​Integrative Analysis of miRNA and mRNA in Dormant Alfalfa under Different Growth States

Abstract

Background: Alfalfa is one of the most important legume forages in the world; it includes three fall dormancy (FD) types. There is previous difference between FD alfalfa and non-FD alfalfa. However, the molecular basis of these differences remains largely dim. MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; the reverse differential expression of genes and miRNAs can help us to reveal the regulation mechanism of fall dormancy in alfalfa. Methods: We carried out integrative analysis of miRNA and mRNA in dormant alfalfa under different growth conditions based on miRNA and transcriptome sequencing analysis. The differential genes were obtained by transcriptome analysis and the differential miRNAs were obtained by small RNA analysis. Then the integration analysis of miRNAs and mRNAs was performed to screen reverse different expressions between genes and miRNAs to construct the key miRNA-mRNA regulatory network. Result: Our results indicated the biological process was the key factor in the fall dormancy of alfalfa, 24 miRNAs downregulated with transcript genes upregulated and 24 miRNAs upregulated with transcript genes downregulated, respectively. Key factors of the regulatory network showed that MiR5287b and miR2643a had a more complex network. MiR5287b had 22 corresponding regulatory transcript factors and miR2643a had 17 corresponding regulatory transcript factors and some conserved miRNAs (e.g., miR172a, miR156e and miRNA169h). Most of them play the vital role in plant growth and development and also participate in regulating fall dormancy in alfalfa.