A Grass Model to Help Improve Giant Miscanthus

Miscanthus sequence offers insights into benefits of polyploidy and perenniality.

The Science

Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)

A reference genome sequence and genomic toolkit for the perennial grass Miscanthus sinensis has been published. Analysis of the genome sequence also provides insights into how the multiple chromosomes of Miscanthus arose by ancient hybridization (polyploidy) and insights into the dynamics of gene expression as it grows back vigorously year after year (perenniality).

The Impact

Among the long-term aims for bioenergy feedstock crops are increasing their yields and improving their abilities to adapt to extreme environments such as poor soils and drought. The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum. The M. sinensis genome analysis explains the hybrid origin of giant miscanthus (M. x giganteus), a high-yield candidate bioenergy feedstock known for its ability to grow on marginal lands and to tolerate stressors such as drought and temperatures.

Summary

CABBI investigators Daniel Rokhsar and Kankshita Swaminathan stand in front of Miscanthus at CABBI’s SoyFACE Facility at the University of Illinois. (Stephen Moose)

Images of giant miscanthus often appear in discussions of rapidly growing plants whose biomass can be renewably converted into energy or biofuels. Although a member of the grass family, as its name suggests giant miscanthus literally towers over most researchers due to its prodigious capability for growth. While many desirable features of biofuel grasses can be studied from simpler (and smaller) models, Miscanthus has a large and complex genome whose evolutionary history and perennial lifecycle makes it important to study directly.

The large and complex genome of M. sinensis was recently published in Nature Communications by an international, multi-institutional team. The work was a joint effort led by scientists at the Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), a Department of Energy (DOE) Bioenergy Research Center, along with researchers from the Energy Biosciences Institute, the DOE Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab), and collaborators across Europe and Asia. CABBI partners include the University of California, Berkeley and the HudsonAlpha Center for Biotechnology.

Most plants are diploids with two copies of each chromosome, one inherited from each parent. Some plants, known as polyploids, have more than two copies of each chromosome, and more complex patterns of inheritance. The additional genes provided by these chromosomes can contribute to novel traits. M. sinensis is a tetraploid, with four sets of chromosomes; the study showed that these sets descend from two now-extinct progenitors. Giant miscanthus is a triploid, the result of a highly productive cross between a diploid M. sinensis and a tetraploid M. sacchariflorus, another species of Miscanthus that was sequenced. Understanding the evolution of polyploidy, and how genomes respond to extra chromosome and gene copies, will help researchers improve Miscanthus breeding programs. The team also sequenced genomes of numerous wild Miscanthus lineages to better understand the genetic diversity of the grass, which could help in optimizing highly productive hybrids.

Like other perennials, Miscanthus is dormant during the winter and grows anew the following spring without requiring replanting. Miscanthus is especially efficient at this process thanks to a specialized kind of underground stem, the rhizome, that stores nutrients from one growing season to the next. By studying genes that are turned “on” or “off” at different times and in different parts of the plant, the team identified genes that may regulate nutrient transport to and from the rhizome and contribute to the grass’ efficient perennial life cycle. For example, in the fall the plants store nitrogen in its rhizomes – in the form of the nitrogen-rich amino acid asparagine – and remobilize this nitrogen in the spring so that the stems and leaves can grow without added fertilizer. Researchers at CABBI and elsewhere are following up on these discoveries to develop new varieties of Miscanthus as a source of renewable bioenergy.

Contacts:

BER Contact
Ramana Madupu, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
Ramana.Madupu@science.doe.gov

JGI Contact
Dan Rokhsar
Computational Genomics Lead, West Coast Plant Genomics
Joint Genome Institute
DSRokhsar@lbl.gov

Funding:

This work was supported by the Energy Biosciences Institute and the DOE Center for Advanced Bioenergy and Bioproducts Innovation, which is supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Number DE-SC0018420. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The collection of the M. sinensis and M. sacchariflorus accessions and RAD-seq work was supported by EU FP7 KBBE.2011.3.1-02, grant number 289461 (GrassMargins) and the DOE Office of Science, Office of Biological and Environmental Research (BER), grant nos. DE-SC0006634 and DE- SC0012379. The generation of the tetraploid M. sacchariflorus whole genome sequence data was funded by the BBSRC Core Strategic Programme in Resilient Crops: Miscanthus, award number BBS/E/W/0012843A. DSR is grateful for support from the Chan-Zuckerberg BioHub and the Marthella Foskett Brown family.

Publication:

Mitros T et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nature Communications. 2020 Oct 28. doi: 10.1038/s41467-020-18923-6