User guide for mapping-by-sequencing in Arabidopsis

Genome Biol. 2013 Jun 17;14(6):R61. doi: 10.1186/gb-2013-14-6-r61.


Mapping-by-sequencing combines genetic mapping with whole-genome sequencing in order to accelerate mutant identification. However, application of mapping-by-sequencing requires decisions on various practical settings on the experimental design that are not intuitively answered. Following an experimentally determined recombination landscape of Arabidopsis and next generation sequencing-specific biases, we simulated more than 400,000 mapping-by-sequencing experiments. This allowed us to evaluate a broad range of different types of experiments and to develop general rules for mapping-by-sequencing in Arabidopsis. Most importantly, this informs about the properties of different crossing scenarios, the number of recombinants and sequencing depth needed for successful mapping experiments.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Breeding
  • Chromosome Mapping / methods*
  • Chromosomes, Plant*
  • Crosses, Genetic
  • Genome, Plant*
  • High-Throughput Nucleotide Sequencing / methods*
  • Mutation
  • Recombination, Genetic