Comparison of Cheng's Index- and SSR Marker-based Classification of Asian Cultivated Rice

A total of 100 cultivated rice accessions, with a clear isozyme-based classification, were analyzed based on Cheng's index and simple sequence repeat (SSR) marker. The results showed that the isozyme-based classification was in high accordance with that based on Cheng's index and SSR markers. Mantel-test revealed that the Euclidean distance of Cheng's index was significantly correlated with Nei's unbiased genetic distance of SSR markers (r = 0.466, P ≤ 0.01). According to the model-based group and cluster analysis, the Cheng's index- and SSR-based classification coincided with each other, with the goodness of fit of 82.1% and 84.7% in indica, 97.4% and 95.1% in japonica, respectively, showing higher accordance than that within subspecies. Therefore, Cheng's index could be used to classify subspecies, while SSR marker could be more efficient to analyze the subgroups within subspecies.