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Open Access Research article

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

Istvan Nagy12, Susanne Barth1, Jeanne Mehenni-Ciz1, Michael T Abberton34 and Dan Milbourne1*

Author affiliations

1 Crops, Environment and Land Use Programme, Teagasc, Oak Park, Carlow, Ireland

2 Current address: Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, Slagelse, DK-4200, Denmark

3 Institute of Biological, Environmental & Rural Sciences, Aberystwyth University Penglais, Penglais, Aberystwyth, Ceredigion, SY23 3DA, UK

4 Current address: International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria

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Citation and License

BMC Genomics 2013, 14:100  doi:10.1186/1471-2164-14-100

Published: 13 February 2013

Abstract

Background

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.

Keywords:
Allelic variants; Allotetraploid; Haplotype reconstruction; Next generation sequencing; Single nucleotide polymorphisms; Sub-genome; Transcript assembly; Trifolium; White clover