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Supercomputing through the grapevine

Speed read
  • Distinguishing between male and female grapevines is key to produce high yielding and disease-resistant crops
  • Genomics studies could help breeders produce more food for an expanding population
  • Jetstream enables researcher to save time and money

In Greek mythology, the god Dionysus was a patron of the theatre, overseer of the grain harvest, and devotee of libations. In many paintings of Dionysus, he is often depicted with grapevines, symbolic for making wine, the juice of the gods.

In genomics, however, grapevines take on another significance. Wild grapes are strongly resistant to fungal infection, giving scientists a clue for how to breed disease-resistant cultivated grapevines.

One obstacle, however, is that half of the offspring of a wild grape don’t produce fruit because cultivated grapes are hermaphrodites and the wild grape is a male. It can take up to two to five years for a grape breeder to distinguish between male and female vines, and in that time, the grapevine takes up valuable field space.

<strong>Outstanding in his field. </strong> Michael Campbell is a geneticist at the Ware Lab. His use of Jetstream HPC resources furthers our understanding of how to employ genetic variability to feed an expanding human population. Courtesy Michael Campbell.

“Understanding the genomic history of plants, such as grapevines, helps us predict the behavior of crops in the field and plan for the future,” says Michael Campbell, geneticist at Cold Spring Harbor Laboratory. “This ultimately results in enhanced food security for populations.”

If breeders could determine whether a grapevine is male or female before permanently planting a seed, they could save plenty of time and money ensuring they’re raising the most fruitful crops possible.

To investigate this genetic puzzle, Campbell turned to Jetstream, the first US National Science Foundation-supported cloud resource for science and engineering research.  

“Limited or oversubscribed computational resources are probably the greatest challenges I face,” Campbell says. “Jetstream provides an onramp to resources for researchers with limited or no access to high-performance computing.”

Extracto magnifico

For Campbell, researching genomics follows a typical pattern. He selects an organism that he is interested in studying, extracts and sequences DNA from the organism, then assembles the sequenced DNA into a genome to reference later on. He annotates the genes and designs experiments to test the genome, such as determining the sex characteristics of a grapevine.

Jetstream takes care of the overhead associated with computational research methods, allowing the scientist to focus on the science instead. ~Michael Campbell

The process is highly collaborative, and Jetstream helps him to work with researchers from different universities quickly and efficiently, including partners at Cornell University and undergraduate trainees at Cold Spring Harbor Laboratory.

“Jetstream allows multiple users from multiple institutions to use the same machine, without having to go through the pain of getting user accounts for everyone,” says Lance Cadle-Davidson, grape geneticist at the US Department of Agriculture Agricultural Research Service in Geneva, New York and collaborator on the project. “This also helps prevent duplicating data at multiple institutions.”

One cost-saving benefit of Jetstream Campbell appreciates is that the service is free for users, saving him and his team valuable research dollars in the process. Time on Jetstream is allocated through the Extreme Science and Engineering Discovery Environment (XSEDE).

“It’s great to be able to suspend a machine when it’s not in use,” Campbell says. “If you own the machine, you still have to pay for its upkeep and maintenance even when you aren’t using it.”

<strong>Knowledge is power.</strong> Understanding the genetic variation in a plant tells farmers how best to cultivate it and manage the land it grows in. This knowledge is needed to respond quickly to changes in climate. Courtesy Krzysztof Czeronko. <a href= 'https://creativecommons.org/licenses/by-sa/2.0/legalcode'> (CC BY-SA 2.0)</a>

One of the main benefits of Jetstream for Campbell is that it allows him to pursue the science he is passionate about, rather than focusing on complicated high-performance computing administration.

“Plant genomics is a critical branch of plant science that gives us insights into the evolution of all plants,” Campbell says. “Jetstream takes care of the overhead associated with computational research methods, allowing the scientist to focus on the science instead.”

Next time you have a glass of wine, don’t bother toasting Dionysus: He probably didn’t contribute as much to your drink as did the computational science enabled by Jetstream. 

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