Features and genetic basis of chlorogenic acid formation in diploid potatoes

•A diversity panel of lines was used to study the CGA formation in diploid potatoes.•Decreased tuber CGA level was observed in the domesticated diploid potatoes.•Potential factors affecting the CGA level in diploid potatoes were revealed. The concentration of chlorogenic acids (CGAs), is tightly associated with the appearance, taste, and nutrient content of potato tubers. Manipulation of tuber CGA concentrations allows for the breeding of quality traits in potatoes. Currently, a hybrid potato breeding system that aims to convert tetraploid potato into a diploid seed crop represents a new development in potato breeding. Unfortunately, however, a systematic study of CGA formation is very limited in diploid potatoes. Here, using a diverse panel of diploid potatoes, including 40 ancestors and 374 landraces, we analyzed the influence of location, environment, genetic basis, as well as expression of enzymes, in affecting the CGA concentrations in diploid lines. We revealed a selection of the decreased CGA level of tuber flesh in the domestication of diploid potatoes. Moreover, we identified 18 SNPs associated with tuber CGA levels using re-sequenced genome data. This study provides a basis for the breeding of high-quality potato by taking into consideration customer preferences.