Organic acids are major determinants of fruit flavor and a primary focus of fruit crop breeding. The accumulation of organic acids is determined by their synthesis, degradation, and transport, all of which are manipulated by sophisticated genetic mechanisms. Constant exploration of the genetic basis of organic acid accumulation, especially through linkage analysis, association analysis, and evolutionary analysis, have identified numerous loci in recent decades. In this review, the genetic loci and genes responsible for malate and citrate contents in fruits are discussed from the genetic perspective. Technologies such as gene transformation and genome editing as well as efficient breeding using marker-assisted selection (MAS) and genomic selection (GS) are expected to break the bottleneck of traditional fruit crop breeding and promote fruit quality improvement.

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