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Acid soils limit agricultural production all over the world. Major reason of crop losses in acid soils is toxicity of aluminum (Al). In the present work, we investigated expression alterations of microRNAs in flax (Linum usitatissimum L.) plants under Al exposure. Flax seedlings of resistant and susceptible to Al lines and cultivars were exposure in AlCl3 solution for 4 and 24 hours. Twelve small RNA libraries were constructed and sequenced using Illumina GAIIx. In total, 97 miRNAs from 18 conserved families were predicted. Definite regularities were revealed for expression alterations of miR319, miR390 and miR393 in flax plants under Al exposure. Moreover, diverse expression alterations were revealed for miR390 and miR393 in susceptible and resistant to Al genotypes. Thus, the involvement of miR319, miR390 and miR393 in response to Al stress in flax was shown for the first time. We firstly identified TCPs as potential targets for miR319, TAS3 and GRF5 as potential targets of miR390, and AFB2 as potential targets for miR393 in flax. TCPs, TAS3, GRF5, and AFB2 participate in regulation of plant growth and development. We discussed that miR319, miR390, and miR393 play important role in Al response via regulation of growth processes in flax plants. |