Whole genome scanning of a Mediterranean basin hotspot collection provides new insights into olive tree biodiversity and biology.

Olive tree (Olea europaea L. subsp. europaea var. europaea) is one of the most important species of the Mediterranean region and one of the most ancient species domesticated. The availability of whole genome assemblies and annotations of olive tree cultivars and oleaster (O. europaea subsp. europaea var. sylvestris) has contributed to a better understanding of genetic and genomic differences between olive tree cultivars. However, compared to other plant species there is still a lack of genomic resources for olive tree populations that span the entire Mediterranean region. In the present study we developed the most complete genomic variation map and the most comprehensive catalog/resource of molecular variation to date for 89 olive tree genotypes originating from the entire Mediterranean basin, revealing the genetic diversity of this commercially significant crop tree and explaining the divergence/similarity among different variants. Additionally, the monumental ancient tree 'Throuba Naxos' was studied to characterize the potential origin or routes of olive tree domestication. Several candidate genes known to be associated with key agronomic traits, including olive oil quality and fruit yield, were uncovered by a selective sweep scan to be under selection pressure on all olive tree chromosomes. To further exploit the genomic and phenotypic resources obtained from the current work, genome-wide association analyses were performed for 23 morphological and two agronomic traits. Significant associations were detected for eight traits that provide valuable candidates for fruit tree breeding and for deeper understanding of olive tree biology.

Introducing Three-Dimensional Scanning for Phenotyping of Olive Fruits Based on an Extensive Germplasm Survey.

Morphological characterization of olive (Olea europaea L.) varieties to detect desirable traits has been based on the training of expert panels and implementation of laborious multiyear measurements with limitations in accuracy and throughput of measurements. The present study compares two- and three-dimensional imaging systems for phenotyping a large dataset of 50 olive varieties maintained in the National Germplasm Depository of Greece, employing this technology for the first time in olive fruit and endocarps. The olive varieties employed for the present study exhibited high phenotypic variation, particularly for the endocarp shadow area, which ranged from 0.17−3.34 cm2 as evaluated via 2D and 0.32−2.59 cm2 as determined by 3D scanning. We found significant positive correlations (p < 0.001) between the two methods for eight quantitative morphological traits using the Pearson correlation coefficient. The highest correlation between the two methods was detected for the endocarp length (r = 1) and width (r = 1) followed by the fruit length (r = 0.9865), mucro length (r = 0.9631), fruit shadow area (r = 0.9573), fruit width (r = 0.9480), nipple length (r = 0.9441), and endocarp area (r = 0.9184). The present study unraveled novel morphological indicators of olive fruits and endocarps such as volume, total area, up- and down-skin area, and center of gravity using 3D scanning. The highest volume and area regarding both endocarp and fruit were observed for 'Gaidourelia'. This methodology could be integrated into existing olive breeding programs, especially when the speed of scanning increases. Another potential future application could be assessing olive fruit quality on the trees or in the processing facilities.

Characterization of Fungi Associated With Wood Decay of Tree Species and Grapevine in Greece.

A two-year survey was conducted to identify fungi associated with wood decay in a range of tree species and grapevine. Fifty-eight fungal strains isolated from plants of 18 species showing typical wood decay symptoms were characterized by morphological, physiological, and molecular analyses. By 5.8S rRNA gene-ITS sequencing analysis, these isolates were classified into 25 distinct operational taxonomic units, including important phytopathogenic species of the phyla Pezizomycotina and Agaricomycotina, such as Fomitiporia, Inonotus, Phellinus, Inocutis, Fuscoporia, Trametes, Fusarium, Eutypa, Phaeomoniella, Phaeoacremonium, and Pleurostomophora spp. The white rot basidiomycetes Fomitiporia mediterranea (20 isolates, 34.5%) and Inonotus hispidus (6 isolates, 10.3%) were the most prevalent. Pathogenicity tests revealed for the first time that certain fungal species of the genera Fomitiporia, Inonotus, Phellinus, Pleurostomophora, and Fusarium caused wood infection of various tree species in Greece and worldwide. To the best of our knowledge, this is the first report of F. mediterranea as the causal agent of wood decay in pear, pomegranate, kumquat, and silk tree. This is also the first record of Inonotus hispidus, Phellinus pomaceus, Pleurostomophora richardsiae, and Fusarium solani in apple, almond, avocado, and mulberry tree, respectively, whereas P. richardsiae was associated with wood infection of olive tree for the first time in Greece. Cross pathogenicity tests with F. mediterranea strains originated from grapevine applied on other woody hosts and from olive on grapevine demonstrated partial host specificity of the fungus. The potential of F. mediterranea to transinfect hosts other than those originated, along with the host range extension of the fungus, is discussed.