Linked Life Data

19207216

Source:http://linkedlifedata.com/resource/pubmed/id/19207216

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4
pubmed:dateCreated
2009-4-21
pubmed:abstractText
Oilseed rape (Brassica napus) was selected as an example of a polyploid crop, and the Solexa sequencing system was used to generate approximately 20 million expressed sequence tags (ESTs) from each of two cultivars: Tapidor and Ningyou 7. A methodology and computational tools were developed to exploit, as a reference sequence, a publicly available set of approximately 94,000 Brassica species unigenes. Sequences transcribed in the leaves of juvenile plants were aligned to approximately 26 Mb of the reference sequences. The aligned sequences enabled the detection of 23,330-41,593 putative single nucleotide polymorphisms (SNPs) between the cultivars, depending on the read depth stringency applied. The majority of the detected polymorphisms (87.5-91.2%) were of a type indicative of transcription from homoeologous genes from the two parental genomes within oilseed rape, and are termed here 'hemi-SNPs'. The overall estimated polymorphism rate (approximately 0.047%-0.084%) is consistent with that previously observed between the cultivars analysed. To demonstrate the heritability of SNPs and to assess their suitability for applications such as linkage map construction and association genetics, approximately nine million ESTs were generated, using the Solexa system, from each of four lines of a doubled haploid mapping population derived from a cross between Tapidor and Ningyou 7. Computational tools were developed to score the alleles present in these lines for each of the potential SNPs identified between their parents. For a specimen region of the genome analysed in detail, segregation of alleles largely, although not entirely, followed the pattern expected for genomic markers.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
May
pubmed:issn
1467-7652
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
7
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
334-46
pubmed:meshHeading
pubmed:year
2009
pubmed:articleTitle
Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing.
pubmed:affiliation
John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't