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Apples are available all year round since they can be stored for long time. However, the expression of the major apple allergen Mal d 1 can increase in the fruit during storage and incease so the risk of allergies in sensitive consumers. Therefore, we studied the change in the expression of the Mal d 1 gene during storage in the modern cultivar UEB 32642 (known under the brand name Opal^®) and the cultivar Gala Brookfield (cv. Gala) as a reference. The cultivars were stored under two different conditions, ultra-low oxygen (ULO) and standard cold conditions. The gene expression was evaluated both in fresh fruits and in fruits stored for four, six, and nine months. Nine isoforms of the gene Mal d 1 with the highest published expression were quantified using real-time PCR. The most expressed isoforms Mal d 1.01, Mal d 1.02 and Mal d 1.06A were found in the fresh and also in the stored fruits. The expression of the Mal d 1.03G and Mal d 1.06D isoforms was higher the sored fruits. Our study confirmed that (i) Opal^® had a lower overall expression of the Mal d 1 gene than cv. Gala, both in the fresh and stored fruits; (ii) standard cold storage is superior in preserving lower Mal d 1 levels in Opal^®apples compared to the ULO conditions; and (iii) less expressed isoforms may be responsible for the general increase in the Mal d 1 gene expression during storage.

Apple scab caused by Venturia inaequalis has the most destructive effects among other phytopathogens in apple crops all over the world. The integration of resistance genes from local and domestic cultivars is a prerequisite for the efficient control of this disease and is a main target in efficient breeding approaches. Across Greece, many domestic apple cultivars are reported without deep knowledge about the presence and diversity of scab resistance genes. In this study, the presence of five resistance genes (Rvi2, Rvi4, Rvi6, Rvi8 and Rvi11) was evaluated across twenty local and domestic apple genotypes, employing twelve molecular markers closely linked to known apple scab resistance loci. Significant differences and polymorphisms among the tested cultivars were detected suggesting that some of them carry a sufficient number of resistance genes. This observed genetic diversity could be exploited in ongoing breeding approaches as a natural source of polygenic resistance against apple scab.

DNA methylation is one of the major epigenetic modifications. It is very important to the regulation of gene expression. Methylation-sensitive amplification polymorphism (MSAP) profiling was applied to a diploid apple cultivar and its derived autotetraploid in order to characterize the level and pattern of DNA methylation at the two different ploidies. The frequency of methylated restriction sites was very similar between the two types (28.0% vs 27.3%), implying that polyploidization had a low effect on the global level of DNA methylation. However, with respect to the pattern of methylation, the frequency of hemi-methylated sites was higher in the tetraploid. When the transcription level of three genes encoding DNA methyltransferase was investigated in various tissues, it was established that MET1 transcript abundance was the lowest of the three genes throughout the plant, while that of DRM2 was high in the leaf, flower and fruit, as was that of CTM3 in the fruit. Polyploidization had no discernible effect on the transcription level of any of the three genes.

The flowering onset of 19 apple progeny was evaluated in 2005-2014 on a total number of 715 seedlings in comparison with their parents and grandparents. A very low flower set delays generally the onset of flowering by one day in comparison with a higher flower set. The maximum span between the first flowering onset and the last one within all the progeny of the study was 11 days. With one exception, the incidence of the first flowering dates of all the progeny fluctuated only within four days - April 28 and May 1. Among them, the great majority of the seedlings had the first flowering date span of not more than ± one day. The progeny of Pink Lady × Discovery was the most exceptional having the mean day on the April 17 and the span about two days longer. The means of the first flowering dates within seedling populations and corresponding dates of both their parents and grandparents were very highly correlated (r = 0.926 for parents and r = 0.877 for grandparents). The incidence of flowering onset dates in almost all progeny followed a typical Gaussian distribution, in which the majority of seedlings start flowering within 3 or 4 days. The maximum difference between both extremes (found only in one progeny) was 11 days. The share of seedlings in both extremes was, however, very small - less than 2%.

The present paper summarized some knowledge of modern technologies, applied in apple (Malus domestica) genome studies. New generation sequencing allowed single nucleotide polymorphism (SNP) chip technologies for genotyping, description of functional apple genes, characterization of the evolutionary results in apple genome fragment transition, as well as phylogenetic reconstruction of the genus Malus, being the confirmed progeny of M. sieviersii. Based on these technologies, newly developed putative markers may give the most important biological data such as age, geographical origins, tissue type determination, and external visible characters. The new generation genotyping platforms, representing very high efficiency, are now successfully applied for random apple genome-wide association (GWA) studies as well pedigree-based analysis and marker-assisted selection (MAS).

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Variation with respect to both ploidy level and morphology was characterized for a set of 690 seedlings of the triploid apple variety Jonagold, of which 481 were obtained via in vitro culture of mature embryos, and 209 via conventional germination. Their ploidy level was determined by a combination of flow cytometry and root tip chromosome counting. The assessed morphological traits were leaf length, width and shape, stomatal density, guard cell length and chloroplast width and number. A total of 452 seedlings were aneuploid, 225 diploid, nine triploid and four tetraploid. All four tetraploid seedlings were derived by in vitro culture. When the triploid seedlings were genotyped at the S-locus and at selected microsatellite loci, we found that the Jonagold stigma was compatible with pollen which shared some of the maternal parent S-locus alleles.

Aloe vera and A. arborescens are succulent plants widely used in cosmetics, pharmaceuticals, and food supplements. The objective of this study was to perform interspecific crosses and agronomically characterise three genotypes cultivated in a Venezuelan highland region (altitude 1 727 m, 13–17.9 °C). Successful hybridisation was achieved only when A. arborescens pollen (P1) was used on A. vera pistils (P2), whereas the reciprocal cross was largely unsuccessful. Hybrid seed germination reached 11.86%, and adult hybrids exhibited significant vegetative superiority over P1, particularly in leaf volume, leaf weight, and flower number. The progeny outperformed both parents in leaf base width and lateral tooth size, thereby enhancing its ornamental value. The expected 2n = 2x = 14 karyotype was confirmed in the root meristems of hybrids. The analysis of leaf pulp processing indicated that the hybrid was promising for juice production (39.8% yield, 1 203 ppm acemannan), thus highlighting its potential for agro-industrial applications in tropical highlands or comparable temperate regions. Other agronomic traits, including number, thickness, colour, and shape of leaves; sprouting of stem branches and basal suckers, flowering period, inflorescence, eggs/ovary, and details of the colour and dimensions of bracts, perianth, pedicel, and ovary, were also evaluated.

With climate change, plants face numerous stresses, notably drought for rice cultivation. Improving rice drought tolerance is vital for sustainable production in water-scarce regions. Identification of drought tolerant genotypes at the seedling stage of the crop contributes to build a climate resilient genotype during the period of water scarcity and under challenging environmental conditions. Hence, polyethylene glycol-6000 (PEG-6000) induced drought conditions could be used for testing the drought tolerance in rice at an earlier stage of the crop. Optimization of PEG-6000 concentration for screening index at -6 bar was done using three drought-tolerant and two drought-susceptible check varieties based on probit analysis. Subsequently, 100 rice landraces underwent PEG-6000 induced drought screening at –6 bar and a total of 32 genotypes were selected as tolerant. After 14 days of treatment, the nine observations viz. germination %, root length (cm), shoot length (cm), number of secondary roots, fresh weight (g), dry weight (g), shoot/root ratio, root/shoot ratio and vigour index were recorded. Variance analysis, revealing significant genetic variation among genotypes for all studied traits, indicating genetic variability. Post hoc analysis confirmed notable variation among treatments. Principal component analysis revealed three components, with the first three accounting for 88.89% of total variability. With respect to the biplot, the ten genotypes viz., IRGC109, IRGC403, IRGC448, IRGC461, IRGC466, IRGC486, IRGC508, IRGC518, IRGC527 and IRGC535 are the seedling stage drought tolerant genotypes based on shoot length, number of secondary roots and vigour index. Population structure classified the accessions into two subpopulations, reflecting diversity. The allele frequency divergence is 0.095 which is a measure of fixation index revealing that the moderate divergence is not extremely pronounced. Genetic diversity, assessed through 26 SSR markers selected from drought tolerant QTLs and markers related to vigour index, exhibited 100% polymorphism with 115 alleles and an average PIC value of 0.61 per primer. Shannon index varied between 0.34 (RM212) and 1.96 (RM252), averaging 1.18. Six SSR markers viz., RM246, RM302, RM252, RM219, RM251, and RM486 were associated with the six key traits viz., shoot length, root length, number of secondary roots, dry weight, shoot/root ratio, and root/shoot ratio respectively offering valuable resources for selecting drought-tolerant accessions as it provides the first step in the selection of genotypes based on the key traits.

Pattern recognition receptors (PRRs) play multiple roles in plants. As a kind of PRRs, chitin elicitor receptor kinase 1 (CERK1) proteins were reported to function in plant resistance to fungal and bacterial pathogens, and tolerance to salt stress. In this study, a predicted cowpea CERK1 homologous gene, designated as VuCERK1, was identified by database search. VuCERK1 protein contains 618 amino acid residues, with a predicted molecular mass of 67.5 kDa and a predicted isoelectric point of 5.04. VuCERK1 shows 58% and 60% sequence identity with AtCERK1 and OsCERK1, respectively. VuCERK1 also shows similar subcellular pattern with AtCERK1 and OsCERK1, suggesting VuCERK1 may function in cowpea immune responses. Gene expression assay indicated, that VuCERK1 was expressed in four different seedling tissues tested, comprising first leave, epicotyl, hypocotyl and root, and it could be induced by salt stress. Furthermore, transient expression of VuCERK1 in Nicotiana benthamiana induced obvious cell death. In addition, heterologous overexpression of VuCERK1 in Arabidopsis thaliana conferred enhanced disease resistance to Pseudomonas syringae pv. tomato strain DC3000 hrcC^- (Pto DC3000 hrcC^-).

Graphene-based materials (GBMs) have become potential soil pollutants due to their wide applications in agricultural environments. Although physiological mechanisms of plant responses to GBMs have been previously explored, the underlying molecular mechanisms remain unclear. In this paper, we analysed the physiological and transcriptomic changes of buckwheat (Fagopyrum spp.) roots exposed to 100 mg/L graphene oxide (GO) with different diameter. GO negatively affected root growth and higher diameters of GO caused more adverse effects on the root. In total 3 724 GO-responsive genes were identified in root by transcriptome analysis. 70 differentially expressed genes (DEGs) were involved in ROS detoxification, and 37 transporter-encoding genes were found to be involved in GO response. These transporters may regulate the uptake and transport of GO in buckwheat. The gene expression of 84 transcription factors (TFs) showed a response to GO stress in the root, which may regulate the transporters and reactive oxygen species (ROS) detoxification-related genes. Finally, the difference in the transcriptomic response of the root to the three GO materials with different diameters was investigated. 49 GO-responsive genes may be involved in the difference in the toxicity of GO with different diameters. This study provides new insights into the molecular mechanisms of plant roots to GBMs.

Iris × germanica L. (bearded iris) is a popular ornamental plant with numerous commercially important cultivars; however, little is known about the genetic diversity and population structure of the species, as limited DNA markers have been explored. In this study, 34 722 expressed sequence tag (EST)-simple sequence repeat (SSR) loci were identified from RNA sequencing data. The most abundant SSR motifs belonged to the tri-nucleotide type, of which the most common were AGG/CCT followed by AAG/CTT. Overall, 50 primer pairs derived from these EST-SSRs were randomly selected and synthesized, and 22 primer pairs with good polymorphism effects were used for the following experiment. Correlation analysis of nine floral traits showed that most floral traits had significant correlations with each other. Association analysis between SSR molecular markers and nine floral traits showed that 11 EST-SSR markers were associated with 3–6 floral traits. The cluster tree constructed by using the unweighted pair group method demonstrated that the cultivars that had the same parents or similar colour were clustered together. The genotypic relations of most cultivars were consistent with their pedigree-based relationships. The EST-SSR loci identified in this study will facilitate the exploitation of genetic resources and molecular breeding of I. × germanica.

Sunflower (Helianthus annuus L.), a globally significant oilseed crop, faces substantial yield losses due to drought stress, a major environmental constraint. In this study, the effects of nitric oxide (NO) to increase drought tolerance in four sunflower genotypes (resistant Irtysh, RAR 56 and sensitive Zarya, RAR 133) showing different stress responses were investigated. Conducted in a controlled hydroponic system, the experiment applied 100 µM NO under 12% polyethylene glycol (PEG)-induced drought, assessing growth, physiological, and biochemical parameters. PEG alone reduced shoot and root growth, relative water content (RWC), and ion levels (K, Ca, Mg, Na), while increasing oxidative stress markers (malondialdehyde (MDA), H₂O₂, •OH) and electrolyte leakage, particularly in sensitive genotypes. NO application, both alone and with PEG, significantly mitigated these effects, enhancing root fresh weight, RWC, and antioxidant enzyme activities (superoxide dismutase (SOD), peroxidase (POX), catalase (CAT) and glutathione reductase (GR)), while reducing reactive oxygen species (ROS) and lipid peroxidation. Resistant genotypes (Irtysh, RAR 56) exhibited superior stress amelioration. These findings highlight NO’s role as a signalling molecule in augmenting drought resilience through genotype-specific mechanisms. The differential responses among genotypes suggest opportunities for identifying genetic markers associated with NO-mediated drought tolerance, which could guide marker-assisted breeding programs. Additionally, integrating these insights with genomic editing techniques may accelerate the development of drought-resistant sunflower cultivars tailored for water-scarce regions. Future research should optimise NO delivery methods and evaluate field-scale efficacy to advance sustainable sunflower production in water-limited environments.

The presence of genes for resistance to scab (Venturia inaequalis) and powdery mildew (Podosphaera leucotricha) was studied using molecular markers in a sample of 279 apple cultivars from the Czech collection of apple genetic resources. The sample comprised 37 cultivars supposed to have the Vf gene for scab resistance, 97 reference world cultivars and 145 old and local cultivars. Six PCR molecular markers for the scab resistance genes Vf, Vm, Vbj, Vr and Vh and three PCR molecular markers for the powdery mildew resistance genes Pl-w, Pl-1 and Pl-d were used. The marker for the major scab resistance gene Vf was detected in all cultivars supposed to have Vf, except in Romus 1, and in the three small-fruited cultivars Malus Evereste, Golden Gem and Hilleri. The markers of the Vr and Vh scab resistance genes were detected in 22 cultivars in combination with the marker for Vf, in 56 reference world cultivars and in 82 old and local apple cultivars. PCR molecular markers for one or two of the powdery mildew resistance genes were detected in the small-fruited cultivars Malus Evereste, Golden Gem, prof. Sprengeri and Hilleri; and in the larger fruited cultivars Hagloe Crab, Borovinka and Tita Zetei. We did not find markers for the scab resistance genes Vm and Vbj in any of the studied cultivars. They are absent also in the remaining part of the Czech collection of apple genetic resources. PCR molecular markers are useful tools for the identification of resistance genes within apple germplasm collections and can be used to increase the number of sources for disease resistance in breeding programmes.

To investigate the role of the HvnAnt2 gene in the formation of different qingke barley grain colours, HvnAnt2 was isolated from the leaves of the White 91-97-3 (white), Blue qingke (blue), Kunlun 17 (black), and Purple qingke (purple). The HvnAnt2 gene encodes a hydrophilic unstable protein consisting of 561 amino acids, without a transmembrane structure and without a signal peptide, with one bHLH-MYC_N and one HLH domain at amino acids 22–204 and 387–436, respectively. The HvnAnt2 of qingke barley was most closely related to Hordeum vulgare and most distantly related to Triticum monococcum; it was mainly related to light responsiveness and methyl jasmonate responsiveness. The Ant2 gene was highly expressed in Kunlun 17 and Purple qingke barley grains during the later stage of development. The protein interaction prediction showed that flavonoid 3’-monooxygenase, anthocyanin biosynthesis gene regulators, and key enzymes in folate metabolism interacted with the Ant2 protein. This study provides a reference for further analysis of the Ant2 gene in the anthocyanin synthesis pathways of qingke barley with different grain colours.

Strigolactones (SLs) are a comparatively novel class of phytohormones that are involved in the maintenance of plant architecture with key regulation of lateral branching. They are also reported to play an important role in regulating plant responses to various abiotic stresses. The potential of SLs to improve crop resilience and productivity needs to be effectively translated into agriculture. Therefore, both the endogenous biosynthesis of SLs and their exogenous application need to be thoroughly investigated to understand and exploit the mechanism underlying the alleviation of abiotic stress responses. Although several reviews have emphasised the biosynthesis of SLs in plants under abiotic stress, the mechanism underlying the alleviation of stress responses upon exogenous application has been less explored. Accordingly, in this review, although we have briefly discussed the beneficial effects of endogenous production of SLs in different sections, our main focus is to summarise the influence of exogenous SLs on the growth and development of different plant species grown under various abiotic stresses, including drought, nutrient, heavy metal, and salinity stress. Apart from providing an overview of the transcriptomic studies conducted to observe the alleviating effects of SLs on abiotic stress responses, the research gaps in this field were briefly discussed. The review provides insight for researchers to conduct further research on SLs and fill the gap so that they can be effectively used for sustainable agriculture.

The basic Helix-Loop-Helix (bHLH) superfamily is the most widespread family of transcription factors in eukaryotic organisms, which can activate the expression of genes by interacting with specific promoters in the genes. The bHLH transcription factors direct the development and metabolic process of plants, including flowering initiation and secondary metabolite production, by attaching to specific sites on their promoters. These transcription factors are essential for encouraging plant tolerance or the adjustment to harsh environmental conditions. The involvement of bHLH genes in anthocyanin formation in fleshy fruit-bearing plants, as well as the role of these genes in response to stimuli including drought, salt, and cold stress, are discussed in this article. New concepts and goals for the production of stress-tolerant fruit species are suggested. Furthermore, solid evidence for the critical role of bHLH genes in the growth and development, as well as anthocyanin biosynthesis in fleshy fruit plants, are also presented in this article. This review identifies several future research directions that can shed light on the roles of bHLH genes in fruit-bearing plants and will assist the use of these genes in efforts to breed fruit crop varieties that are more resistant to stress. Generally, there has been little research carried out on the role of bHLHs transcription factor family genes in fleshy fruit-bearing plant species and more in-depth studies are required to fully understand the diverse role of bHLH genes in these species.

The CBF (C-repeat binding factors) genes play important roles in response to abiotic stress and environmental changes. In the present study, a total of 18 CBF genes were identified from a grapevine. Their domains, phylogenetics, and collinearity were analysed. The results revealed, that 18 VviCBF genes were distributed on 10 chromosomes unevenly in the grape genome. Promoter data analysis showed that the CBF gene has many cis-acting elements related to plant growth and development, light response, hormone, and abiotic stress response. We found that six VviCBF genes including, VviCBF5, VviCBF13, VviCBF14, VviCBF15, VviCBF16, and VviCBF18 differentially expressed during fruit developmental stages. Furthermore, four VviCBF genes including, VviCBF1, VviCBF3, VviCBF6, and VviCBF11 were expressed at the early stage of bud dormancy, whereas, nine VviCBF genes were expressed at the bud dormancy-breaking stage. Additionally, various VviCBFs genes respond to different abiotic and biotic stress. These findings will lay a foundation for further study of the CBF genes in bud dormancy, downy mildew, and abiotic and biotic stresses.

BTB-TAZ (BT) proteins are plant-specific transcription factors containing a BTB domain and a TAZ domain. They play vital roles in various biological processes and stress responses. In this study, a total of three BT genes (CsBT1-3) were identified from cucumber genome, and they were unevenly distributed in two of the seven chromosomes. Phylogenetic analysis of the BT proteins from cucumber, Arabidopsis, apple, tomato, and rice revealed that these proteins could be distinctly divided into two groups in accordance with their motif distributions. We also determined the structures of BT genes from cucumber, Arabidopsis, and rice to demonstrate their differences. The quantitative real-time PCR (qRT-PCR) results showed that the CsBT genes displayed differential expression patterns in cucumber tissues, and their expression was regulated by cold, salt, and drought stresses. These findings suggest that CsBT genes may participate in cucumber development and responses to various abiotic stresses.

In vitro meristem cultures have been used for the production of hop (Humulus lupulus L.) virus-free rootstocks worldwide, because multipropagation is considered to preserve the genetic stability of the produced plantlet. Nevertheless, in vitro tissue cultures can cause genetic and epigenetic changes. Therefore, we studied the genetic and epigenetic variability of Saaz Osvald's clones, Sládek and Premiant cultivars on the DNA methylation level by methylation-sensitive amplification polymorphism (MSAP). In vitro propagated plants, acclimatised glasshouse rootstocks as well as derived mericlones and control plants under field conditions were used for the analyses. A total of 346 clearly and highly reproducible amplified products were detected in the MSAP analyses within the studied hop plants. We found 16 polymorphic products (4.6% of products) and 64 products with methylation changes (18.5% of products) in the analyses. The demethylation events were comparable to the de novo methylation events. Most demethylation changes were found in the in vitro plants, but only a few of them were found in the derived mericlones under field conditions. In contrast, the de novo methylation changes persisted in the acclimatised plants under glasshouse or field conditions. A hierarchical cluster analysis was used for the evaluation of the molecular genetic variability within the individual samples. The dendrogram showed that the individual samples of the same variety, more or less, clustered together. Because the methylation status varied during the virus-free rootstock production process, we suppose that de/methylation process is a natural tool of epigenetics and evolution in vegetatively propagated plants.

Fire blight is one of the most destructive diseases of pome fruits, especially pears. In current conditions when the demand for organic products is increasing, improvement of resistant rootstock and varieties is becoming important due to the lack of an effective disease management method against fire blight caused by Erwinia amy-lovora as well as the harmful effects of chemicals on environment, human and animal health. The findings of the researchers as to which variety performs well in terms of the transmission of fire blight resistance are quite important for new breeding programs. In the study, three varieties with high commercial value (Magness, Santa Maria and Williams) were identified as the maternal parents and 21 hybridization combinations were made with seven varieties (Akça, Ankara, Conference, Güz, Kaiser Alexandre, Kieffer and Taş) as pollinators. The Magness maternal parent was found superior when compared with the other maternal parents for the variety susceptibility level to fire blight. Apart from the differences in the susceptibility level of 21 different combinations of hybrids to fire blight, the commercially superior ten hybrids (I-15-24, II-13-1, II-13-19, II-13-34, II-13-73, II-27-21, II-27-55, II -32-44, III-22-638, III-27-590) have been determined via the weighted ranking method from the parameters of disease resistance and different fruit characteristics measuring the commercial preference of the fruits such as fruit quality, attractiveness, size, firmness and rustiness

In the past decade, next-generation sequencing (NGS) platforms have changed the impact of sequencing on our knowledge of crop genomes and gene regulation. These techniques are today acquiring a great potential in metagenomic and agrigenomic research while showing prospects for their utilization in plant breeding. We can now obtain new and beneficial information about gene regulation on the cellular as well as whole-plant level through RNA-sequencing and subsequent expression analyses of genes participating in plant defence reactions to pathogens and in abiotic stress tolerance. NGS has facilitated the development of methods to genotype very large numbers of single-nucleotide polymorphisms. Genotyping- by-sequencing and whole-genome resequencing can lead to the development of molecular markers suited to studies of genetic relationships among breeding materials, creation of detailed genetic mapping of targeted genes and genome-wide association studies. Plant genotyping can benefit plant breeding through selection of individuals resistant to climatic stress and to pathogens causing substantial losses in agriculture.

In situ conservation is considered as conservation of wild biota in the natural habitat (locality). The authors extend the term to cultivated fruit species naturalised in the landscape, such as occasional spontaneous seedlings, and planted material such as old solitary trees among fields, old groves, avenues (country lanes), wind-breaks, and abandoned remnants of orchards. In situ conservation is also used to mark unique materials during collecting expeditions, before they will be taken as ex situ or proclaimed as permanent in situ. Important landraces found within 12 regions of the Czech Republic were registered, evaluated, and in situ localised by Global Positioning System (GPS). The following accessions were marked for in-situ conservation: apple (401), sweet cherry (263), pear (91), plum (42), sour cherry (27), and berry fruits (18).