Fig. 3

The iterative process of reduced representation sequencing (RRS) optimization. Empirical (in vitro, left of the dotted line) and computational (in silico, right of dotted line) analyses are part of this process. Core procedures to identify suitable experimental setups are in silico and empirical enzyme digestion and sequencing of a pilot RRS library (blue boxes). The coverage and marker density that can be achieved with a given setup needs to be repeatedly checked and fine-tuned (red box). We used 30 × coverage and a density of at least one SNP per 10,000 bp as target values but emphasize that these values need to be defined depending on the specific goals of a research project