Single nucleotide polymorphism discovery in barley using autoSNPdb

Duran, C, Appleby, N, Vardy, M, Imelfort, M, Edwards, D and Batley, J (2009) Single nucleotide polymorphism discovery in barley using autoSNPdb. Plant Biotechnology Journal, 7 4: 326-333. doi:10.1111/j.1467-7652.2009.00407.x

Author Duran, C
Appleby, N
Vardy, M
Imelfort, M
Edwards, D
Batley, J
Title Single nucleotide polymorphism discovery in barley using autoSNPdb
Journal name Plant Biotechnology Journal   Check publisher's open access policy
ISSN 1467-7644
Publication date 2009-05
Year available 2009
Sub-type Article (original research)
DOI 10.1111/j.1467-7652.2009.00407.x
Volume 7
Issue 4
Start page 326
End page 333
Total pages 8
Editor Keith J. Edwards
Place of publication United Kingdom
Publisher Wiley-blackwell Publishing
Collection year 2010
Language eng
Subject C1
820501 Barley
060102 Bioinformatics
Abstract Molecular markers are used to provide the link between genotype and phenotype, for the production of molecular genetic maps and to assess genetic diversity within and between related species. Single nucleotide polymorphisms (SNPs) are the most abundant molecular genetic marker. SNPs can be identified in silico, but care must be taken to ensure that the identified SNPs reflect true genetic variation and are not a result of errors associated with DNA sequencing. The SNP detection method autoSNP has been developed to identify SNPs from sequence data for any species. Confidence in the predicted SNPs is based on sequence redundancy, and haplotype co-segregation scores are calculated for a further independent measure of confidence. We have extended the autoSNP method to produce autoSNPdb, which integrates SNP and gene annotation information with a graphical viewer. We have applied this software to public barley expressed sequences, and the resulting database is available over the Internet. SNPs can be viewed and searched by sequence, functional annotation or predicted synteny with a reference genome, in this case rice. The correlation between SNPs and barley cultivar, expressed tissue type and development stage has been collated for ease of exploration. An average of one SNP per 240 bp was identified, with SNPs more prevalent in the 5' regions and simple sequence repeat (SSR) flanking sequences. Overall, autoSNPdb can provide a wealth of genetic polymorphism information for any species for which sequence data are available.
Keyword autoSNPdb
expressed sequence tag (EST)
genetic variation
in silico
single nucleotide polymorphism (SNP)
Q-Index Code C1
Q-Index Status Confirmed Code

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Created: Thu, 03 Sep 2009, 08:17:29 EST by Mr Andrew Martlew on behalf of School of Land, Crop and Food Sciences