technical aspects such as harvest maturity and storage conditions also play a role. Multi-omics approaches have been used to provide an integrated explanation of chilling injury development. Metabolomics in pome fruits specifically targets the identification of ethylene, phenols, lipids, and oxidation products. Genomics and transcriptomics have revealed interesting connections with metabolomic datasets, pinpointing specific genes linked to cold stress, wax synthesis, farnesene metabolism, and the metabolic pathways of ascorbate and glutathione. When applied to Prunus species, these cutting-edge approaches have uncovered that the development of mealiness symptoms is linked to ethylene signaling, cell wall synthesis, lipid metabolism, cold stress genes, and increased DNA methylation levels. Emphasizing the findings from multi-omics studies, this review reports how the integration of omics datasets can provide new insights into understanding of chilling injury development. This new information is essential for successfully creating more resilient fruit varieties and developing novel postharvest strategies.

Targeting ripening regulators to develop fruit with high quality and extended shelf life

Fruit quality directly impacts fruit marketability and consumer acceptance. Breeders have focused on fruit quality traits to extend shelf life, primarily through fruit texture, but, in some cases, have neglected other qualities such as flavor and nutrition. In recent years, integrative biotechnology and consumer-minded approaches have surfaced, aiding in the development of flavorful, long-lasting fruit. Here, we discussed how specific transcription factors and hormones involved in fruit ripening can be targeted to generate high-quality fruit through traditional breeding and bioengineering. We highlight regulators that can be used to generate novel-colored fruit or biofortify fresh produce with health-promoting nutrients, such as vitamin C. Overall, we argue that addressing grower and industry needs must be balanced with consumer-based traits.

Epigenetic reprogramming of H3K27me3 and DNA methylation during leaf-to-callus transition in peach

Plant tissues are capable of developing unorganized cell masses termed calluses in response to the appropriate combination of auxin and cytokinin. Revealing the potential epigenetic mechanisms involved in callus development can improve our understanding of the regeneration process of plant cells, which will be beneficial for overcoming regeneration recalcitrance in peach. In this study, we report on single-base resolution mapping of DNA methylation and reprogramming of the pattern of trimethylation of histone H3 at lysine 27 (H3K27me3) at the genome-wide level during the leaf-to-callus transition in peach. Overall, mCG and mCHH were predominant at the genome-wide level and mCG was predominant in genic regions. H3K27me3 deposition was mainly detected in the gene body and at the TSS site, and GAGA repetitive sequences were prone to recruit H3K27me3 modification. H3K27me3 methylation was negatively correlated with gene expression. In vitro culture of leaf explants was accompanied by DNA hypomethylation and H3K27me3 demethylation, which could activate auxin- and cytokinin-related regulators to induce callus development. The DNA methylation inhibitor 5-azacytidine could significantly increase callus development, while the H3K27me3 demethylase inhibitor GSK-J4 dramatically reduced callus development. These results demonstrate the roles of DNA methylation and H3K27me3 modification in mediating chromatin status during callus development. Our study provides new insights into the epigenetic mechanisms through which differentiated cells acquire proliferative competence to induce callus development in plants.

Absence of major epigenetic and transcriptomic changes accompanying an interspecific cross between peach and almond

Hybridization has been widely used in breeding of cultivated species showing low genetic variability, such as peach (Prunus persica). The merging of two different genomes in a hybrid often triggers a so-called "genomic shock" with changes in DNA methylation and in the induction of transposable element expression and mobilization. Here, we analysed the DNA methylation and transcription levels of transposable elements and genes in leaves of Prunus persica and Prunus dulcis and in an F1 hybrid using high-throughput sequencing technologies. Contrary to the "genomic shock" expectations, we found that the overall levels of DNA methylation in the transposable elements in the hybrid are not significantly altered compared with those of the parental genomes. We also observed that the levels of transcription of the transposable elements in the hybrid are in most cases intermediate as compared with that of the parental species and we have not detected cases of higher transcription in the hybrid. We also found that the proportion of genes whose expression is altered in the hybrid compared with the parental species is low. The expression of genes potentially involved in the regulation of the activity of the transposable elements is not altered. We can conclude that the merging of the two parental genomes in this Prunus persica x Prunus dulcis hybrid does not result in a "genomic shock" with significant changes in the DNA methylation or in the transcription. The absence of major changes may facilitate using interspecific peach x almond crosses for peach improvement.

Challenges and Perspectives in the Epigenetics of Climate Change-Induced Forests Decline

Forest tree species are highly vulnerable to the effects of climate change. As sessile organisms with long generation times, their adaptation to a local changing environment may rely on epigenetic modifications when allele frequencies are not able to shift fast enough. However, the current lack of knowledge on this field is remarkable, due to many challenges that researchers face when studying this issue. Huge genome sizes, absence of reference genomes and annotation, and having to analyze huge amounts of data are among these difficulties, which limit the current ability to understand how climate change drives tree species epigenetic modifications. In spite of this challenging framework, some insights on the relationships among climate change-induced stress and epigenomics are coming. Advances in DNA sequencing technologies and an increasing number of studies dealing with this topic must boost our knowledge on tree adaptive capacity to changing environmental conditions. Here, we discuss challenges and perspectives in the epigenetics of climate change-induced forests decline, aiming to provide a general overview of the state of the art.