Cultivated Prunus Research Articles

Modern methods of molecular diagnostics and study the genetic diversity of fruit and small fruit crops viruses based on sequencing

Fruit and small fruit crops are aff ected by various viral diseases, leading to a decrease in yield and product quality, in connection with which the urgent task is to increase the reliability, sensitivity and productivity of diagnosing viruses and other dangerous pathogens. The solution to this problem is carried out by introducing new methods and technologies of molecular diagnostics, with the main attention being paid to decoding nucleotide sequences by sequencing. Sequencing provides a detailed description of the genome of the virus and allows one to get complete epigenomic information. Next generation sequencing (NGS) methods provide parallel testing for the presence of all malicious viruses in a single sample, including identifi cation with a high degree of certainty of non-specifi c and new viruses with the possibility of using diff erent types of samples, for example, pollen. An example of NGS is the Illumina method, based on sequencing and bioinformatics analysis of short RNAs. Modern sequencers can generate from 4 million to 20 billion reads per cycle with read lengths from 50 to 300 nucleotides. The use of high-throughput sequencing (HTS) in conjunction with barcoding allows mass genotyping and characterization of viruses, analysis and elimination of PCR errors while maintaining the real diversity of gene libraries, as well as recognition of mutations in samples. New sequencing methods allow a deeper study of the genetic diversity of the strain composition of the viruses of fruit and small fruit crops. Some of the recently identifi ed and infecting fruit crops belong to the genera of viruses previously unknown for these plant species (for example, Fabavirus, Luteovirus). Complete RNA sequencing was used to identify and characterize the viruses of grape, apple, pear, and cherry. In cultivated Prunus species, 44 viruses have been identifi ed. A new ilarvirus was discovered on the apple tree – the Apple necrotic mosaic virus. The use of HTS for the analysis of fruit and small fruit viruses is becoming increasingly widespread. With a decrease in the cost of sequencing, the introduction and validation of new molecular methods will make it possible in the near future to use them in the diagnosis of viruses by State surveillance authorities.

Multi-scale spatial genetic structure of the vector-borne pathogen \u2018Candidatus Phytoplasma prunorum\u2019 in orchards and in wild habitats

Inferring the dispersal processes of vector-borne plant pathogens is a great challenge because the plausible epidemiological scenarios often involve complex spread patterns at multiple scales. The spatial genetic structure of ‘Candidatus Phytoplasma prunorum’, responsible for European stone fruit yellows disease, was investigated by the application of a combination of statistical approaches to genotype data of the pathogen sampled from cultivated and wild compartments in three French Prunus-growing regions. This work revealed that the prevalence of the different genotypes is highly uneven both between regions and compartments. In addition, we identified a significant clustering of similar genotypes within a radius of 50 km or less, but not between nearby wild and cultivated Prunus. We also provide evidence that infected plants are transferred between production areas, and that both species of the Cacopsylla pruni complex can spread the pathogen. Altogether, this work supports a main epidemiological scenario where ‘Ca. P. prunorum’ is endemic in — and generally acquired from — wild Prunus by its immature psyllid vectors. The latter then migrate to shelter plants that epidemiologically connect sites less than 50 km apart by later providing infectious mature psyllids to their “migration basins”. Such multi-scale studies could be useful for other pathosystems.

Morphological characteristics as a key attribute for a successful determination of selected Cotoneaster species

Article Details: Received: 2019-12-17 | Accepted: 2019-01-24 | Available online: 2020-03-31 https://doi.org/10.15414/afz.2020.23.01.15-23 In this paper, morphological features, such as the number of pyrenes in pome and the number of pomes in infructescence, were used for determination of closely related tetraploid Cotoneaster species. Samples were collected from various localities in the Western Carpathians. The collection of samples, designed for counting of pyrenes in pome, included 2353 pomes of >130 individuals. Number of pyrenes in pome ranged from 1 to 5. Statistical analysis revealed a significant difference in pyrenes per pome mean values between C. integerrimus (3.01), C. melanocarpus agg. (2.46; including C. matrensis) and C. tomentosus (3.93). The collection of samples, designed for counting of pomes in infructescence, included 1019 infructescences of 141 individuals. Number of pomes in infructescence ranged from 1 to 5. Statistical analysis also revealed a significant difference in pomes per infructescence mean values between C. integerrimus (1.14) and C. melanocarpus agg. (1.54; including C. matrensis), and between C. integerrimus and C. tomentosus (1.50). Keywords: pyrenes, pomes, infructescence, Cotoneaster, Western Carpathians

Epidemiological and molecular study on ‘Candidatus Phytoplasma prunorum’ in Austria and Hungary

AbstractThe epidemiology of ‘Candidatus Phytoplasma prunorum’ was studied in Austria and Hungary from 2014 to 2018. Testing of root samples showed average infections rates of 61 and 40% of the Austrian Prunus spinosa and Prunus domestica spp. insititia samples, respectively. In Hungary, on average 21% of the P. spinosa and 13% of the feral Prunus cerasifera samples were infected. The pathogen was found in 18 out of 19 apricot orchards and PCR positive Cacopsylla pruni were observed at 11 out of 17 sampling locations in both countries. In cage experiments with C. pruni remigrants successful pathogen transmission to Prunus armeniaca, P. domestica and P. spinosa seedlings in budding and foliated developmental stages was recorded, an inoculation access period of 4 hr was sufficient for transmission. A field experiment with ungrafted apricot seedlings planted in 2012 and 2014 indicated a prominent role of the insect vectors for disease spread. In 2017, 40 and 28% of the trees planted in 2012 and 2014, respectively, were infected. Molecular characterisation based on the genes aceF and imp allowed the discrimination between 10 phytoplasma types in apricots. Around 70% of the phytoplasma types in apricots were also common in P. spinosa, in P. domestica spp. insititia and in remigrant C. pruni pointing to a possible pathogen exchange by insects between wild and cultivated Prunus spp. For disease control, vector management over the entire flight period of the remigrants seems necessary; when selecting active compounds, the short inoculation access period of not more than 4 hr should be considered.

Genome size and ploidy level among wild and cultivated Prunus taxa in Slovakia

2C DNA content and ploidy level variation of Prunus spinosa and closely related taxa together with Prunus domestica L. and Prunus insititia L. was studied in Slovakia. The aim of the study was to define genome sizes and find differences between closely related taxa within Prunus spinosa sensu lato mentioned in previous works. According to our results, investigated taxa can be divided into three groups according to ploidy level: Prunus spinosa, Prunus dasyphylla, Prunus ×fruticans, Prunus ×dominii and Prunus ×schurii are tetraploids, Prunus ×fechtneri is pentaploid, and P. domestica and P. insititia are hexaploids. Genome size differences within tetraploid taxa were relatively small (Prunus spinosa: 1.40 ± 0.02, P. ×domini: 1.44 ± 0.01, P. ×fruticans: 1.48 ± 0.02, P. ×schurii: 1.44 ± 0.02), but statistically significant. Although further research is needed, it seems that the concept of several taxa as product of hybridization between P. spinosa and cultivated plum species has been supported by our study.

Resistance to Phytophthora Species among Rootstocks for Cultivated Prunus Species

Many species of Phytophthora de Bary are important pathogens of cultivated Prunus L. species worldwide, often invading the trees via their rootstocks. In a series of greenhouse trials, resistance to Phytophthora was tested in new and standard rootstocks for cultivated stone fruits, including almond. Successive sets of the rootstocks, propagated as hardwood cuttings or via micropropagation, were transplanted into either noninfested potting soil or potting soil infested with Phytophthora cactorum (Lebert & Cohn) J. Schöt., Phytophthora citricola Sawada, Phytophthora megasperma Drechs, or Phytophthora niederhauserii Z.G. Abad & J.A. Abad. Soil flooding was included in all trials to facilitate pathogen infection. In some trials, soil flooding treatments were varied to examine their effects on the rootstocks in both the absence and presence of Phytophthora. Two to 3 months after transplanting, resistance to the pathogens was assessed based on the severity of root and crown rot. ‘Hansen 536’ was consistently more susceptible than ‘Lovell’, ‘Nemaguard’, ‘Atlas’, ‘Viking’, ‘Citation’, and ‘Marianna 2624’ to root and/or crown rot caused by P. cactorum, P. citricola, and P. megasperma. By contrast, susceptibility to P. niederhauserii was similarly high among all eight tested genotypes of peach, four genotypes of peach × almond, two genotypes of (almond × peach) × peach, and one genotype of plum × almond. Most plum hybrids were highly and consistently resistant to crown rot caused by P. niederhauserii, but only ‘Marianna 2624’ was highly resistant to both crown and root rot caused by all of the Phytophthora species. The results indicate that there is a broad tendency for susceptibility of peach × almond rootstocks and a broad tendency for resistance of plum hybrid rootstocks to multiple species of Phytophthora.

Chloroplast Noncoding DNA Sequences Reveal Genetic Distinction and Diversity between Wild and Cultivated Prunus yedoensis

Cultivated flowering cherries (Prunus subgenus Cerasus), which are one of the most popular ornamental trees around the world, have been developed through artificial hybridizations among wild flowering cherries. Among the hundreds of cultivars of flowering cherries, Prunus ×yedoensis ‘Somei-yoshino’ is the most common and widespread. However, its origin and genetic relationship to wild P. yedoensis, naturally occurring on Jeju Island, South Korea, have long been debated. We used sequence polymorphisms in eight chloroplast DNA (cpDNA) noncoding regions to distinguish wild and cultivated flowering cherries among 104 individuals (55 accessions). We were able to distinguish two distinct groups, one corresponding to wild P. yedoensis collections from Jeju Island and the other collections of cultivated P. ×yedoensis from Korea, Japan, and the United States. The chlorotype diversity of wild P. yedoensis in Jeju Island and cultivated P. ×yedoensis collections in the United States was quite high, suggesting multiple natural hybrid origins and long history of cultivation from different original sources, respectively.

Recent advances and prospects in Prunus virology

AbstractThe stone fruit genus Prunus, within the family Rosaceae, comprises more than 230 species, some of which have great importance or value as ornamental or fruit crops. Prunus are affected by numerous viruses and viroids linked to the vegetative propagation practices in many of the cultivated species. To date, 44 viruses and three viroids have been described in the 9 main cultivated Prunus species. Seven of these viruses and one viroid have been identified in Prunus hosts within the last 5 years. This work addresses recent advances and prospects in the study of viruses and viroids affecting Prunus species, mostly concerning the detection and characterisation of the agents involved, pathogenesis analysis and the search for new control tools. New sequencing technologies are quickly reshaping the way we can identify and characterise new plant viruses and isolates. Specific efforts aimed at virus identification or data mining of high‐throughput sequencing data generated for plant genomics‐oriented purposes can efficiently reveal the presence of known or novel viruses. These technologies have also been used to gain a deeper knowledge of the pathogenesis mechanisms at the gene and miRNA expression level that underlie the interactions between Prunus spp. and their main viruses and viroids. New biotechnological control tools include the transfer of resistance by grafting, the use of new sources of resistance and the development of gene silencing strategies using genetic transformation. In addition, the application of next generation sequencing and genome editing techniques will contribute to improving our knowledge of virus–host interactions and the mechanisms of resistance. This should be of great interest in the search to obtain new Prunus cultivars capable of dealing both with known viruses and viroids and with those that are yet to be discovered in the uncertain scenario of climate change.

Comparative phylogenetic relationship between wild and cultivated <i>Prunus yedoensis</i> Matsum. (Rosaceae) with regard to Taquet’s collection

As an attempt to determine the identity of the old trees of flowering cherries planted in the yard of the Catholic Archdiocese of Daegu, we conducted comparative phylogenetic analyses between wild and cultivated Prunus yedoensis Matsum. We generated the phylogeny (MP) and haplotype network (TCS) of 25 individuals, including wild P. yedoensis, from Jeju Island, cultivated P. yedoensis `Somei-yoshino` from Korea and Japan, and P. spachiana f. ascendens (Makino) Kitam. from Jeju Island and Japan based on highly informative sequences of two cpDNA regions (rpl16 gene and trnS-trnG intergenic spacer). The wild and cultivated P. yedoensis were distinguished from each other in both the phylogeny and haplotype networks, and the old flowering cherry trees in Daegu had a cpDNA haplotype identical to that of the cultivated P. yedoensis `Someiyoshino`. Compared to the cultivated P. yedoensis `Somei-yoshino`, wild P. yedoensis appears to have greater haplotype diversity, presumably originating from the genetic diversity of P. spachiana f. ascendens that functioned as a maternal parent in the hybrid origin of wild P. yedoensis. A future detailed study requires extensive sampling of P. spachiana f. ascendens from Japan and Korea to determine their precise phylogenetic relationships relative to wild and cultivated P. yedoensis. We concluded that the old flowering cherry trees planted in the yard of the Catholic Archdiocese of Daegu are highly likely to be of cultivated origin rather than wild types from Jeju Island, as previously speculated.

Genetic differentiation and gene flow between wild and cultivated Prunus avium: An analysis of molecular genetic evidence at a regional scale

The presence of conspecific wild-type and cultivar populations has been a common landscape feature for centuries. As orchards generally continue to expand towards the natural forest, two important issues are raised: the potential reduction of cultivar genetic diversity compared to wild populations and the extent of gene flow between the two population types. These questions were addressed in a study of Prunus avium in northern Greece using nine simple sequence repeat loci to analyse genetic variation in 93 wild-type individuals and 21 cultivars representing the local cultivated germplasm. Results showed a significant reduction of genetic diversity parameters in the cultivated germplasm compared to natural populations. Bayesian, frequency-based and Markov chain – Monte Carlo analyses have revealed that the wild and cultivar groups are genetically divergent and that realized between-group gene flow is almost completely absent. This result was further verified by a principal component analysis showing a clear separation of the two groups in low multivariate space after a principal coordinate analysis. The significant disjunction in flowering time and a considerable geographic distance between the two groups could primarily account for the absence of substantial gene flow. These findings indicate that local wild cherry can provide a source of genetic variation for future breeding in the genetically restricted cultivar group.

Insights into the genome of the xanthan-producing phytopathogen Xanthomonas arboricola pv. pruni 109 by comparative genomic hybridization

The phytopathogenic bacterium Xanthomonas arboricola pv. pruni is the causal agent of Prunus Bacterial Spot disease that infects cultivated Prunus species and their hybrids. Furthermore, X. arboricola pv. pruni (Xap) plays a role in biotechnology since it produces xanthan gum, an important biopolymer used mainly in the food, oil, and cosmetics industry. To gain first insights into the genome composition of this pathovar, genomic DNA of X. arboricola pv. pruni strains was compared to the genomes of reference strains X. campestris pv. campestris B100 (Xcc B100) and X. campestris pv. vesicatoria 85-10 (Xcv 85-10) applying microarray-based comparative genomic hybridizations (CGH). The results implied that X. arboricola pv. pruni 109 lacks 6.67% and 5.21% of the genes present in the reference strains Xcc B100 and Xcv 85-10, respectively. Most of the missing genes were found to be organized in clusters and do not belong to the core genome of the two reference strains. Often they encode mobile genetic elements. Furthermore, the absence of gene clusters coding for the lipopolysaccharide (LPS) O-antigens of Xcc B100 and Xcv 85-10 indicates that the structure of the O-antigen of X. arboricola pv. pruni 109 differs from that of Xcc B100 and Xcv 85-10.

Graft-transmissible agent causes bark necrosis and stem pitting in plum trees

In two Central Valley plum orchards, nearly all the trees started exhibiting copious amounts of dark gumballs on scaffold branches and main trunks. Exposed bark showed extensive tissue necrosis and necrotic stem-pitting on the surface of the woody cylinders. Eventually, both orchards had to be removed and replanted. The symptoms were highly suggestive of a viral or viruslike disease agent. We began studies to characterize the pathogen associated with the failure of these orchards and were successful in associating the disease with a new virus that proved to have an extensive host range in many cultivated Prunus. Characterization of this virus is under way.

Phylogenetic Relationship Among Selected Taxa of Prunus in Mt. Halla and Cultivated Prunus yedoensis by the RAPD Analysis

Phylogenetic Relationship Among Selected Taxa of Prunus in Mt. Halla and Cultivated Prunus yedoensis by the RAPD Analysis