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

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Relation http://oar.icrisat.org/3009/
http://dx.doi.org/10.1007/s00122-006-0289-z
 
Title Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome
 
Creator Varshney, R K
Grosse, I
Hahnel, U
Siefken, R
Prasad, M
Stein, N
Langridge, P
Altschmied, L
Graner, A
 
Subject Genetics and Genomics
 
Description 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.
 
Publisher Springer Verlag
 
Date 2006
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
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Identifier http://oar.icrisat.org/3009/1/Genetic_mapping_and_BAC_assignment_of_EST-derived_SSR_markers_shows_non-uniform_distribution_of_genes_in_the_barley_genome.pdf
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