Genome biology of the paleotetraploid perennial biomass crop Miscanthus

Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. x giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses

Classification of ornamental accessions of Miscanthus with molecular techniques

The perennial C4 grass genus Miscanthus has a long history of use as valued landscaping and garden ornamentals. More recently, interest in domestic energy security and sustainable fuel sources have brought it to the forefront as a sustainable and productive bioenergy feedstock. In particular, the sterile inter-specific hybrid Miscanthus x giganteus, has proven to be particularly productive over a wide range of habitats and sustainable. But it lacks genetic variation, a serious limitation to wide scale production. New forms of M. x giganteus could be achieved by crosses of the parent species. Not only are the parents of the hybrid uncertain, but the degree of diversity in accessions of the parent species in the USA is unknown, as is the relationship to other putative Miscanthus spp. Identification at the species level depends predominantly on floral characteristics, which is a major limitation for plants which may not flower in some locations and which are supplied as vegetative propagules. DNA based methods should overcome these limitations This study tested the efficacy of three emergent DNA based methods for inter- and intra-specific separation. Simultaneously it also tested the proper categorization of accessions within species and the degree of diversity of commercially available Miscanthus accessions within the United States. 1) High Resolution Melting analysis was used to determine if accessions of Miscanthus could be distinguished at the species level. HRM was able to distinguish species and furthermore, it was found that material provided as M. x giganteus ‘Kurt Bluemel’ and M. sinensis ‘Hercules’ in fact corresponded to M. sacchariflorus. The method is low cost at scale and rapid. It could be particularly valuable for establishing the veracity of material supplied as a named accession. 2) Simple Sequence Repeats were used to look at both interspecific and intraspecific relationships of over 80 accessions of Miscanthus by using primers designed from sugarcane. That study showed that there was a clear separation of accessions at the species level and there was a low level of similarity between accessions even within the same species. This also showed that genetic variation in the ornamental accessions of M. sinensis commercially available in the USA, was high compared to material recently collected from known sites that were geographically widely separated. 3) A high throughput method of single nucleotide detection was applied to over 300 Miscanthus accessions that identified 803 SNP markers that allowed for individual fingerprints of each plant to be obtained. Overall, this method proved the most effective. It separated all accessions and provided clear evidence that at least three had been misclassified at the species level. It also confirmed the SSR study finding that there was wide diversity in the extant ornamental collections of M. sinensis. Overall, this study established that the emergent DNA based screening methods are highly effective in both inter-specific and intra-specific differentiation of Miscanthus an important pre-requisite to an effective breeding program

Genome biology of the paleotetraploid perennial biomass crop Miscanthus.

Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses