Background: Small RNAs play an important role in the regulation of gene expression. Recent genome-wide profiling studies of small RNAs in Arabidopsis thaliana have revealed the complexity of small RNA in plant genomes. Since soybean small RNA populations in Soybean [Glycine max] may regulate important processes in this crop plant, we used illumina sequencing-by-synthesis technology to sequence approximately 30 million small RNAs from seed coat and cotyledon tissues to identify small regulatory RNAs that are differentially expressed between these tissues.Results: Glycine max genome locations, genomic features, and small RNA sequence abundance information from the seed coat and cotyledon libraries were used to characterize the small RNA population and its expression. By analyzing small RNAs as clusters based on their closeness of the genomic matching location, we identified 177,314 small RNA generating loci from 20 chromosomes. 89% of small RNA generating loci mapped to the annotated repeat regions. More than 1% of small RNA generating loci mapped to genomic region where no functional information is available. 3017 small RNA generating loci also showed significant expression differences between libraries in our comparison. In addition, we identified 6 potential secondary siRNA triggers, 94 potential trans-acting siRNA (ta-siRNA) generation loci, at least 5 natural cis-antisense siRNA (cis-nat-siRNAs) generating loci.Conclusions: Identification of distinct candidate small RNA populations such as ta-siRNA, cis-nat-siRNAs, secondary siRNA triggers, and genomic regions where small RNAs are potentially involved in the regulation of gene expression in soybean seed coat and cotyledon gives a better understanding of small RNA populations in the Glycine max genome. In particular, the potential new ta-siRNA loci identified show that the ta-siRNA system in soybean is significantly more complex than the system previously characterized in the model system Arabidopsis.
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