Genome-Wide Mining, Characterization and Development of miRNA-SSRs in Arabidopsis thaliana

Kumar, A.; Aditi Chauhan, A.; Kompelli, S. K.; Gahlaut, V.; Ijaq, J.; Singh, K. P.; Gajula, M. P.; Suravajhala, P.; Mishra, A.; Balyan, H. S.; Gupta, P. K.

doi:10.1101/203851

bioRxiv · 10.1101/203851

Genome-Wide Mining, Characterization and Development of miRNA-SSRs in Arabidopsis thaliana

Kumar, A.·Aditi Chauhan, A.·Kompelli, S. K.·Gahlaut, V.·Ijaq, J.·Singh, K. P.·Gajula, M. P.·Suravajhala, P.·Mishra, A.·Balyan, H. S.·Gupta, P. K.

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Abstract

Simple Sequence Repeats (SSRs), also known as microsatellites are short tandem repeats of DNA sequences that are 1-6 bp long. In plants, SSRs serve as a source of important class of molecular markers because of their hypervariabile and co-dominant nature, making them useful both for the genetic studies and marker-assisted breeding. The SSRs are widespread throughout the genome of an organism, so that a large number of SSR datasets are available, most of them from either protein-coding regions or untranslated regions. It is only recently, that their occurrence within microRNAs (miRNA) genes has received attention. As is widely known, miRNA themselves are a class of non-coding RNAs (ncRNAs) with varying length of 19-22 nucleotides (nts), which play an important role in regulating gene expression in plants under different biotic and abiotic stresses. In this communication, we describe the results of a study, where miRNA-SSRs in full length pre-miRNA sequences of Arabidopsis thaliana were mined. The sequences were retrieved by annotations available at EnsemblPlants using BatchPrimer3 server with miRNA-SSR flanking primers found to be well distributed. Our analysis shows that miRNA-SSRs are relatively rare in protein-coding regions but abundant in non-coding region. All the observed 147 di-, tri-, tetra-, penta- and hexanucleotide SSRs were located in non-coding regions of all the 5 chromosomes of A. thaliana. While we confirm that miRNA-SSRs were commonly spread across the full length pre-miRNAs, we envisage that such studies would allow us to identify newly discovered markers for breeding studies.

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Kumar, A., Aditi Chauhan, A., Kompelli, S. K., Gahlaut, V., Ijaq, J., Singh, K. P., Gajula, M. P., Suravajhala, P., Mishra, A., Balyan, H. S., Gupta, P. K.. 2017-10-16. Genome-Wide Mining, Characterization and Development of miRNA-SSRs in Arabidopsis thaliana. https://doi.org/10.1101/203851

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