Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome

Varshney, R K and Grosse, I and Hahnel, U and Siefken, R and Prasad, M and Stein, N and Langridge, P and Altschmied, L and Graner, A (2006) Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome. TAG Theoretical and Applied Genetics, 113 (2). pp. 239-250. ISSN 1432-2242

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Abstract

A set of 111,090 barley expressed sequence tags (ESTs) was searched for the presence of microsatellite motifs [simple sequence repeat (SSRs)] and yielded 2,823 non-redundant SSR-containing ESTs (SSR–ESTs). From this, a set of 754 primer pairs was designed of which 525 primer pairs yielded an amplicon and as a result, 185 EST-derived microsatellite loci (EST–SSRs) were placed onto a genetic map of barley. The markers show a uniform distribution along all seven linkage groups ranging from 21 (7H) to 35 (3H) markers. Polymorphism information content values ranged from of 0.24 to 0.78 (average 0.48). To further investigate the physical distribution of the EST–SSRs in the barley genome, a bacterial artificial chromosomes (BAC) library was screened. Out of 129 markers tested, BAC addresses were obtained for 127 EST– SSR markers. Twenty-seven BACs, forming eight contigs, were hit by two or three EST–SSRs each. This unexpectedly high incidence of EST–SSRs physically linked at the sub-megabase level provides additional evidence of an uneven distribution of genes and the segmentation of the barley genome in gene-rich and gene-poor regions.

Item Type:	Article
Divisions:	UNSPECIFIED
CRP:	UNSPECIFIED
Subjects:	Others > Genetics and Genomics
Depositing User:	Library ICRISAT
Date Deposited:	21 Oct 2011 08:31
Last Modified:	21 Oct 2011 08:42
URI:	http://oar.icrisat.org/id/eprint/3009
Official URL:	http://dx.doi.org/10.1007/s00122-006-0289-z
Projects:	UNSPECIFIED
Funders:	Grain Research and Development Corporation, Federal Ministry of Education and Research , BMBF Bioinformatics Centre, Gatersleben
Acknowledgement:	We are grateful to Timothy J. Close (University of California, Riverside, USA) for his valuable suggestions on the physical mapping data. We thank Uwe Scholz and Christian Künne (IPK) for performing cluster analysis of SSR-ESTs of IPK and non-IPK ESTs, and Paul Krapivsky (Boston University, Boston, USA), Stefan Posch (Martin Luther University Halle-Wittenberg, Halle, Germany) and Roland Schnee (IPK) for helpful discussions. We also thank Christine Künzel, Anita Czech, Brigitte Schmidt and Ingelore Dommers for technical assistance. The present work was funded by grants from the Grain Research and Development Corporation, Australia (GRDC, UA476), the Federal Ministry of Education and Research (BMBF, GABI-PLANT 312271A,B,C) and BMBF Bioinformatics Centre, Gatersleben/Halle 0312706A).
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