Identification and cross-species amplification of EST derived SSR markers in different bamboo species

Abstract

The availability of expressed sequence data derived from gene discovery programs became an alternative source of mining simple sequence repeat (SSR) and developing inexpensive genetic markers for the crop improvements. In present study, 10 express sequence tags (EST)-SSR markers were identified from Bambusa oldhamii public sequence data base. Transferability to 25 species of Bambusoideae ranged from 30% to 100%. The number of alleles detected per locus ranged from 2 to 10. All the newly identified SSR markers were found to be moderately to highly polymorphic with an average Polymorphic Information Content (PIC) value of 0.54. As these loci represents transcribed region and recorded high level of cross transferability and reliable amplification across the species, demonstrating the utility of these markers for functional and genetic analyses of bamboo species.

Analysis of genetic structure and interrelationships in lentil species using morphological and SSR markers

“…Thirty-one SSR primers showing polymorphic and reproducible bands were selected based on the published reports (Hamwieh et al 2005;Phan et al 2007;Saha et al 2010). PCR reactions were comprised of 10 ll reaction volume as per Sharma et al (2009). The total PCR reaction volume contained 20 ng of template DNA, 15 ng of each primer, 200 lM of each dNTP, 10 mM Tris-HCl (pH 8.3), 50 mM KCL, 1.5 mM MgCl 2 , 0.01% gelatin and 0.5 U of Taq DNA polymerase.…”

Development and crosstransferability of functionally relevant microsatellite markers in Dendrocalamus latiflorus and related bamboo species

“…Microsatellite markers are used as tools for assessing genetic variation and dissecting complex traits. Nevertheless, such marker resource is severely limited in bamboo (Sharma et al 2009;Lu et al 2009;Ramalakshmi and Piramanayagam 2010) and nonexistent in D. latiflorus. Genic microsatellites derived from publicly available expressed sequence tag (EST) database have gained considerable importance because they are inexpensive to develop, ubiquitously dispersed in genome, codominantly inherited and often a putative function can be assigned (Provan et al 2001;Chung et al 2006).…”

Analysis of genetic diversity and population structure in Asparagus species using SSR markers

“…Of 40, 15 SSR primers (PN1-PN15) were newly designed and rest were adopted from related Asparagus species ( A. officinalis ) [ 26 , 35 ]. Out of 40, 24 polymorphic SSR primers were used to achieve PCR amplifications in Veriti™ 96-Well Thermal Cycler (Applied Biosystems, CA, USA), in a 12.5 μl reaction volume as per Sharma et al 2009 [ 27 ]. The ingredients present in reaction mixture were 2 μl genomic DNA (13 ng/μl), 1.25 μl 10× PCR Buffer (10 mM Tris-HCl, 50 mM KCl, pH 8.3), 1.0 μl MgCl 2 (25 mM), 1.0 μl dNTP mix (0.2 mM each of dATP, dGTP, dTTP, dCTP ), 0.5 μl of each of two primers and 0.1 μl Taq DNA polymerase (5 U/μl).…”