ARS | Publication request: Flux in the coding and small RNA transcriptomes during soybean seed and seedling development

Submitted to: Biennial Conference on Molecular and Cellular Biology of the Soybean
Publication Type: Abstract Only
Publication Acceptance Date: May 27, 2008
Publication Date: July 20, 2008
Citation: Vodkin, L., Jones, S., Gonzalez, D.O., Zabala, G., Hunt, M., Tuteja, J., Radwan, O., Calla, B., Clough, S.J., Varala, K., Win, H., Hudson, M. 2008. Flux in the coding and small RNA transcriptomes during soybean seed and seedling development [abstract]. In: Proceedings of the 12th Biennial Conference on Molecular and Cellular Biology of the Soybean. July 20-23, 2008. Indianapolis, Indiana. p. 27.

Technical Abstract: Soybean cotyledons undergo major developmental transitions during seed development. Changes in the transcriptome of seed tissues from a few days after flowering through maturation, and in the cotyledons during germination and early seedling growth, have been revealed using cDNA and 70-mer oligonucleotide arrays containing over 36,000 different probes. We use custom arrays with up to 40 repeats of specific oligos to reaffirm the changes in gene expression during these developmental transitions. We have also explored the flux of small RNA populations (the smRNAome of 21-27 nt RNAs) for several stages and tissues of seed, seedling development, and treated plants using Illumina Sequence-by-Synthesis deep sequencing yielding over 10 million reads. These small RNAs are being characterized by enumerating the species present and alignment of each to the curated miRNA Sanger database and to the non-redundant nucleotide database at NCBI. Many match known miRNAs from other organisms in the database, while many others appear to be novel siRNAs. We have also developed statistical techniques to identify differentially expressed small RNAs. Similar to the coding transcriptome, the small RNAome reveals many organ, tissue specific and developmental shifts in the population of small RNAs. Finally, we have investigated the molecular basis of several mutations affecting seed or seedling traits using microarrays to identify downstream genes and/or candidate genes. Likewise the flux of small RNA populations is also being examined in some of these soybean mutant lines.