Transcriptome and miRNAome reveal components regulating primary thickening of bamboo shoots

Abstract Primary thickening determines bamboo yield and wood property. However, little is known about the regulatory networks involved in this process. The present study identified a total of 58,652 genes and 521 miRNAs via transcriptome and small RNA sequencing using the underground thickening shoot samples of wild type (WT) Moso bamboo ( Phyllostachys edulis ) and a thick wall (TW) variant ( P. edulis cv. Pachyloen ) at five developmental stages (WTS1/TWS1-WTS5/TWS5). A total of 11,636 (54.05%) differentially expressed genes (DEGs) and 515 (98.85%) differentially expressed miRNAs (DEmiRs) were identified from the WT, TW, and WTTW groups. The first two groups were composed of four pairwise combinations each between two successive stages (WTS2/TWS2_vs_WTS1/TWS1, WTS3/TWS3_vs_WTS2/TWS2, WTS4/TWS4_vs_WTS3/TWS3 and WTS5/TWS5_vs_WTS4/TWS4), and the WTTW group was composed of five between two relative stages (TWS1–5_vs_WTS1–5). Additionally, among the phytohormones, zeatin (ZT) showed more remarkable changes in concentrations than indole-3-acetic acid (IAA), gibberellic acid (GA 3 ), and abscisic acid (ABA) throughout the five stages in the WT and the TW groups. Moreover, 118 sites were identified for 590 miRNA-mRNA pairs via degradome sequencing. The dual-luciferase reporter assay confirmed that 14 miRNAs bound to 12 targets. Fluorescence in situ hybridization (FISH) localized miR166 and miR160 in the shoot apical meristem (SAM) and the procambium of Moso bamboo shoots at the S1 stage. Thus, primary thickening is a complex process regulated by miRNA-gene-phytohormone networks, and the miRNAome and transcriptome dynamics regulate phenotypic plasticity. These findings provide insights into the molecular mechanisms underlying wood formation and properties and propose targets for bamboo breeding.