Differentiated expression of microRNAs may regulate genotype-dependent traits in cotton

miRNA is an exogenous non-coding RNA with 21-24nt in length, which plays a crucial role in almost all biological processes. In plants, miRNAs regulate organ development, phase change, signal transduction and response to different biotic and abiotic stresses at the post-transcriptional levels. Although there are many studies on plant miRNAs, no studies have been focused on the genotype dependence. Genotype-dependent traits may be controlled by the differential expression of certain miRNAs. To test this hypothesis, we investigated the expression profile patterns of 11 selected miRNAs in 5 different organs in 5 different cotton cultivars and their implication on plant development. Our results demonstrate that miRNAs have different expression patterns in different plant organs in different genotypes, which implicate their different traits, including early flowering. miR172 is a miRNA controlling floral development and phase change; our results show that miR172 has a higher expression level in the flower bud than in any other organ, our results also show that Baimian cultivars have a higher expression of miR172 than TM-1. This suggests that Baimian cultivars have an earlier transition from vegetable growth to reproductive growth, which is confirmed by our development data on floral branch development. Our result also shows that several miRNAs, including miR159 and miR162, were highly expressed in Baimian cultivars. The results obtained in this study would provide new insight for improving cotton using miRNA-based biotechnology.