Co-Selection of Low Cadmium Accumulation and High Yield During Tomato Improvement

Enhancing crop production and yield is necessary to feed an increasing population, but cadmium (Cd) accumulation in crops poses a serious threat to human health. It is found that a trend during domestication is for the co-selection of improved tomato yield and reduced Cd accumulation. A genome-wide association study (GWAS) of 506 tomato accessions identifies a natural allele, LCT1^AA, which confers low Cd accumulation in the shoots and fruits of tomato. The linkage disequilibrium (LD) analysis reveals a tight linkage between LCT1^A and a large fruit allele fw3.2^T. Evolution analysis shows that fw3.2 and LCT1 experience similar selection pressure. Grafting experiments using tomato hypocotyls as the junction point further demonstrate that LCT1 reduces Cd accumulation primarily through regulation in the root rather than the shoot of the plant. These findings collectively highlight the importance of LCT1 in regulating Cd accumulation and indicate that the widespread presence of low Cd accumulating types in cultivated tomato is due to genetic hitchhiking and co-selection of LCT1^A with fw3.2^T during yield breeding.