Open Access Highly Accessed Research article

Identification of novel MiRNAs and MiRNA expression profiling during grain development in indica rice

Ying Lan12, Ning Su2, Yi Shen1, Rongzhi Zhang2, Fuqing Wu2, Zhijun Cheng2, Jiulin Wang2, Xin Zhang2, Xiupin Guo2, Cailin Lei2, Jie Wang2, Ling Jiang1, Long Mao2 and Jianmin Wan12*

Author affiliations

1 National Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China

2 National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agriculture Sciences, Beijing, 100081, China

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Citation and License

BMC Genomics 2012, 13:264  doi:10.1186/1471-2164-13-264

Published: 21 June 2012



MicroRNAs (miRNAs) modulate gene expression in different tissues and at diverse developmental stages, including grain development in japonica rice. To identify novel miRNAs in indica rice and to study their expression patterns during the entire grain filling process, small RNAs from all stages of grain development were sequenced and their expression patterns were studied using customized miRNA chips.


A total of 21 conserved and 91 non-conserved miRNA families were found in developing indica grains. We also discovered 11 potential novel miRNAs based on the presence of their miRNA*s. Expression patterns of these identified miRNAs were analyzed using customized miRNA chips. The results showed that during the filling phase about half of the detected miRNAs were up-regulated, whereas the remainder were down-regulated. Predicted targets of differentially expressed miRNAs may participate in carbohydrate metabolism, hormone signaling and pathways associated with seed maturity, suggesting potentially important roles in rice grain development.


This study is the first genome-wide investigation of miRNAs during the grain-filling phase of an indica variety of rice. The novel miRNAs identified might be involved in new miRNA regulatory pathways for grain development. The complexity of these miRNAs and their targets and interactions require further study to obtain a better understanding of the molecular mechanisms underlying grain development.

miRNA; Grain filling; Indica rice