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The diversity of climate, from subarctic to subtropical, and the complex geological history of Japan have produced a rich biodiversity. The flora includes several hundred species of native woody plants with edible fleshy fruits or nuts. People have eaten them from prehistoric times until about a half century ago. In Hokkaidō and the Ryūkyū Islands nut species had an important role in the diet, but fleshy fruits were also eaten until recently. Only Castanea crenata and a few minor species became domesticated as edible fruit trees in pre-modern times. Recently, Vitis coignetiae, Lonicera caerulea, Akebia quinata, Akebia trifoliata, Stauntonia hexaphylla, and Actinidia arguta have entered small-scale cultivation. The conservation of the germplasm of many of these native species, both in situ and ex situ, is precarious.

For AFLP analysis of grapes, three different concentrations of restriction enzymes were examined to reduce artifact bands due to incomplete digestion or star activity of the restriction enzymes. Differences among band intensities were neglected, and all the detected bands were used in the analysis. A phenogram of 12 cultivars of Vitis vinifera, two cultivars of V. labrusca and two wild species, V. ficifolia var. lobata (V. thunbergii, Ebizuru) and V. coignetiae (Yamabudou) was obtained by UPGMA (unweighted pair group method arithmetic averages) based on the percentage of unshared AFLP bands of each sample pair, using four primer pairs. This phenogram revealed a clear separation of the tested species and proles with high bootstrap probabilities, except for the clusters with a longer phenetic distance in the Oriental cultivars of V. vinifera. The cluster of Occidental cultivars split into a cluster consisting of Cabernet Sauvignon and Cabernet franc, and another cluster consisting of Pinot noir, Pinot blanc, Chardonnay and Riesling. Among the Oriental cultivars, two Japanese cultivars, Koshu and Koshu-Sanjaku, formed a cluster. Thus, this phenogram agreed well with the classification based on morphological properties and geographical location.