Comparative Genomics Approach to Understanding the Crop Root Development

Growth and patterning of multicellular organs are controlled by complex gene regulatory programs. Gene expression dynamics during the organ growth can provide clues of how regulatory programs are operated.  Our long term goal is to comprehensively understand the molecular programs underlying the organ growth and to apply this knowledge to enhancing yields. Cambium is the stem cell population for plant vascular tissues that grow radially. Cambium activity plays an important role in controlling plant growth forms and biomass yields. In our research, we profiled transcripts in the procambium/cambium of Arabidopsis roots using the cell sorting-microarray technique.  From these data, together with the rest of the root cell type specific transcript profile data (a total of 23 data sets), groups of differentially expressed genes in the cambium were identified. Using upstream sequences of each gene set, highly enriched regulatory motifs were identified by statistical analysis. We searched for potential transcriptional regulators of gene sets with these motifs and addressed their regulatory roles in the cambium. Among these are transcriptional regulators involved in the cell cycle regulation and cell differentiation in stem cells of plants and animals.  Using a cell cycle regulator showing enriched gene expression in the cambium in Arabidopsis roots, we further analyzed its expression in the cambium area of radish (Raphanus sativus) roots. We found that this cell cycle regulator is specifically expressed in the cambial cells and its expression increases in the roots that are at a stage of rapid radial growth. In summary, our comparative study of a model organism Arabidopsis thaliana and a root crop in Brassicaceae provides a new framework towards a systematic understanding of gene regulatory programs underlying the growth of root crops.