Abstract
In silico analysis provides an economical approach in the development of simple sequence repeat (SSR) markers through utilization of genome sequences generated from high throughput sequencing platform. In this study, we present the potential SSR markers of maize mining from its reference genome of cultivar B73. In total, 94, 534 putative SSRs were detected in maize reference genome B73. Dinucleotide repeats (57.00%) were found the most frequent repeats in maize genome, followed by trinucleotide (38.90%), tetranucleotide (2.77%), pentanucleotide (0.85%) and hexanucleotide (0.48%) repeats. A total of 2239 primer pairs were successfully designed for experimental validation. Of these, 99 SSR markers were selected for optimization and only 71(71.71%) SSR primer pairs produced DNA amplification products and therefore validated as developed SSR markers for maize. This in silico approach through genome wide analysis of maize genome not only provides rapid discovery and cost effective methods in SSR markers development but also will act as useful tool for genetic diversity and marker-trait association in maize.
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