A transposon insertion in the 5′ UTR of OsPT1 reprograms its expression pattern and promotes cadmium accumulation in rice grains

TL;DR

A transposon insertion in the OsPT1 gene helps rice absorb more cadmium, a harmful metal, and this discovery could help breed safer rice varieties.

Contribution

A novel genetic mechanism involving a transposon and a transcription factor that increases cadmium accumulation in rice grains is identified.

Findings

A transposon insertion in the 5′ UTR of OsPT1 alters its expression and increases cadmium accumulation in rice grains.

The transcription factor OsbHLH35 binds to the OsPT1 promoter and regulates its transcription in response to cadmium stress.

CRISPR-Cas9 gene editing of OsPT1 or OsbHLH35 reduced grain cadmium content by 61.7% to 80.6%.

Abstract

Cadmium (Cd) accumulation in rice grains presents a serious risk to human health; however, the mechanisms underlying this process remain incompletely understood. In this study, a genome-wide association analysis identified 29 loci associated with grain Cd content (LAGCCs). Among these, one of the most strongly associated loci, LAGCC4, contains the transporter gene OsPT1, whose haplotypes show a strong correlation with Cd content in rice grains. A transposon, H-MITE, inserts into the 5′ untranslated region (UTR) of OsPT1, altering its expression pattern and leading to increased Cd accumulation. Furthermore, we identified the transcription factor OsbHLH35, which specifically binds to the OsPT1H-MITE promoter to regulate its transcription in response to Cd stress. Targeted knockout of either OsPT1H-MITE or OsbHLH35 via CRISPR-Cas9 gene editing significantly reduced grain Cd content, with reductions ranging from 61.7% to 80.6%. This study reveals a previously unrecognized mechanism contributing to high Cd accumulation in rice and identifies genetic targets for breeding rice varieties with reduced Cd content.

This study reports the identification of a transposon insertion in the 5' UTR of OsPT1, which enables its cadmium (Cd)-induced transcriptional activation by the transcription factor OsbHLH35, thereby indirectly enhancing Cd accumulation in rice grains. The findings highlight a genetic mechanism linking the regulation of phosphate transporters to heavy metal accumulation in crops.

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