Development of simple sequence repeat DNA markers and their integration into a barley linkage map

Abstract

Simple sequence repeats (SSRs), or microsatellites, are a new class of PCR-based DNA markers for genetic mapping. The objectives of the present study were to develop SSR markers for barley and to integrate them into an existing barley linkage map. DNA sequences containing SSRs were isolated from a barley genomic library and from public databases. It is estimated that the barley genome contains one (GA)n repeat every 330 kb and one (CA)n repeat every 620 kb. A total of 45 SSRs were identified and mapped to seven barley chromosomes using doubled-haploid lines and/or wheat-barley addition-line assays. Segregation analysis for 39 of these SSRs identified 40 loci. These 40 markers were placed on a barley linkage map with respect to 160 restriction fragment length polymorphism (RFLP) and other markers. The results of this study demonstrate the value of SSRs as markers in genetic studies and breeding research in barley.

A high density barley microsatellite consensus map with 775 SSR loci

“…The consensus map integrates already published (Saghai Maroof et al 1994;Becker and Heun 1995;Liu et al 1996;Struss and Plieske 1998;Ramsay et al 2000;Li et al 2003;Thiel et al 2003) and very recently developed (mainly GBM and scssr; Rostoks et al 2005;Varshney et al 2006a;Marcel et al 2007) barley SSR markers.…”

“…Within the latter set of 230 microsatellite loci, 34 are new scssr (SCRI-SSR) loci recently integrated into a SNP map of barley (Rostoks et al 2005) and provided by Joanne Russell. Finally, the segregation data of 418 Liu et al (1996) Theor Appl Genet (2007) …”

“…This is largely because they require small amounts of sample DNA, are easy to detect by PCR, are amenable to high-throughput analysis, co-dominantly inherited, multi-allelic, highly informative and abundant in genomes (Powell et al 1996;Gupta and Varshney 2000). The value of microsatellite markers for both genetic diversity studies and for barley breeding was demonstrated as early as 1994 (Saghai Maroof et al 1994;Becker and Heun 1995;Liu et al 1996;Struss and Plieske 1998). Later, comprehensive microsatellite genetic maps integrating 242 SSR loci and 127 SSR loci were prepared by Ramsay et al (2000) and by Li et al (2003), respectively.…”

Inheritance and identification of molecular markers associated with spot blotch (Cochliobolus sativus L.) resistance through microsatellites analysis in barley

“…Forty five SSRs primers (Table 1), based on the map of Becker and Heun (1995), Liu et al (1996), Ramsay et al (2000) and Li et al (2003), specific for 1H and 5H were used to screen for polymorphism between IBON 18 and RD 2508. Then the polymorphic markers were screened against the two DNA bulks.…”

“…DNA amplification was carried out in a 20 well thermocycler (TECHNE, England) each containing 50-100 ng template DNA, 0.2 μM of each primer, 200 μM of each of the dNTPs, 2.5 mM MgCl 2 , 1X PCR buffer and 1U of Taq DNA Polymerase (Bangalore Genei, India; The composition for 10x buffer was = 100 mM Tris-HCl, pH 8.3 at 25°C; 500 mM KCl; 15 mM MgCl 2 ; 0.5% (vol) Tween 20). The temperature profile for annealing was used according to the information provided for the primers (Becker and Heun, 1995;Liu et al, 1996;Ramsay et al, 2000;Li et al, 2003) (Table 1). The amplification products were separated on 2.5% agarose gels with TBE buffer (100 mM Tris-borate, 2.5 mM EDTA, pH 8).…”