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Open Access Research

Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production

Carrie S Thurber1, Justin M Ma1, Race H Higgins12 and Patrick J Brown12*

Author Affiliations

1 Energy Biosciences Institute, University of Illinois, Urbana, IL, USA

2 Department of Crop Sciences, University of Illinois, Urbana, IL, USA

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Genome Biology 2013, 14:R68  doi:10.1186/gb-2013-14-6-r68

Published: 26 June 2013

Additional files

Additional File 1:

Table S1. SC and EP lines used in this study. Principal components analysis in the EP lines was used to assign SC-EP pairs to subpopulations. Plant height and flowering time phenotypes used for association mapping in the SC lines are also provided.

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Additional File 2:

Figure S1. Enzyme effects on SNP output. Combining two double digests (PstI-HF/HinP1I and PstI-HF/BfaI) nearly doubles the number of SNPs called per sample over one double digest (Pst1-HF/HinP1I).

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Additional File 3:

Figure S2. Principal Component Analysis (PCA) of BTx406 seed source libraries. Twenty-eight libraries were created for BTx406 seed from three different sources (GRIN, Cornell, and Lubbock). The three outlier libraries from the GRIN collection were removed due to low concordance.

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Additional File 4:

Figure S3. Introgression maps for 390 SC lines.

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Additional File 5:

Table S2. Number and percentage of introgressed, unexpected, and informative markers for each SC-EP pair.

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Additional File 6:

Table S3. Physical map positions of unanchored SNPs

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Additional File 7:

Figure S4. Introgression frequency, phenotypic associations, and population differentiation in the Ma1-Dw2 region on sorghum chromosome 6. Panels are the same as in Figures 3 to 6. The locations of Ma1 at 40.3 Mb is shown with a vertical dashed gray line.

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Additional File 8:

Figure S5. PCA of SC lines with and without SNPs in the three major introgressed regions.

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Additional File 9:

Figure S6. Subpopulation-specific introgression frequencies.

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Additional File 10:

Table S4. Phenotypic associations with plant height and flowering time in 580 SC lines.

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Additional File 11:

Table S5. List of barcoded adapters used in library preparation.

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Additional File 12:

Table S6. Raw introgression scores.

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