SHORT COMMUNICATION Chloroplast DNA markers (cpSSRs, SNPs) for Miscanthus, Saccharum and related grasses (Panicoideae, Poaceae) Mariateresa de Cesare • Trevor R. Hodkinson • Susanne Barth Received: 7 January 2010 / Accepted: 19 April 2010 Ó Springer Science+Business Media B.V. 2010 Abstract Miscanthus and Saccharum are closely related perennial C 4 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,con- taining 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. 9giganteus 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 cytoplas- mic genepools of Miscanthus for breeding purposes. Keywords Chloroplast microsatellites Á cpSSR Á Miscanthus Á Saccharum The genus Miscanthus comprises 11–12 species of perennial C 4 plants. The uncertainty regarding the number of species included in the genus is due to the lack of taxonomic consensus for a number of taxa, such as M. sinensis ssp. condensatus, which is sometimes listed as M. condensatus (Clifton-Brown et al. 2008), and a few other species that are closely allied with other genera based on molecular phylog- enetics analysis (Hodkinson et al. 2002a). The centre of diversity of Miscanthus is Southeast Asia, where it is distributed under a wide range of climatic condi- tions, from temperate to tropical areas (Greef and Deuter 1993). It is closely related to sugarcane (Saccharum officinarum) but differs from the latter in basic chromosome number (19 vs. 10, respec- tively). In 1935, the botanist Aksel Olsen introduced the allotriploid hybrid M. 9giganteus (Hodkinson and Renvoize 2001) native to Japan into Denmark. This species has attracted the interest of researchers as a potential source of renewable energy due to its ability to produce a high biomass yield under different climatic conditions (Venendaal et al. 1997) and, consequently, field trials of the sterile clone M. 9giganteus have been conducted throughout Europe during the past few decades (Lewandowski et al. 2000; Clifton-Brown et al. 2008). The allotrip- loid nature of M. 9giganteus (Hodkinson et al. 2002a) M. de Cesare Á S. Barth (&) Teagasc Crops Research Centre, Oak Park, Carlow, Ireland e-mail: susanne.barth@teagasc.ie M. de Cesare Á T. R. Hodkinson School of Natural Sciences, Trinity College Dublin, Dublin, D2, Ireland 123 Mol Breeding DOI 10.1007/s11032-010-9451-z