HPC Unlocks Secret to Drought-Resistant Crops

April 20, 2017

This network shows the cross-species co-expression relationships between genes in Arabidopsis and Agave. Dark green nodes represent Agave genes, light green nodes represent Arabidopsis genes, blue edges represent positive co-expression relationships, and red edges represent negative co-expression relationships. The co-expression network was used in the paper to investigate the co-expression relationships of genes within the same gene family.

OAK RIDGE, Tenn., April 20, 2017 — A multi-institution research team has used supercomputing to understand processes leading to increased drought resistance in food and fuel crops.

Photosynthesis, the method plants use to convert energy from the sun into food, is a ubiquitous process many people learn about in elementary school. Almost all plants use photosynthesis to gather energy and stay alive.

Not all photosynthetic processes are the same, though. In recent years, researchers have grown increasingly interested in desert plants’ preferred method of photosynthesis—crassulacean acid metabolism (CAM), a process named after the Crassulaceae family of plants, which include succulents like friendship plants, pig’s ears, and hens and chicks.

These plants caught researchers’ attention because of their seemingly opposite photosynthetic schedule, and understanding this process may be the genetic key to helping plants of all kinds conserve water. With a more fundamental understanding of CAM, scientists aim to help the plants upon which society relies for food and fuel become more drought resistant, thereby expanding the area where crops can grow and thrive.

“One of the benefits of CAM photosynthesis is water efficiency,” said Oak Ridge National Laboratory (ORNL) computational biologist Dan Jacobson, who is part of a multi-institutional team that recently published a CAM study in Nature Plants. “When you think of bioenergy and food crops, you want them to be able to tolerate drought stress or grow in areas that aren’t currently arable land. That means they have to be able to withstand some kind of environmental stress, most commonly drought stress. CAM species are very good at this.”

To that end, Jacobson works with a large group of experimentalists and computational scientists to more fully understand the CAM process. This cross-omics team (combining expertise in metabolomics, proteomics, and genomics) uses computing resources at the Oak Ridge Leadership Computing Facility (OLCF)—a US Department of Energy Office of Science User Facility located at ORNL—to catalog how plants’ CAM processes vary and ultimately uncover how CAM processes may be genetically engineered into feed stock, food crops, and crops for bioenergy applications.

Shining a light on photosynthesis

When most people think of photosynthesis, they are actually thinking of a specific form, called C3 photosynthesis. This process follows the Calvin Cycle, in which plants capture light energy during the day and convert it into energy-bearing adenosine triphosphate (ATP).

ATP helps plants split water atoms into their hydrogen and oxygen constituent particles. Meanwhile, a C3 photosynthetic plant opens up small pores—called stomata—to absorb carbon dioxide from the atmosphere. Then at night, the newly freed hydrogen particles combine with carbon dioxide absorbed during the day to create the carbohydrates plants use to live and grow.

CAM photosynthesis works the same way, but stomata open for respiration at night and stay tightly closed during the day, allowing plants to conserve more water. This helps plants like cactus and Agave survive in climates where water is scarce.

Less than 10 percent of known plant species use this specialized form of photosynthesis, but researchers hope that by understanding how CAM works, they can apply this water-saving method to other plants. To do that, though, researchers need to understand how molecules interact during CAM photosynthesis and how metabolites and proteins change over time.

Data-intensive design

In addition to simulating processes too dangerous or complex for experiments, supercomputers also help scientists make connections in vast amounts of data. For this project, researchers from ORNL, the University of Tennessee, Newcastle University in the United Kingdom, and the University of Nevada, Reno gathered photosynthesis data from Agave (a CAM plant) and compared it with the Arabidopsis genus of plants (C3 plants). To conduct a study between Agave and a C3 plant, the team selected the Arabidopsis genus plant thale cress, one of the first plants to have its genome sequenced and a good candidate for plant studies.

The team then studied what gene expressions control stomata opening and closing in both CAM and C3 plants and how proteins regulated this process. Collecting this data in both a common CAM and a C3 species allowed the team to distinguish traits ubiquitous to CAM plants from species-specific traits. However, finding these connections required a machine capable of comparing large data sets against themselves.

Jacobson and his collaborators used the OLCF’s Eos analysis cluster to run “all-versus-all” comparisons of the team’s data sets. These comparisons scan large data sets and compare each individual plant’s data with all others. This helps the team form relationships between the metabolic processes underpinning CAM in individual Agave specimens as well as the differences between Agave’s CAM properties from thale cress’s C3 properties.

“These all-against-all vector comparisons for correlation networks allowed us to look for different types of patterns and different times of day where the [gene expression] transcripts are correlated with each other, where they were correlated to proteins or metabolites, or times of the day where they shift dramatically,” Jacobson said.

The team members gained access to OLCF resources through the OLCF’s Director’s Discretionary program, and after familiarizing themselves with Titan’s hybrid architecture, they plan to expand research into other CAM species, comparing larger data sets and more fully cataloging CAM processes. “As we gain more knowledge from these various approaches, we hope to tease apart the underlying mechanisms for CAM and how it is regulated,” Jacobson said. “That starts to build toward having enough knowledge to deploy CAM in a new species.”

Jacobson also indicated that without access to high-performance computing, the team would not have been able to find these meaningful connections in a timely manner. “This is the first study looking at a cross-omics, time-course experiment to try and explore CAM at this molecular detail,” he said. “I think the ability to use supercomputing infrastructure enabled things that wouldn’t have been possible otherwise. We were able to have a pretty big impact on the analysis of this work because of those resources.”

Related Publication: P. Abraham, H. Yin, A. Borland, D. Weighill, et al., “Transcript, Protein, and Metabolite Temporal Dynamics in the CAM Plant Agave.” Nature Plants 12, no. 2 (2016): 1–10, doi:10.1038/nplants.2016.178.

About Oak Ridge National Laboratory

Oak Ridge National Laboratory is supported by the US Department of Energy’s Office of Science. The single largest supporter of basic research in the physical sciences in the United States, the Office of Science is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.


Source: ORNL

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

UCSD, AIST Forge Tighter Alliance with AI-Focused MOU

January 18, 2018

The rich history of collaboration between UC San Diego and AIST in Japan is getting richer. The organizations entered into a five-year memorandum of understanding on January 10. The MOU represents the continuation of a 1 Read more…

By Tiffany Trader

New Blueprint for Converging HPC, Big Data

January 18, 2018

After five annual workshops on Big Data and Extreme-Scale Computing (BDEC), a group of international HPC heavyweights including Jack Dongarra (University of Tennessee), Satoshi Matsuoka (Tokyo Institute of Technology), Read more…

By John Russell

Researchers Measure Impact of ‘Meltdown’ and ‘Spectre’ Patches on HPC Workloads

January 17, 2018

Computer scientists from the Center for Computational Research, State University of New York (SUNY), University at Buffalo have examined the effect of Meltdown and Spectre security updates on the performance of popular H Read more…

By Tiffany Trader

HPE Extreme Performance Solutions

HPE and NREL Take Steps to Create a Sustainable, Energy-Efficient Data Center with an H2 Fuel Cell

As enterprises attempt to manage rising volumes of data, unplanned data center outages are becoming more common and more expensive. As the cost of downtime rises, enterprises lose out on productivity and valuable competitive advantage without access to their critical data. Read more…

Fostering Lustre Advancement Through Development and Contributions

January 17, 2018

Six months after organizational changes at Intel's High Performance Data (HPDD) division, most in the Lustre community have shed any initial apprehension around the potential changes that could affect or disrupt Lustre Read more…

By Carlos Aoki Thomaz

UCSD, AIST Forge Tighter Alliance with AI-Focused MOU

January 18, 2018

The rich history of collaboration between UC San Diego and AIST in Japan is getting richer. The organizations entered into a five-year memorandum of understandi Read more…

By Tiffany Trader

New Blueprint for Converging HPC, Big Data

January 18, 2018

After five annual workshops on Big Data and Extreme-Scale Computing (BDEC), a group of international HPC heavyweights including Jack Dongarra (University of Te Read more…

By John Russell

Researchers Measure Impact of ‘Meltdown’ and ‘Spectre’ Patches on HPC Workloads

January 17, 2018

Computer scientists from the Center for Computational Research, State University of New York (SUNY), University at Buffalo have examined the effect of Meltdown Read more…

By Tiffany Trader

Fostering Lustre Advancement Through Development and Contributions

January 17, 2018

Six months after organizational changes at Intel's High Performance Data (HPDD) division, most in the Lustre community have shed any initial apprehension aroun Read more…

By Carlos Aoki Thomaz

When the Chips Are Down

January 11, 2018

In the last article, "The High Stakes Semiconductor Game that Drives HPC Diversity," I alluded to the challenges facing the semiconductor industry and how that may impact the evolution of HPC systems over the next few years. I thought I’d lift the covers a little and look at some of the commercial challenges that impact the component technology we use in HPC. Read more…

By Dairsie Latimer

How Meltdown and Spectre Patches Will Affect HPC Workloads

January 10, 2018

There have been claims that the fixes for the Meltdown and Spectre security vulnerabilities, named the KPTI (aka KAISER) patches, are going to affect applicatio Read more…

By Rosemary Francis

Momentum Builds for US Exascale

January 9, 2018

2018 looks to be a great year for the U.S. exascale program. The last several months of 2017 revealed a number of important developments that help put the U.S. Read more…

By Alex R. Larzelere

ANL’s Rick Stevens on CANDLE, ARM, Quantum, and More

January 8, 2018

Late last year HPCwire caught up with Rick Stevens, associate laboratory director for computing, environment and life Sciences at Argonne National Laboratory, f Read more…

By John Russell

Inventor Claims to Have Solved Floating Point Error Problem

January 17, 2018

"The decades-old floating point error problem has been solved," proclaims a press release from inventor Alan Jorgensen. The computer scientist has filed for and Read more…

By Tiffany Trader

US Coalesces Plans for First Exascale Supercomputer: Aurora in 2021

September 27, 2017

At the Advanced Scientific Computing Advisory Committee (ASCAC) meeting, in Arlington, Va., yesterday (Sept. 26), it was revealed that the "Aurora" supercompute Read more…

By Tiffany Trader

Japan Unveils Quantum Neural Network

November 22, 2017

The U.S. and China are leading the race toward productive quantum computing, but it's early enough that ultimate leadership is still something of an open questi Read more…

By Tiffany Trader

AMD Showcases Growing Portfolio of EPYC and Radeon-based Systems at SC17

November 13, 2017

AMD’s charge back into HPC and the datacenter is on full display at SC17. Having launched the EPYC processor line in June along with its MI25 GPU the focus he Read more…

By John Russell

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Nvidia highlights strengths of its newest GPU silicon in response to Google's report on the performance and energy advantages of its custom tensor processor. Read more…

By Tiffany Trader

IBM Begins Power9 Rollout with Backing from DOE, Google

December 6, 2017

After over a year of buildup, IBM is unveiling its first Power9 system based on the same architecture as the Department of Energy CORAL supercomputers, Summit a Read more…

By Tiffany Trader

Fast Forward: Five HPC Predictions for 2018

December 21, 2017

What’s on your list of high (and low) lights for 2017? Volta 100’s arrival on the heels of the P100? Appearance, albeit late in the year, of IBM’s Power9? Read more…

By John Russell

GlobalFoundries Puts Wind in AMD’s Sails with 12nm FinFET

September 24, 2017

From its annual tech conference last week (Sept. 20), where GlobalFoundries welcomed more than 600 semiconductor professionals (reaching the Santa Clara venue Read more…

By Tiffany Trader

Leading Solution Providers

Chip Flaws ‘Meltdown’ and ‘Spectre’ Loom Large

January 4, 2018

The HPC and wider tech community have been abuzz this week over the discovery of critical design flaws that impact virtually all contemporary microprocessors. T Read more…

By Tiffany Trader

Perspective: What Really Happened at SC17?

November 22, 2017

SC is over. Now comes the myriad of follow-ups. Inboxes are filled with templated emails from vendors and other exhibitors hoping to win a place in the post-SC thinking of booth visitors. Attendees of tutorials, workshops and other technical sessions will be inundated with requests for feedback. Read more…

By Andrew Jones

Tensors Come of Age: Why the AI Revolution Will Help HPC

November 13, 2017

Thirty years ago, parallel computing was coming of age. A bitter battle began between stalwart vector computing supporters and advocates of various approaches to parallel computing. IBM skeptic Alan Karp, reacting to announcements of nCUBE’s 1024-microprocessor system and Thinking Machines’ 65,536-element array, made a public $100 wager that no one could get a parallel speedup of over 200 on real HPC workloads. Read more…

By John Gustafson & Lenore Mullin

Delays, Smoke, Records & Markets – A Candid Conversation with Cray CEO Peter Ungaro

October 5, 2017

Earlier this month, Tom Tabor, publisher of HPCwire and I had a very personal conversation with Cray CEO Peter Ungaro. Cray has been on something of a Cinderell Read more…

By Tiffany Trader & Tom Tabor

Flipping the Flops and Reading the Top500 Tea Leaves

November 13, 2017

The 50th edition of the Top500 list, the biannual publication of the world’s fastest supercomputers based on public Linpack benchmarking results, was released Read more…

By Tiffany Trader

GlobalFoundries, Ayar Labs Team Up to Commercialize Optical I/O

December 4, 2017

GlobalFoundries (GF) and Ayar Labs, a startup focused on using light, instead of electricity, to transfer data between chips, today announced they've entered in Read more…

By Tiffany Trader

How Meltdown and Spectre Patches Will Affect HPC Workloads

January 10, 2018

There have been claims that the fixes for the Meltdown and Spectre security vulnerabilities, named the KPTI (aka KAISER) patches, are going to affect applicatio Read more…

By Rosemary Francis

HPC Chips – A Veritable Smorgasbord?

October 10, 2017

For the first time since AMD's ill-fated launch of Bulldozer the answer to the question, 'Which CPU will be in my next HPC system?' doesn't have to be 'Whichever variety of Intel Xeon E5 they are selling when we procure'. Read more…

By Dairsie Latimer

  • arrow
  • Click Here for More Headlines
  • arrow
Share This