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
相关论文
共 37 条
[31]   The recombination landscape in Arabidopsis thaliana F2 populations [J].
Salome, P. A. ;
Bomblies, K. ;
Fitz, J. ;
Laitinen, R. A. E. ;
Warthmann, N. ;
Yant, L. ;
Weigel, D. .
HEREDITY, 2012, 108 (04) :447-455
[32]   Reference-guided assembly of four diverse Arabidopsis thaliana genomes [J].
Schneeberger, Korbinian ;
Ossowski, Stephan ;
Ott, Felix ;
Klein, Juliane D. ;
Wang, Xi ;
Lanz, Christa ;
Smith, Lisa M. ;
Cao, Jun ;
Fitz, Joffrey ;
Warthmann, Norman ;
Henz, Stefan R. ;
Huson, Daniel H. ;
Weigel, Detlef .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2011, 108 (25) :10249-10254
[33]   SHOREmap: simultaneous mapping and mutation identification by deep sequencing [J].
Schneeberger, Korbinian ;
Ossowski, Stephan ;
Lanz, Christa ;
Juul, Trine ;
Petersen, Annabeth Hogh ;
Nielsen, Kare Lehmann ;
Jorgensen, Jan-Elo ;
Weigel, Detlef ;
Andersen, Stig Uggerhoj .
NATURE METHODS, 2009, 6 (08) :550-551
[34]   Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat [J].
Trick, Martin ;
Adamski, Nikolai Maria ;
Mugford, Sarah G. ;
Jiang, Cong-Cong ;
Febrer, Melanie ;
Uauy, Cristobal .
BMC PLANT BIOLOGY, 2012, 12
[35]   Massively parallel exon capture and library-free resequencing across 16 genomes [J].
Turner, Emily H. ;
Lee, Choli ;
Ng, Sarah B. ;
Nickerson, Deborah A. ;
Shendure, Jay .
NATURE METHODS, 2009, 6 (05) :315-316
[36]   Identification of EMS-Induced Causal Mutations in a Non-Reference Arabidopsis thaliana Accession by Whole Genome Sequencing [J].
Uchida, Naoyuki ;
Sakamoto, Tomoaki ;
Kurata, Tetsuya ;
Tasaka, Masao .
PLANT AND CELL PHYSIOLOGY, 2011, 52 (04) :716-722
[37]   A Strategy for Direct Mapping and Identification of Mutations by Whole-Genome Sequencing [J].
Zuryn, Steven ;
Le Gras, Stephanie ;
Jamet, Karine ;
Jarriault, Sophie .
GENETICS, 2010, 186 (01) :427-430