Cadmium (Cd) accumulation in rice grain poses a serious threat to human health. While several transport systems have been reported, the complexity of rice Cd transport and accumulation indicates the necessity of identifying additional genes, especially those that are responsible for Cd accumulation divergence between
indica
and
japonica
rice subspecies. Here, we show that a gene,
OsCd1
, belonging to the major facilitator superfamily is involved in root Cd uptake and contributes to grain accumulation in rice. Natural variation in
OsCd1
with a missense mutation Val449Asp is responsible for the divergence of rice grain Cd accumulation between
indica
and
japonica
. Near-isogenic line tests confirm that the
indica
variety carrying the
japonica
allele
OsCd1
V449
can reduce the grain Cd accumulation. Thus, the
japonica
allele
OsCd1
V449
may be useful for reducing grain Cd accumulation of
indica
rice cultivars through breeding.
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