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Inter species testing of Brassica microsatellites available in public domain and their potential utilization for comparative genomics in Cruciferae

MUNAZZA SADIA¹*, MALIK ASHIQ RABBANI², M. SHAHID MASOOD², S.R. PEARCE³ AND SALMAN A. MALIK¹

Abstract: Many of the microsatellites available in the public domain have been used successfully or tested on species other than that from which they were originally isolated. In this study we report on the distribution of more SSR loci within Brassicaceae species. A selection of available primer pairs was screened against a panel of Brassica rapa, B. carinata, B. juncea, B. napus and B. nigra lines. PCR conditions were kept uniform to facilitate high throughput genotyping.  Initial screening comprised of separation of PCR products on 3.5% metaphor agarose gels and visualization by staining with Ethidium bromide. The PCR products were assessed on the basis of polymorphism and number of fragments amplified. Those with a small number of fragments (1-4) that showed polymorphism either within or between species were then screened again using a larger panel of lines. All the primer pairs that could be used successfully in B. rapa were examined in other Brassica and Cruciferous species. More than 90% of the primer pairs successfully amplified the corresponding microsatellite regions in the Brassica species tested. Based on these results, we concluded that the selected microsatellites have a high potential for the development of DNA markers that could contribute to the genetic analysis of Brassica and other Cruciferae.

¹Department of Biochemistry, Quaid-I-Azam University, Islamabad, Pakistan.

²Institute of Agri-Biotechnology & Genetic Resources, NARC, Islamabad, Pakistan

³School of Life Sciences, University of Sussex, Brighton, UK.