Small RNA Expression Profiles During Determinate Primary Root Growth in Cardon Pachycereus pringlei (Cactaceae)

We sequenced and compared small RNA populations from the primary root tips of cardon Pachycereus. pringlei. The primary root of P.pringlei, a Sonoran Desert Cactaceae, exhibits determinate growth. The root apical meristem of seedling primary root exhausts and all cells in the root tip differentiate. Determinate growth of primary and most lateral roots results in the formation of a compact root system that provides seedlings an advantage for survival in desert environment. In order to identify and characterize small RNAs involved in root meristem maintenance and determinate root growth in P.pringlei, we employed smRNA sequencing using SOLID5500.  The 35nt reads were analysed using the small RNA analysis tools in CLC Genomics Workbench.  Using miRBase data, we annotated small RNAs differentially expressed in the root tip during initial growth phase soon after germination and terminal growth phase after meristem exhaustion.

A number of known smRNAs were significantly down regulated in the terminal root growth phase: MIR156, MIR169, MIR390, MIR395b, MIR399e, and MIR529b.  The small RNAs that were up-regulated in the terminal phase: MIR167c, MIR395l, MIR396, and MIR398c.

The most up-regulated smRNA in the terminal phase is MIR167c that was shown to be involved into inhibition of auxin response factors (Lv et al, 2012). The significantly downregulated in the terminal phase MIR390 was shown to be involved into leaf development, particularly in establishing patterning events (Nogueira et al, 2009).

We also identified hundreds of novel, the species specific smRNAs that show differential expression in these growth phases.

Acknowlegment: PAPIIT/UNAM IN204912 to SS.