English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  Large-scale identification and analysis of genome-wide single- nucleotide polymorphisms for mapping in Arabidopsis thaliana

Schmid, K. J., Rosleff Sorensen, T., Stracke, R., Torjek, O., Altmann, T., Mitchell-Olds, T., et al. (2003). Large-scale identification and analysis of genome-wide single- nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Research, 13(6), 1250-1257.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0012-3CC2-B Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0012-3CC3-9
Genre: Journal Article

Files

show Files

Locators

show

Creators

show
hide
 Creators:
Schmid, K. J., Author
Rosleff Sorensen, T.1, Author              
Stracke, R.1, Author              
Torjek, O., Author
Altmann, T., Author
Mitchell-Olds, T., Author
Weisshaar, B.1, 2, Author              
Affiliations:
1ADIS, MPI for Plant Breeding Research, Max Planck Society, ou_1113564              
2Dept. of Biochemistry (Klaus Hahlbrock), MPI for Plant Breeding Research, Max Planck Society, ou_1113566              

Content

show
hide
Free keywords: -
 Abstract: Genetic markers such as single nucleotide polymorphisms (SNPs) are essential tools for positional cloning, association, or quantitative trait focus mapping and the determination of genetic relationships between individuals. We identified and characterized a genome-wide set of SNP markers by generating 10,706 expressed sequence tags (ESTs) from cDNA libraries derived from 6 different accessions, and by analysis of 606 sequence tagged sites (STS) from up to 12 accessions of the model flowering plant Arabidopsis thaliana. The cDNA libraries for EST sequencing were made from individuals that were stressed by various means to enrich for transcripts from genes expressed under such conditions. SNPs discovered in these sequences may be useful markers for mapping genes involved in interactions with the biotic and abiotic environment. The STS loci are distributed randomly over the genome. By comparison with the Col-O genome sequence, we identified a total of 8051 SNPs and 637 insertion/deletion polymorphisms (InDel). Analysis of STS-derived SNPs shows that most SNPs are rare, but that it is possible to identify intermediate frequency framework markers that can be used for genetic mapping in many different combinations of accessions. A substantial proportion of SNPs located in ORFs caused a change of the encoded amino acid. A comparison of the density of our SNP markers among accessions in both the EST and STS datasets, revealed that Cvi-O is the most divergent accession from Col-O among the 12 accessions studied. All of these markers are freely available via the internet.

Details

show
hide
Language(s): eng - English
 Dates: 2003-06
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: eDoc: 42414
ISI: 000183346500021
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: Genome Research
  Alternative Title : Genome Res.
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: - Volume / Issue: 13 (6) Sequence Number: - Start / End Page: 1250 - 1257 Identifier: ISSN: 1088-9051