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dc.contributor.author
Studer, Bruno
dc.contributor.author
Byrne, Stephen
dc.contributor.author
Nielsen, Rasmus O.
dc.contributor.author
Panitz, Frank
dc.contributor.author
Bendixen, Christian
dc.contributor.author
Islam, Shofiqul Md.
dc.contributor.author
Pfeifer, Matthias
dc.contributor.author
Lübberstedt, Thomas
dc.contributor.author
Asp, Torben
dc.date.accessioned
2018-10-09T12:34:29Z
dc.date.available
2017-06-10T14:39:46Z
dc.date.available
2018-10-09T12:34:29Z
dc.date.issued
2012-04
dc.identifier.other
10.1186/1471-2164-13-140
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/64454
dc.identifier.doi
10.3929/ethz-b-000064454
dc.description.abstract
Background Single nucleotide polymorphisms (SNPs) are increasingly becoming the DNA marker system of choice due to their prevalence in the genome and their ability to be used in highly multiplexed genotyping assays. Although needed in high numbers for genome-wide marker profiles and genomics-assisted breeding, a surprisingly low number of validated SNPs are currently available for perennial ryegrass. Results A perennial ryegrass unigene set representing 9,399 genes was used as a reference for the assembly of 802,156 high quality reads generated by 454 transcriptome sequencing and for in silico SNP discovery. Out of more than 15,433 SNPs in 1,778 unigenes fulfilling highly stringent assembly and detection parameters, a total of 768 SNP markers were selected for GoldenGate genotyping in 184 individuals of the perennial ryegrass mapping population VrnA, a population being previously evaluated for important agronomic traits. A total of 592 (77%) of the SNPs tested were successfully called with a cluster separation above 0.9. Of these, 509 (86%) genic SNP markers segregated in the VrnA mapping population, out of which 495 were assigned to map positions. The genetic linkage map presented here comprises a total of 838 DNA markers (767 gene-derived markers) and spans 750 centi Mogan (cM) with an average marker interval distance of less than 0.9 cM. Moreover, it locates 732 expressed genes involved in a broad range of molecular functions of different biological processes in the perennial ryegrass genome. Conclusions Here, we present an efficient approach of using next generation sequencing (NGS) data for SNP discovery, and the successful design of a 768-plex Illumina GoldenGate genotyping assay in a complex genome. The ryegrass SNPs along with the corresponding transcribed sequences represent a milestone in the establishment of genetic and genomics resources available for this species and constitute a further step towards molecular breeding strategies. Moreover, the high density genetic linkage map predominantly based on gene-associated DNA markers provides an important tool for the assignment of candidate genes to quantitative trait loci (QTL), functional genomics and the integration of genetic and physical maps in perennial ryegrass, one of the most important temperate grassland species.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
BioMed Central
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/2.0/
dc.subject
Illumina GoldenGate genotyping
en_US
dc.subject
In silico SNP discovery
en_US
dc.subject
Next generation sequencing (NGS)
en_US
dc.subject
Perennial ryegrass (Lolium perenne L.)
en_US
dc.subject
Single nucleotide polymorphism (SNP)
en_US
dc.subject
Transcriptome sequencing
en_US
dc.title
A transciptome map of perennial ryegrass (Lolium perenne L.)
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 2.0 Generic
ethz.journal.title
BMC Genomics
ethz.journal.volume
13
en_US
ethz.pages.start
140
en_US
ethz.size
13 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.nebis
004256340
ethz.publication.place
London
en_US
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02350 - Dep. Umweltsystemwissenschaften / Dep. of Environmental Systems Science::02703 - Institut für Agrarwissenschaften / Institute of Agricultural Sciences::03969 - Studer, Bruno / Studer, Bruno
en_US
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02350 - Dep. Umweltsystemwissenschaften / Dep. of Environmental Systems Science::02703 - Institut für Agrarwissenschaften / Institute of Agricultural Sciences::03969 - Studer, Bruno / Studer, Bruno
ethz.date.deposited
2017-06-10T14:41:18Z
ethz.source
ECIT
ethz.identifier.importid
imp5936506922fc698492
ethz.ecitpid
pub:102434
ethz.eth
no
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2017-07-26T18:56:00Z
ethz.rosetta.lastUpdated
2018-10-09T12:34:32Z
ethz.rosetta.exportRequired
true
ethz.rosetta.versionExported
true
ethz.COinS
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