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 possible to align the allele lengths and compare the molecular genetic profiles of 20 randomly derived cultivars, which were analysed in both studies. This comparison evidenced an exact correspondence of the microsatellite profiles contained in the two datasets, further pointing to the accuracy of our database. Apart from its application to characterise genetic resources or to manage germplasm collections, the here presented database could serve as an important tool for quality control or as a useful instrument in breeding programmes.

South Tyrol (northern Italy) harbors one of the largest interconnected apple farming areas in Europe, contributing approximately 10% to the apple production of the European Union. Despite the availability of sophisticated storage facilities, postharvest diseases occur, one of which is bitter rot of apple. In Europe, this postharvest disease is mainly caused by the Colletotrichum acutatum species complex. This study aimed to characterize the Colletotrichum spp. isolated from decayed apple fruit collected in 2018 and 2019 in South Tyrol. The characterization of Colletotrichum spp. was accomplished based on multilocus DNA sequences of four different genomic regions—actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone H3 (HIS3), and the internal transcribed spacer (ITS) region—as well as morphological and pathogenicity assessment. A phylogenetic analysis based on multilocus DNA sequences showed that the isolates obtained from apples with symptoms of bitter rot belonged to the species Colletotrichum godetiae and Colletotrichum fioriniae, which are part of the Colletotrichum acutatum species complex. A third species isolated from apples belonging to the same species complex, Colletotrichum salicis, was described in this area. Moreover, the Colletotrichum isolates found in this study proved to be virulent on Cripps Pink, Golden Delicious, and Roho 3615/Evelina. To the best of our knowledge, C. godetiae and C. fioriniae have so far never been mentioned as postharvest pathogens of apple in Italy, although the reanalysis of samples collected in the past indicates that these pathogens have been occurring in Italy for at least a decade. So far, bitter rot seems to play a minor role as a postharvest disease in South Tyrol, but it was disproportionately represented on a few scab-resistant apple cultivars, which are increasingly planted in organically managed orchards. Considering that the expansion of organic apple production and the conversion to new potentially Colletotrichum-susceptible cultivars will continue, the present study represents an important contribution toward a better understanding of bitter rot in this geographic area. [ ] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Recently, Cadophoraluteo-olivacea has been reported as a post-harvest pathogen of side rot of apple (Malusdomestica) in Latvia, and of pear (Pyruscommunis) in Italy and the Netherlands. In 2018 and 2019, in South Tyrol (northern Italy) 11 fungal cultures, identified as C.luteo-olivacea based on ITS (internal transcribed spacer region) sequence data, were obtained from apple fruit displaying post-harvest side rot symptoms. The fruit were sampled in packinghouses representing different apple growing areas of South Tyrol. For a more accurate taxonomic assignment, two additional molecular genetic loci, β-tubulin (TUB2) and translation elongation factor 1α (TEF-1α), of seven isolates were amplified and sequenced. Phylogenetic analysis based on multi-locus DNA sequence data confirmed that isolates from apple fruit with side rot symptoms indeed represented C.luteo-olivacea. A pathogenicity test performed on apple fruit of ‘Golden Delicious’ confirmed the virulence of a representative isolate. So far, C.luteo-olivacea represents a minor post-harvest pathogen of apple but considering the losses that this fungus can cause to other crops, the awareness about this potential apple disease should be raised.

Bull’s eye rot, caused by Phlyctema vagabunda and Neofabraea species, is one of the most important postharvest diseases of apple. South Tyrol (northern Italy) is the largest continuous apple-producing area in Europe, with approximately 1 million tons being produced yearly and conserved in technologically advanced storage facilities for several months. Still, studies on the pathogen species causing postharvest bull’s eye rot of apple, as well as their diversity and biology, are lacking for this region. Therefore, the main purpose of the present work was to identify and characterize fungal isolates obtained from decayed apple fruit with symptoms of bull’s eye rot that were collected in 2018 and 2019 in different packinghouses in South Tyrol. Among more than 1,000 fungal isolates that were obtained, 419 could be assigned to the genera Phlyctema and/or Neofabraea based on rot symptoms on apple fruit and colony morphology on potato dextrose agar. A smaller subset of 101 representative isolates was further analyzed by DNA sequencing of the internal transcribed spacer region. Furthermore, partial segments of the β-tubulin gene, the translation elongation factor 1α gene, and the 16S mitochondrial ribosomal RNA gene were studied. The phylogenetic analyses, including sequences of reference species, showed that P. vagabunda is the dominant species associated with bull’s eye rot of apple in the study area, whereas Neofabraea kienholzii was found only on a small number of apple fruit samples. The combination of multilocus sequence data revealed 11 unique genotypes that belonged to P. vagabunda and four to N. kienholzii. To the best of our knowledge, this study is the first to report N. kienholzii as a postharvest pathogen of apple in Italy. Finally, a pathogenicity test demonstrated different degrees of virulence among selected isolates of P. vagabunda and N. kienholzii on the cultivar Golden Delicious. The present study emphasizes the importance of accurate species identification, because different species may vary in their biological and pathogenic characteristics, and consequently require distinct disease management strategies, both in the field and during the postharvest stages. [ ] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

European chestnut (Castanea sativa) is threatened by the invasive fungus Cryphonectria parasitica, which causes chestnut blight. The virulence of the fungus can be reduced by a group of mycoviruses that can spread among vegetatively compatible strains through hyphal anastomosis. Hypovirulent isolates are used as biocontrol agents, but their efficiency can be diminished by restricted hyphal anastomosis if the variability of vegetative compatibility (vc) types in a population is high. Sexual reproduction could increase the vc type diversity and further complicate biocontrol in a region. Therefore, knowledge of genetic diversity of C. parasitica is important to assess the effectiveness of a biological control program. The present study was performed in the Autonomous Province of Bozen-Bolzano (South Tyrol) in northern Italy, where chestnut cultivation provides an additional income to farmers. The genetic characterization of C. parasitica isolates from 35 chestnut stands and one forest population in different districts of South Tyrol was performed based on the analysis of vegetative incompatibility loci, the mating type locus, and the internal transcribed spacer (ITS) region. In this study, a total of 23 different vc types were found all over South Tyrol with a Shannon diversity index of 1.86. EU-2, EU-1, and EU-13 were the most widespread vc types comprising 51%, 13%, and 9% of the fungal isolates, respectively. Both mating types were present in the region with a ratio close to 1:1. Three different haplotypes were identified based on ITS sequence analysis, which pointed to two introduction events of the fungus to the region and allowed placing C. parasitica from South Tyrol into a larger phylogeographic context.

Apple (Malus domestica Borkh.) is the most important fruit crop in South Tyrol (northern Italy), with a total production of 905.089 tons in 2019 (Chamber of Commerce, Industry, Crafts and Agricultu...