Development and applications of EST-SSR markers in sorghum

Ramu, P (2009) Development and applications of EST-SSR markers in sorghum. PHD thesis, Osmania University.

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Supervisors NameSupervisors ID
Ananda Reddy, LOU


Microsatellites or simple sequence repeat (SSR) markers are playing a significant role in molecular breeding programs. But, conventional methods of SSR markers development are laborious and expensive. The alternative way is to explore the existing databases for the development of new markers. Complete genome sequencing projects depositing numerous amounts of genomic and genic (expressed sequence tag, EST) sequence in the public databases. This facilitates to explore for the development of new marker systems including SSRs, SNPs, etc. In the present study, 600 EST-SSR markers were developed in sorghum by mining the J. Craig Research Institute [formerly, The Institute for Genome Research (TIGR)] database. Non-redundant EST sequences which are having the homology with rice genome were selected for the designing these 600 markers (by exploiting rice-sorghum synteny). PCR conditions for these primer pairs were optimized on four parental pairs of sorghum genotypes constituting two mapping populations. About 23% of markers were found polymorphic in parents of shootfly resistance mapping population (BTx623  IS18551). These polymorphic markers were screened against the shootfly RIL mapping population. A total of 82 EST-SSR markers were mapped onto the previously existing skeleton map of the sorghum using shootfly resistance mapping population. After adding these 82 new EST-SSR markers, the map distance was extended to 2966.4 cM. This map distance was ~250 cM larger than the previously reported longest linkage map in sorghum. These EST-SSR markers, however, filled gaps or marker-rare regions in the existing linkage map of sorghum targeted based on rice-sorghum sequence similarity. This study demonstrates the utility of comparative genomic information in targeted development of markers to fill gaps in linkage maps of related crop species for which sufficient genomic tools are not available...

Item Type: Thesis (PHD)
Subjects: Mandate crops > Sorghum
Depositing User: Users 6 not found.
Date Deposited: 28 Oct 2011 10:37
Last Modified: 27 Sep 2013 11:27
Acknowledgement: UNSPECIFIED
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