Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Signatures of selection inscribed on poplar genomes

25.08.2014

Genome-wide study shows evidence of genetic selection

One aspect of the climate change models researchers have been developing looks at how plant ranges might shift, and how factors such as temperature, water availability, and light levels might come into play. Forests creeping steadily north and becoming established in the thawing Arctic is just one of the predicted effects of rising global temperatures.

A recent study published online August 24, 2014 in Nature Genetics offers a more in-depth, population-based approach to identifying such mechanisms for adaptation, and describes a method that could be harnessed for developing more accurate predictive climate change models. For the U.S. Department of Energy, which is developing biomass crops for biofuels production, this knowledge could determine which genotypes – genetic makeup of an organism – of biomass crop may thrive better than others in certain environments. The team led by Gerald Tuskan of Oak Ridge National Laboratory (ORNL), the Department of Energy Joint Genome Institute (DOE JGI) – a DOE Office of Science user facility – and Stephen DiFazio of West Virginia University, used a combination of genome-wide selection scans and analyses to understand the processes involved in shaping the genetic variation of natural poplar (Populus trichocarpa) populations.

As part of this long-term study, the team took samples from 1,100 poplar trees growing in wild populations in California, Oregon, Washington and British Columbia. They then clonally propagated (through cuttings) these trees in three plantations in California and Oregon. For their analyses, they pared the group down to 544 unrelated individuals whose genotypes could be accurately determined so as to characterize the genetic basis for variation in adaptation. The shift from an approach focused on single candidate genes to the large-scale computational approach analyzing all of them is made possible by the availability of the poplar genome, which was published in the journal Science in 2006 by the DOE JGI. Since the genome was made publicly available, it has been used to understand woody perennial plant development and served as a model for genome-level insights in forest trees. The publication itself has been cited more than 1,000 times in a wide variety of journals.

"This is the first time that deep genomics resources have ever been applied to an ecological question, in this case: 'What does selection do at the genome level?'" said Tuskan. "In the past, people looked at adaptation to factors such as temperature and light levels, and they examined variation in those genes as they vary across environmental gradients. There was a preconceived notion and a very narrow view of what was causing the response. Here, we took five major approaches, applied them blindly to the whole genome, and let the analysis show us where the fingerprints of selection are and what genes fall under those fingerprints." Watch a video of Tuskan on the importance of selection in trees at http://bit.ly/Tuskan14fingerprints.

Going from 1,000 genotypes and 45,000 genes "to figuring out what's not just statistically significant but biologically meaningful" wasn't easy, said study first author Luke Evans of West Virginia University. "We did it by determining selection targets – things that looked like they might be under natural selection in wild populations and looked at growth and performance evidence that they affect adaptive traits. If these targets showed not only computational evidence of selection but also influenced phenotypes, it was a nice sort of dovetailing that was mutually supportive."

DiFazio highlighted the significance of the computational work. "Our approach is particularly powerful because we are mining standing natural variation resulting from tens of thousands of years of evolution and selection such that the alleles or gene variants that we have identified have great promise to provide robust, long-term improvements to biofuel feedstocks."

Evans also noted that their study yielded nearly 18 million single base pair variants of DNA sequence (called "SNPs") in poplar. These data can be accessed at Phytozome, DOE JGI's plant comparative genomics portal. "That's a massive number of naturally occurring variants, a lot in cell wall chemistry genes and other known productivity genes. This provides an immediate resource for tree breeding programs," he said.

The team identified 397 genomic regions that contribute to adaptive traits for wild populations of poplars. For example, data gathered on height, spring bud flush and fall bud set from the clonally-replicated poplars growing in three plantations indicated that in warmer climates, trees with earlier bud flush and later bud set were favored.

Given the importance of poplar trees, not just for their role in the ecosystem, for instance, in capturing carbon, but also for their economic importance in fields ranging from timber to bioenergy, Evans noted that the ability to have plantations of poplars through vegetative propagation is a significant tree-breeding tool for picking the appropriate stocks for the task. "If you know every base in a genome, you can skip whole generations and use genomic information to predict how well an individual will do," he said. "Plantations serve as the initial tests where you can take that genomic information and calibrate those predictions. With those reference points, you can scale everything."

###

Aside from Evans, Tuskan, and DiFazio, other authors on the study were Gancho Slavov of Aberystwyth University, UK; Eli Rodgers-Melnick of West Virginia University, Joel Martin and Wendy Schackwitz of the DOE JGI; Priya Ranjan, Wellington Muchero, Lee Gunter, Jin-Gui Chen of ORNL; and Amy Brunner of Virginia Tech.

Members of the BioEnergy Science Center (BESC), a U.S. DOE Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science, contributed to the published work, in particular the collection, propagation, and maintenance of the common gardens.

The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI, headquartered in Walnut Creek, Calif., provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @doe_jgi on Twitter.

DOE's Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

David Gilbert | Eurek Alert!

Further reports about: Genome Science genes genomes genomic genotypes importance plantations poplar populations variants

More articles from Life Sciences:

nachricht Multi-institutional collaboration uncovers how molecular machines assemble
02.12.2016 | Salk Institute

nachricht Fertilized egg cells trigger and monitor loss of sperm’s epigenetic memory
02.12.2016 | IMBA - Institut für Molekulare Biotechnologie der Österreichischen Akademie der Wissenschaften GmbH

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Novel silicon etching technique crafts 3-D gradient refractive index micro-optics

A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.

Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...

Im Focus: Quantum Particles Form Droplets

In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.

“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...

Im Focus: MADMAX: Max Planck Institute for Physics takes up axion research

The Max Planck Institute for Physics (MPP) is opening up a new research field. A workshop from November 21 - 22, 2016 will mark the start of activities for an innovative axion experiment. Axions are still only purely hypothetical particles. Their detection could solve two fundamental problems in particle physics: What dark matter consists of and why it has not yet been possible to directly observe a CP violation for the strong interaction.

The “MADMAX” project is the MPP’s commitment to axion research. Axions are so far only a theoretical prediction and are difficult to detect: on the one hand,...

Im Focus: Molecules change shape when wet

Broadband rotational spectroscopy unravels structural reshaping of isolated molecules in the gas phase to accommodate water

In two recent publications in the Journal of Chemical Physics and in the Journal of Physical Chemistry Letters, researchers around Melanie Schnell from the Max...

Im Focus: Fraunhofer ISE Develops Highly Compact, High Frequency DC/DC Converter for Aviation

The efficiency of power electronic systems is not solely dependent on electrical efficiency but also on weight, for example, in mobile systems. When the weight of relevant components and devices in airplanes, for instance, is reduced, fuel savings can be achieved and correspondingly greenhouse gas emissions decreased. New materials and components based on gallium nitride (GaN) can help to reduce weight and increase the efficiency. With these new materials, power electronic switches can be operated at higher switching frequency, resulting in higher power density and lower material costs.

Researchers at the Fraunhofer Institute for Solar Energy Systems ISE together with partners have investigated how these materials can be used to make power...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ICTM Conference 2017: Production technology for turbomachine manufacturing of the future

16.11.2016 | Event News

Innovation Day Laser Technology – Laser Additive Manufacturing

01.11.2016 | Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

 
Latest News

UTSA study describes new minimally invasive device to treat cancer and other illnesses

02.12.2016 | Medical Engineering

Plasma-zapping process could yield trans fat-free soybean oil product

02.12.2016 | Agricultural and Forestry Science

What do Netflix, Google and planetary systems have in common?

02.12.2016 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>