The taproots of plants are high value-added plant organs providing high levels of digestible nutrients and fibers. The molecular mechanism underlying taproot development, however, is totally unknown. In an earlier study, we isolated a sweetpotato (Ipomoea batat as cv. “Jinhongmi”) MADS-box protein cDNA (SRD1) from an early stage storage root cDNA library and investigated the role of the SRD1 gene in the formation of the storage root in sweetpotato using SRD1-overexpressing (ox) transgenic sweetpotato plants. SRD1 was found to play a role in the formation of storage roots by activating the proliferation of cambium and metaxylem cells to induce the initial thickening growth of storage roots in an auxin-dependent manner. To identify genes involved in taproot development, we generated SRD1-ox transgenic carrot (Daucus carota L. cv. ‘Hapa-ochon’) plants. In vitro-cultured SRD1-ox carrot plants produced thicker taproots than wild-type plants. The metaxylem and cambium cells of the taproots of SRD1-ox plants showed markedly enhanced proliferation, resulting in the taproots of these plants showing an earlier thickening growth than those of wild-type plants. These results indicate that the initial thickening growth of taproots in SRD1-ox plants was accelerated by the enhnced proliferation of cambium and metaxylem cells relative to wild-type. To screen genes involved in the thickening growth of taproots, transcriptome of the taproots from the SRD1-ox and wild-type carrot plants were sequenced using Illumina paired-end sequencing technology. A de novo assembly of transcriptome sequence produced 55,383 contigs and singletons from the SRD1-ox and wild-type taproots and these assembled sequences were annotated. Digital expression analysis identified differentially expressed genes between SRD1-ox and wild-type taproots. These differentially expressed genes are candidates for the genes controlling taproot development.