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Recent studies have revealed associations between single nucleotide polymorphisms (SNPs) in microRNA (miRNA) genes and diseases. However, association studies to decipher the interactions between miRNAs and their target genes remain to be conducted. Here, we investigated the association of growth and wood traits with SNPs in  Pt-miR397a  and its targets, in 261 individuals from a natural population of  Populus tomentosa . Of the 57 SNPs identified in  Pt-miR397a , three strongly affect its secondary stability, and SNPs in target sites in  Pt-LAC20  and  Pt-HSP40  changed the binding affinity of Pt-miR397a. Single-SNP association analysis revealed that SNPs in  Pt-miR397a  significantly associated with α-cellulose content and stem volume, and SNPs in target genes also associated with growth and wood-property traits. Multi-SNP association analysis with additive and dominant models found that SNPs in six potential target genes associated with at least one trait in common with  Pt-miR397a , revealing a possible genetic interaction between  Pt-miR397a  and its targets. Furthermore, epistasis analysis revealed epistatic interactions between SNPs in  Pt-miR397 a and its target genes. Thus, our study indicated that SNPs in  Pt-miR397a  and six target genes affect wood formation and that association studies can reveal the interactions between miRNAs and their target genes.

Association genetics in Populus reveals the interactions between Pt-miR397a and its target genes