Automated Seed Morphometry Identifies Morphotypes Associated with Major Grapevine Haplotypic Lineages

High-throughput DNA sequencing has revealed that the extensive diversity of Vitis vinifera L. cultivars is structured into several major genetic lineages. Identifying phenotypic traits that reflect these genetic relationships remains an important challenge for grapevine taxonomy, germplasm characterization, and archaeobotany. Here, we present an automated computational workflow implemented in R that reconstructs seed outlines from Elliptic Fourier Descriptors (EFDs) and calculates the J index, a measure of similarity to predefined reference morphotypes, together with curvature profiles along the seed outline. The workflow is reproducible and suitable for high-throughput morphometric analysis. A dataset comprising 2895 seeds from 143 populations representing 85 V. vinifera cultivars was initially organized into three groups according to available pedigree information and previously characterized seed morphotypes. Geometric reference models representing the Hebén, Savagnin Blanc, and Muscat morphotypes were then used to calculate J index values for each population. Based on these values, 74 populations were assigned unambiguously to one of the three reference morphotypes, whereas 69 showed similar affinities to two or three models and were therefore classified as intermediate or undifferentiated. The three primary morphometric groups comprised 41 populations assigned to the Hebén morphotype, 12 to the Savagnin Blanc morphotype, and 21 to the Muscat morphotype. Curvature analysis of the reconstructed seed outlines was subsequently used to characterize local geometric variation and to identify representative populations within each group. The resulting morphotypes showed substantial correspondence with major grapevine haplotypic lineages while also revealing intermediate phenotypes associated with the complex genetic and developmental history of cultivated grapevine. Overall, the workflow provides an objective and reproducible approach for high-throughput seed phenotyping and represents a complementary phenotypic tool for investigating grapevine genetic diversity, germplasm characterization, and the relationships between seed morphology and genetic lineage.