A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover

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A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover. / Nagy, Istvan; Barth, Susanne; Mehenni-Ciz, Jeanne; Abberton, Michael T; Milbourne, Dan.

I: B M C Genomics, Bind 14, 100, 2013.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

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@article{4c0c743ff68848a0bf01fce4ac77b4d3,
title = "A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover",
abstract = "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.",
keywords = "Alleles, Expressed Sequence Tags, Haplotypes, Homozygote, Inbreeding, Polymorphism, Single Nucleotide, RNA, Messenger, Sequence Analysis, RNA, Sequence Homology, Nucleic Acid, Tetraploidy, Trifolium",
author = "Istvan Nagy and Susanne Barth and Jeanne Mehenni-Ciz and Abberton, {Michael T} and Dan Milbourne",
year = "2013",
doi = "10.1186/1471-2164-14-100",
language = "English",
volume = "14",
journal = "B M C Genomics",
issn = "1471-2164",
publisher = "BioMed Central Ltd.",

}

RIS

TY - JOUR

T1 - A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover

AU - Nagy, Istvan

AU - Barth, Susanne

AU - Mehenni-Ciz, Jeanne

AU - Abberton, Michael T

AU - Milbourne, Dan

PY - 2013

Y1 - 2013

N2 - 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.

AB - 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.

KW - Alleles

KW - Expressed Sequence Tags

KW - Haplotypes

KW - Homozygote

KW - Inbreeding

KW - Polymorphism, Single Nucleotide

KW - RNA, Messenger

KW - Sequence Analysis, RNA

KW - Sequence Homology, Nucleic Acid

KW - Tetraploidy

KW - Trifolium

U2 - 10.1186/1471-2164-14-100

DO - 10.1186/1471-2164-14-100

M3 - Journal article

C2 - 23402685

VL - 14

JO - B M C Genomics

JF - B M C Genomics

SN - 1471-2164

M1 - 100

ER -