Seq-Array – Leveraging the Power of both NGS and Microarray for Plant microRNA Studies
A study led by researchers at Nanjing Agricultural University, China provides the first small RNA expression analysis throughout the entire grain filling phase in an indica rice cultivar.
MicroRNAs (miRNAs) modulate gene expression in different tissues and at diverse developmental stages in plants. In this study, the researchers used a Seq-Array approach to first, identify novel miRNAs in indica rice by small RNA sequencing and then, to study their expression patterns during all stages of grain development by custom microarray.
Using LC Sciences microRNA discovery and profiling services, sequenced small RNAs from all stages of grain development and discovered 11 potential novel miRNAs based on the presence of their miRNA*s. A total of 21 conserved and 91 non-conserved miRNA families were found in developing indica grains.
Expression patterns of these identified miRNAs were analyzed using customized miRNA chips. Comparison between the three phases of grain filling revealed that these miRNAs and their targets may be involved in diverse pathways, which may also be conserved in other cereal plants. 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.
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.
- Lan Y, Su N, Shen Y, Zhang R, Wu F, Cheng Z, Wang J, Zhang X, Guo X, Lei C, Wang J, Jiang L, Mao L, Wan J. (2012) Identification of novel MiRNAs and MiRNA expression profiling during grain development in indica rice. BMC Genomics 13(1), 264. [Epub ahead of print]. [article]