WP 1: Phenotypic analysis of released varieties based on variety release trial dataTo compare the phenotypic distance with the distances of markers, the field trial data generated during the variety testing process will be obtained from the granting authorities in Poland (COBORU) and Germany (BSA). They will be stored in a database and analysed further by the academic partners. Central goals and outcomes of this WP are empirical phenotypic distances between and variation estimates within released varieties, which represents the current status quo and reference to which any new phenotype/marker or marker-based approaches in DUS testing are being compared.
WP 2: Genotyping and analysis of released rye varietiesWithin this WP, the markers used for the 384 SNP reference genotyping array will be defined based on the results and annotation of the 5k SNP array. The markers used for the genotyping will be identified from the published data of the rye cDNA sequencing project. The following criteria will be applied for design of the marker array:
Simulations will be used to evaluate the effect of different marker selection strategies on the outcome based on the smaller SNP set.
- Equal distribution of markers over the genome;
- High polymorphism information content (PIC) value in the ascertainment panel;
- Functional annotation.
WP 3: Development of computational tools for marker-based DUS analysis and a best practice recommendationThe objective of this WP is to implement a database structure as well as a software package that is well documented and harbors all routines required for the marker-based DUS testing. The package will be implemented in the R statistical language. A modified version of the widely adopted Genomic Diversity and Database Model will be used as a database structure. Maximum likelihood and Bayesian assignment tests will be implemented to differentiate between varieties and to allow the inclusion of prior information such as variety type. The goal of this WP is the analysis of the genotypic distance and the phenotypic distance of the variety data generated in WP1.