Sweetpotato transcriptome data have increased enormously during the last two years. The goal of the present work was to use this information to build a core set of Unigenes for functional genomics studies in sweetpotato. The primary objective was to discover the genes associated with the onset of storage root formation. Sweetpotato transcriptome derived from root, stem and leaf were assembled using cap3 and Newbler program. The transcripts (contigs + singlets) were functionally annotated for their homologies to known proteins by blasting against the Uniprot database. Further functional characterization was done using b2go and KEGG analysis. Using the results of these bioinformatic analyses along with the in silico quantitative analysis of transcripts from initiating storage and fibrous roots, a set of candidate genes with regulatory roles and in signaling pathway were selected mostly from the root transcriptome. Expression profiling of these genes between initiating storage root and fibrous root was done using quantitative reverse transcription PCR. The results showed that a set of 17 genes were implicated in sweetpotato storage root formation of which 15 were considered novel. These include transcription factors for meristem maintenance and cell differentiation, and genes for calcium signaling. They are up-regulated in storage roots with fold changes up to 30 times. Additionally, we correlated potential single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) to variation in expression of genes in fibrous and early developing storage roots. Work is in progress in the design of a microarray for functional genomic research, and to develop a database.