Genetic variations and miRNA–target interactions contribute to natural phenotypic variations in Populus

Summary Variation in regulatory factors, including micro RNA s (mi RNA s), contributes to variation in quantitative and complex traits. However, in plants, variants in mi RNA s and their target genes that contribute to natural phenotypic variation, and the underlying regulatory networks, remain poorly characterized. We investigated the associations and interactions of single‐nucleotide polymorphisms ( SNP s) in mi RNA s and their target genes with phenotypes in 435 individuals from a natural population of Populus . We used RNA ‐seq to identify 217 mi RNA s differentially expressed in a tension wood system, and identified 1196 candidate target genes; degradome sequencing confirmed 60 of the target sites. In addition, 72 mi RNA –target pairs showed significant co‐expression. Gene ontology ( GO ) term analysis showed that most of the genes in the co‐regulated pairs participate in biological regulation. Genome resequencing found 5383 common SNP s (frequency ≥ 0.05) in 139 mi RNA s and 31 037 SNP s in 819 target genes. Single‐ SNP association analyses identified 232 significant associations between wood traits ( P ≤ 0.05) and SNP s in 102 mi RNA s and 1387 associations with 478 target genes. Among these, 102 mi RNA –target pairs associated with the same traits. Multi‐ SNP associations found 102 epistatic pairs associated with traits. Furthermore, a reconstructed regulatory network contained 12 significantly co‐expressed pairs, including eight mi RNA s and nine targets associated with traits. Lastly, both expression and genetic association showed that miR156i, miR156j, miR396a and miR6445b were involved in the formation of tension wood. This study shows that variants in mi RNA s and target genes contribute to natural phenotypic variation and annotated roles and interactions of mi RNA s and their target genes by genetic association analysis.