Comparative transcriptomics reveals the key pathways and genes of cadmium accumulation in the high cadmium-accumulating rice (Oryza Sativa L.) line

The high cadmium (Cd)-accumulating rice line Lu527-8 (H8) has already been proven to exhibit elevated Cd concentration and translocation over the normal rice line Lu527-4 (N4). H8 and N4 are sister lines that diverged from the same parents, while the molecular mechanisms underlying the genotypic differences in Cd enrichment between the two rice lines remains unclear. Here an in-depth exploration was performed via transcriptome analysis with 2919 and 2563 differentially expressed genes (DEGs) in H8 and N4 identified, respectively. Gene ontology (GO) enrichment revealed that Cd-stressed rice both exhibited enhanced defense and antioxidant responses, while N4 displayed unique categories related to cell wall biosynthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 5 mutual pathways between H8 and N4. Many genes associated with cell wall biosynthesis were identified as the Cd-responsive DEGs. Enhanced phenylpropanoid biosynthesis and unique diterpenoid biosynthesis resulted in intensified lignin biosynthesis, which likely led to apoplastic barrier formation, subsequently blocked Cd inflow and reduced radial Cd transport in the root, thereby limited Cd translocation into aerial parts in N4. The key genes OsPAL6 and OsPAL8 that encode phenylalanine ammonia lyase (PAL), and gibberellin (GA) biosynthesis-related key genes including OsCPS2, OsCPS4, OsKSL4, OsKSL7 and some CYP superfamily members played vital roles in the process. Meanwhile, the greater upregulation of Cd transporters, such as OsIRT1/2, some OsABCs, OsYSLs, and OsZIPs in H8, accounted for the higher root absorption of Cd compared to N4. These findings unveil the molecular basis of the differential Cd concentration and translocation between the two rice lines, contributing valuable insights to the theory of Cd accumulation in rice.