Identification of root transcriptional responses to shoot illumination in Arabidopsis thaliana.

KEY MESSAGE: The transcriptional profile of roots is highly affected by shoot illumination. Transcriptogram analysis allows the identification of cellular processes that are not detected by DESeq. Light is a key environmental factor regulating plant growth and development. Arabidopsis thaliana seedlings grown under light display a photomorphogenic development pattern, showing short hypocotyl and long roots. On the other hand, when grown in darkness, they display skotomorphogenic development, with long hypocotyls and short roots. Although many signals from shoots might be important for triggering root growth, the early transcriptional responses that stimulate primary root elongation are still unknown. Here, we aimed to investigate which genes are involved in the early photomorphogenic root development of dark grown roots. We found that 1616 genes 4 days after germination (days-old), and 3920 genes 7 days-old were differently expressed in roots when the shoot was exposed to light. Of these genes, 979 were up regulated in 4 days and 2784 at 7 days-old. We compared the functional categorization of differentially regulated processes by two methods: GO term enrichment and transcriptogram analysis. Expression analysis of nine selected candidate genes in roots confirmed the data observed in the RNA-seq analysis. Loss-of-function mutants of these selected differentially expressed genes suggest the involvement of these genes in root development in response to shoot illumination. Our findings are consistent with the observation that dark grown roots respond to the shoot-perceived aboveground light environment.