In-Silico Approach for Development of SSR Markert in Foxtail Millet (Setaria Italica)

Abstract

Foxtail millet (Setaria italica) is one of the oldest cultivated cereal grain and the most economically important species of the setaria genus. Foxtail millet (Setaria italica) possesses a small genome (-515Mb; 2n=2x=18) with a relatively lower repetitive DNA and its inbreeding nature coupled to short life-cycle. Molecular markers are indispensable for genomic study. Among various marker systems Simple Sequence Repeats (SSRs) have occupied a pivotal place because of their reproducibility, multiallelic nature, codominant inheritance, relative abundance and good genetic coverage. Its major features that SSRs shows abundant distribution in the genomes and were hyper variable in nature. The traditional method of SSR marker development involves construction of SSRenriched library, cloning and sequencing, which is costly and labour intensive. Bioinformatics approaches are increasingly being used for molecular marker development since the sequences from many genomes are made freely available in the public databases. The source of sequences for marker development are expressed sequence tags (ESTs) that are obtained by sequencing 5' and/or 3' ends of a complementary DNA (eDNA) molecule synthesized from a messenger RNA (q~RNA). However in Setaria italica, development of EST-SSR markers is in its infancy. The primers were designed for SSR markers isolated from Setaria italica EST sequences using in silico techniques. The sequence were retrieved from the EST sequences related to Setaria italica from National Center for Biotechnology Information (NCBI). Analysis of the repeat patterns and designing of SSR primers were done through SSRIT for repeat motifs. The specificity of the pre-existing primers and designing target-specific primer was done by the Primer 3 and Primer BLAST software. This study concludes that the insilica designing of EST-SSR marker were cheap and much effective, shows more efficacy than the than the conventional method. They are useful for the genome mapping, comparative analysis with other crop and to determine the genetic diversity of the Setaria italica.