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

User guide for mapping-by-sequencing in Arabidopsis.

Abstract

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.

PMID:
23773572
PMCID:
PMC3706810
DOI:
10.1186/gb-2013-14-6-r61
[Indexed for MEDLINE]
Free PMC Article

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