Assessing indica-japonica differentiation of improved rice varieties using microsatellite markers

a.
Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100094, China
b.
Guangdong Key Laboratory of Sugarcane Improvement & Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou 510316, China
c.
Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
d.
The Centre of Biotechnology Research, Jilin Academy of Agricultural Sciences, Changchun 130124, China

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Corresponding author: E-mail address: lizichao@cau.edu.cn (Zichao Li)

摘要

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Abstract: To assess the indica-japonica differentiation of improved rice varieties, a total of 512 modern varieties including 301 indica and 211 japonica accessions were analyzed using 36 microsatellites. The Fst coefficients ranged from 0.002 to 0.730 among the loci with an average of 0.315. Significant differentiation was detected at 94.4% of the loci studied (P < 0.05, pairwise Fst tests), indicating that there was a high level of indica-japonica differentiation within the improved varieties. At 18 loci, about 74%–98% of the alleles of indica and japonica accessions were distributed in two ranges of amplicon length. Linkage disequilibrium analysis showed that the distribution trends were significantly nonrandomly associated. Using the differentiation trends at the 18 loci, microsatellite index (MI) was proposed for discrimination of the two subspecies. When rice accessions with MI value greater than zero were classified as indica, and those with MI value smaller than zero were classified as japonica, about 96.1% of the accessions could be classified. This result agrees with the classification based on morphological-physiological characters, indicating that this method is feasible and effective.
- improved rice varieties /
- microsatellite index (MI)

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