Identification and expression analysis of critical microRNA-transcription factor regulatory modules related to seed development and oil accumulation in developing Hippophae rhamnoides seeds

Sea buckthorn (Hippophae rhamnoides) seed oil is rich in omega fatty acids and various other bioactive compounds, which not only have high antioxidant activity but may also prevent cardiovascular diseases. However, the molecular mechanisms of oil biosynthesis and fatty acid accumulation in developing sea buckthorn seeds remain unknown. Altering the levels of certain miRNAs and transcription factors can affect the expression of multiple genes involved in seed development and fatty acid biosynthesis, resulting in changed seed oil contents. Considering that previous studies have focused mainly on these two regulators separately, we attempted to combine the study of miRNAs and transcription factors to construct a coregulatory network. In the present study, we generated cDNA libraries and small RNA libraries from the seeds of high-oil-content and low-oil-content sea buckthorn cultivars at four developmental stages, and then used high-throughput sequencing technology and bioinformatics methods to identify 140 differentially expressed transcription factors, 137 known miRNAs, and 250 novel miRNAs. Through target relationship prediction, 31 potential transcription factors were found to be associated with 27 miRNAs in 18 independent networks, showing the multiplicity of the regulators. In particular, 9 miRNAs and 5 transcription factors were found as hubs in the network. Furthermore, we hypothesized that 12 regulatory modules might play combinatory regulatory roles in seed development and oil accumulation. In developing seeds, the expression levels of these miRNAs and transcription factors were significantly different between the two cultivars. Taken together, these data describe the first miRNA-transcription factor coregulatory network in developing seeds of sea buckthorn. These findings will be helpful for understanding seed development and oil accumulation at the molecular level in sea buckthorn