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Maps of miscanthus genome offer insight into grass evolution

Stephen Moose
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L. Brian Stauffer

University of Illinois crop sciences professor and Energy Biosciences Institute program leader Stephen Moose and his colleagues mapped the Miscanthus sinensis genome, a first step toward a full genome sequence.

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5/15/2012 | Diana Yates, Life Sciences Editor | 217-333-5802; diya@illinois.edu

CHAMPAIGN, lll. — Miscanthus grasses are used in gardens, burned for heat and energy, and converted into liquid fuels. They also belong to a prominent grass family that includes corn, sorghum and sugarcane. Two new, independently produced chromosome maps of Miscanthus sinensis (an ornamental that likely is a parent of Miscanthus giganteus, a biofuels crop) are a first step toward sequencing the M. sinensis genome. The studies reveal how a new plant species with distinctive traits can arise as a result of chromosome duplications and fusions.

The two studies were published this year: The first, led by the energy crop company Ceres, appeared in the journal PLoS ONE; the second, from a team led by researchers at the University of Illinois, is in the journal BMC Genomics. The data, materials, methods and genetic markers used in the latter study are available to the public for further research.

Before this work, scientists knew that M. sinensis had a base set of 19 chromosomes and was closely related to sorghum, which has a base set of 10. (Humans have a base set of 23). But without a map and sequence of the Miscanthus genome, researchers who hope to maximize yields or discover which genes give Miscanthus its desirable traits are working in the dark, said Stephen Moose, a University of Illinois crop sciences professor and Energy Biosciences Institute program leader, who led the BMC Genomics study.

Moose and his colleagues used information gleaned from the sugarcane genome to develop hundreds of genetic markers to target specific regions of the M. sinensis genome. Then they crossed two M. sinensis plants and grew 221 offspring in a laboratory. By comparing how the genetic markers from each parent were sorted in the offspring, the team reconstructed 19 “linkage groups” corresponding to the 19 chromosomes of Miscanthus. This rough map of the chromosomes is a first step toward a Miscanthus genome, Moose said.

The researchers also used the sorghum genome as a comparative reference. Their analysis indicated that M. sinensis arose as a result of a duplication of the sorghum genome, with a later fusion of some chromosome parts.

“Some plants will duplicate their genomes and then there’s some sorting that goes on,” Moose said. “Sometimes whole chromosomes are lost and sometimes there are fusions.” Once there are two copies of each chromosome in a base set, each will proceed along its own evolutionary trajectory. “Often what will happen is even though there are two (versions of the same chromosome), one of them will start to deteriorate over time,” Moose said. “Some positions and some genes will win out over the others.”

Genome duplications may undermine the viability of a plant or give it an advantage. One immediate advantage of doubling, tripling or otherwise duplicating the genome is that it increases the size of the plant, or of certain plant parts, Moose said.

“Humans have selected for these traits,” he said. “Strawberries, for example, are octoploids; they have eight chromosome sets. Sugarcane has eight sets, and it’s bigger (than its wild cousins).”

Moose and his colleagues were surprised to find a high degree of similarity between the Miscanthus and sorghum genomes.

“I would say that for about 90 percent of the Miscanthus markers, their chromosomal order corresponds to what is known for sorghum,” he said.

The new findings and the eventual publication of the Miscanthus genome will help scientists understand the evolution of grasses and the genetic mechanisms that give them their desirable traits, Moose said.

The BMC Genomics team also included researchers from the University of California, Berkeley; the Polish Academy of Sciences; the department of plant biology at the U. of I.; the Department of Energy Joint Genome Institute; and the National Institute of Horticultural and Herbal Science, in South Korea. Moose is an affiliate of the Institute for Genomic Biology at Illinois.

The Energy Biosciences Institute supported this research.

Editor's note: To contact Stephen Moose, call 217-244-6308; email smoose@illinois.edu. The paper, “A Framework Genetic Map for Miscanthus sinensis From RNAseq-based Markers Shows Recent Tetraploidy,” is available online and from the U. of I. News Bureau.
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