miRNA regulation in fast- and slow-growing hybrid Larix trees

Variation in the growth of Larix hybrid trees is under complex genetic regulation. To examine whether microRNAs (miRNAs) are involved in this complex regulation, we compared miRNA expression profiles between six fast- and six slow-growing Larix hybrid lines from two full-sib families. Five miRNAs were differentially expressed between the fast- and slow-growing lines, of which ppt-miR477g-3p, mml-miR-675 and smo-miR1083 were down-regulated, and cre-miR905* and vvi-miR171a were up-regulated in the six fast-growing lines. Analyses of the target genes of these five miRNAs revealed a common functional feature—changes in the expression of those miRNAs in the fast-growing trees can potentially lead to an enhanced cell proliferation and superior ability to adapt to environmental changes/stresses. Comparison of the expression profiles between families revealed a family specific expression signature—eight members of miR395 family were differentially expressed between the fast- and slow-growing trees in one full-sib family but not in another, suggesting a family dependent unique miRNA regulation. Differential miRNA expression was confirmed and independently validated by QRT-PCR. Orthologous miRNA hybridization between species was verified by sequencing some of the Larix miRNA. Taken together, our data suggested that rapid growth in Larix is subject to complex miRNA regulation. Some of the regulatory mechanisms are common among families while others are unique to a given family. Five differentially expressed miRNAs between the fast- and slow-growing trees may play a role in regulating growth of Larix trees.