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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  • Istvan Nagy
  • Susanne Barth, Crops, Environment and Land Use Programme, Teagasc, Irland
  • Jeanne Mehenni-Ciz, Crops, Environment and Land Use Programme, Teagasc, Irland
  • Michael T Abberton, Institute of Biological, Environmental & Rural Sciences, Aberystwyth University Penglais, Storbritannien
  • Dan Milbourne, Crops, Environment and Land Use Programme, Teagasc, Irland
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.
TidsskriftB M C Genomics
Antal sider19
StatusUdgivet - 2013

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