Most traits of agricultural importance are quantitative traits controlled by numerous genes. However, it remains unclear about the molecular mechanisms underpinning quantitative traits. Here, we report the molecular characteristics of the genes controlling three quantitative traits randomly selected from three diverse plant species, including ginsenoside biosynthesis in ginseng (Panax ginseng C.A. Meyer), fiber length in cotton (Gossypium hirsutum L. and G. barbadense L.) and grain yield in maize (Zea mays L.). We found that a vast majority of the genes controlling a quantitative trait were significantly more likely spliced into multiple transcripts while they expressed. Nevertheless, only one to four, but not all, of the transcripts spliced from each of the genes were significantly correlated with the phenotype of the trait. The genes controlling a quantitative trait were multiple times more likely to form a co-expression network than other genes expressed in an organ. The network varied substantially among genotypes of a species and was associated with their phenotypes. These findings indicate that the genes controlling a quantitative trait are more likely pleiotropic and functionally correlated, thus providing new insights into the molecular basis underpinning quantitative traits and knowledge necessary to develop technologies for efficient manipulation of quantitative traits.