Transcriptome analysis revealed key genes and pathways related to cadmium tolerance and accumulation in coix (Coix lacryma-jobi L.)

Coix ( Coix lacryma-jobi L.) is an essential medicinal and edible plant with great economic value. Nevertheless, little is known about the molecular mechanisms underlying coix response to cadmium (Cd) stress. Coix germplasm, YY03-03, was exposed to 0 (control), 15, and 30 mg kg −1 Cd. We observed that YY03–03 exhibited low Cd absorption and transportation capacity. Further, various enrichment and translocation factors decreased under Cd stress. Moreover, under Cd stress levels of 15 and 30 mg kg - ¹, transpiration rate, stomatal conductance, and photosynthetic rate significantly decreased (by 54.0% and 64.8%, 40.4% and 47.9%, 27.7% and 37.6%, respectively), while intercellular carbon dioxide concentration significantly increased (by 82.1% and 111.5%, respectively).Next, we conducted a transcriptome analysis of plants in control or 30 mg kg −1 Cd group. Transcriptome sequencing generated a total of 6.28–8.79, 7.93–9.37, 8.51–9.79, 6.62–7.38, 7.75–8.47, 7.31–8.37, 6.92–7.75, and 6.40–8.51 billion base pairs (bp) in the control roots, stems, leaves, and grains and Cd-treated roots, stems, leaves, and grains, respectively. Furthermore, 1144, 2924, 3818, and 1702 DEGs were identified in Cd-treated root, stem, leaf, and grain with 682, 942, 1907, and 877 upregulated and 462, 1982, 1911, and 825 downregulated genes, respectively. Quantitative real time-polymerase chain reaction was used to assess 12 stress-responsive differentially expressed genes (DEGs) and validate transcriptomic data. Gene ontology analyses demonstrated that DEGs were primarily engaged in catalytic activity, cellular processes, cell, cell component, binding, and metabolic processes. The Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that Cd stress altered DEGs primarily involved in environmental adaptability, transport and catabolism, signal transduction, translation, and glucose metabolism. These findings provide a molecular basis for breeding low-Cd coix varieties, which is of significant importance for ensuring the safety of coix as a medicinal and edible resource in Cd-contaminated areas.