Classification of fruit shape based on decision tree model and identification of QTLs and genes controlling fruit shape in eggplant

• Thirteen shape categories and ten key attributes determining fruit shape were identified based on decision tree model in eggplant • Classification rules achieving an accuracy of 92.59% were generated. • Four QTLs controlling FSI and PAMi were detected using GWAS and QTL-seq. • Overexpression of the candidate gene SmFSI3.1 / SmFL resulted in the production of elongated tomato fruits Eggplant ( Solanum melongena L.) shows remarkable diversity in fruit shape, making it an excellent model for studying shape variation. Eggplant fruit shape influences consumer preference and plays an important role in the classification of commercial varieties and germplasm. Despite its importance, existing classification systems are limited to description without quantitative criteria, differ by country or region and fail to fully capture the diversity of eggplant fruit shapes. In the present study, thirteen shape categories were identified using a decision tree model with Gini index-based variable selection. Ten key attributes that largely determine fruit shape were identified and high accuracy (92.59%) classification rules were generated. Five other methods, including random forest, XGBoost, SVM, K-means and GMM, were also applied to fruit shape classification, but they proved less robust for classification compared to the decision tree. The shape modeling informed the key attribute selection for the QTL-seq and GWAS analyses. Four QTLs controlling Fruit Shape Index (FSI) and Proximal Angle Micro (PAMi) were detected using GWAS and QTL-seq. The candidate gene SmFSI3.1 / SmFL , a member of the SUN/IQD family, was over-expressed in tomato and resulted in elongated fruits, indicating the positive roles of this gene in regulating fruit elongation in eggplant. In summary, we developed an accurate and reproducible model for classifying eggplant fruit shapes, which is of significance for eggplant breeding and variety classification. Moreover, we verified the function of the causal gene responsible for fsi3.1 / fl3.1 locus, providing a foundation for understanding the genetic regulation of fruit shape in eggplant.