DEMETRA relies on the availability of two germplasm collections of grapevines: a full-sib family and a germplasm collection. The high-throughput genotyping of the two collections combined with the integration of the phenotypic data generated in Milestone 2 will allow the set-up marker-trait association analysis (Milestone 3) and the study of coding and small non-coding RNAs (Milestone 4).

Activity 1.1: Sampling of plant material and DNA extraction

Objective: Extraction of the DNA

Expected results: Extraction of high-quality DNA for genotyping analysis (ER 1.1)

Methodology:

Germplasm material:
- Full-sib family population is composed of 120 offspring and was ad-hoc developed to investigate the segregation of the resistance/susceptibility allele to PM, since the maternal line, the seeded table grape cv ‘Terez’, a Hungarian white variety derived from Vitis interspecific crossing ‘Seyve Villard 12374’ x ‘Olimpia’, is characterized by resistance to PM while the paternal line, the seedless table grape cv. ‘Autumn Giant’, is susceptible to PM instead.
- The germplasm collection is composed of 126 individuals encompassing the most important cultivars and local selections characterizing the grapevine panorama of Sicily and Campania

Activity 1.2: Genotyping and SNP filtering

Objective: High-Throughput genotyping of the two germplasm collections

Expected results: - Definition of a list of robust SNPs 

Methodology:
A novel chip array composed by the most robust SNPs included in the Vitis 18k chip (GrapeReSeq Consortium) complemented with novel SNPs targeting coding sequences is under development (Troggio M., personal communication). Robust SNPs will be filtered using the ASSIsT software (raw data from Illumina arrays), Axiom Analysis suite (ThermoFisher scientific) or pipeline for SNP filtering and/or SNP selection developed in house. The final set of robust SNPs segregating in the two germplasms in analysis will be made available for the analysis of Milestone 3.