Insight on Rosaceae Family with Genome Sequencing and Functional Genomics Perspective

Overexpression of a Fragaria × ananassa AP2/ERF Transcription Factor Gene (FaTINY2) Increases Cold and Salt Tolerance in Arabidopsis thaliana

The AP2/ERF family of transcription factors is one of the most conserved and important transcription factor families, and it is ubiquitous in plants. It plays an essential role in plant morphogenesis, molecular mechanisms of stress responses, hormone signaling pathways, and synthesis of secondary metabolites. FaTINY2 was cloned from the octaploid strawberry Fragaria × ananassa for this investigation. Bioinformatics revealed that the protein possesses a conserved AP2 domain and is localized in the nucleus. When FaTINY2 was expressed in plants, quantitative analysis revealed that the gene was tissue-specific. There are lower contents of reactive oxygen species (ROS) and malondialdehyde (MDA), higher contents of proline, chlorophyll, and higher activities of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) in transgenic Arabidopsis thaliana than wild type (WT) and unload line (UL) plants under cold and salt stress. FaTINY2 plays a role in enhancing stress tolerance by regulating a few genes linked to the stress response. The findings of this study were that FaTINY2 transgenic Arabidopsis thaliana plants were more tolerant to salt and cold than WT and UL plants. In addition to offering a theoretical reference for strawberry production under stress, this research established a groundwork for exploration into the molecular mechanisms in which strawberries respond to cold and high salt stress.

Genetic Variation, Polyploidy, Hybridization Influencing the Aroma Profiles of Rosaceae Family

BACKGROUND

The fragrance and aroma of Rosaceae plants are complex traits influenced by a multitude of factors, with genetic variation standing out as a key determinant which is largely impacted by polyploidy. Polyploidy serves as a crucial evolutionary mechanism in plants, significantly boosting genetic diversity and fostering speciation.

OBJECTIVE

This review focuses on the Rosaceae family, emphasizing how polyploidy influences the production of volatile organic compounds (VOCs), which are essential for the aromatic characteristics of economically important fruits like strawberries, apples, and cherries. The review delves into the biochemical pathways responsible for VOC biosynthesis, particularly highlighting the roles of terpenoids, esters alcohols, aldehydes, ketones, phenolics, hydrocarbons, alongside the genetic mechanisms that regulate these pathways. Key enzymes, such as terpene synthases and alcohol acyltransferases, are central to this process. This review further explores how polyploidy and hybridization can lead to the development of novel metabolic pathways, contributing to greater phenotypic diversity and complexity in fruit aromas. It underscores the importance of gene dosage effects, isoenzyme diversity, and regulatory elements in determining VOC profiles.

CONCLUSIONS

These findings provide valuable insights for breeding strategies aimed at improving fruit quality and aligning with consumer preferences. Present review not only elucidates the complex interplay between genomic evolution and fruit aroma but also offers a framework for future investigations in plant biology and agricultural innovation.

Viral Diversity in Mixed Tree Fruit Production Systems Determined through Bee-Mediated Pollen Collection

Commercially cultivated Prunus species are commonly grown in adjacent or mixed orchards and can be infected with unique or commonly shared viruses. Apple (Malus domestica), another member of the Rosacea and distantly related to Prunus, can share the same growing regions and common pathogens. Pollen can be a major route for virus transmission, and analysis of the pollen virome in tree fruit orchards can provide insights into these virus pathogen complexes from mixed production sites. Commercial honey bee (Apis mellifera) pollination is essential for improved fruit sets and yields in tree fruit production systems. To better understand the pollen-associated virome in tree fruits, metagenomics-based detection of plant viruses was employed on bee and pollen samples collected at four time points during the peak bloom period of apricot, cherry, peach, and apple trees at one orchard site. Twenty-one unique viruses were detected in samples collected during tree fruit blooms, including prune dwarf virus (PDV) and prunus necrotic ringspot virus (PNRSV) (Genus Ilarvirus, family Bromoviridae), Secoviridae family members tomato ringspot virus (genus Nepovirus), tobacco ringspot virus (genus Nepovirus), prunus virus F (genus Fabavirus), and Betaflexiviridae family member cherry virus A (CVA; genus Capillovirus). Viruses were also identified in composite leaf and flower samples to compare the pollen virome with the virome associated with vegetative tissues. At all four time points, a greater diversity of viruses was detected in the bee and pollen samples. Finally, the nucleotide sequence diversity of the coat protein regions of CVA, PDV, and PNRSV was profiled from this site, demonstrating a wide range of sequence diversity in pollen samples from this site. These results demonstrate the benefits of area-wide monitoring through bee pollination activities and provide new insights into the diversity of viruses in tree fruit pollination ecosystems.

Understanding the salt overly sensitive pathway in Prunus: Identification and characterization of NHX, CIPK, and CBL genes

Salinity is a major abiotic stress factor that can significantly impact crop growth, and productivity. In response to salt stress, the plant Salt Overly Sensitive (SOS) signaling pathway regulates the homeostasis of intracellular sodium ion concentration. The SOS1, SOS2, and SOS3 genes play critical roles in the SOS pathway, which belongs to the members of Na+/H+ exchanger (NHX), CBL-interacting protein kinase (CIPK), and calcineurin B-like (CBL) gene families, respectively. In this study, we performed genome-wide identifications and phylogenetic analyses of NHX, CIPK, and CBL genes in six Rosaceae species: Prunus persica, Prunus dulcis, Prunus mume, Prunus armeniaca, Pyrus ussuriensis × Pyrus communis, and Rosa chinensis. NHX, CIPK, and CBL genes of Arabidopsis thaliana were used as controls for phylogenetic analyses. Our analysis revealed the lineage-specific and adaptive evolutions of Rosaceae genes. Our observations indicated the existence of two primary classes of CIPK genes: those that are intron-rich and those that are intron-less. Intron-rich CIPKs in Rosaceae and Arabidopsis can be traced back to algae CIPKs and CIPKs found in early plants, suggesting that intron-less CIPKs evolved from their intron-rich counterparts. This study identified one gene for each member of the SOS signaling pathway in P. persica: PpSOS1, PpSOS2, and PpSOS3. Gene expression analyses indicated that all three genes of P. persica were expressed in roots and leaves. Yeast two-hybrid-based protein-protein interaction analyses revealed a direct interaction between PpSOS3 and PpSOS2; and between PpSOS2 and PpSOS1C-terminus region. Our findings indicate that the SOS signaling pathway is highly conserved in P. persica.

Polyphenol-enriched extracts of Sarcopoterium spinosum fruits for counteracting lipid accumulation and oxidative stress in an in vitro model of hepatic steatosis

Sarcopoterium spinosum (L.) Spach is a Rosaceae shrub employed in the folk medicine in the Eastern Mediterranean basin. The previous few studies have focused on the S. spinosum roots, while the fruits have been poorly investigated. The present study aims to assess the biological properties of S. spinosum fruits collected in Lebanon and subjected to ethanolic, water or boiling water extraction. The extracts were compared for the phenol and flavonoid contents, and for the in vitro radical scavenging ability. The ethanolic extract (SEE) was selected and characterized by high-performance liquid chromatography coupled with mass spectrometry (HPLC-MS/MS) showing a phenolome rich in tannins (ellagitannins), flavonoids (quercetin derivatives), and triterpenes. The biological activity of SEE was tested on a cellular model of moderate steatosis consisting of lipid-loaded hepatic cells treated with increasing concentrations of SEE (1-25 μg/mL), or with corilagin or quercetin as comparison. In steatotic hepatocytes the SEE was able (i) to ameliorate the hepatosteatosis; (ii) to counteract the excess ROS and lipid peroxidation; (iii) to restore the impaired catalase activity. The results indicate that the ethanolic extract from S. spinosum fruits is endowed with relevant antisteatotic and antioxidant activities and might find application as nutraceutical product.

Do Abiotic Stresses Affect the Aroma of Damask Roses?

Roses are popular ornamental plants all over the world. Rosa damascena Mill., also known as the damask rose, is a well-known scented rose species cultivated to produce essential oil. The essential oils obtained are high in volatile organic compounds (VOCs), which are in demand across the pharmaceutical, food, perfume, and cosmetic industries. Citronellol, nonadecane, heneicosane, caryophyllene, geraniol, nerol, linalool, and phenyl ethyl acetate are the most important components of the rose essential oil. Abiotic factors, including as environmental stress and stress generated by agricultural practises, frequently exert a selective impact on particular floral characteristics, hence influencing the overall quality and quantity of rose products. Additionally, it has been observed that the existence of stress exerts a notable impact on the chemical composition and abundance of aromatic compounds present in roses. Therefore, understanding the factors that affect the biosynthesis of VOCs, especially those representing the aroma and scent of rose, as a response to abiotic stress is important. This review provides comprehensive information on plant taxonomy, an overview of the volatolomics involving aromatic profiles, and describes the influence of abiotic stresses on the biosynthesis of the VOCs in damask rose.

Molecular mechanisms involved in fruit cracking: A review

Several fleshy fruits are highly affected by cracking, a severe physiological disorder that compromises their quality and causes high economical losses to the producers. Cracking can occur due to physiological, genetic or environmental factors and may happen during fruit growth, development and ripening. Moreover, in fleshy fruits, exocarp plays an important role, acting as a mechanical protective barrier, defending against biotic or abiotic factors. Thus, when biochemical properties of the cuticle + epidermis + hypodermis are affected, cracks appear in the fruit skin. The identification of genes involved in development such as cell wall modifications, biosynthesis and transport of cuticular waxes, cuticular membrane deposition and associated transcription factors provides new insights to better understand how fruit cracking is affected by genetic factors. Amongst the major environmental stresses causing cracking are excessive water during fruit development, leading to imbalances in cations such as Ca. This review focus on expression of key genes in these pathways, in their influence in affected fruits and the potential for molecular breeding programs, aiming to develop cultivars more resistant to cracking under adverse environmental conditions.

Modulation of Cytoskeleton, Protein Trafficking, and Signaling Pathways by Metabolites from Cucurbitaceae, Ericaceae, and Rosaceae Plant Families

One promising frontier within the field of Medical Botany is the study of the bioactivity of plant metabolites on human health. Although plant metabolites are metabolic byproducts that commonly regulate ecological interactions and biochemical processes in plant species, such metabolites also elicit profound effects on the cellular processes of human and other mammalian cells. In this regard, due to their potential as therapeutic agents for a variety of human diseases and induction of toxic cellular responses, further research advances are direly needed to fully understand the molecular mechanisms induced by these agents. Herein, we focus our investigation on metabolites from the Cucurbitaceae, Ericaceae, and Rosaceae plant families, for which several plant species are found within the state of Florida in Hillsborough County. Specifically, we compare the molecular mechanisms by which metabolites and/or plant extracts from these plant families modulate the cytoskeleton, protein trafficking, and cell signaling to mediate functional outcomes, as well as a discussion of current gaps in knowledge. Our efforts to lay the molecular groundwork in this broad manner hold promise in supporting future research efforts in pharmacology and drug discovery.

Cancer and Traditional Plant Knowledge, an Interesting Field to Explore: Data from the Catalan Linguistic Area

Cancer is the second cause of death in the world and is foreseen to be responsible for about 16 million deaths in 2040. Approximately, 60% of the drugs used to treat cancer are of natural origin. Besides the extensive use of some of these drugs in therapies, such as those derived from the genus Taxus, a significant number of plants have revealed themselves as useful against cancer in recent years. The field of ethnobotany focuses on documenting traditional knowledge associated with plants, constituting a starting point to uncover the potential of new plant-based drugs to treat or prevent, in this case, tumour diseases and side effects of chemotherapy and radiotherapy. From a series of extensive ethnobotanical prospections across the Catalan linguistic area (CLA), we have recorded uses for 41 taxa with antitumour effects. The two most quoted botanical families are Asteraceae and Ranunculaceae, and the most frequently reported species is Ranunculus parnassifolius, a high-mountain species, which is widely collected for this purpose. The reported species have been used to treat an important number of cancer types, focusing on preventive, palliative, and curative uses, as well as to deal with the side effects of conventional treatments. Comparing our results in CLA with previous data available in the most comprehensive databases of pharmacology and a review of cytotoxicity assays revealed that for the several species reported here, there was no previous evidence of traditional uses against cancer. Despite the need for further analyses to experimentally validate the information presented here, combining traditional uses and phylogenetically-informed strategies to phytochemical and pharmacological research would represent new avenues to establish more integrative approaches, hence improving the ability to select new candidate taxa in cancer research.

Root Breeding in the Post-Genomics Era: From Concept to Practice in Apple

The development of rootstocks with a high-quality dwarf-type root system is a popular research topic in the apple industry. However, the precise breeding of rootstocks is still challenging, mainly because the root system is buried deep underground, roots have a complex life cycle, and research on root architecture has progressed slowly. This paper describes ideas for the precise breeding and domestication of wild apple resources and the application of key genes. The primary goal of this research is to combine the existing rootstock resources with molecular breeding and summarize the methods of precision breeding. Here, we reviewed the existing rootstock germplasm, high-quality genome, and genetic resources available to explain how wild resources might be used in modern breeding. In particular, we proposed the 'from genotype to phenotype' theory and summarized the difficulties in future breeding processes. Lastly, the genetics governing root diversity and associated regulatory mechanisms were elaborated on to optimize the precise breeding of rootstocks.

Integrating Omics and Gene Editing Tools for Rapid Improvement of Traditional Food Plants for Diversified and Sustainable Food Security

Indigenous communities across the globe, especially in rural areas, consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many TFPs are highly nutritious as they contain health beneficial metabolites, vitamins, mineral elements and other nutrients. Excessive reliance on the mainstream staple crops has its own disadvantages. Traditional food plants are nowadays considered important crops of the future and can act as supplementary foods for the burgeoning global population. They can also act as emergency foods in situations such as COVID-19 and in times of other pandemics. The current situation necessitates locally available alternative nutritious TFPs for sustainable food production. To increase the cultivation or improve the traits in TFPs, it is essential to understand the molecular basis of the genes that regulate some important traits such as nutritional components and resilience to biotic and abiotic stresses. The integrated use of modern omics and gene editing technologies provide great opportunities to better understand the genetic and molecular basis of superior nutrient content, climate-resilient traits and adaptation to local agroclimatic zones. Recently, realizing the importance and benefits of TFPs, scientists have shown interest in the prospection and sequencing of TFPs for their improvements, cultivation and mainstreaming. Integrated omics such as genomics, transcriptomics, proteomics, metabolomics and ionomics are successfully used in plants and have provided a comprehensive understanding of gene-protein-metabolite networks. Combined use of omics and editing tools has led to successful editing of beneficial traits in several TFPs. This suggests that there is ample scope for improvement of TFPs for sustainable food production. In this article, we highlight the importance, scope and progress towards improvement of TFPs for valuable traits by integrated use of omics and gene editing techniques.

An Atlas of Genomic Resources for Studying Rosaceae Fruits and Ornamentals

Rosaceae, a large plant family of more than 3,000 species, consists of many economically important fruit and ornamental crops, including peach, apple, strawberry, raspberry, cherry, and rose. These horticultural crops are not only important economic drivers in many regions of the world, but also major sources of human nutrition. Additionally, due to the diversity of fruit types in Rosaceae, this plant family offers excellent opportunities for investigations into fleshy fruit diversity, evolution, and development. With the development of high-throughput sequencing technologies and computational tools, an increasing number of high-quality genomes and transcriptomes of Rosaceae species have become available and will greatly facilitate Rosaceae research and breeding. This review summarizes major genomic resources and genome research progress in Rosaceae, highlights important databases, and suggests areas for further improvement. The availability of these big data resources will greatly accelerate research progress and enhance the agricultural productivity of Rosaceae.

Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume

BACKGROUND

Phosphatidylethanolamine-binding proteins (PEBPs) constitute a common gene family found among animals, plants and microbes. Plant PEBP proteins play an important role in regulating flowering time, plant architecture as well as seed dormancy. Though PEBP family genes have been well studied in Arabidopsis and other model species, less is known about these genes in perennial trees.

RESULTS

To understand the evolution of PEBP genes and their functional roles in flowering control, we identified 56 PEBP members belonging to three gene clades (MFT-like, FT-like, and TFL1-like) and five lineages (FT, BFT, CEN, TFL1, and MFT) across nine Rosaceae perennial species. Structural analysis revealed highly conserved gene structure and protein motifs among Rosaceae PEBP proteins. Codon usage analysis showed slightly biased codon usage across five gene lineages. With selection pressure analysis, we detected strong purifying selection constraining divergence within most lineages, while positive selection driving the divergence of FT-like and TFL1-like genes from the MFT-like gene clade. Spatial and temporal expression analyses revealed the essential role of FT in regulating floral bud breaking and blooming in P. mume. By employing a weighted gene co-expression network approach, we inferred a putative FT regulatory module required for dormancy release and blooming in P. mume.

CONCLUSIONS

We have characterized the PEBP family genes in nine Rosaceae species and examined their phylogeny, genomic syntenic relationship, duplication pattern, and expression profiles during flowering process. These results revealed the evolutionary history of PEBP genes and their functions in regulating floral bud development and blooming among Rosaceae tree species.

An Overview of the Genus Cotoneaster (Rosaceae): Phytochemistry, Biological Activity, and Toxicology

Traditional herbal medicines have become a subject of global importance with both medical and economic implications. The regular consumption of herbal drugs has led to serious concerns regarding their quality, effectiveness, and safety. Thus, relevant scientific evidence has become an important criterion for the acceptance of traditional health claims. The genus Cotoneaster Medikus provides numerous species traditionally used in Asian medicine for the treatment of haemorrhoids, diabetes, and cardiovascular diseases. This review summarises the achievements of modern research on the Cotoneaster taxa, including ethnobotany, phytochemistry, pharmacology, and toxicology. To date, more than 90 compounds have been isolated or analytically identified in Cotoneaster leaves, fruits, flowers or twigs. These phytochemicals are categorised into flavonoids, procyanidins, phenolic acids, cotonefurans, cyanogenic glycosides, triterpenes, sterols, fatty acids, volatile compounds, and carbohydrates, and many of them are responsible for Cotoneaster pharmacological properties including antioxidant, anti-inflammatory, antimicrobial, antiparasitic, hepatoprotective, anti-diabetic or anti-dyslipidaemic activity. In order to ensure the safety of pharmaceutical applications, the potential toxicity of Cotoneaster extracts has also been investigated. In conclusion, this systematic review provides an important reference base for further study into the various medical applications of both the dry extracts and pure isolates of Cotoneaster species.