Association Studies in Populus tomentosa Reveal the Genetic Interactions of Pto-MIR156c and Its Targets in Wood Formation.

Mingyang Quan,Qingzhang Du,Souksamone Phangthavong,Qingshi Wang,Xiaohui Yang,Yuepeng Song,Deqiang Zhang

doi:10.3389/fpls.2016.01159

Abstract

MicroRNAs (miRNAs) regulate gene expression in many biological processes, but the significance of the interaction between a miRNA and its targets in perennial trees remains largely unknown. Here, we employed transcript profiling and association studies in Populus tomentosa (Pto) to decipher the effect of genetic variation and interactions between Pto-miR156c and its potential targets (Pto-SPL15, Pto-SPL20, and Pto-SPL25) in 435 unrelated individuals from a natural population of P. tomentosa. Single-SNP (single-nucleotide polymorphism) based association studies with analysis of the underlying additive and dominant effects identified 69 significant associations (P < 0.01), representing 51 common SNPs (minor allele frequency > 0.05) from Pto-MIR156c and its three potential targets, with six wood and growth traits, revealing their common roles in wood formation. Epistasis analysis uncovered 129 significant SNP-SNP associations with ten traits, indicating the potential genetic interactions of Pto-MIR156c and its three putative targets. Interestingly, expression analysis in stem (phloem, cambium, and xylem) revealed that Pto-miR156c expression showed strong negative correlations with Pto-SPL20 (r = −0.90, P < 0.01) and Pto-SPL25 (r = −0.65, P < 0.01), and a positive correlation with Pto-SPL15 (r = 0.40, P < 0.01), which also indicated the putative interactions of Pto-miR156c and its potential targets and their common roles in wood formation. Thus, our study provided an alternative approach to decipher the interaction between miRNAs and their targets and to dissect the genetic architecture of complex traits in trees.

Highlights

MicroRNAsare small non-coding RNAs (20–24 nt) that function in gene regulation as sequence-specific regulators, via post-transcriptional mRNA cleavage or inhibition of gene expression in eukaryotes (Voinnet, 2009)
To examine the expression patterns of P. tomentosa (Pto)-MIR156 gene family in different tissues and organs, we first measured the expression abundance of 12 members in Pto-MIR156 family, which showed that Pto-MIR156c exhibited high abundance in vascular tissue, indicating that Pto-miR156c might function in wood formation of trees (Figure S1)
Comparison of the Pto-MIR156c pre-miRNA sequence with homologous miRNAs in P. trichocarpa, Oryza sativa, Zea mays, and Arabidopsis thaliana revealed that the mature region of these miRNAs were completely conserved, despite the diverse degrees of similarity (52.32–100%) in the pre-miRNA region (Figure 1A)

Summary

Introduction

MicroRNAs (miRNAs)are small non-coding RNAs (20–24 nt) that function in gene regulation as sequence-specific regulators, via post-transcriptional mRNA cleavage or inhibition of gene expression in eukaryotes (Voinnet, 2009). In Arabidopsis and maize, miR156 functions in shoot maturation during the juvenile to adult transition, and is highly expressed in early shoot development but decreases after this stage. The juvenile to adult phase was delayed when miR156 was overexpressed (Wu and Poethig, 2006; Chuck et al, 2007). The SPLs encode a plant-specific transcription factor family that plays pivotal roles throughout different stages of plant development (Birkenbihl et al, 2005); for example, AtSPL2, AtSPL10, and AtSPL11 function in morphological regulation of cauline leaves and flowers during the Arabidopsis reproductive phase (Shikata et al, 2009)

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Conclusion