Metabolic and transcriptional changes reveal the molecular mechanism that regulates taproot thickening in root chicory (Cichorium intybus L.)

Root chicory (Cichorium intybus L.) is a plant whose belowground parts are mainly used as raw material for the industrial production of inulin. To investigate the molecular mechanism responsible for regulating the process of taproot thickening in root chicory, both mRNA-seq and non-targeted metabolome detection were performed for taproots at five developmental stages in the first year of field growth. Results showed a faster increase in root diameter and root fresh weight in the early stage of taproot thickening, whereas in its late stage the dry weight content increased rapidly. In tandem, the abundance of carbohydrates and fatty acids was relatively high at the early stage, in contrast to the late stage of taproot thickening, when amino acids substantially accumulated. Differentially expressed genes (DEGs) were enriched to pathways or biological processes closely related to taproot thickening, namely, ‘transcriptional regulation’, ‘hormone signal transduction’, ‘starch and sucrose metabolism’, ‘cell wall organization and biosynthesis’, and ‘phenylpropanoid and lignin biosynthesis’. Further, transcripts–metabolites regulatory network revealed that sucrose, D-fructose 6-P, and phenylalanine, together with the transcription factors CiMYB20 and CiERF13, as well as the structural genes CiEXPA, Ci1-FFT, CiSPS, and CiPAL, could be critical molecules that operate to regulate chicory’s taproot thickening. We conclude that the differential expression of metabolites and genes plays a crucial role in the taproot thickening of root chicory. This study lays a foundation for future in-depth elucidation of the molecular regulatory mechanism of taproot thickening in root chicory plants.