Integrated analysis of mRNA and miRNA transcriptomes reveals the mechanism of regulatory interspecific fiber heterosis

Interspecific hybridization contributes to improving cotton fiber quality, thus addressing the parental genetic diversity bottleneck problems. To elucidate the molecular mechanisms underlying fiber heterosis in interspecific hybrid cotton, an integrated analysis of phenotypes, mRNAs, and miRNAs was performed to compare the immature fibers of the parents (Gossypium hirsutum and Gossypium barbadense) with those of their hybrid at various development stages. The results showed that fiber heterosis was most obvious at 10 days post anthesis. Comprehensive analysis of mRNA and miRNA demonstrated that the main expression pattern was transgressive up-regulation (TUR) at mRNA level, while it was transgressive down-regulation (TDR) at miRNA level. The miR160-ARF and miR319-TCP pairs were mainly responsible for the changes in endogenous auxin content and secondary cell wall deposition in the fiber development stage, and they played an important role in the formation of interspecific fiber heterosis. Meanwhile, the results of indole-3-acetic acid (IAA) content determination and in vitro ovule culture indicated that auxin affected fiber heterosis. This study reveals the mechanism by which miRNA-mRNA regulates fiber heterosis, and it will promote the applications of interspecific hybrid cotton between G. hirsutum and G. barbadense.