Application of geometric morphometrics for variety identification in Rubus crataegifolius : a comparison of primocane and floricane leaf morphology.

Abstract

Accurate identification of crop varieties is essential for plant breeding programs and the protection of Plant Breeders' Rights (PBR), yet traditional morphological assessment methods remain subjective and time-consuming, particularly for species with complex morphological diversity such as Rubus crataegifolius . This study demonstrates that geometric morphometric techniques provide an objective, quantitative complementary approach for distinguishing Korean raspberry varieties, addressing the limitations of subjective visual assessment while remaining compatible with molecular marker analysis. We employed three complementary morphometric approaches: landmark-based analysis (19 anatomical points capturing vein junctions and leaf margins), Elliptic Fourier Descriptors (EFD) for outline contours, and a hybrid landmark-EFD dataset. Using these approaches, we analyzed primocane and floricane leaves from 10 accessions of R. crataegifolius comprising 8 varieties and 2 landraces and performed principal component analysis (PCA) and linear discriminant analysis (LDA) with leave-one-out cross-validation. As a result, among the three morphometric approaches applied to primocane and floricane leaves, landmark-based analysis of primocane leaves achieved the highest classification accuracy (87.2%), with an overall average accuracy of 72.0% (range: 51.1-87.2%) across all six analytical combinations. LDA visualization suggested the presence of four major morphological groups, and primocane leaves exhibited higher discriminatory power than floricane leaves, which may reflect greater morphological uniformity under normal growing conditions. Landmark analysis effectively detected subtle differences in leaf venation and leaflet architecture that are difficult to distinguish visually, highlighting the capacity of morphometrics for objective and multidimensional morphological analysis. These findings suggest that morphometric analysis provides a practical and cost-effective preliminary screening tool, complementary to molecular approaches, for supporting Distinctness, Uniformity, and Stability (DUS) examination in raspberry variety evaluation. This approach shows strong potential for offering a scalable solution for variety registration and protection and supporting sustainable horticultural development.

Plant phenotyping relevance

葉の形態を幾何学的モルフォメトリクスで定量化し、品種識別とDUS評価に応用した研究で、表現型の取得・解析手法が中心である。

Code and data availability

The paper reports leaf image scans, landmark coordinates, and morphometric analyses of Rubus crataegifolius, but no public repository deposit or authors' public URL for the data or code is provided. The data availability statement only promises data from the authors on request. The supplementary material link is given,

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