Simultaneous Agronomic and Molecular Characterization of Genotypes via the Generalised Procrustes Analysis: An Application to Cucumber

Abstract

Characterizing entries in a germplasm bank by molecular markers and/or agronomic attributes is a common practice, but studies that simultaneously use molecular and agronomic traits are less frequent. Generalised Procrustes Analysis (GPA) was used to determine the relationships among 41 entries of cucumber ( Cucumis sativus L.) via the simultaneous use of 16 agronomic traits (nine qualitative variables and seven quantitative variables) and 33 random amplified polymorphic DNA (RAPD) markers using a set of 11 primers. Other techniques like generalization of the simple matching coefficient, Gower's general similarity coefficient, and discretizing the quantitative variables were compared with GPA. The ordinations of cultivars using each trait individually did not fully characterize the cultivars. In fact, on the basis of the qualitative traits, only two groups were formed, with cultivars belonging to Beth‐α and Dutch constituting a single group and the slice and gherkin types another group. The quantitative traits and also the molecular traits further separated the cultivars belonging Beth‐α and Dutch types. The utilization of all variables together showed a greater discrimination power of genotypes. Four groups were defined which were consistent with Dutch, gherkin, slice, and Beth‐α types. GPA was the most precise technique to cluster the entries. The final configuration was an average of the individual configurations. For other methods, those traits with more variants (but not necessarily more genetic information) had more influence on the final results. Besides, GPA allowed a deeper study of the relationships among relative ordinations of a same genotype under different types of descriptors to establish concordance between characterizations.