biologia plantarum

International journal on Plant Life established by Bohumil Němec in 1959

Biologia plantarum 58:627-640, 2014 | DOI: 10.1007/s10535-014-0441-6

Natural genetic variation in MIR172 isolated from Brassica species

S. M. Shivaraj1, P. Dhakate1, P. Mayee1, M. S. Negi1, A. Singh1,*
1 Department of Biotechnology, TERI University, Vasant Kunj, India

The present study reports a natural variation in microRNA172 (MIR172) family members isolated from six species of genus Brassica. The analysis of nucleotide polymorphism across 44 Brassica MIR172 homologs revealed a higher conservation in the predicted precursors relative to flanking regions. Single nucleotide polymorphisms (SNPs) were detected in miRNA and miRNA*. The 21-nt miRNA sequence was conserved in all MIR172 members except MIR172a. However, the miRNA* sequence was conserved only in MIR172a compared to A. thaliana. Non-canonical Brassica variants of precursor miR172a were detected wherein SNP at 5' terminal in mature miR172a resulted in a sequence identical to mature miR172e. SNPs and indels in precursors resulted in varied stem-loop structures of differing stabilities (ΔG) implying a differential efficiency of miRNA biogenesis. A sequence based phylogram revealed ortholog specific groupings of MIR172 irrespective of genetic background. A Northern analysis in Brassica juncea displayed the cumulative expression of miR172 isoforms in all tissues representing different developmental stages with levels gradually increasing from vegetative to reproductive stages. Detection of high content of miR172 in roots indicates the possibility of additional roles of Brassica miR172 in root development.

Keywords: Arabidopsis thaliana; evolution; flowering; orthologs; polyploidy; single nucleotide polymorphism
Subjects: microRNA; flowering; single nucleotide polymorphism; evolution; Northern blot

Received: October 16, 2013; Revised: February 11, 2014; Accepted: February 25, 2014; Published: December 1, 2014  Show citation

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Shivaraj, S.M., Dhakate, P., Mayee, P., Negi, M.S., & Singh, A. (2014). Natural genetic variation in MIR172 isolated from Brassica species. Biologia plantarum, 58(4), 627-640. doi: 10.1007/s10535-014-0441-6
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