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Open Access Research article

Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content

Wolfgang Goettel1, Eric Xia2, Robert Upchurch3, Ming-Li Wang4, Pengyin Chen5 and Yong-Qiang Charles An1*

Author Affiliations

1 USDA-ARS, Midwest Area, Plant Genetics Research Unit at Donald Danforth Plant Science Center, 975 N Warson Rd, St. Louis, MO 63132, USA

2 508 East Stoughton Street, Champaign, IL 61820, USA

3 USDA-ARS, Soybean and Nitrogen Fixation Research, 2417 Gardner Hall, Raleigh, NC 27695, USA

4 USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment St., Griffin, GA 30223, USA

5 Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA

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BMC Genomics 2014, 15:299  doi:10.1186/1471-2164-15-299

Published: 23 April 2014

Additional files

Additional file 1: Figure S1:

Accumulative transcript amount of most highly expressed genes in seeds. Genes were sorted by average expression in percent across nine lines. The smallest number of genes (i.e. top expressers) required to reach the accumulative transcript amounts in percent as indicated on the X-axis are shown. Figure S2. Distribution of expression variation per line. For each of the 8,037 differentially expressed genes, we determined the line that exhibits the largest expression variation (i.e. absolute Z-score) compared to the average expression across all nine lines. The total count for up-regulated (blue columns) and down-regulated (red columns) genes per line is presented.

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Additional file 2: Table S1:

100 most abundant transcripts in seeds. Table S2. Genes showing expression variation across nine lines. Table S3. Expression variation by fold-change. Table S4. Average expression ratio of genes with and without SNPs that led to pre-mature stop codons. Table S5. Possibly damaging non-synonymous SNPs in putative acyl lipid genes.

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