User guide for mapping-by-sequencing in Arabidopsis

被引：89

作者：

James, Geo Velikkakam ^{[1
]}

Patel, Vipul ^{[1
]}

Nordstroem, Karl J. V. ^{[1
,2
]}

Klasen, Jonas R. ^{[1
]}

Salome, Patrice A. ^{[3
]}

Weigel, Detlef ^{[3
]}

Schneeberger, Korbinian ^{[1
]}

机构：

[1] Max Planck Inst Plant Breeding Res, Dept Plant Dev Biol, D-50829 Cologne, Germany

[2] Univ Saarland, Inst Genet Epigenet, Dept Biol Sci, D-66123 Saarbrucken, Germany

[3] Max Planck Inst Dev Biol, Dept Mol Biol, D-72076 Tubingen, Germany

来源：

GENOME BIOLOGY | 2013年 / 14卷 / 06期

关键词：

Mapping-by-sequencing; SHOREmapping; genetic mapping; whole; genome sequencing; Arabidopsis thaliana; MUTATION IDENTIFICATION; SNP DISCOVERY; GENOME; THALIANA; MUTANT; REVEALS; MAP; RECOMBINATION; SELECTION; MARKERS;

D O I：

10.1186/gb-2013-14-6-r61

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

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