RT Journal Article SR Electronic T1 Genome-Wide Mining, Characterization and Development of miRNA-SSRs in Arabidopsis thaliana JF bioRxiv FD Cold Spring Harbor Laboratory SP 203851 DO 10.1101/203851 A1 Anuj Kumar A1 Aditi Chauhan A1 Sai Kumar Kompelli A1 Vijay Gahlaut A1 Johny Ijaq A1 Krishna Pal Singh A1 MNV Prasad Gajula A1 Prashanth Suravajhala A1 AK Mishra A1 Harindra Singh Balyan A1 Pushpendra Kumar Gupta YR 2017 UL http://biorxiv.org/content/early/2017/10/16/203851.abstract AB 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 (Gupta et al., 2015, and references therein). 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.