Integrated transcriptome and physiological analysis of rice seedlings reveals different cadmium response mechanisms between indica and japonica varieties

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Cadmium (Cd) is one of the most toxic heavy metals to all plant species. However, the underlying molecular mechanisms of Cd tolerance in rice remains largely unknown. In this study, the comparative changes of physiological indexes and gene expression patterns between the rice subspecies indica (‘LY0861’ variety) and japonica (‘ZH6’ variety) were evaluated under the same Cd stress. Biochemical and physiological analysis of malondialdehyde (MDA), H 2 O 2 , proline (Pro) and glutathione (GSH) contents and the antioxidant enzyme activities showed that ZH6 exhibited a stronger Cd detoxification capacity than LY0861. Meanwhile, we found that Cd was mainly distributed in the roots of both rice varieties and ZH6 had a lower Cd translocation ability than LY0861. The transcriptomic analysis revealed 4862 and 1849 differentially expressed genes (DEGs) in the shoots and roots of LY0861 between Cd-stressed plants and control, while 2085 and 4385 DEGs were found in the shoots and roots of ZH6, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that more DEGs functioning in Phenylpropanoid biosynthesis’, ‘Plant hormone signal transduction’ and ‘Starch and sucrose metabolism’ were enriched in the shoots of LY0861 and in the roots of ZH6, respectively. Furthermore, MapMan pathway analysis indicated that the Cd-regulated genes related to the antioxidant defense system, cell wall synthesis, metal transporters, transcription factors and hormone metabolism were more active in the shoots of LY0861 and roots of ZH6 under Cd stress, and thus might be one of the key processes associated with the genotype difference in Cd tolerance and transport. Taken together, these findings provide new insights into the genome-wide transcriptome profiles of rice under Cd stress, as well as the selection of rice varieties and field management measures to mitigate Cd exposure in rice production. • Cadmium caused severe growth inhibition in both ZH6 and LY0861 varieties. • ZH6 had a stronger Cd tolerance and a lower Cd transportation capability than LY0861 • Key Cd-response genes and pathways were more active in the shoots of LY0861 and roots of ZH6. • Improving the understanding of the complex molecular response mechanisms of rice under Cd stress