Overview of different strategies for mapping-by-sequencing. Establishing mutant pools or individual mutant recombinant genomes requires decisions on different aspects of mapping-by-sequencing. Common questions are shown in red. (I) Mutants can be crossed to diverged accessions or backcrossed to the wild-type. (II) The number of backcrosses and number of plants used as parents contribute to the outcome of mapping-by-sequencing. (III) The number of mutant plants sampled from mapping population greatly impacts on the mapping results. (IV) Finally, the sequencing coverage as well as type of sequencing (single-end or paired-end) affects the outcome of mapping-by-sequencing.