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Flax (Linum usitatissimum L.), is important agricultural crop.Flax stem fiber and seed oil have multiple industrial applications.Flax undergoes heritable changes in phenotype and genotype inresponse to the growth environment [1]. Flax lines in which stableinherited changes were observed were named genotrophs. Very lit-tle is known about mechanisms of genetic changes during flaxdevelopment under defined environment conditions. Small non-coding RNAs are a distinct class of regulatory RNAs in plantsthat control a variety of biological processes. Small RNAs regu-late growth and development, maintenance of genome integrity,and are also important components in plant stress responses.The comparison of miRNA expression profiles was performedfor flax cultivar Stormont Cirrus grown under normal (1),inadequate (2) and excessive (3) nutrition using the miRNAsequencing with genome analyzer Illumina GAIIx.A total of 7.2 M (1), 11.6 M (2), and 7.6 M (3) raw readswere obtained from deep sequencing of flax sRNA. The highestread abundance was found for 24-nt (over 25%) and 21-nt (23%)sRNAs. We identified 76 conserved miRNA homologues whichbelong to 20 distinct miRNAs families The highest read abun-dance was detected for miR166 family. In total, we predicted 50potential novel miRNAs for (1), (2) and (3) libraries respectively.Some of the conserved and novel miRNAs showed differentialexpression among (1), (2) and (3) libraries.Thus, we ide ntified conserved and novel miRNA tha t wereexpressed in flax seedlings and perform expression analysis of miR-NA in flax genotrophs. It gives new information about the processesoccurring while the plants were growing under different condition sand the role of the environmen t in generating adaptive mutation.