A Spatiotemporal Transcriptome Revealed Stalk Development in Pearl Millet

Pearl millet is a major cereal crop that feeds more than 90 million people worldwide in arid and semi-arid regions. The stalk phenotypes of Poaceous grasses are critical for their productivity and stress tolerance, however, the molecular mechanisms governing stalk development in pearl millet remained to be deciphered. In this study, we spatiotemporally measured 19 transcriptomes for stalk internodes of four different early developmental stages. Data analysis of the transcriptomes defined 4 developmental zones on the stalks and identified 12 specific gene sets with specific expression patterns across the zones. Using weighted gene co-expression network analysis (WGCNA), we found that 2 co-expression modules together with candidate genes were involved in stalk elongation and thickening of pearl millet. Among the elongation-related candidate genes, we established by SELEX that a MYB-family transcription factor PMF7G02448 can bind to the promoters of three cell wall synthases genes (CesAs). In summary, these findings provide insights into stalk development and offer potential targets for future genetic improvement of pearl millet. To understand the dynamics of gene expression during stalk elongation of pearl millet, we collected 19 internodes for stalks of four early developmental stages. To verify the regulatory role of the MYB-family TF PMF7G02448 on the PmCesAs, we performed SELEX for PMF7G02448 to examine its specificity.