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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页数:13
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