National Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China.
BMC Genomics. 2012 Jun 21;13:264. doi: 10.1186/1471-2164-13-264.
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.
微小 RNA（miRNAs）在不同组织和不同发育阶段调节基因表达，包括粳稻的籽粒发育。为了鉴定籼稻中的新 miRNAs，并研究它们在整个灌浆过程中的表达模式，我们对不同发育阶段的籽粒小 RNA 进行了测序，并使用定制的 miRNA 芯片研究了它们的表达模式。
在发育中的籼稻粒中发现了 21 个保守和 91 个非保守的 miRNA 家族。我们还根据 miRNA*的存在发现了 11 个潜在的新 miRNAs。使用定制的 miRNA 芯片分析了这些鉴定出的 miRNAs 的表达模式。结果表明，在灌浆阶段，大约一半的检测到的 miRNAs 上调，而其余的下调。差异表达 miRNA 的预测靶标可能参与碳水化合物代谢、激素信号和与种子成熟相关的途径，表明它们在水稻籽粒发育中可能具有重要作用。
本研究首次对籼稻品种灌浆期的 miRNAs 进行了全基因组研究。鉴定出的新 miRNAs 可能参与新的 miRNA 调控途径，以促进籽粒发育。这些 miRNAs 及其靶标和相互作用的复杂性需要进一步研究，以更好地理解籽粒发育的分子机制。
