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Comprehensive genotyping of the USA national maize inbred seed bank

Maria C Romay1, Mark J Millard23, Jeffrey C Glaubitz1, Jason A Peiffer4, Kelly L Swarts5, Terry M Casstevens1, Robert J Elshire1, Charlotte B Acharya1, Sharon E Mitchell1, Sherry A Flint-Garcia26, Michael D McMullen26, James B Holland27, Edward S Buckler125* and Candice A Gardner23*

Author Affiliations

1 Institute for Genomic Diversity, Biotechnology bldg., Cornell University, Ithaca, NY, 14853, USA

2 USA Department of Agriculture (USDA) - Agricultural Research Service (USDA-ARS

3 North Central Regional Plant Introduction Station, Agronomy bldg., Department of Agronomy, Iowa State University, Ames, IA, 50001, USA

4 Bioinformatics Research Center, Thomas Hall, North Carolina State University, Raleigh, NC, 27606, USA

5 Department of Plant Breeding and Genetics, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA

6 Division of Plant Sciences, Curtis Hall, University of Missouri, Columbia, MO, 65211,USA

7 Department of Crop Science, Williams Hall, North Carolina State University, Raleigh, NC, 27695, USA

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Genome Biology 2013, 14:R55  doi:10.1186/gb-2013-14-6-r55

Published: 11 June 2013

Additional files

Additional file 1:

Table S1. Details for the 2,815 accessions (accession number, number of samples, number of plants, average identical by state (IBS) value for all the samples, percentage of missing data, breeding program, and pedigree group).

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Additional file 2:

Table S2. The 10 closest neighbors for each unique entry in our maize list based on identical by state (IBS) values. IBS value for each neighbor is presented between brackets.

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Additional file 3:

Figure S1. Network diagram showing the relationships of maize inbred lines with identical by state (IBS) values greater than 0.96.

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Additional file 4:

Figure S2. Median linkage disequilibrium (LD) decay measured as pairwise r2 between all single-nucleotide polymorphisms (SNPs) in the collection. Each line represents a different group of germplasm.

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Additional file 5:

Figure S3. Relationships between nested association mapping (NAM) recombination rate (log10 cM/Mb), average haplotype length (bp), average linkage disequilibrium (LD) (r2), and fixation index (Fst) between stiff stalk, non-stiff stalk, and tropical lines at the NAM genetic map bin scale for each chromosome. The numbers indicate the coefficient of determination (r2) calculated using Spearman's rank correlation.

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Additional file 6:

Figure S4 Quantile-quantile (QQ) plot for kernel color genome-wide association study (GWAS) analysis.

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Additional file 7:

Figure S5 Quantile-quantile (QQ) plot for sweet corn genome-wide association study (GWAS) analysis.

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Additional file 8:

Figure S6 Quantile-quantile (QQ) plot for flowering-time genome-wide association study (GWAS) analysis.

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