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

R.K. Varshney; I. Grosse; U. Hähnel; R. Siefken; M. Prasad; N. Stein; P. Langridge; L. Altschmied; A. Graner

doi:10.1007/s00122-006-0289-z

Back

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

Journal article

Peer reviewed

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

R.K. Varshney, I. Grosse, U. Hähnel, R. Siefken, M. Prasad, N. Stein, P. Langridge, L. Altschmied and A. Graner

Theoretical and Applied Genetics, Vol.113(2), pp.239-250

2006

DOI: https://doi.org/10.1007/s00122-006-0289-z

Files and links (1)

url

Link to Published Version *Subscription may be requiredView

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.

Details

Title: Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome
Authors/Creators: R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
I. Grosse (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
U. Hähnel (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
R. Siefken (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
M. Prasad (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
N. Stein (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
P. Langridge (Author/Creator) - The University of Adelaide
L. Altschmied (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
A. Graner (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
Publication Details: Theoretical and Applied Genetics, Vol.113(2), pp.239-250
Publisher: Springer Verlag
Identifiers: 991005546359107891
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

UN Sustainable Development Goals (SDGs)

This output has contributed to the advancement of the following goals:

Source: InCites

Metrics

37 Record Views

91 Times Cited - Web of Science

InCites Highlights

These are selected metrics from InCites Benchmarking & Analytics tool, related to this output

Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Agronomy; Genetics & Heredity; Horticulture; Plant Sciences
ESI research areas: Agricultural Sciences