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Chloroplast DNA markers (cpSSRs, SNPs) for Miscanthus, Saccharum and related grasses (Panicoideae, Poaceae)

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Abstract

Miscanthus and Saccharum are closely related perennial C4 grasses. Miscanthus has recently attracted interest as a non-food crop for energy and fibre production. However, molecular genetic tools for the selection of new Miscanthus genotypes and study of its genetic resources are limited. We have identified six chloroplast (plastid) marker loci,containing both microsatellites (cpSSRs) and single nucleotide polymorphisms (SNPs) and developed primers to amplify and sequence these regions. The primers were designed using the complete chloroplast genome sequence of sugarcane and were tested on a collection of 164 Miscanthus genotypes and 14 related species of the subfamily Panicoideae. The cpSSR markers were highly polymorphic, with the number of alleles ranging from 10 to 16 per locus. Within the six cpSSR marker loci, the hybrid M. ×giganteus exhibits virtually no cpDNA variation compared with its putative parents M. sinensis and M. sacchariflorus. These SNP markers enable the differentiation of most Miscanthus species and detect infraspecific variation suitable for defining cytoplasmic genepools of Miscanthus for breeding purposes.

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Acknowledgements

The project is funded by the National Development Plan of Ireland through Teagasc core funding. MdC is financed under the Teagasc Walsh Fellowship Scheme. We are grateful to TCD Botanic Gardens Dublin, Svalöf Weibull/Sweden and the University of Hohenheim/Germany for sharing their Miscanthus resources for this study.

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Authors and Affiliations

  1. Teagasc Crops Research Centre, Oak Park, Carlow, Ireland

    Mariateresa de Cesare & Susanne Barth

  2. School of Natural Sciences, Trinity College Dublin, Dublin, D2, Ireland

    Mariateresa de Cesare & Trevor R. Hodkinson

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  1. Mariateresa de Cesare
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  2. Trevor R. Hodkinson
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  3. Susanne Barth
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Correspondence to Susanne Barth.

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de Cesare, M., Hodkinson, T.R. & Barth, S. Chloroplast DNA markers (cpSSRs, SNPs) for Miscanthus, Saccharum and related grasses (Panicoideae, Poaceae). Mol Breeding 26, 539–544 (2010). https://doi.org/10.1007/s11032-010-9451-z

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  • DOI: https://doi.org/10.1007/s11032-010-9451-z

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