'Rules' may govern genome evolution in young plant species

Researchers analyzed genes of a naturally occurring hybrid species, Tragopogon miscellus, and the study, recently published online in Current Biology, suggests genome evolution in hybrid plants may follow a set of "rules" that determine which parental genes are lost. The research may be used to create higher and more stable yields in other hybrid polyploid plants, including agricultural crops such as wheat, corn, coffee and apples.

"The repeatability of gene loss in populations of separate origin is a really exciting result," said co-author Pam Soltis, distinguished professor and curator of molecular systematics and evolutionary genetics at the Florida Museum of Natural History on the UF campus. "Scientists have often wondered if there are 'rules' that govern patterns of evolution, and data for Tragopogon polyploids suggest that such rules may actually operate at the genetic level."

Scientists analyzed about 70 of the hybrid plants commonly known as goatsbeard, a species in the daisy family that originated in the northwestern U.S. about 80 years ago. The new species formed naturally when two plants introduced from Europe mated to produce a hybrid offspring, and hybridization was accompanied by polyploidy, or whole genome duplication. Following a polyploidy event, the hybrid offspring contains twice the number of chromosomes, totaling 24.

Researchers compared the patterns of gene loss in the hybrid to patterns of gene loss in other species from the same family that experienced an ancient polyploidy event about 40 million years ago, and found similar results. The data support an evolutionary hypothesis that genes whose products interact closely with other gene products are more likely to be maintained in duplicate after polyploid formation, meaning some aspects of genome evolution are predictable and repeatable in independent lines.

"We were surprised at the speed at which patterns seemed to form in which genes show loss versus retention," said lead author Richard Buggs of Queen Mary University of London, who worked on the study as a postdoctoral researcher at the Florida Museum.

Soltis said one possible mechanism of gene loss may be linked with changes in chromosome structure, an occurrence documented in a study published Jan. 6 in the Proceedings of the National Academy of Sciences. By further researching the connection between specific gene losses and chromosomal changes, researchers hope to better understand how these patterns affect fertility and physical characteristics of hybrid plants.

"Hybridization and chromosome doubling have played a major role in the evolution of flowering plants, and Tragopogon miscellus gives us an amazing window into this process," said study co-author Doug Soltis, a distinguished professor in UF's biology department.

The polyploid's two parent species, Tragopogon dubius and Tragopogon pratensis, were introduced to the U.S. in the 1920s. Because their flowers only bloom for a few hours in the morning, Tragopogon plants are often referred to as "John-go-to-bed-at-noon." It looks like a daisy except for being yellow in color.

Researchers analyzed genes from five natural populations of T. miscellus, as well as polyploid plants re-created in UF greenhouses. The DNA was extracted from the leaf tissue.

"Although Tragopogon miscellus is perfectly positioned to allow examination of genome evolution after hybridization, it is not a traditional research model organism and virtually none of the tools and resources that allow these types of studies had been developed for it," said co-author Brad Barbazuk, a UF associate professor in biology and member of the UF Genetics Institute. "The availability of cost-effective, high-throughput genomics technologies has enabled us to examine this important phenomenon in this young species."

The two-year study was funded by UF and the National Science Foundation. Study co-authors include Srikar Chamala of the UF Genetics Institute, Wei Wu and Pat Schnable of Iowa State University and Jennifer Tate of Massey University in New Zealand.

"Polyploidy, the duplication of whole genomes, is a huge and really important process in plant genetics and plant evolution, and what the Soltises have is a beautiful system for studying these early stages of polyploid formation in nature," said Jeffrey Doyle, a plant biology professor at Cornell University. "If you know something about the rules by which genomes evolve, you may be able to predict what's going to happen when you try to genetically engineer something."