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User guide for mapping-by-sequencing in Arabidopsis

Geo Velikkakam James1, Vipul Patel1, Karl JV Nordström12, Jonas R Klasen1, Patrice A Salomé3, Detlef Weigel3 and Korbinian Schneeberger1*

Author Affiliations

1 Max Planck Institute for Plant Breeding Research, Department for Plant Developmental Biology, 50829 Cologne, Germany

2 Department of Biological Sciences, Institute of Genetics/Epigenetics, University of Saarland, Campus Saarbrücken, 66123 Saarbrücken, Germany

3 Max Planck Institute for Developmental Biology, Department of Molecular Biology, 72076 Tübingen, Germany

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Genome Biology 2013, 14:R61  doi:10.1186/gb-2013-14-6-r61

Published: 17 June 2013

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.

Keywords:
Mapping-by-sequencing; SHOREmapping; genetic mapping; whole-genome sequencing; Arabidopsis thaliana