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We have created a high-resolution linkage map of  Miscanthus sinensis , using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since  Miscanthus  has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the  M. sinensis  composite linkage map to the genomes of sorghum, maize, rice, and  Brachypodium distachyon  indicate that sorghum has the closest syntenic relationship to  Miscanthus  compared to other species. The comparative results revealed that each pair of the 19  M. sinensis  linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of  M. sinensis  and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of  M. sinensis . The results clearly demonstrate, for the first time, that the diploid  M. sinensis  is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of  Miscanthus  as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the  Miscanthus  genus.

High Resolution Genetic Mapping by Genome Sequencing Reveals Genome Duplication and Tetraploid Genetic Structure of the Diploid Miscanthus sinensis