title: 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.
authors.forename: Geo Velikkakam
authors.initials: GV
authors.lastname: James
authors.forename: Vipul
authors.initials: V
authors.lastname: Patel
authors.forename: Karl J V
authors.initials: KJ
authors.lastname: Nordström
authors.forename: Jonas R
authors.initials: JR
authors.lastname: Klasen
authors.forename: Patrice A
authors.initials: PA
authors.lastname: Salomé
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.forename: Korbinian
authors.initials: K
authors.lastname: Schneeberger
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001947:Breeding; D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant; D003433:Crosses, Genetic; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D009154:Mutation; D011995:Recombination, Genetic