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.

根菊苣 ( Cichorium intybusL.)是一种植物，其地下部分主要用作工业生产菊粉的原料。为了研究负责调节根菊苣主根增厚过程的分子机制，对田间生长第一年五个发育阶段的主根进行了 mRNA-seq 和非靶向代谢组学检测。结果表明，在主根增粗早期，根粗和根鲜重增加较快，而在增粗后期干重增加较快。串联地，碳水化合物和脂肪酸的丰度在早期相对较高，这与主根增厚的后期形成鲜明对比，此时氨基酸大量积累。差异表达基因 (DEG) 富集到与主根增厚密切相关的途径或生物过程，即“转录调控”、“激素信号转导”、“淀粉和蔗糖代谢”、“细胞壁组织和生物合成”以及“苯丙素”和木质素生物合成'。此外，转录本-代谢物调控网络显示蔗糖、D-果糖 6-P 和苯丙氨酸，连同转录因子CiMYB20和CiERF13，以及结构基因CiEXPA、Ci1-FFT、CiSPS和CiPAL，可能是调节菊苣主根增厚的关键分子。我们得出结论，代谢物和基因的差异表达在根菊苣的主根增厚中起着至关重要的作用。本研究为今后深入阐明根菊苣植物主根增粗的分子调控机制奠定了基础。