Co-selection of low cadmium accumulation and high yield during tomato breeding

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. We found that there has been a trend during domestication for co-selection of improved tomato yield and reduced Cd accumulation. A genome-wide association study (GWAS) of 506 tomato accessions identified a natural allele, SlF3’H ^AA , which confers low Cd accumulation in the shoots of tomato. The linkage disequilibrium (LD) analysis revealed a tight linkage between SlF3’H ^AA and a fruit weight gene fw3.2 . Evolution analysis showed that fw3.2 and SlF3’H experienced similar selection pressure. These findings indicate that the widespread presence of low Cd accumulating types in cultivated tomato is due to genetic hitchhiking and co-selection of SlF3’H with fw3.2 during yield breeding.