Molecular characterization and bioinformatics analysis of transporter genes associated with Cd-induced phytotoxicity in rice (Oryza sativa L.)

Cadmium (Cd) adversely affects the yield and quality of rice. It is, therefore, crucial to elucidate the consequences of Cd toxicity. Plant height, biomass, SPAD score, PSII efficiency, and photosynthetic performance index were all significantly reduced in Cd-stressed rice. Cd stress resulted in a simultaneous increase in Cd and Fe concentrations in both the roots and the shoots, accompanied by the significant upregulation of heavy metal ATPase (OsHMA2, OsHMA3), natural resistance-associated macrophage proteins (OsNramp1, OsNramp5), Fe-regulated transporters (OsIRT1), Fe-reductase oxidase (OsFRO1) genes, and FCR activity in roots. This implies that Cd uptake may be closely associated with Fe transporters resulted in physiological and photosynthetic damages in Cd-stressed rice. In silico analysis suggested that the localization of Cd-uptake proteins in the plasma membrane exhibiting transporter activity, among which two motifs were linked to the pfam_fs: Nramp domain. In a phylogenetic tree, HMA and Nramp genes were consistently positioned in the same cluster, while OsIRT1 and OsFRO1 were independently located. The key cis-acting elements were abscisic acid-responsiveness, methyl jasmonate-responsiveness, zein metabolism regulation, stress-responsiveness, salicylic acid-responsiveness, and gibberellin-responsiveness. An interactome map revealed the diverse functional partners of Cd-uptake genes, including MTP1 (metal tolerance protein 1), YSL6 (metal-nicotianamine transporter), IRO2 (Fe-regulated transcription factor 2), OsJ_16707 (a vacuolar Fe transporter homolog), YSL15 (an Fe-phytosiderophore transporter), and NAS2 (nicotianamine synthase), which were predominantly linked to Fe homeostasis. These findings greatly elucidate the Cd uptake mechanism in rice plants and can help to regulate Cd uptake either by breeding or silencing these transporters. •Cd-toxicity severely affected plant biomass, chlorophyll synthesis, and PSII efficiency in rice.•Cd stress caused a simultaneous increase of Cd and Fe in both root and shoot tissues.•Results suggest the involvement of a common channel involving Cd and Fe uptake in Cd-stressed rice.•Cd-uptake genes in rice have a close partnership with MTP1, YSL6, IRO2, OsJ_16707, YSL15, and NAS2.•Abscisic acid and salicylic acid cis-acting elements are possibly involved in the regulatory process in Cd-stressed rice.