Molecular Tools Applied to the Advancement of Fruit Growing in South Tyrol: a Review

Baric, Sanja

doi:10.1007/s10341-012-0170-y

Cited by 5 publications

(3 citation statements)

References 54 publications

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“…Our database furthermore allowed identifying several synonym names, such as the synonymy of 'Köstlicher von Zallinger', 'Napoleone' and 'Carla' or the synonymy of 'Stina Lohmann' and 'Korbiniansapfel'. Finally, the here presented database proved useful at several occasions to identify unknown or misidentified apple cultivars (Baric 2012). Therefore, apart from its application to characterise genetic resources or to manage germplasm collections, the database could serve as an important tool for quality control.…”

Section: Discussionmentioning

confidence: 99%

Molecular Genetic Identification of Apple Cultivars Based on Microsatellite DNA Analysis. I. The Database of 600 Validated Profiles

et al. 2020

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Apple (Malus × domestica Borkh.) is the most widely grown permanent fruit crop of temperate climates. Although commercial apple growing is based on a small number of globally spread cultivars, its diversity is much larger and there are estimates about the existence of more than 10,000 documented varieties. The varietal diversity can be described and determined based on phenotypic characters of the external and internal traits of fruit, which, however, can be modulated by environmental factors. Consequently, molecular methods have become an important alternative means for the characterisation of apple cultivar diversity. In order to use multilocus microsatellite data for determination of unidentified or misidentified apple varieties, a database with molecular genetic fingerprints of well-determined reference cultivars needs to be available. The objective of the present work was to establish such a database that could be applied for the molecular genetic determination of a large number of historic and modern, diploid and triploid apple cultivars. Based on the analysis of more than 1600 accessions of apple trees sampled in 37 public and private cultivar collections in different European countries at 14 variable microsatellite loci, a database with 600 molecular genetic profiles was finally obtained. The key criterion for considering a molecular genetic profile as confirmed and for including it into the reference database was that at least two accessions of the same cultivar of different provenances generated an identical result, which was achieved for 98% of the apple cultivars present in the database. For the remaining genotypes, the cultivar assignment was supported by a parentage analysis or by comparison to molecular genetic profiles available in published works. The database is composed of 574 scion cultivars, 24 rootstock genotypes and two species of crab apples. Of the 574 scion cultivars, 61% were derived from historic or old cultivars, many of which were grown in Central Europe in the past. The remaining scion cultivars are currently grown or available in testing programmes and may gain importance in the future. In order to validate the genotyping data, parentage analysis was performed involving cultivars and rootstocks that arose after 1900, for which information about at least one parent cultivar was available from pomological and scientific literature and the molecular genetic profiles of the assumed parent(s) were also present in our database. This analysis revealed the presence of null alleles at locus COL, however, when excluding this locus, a mean genotyping error rate of only 0.28% per locus was revealed, which points to a high reliability of the dataset. The datasets with 14 and 13 loci (excluding locus COL) showed a high degree of discrimination power, with a combined non-exclusion probability of identity of 2.6 × 10 -20 and 3.4 × 10 -19 . Five of the microsatellite loci analysed in the present study overlapped with another published dataset and after the application of conversion values, it was p...

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Section: Discussionmentioning

confidence: 99%

Molecular Genetic Identification of Apple Cultivars Based on Microsatellite DNA Analysis. I. The Database of 600 Validated Profiles

et al. 2020

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“…The lack of positive correlation between infected vectors and AP symptoms hint at other infection sources not considered in this study. For example, recently, a phytoplasma transmission via root-bridges between apple trees was hypothesized [27].…”

Section: Influence Of Environment On Apple Proliferation Epidemiologymentioning

confidence: 99%

Using Bayesian Inference to Investigate the Influence of Environmental Factors on a Phytoplasma Disease

Panassiti¹

2018

New Insights Into Bayesian Inference

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Phytoplasma diseases cause major economic damage on crops worldwide. To draw inferences from such a system, joint estimation of dependencies and high flexibility in the model structure are required. Using Bayesian inference, the aim of this chapter was to infer the apple proliferation (AP) disease epidemiology in South Tyrol, Italy. The data consisted of (1) presence/absence of the AP vector Cacopsylla picta collected in 44 orchards in 2014; (2) prevalence of the AP pathogen "Candidatus Phytoplasma mali" in the vector population; and (3) AP symptomatic trees visually assessed in 2015. Generalized linear mixed models evaluated in a Bayesian framework were used to test species-environment relationships. The model results indicated that the occurrence of the AP vector and symptomatic plants are positively influenced by elevation and temperature and negatively by management. Vector and pathogen predictions in the disease symptoms model correlated negatively or not at all with the prevalence of AP symptoms occurrence. In conclusion, the model results suggest that the presence/absence of the AP vector alone may not be the only cause for disease occurrence. Considering factors such as phytoplasma transmission via root-bridges and specific management strategies, may help to improve inference and finally to optimize the existing pest management.

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“…Nowadays, most tools for phytoplasma detection are based on quantitative PCR (qPCR) techniques, using intercalating DNA dyes (SYBR-Green) or hybridization probes (TaqMan ® ) [13]. Several qPCR protocols are available for the detection of phytoplasmas using different host specific endogenous internal controls [13][14][15][16][17][18][19]. Some of the available host specific internal controls can be used simultaneously with the phytoplasma specific primers in a multiplex qPCR assay [14,15,18,19], for others it is necessary to perform a separate qPCR run [20].…”

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Development of a universal endogenous qPCR control for eukaryotic DNA samples

Mittelberger¹,

Obkircher²,

Oberkofler³

et al. 2020

Plant Methods

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Background: Phytoplasma are obligate intracellular plant-pathogenic bacteria that infect a broad range of plant species and are transmitted by different insect species. Quantitative real-time PCR (qPCR) is one of the most commonly used techniques for pathogen detection, especially for pathogens that cannot be cultivated outside their host like phytoplasma. PCR analysis requires the purification of total DNA from the sample and subsequent amplification of pathogen DNA with specific primers. The purified DNA contains mainly host DNA and only a marginal proportion is of phytoplasmal origin. Therefore, detection of phytoplasma DNA in a host DNA background must be sensitive, specific and reliable and is highly dependent on the quality and concentration of the purified DNA. DNA quality and concentration and the presence of PCR-inhibitors therefore have a direct impact on pathogen detection. Thus, it is indispensable for PCR-based diagnostic tests to validate the DNA preparation and DNA integrity before interpreting diagnostic results, especially in case that no pathogen DNA is detected. The use of an internal control allows to evaluate DNA integrity and the detection of PCR-inhibiting substances. Internal controls are generally host-specific or limited to a defined group of related species. A control suitable for the broad range of phytoplasma hosts comprising different insect and plant species is still missing. Results: We developed a primer and probe combination that allows amplification of a conserved stretch of the eukaryotic 28S rDNA gene. The developed endogenous qPCR control serves as a DNA quality control and allows the analysis of different eukaryotic host species, including plants, insects, fish, fungi, mammals and human with a single primer/probe set in single-or multiplex assays. Conclusions: Quality and performance control is indispensable for pathogen detection by qPCR. Several plant pathogens are transmitted by insects and have a broad range of host species. The newly developed endogenous control can be used with all so far tested eukaryotic species and since multiplexing is possible, the described primer and probe set can be easily combined with other PCR-based pathogen detection systems.

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Molecular Tools Applied to the Advancement of Fruit Growing in South Tyrol: a Review

Cited by 5 publications

References 54 publications

Molecular Genetic Identification of Apple Cultivars Based on Microsatellite DNA Analysis. I. The Database of 600 Validated Profiles

Molecular Genetic Identification of Apple Cultivars Based on Microsatellite DNA Analysis. I. The Database of 600 Validated Profiles

Using Bayesian Inference to Investigate the Influence of Environmental Factors on a Phytoplasma Disease

Development of a universal endogenous qPCR control for eukaryotic DNA samples

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