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Background  Cadmium (Cd) is a widespread toxic heavy metal pollutant in agricultural soil, and Cd accumulation in rice grains is a major intake source of Cd for Asian populations that adversely affect human health. However, the molecular mechanism underlying Cd uptake, translocation and accumulation has not been fully understood in rice plants.    Results  In this study, a mutant displaying extremely low Cd accumulation ( lcd1 ) in rice plant and grain was generated by EMS mutagenesis from  indica  rice cultivar 9311 seeds. The candidate SNPs associated with low Cd accumulation phenotype in the  lcd1  mutant were identified by MutMap and the transcriptome changes between  lcd1  and WT under Cd exposure were analyzed by RNA-seq. The  lcd1  mutant had lower Cd uptake and accumulation in rice root and shoot, as well as less growth inhibition compared with WT in the presence of 5 μM Cd. Genetic analysis showed that  lcd1  was a single locus recessive mutation. The SNP responsible for low Cd accumulation in the  lcd1  mutant located at position 8,887,787 on chromosome 7, corresponding to the seventh exon of  OsNRAMP5 . This SNP led to a Pro236Leu amino acid substitution in the highly conserved region of OsNRAMP5 in the  lcd1  mutant. A total of 1208 genes were differentially expressed between  lcd1  and WT roots under Cd exposure, and DEGs were enriched in transmembrane transport process GO term. Increased  OsHMA3  expression probably adds to the effect of  OsNRAMP5  mutation to account for the significant decreases in Cd accumulation in rice plant and grain of the  lcd1  mutant.    Conclusions  An extremely low Cd mutant  lcd1  was isolated and identified using MutMap and RNA-seq. A Pro236Leu amino acid substitution in the highly conserved region of OsNRAMP5 is likely responsible for low Cd accumulation in the  lcd1  mutant. This work provides more insight into the mechanism of Cd uptake and accumulation in rice, and will be helpful for developing low Cd accumulation rice by marker-assisted breeding.    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1867-y) contains supplementary material, which is available to authorized users.

Gene identification and transcriptome analysis of low cadmium accumulation rice mutant (lcd1) in response to cadmium stress using MutMap and RNA-seq