Abstract

MicroRNAs (miRNAs) play crucial roles in plant growth and development, but few studies have illuminated the allelic interactions among miRNAs and their targets in perennial plants. Here, we combined analysis of expression patterns and single-nucleotide polymorphism (SNP)-based association studies to explore the interactions between Pto-MIR475b and its four target genes (Pto-PPR1, Pto-PPR2, Pto-PPR3, and Pto-PPR4) in 435 unrelated individuals of Populus tomentosa. Expression patterns showed a significant negative correlation (r = -0.447 to -0.411, P < 0.01) between Pto-MIR475b and its four targets in eight tissues of P. tomentosa, suggesting that Pto-miR475b may negatively regulate the four targets. Single SNP-based association studies identified 93 significant associations (P < 0.01, Q < 0.1) representing associations of 80 unique SNPs in Pto-MIR475b and its four targets with nine traits, revealing their potential roles in tree growth and wood formation. Moreover, one common SNP in the precursor region significantly altered the secondary structure of the pre-Pto-miR475b and changed the expression level of Pto-MIR475b. Analysis of epistatic interactions identified 115 significant SNP–SNP associations (P < 0.01) representing 45 unique SNPs from Pto-MIR475b and its four targets for 10 traits, revealing that genetic interactions between Pto-MIR475b and its targets influence quantitative traits of perennial plants. Our study provided a feasible strategy to study population genetics in forest trees and enhanced our understanding of miRNAs by dissecting the allelic interactions between this miRNA and its targets in P. tomentosa.

Highlights

  • MicroRNAs are small, non-coding RNAs of 20 to 24 nucleotides and play key roles in post-transcriptional regulation of gene expression in eukaryotes (He and Hannon, 2004; Rogers and Chen, 2013)

  • The 21 nt mature sequence of Pto-miR475b and the mature xylem complementary DNA (cDNA) library of P. tomentosa were analyzed in psRNATarget to predict its target genes, which identified 78 candidate targets

  • We found that 17 single-nucleotide polymorphism (SNP) in Pto-PPR1, Pto-PPR2, Pto-PPR3, and Pto-PPR4 were significantly associated with H and fiber width (FW)

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Summary

Introduction

MicroRNAs (miRNAs) are small, non-coding RNAs of 20 to 24 nucleotides and play key roles in post-transcriptional regulation of gene expression in eukaryotes (He and Hannon, 2004; Rogers and Chen, 2013). MiRNAs function by cleaving the transcripts or suppressing the translation of their target genes through near-perfect sequence complementation (Chen, 2005). Lu et al (2013) overexpressed Ptr-MIR397a in nine transgenic Populus trichocarpa lines, which resulted in notably down-regulated expression of Ptr-LACs and decreased total laccase activity, which further reduced the Klason lignin content by as much as 22%. These results suggested that Ptr-miR397a is a master regulator of lignin polymerization and is involved in the regulation of the lignin biosynthesis pathway

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