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MicroRNAs (miRNAs) play crucial regulatory roles in plant growth and development by interacting with RNA molecules, including messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs); however, the genetic networks of miRNAs and their targets influencing the phenotypes of perennial trees remain to be investigated. Here, we integrated expression profiling and association analysis of underlying physiology and expression traits to dissect the allelic variations and genetic interactions of  Pto-MIR167a  and its targets, sponge lncRNA  ARFRL , and  Pto-ARF8 , in 435 unrelated individuals of  Populus tomentosa . Tissue-specific expression analysis in eight tissues, including stem, leaf, root, and shoot apex, revealed negative correlations between  Pto-MIR167a  and lncRNA  ARFRL  and  Pto-ARF8  ( r  = −0.60 and −0.61, respectively,  P  < 0.01), and a positive correlation between sponge lncRNA  ARFRL  and  Pto-ARF8  ( r  = 0.90,  P  < 0.01), indicating their potential regulatory roles in tree growth and wood formation. Single nucleotide polymorphism (SNP)-based association studies detected 53 significant associations ( P  < 0.01,  Q  < 0.1) representing 41 unique SNPs from the three genes and six traits, suggesting their potential roles in wood formation. Epistasis uncovered 88 pairwise interactions for 10 traits, which provided substantial evidence for genetic interactions among  Pto-MIR167a , lncRNA  ARFRL , and  Pto-ARF8 . Using gene expression-based association mapping, we also examined SNPs within the three genes that influence phenotypes by regulating the expression of  Pto-ARF8 . Interestingly, SNPs in the precursor region of  Pto-MIR167a  altered its secondary structure stability and transcription, thereby affecting the expression of its targets. In summary, we elucidated the genetic interactions between  Pto-MIR167a  and its targets, sponge lncRNA  ARFRL , and  Pto-ARF8 , in tree growth and wood formation, and provide a feasible method for further investigation of multi-factor genetic networks influencing phenotypic variation in the population genetics of trees.

Association Genetics in Populus Reveal the Allelic Interactions of Pto-MIR167a and Its Targets in Wood Formation