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Study – 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.

In this study is reported 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.

In addition to its historical roles in paper production and as ornamentals, varieties of the wild grass Miscanthus can produce high yields of harvestable vegetative biomass while maintaining and potentially increasing soil carbon. These features, enabled by C4 photosynthesis, perenniality, and related high efficiencies of light, nutrient, and water use, make Miscanthus and its close relatives (including sugarcanes and energy canes) promising candidates for economically feasible and sustainable bioenergy crops. Continued genetic improvement of bioenergy feedstocks is needed to enhance productivity and ensure that these crops remain robust in the face of ongoing biotic and abiotic stresses. This is particularly true for perennial grasses, where the advantages in economic and environmental sustainability relative to annuals depend on the longevity of the crop once established. Although perennial crops have tremendous potential for maximizing agricultural yields and minimizing environmental impacts, our knowledge of their biology and ability to manipulate their genetics lags well behind that in annual crops5.

A key limitation to the genetic improvement of perennial bioenergy grasses is the complexity of their genomes, which hinders the application of modern breeding approaches. Miscanthus sinensis is a genetic diploid (2n = 38) with a genome size of 1C = 2.4–2.6 Gb; the related M. sacchariflorus occurs in both diploid (2n = 38) and tetraploid (2n = 76) forms. The n = 19 monoploid chromosome set of Miscanthus arose by ancient doubling of a sorghum-like n = 10 ancestor, with a single chromosomal fusion. Interspecific hybrids of Miscanthus form readily, even between individuals of different ploidy. Indeed, the predominant commercially grown miscanthus bioenergy variety is the high-yielding, sterile, asexually propagated triploid hybrid M. × giganteus “Illinois” (3n = 57). It is a clone of the taxonomic-type specimen, holotypus 1993–1780 Kew. Polyploidy is also common within the Saccharum complex, a group of closely related and highly productive perennial C4 grass species in the subtribe Saccharinae that includes sugarcanes (Saccharum spp.) and miscanthus. Intergeneric hybrid “miscanes” have been made by crossing miscanthus with hybrid sugarcanes, suggesting that natural genetic variation in these two genera could be combined in order to blend desirable traits (e.g., cold tolerance and disease resistance).

Here we establish miscanthus as a genomic model for perenniality and polyploidy, and develop a foundation for genomic variation that will enable the future improvement of perennial biomass crops. We describe a draft chromosome-scale genome sequence for M. sinensis, prove that miscanthus is a paleo-allotetraploid by analyzing the distribution of transposable elements across its genome, and establish the timing of key evolutionary events. By mRNA sequencing, we identify genes preferentially expressed in rhizomes, stems, and leaves, and explore the unique transcriptional dynamics of nutrient mobilization in this rhizomatous perennial grass.

Unlike most perennial Andropogoneae, which are restricted to tropical or subtropical regions, the Miscanthus genus comprises species that naturally range from tropical to subarctic regions. Genomic analysis of 18 miscanthus accessions sequenced for this study, in addition to reduced representation genotyping of over 2000 accessions collected in the wild from east Asia, reveals extensive population structure and interspecific introgression, which further contributes to the genomic diversity of the genus Miscanthus.


You can find the study here.