The molecular mechanism of eggplant parthenocarpy revealed through a combined analysis of the transcriptome and the metabolome

Feral eggplant (Solanum melongena L.) breeding relies heavily on the parthenocarpic trait, so facultative parthenocarpy is a definite advantage. The molecular mechanism of facultative parthenogenesis, however, remains uncertain. To better understand the genetic regulators of this trait in eggplant, we compared the transcriptome and metabolome of the nonpollinated buds/flowers/fruits of the parthenocarpic (D6) and nonparthenocarpic (JDX8) lines at 3 days before flowering (DBF3), on the day of flowering (DOF), and 5 days after flowering (DAF5). ABA-, GA-, ZR-, and CTK-related genes, as well as ethelye-responsive and auxin-responsive genes, were significantly different between JDX8 and D6, as determined by a transcriptome comparison. ZR-related genes exhibited significant variations in expression between JDX8 and D6 at the DAF5 stage, while other hormone-related genes exhibited substantial expression differences at the DOF and DAF5 phases. K-means clustering and functional analysis of differentially expressed genes (DEGs) demonstrated that JDX8 and D6 exhibited substantial changes in pathway-related genes, such as those involved in biosynthesis of secondary metabolites, plant hormone signal transduction, and carbon metabolism. Twenty-five MADS-box transcription factor family genes were also differentially expressed between JDX8 and D6, and additional transcription factor families, such as MYB, bHLH, and WRKY, may potentially be possible regulators of eggplant parthenogenesis. Phosphatidylethanolamine, phosphatidylcholine, and free fatty acids were considerably upregulated in D6 strains at the DOF stage, whereas flavonoids were the most significantly upregulated metabolites in D6 at the DAF5 stage, as shown by comparative metabolome analysis. Similarly, the major structural genes associated with flavonoid metabolism were highly upregulated in D6 at the DAF5 stage. These findings indicate that eggplant parthenocarpy is a feature that is controlled by the hormone signalling system, transcription factor regulation, flavonoid metabolism, and lipid metabolism. This work provides detailed molecular pathways and possible regulators for eggplant parthenocarpy research, which is advantageous for the breeding of parthenocarpic lines.