Long non-coding RNAs and mRNAs interaction networks in maize roots treated with biostimulants

Long non-coding RNAs (lncRNAs) constitute a class of non-coding RNAs (ncRNAs) responsible for playing critical regulatory roles at different stages of development and in plants subjected to diverse types of biotic and abiotic stress. Research with plants subjected to biostimulants (e.g., plant growth-promoting bacteria and humic acid) has shown promising results regarding increased productivity and resistance to stress. However, despite the increase of studies on plant lncRNAs in recent years, the functions of lncRNAs in maize (Zea mays L.) subjected to colonization by beneficial microorganisms and its response to humic acids remain unknown. To identify and characterize maize lncRNAs, we used single-end RNA-seq libraries constructed from roots of non-inoculated seedlings and inoculated with diazotrophic endophytic bacterium Herbaspirillum seropedicae and humic acid. Through a computational pipeline, we identified a total of 32 501 known High-Confidence lncRNAs (HC-lncRNAs) and 6 418 novel candidate lncRNAs (NC-lncRNAs) in the transcriptome. The expression profile of lncRNAs revealed 3 263 HC-lncRNAs and 1 050 NC-lncRNAs significantly differentially expressed (DE) when treated plants are compared to controls. We also identified the regulatory networks of DE-lncRNAs by predicting cis-target genes and miRNAs. The results showed that lncRNAs target genes related to different processes, including the participation of elements associated with distinct plant hormones. Furthermore, interaction networks of lncRNA-mRNA-miRNA were constructed and showed the potential of lncRNAs as a key regulatory element.