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

• Published in: Rice science Vol. 20; no. 2; pp. 103 - 110
• Main Authors: WANG, Cai-hong, YU, Han-yong, XU, Qun, YU, Ping, YUAN, Xiao-ping, WANG, Yi-ping, TANG, Sheng-xiang, WEI, Xing-hua
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.03.2013; State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
• Subjects: Cheng's index; classification; cluster analysis; genetic distance; microsatellite repeats; Oryza sativa; rice; simple sequence repeat marker; Oryza sativa; classification; simple sequence repeat marker; Cheng's index
• ISSN: 1672-6308; 1876-4762
• DOI: 10.1016/S1672-6308(13)60120-1

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.