Cells, Genes & Molecules Growth & Development

A step to the biofuels of the future?

Compiling a genome of an Asian grass is already producing useful results for breeding.

Two new publications could aid the development of biofuels. A team of scientists has recently published the genome of Miscanthus sinensis, a plant commonly found in gardens as an ornamental grass. The research has already yielded some results in finding a part of the genome associated with flowering time in the grass. Being able to synchronise flowering times will aid scientists in crossing different Miscanthus plants, to breed for the most productive traits.

Miscanthus. Image: Canva.

Which plants get sequenced?

Despite being a popular ornamental grass, gathering the material wasn’t as simple as visiting the local garden centre for supplies. “This paper made use of a M. sinensis haploid genotype which was characterized by the University of Illinois and created by the Institute of Plant Genetics, Polish Academy of Science,” said Daniel Rokhsar, who co-directed the genome publication. “The plant was small and hard to keep alive so not optimal for biomass crop production but because of its reduced genome complexity made the genome assembly easier – that said even the basic genome is the result of a relatively recent whole genome duplication.”

The team switched to exploring M. sinensis after beginning a project with a hybrid species of Miscanthus, said co-director, Kankshita Swaminathan. “We initially started with exploring the genome of Miscanthus × giganteus. While we knew this was a triploid (3 genomes instead of the typical 2 that most organisms have), we didn’t know about the whole genome duplication. These initial studies told us that this was a complex genome that was hard to assemble. Using independent mapping populations of diploid M. sinensis lines, a team at IBERS as well as the University of Illinois generated genetic maps of M. sinensis and discovered that Miscanthus harbored a whole genome duplication which further increased the complexity of this large genome. This data started the search for a doubled haploid Miscanthus and added researchers from the Polish Academy of Science to the collaboration.”

Iain Donnison, who supervised the flowering paper had a different source for his material. “The flowering time mapping family cross was made in the Miscanthus breeding programme involving John Clifton-Brown and Charlotte Hayes. Dr. Karen Petersen supplied the female clone, selected in 1988 from temperate Japan (Honshu Island) by Danish plant collector Dr Poul Erik Brander. It was part of the European Miscanthus Improvement (EMI) programme (1997–2000). Dr. Oene Dolstra supplied the male genotype from the BIOMIS population as part a Department for Environment Food and Rural Affairs (Defra) funded United Kingdom–Netherlands collaborative project.  This family is an outcrossing full-sibling F1 mapping population between female EMI11 (Danish accession number MS-88-110) and male H0023.”

“In addition, IBERS has collected new accessions of Miscanthus species and genotypes from the wild in Taiwan, Japan, China, South Korea (under the UN protocols Convention of Biological Diversity, and Access and Benefit Sharing).”

How do so many people get involved?

The papers are the result of co-operation of people working in multiple institutes, a process that began organically. “Most of these groups started working on Miscanthus independently,” said Kankshita Swaminathan. “Miscanthus is native the Asia subcontinent and to really understand Miscanthus diversity and collect germplasm for breeding we needed to collect representative plants from the entire range. This led to the many international collaborations you see here.”

The researchers came together at conferences, said Daniel Rokhsar. “Kankshita and Kerrie Farar run an annual workshop at the Plant & Animal Genome meeting in San Diego that brings many members of this community together. The conference has provided an annual opportunity for many involved in the project and paper to catch up at intervals. Kankshita led the sequencing project and the manuscript, including coordinating with all authors.”

For the flowering paper, the collaboration came about to due to BBSRC funding for a UK-US collaboration awarded to Iain Donnison with Malay Saha at the Samuel Roberts Noble Foundation in Oklahoma. “IBERS scientists started working with US biotechnology company Ceres, where Richard Flavell was Chief Scientific Officer. IBERS had also received BBSRC funding into flowering time in Miscanthus, and Ceres were interested in identifying molecular markers for this trait. Ceres were also already working with switchgrass researchers at the Noble Foundation, and the cross-species collaboration evolved when we realized we had similar aspirations and approaches in breeding for bioenergy. IBERS visited Ceres and Noble on several occasions and found the interactions beneficial scientifically, and fun.” said Iain Donnison

“When researchers have a common and complex interest its not hard for them to come together,” added Kankshita Swaminathan. “A few emails, calls, and the exchange of ideas at scientific conferences is often all it takes to establish an interest in working together towards a common goal. If there are no other conflicts a collaboration forms naturally.”

New Opportunities

“This manuscript opens up opportunities to understand the biology of this highly successful perennial grass. It provides breeders and geneticists to understand genes behind traits and use markers to bring traits of interest together,” said Kankshita Swaminathan.

“It’s also great to have the new reference genome as this will be used for further comparative genomics, and also genetic & QTL mapping to locate traits of interest to regions of the genome, transcriptome analyses to understand how Miscanthus genes are regulated in different parts of the plant and how they respond under various conditions, and for GxE studies. This can accelerate future plant breeding of Miscanthus and both IBERS and Illinois groups are seeking to do this through genomic prediction methods. Most importantly this has real potential to tackle climate change in the near future through approaches such as bioenergy with carbon capture and storage (BECCS) to create negative (carbon) emissions and therefore allow economies to decarbonize and meet net zero targets.”

The publication of a study of flowering time in Miscanthus shows that the genome already has value for researchers. “Flowering time is such a key trait and exciting to study, especially when so little is known about it in a relatively recently studied species,” said Elaine Jensen, one of the first authors of the flowering study. “The Miscanthus genus is incredibly diverse.” 

“We have collected accessions from a latitudinal range extending from 18oN in Hainan, China, to 45oN in Preide, China. We know from other species that flowering time is a complex trait and that latitude of origin is likely to have some bearing on flowering time (where northerly latitude derived accessions will flower earlier), and we have found that M. sinensis genotypes demonstrate a complex geographical relationship reflecting climate variation. The only way to make crosses is to synchronize flowering, which is why we’ve invested into determining what factors impact its timing. However, once we’ve made the crosses, we want a means of screening progeny to determine whether they will have the desired late-flowering characteristic to enable maximum use of the growing season: optimal flowering maximizes yield and quality of the biomass and ensures the sustainability of this perennial crop.”

Another pressure on farm land?

But does the promise of a more efficient biofuel crop mean that there will be more demand on farm land, leading to increased pressure on food supply? Not necessarily, says Iain Donnison.  “Bioenergy research is often pitched as food versus fuel, either directly or via land use change. Our aim is to utilise dedicated crops that grow on (marginal) land less suited to food production. Perennial crops such as Miscanthus are more sustainable than annuals as they don’t require such an intensive annual cycle of ploughing, herbicide, pesticide and fertilizer applications.” 

“The energy ratios of energy in to energy out can be extremely high, eg x30 or even more. Miscanthus is unique in having efficient C4 photosynthesis that functions at lower temperatures, which is why the yields are so impressive, even in temperate climates. Our options for carbon-based renewable fuels are very limited, energy crops have a distinctive role to play in the energy system. Most importantly to meet ambitious climate change targets such as agreed in the Paris 2015 agreement in COP21, we need GHG removal technologies such as BECCS that can create the negative emissions needed for industrial economies to go net zero. In other words, these negative emissions are needed to compensate for the hard to fully decarbonize sectors such as aviation, heavy industry and livestock agriculture (eg red meat and dairy), and also to go even further and help remove the historic emissions from the burning of fossil fuels. In addition, to helping to tackle climate change these new green technologies can contribute to a post-Covid recovery and create jobs, as described in the Government’s announcement of a Green Industrial revolution this week.”

“However hard we decarbonise the rest of the sectors we need these negative emissions where carbon is fixed by fast growing crops through photosynthesis and the carbon either manufactured into long lived products or combusted in a power station and the CO2 captured, compressed and then pumped into underground stores. Further alternatives being the use of the CO2 in greenhouses for horticulture and again fixation by plants, or use industrially as part of the circular economy. Such discussions including on the setting of targets will be continuing at COP26 in Glasgow next year.”

A growing field

Anyone wanting to get into the research should be able to find a space for themselves. “We have a very diverse team with people with expertise in molecular biology, botany, genetics, mathematics, computational analysis and programming, statistics and quantitative analyses etc. What is important is to love your what you do and develop expertise in it. If there is a gap in your expertise to explore a specific topic (and with today’s interdisciplinary science there always will be), you find a good collaborator who can help,” said Kankshita Swaminathan

““Research teams today are diverse and interdisciplinary. The important thing, as well as developing your own areas of interest, is to be able to communicate with diverse researchers and users at different parts of the commercial pipeline to contribute to research beyond your own area of expertise,” said Iain Donnison.

“We believe this so passionately that we have even set up a degree programme where biologists each year will also study with students from other disciplines including business, economics, international politics, and English and creative writing.”

As climate change will be a long-term problem, this is likely to remain a source of research for many years to come.

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