Single-cell RNA sequencing uncovers cell-type-specific reprogramming of water-channel and cell-wall genes in PFOA uptake by lettuce root tips

Per- and polyfluoroalkyl substances (PFAS) are persistent organic pollutants that accumulate in edible crops, posing threats to food safety and human health. Breeding varieties with reduced PFAS accumulation offers a promising mitigation strategy, yet the underlying cellular mechanisms remain elusive. Here, we integrated short- and long-read single-cell RNA sequencing to generate a high-resolution transcriptomic atlas of lettuce (Lactuca sativa L.) root tips, comparing varieties with contrasting perfluorooctanoic acid (PFOA) accumulation capacities. Our analyses uncovered a synergistic mechanism underlying PFOA uptake: up-regulation of aquaporin genes in epidermal and xylem cells, coupled with down-regulation of cell-wall biosynthesis genes specifically in epidermal and xylem. Furthermore, we identified distinct RNA isoforms-including variants with altered coding potential-that may contribute to PFOA transport and deposition through structural modulation of the encoded proteins. This study represents the first application of single-cell sequencing to elucidate the cellular and molecular basis of crop responses to PFOA, providing new insights into pollutant-crop interactions and informing strategies for sustainable agriculture and food safety.