Genetic and physical mapping of genic microsatellites in barley (Hordeum vulgare L.)
2005
Varshney, R.K.(Institute of Plant Genetics and Crop Plant Research, Gatersleben (Germany)) E-mail:rajeev@ipk-gatersleben.de | Haehnel, U.(Institute of Plant Genetics and Crop Plant Research, Gatersleben (Germany)) | Thiel, T.(Institute of Plant Genetics and Crop Plant Research, Gatersleben (Germany)) | Stein, N.(Institute of Plant Genetics and Crop Plant Research, Gatersleben (Germany)) | Altschmied, L.(Institute of Plant Genetics and Crop Plant Research, Gatersleben (Germany)) | Langridge, P.(University of Adelaide (Australia). Centre for Plant Functional Genomics) | Graner, A.(Institute of Plant Genetics and Crop Plant Research, Gatersleben (Germany))
A set of 111,090 barley expressed sequence tags (ESTs, corresponding to 55.9 Mb of sequence) was employed for the identification of microsatellites with the help of a PERL5 script called MISA. A total of 9,564 microsatellites were identified in 8,766 ESTs (simple sequence repeat-ESTs, SSR-ESTs). Cluster analysis revealed the presence of 2,823 non-redundant SSR-ESTs. From these, 754 primer pairs were designed and analysed in a set of seven genotypes including the parents of three mapping populations. Finally, 185 microsatellite (EST-SSRs) loci were placed onto the barley genetic map. These markers show a uniform distribution on all the linkage groups ranging from 21 markers (on 7H) to 35 markers (3H). The polymorphism information content (PIC) for the developed markers ranged from 0.24 to 0.78 with an average of 0.48. A PCR-based strategy was established to screen the "Morex"-BAC library. BAC addresses were obtained for 127 mapped EST-SSRs.
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