Age-Related miRNA-Mediated Regulatory Networks Orchestrating Chronological Development of Meristems in Larix Kaempferi

Plant growth and development is usually characterized by chronological age over the plants’ lifetimes. Age-related changes actually originate with meristems because they control if, where, when, and how new tissues are formed along the axis of the shoot. The “time-keeping” of plant meristem development is a complex process. To uncover the post-transcriptional regulation underlying the chronological development of Larix kaempferi (Japanese larch) meristems, we investigated the miRNA-mediated regulatory network in the defoliated, uppermost main stems of 1-, 2-, 5-, 10-, 25-, and 50-year-old L. kaempferi using RNA-seq methods. We identified 29 high-confidence miRNAs, three of which were defined, age-related miRNAs whose expression changed depending on L. kaempferi age, and 17 showed coordinated expression patterns with three age-related miRNAs based on hierarchical correlations. All hierarchically coordinated miRNAs and their targets constituted a miRNA-mediated regulatory network. The developmental timing pathway lka-miR-1-5p-156-SBP/SPL (Squamosa Promoter Binding Protein-Like), the lignin biosynthesis pathway lka-miR-7,13-5p-397-LAC (Laccase), and an unknown pathway lka-miR-3-5p-CMSS1 (Cms1 Ribosomal Small Subunit Homolog) were age-driven, and information from auxin and light could be integrated by the lka-miR-9-5p-390-TAS/ARF (Trans-Acting siRNA3/Auxin Response Factor) and lka-miR-8-5p-IRL4 (Plant Intracellular Ras-Group-Related LRR Protein 4) pathways, respectively. Age-driven regulatory network will lead the way to understand which and how genes mutually cross-regulate their activity orchestrating development of meristems of L. kaempferi with age. We also discussed and contributed to miRNA annotation and nomenclature.