Publication: Diversity of Mediterranean Vitis spp. genetic resources

Publication: Diversity of Mediterranean Vitis spp. genetic resources

Title of the project:

Protecting the Diversity of Mediterranean Vitis in a Changing Environment

Acronym: MedVitis

Project duration

1th of April 2018 - 31th of March 2021

Leader of the Slovenian research group:

dr. Barbara Pipan

Members of the Slovenian research group: dr. Lovro Sinkovič, (Radojko Pelengić), izr. prof.dr. Vladimir Meglič

Coordinator:

Hellenic Agricultural Organisation-Demeter, Grčija (dr.Aliki Kapazoglou)
Partners: University Abdelmalek Essaadi, Morocco (Younes Hmimsa); Agricultural Institute of Slovenia, Slovenia (dr. Barbara Pipan)
Collaborators: Institut National de la Recherche Agronomique, Morocco (dr. Aicha El Oualkadi)

Funding:

By ERA-NET ARIMNet2 iniciative; national funder is Ministry of Agriculture, Forestry and Food (contract no. 2330-18-000077)

Project summary:

Viticulture and wine production are important agricultural activities in Mediterranean countries, such as Greece, Slovenia and Morocco. In all three countries diverse geographical terrains and microclimates have favored wide Vitis diversity and led to local varieties that are well adapted to the specific agro-climatic conditions of each region, supporting sustainable agricultural systems of low inputs. However, introduction of foreign commercial varieties have resulted in genetic erosion and loss of genetic diversity, necessitating the undertaking of collaborative actions to preserve the diversity of Vitis genetic resources. Moreover, environmental changes across the Mediterranean region, linked to the ongoing global climatic changes, and the threat of diseases may have a negative impact for Mediterranean viticulture. This requires the implementation of activities to preserve well adapted local varieties or develop improved varieties with tolerance to changing environmental conditions and resistance to pathogens. The project, MedVitis, proposes an integrated effort by four partners originating from Greece (1), Slovenia (1), and Morocco (2), aiming to protect the diversity of grapevine germplasm across the three countries, in order to better manage issues of grapevine identification, genetic erosion, climate change and Vitis pathogenicity.

Phenotypic characterization included 33 genetic resources of the genus Vitis from different areas of Slovenia (Primorska, Podravje, Posavje) and evaluated them on the basis of a total of 108 O.I.V. descriptors standardized by the OIV organization and proposed for characterization of new and unknown grape varieties and species. We evaluated the visual parameters of the different parts of the vine with 82 descriptive traits. Morphometric parameters on grapes, grape berries and tendrils were measured and evaluated with 11 numerical descriptors. Based on the measurements, the obtained results were converted into corresponding estimates of descriptive descriptors. The morphometric parameters on fully developed leaves were estimated using 15 phylometric descriptors. Measurements on fully developed leaves were performed using the SuperAmpelo program. We imported the taken photographs into the program, marked important points on the leaf, and the program then calculated the distances, angles, and relationships between them. Based on the measurements, the program calculated and outputted descriptive estimates. We found that the studied genetic resources of the genus Vitis are highly variable at the morphological level. The genetic resources show great variability in some traits, and in some, the results showed that the genetic resources are very similar or even identical in certain traits. Variations in some morphological traits can be observed in genetic resources that do not belong to the species Vitis vinifera L., especially in some descriptive ones (O.I.V. 004, O.I.V. 011, O.I.V. 012, O.I.V. 015-1, O.I.V. 015-2, O.I.V. 016 ., O.I.V. 065, O.I.V. 077, O.I.V. 084, O.I.V. 202, O.I.V. 236, O.I.V. 243, O.I.V. 502) and six phylometric descriptors (O.I.V. 601, O.I.V. 602, O.I.V. 60). Some descriptors were also found to deviate from genetic resources from a specific geographical area. Within the WP2 and WP3 workpackages, we also characterized 10 previously unexplored Slovenian genetic resources.

Genetic characterization was performed for collected genetic resources in all three member countries of the consortium: Slovenia, Greece and Morocco. We genotyped a total of 136 genotypes at 12 SSR (Simple Sequence Repeats) loci. The study included 9 markers that the OIV has included in the O.I.V. descriptors for Vitis sp.description and characterization and recommends for species and varietal description (O.I.V. 801-809, loci VVS2, VVMD5, VVMD7, VVMD27, VrZAG62, VrZAG79, VVMD32, VVMD25, VVMD28). To obtain better genetic information, we included three additional SSR loci (VrZAG67, VMC5G6.1, VMC3C9). Based on allele profiles at 12 loci for each included genetic resource, we applied population genetics tools to analyze genetic diversity, variability, association, and genetic structure (parameters of variability by loci and geographic origin, HWE, AMOVA, PCoA, Bayesian cluster analysis). Based on the results, we can conclude that the most informative locus in the analysis was VVMD28 (PIC = 0.91) where we also calculated the highest determined level of genetic variability between Slovenian, Moroccan and Greek genotypes (He = 0.92). Measures of relatedness, where the highest genetic differentiation occurs in the case of random mating, were found at the VVS2 locus (Fis = 0.27, Fit = 0.30), while the highest overall degree of genetic differentiation was determined at the VrZAG79 locus (Fst=0.10). The highest number of genetic migrants was determined at the VrZAG62 locus (Nm = 6.74), indicating that this locus is the most informative in terms of studying gene flow by spontaneous/target pollination. Considering that the project includes genetically very diverse genetic resources of the genus Vitis from three Mediterranean regions, we were expected to calculate a high level of genetic variability at each locus using different parameters and selected set of markers were proven to be informative and relevant (mean PIC and He > 0.85). From deviations from the Hardy-Weinberg equilibrium, we can see that only for the Greek genotypes at the loci VVMD5, VVMD27 and VrZAG79 there is no statistical significance, which means that these parts of the genome are uniform for Greek genetic resources comparing with other ones from other origins that are statistically significantly different at all analyzed loci / parts of the genome. Based on the results of allele profiles by the parameters of population genetics (number of different alleles, number of private alleles, expected heterozygosity, number of effective alleles) and genetic comparisons between genetic sources from Slovenia, Greece and Morocco, we can conclude that the most diverse genetic sources were found in Morocco (He=0,86). Based on calculations of the degree of genetic association of genetic resources from Slovenia, Greece and Morocco according to Nei genetic distance, we find that the genetic association follows geographically, as the most genetically related genetic resources are from Slovenia and Greece, which are also geographically closer (0.642). This is continued by the Greece-Morocco relation; the least related genetic sources in the analysis are from Slovenia and Morocco. The analysis of molecular variability (AMOVA) showed that all three Mediterranean countries are sharing 89% of germplasm; only 11% of it is different/variable. The analysis of the genetic structure and the analysis of the principal coordinates confirmed the AMOVA results, as we divided all 136 genetic resources into two genetic groups based on the allele profiles. In PCoA, the first two coordinates together explained 52% of the molecular variability. According to the results, the genetic groups formed have no association with the color of the skin of the berries or whether a genetic resource is primarily intended as a table or wine variety, but most likely with the geographically determined distribution and adaptation of genotypes to the environment in which they grow. Thus, we have confirmed that much of the Vitis sp. germplasm is common to these three Mediterranean countries, and within them there are two different genetic pools indicating separate adaptation to local Mediterranean growing conditions.

The obtained results allow us to accurately describe and characterize the studied genetic resources of the genus Vitis. Particularly important is the description of genetic resources that were completely unknown and unexplored until now. In the future, the descriptions of the studied genetic resources can serve various breeding programs in the search for new species and varieties that can successfully resist the changing conditions in which the Vitis plants thrives and new pests and diseases that affect the Vitis plants. Unknown local sources can thus be a potential treasure trove of endangered genetic variability, making it worthwhile to preserve such genetic resources for future generations.

 

Publication: Diversity of Mediterranean Vitis spp. genetic resources