Open Access Highly Accessed Methodology article

Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat

Martin Trick1, Nikolai Maria Adamski1, Sarah G Mugford1, Cong-Cong Jiang1, Melanie Febrer2 and Cristobal Uauy13*

Author Affiliations

1 John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK

2 The Genome Analysis Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK

3 National Institute of Agricultural Botany, Huntingdon Road, Cambridge CB3 0LE, UK

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BMC Plant Biology 2012, 12:14  doi:10.1186/1471-2229-12-14

Published: 26 January 2012

Additional files

Additional file 1:

Figure S1: Flow-chart summarizing the main steps of the NGS-BSA approach. Figure S2: Chromatograms of LDN and RSL65 for Ta#S32574498. Figure S3: BFR of validated and mapped SNPs across the GPC-B1 interval. Figure S4: Mapping of wheat unigenes with putative SNP to the Brachypodium genome. Figure S5: View of MAQ alignment of Ta#S37941845 reads for LDN and RSL65 encompassing the hemi-SNP (R = A/G) at position 582. Figure S6: Visualization of fluorescence output for two hemi-SNPs Table S1: Breakdown of SNPs lost during the validation and mapping process Table S2: Collinearity between most closely identified markers in the present study and previous markers used for physical map construction.

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Open Data

Additional file 2:

Characteristics of all putative SNPs identified in the bulk samples by Maq-default analysis.

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Additional file 3:

Characteristics of all putative SNPs identified in the bulk samples by Maq-120 analysis.

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Additional file 4:

Characteristics of SNPs mapped to the GPC-B1 region.

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Additional file 5:

SNP_parser.pl Perl script.

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Additional file 6:

bulk_frequencies.pl Perl script.

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Additional file 7:

Primers used in this study and characteristics of all SNPs tested.

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