In most cases, plant miRNA functions by suppressing expression of its target genes. MiRNAs recognize their mRNA targets based on sequence complementarity. Unlike the animal miRNAs, a specificity of plant miRNAs is that they share very high complementarity to their targets with few or no mismatches (Chuck et al. 2009; Poethig 2009; Voinnet 2009). Since plant miRNAs recognize their target mRNAs by near-perfect base pairing, identifying potential target by computational approaches is easier than in animals. Currently, a number of miRNA target prediction algorithms, programs and web servers have been developed (Zhang 2005; Kruger and Rehmsmeier 2006; Bonnet et al. 2010; Wu et al. 2012), and many plant miRNA-target genes have been predicted and experimentally validated (Addo-Quaye et al. 2008; Li et al. 2010; Zhou et al. 2010).

Many plant miRNAs are encoded by gene families. The mature miRNAs often have multiple targets with similar complementary sequence in their mRNAs (Axtell and Bowman 2008; Bartel 2009). In animals, approximately 60% of protein-coding genes appear to be regulated by miRNAs (Friedman et al. 2009). However, plant miRNAs target only a small number of mRNAs (Addo-Quaye et al. 2008; German et al. 2008; Li et al. 2010).

Plant miRNAs target many kinds of genes, suggesting that they play critical roles in a variety of developmental and physiological processes (Llave et al. 2002; Aukerman and Sakai 2003; Chen 2004). Interestingly, many of the target mRNAs are transcription factors. For example, miR156 has been reported to target SQUAMOSA promoter-binding-like (SPL) transcription factor genes (Xie et al. 2006; Schwarz et al. 2008; Yang et al. 2008; Yamaguchi et al. 2009); miR159 could target several members of MYB genes; miR166 could target some members of Class III HD-Zip and KANADI families; miR319 has been reported to target TEOSINTE BRANCHED/CYCLOIDEA/ PCF (TCP) genes (Palatnik et al. 2003).