Int J Biol Sci 2013; 9(6):578-586. doi:10.7150/ijbs.6357

Research Paper

Loop Nucleotide Polymorphism in a Putative miRNA Precursor Associated with Seed Length in Rice (Oryza sativa L.)

Chunming Wang1✉, Jian Ye2, Weijie Tang1, Zhiyi Liu1, Chengsong Zhu3, Maoqing Wang1, Jianmin Wan1✉

1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China;
2. Laboratory of Host-Pathogen Interaction, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore;
3. Department of Agronomy, Iowa State University, Ames, IA 50011, USA.

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Wang C, Ye J, Tang W, Liu Z, Zhu C, Wang M, Wan J. Loop Nucleotide Polymorphism in a Putative miRNA Precursor Associated with Seed Length in Rice (Oryza sativa L.). Int J Biol Sci 2013; 9(6):578-586. doi:10.7150/ijbs.6357. Available from

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The terminal loop region of primary miRNA transcripts is an important determinant controlling miRNA function in human, animals and plants. However, the effects of polymorphisms in loop region of miRNA precusors on phenotypic variation have not been reported, especially on agronomic traits in rice. From rice japonica variety Koshihikari and indica Guichao2, we isolated a precursor of putative miRNA osa-MIR2923a. We detected a GG/AA polymorphism in the loop structure from japonica and indica rice varieties, which was corresponding to japonica/indica rice differentiation. By using high-resolution melting (HRM) analysis, we measured the polymorphisms in a RIL (recombinant inbred lines) population derived from japonica variety Koshihikari and indica Guichao2. We found that the GG/AA polymorphism in the osa-MIR2923a loop was correlated to grain length and length-width ratio. We further found the significant association between seed length and GG/AA polymorphism in a population consisting of 72 rice landraces. Three targets were predicted, whose expressions showed significant differences between the two varieties. Our results suggested that the putative miRNA precursor and the three target genes could play functional roles for indica/japonica seed differentiation.

Keywords: rice, miRNA, polymorphism, seed length.