|Rapid Genome Evolution Observed In Polyploid Plants|
|SciMed - Genetics & Genome|
|TS-Si News Service|
|Sunday, 22 January 2012 15:00|
Gainesville, FL, USA. A hybrid plant species may experience rapid genome evolution in predictable patterns, suggesting that evolution in hybrid plants may follow a set of rules that determine which parental genes are lost.
The repeatability of gene loss in populations of separate origin suggests that evolutionary patterns operate at the genetic level, with parental gene loss possibly linked to changes in chromosome structure.
Researchers analyzed the genes of Tragopogon miscellus, a naturally occurring hybrid species. The results published in the journal Current Biology suggest 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.
Tragopogon dubius, a parent of the hybrid species T. miscellus.
Tragopogon pratensis, a parent of the hybrid species T. miscellus.The analysis covered 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 plant's two parent species, Tragopogon dubius and Tragopogon pratensis, were introduced from Europe to the United States 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.
Also, hybridization was accompanied by polyploidy, or whole genome duplication where cells and organisms contain more than two paired (homologous) sets of chromosomes. The phenomemon occurs in some organisms, but is especially common in plants. Less common (but very important) is a condition known as endopolyploidy, where polyploidy occurs in specific animal tissues (such as human muscle tissues).
A cell or organism is considered polyploid if there is a numerical change in a whole set of chromosomes. During this research, the hybrid offspring following a polyploidy event contains twice the number of chromosomes, totaling 24.
Researchers analyzed genes from five natural populations of T. miscellus, as well as polyploid plants recreated in UF greenhouses. The DNA was extracted from the leaf tissue. They then 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.
This means some aspects of genome evolution are predictable and repeatable in independent lines.
Lead author Richard Buggs of Queen Mary University of London, who worked on the study as a postdoctoral researcher at the Florida Museum of Natural History.
Buggs said "We were surprised at the speed at which patterns seemed to form in which genes show loss versus retention"."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 University of Florida (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." Soltis said one possible mechanism of gene loss may be linked with changes in chromosome structure, an occurrence documented in a study published in the Proceedings of the National Academy of Sciences (PNAS) (January 6, 2012).
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.
"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 University of Florida (UF) associate professor in biology and member of the University of Florida Genetics Institute (UFGI).
"The availability of cost-effective, high-throughput genomics technologies has enabled us to examine this important phenomenon in this young species," said Barbazuk.
"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."
FundingThe study was funded by the University of Florida (UF) and the National Science Foundation (NSF).
ParticipationStudy co-authors include Srikar Chamala of the University of Florida Genetics Institute (UFGI), Wei Wu and Pat Schnable of Iowa State University, and Jennifer Tate of Massey University (Maori: Te Kunenga ki Purehuroa) in New Zealand.
CitationRapid, Repeated, and Clustered Loss of Duplicate Genes in Allopolyploid Plant Populations of Independent Origin. Richard J.A. Buggs, Srikar Chamala, Wei Wu, Jennifer A. Tate, Patrick S. Schnable, Douglas E. Soltis, Pamela S. Soltis, W. Brad Barbazuk. Current Biology 2012. doi:10.1016/j.cub.2011.12.027
● Duplicate genes are rapidly lost in young allotetraploid T. miscellus populations
● Clusters of genes tend to be lost together repeatedly in independent populations
● Patterns of loss are similar to those in ancient polyploids of the same plant family
● The connectivity of gene products in networks may determine which genes are lost
The predictability of evolution is debatable, with recent evidence suggesting that outcomes may be constrained by gene interaction networks. Whole-genome duplication (WGD; polyploidization—ubiquitous in plant evolution) provides the opportunity to evaluate the predictability of genome reduction, a pervasive feature of evolution. Repeated patterns of genome reduction appear to have occurred via duplicated gene (homeolog) loss in divergent species following ancient WGD, with evidence for preferential retention of duplicates in certain gene classes. The speed at which these patterns arise is unknown. We examined presence/absence of 70 homeologous loci in 59 Tragopogon miscellus plants from five natural populations of independent origin; this allotetraploid arose ~80 years ago via hybridization between diploid parents and WGD. Genes were repeatedly retained or lost in clusters, and the gene ontology categories of the missing genes correspond to those lost after ancient WGD in the same family (Asteraceae; sunflower family) and with gene dosage sensitivity. These results provide evidence that the outcomes of WGD are predictable, even in 40 generations, perhaps due to the connectivity of gene products. The high frequency of single-allele losses detected and low frequency of changes fixed within populations provide evidence for ongoing evolution.
|Last Updated on Sunday, 22 January 2012 15:11|