Morphological Traits Evaluated with Random Forest Method Explains Natural Classification of Grapevine (Vitis vinifera L.) Cultivars

There are hundreds of morphologic and morphometric traits available to classify and identify grapevine (Vitis vinifera L.) genotypes, while statistical evaluation of those has certain limitations, especially when we have no information about the traits that are discriminative to a certain sample set. High numbers of investigated characters could cause redundancy, while reducing those numbers may result in data loss. Grapevine is one of the most important horticultural crops, with many cultivars in production. The characterization of the genotypes is of undeniably high importance. In this study, we analyzed a dataset of scientific and historical importance with 125 morphological traits of 97 grapevine cultivars described by Nemeth in 1966. However, the traits are not independent in a set of a large number of categorical traits with too few cultivars. Therefore, the number of traits was first reduced using a simple and effective algorithm to eliminate traits with redundant information content using the asymmetric measure of association Goodman and Kruskal's lambda. We reduced the number of traits from 125 to 59 without any information loss. For the classification, we applied a random forest (RF) method. In this way, 93% of the cultivars were correctly classified using only four traits of the data set. To our knowledge, only a few studies applied a trait elimination algorithm similar to ours in ampelography that can be used for other biological data sets of similar structure. The classification results give a morphological explanation to several cultivars from the Carpathian Basin, a territory where all three Vitis vinifera L. geographical groups, occidentalis, orientalis and pontica, are represented. We found that the information-loss-avoiding data reduction method we applied in our study solved the redundancy-caused interdependencies and provided a suitable dataset for classifying grapevine genotypes. For example, this method may successfully be applied in digital image analysis-based traditional morphometric investigations in ampelography.

Automated summary

In this study, a dataset of 125 morphological traits of 97 grapevine cultivars was analyzed and reduced to 59 traits using a feature elimination algorithm. The classification results using only four traits achieved 93% accuracy. This study provides a suitable dataset and method for classifying grapevine genotypes and can be applied to similar biological datasets.