Show simple item record

dc.contributor.authorNagy, Istvan*
dc.contributor.authorBarth, Susanne*
dc.contributor.authorMehenni-Ciz, Jeanne*
dc.contributor.authorAbberton, Michael T*
dc.contributor.authorMilbourne, Dan*
dc.date.accessioned2013-08-12T14:25:06Z
dc.date.available2013-08-12T14:25:06Z
dc.date.issued13/02/2013
dc.identifier.citationIstvan Nagy, et al. A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover. BMC Genomics, 2013, 14:100. DOI:10.1186/1471-2164-14-100en_GB
dc.identifier.issn1471-2164
dc.identifier.urihttp://hdl.handle.net/11019/420
dc.descriptionpeer-revieweden_GB
dc.description.abstractBackground: White clover (Trifolium repens L.) is an allotetraploid species possessing two highly collinear ancestral sub-genomes. The apparent existence of highly similar homeolog copies for the majority of genes in white clover is problematic for the development of genome-based resources in the species. This is especially true for the development of genetic markers based on single nucleotide polymorphisms (SNPs), since it is difficult to distinguish between homeolog-specific and allelic variants. Robust methods for categorising single nucleotide variants as allelic or homeolog-specific in large transcript datasets are required. We illustrate one potential approach in this study. Results: We used 454-pyrosequencing sequencing to generate ~760,000 transcript sequences from an 8th generation white clover inbred line. These were assembled and partially annotated to yield a reference transcript set comprising 71,545 sequences. We subsequently performed Illumina sequencing on three further white clover samples, generating 14 million transcript reads from a mixed sample comprising 24 divergent white clover genotypes, and 50 million reads on two further eighth generation white clover inbred lines. Mapping these reads to the reference transcript set allowed us to develop a significant SNP resource for white clover, and to partition the SNPs from the inbred lines into categories reflecting allelic or homeolog-specific variation. The potential for using haplotype reconstruction and progenitor genome comparison to assign haplotypes to specific ancestral sub-genomes of white clover is demonstrated for sequences corresponding to genes encoding dehydration responsive element binding protein and acyl-coA oxidase. Conclusions: In total, 208,854 independent SNPs in 31,715 reference sequences were discovered, approximately three quarters of which were categorised as representing allelic or homeolog-specific variation using two inbred lines. This represents a significant resource for white clover genomics and genetics studies. We discuss the potential to extend the analysis to identify a “core set” of ancestrally derived homeolog specific variants in white clover.en_GB
dc.description.sponsorshipDepartment of Agriculture Food & the Marine, Ireland - Research Stimulus Fund (RSF 07–566)en_GB
dc.language.isoenen_GB
dc.publisherBiomed Central
dc.relation.ispartofseriesBMC Genomics;vol 14
dc.subjectAllelic variants
dc.subjectAllotetraploid
dc.subjectHaplotype reconstruction
dc.subjectNext generation sequencing
dc.subjectSingle nucleotide polymorphisms
dc.subjectSub-genome
dc.subjectTranscript assembly
dc.subjectTrifolium
dc.subjectWhite clover
dc.titleA hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white cloveren_GB
dc.typeArticleen_GB
dc.identifier.doihttp://dx.doi.org/10.1186/1471-2164-14-100
dc.contributor.sponsorDepartment of Agriculture, Food and the Marine, Ireland
dc.contributor.sponsorGrantNumberRSF 07–566
refterms.dateFOA2018-01-12T07:57:23Z


Files in this item

Thumbnail
Name:
1471-2164-14-100.pdf
Size:
1.604Mb
Format:
PDF
Thumbnail
Name:
1471-2164-14-100-S1.CSV
Size:
10.70Mb
Format:
Microsoft Excel
Thumbnail
Name:
1471-2164-14-100-S3.CSV
Size:
4.367Mb
Format:
Microsoft Excel
Thumbnail
Name:
1471-2164-14-100-S4.PDF
Size:
78.11Kb
Format:
PDF
Thumbnail
Name:
1471-2164-14-100-S5.PDF
Size:
96.94Kb
Format:
PDF

This item appears in the following Collection(s)

Show simple item record