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BMC Genomics

, 13:264

First Online: 21 June 2012Received: 13 September 2011Accepted: 03 April 2012DOI: 10.1186-1471-2164-13-264

Cite this article as: Lan, Y., Su, N., Shen, Y. et al. BMC Genomics 2012 13: 264. doi:10.1186-1471-2164-13-264


BackgroundMicroRNAs 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.

ResultsA 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.

ConclusionsThis 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.

KeywordsmiRNA Grain filling Indica rice Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-13-264 contains supplementary material, which is available to authorized users.

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Autor: Ying Lan - Ning Su - Yi Shen - Rongzhi Zhang - Fuqing Wu - Zhijun Cheng - Jiulin Wang - Xin Zhang - Xiupin Guo - Cailin 


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