Comparison of Cheng&rsquo;s Index- and SSR Marker-based Classification of Asian Cultivated Rice

WANG Cai-hong, XU Qun, YU Ping, YUAN Xiao-ping, YU Han-yong, WANG Yi-ping, TANG Sheng-xiang, WEI Xing-hua

doi:10.1016/S1672-6308(13)60120-1

Rice Science >

2013 , Vol. 20 >Issue 2: 103 - 110

DOI: https://doi.org/10.1016/S1672-6308(13)60120-1

Research Paper

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

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State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China

Online published: 2013-01-30

Supported by

This work was supported by the Crop Genetic Resources Protection Project of Ministry of Agriculture, China, and the Basic Research Budget of China National Rice Research Institute (Grant No. 2009RG001-3).

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Abstract

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.

Key words： Oryza sativa; classification; Cheng’s index; simple sequence repeat marker

Cite this article

WANG Cai-hong, XU Qun, YU Ping, YUAN Xiao-ping, YU Han-yong, WANG Yi-ping, TANG Sheng-xiang, WEI Xing-hua . Comparison of Cheng’s Index- and SSR Marker-based Classification of Asian Cultivated Rice[J]. Rice Science, 2013 , 20(2) : 103 -110 . DOI: 10.1016/S1672-6308(13)60120-1

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