Abstract
Whole-genome resequencing of pools of recombinant mutant genomes allows direct linking of phenotypic traits to causal mutations. Such analysis, called mapping-by-sequencing, combines classical genetic mapping and next-generation sequencing by relying on selection-induced patterns within genome-wide allele frequency (AF) in pooled genomes. Mapping-by-sequencing can be performed with computational tools such as SHOREmap. Previous versions of SHOREmap, however, did not implement standardized analyses, but were specifically designed for particular experimental settings. Here, we introduce the usage of a novel and advanced implementation of SHOREmap (version 3.0), including several new features like file readers for commonly used file formats, SNP marker selection, and a stable calculation of mapping intervals. SHOREmap can be downloaded at shoremap.org.
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References
Ossowski S et al (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res 18:2024–2033
Nordström KJ et al (2013) Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers. Nat Biotechnol 31:325–330
Schneeberger K et al (2009) SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nat Methods 6:550–551
Schneeberger K, Weigel D (2011) Fast-forward genetics enabled by new sequencing technologies. Trends Plant Sci 16:282–288
Galvão VC et al (2012) Synteny-based mapping-by-sequencing enabled by targeted enrichment. Plant J 71:517–526
Schneeberger K (2014) Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nat Rev Genet 15(10):662–676
Austin RS et al (2011) Next-generation mapping of Arabidopsis genes. Plant J 67:715–725
Cuperus JT et al (2010) Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing. Proc Natl Acad Sci U S A 107:466–471
Lindner H et al (2012) SNP-Ratio Mapping (SRM): identifying lethal alleles and mutations in complex genetic backgrounds by next-generation sequencing. Genetics 191:1381–1386
Minevich G, Park DS, Blankenberg D, Poole RJ, Hobert O (2012) CloudMap: a cloud-based pipeline for analysis of mutant genome sequences. Genetics 192:1249–1269
Leshchiner I et al (2012) Mutation mapping and identification by whole genome sequencing. Genome Res 22:1541–1548
Abe A et al (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30:174–178
Hartwig B, James GV, Konrad K, Schneeberger K, Turck F (2012) Fast isogenic mapping-by-sequencing of ethyl methanesulfonate-induced mutant bulks. Plant Physiol 160:591–600
Allen RS, Nakasugi K, Doran RL, Millar AA, Waterhouse PM (2013) Facile mutant identification via a single parental backcross method and application of whole genome sequencing based mapping pipelines. Front Plant Sci 4
Fekih R et al (2013) MutMap+: genetic mapping and mutant identification without crossing in rice. PLoS One 8:e68529
Velikkakam James G et al (2013) User guide for mapping-by-sequencing in Arabidopsis. Genome Biol 14:R61
Li H, Durbin R (2009) Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics 25:1754–1760
Schneeberger K et al (2009) Simultaneous alignment of short reads against multiple genomes. Genome Biol 10:R98
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359
Li H et al (2009) The sequence alignment/Map format and SAMtools. Bioinformatics 25:2078–2079
DePristo MA et al (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491–498
Danecek P et al (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158
Schneeberger K et al (2011) Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proc Natl Acad Sci U S A 108:10249–10254
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Sun, H., Schneeberger, K. (2015). SHOREmap v3.0: Fast and Accurate Identification of Causal Mutations from Forward Genetic Screens. In: Alonso, J., Stepanova, A. (eds) Plant Functional Genomics. Methods in Molecular Biology, vol 1284. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2444-8_19
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DOI: https://doi.org/10.1007/978-1-4939-2444-8_19
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