Although the selection of coding genes during plant domestication has been well studied, the evolution of MIRNA genes (MIRs) and the interaction between microRNAs (miRNAs) and their targets in this process are poorly understood. Here, we present a genome-wide survey of the selection of MIRs and miRNA targets during soybean domestication and improvement. Our results suggest that, overall, MIRs have higher evolutionary rates than miRNA targets. Nonetheless, they do demonstrate certain similar evolutionary patterns during soybean domestication: MIRs and miRNA targets with highly expressed, duplication status, and with greater numbers of partners exhibit lower nucleotide divergence than their counterparts without these characteristics, suggesting that expression level, duplication status, and miRNA-target interaction are essential to the evolution of MIRs and miRNA targets. Further investigation reveals that miRNA-target pairs that are subjected to strong purifying selection have higher similarities than that exhibited genetic diversity. Moreover, mediated by domestication and improvement, the similarities of a large number of miRNA-target pairs in cultivated soybean populations were increased compared to those in wild soybeans, whereas a small number of miRNA-target pairs exhibited decreased similarity, which might be associated with the adoption of particular domestication traits. Taken together, our results shed light on the coevolution of MIRs and miRNA targets during soybean domestication.

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