A transposon insertion into the 5’ UTR of OsPT1 reprograms its expression pattern and leads to high cadmium accumulation in rice grains

Cadmium (Cd) accumulation in rice grains poses a serious threat to human health, however the underlying mechanisms remain incompletely understood. Here, we conducted a genome-wide association study and identified 29 loci associated with grain Cd content (LAGCCs). One of the top associated loci, LAGCC4, harbors the transporter gene OsPT1, whose haplotypes are tightly associated with Cd content in rice grains. A transposon, H-MITE, inserts into the 5' untranslated region of OsPT1, altering its expression pattern and leading to higher Cd accumulation. We further identified a transcription factor OsbHLH35 that specifically binds to the OsPT1^H-MITE promoter to regulate its transcription in response to Cd stress. Knocking out either the OsPT1^H-MITE or OsbHLH35 gene through CRISPR/Cas9 gene editing significantly reduced grain Cd content, with a reduction ranging from 61.7% to 80.6%. Our study uncovered a previously unknown mechanism responsible for high Cd accumulation in rice and identified targets for breeding rice varieties with lower Cd content.