Tissue-specific transcriptome and proteome analyses of Taraxacum kok-saghyz reveal key genes for natural rubber biosynthesis

Abstract Background Taraxacum kok-saghyz (TKS) accumulates high-added-value compounds such as natural rubber (NR) and inulin, making it a promising alternative industrial crop. However, the tissue-specific regulation of NR biosynthesis (NRB) in TKS still requires further investigation. Here, we integrated transcriptomic and proteomic analyses of four TKS samples (main roots (MR), lateral roots (LR), main leaves (ML) and latex (LAT)) to dissect the molecular framework controlling NRB. Results A total of 31,569 genes and 2,782 proteins were identified, among which a subset exhibited pronounced tissue specificity. For example, LAT-specific genes/proteins were mainly enriched in terpenoid backbone biosynthesis. Furthermore, nine-quadrant analysis highlighted 19 NRB-related candidates with positively correlated expression, among which SRPP5, SRPP9 and REF1 were consistently shared across tissue comparisons. NRB-centered co-expression subnetworks derived from LAT-associated modules highlighted SRPP4, SRPP5, SRPP6, SRPP9, REF1, CPTL1 and ACAT4 as highly connected nodes. In addition, bHLH, C3H and TCP transcription factors together with HP, LEA and R40G3 were linked to multiple NRB-related genes/proteins, suggesting an additional coordinated regulatory layer superimposed on the structural biosynthetic machinery. Quantitative real-time PCR validation of selected NRB genes corroborated the robustness of the transcriptomic data. Conclusions Two omics data indicate that a latex-centered regulatory module, comprising SRPP/REF proteins and associated transcription factors, plays a pivotal role in coordinating NRB. Therefore, our findings provide insight into the molecular network underlying NRB in TKS and offer prioritized candidate regulators for future molecular breeding of high-rubber-yielding lines.