Domestication may have unintentionally increased arsenic accumulation in japonica rice

Arsenic contamination in soil and water poses significant health risks globally through contaminated crops.^1,2,3 Modern cultivated rice (Oryza sativa), particularly the subspecies japonica, accumulates high levels of arsenic.^1,3,4,5,6 This may possibly result from unintended physiological and genomic changes during rice domestication, which have significantly altered traits such as plant architecture and phosphorus nutrition,^{7,8,9,10,11,12} some of which are closely linked to arsenic accumulation in rice.^{13,14,15,16,17,18,19} This study compared arsenic accumulation in domesticated rice subspecies japonica and indica with their wild ancestor O. rufipogon and explored the mechanisms underlying their differences. Results show significantly higher arsenic levels in japonica genotypes compared with their wild ancestors, a trend not observed in subspecies indica. Phylogenetic and genomic analyses indicate that domestication influenced the arsenic-accumulation trait, particularly through selection on phosphorus (P)-arsenic co-transporter genes. Physiological analyses revealed that domestication altered plant architecture and P-nutrition traits, with the latter accounting for most of the variation in arsenic accumulation. Specifically, arsenic and P contents were positively correlated in japonica genotypes, which demonstrated significantly increased affinity, uptake rates, and specific uptake of arsenic compared with their wild ancestors in the presence of P. Profiling of P-arsenic co-transporter genes showed increased Phosphate Transporter 1-1 (PT1) expression in japonica relative to its wild ancestor, along with upregulated PT8 transcription upon arsenic addition. These findings suggest that domestication may have unintentionally increased arsenic accumulation in japonica rice due to artificial selection on P-nutrition traits, providing insights for reducing arsenic contamination in future rice breeding programs.